PaperPlayer biorxiv bioinformatics
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Episodes: 1953
Description
Audio versions of bioRxiv and medRxiv paper abstracts
| Episode | Date |
|---|---|
|
AAontology: An ontology of amino acid scales for interpretable machine learning
|
Aug 05, 2023 |
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A dose-response based model for statistical analysis of chemical genetic interactions in CRISPRi libraries
|
Aug 05, 2023 |
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PxBLAT: An Ergonomic and Efficient Python Binding Library for BLAT
|
Aug 05, 2023 |
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CellGO: A novel deep learning-based framework and webserver for cell type-specific gene function interpretation
|
Aug 05, 2023 |
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Chrombus-XMBD: A Graph Generative Model Predicting 3D-Genome, ab initio from Chromatin Features
|
Aug 05, 2023 |
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Bioinformatics and next generation data analysis reveals the potential role of inflammation in sepsis and its associated complications
|
Aug 05, 2023 |
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Compound models and Pearson residuals for normalization of single-cell RNA-seq data without UMIs
|
Aug 05, 2023 |
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Multi-representation DeepInsight: an improvement on tabular data analysis
|
Aug 05, 2023 |
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Can a Sparse 29 x 29 Pixel Chaos Game Representation Predict Protein Binding Sites using Fine-Tuned State-of-the Art Deep Learning Semantic Segmentation Models?
|
Aug 04, 2023 |
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Single-linkage molecular clustering of viral pathogens
|
Aug 04, 2023 |
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memerna: Sparse RNA Folding Including Coaxial Stacking
|
Aug 04, 2023 |
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Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS
|
Aug 04, 2023 |
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Comparing full variation profile analysis with the conventional consensus method in SARS-CoV-2 phylogeny
|
Aug 04, 2023 |
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Neo-epitope identification by weakly-supervised peptide-TCR binding prediction
|
Aug 03, 2023 |
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A versatile framework for drug-target interaction prediction by considering domain specific features
|
Aug 03, 2023 |
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An AI-assisted Investigation of Tumor-Associated Macrophages and their Polarization in Colorectal Cancer
|
Aug 03, 2023 |
|
FiTMuSiC: Leveraging structural and (co)evolutionary data for protein fitness prediction
|
Aug 03, 2023 |
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From Proteins to Ligands: Decoding Deep Learning Methods for Binding Affinity Prediction
|
Aug 03, 2023 |
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Continuous lifelong learning for modeling of gene regulation from single cell multiome data by leveraging atlas-scale external data
|
Aug 03, 2023 |
|
SAMPLER: Empirical distribution representations for rapid analysis of whole slide tissue images
|
Aug 03, 2023 |
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PoMeLo: a systematic computational approach to predicting metabolic loss in pathogen genomes
|
Aug 03, 2023 |
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Non-sequential alignment of binding sites for fast peptide screening
|
Aug 03, 2023 |
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The importance of DNA sequence for nucleosome positioning in the process of transcriptional regulation
|
Aug 03, 2023 |
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Unraveling the Pathogenesis of Idiopathic Pulmonary Fibrosis Complicated with Type 2 Diabetes through Microarray Data Analysis
|
Aug 02, 2023 |
|
MousiPLIER: A Mouse Pathway-Level Information Extractor Model
|
Aug 02, 2023 |
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NetActivity enhances transcriptional signals by combining gene expression into robust gene set activity scores through interpretable autoencoders
|
Aug 02, 2023 |
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SR2: Sparse Representation Learning for Scalable Single-cell RNA Sequencing Data Analysis
|
Aug 02, 2023 |
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ProjectSVR: Mapping single-cell RNA-seq data to reference atlases by supported vector regression
|
Aug 02, 2023 |
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Machine Learning Gene Signature to Metastatic ccRCC based on ceRNA Network
|
Aug 02, 2023 |
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Unveiling a Potential Prognostic Biomarker in KRAS-Mutant Lung Adenocarcinoma Using Weighted Gene Co-Expression Network Analysis
|
Aug 02, 2023 |
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A systematic comparison of computational methods for expression forecasting
|
Jul 31, 2023 |
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NetVA: An R Package for Network Vulnerability and Influence Analysis
|
Jul 31, 2023 |
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Model-based compound hypothesis testing for snATAC-seq data with PACS
|
Jul 31, 2023 |
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disperseNN2: a neural network for estimating dispersal distance from georeferenced polymorphism data
|
Jul 31, 2023 |
|
A diversified, widespread microbial gene cluster encodes homologs of methyltransferases involved in methanogenesis.
|
Jul 31, 2023 |
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The Role of C-to-U RNA Editing in Human Biodiversity
|
Jul 31, 2023 |
|
ISMI-VAE: A Deep Learning Model for Classifying Disease Cells Using Gene Expression and SNV Data
|
Jul 31, 2023 |
|
Picky with peakpicking: assessing chromatographic peak quality with simple metrics in metabolomics
|
Jul 30, 2023 |
|
Unraveling cell differentiation mechanisms through topological exploration of single-cell developmental trajectories
|
Jul 30, 2023 |
|
Transfer learning to leverage larger datasets for improved prediction of protein stability changes
|
Jul 30, 2023 |
|
Extended Similarity Methods for Efficient Data Mining in Imaging Mass Spectrometry
|
Jul 30, 2023 |
|
An Optimized Pipeline for Detection of Salmonella Sequences in Shotgun Metagenomics Datasets
|
Jul 30, 2023 |
|
einprot: flexible, easy-to-use, reproducible workflows for statistical analysis of quantitative proteomics data
|
Jul 30, 2023 |
|
Clade-wise alignment integration improves co-evolutionary signals for protein-protein interaction prediction
|
Jul 30, 2023 |
|
Context-Dependent Design of Induced-fit Enzymes using Deep Learning Generates Well Expressed, Thermally Stable and Active Enzymes
|
Jul 29, 2023 |
|
MethyLasso: a segmentation approach to analyze DNA methylation patterns and identify differentially methylation regions from whole-genome datasets
|
Jul 29, 2023 |
|
GAPiM: Discovering Genetic Variations on a Real Processing-in-Memory System
|
Jul 29, 2023 |
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Directly selecting differentially expressed genes for single-cell clustering analyses
|
Jul 29, 2023 |
|
Deep Batch Active Learning for Drug Discovery
|
Jul 29, 2023 |
|
Assessing the basal gene expression of cancer cell lines for in vitro transcriptomic toxicology screening
|
Jul 29, 2023 |
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Mcadet: a feature selection method for fine-resolution single-cell RNA-seq data based on multiple correspondence analysis and community detection
|
Jul 29, 2023 |
|
getphylo: rapid and automatic generation of multi-locus phylogentic trees from genbank files
|
Jul 29, 2023 |
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Time-Informed Dimensionality Reduction for Longitudinal Microbiome Studies
|
Jul 29, 2023 |
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Sensitive remote homology search by local alignment of small positional embeddings from protein language models
|
Jul 29, 2023 |
|
A comprehensive experimental comparison between federated and centralized learning
|
Jul 29, 2023 |
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ProteoMixture: A Cell Type Deconvolution Tool for Bulk Tissue Proteomics Data
|
Jul 29, 2023 |
|
Modeling Kinetics of RNA RNA Interactions on Direct Paths
|
Jul 29, 2023 |
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mAFiA: Detecting m6A at single-molecular resolution via direct-RNA sequencing
|
Jul 29, 2023 |
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Look4LTRs: A Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats
|
Jul 29, 2023 |
|
Star allele search: a pharmacogenetic annotation database and user-friendly search tool of publicly available 1000 Genomes Project biospecimens
|
Jul 29, 2023 |
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Gradient-based implementation of linear model outperforms deep learning models
|
Jul 29, 2023 |
|
Analyzing interaction of rhodacyanine inhibitor MKT-077 with Plasmodium falciparum HSP70 nucleotide binding domains
|
Jul 29, 2023 |
|
LipidSIM: inferring mechanistic lipid biosynthesis perturbations from lipidomics with a flexible, low-parameter, systematic Markov Modeling framework
|
Jul 28, 2023 |
|
ChromaFold predicts the 3D contact map from single-cell chromatin accessibility
|
Jul 28, 2023 |
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AnglesRefine: refinement of 3D protein structures using Transformer based on torsion angles
|
Jul 28, 2023 |
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Quantification of circulating tumor DNA using deep learning
|
Jul 28, 2023 |
|
cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data
|
Jul 27, 2023 |
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Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
|
Jul 27, 2023 |
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Self-targeting spacers reveal new functions of CRISPR systems
|
Jul 27, 2023 |
|
Predicting Relative Populations of ProteinConformations without a Physics Engine UsingAlphaFold2
|
Jul 27, 2023 |
|
GRouNdGAN: GRN-guided simulation of single-cell RNA-seq data using causal generative adversarial networks
|
Jul 27, 2023 |
|
CellSNAP: A fast, accurate algorithm for 3D cell segmentation in quantitative phase imaging
|
Jul 26, 2023 |
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Mining drug-target interactions from biomedical literature using chemical and gene descriptions based ensemble transformer model
|
Jul 26, 2023 |
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Data-driven probabilistic definition of the low energy conformational states of protein residues
|
Jul 26, 2023 |
|
ursaPGx: a new R package to annotate pharmacogenetic star alleles using phased whole genome sequencing data
|
Jul 26, 2023 |
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Structural Coverage of the Human Interactome
|
Jul 26, 2023 |
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Discovering genetic biomarkers for targeted cancer therapeutics with eXplainable AI
|
Jul 26, 2023 |
|
scViralQuant: A tool for efficient alignment and quantification of viral reads from 10x single cell sequencing data sets
|
Jul 26, 2023 |
|
Benchmarking DNA Isolation Methods for Marine Metagenomics Studies
|
Jul 26, 2023 |
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A Versatile Tool for Precise Variant Calling in Mycobacterium tuberculosis Genetic Polymorphisms
|
Jul 26, 2023 |
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HLA-DR4Pred2: an improved method for predicting HLA-DRB1*04:01 binders
|
Jul 26, 2023 |
|
EPINEST, an agent-based model to simulate epidemic dynamics in large-scale poultry production and distribution networks
|
Jul 26, 2023 |
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AntiBP3: A hybrid method for predicting antibacterial peptides against gram-positive/negative/variable bacteria
|
Jul 26, 2023 |
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Immune Profiling among Colorectal Cancer Subtypes using Dependent Mixture Models
|
Jul 26, 2023 |
|
Differentiable Search of Evolutionary Trees from Leaves
|
Jul 25, 2023 |
|
Deep learning-based cell profiling based on neuronal morphology
|
Jul 25, 2023 |
|
Investigation of latent representation of toxicopathological images extracted by CNN model for understanding compound properties in vivo
|
Jul 25, 2023 |
|
ProstT5: Bilingual Language Model for Protein Sequence and Structure
|
Jul 25, 2023 |
|
hadge: a comprehensive pipeline for donor deconvolution in single cell
|
Jul 25, 2023 |
|
Highly accurate estimation of cell type abundance in bulk tissues based on single-cell reference and domain adaptive matching
|
Jul 25, 2023 |
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Collaborative network analysis for the interpretation of transcriptomics data in rare diseases, an application to Huntington's disease
|
Jul 25, 2023 |
|
ClusterDE: a post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping
|
Jul 25, 2023 |
|
Identification of a botulinum neurotoxin-like gene cluster in Bacillus toyonensis
|
Jul 25, 2023 |
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AlphaFold2 models of the active form of all 437 catalytically-competent typical human kinase domains
|
Jul 25, 2023 |
|
Meta-colored compacted de Bruijn graphs: overview and challenges
|
Jul 25, 2023 |
|
Detection of viral infection in cell lines using ViralCellDetector
|
Jul 25, 2023 |
|
Exploring NCATS In-House Biomedical Data for Evidence-based Drug Repurposing
|
Jul 25, 2023 |
|
Prominent contributions of selective neuronal subtypes to pediatric drug-resistant focal dysplasia
|
Jul 25, 2023 |
|
ScopeViewer: A Browser-Based Solution for Visualizing Spatial Transcriptomics Data
|
Jul 25, 2023 |
|
A Strategy for Differential Abundance Analysis of Sparse Microbiome Data with Group-wise Structured Zeros
|
Jul 25, 2023 |
|
ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning
|
Jul 25, 2023 |
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Looking at the Full Picture: Utilizing Topic Modeling to Determine Disease-Associated Microbiome Communities
|
Jul 25, 2023 |
|
Computational Engineering of a Therapeutic Antibody to Inhibit Multiple Mutants of HER2 Without Compromising Inhibition of the Canonical HER2
|
Jul 25, 2023 |
|
CRUX, a platform for visualising, exploring and analysing cancer genome cohort data
|
Jul 25, 2023 |
|
Using graph-based model to identify cell specific synthetic lethal effects
|
Jul 25, 2023 |
|
Identification of Low-Complexity Domains by Compositional Signatures Reveals Class-Specific Frequencies and Functions Across Reference Proteomes
|
Jul 25, 2023 |
|
MLOsMetaDB, a meta-database to centralize the information on Liquid-liquid phase separation proteins and Membraneless organelles.
|
Jul 25, 2023 |
|
Revisiting structural organization of proteins at high temperature from network perspective
|
Jul 25, 2023 |
|
Unraveling the Potential of Epicatechin Gallate in Targeting Aberrant Cardiac Ca2+ Signaling Protein
|
Jul 25, 2023 |
|
Autoencoder-transformed transcriptome improves genotype-phenotype association studies
|
Jul 25, 2023 |
|
AmpliDiff: An Optimized Amplicon Sequencing Approach to Estimating Lineage Abundances in Viral Metagenomes
|
Jul 24, 2023 |
|
3 Directional Inception-ResUNet: deep spatial feature learning for multichannel singing voice separation with distortion
|
Jul 24, 2023 |
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Addressing persistent challenges in digital image analysis of cancerous tissues
|
Jul 24, 2023 |
|
Predicting gene expression changes upon epigenomic drug treatment
|
Jul 23, 2023 |
|
Mendelian disease comorbidity as a resource for novel therapeutic targets
|
Jul 23, 2023 |
|
Charting cellular differentiation trajectories with Ricci flow
|
Jul 23, 2023 |
|
Taxor: Fast and space-efficient taxonomic classification of long reads with hierarchicalinterleaved XOR filters
|
Jul 22, 2023 |
|
A Motion Transformer for Single Particle Tracking in Fluorescence Microscopy Images
|
Jul 22, 2023 |
|
FocA: A deep learning tool for reliable, near-real-time imaging focus analysis in automated cell assay pipelines
|
Jul 22, 2023 |
|
Identification of five characteristic ferroptosis-related genes as novel biomarkers for ischemic stroke using bioinformatic and machine learning strategies
|
Jul 22, 2023 |
|
Voyager: exploratory single-cell genomics data analysis with geospatial statistics
|
Jul 22, 2023 |
|
PseudoCell: A collaborative network for in silico prediction of regulatory pathways
|
Jul 22, 2023 |
|
BuDDI: Bulk Deconvolution with Domain Invariance to predict cell-type-specific perturbations from bulk
|
Jul 22, 2023 |
|
Cellular proliferation biases clonal lineage tracing and trajectory inference
|
Jul 22, 2023 |
|
Efficient protein structure archiving using ProteStAr
|
Jul 22, 2023 |
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Identifying Clusters in Graph Representations of Genomes
|
Jul 22, 2023 |
|
DIMPLE: AN R PACKAGE TO QUANTIFY, VISUALIZE, AND MODEL SPATIAL CELLULAR INTERACTIONS FROM MULTIPLEX IMAGING WITH DISTANCE MATRICES
|
Jul 22, 2023 |
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PANDORA v2.0: Benchmarking peptide-MHC II models and software improvements
|
Jul 22, 2023 |
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Predicting Gene Spatial Expression and Cancer Prognosis: An Integrated Graph and Image Deep Learning Approach Based on HE Slides
|
Jul 21, 2023 |
|
In-silico identification, characterization, and expression analysis of RNA recognition motif (RRM) containing RNA binding proteins in Aedes aegypti
|
Jul 21, 2023 |
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Hidden Markov Models based search in combination with structural bioinformatics pipeline leads to the identification of DAF-12 distant orthologous in Meloidogyne incognita
|
Jul 21, 2023 |
|
EPIGENOMIC VARIABILITY AND TRANSCRIPTOMICS AS A NOVEL MULTIOMIC COMPLEMENTARY APPROACH FOR PERSONALIZED NUTRITION IN COLORECTAL CANCER PATIENTS
|
Jul 20, 2023 |
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Unified fate mapping in multiview single-cell data
|
Jul 20, 2023 |
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Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in TimsTOF
|
Jul 19, 2023 |
|
Recurrent composite markers of cell types and states
|
Jul 19, 2023 |
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Estimating error rates for single molecule protein sequencing experiments
|
Jul 19, 2023 |
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Predicting cell morphological responses to perturbations using generative modeling
|
Jul 19, 2023 |
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Solving the Pervasive Problem of Protocol Non-Compliance in MRI using an Open-Source tool mrQA
|
Jul 19, 2023 |
|
Molecular Surface Descriptors to Predict Antibody Developability
|
Jul 19, 2023 |
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PhageScanner, a flexible machine learning pipeline for automated bacteriophage genomic and metagenomic feature annotation
|
Jul 19, 2023 |
|
mEthAE: an Explainable AutoEncoder for methylation data
|
Jul 19, 2023 |
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Scalable querying of human cell atlases via a foundational model reveals commonalities across fibrosis-associated macrophages
|
Jul 19, 2023 |
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Contextualizing protein representations using deep learning on protein networks and single-cell data
|
Jul 19, 2023 |
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Zero-Shot Transfer of Protein Sequence Likelihood Models to Thermostability Prediction
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Jul 19, 2023 |
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Microenvironment of metastatic site reveals key predictors of PD-1 blockade response in renal cell carcinoma
|
Jul 19, 2023 |
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A Template for Translational Bioinformatics: Facilitating Multimodal Data Analyses in Preclinical Models of Neurological Injury
|
Jul 19, 2023 |
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Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery
|
Jul 19, 2023 |
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Random, de novo and conserved proteins: How structure and disorder predictors perform differently
|
Jul 19, 2023 |
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A novel machine learning algorithm picks proteome signature to specifically identify cancer exosomes
|
Jul 19, 2023 |
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TULIP - a Transformer based Unsupervised Language model for Interacting Peptides and T-cell receptors that generalizes to unseen epitopes
|
Jul 19, 2023 |
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Using random forests to uncover the predictive power of distance-varying cell interactions in tumor microenvironments
|
Jul 19, 2023 |
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High-throughput complement component 4 genomic sequence analysis with C4Investigator
|
Jul 19, 2023 |
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Profiling the Expression of Transportome Genes in cancer: A systematic approach
|
Jul 19, 2023 |
|
Understanding the structural basis for differential binding of lapachol with PfHSP70s
|
Jul 19, 2023 |
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cycle_finder: de novo analysis of tandem and interspersed repeats based on cycle-finding
|
Jul 19, 2023 |
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Benchmarking and optimization of cell-free DNA deconvolution
|
Jul 19, 2023 |
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Benchmarking software tools for trimming adapters and merging next-generation sequencing data for ancient DNA
|
Jul 19, 2023 |
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A Systematic Identification of RBPs Driving Aberrant Splicing in Cancer
|
Jul 18, 2023 |
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Proteasomal cleavage prediction: state-of-the-art and future directions
|
Jul 18, 2023 |
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Reliable interpretability of biology-inspired deep neural networks
|
Jul 18, 2023 |
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Nucleus basalis of Meynert degeneration signals earliest stage of Alzheimer's disease progression
|
Jul 18, 2023 |
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rvTWAS: identifying gene-trait association using sequences by utilizing transcriptome-directed feature selection
|
Jul 18, 2023 |
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Brightest path tracing: A Python package to trace the brightest path in 2D and 3D images.
|
Jul 18, 2023 |
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Characterizing dysregulations via cell-cell communications in Alzheimer's brains using single-cell transcriptomes
|
Jul 18, 2023 |
|
A data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence (MISIP)
|
Jul 17, 2023 |
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MosaiCatcher v2: a single-cell structural variations detection and analysis reference framework based on Strand-seq
|
Jul 17, 2023 |
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Metabolic Interactive Nodular Network for Omics (MINNO): Refining and investigating metabolic networks based on empirical metabolomics data
|
Jul 17, 2023 |
|
Host species and geography impact bee-associated RNA virus communities with evidence for isolation-by-distance in viral populations
|
Jul 17, 2023 |
|
XA4C: eXplainable representation learning via Autoencoders revealing Critical genes
|
Jul 17, 2023 |
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Apis mellifera filamentous virus from a honey bee gut microbiome survey in Hungary
|
Jul 17, 2023 |
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DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction
|
Jul 17, 2023 |
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Contextual protein encodings from equivariant graph transformers
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Jul 17, 2023 |
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sNucConv: A bulk RNA-seq deconvolution method trained on single-nucleus RNA-seq data to estimate cell-type composition of human subcutaneous and visceral adipose tissues
|
Jul 17, 2023 |
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Introducing PandaNovo for practical large-scale de novo peptide sequencing
|
Jul 16, 2023 |
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The Patent and Literature Antibody Database (PLAbDab): an evolving reference set of functionally diverse, literature-annotated antibody sequences and structures
|
Jul 16, 2023 |
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Synergizing Geometric Deep Learning and Data-Centric Methods for Improved Protein Structural Alignment
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Jul 16, 2023 |
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tfboot: Bootstrapping and statistical analysis for transcription factor binding site-disrupting variants in gene sets
|
Jul 16, 2023 |
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RNA Strain-Match: A tool for matching single-nucleus, single-cell, or bulk RNA-sequencing alignment data to its corresponding genotype
|
Jul 16, 2023 |
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Precise Nanopore Signal Modeling Improves Unsupervised Single-Molecule Methylation Detection
|
Jul 15, 2023 |
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Beam search decoder for enhancing sequence decoding speed in single-molecule peptide sequencing data
|
Jul 15, 2023 |
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FLAG: Find, Label Annotate Genomes, a fully automated tool for genome gene structural and functional annotation of highly fragmented non-model species
|
Jul 15, 2023 |
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TriTan: An efficient triple non-negative matrix factorisation method for integrative analysis of single-cell multiomics data
|
Jul 15, 2023 |
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Integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types
|
Jul 15, 2023 |
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Accurately identifying nucleic-acid-binding sites through geometric graph learning on language model predicted structures
|
Jul 15, 2023 |
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BERLIN: Basic Explorer for single-cell RNAseq analysis and cell Lineage Determination.
|
Jul 15, 2023 |
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Predicting Disease-gene Associations through Self-supervised Mutual Infomax Graph Convolution Network
|
Jul 15, 2023 |
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ChatGPT-Enhanced ROC Analysis (CERA): A Shiny Web Tool for Finding Optimal Cutoff in Biomarker Analysis
|
Jul 15, 2023 |
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DeepETPicker: Fast and accurate 3D particle picking for cryo-electron tomography using weakly supervised deep learning
|
Jul 14, 2023 |
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TFvelo: gene regulation inspired RNA velocity estimation
|
Jul 14, 2023 |
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EnrichMiner: a biologist-oriented web server for mining biological insights from functional enrichment analysis
|
Jul 14, 2023 |
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ScreenDMT reveals linoleic acid diols replicably associate with BMI and stimulate adipocyte calcium fluxes
|
Jul 14, 2023 |
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Functional profiling of the sequence stockpile: a review and assessment of in silico prediction tools
|
Jul 14, 2023 |
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A Conserved Electrostatic Membrane-Binding Surface in Synaptotagmin-Like Proteins Revealed Using Molecular Phylogenetic Analysis and Homology Modeling
|
Jul 13, 2023 |
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AI2BMD: efficient characterization of protein dynamics with ab initio accuracy
|
Jul 13, 2023 |
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Prediction of protein-RNA interactions from single-cell transcriptomic data
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Jul 13, 2023 |
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Integration of variant annotations using deep set networks boosts rare variant association genetics
|
Jul 13, 2023 |
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reanalyzerGSE: tackling the everlasting lack of reproducibility and reanalyses in transcriptomics
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Jul 13, 2023 |
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Characterising neutrophil subtypes in cancer using human and murine single-cell RNA sequencing datasets
|
Jul 13, 2023 |
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Peptriever: A Bi-Encoder approach for large-scale protein-peptide binding search
|
Jul 13, 2023 |
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Identifying Protein Conformational States in the PDB and Comparison to AlphaFold2 Predictions
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Jul 13, 2023 |
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Ecological network inference is not consistent across sales or approaches
|
Jul 13, 2023 |
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RNAGEN: A generative adversarial network-based model to generate synthetic RNA sequences to target proteins
|
Jul 12, 2023 |
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fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing
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Jul 12, 2023 |
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Salmonella enterica serovar Typhimurium ST313 sublineage 2.2 has emerged in Malawi with a characteristic gene expression signature and a fitness advantage
|
Jul 12, 2023 |
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Hyperparameter optimisation in differential evolution using Summed Local Difference Strings, a rugged but easily calculated landscape for combinatorial search problems
|
Jul 12, 2023 |
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The Landscape of Maize-Associated Bacteria and Fungi Across the United States
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Jul 12, 2023 |
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Tutorial: guidelines for manual cell type annotation of single-cell multi-omics datasets using interactive software
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Jul 12, 2023 |
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DNA Storage Designer: A practical and holistic design platform for storing digital information in DNA sequence
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Jul 12, 2023 |
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UNI-RNA: UNIVERSAL PRE-TRAINED MODELS REVOLUTIONIZE RNA RESEARCH
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Jul 12, 2023 |
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Exploiting protein language models for the precise classification of ion channels and ion transporters
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Jul 12, 2023 |
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Distinguishing word identity and sequence context in DNA language models
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Jul 12, 2023 |
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PlantConnectome: knowledge networks encompassing greater than 100,000 plant article abstracts
|
Jul 12, 2023 |
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An interpretable deep learning framework for genome-informed precision oncology
|
Jul 12, 2023 |
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Simulations of sequence evolution: how (un)realistic they really are and why
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Jul 12, 2023 |
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In-Silico analysis of Human Insulin Gene for Mirror repeat sequences
|
Jul 11, 2023 |
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Robust Phylogenetic Tree-based Microbiome Association Test using Repeatedly Measured Data for Composition Bias
|
Jul 11, 2023 |
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Metastatic prognostic ability of lung cancer stromal cells from a single-cell RNA-seq perspective
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Jul 11, 2023 |
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Improving genome-scale metabolic models of incomplete genomes with deep learning
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Jul 11, 2023 |
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The Impact of AI-Based Modeling on the Accuracy of Protein Assembly Prediction: Insights from CASP15
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Jul 11, 2023 |
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An error correction strategy for image reconstruction by DNA sequencing microscopy
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Jul 11, 2023 |
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ESQmodel: biologically informed evaluation of 2-D cell segmentation quality in multiplexed tissue images
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Jul 11, 2023 |
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Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data
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Jul 11, 2023 |
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A workflow combining single-cell CRISPRi screening and a supervised autoencoder neural network to detect subtle transcriptomic perturbations induced by lncRNA Knock-Down
|
Jul 11, 2023 |
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Utility of language model and physics-based approaches in modifying MHC Class-I immune-visibility for the design of vaccines and therapeutics
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Jul 11, 2023 |
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ARCTIC-3D: Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information
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Jul 11, 2023 |
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kGWASflow: a modular, flexible, and reproducible Snakemake workflow for k-mers-based GWAS
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Jul 11, 2023 |
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Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment
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Jul 11, 2023 |
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Petascale Homology Search for Structure Prediction
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Jul 11, 2023 |
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A divide and conquer approach (DACA) to predict high fidelity structure of large multidomain protein BRWD1
|
Jul 11, 2023 |
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Studies on the selectivity of the SARS-CoV-2 papain-like protease reveal the importance of the P2' proline of the viral polyprotein
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Jul 11, 2023 |
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Self-supervised Benchmarking for scRNAseq Clustering
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Jul 10, 2023 |
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Pasa: Leverage population pangenome graph to scaffold prokaryote genome assemblies.
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Jul 10, 2023 |
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ENTRAIN: integrating trajectory inference and gene regulatory networks with spatial data to co-localize the receptor-ligand interactions that specify cell fate
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Jul 10, 2023 |
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Quantifying Cell-State Densities in Single-Cell Phenotypic Landscapes using Mellon
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Jul 10, 2023 |
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Prediction of Alzheimer's Disease from Single Cell Transcriptomics Using Deep Learning
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Jul 10, 2023 |
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Spatial pattern and differential expression analysis with spatial transcriptomic data
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Jul 09, 2023 |
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Indexing and searching petabyte-scale nucleotide resources
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Jul 09, 2023 |
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A microRNA-based Johne's disease diagnostic predictive system: preliminary results
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Jul 09, 2023 |
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Efficient High-Quality Metagenome Assembly from Long Accurate Reads using Minimizer-space de Bruijn Graphs
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Jul 08, 2023 |
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Mass2SMILES: deep learning based fast prediction of structures and functional groups directly from high-resolution MS/MS spectra.
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Jul 08, 2023 |
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Dromi: Python package for parallel computation of similarity measures among vector-encoded sequences
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Jul 07, 2023 |
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Leveraging Permutation Testing to Assess Confidence in Positive-Unlabeled Learning Applied to High-Dimensional Biological Datasets
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Jul 07, 2023 |
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Epigenetic Germline Variants Predict Cancer Prognosis and Risk and Distribute Uniquely in Topologically Associating Domains
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Jul 07, 2023 |
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SPIN-CGNN: Improved fixed backbone protein design with contact map-based graph construction and contact graph neural network
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Jul 07, 2023 |
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Deep FASTQ and BAM co-compression in Genozip 15
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Jul 07, 2023 |
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Accelerated computations for iterative-solver techniques in single-step BLUP models
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Jul 07, 2023 |
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Spontanously breaking of symmetry in overlapping cell instance segmentation using diffusion models
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Jul 07, 2023 |
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SpaceANOVA: Spatial co-occurrence analysis of cell types in multiplex imaging data using point process and functional ANOVA
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Jul 07, 2023 |
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Semi-supervised integration of single-cell transcriptomics data
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Jul 07, 2023 |
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Codon usage bias study of the Vitamin D receptor (VDR) gene of Multiple Sclerosis and Diabetes-1 patients
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Jul 07, 2023 |
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Breaking Down Cell-Free DNA Fragmentation: A Markov Model Approach
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Jul 07, 2023 |
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Prospects for a sequence-based taxonomy of influenza A virus subtypes
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Jul 07, 2023 |
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RamanSPy: An open-source Python package for integrative Raman spectroscopy data analysis
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Jul 07, 2023 |
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SynerGPT: In-Context Learning for Personalized Drug Synergy Prediction and Drug Design
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Jul 07, 2023 |
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Pan-cancer analysis reveals embryonic and hematopoietic stem cell signatures to distinguish different cancer subtypes
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Jul 07, 2023 |
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Exploring multi-omics latent embedding spaces for characterizing tumor heterogeneity and tumoral fitness effects
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Jul 07, 2023 |
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Reusability Report: Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients
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Jul 07, 2023 |
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Learning Complete Protein Representation by Deep Coupling of Sequence and Structure
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Jul 07, 2023 |
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scARE: Attribution Regularization for Single Cell Representation Learning
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Jul 07, 2023 |
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Network-based prediction approach for cancer-specific driver missense mutations using a graph neural network
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Jul 07, 2023 |
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Exploring Leishmania linear motifs directing protein secretion, sorting and autophagy
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Jul 07, 2023 |
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Deep dynamical modelling of developmental trajectories with temporal transcriptomics
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Jul 07, 2023 |
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DeepNeuropePred: a robust and universal tool to predict cleavage sites from neuropeptide precursors by protein language model
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Jul 07, 2023 |
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SPAT: Surface Protein Annotation Tool
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Jul 07, 2023 |
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Using Published Pathway Figures in Enrichment Analysis and Machine Learning
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Jul 07, 2023 |
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DeepCristae, a CNN for the restoration of mitochondria cristae in live microscopy images
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Jul 05, 2023 |
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msqrob2PTM: differential abundance and differential usage analysis of MS-based proteomics data at the post-translational modification and peptidoform level
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Jul 05, 2023 |
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ODAMNet: a Python package to identify molecular relationships between chemicals and rare diseases using overlap, active module and random walk approaches
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Jul 05, 2023 |
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ESGq: Alternative Splicing events quantification across conditions based on Event Splicing Graphs
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Jul 05, 2023 |
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ABDS: tool suite for analyzing biologically diverse samples
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Jul 05, 2023 |
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Hostile: accurate host decontamination of microbial sequences
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Jul 05, 2023 |
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Molecular and Quantum Mechanical Studies of Interaction Between Tetrahydrocurcumin Derivative and PCSK9 Protein to Provide a Basis for an Oral Pill to Remove Bad Cholesterol
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Jul 05, 2023 |
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Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples
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Jul 04, 2023 |
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A pre-trained large language model for translating single-cell transcriptome to proteome
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Jul 04, 2023 |
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Machine Learning Made Easy (MLme): A Comprehensive Toolkit for Machine Learning-Driven Data Analysis
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Jul 04, 2023 |
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Molecular Dynamics Simulations on Quercetin-3-(6-Malonylglucoside) From Morus alba Shows Optimal Inhibition of Bcl-2 with Favorable Anti-Tumor Activities.
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Jul 04, 2023 |
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Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile
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Jul 04, 2023 |
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Cryptic mitochondrial ageing coincides with mid-late life and is pathophysiologically informative in single cells across tissues and species
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Jul 04, 2023 |
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Feature selection by replicate reproducibility and non-redundancy
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Jul 04, 2023 |
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ColabDock: inverting AlphaFold structure prediction model for protein-protein docking with experimental restraints
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Jul 04, 2023 |
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Multi-view integration of microbiome data for predicting host disease and identifying disease-associated features
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Jul 04, 2023 |
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Robust Feature Selection strategy detects a panel of microRNAs as putative diagnostic biomarkers in Breast Cancer
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Jul 04, 2023 |
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ColabSeg: An interactive tool for editing, processing, and visualizing membrane segmentations from cryo-ET data
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Jul 04, 2023 |
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Identification of critical cell-types using genetic modules: A case study of neurodevelopmental disorders
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Jul 04, 2023 |
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T4SEpp: a pipeline integrated with protein language models effectively predicting bacterial type IV secreted effectors
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Jul 03, 2023 |
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Identification and characterization of specific motifs in effector proteins of plant parasites using MOnSTER.
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Jul 03, 2023 |
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Reconstructing the Transcriptional Regulatory Network of Probiotic L. reuteri is Enabled by Transcriptomics and Machine Learning
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Jul 03, 2023 |
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PanTA: An ultra-fast method for constructing large and growing microbial pangenomes
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Jul 03, 2023 |
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In silico characterization of Protein L-Iso-Aspartate-O-Methyltransferases (PIMT) of Shigella flexner
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Jul 03, 2023 |
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EEG Signal Processing to Control a Finger Rehabilitation System
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Jul 03, 2023 |
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Mitigating autocorrelation during spatially resolved transcriptomics data analysis
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Jul 02, 2023 |
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New genome scale network modeling and mining workflow for detecting metabolic changes induced by exposure to chemicals
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Jul 02, 2023 |
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Entropy-based decoy generation methods for accurate FDR estimation in large-scale metabolomics annotations.
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Jul 02, 2023 |
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Optimal Transport Method-Based Gene Filter (GF) Denoising Algorithm for Enhancing Spatially Resolved Transcriptomics Data
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Jul 02, 2023 |
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Identification of treatment-responsive genes in spatial transcriptomics data by leveraging injection site information
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Jul 02, 2023 |
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P-PPI: accurate prediction of peroxisomal protein-protein interactions (P-PPI) using deep learning-based protein sequence embeddings
|
Jul 02, 2023 |
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Concise functional enrichment of ranked gene lists
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Jul 02, 2023 |
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Deep learning microstructure estimation of developing brains from diffusion MRI: a newborn and fetal study
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Jul 02, 2023 |
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CHAPERONg: A tool for automated GROMACS-based molecular dynamics simulations and trajectory analyses
|
Jul 02, 2023 |
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Easing OMERO adoption with ezomero
|
Jul 01, 2023 |
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Juggling offsets unlocks RNA-seq tools for fast scalable differential usage, aberrant splicing and expression analyses.
|
Jul 01, 2023 |
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Pan-cancer characterization of ncRNA synergistic competition uncovers potential carcinogenic biomarkers
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Jul 01, 2023 |
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Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer
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Jul 01, 2023 |
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A more expressive spline representation for SBML models improves code generation performance in AMICI
|
Jul 01, 2023 |
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Discovering Matrix Adducts for Enhanced Metabolite Profiling with Stable Isotope-Labeled MALDI-MSI
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Jun 30, 2023 |
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A Molecular Communication model for cellular metabolism
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Jun 30, 2023 |
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Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy
|
Jun 30, 2023 |
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OrthoPhyl - A turn-key solution for large scale whole genome bacterial phylogenomics
|
Jun 30, 2023 |
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Clinical super-resolution computed tomography of bone microstructure: application in musculoskeletal and dental imaging
|
Jun 30, 2023 |
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PSite: inference of read-specific P-site offsets for ribosomal footprints
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Jun 30, 2023 |
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Quantitative assessment of single-cell RNA-seq clustering with CONCORDEX
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Jun 30, 2023 |
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Machine learning of enhancer-promoter specificity based on enhancer perturbation studies reveals a distinct class of enhancers.
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Jun 30, 2023 |
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A Random Matrix Approach to Single Cell RNA-seq Analysis
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Jun 30, 2023 |
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DrugGPT: A GPT-based Strategy for Designing Potential Ligands Targeting Specific Proteins
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Jun 30, 2023 |
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Contextualising the developability risk of antibodies with lambda light chains using enhanced therapeutic antibody profiling
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Jun 30, 2023 |
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Integrative analysis of microbial 16S gene and shotgun metagenomic sequencing data improves statistical efficiency
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Jun 30, 2023 |
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Nanopore Adaptive Sampling Enriches for Antimicrobial Resistance Genes in Microbial Communities
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Jun 30, 2023 |
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A closer look at Type I left-handed β-helices provides a better understanding in their sequence-structure relationship: towards their rational design
|
Jun 29, 2023 |
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Morc1 re-establishes heterochromatin on activated transposons and shapes the host transcriptome in gonocytes
|
Jun 29, 2023 |
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Optimizing Proteomics Data Differential Expression Analysis via High-Performing Rules and Ensemble Inference
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Jun 29, 2023 |
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Mixed data analysis detected Endocrine Fibroblast Growth Factors (FGF19, FGF21, and FGF23) as Prognostic and Diagnostic Markers of Colorectal Neoplasia and Carcinoma
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Jun 29, 2023 |
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Clustering the Planet: An Exascale Approach to Determining Global Climatype Zones
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Jun 29, 2023 |
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Six novel nsSNPs affect RUNX1 gene may leading to Acute Myeloid Leukemia (AML) using Bioinformatics approach
|
Jun 29, 2023 |
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Automated Extraction and Visualization of Metabolic Networks from Biomedical Literature Using a Large Language Model
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Jun 29, 2023 |
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Computational investigation of cis-1,4-polyisoprene binding to the latex clearing protein LcpK30
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Jun 29, 2023 |
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Prediction of tumor-specific splicing from somatic mutations as a source of neoantigen candidates
|
Jun 29, 2023 |
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Scalable Integration of Multiomic Single Cell Data Using Generative Adversarial Networks
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Jun 29, 2023 |
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Identification of three distinct cell populations for urate excretion in human kidney
|
Jun 29, 2023 |
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Semi-automated retrieval of chemical and phylogenetic information from natural products literature
|
Jun 29, 2023 |
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Development of a CMS Classifier for Clinical CRC Samples
|
Jun 29, 2023 |
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nf-core/marsseq: systematic pre-processing pipeline for MARS-seq experiments
|
Jun 29, 2023 |
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Single-cell transcriptomes identify patient-tailored therapies for selective co-inhibition of cancer clones
|
Jun 28, 2023 |
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SpatialSPM: Statistical parametric mapping for the comparison of gene expression pattern images in multiple spatial transcriptomic datasets
|
Jun 28, 2023 |
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FISHtoFigure: An easy-to-use tool for rapid, multi-target partitioning and analysis of sub-cellular mRNA transcripts in smFISH data
|
Jun 28, 2023 |
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Design, Synthesis, Molecular Docking and Biological Activity of Pyrazolopyridines as Promising Lead Candidates Against Mycobacterium tuberculosis
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Jun 28, 2023 |
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Inference of Genomic Landscapes using Ordered Hidden Markov Models with Emission Densities (oHMMed)
|
Jun 28, 2023 |
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Generation of Super-resolution Images from Barcode-based Spatial Transcriptomics Using Deep Image Prior
|
Jun 28, 2023 |
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SHARK enables homology assessment in unalignable anddisordered sequences
|
Jun 28, 2023 |
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Enteropathway: the metabolic pathway database for the human gut microbiota
|
Jun 28, 2023 |
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CHARR efficiently estimates contamination from DNA sequencing data
|
Jun 28, 2023 |
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SpheroScan: A User-Friendly Deep Learning Tool for Spheroid Image Analysis
|
Jun 28, 2023 |
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Evolutionary potential of the monkeypox genome arising from interactions with human APOBEC3 enzymes
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Jun 28, 2023 |
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MGSurvE: A framework to optimize trap placement for genetic surveillance of mosquito population
|
Jun 27, 2023 |
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Metabolic-Pathway-Presence-Heatmap (MPPH):Constructing phylogenetic trees based on metabolic pathways.
|
Jun 27, 2023 |
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DENetwork: Unveiling Regulatory and Signaling Networks Behind Differentially-Expressed Genes
|
Jun 27, 2023 |
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FM3VCF: A Software Library for Accelerating the Loading of Large VCF Files in Genotype Data Analyses
|
Jun 27, 2023 |
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Catching a wave: on the suitability of traveling-wave solutions in epidemiological modeling
|
Jun 26, 2023 |
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Fusion Neural Network (FusNet) for predicting protein-mediated loops
|
Jun 26, 2023 |
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Incorporating physics to overcome data scarcity in predictive modeling of protein function: a case study of BK channels
|
Jun 26, 2023 |
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Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data
|
Jun 26, 2023 |
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Genome-scale metabolic model predicts mechanistic differences in metabolic gradient of spatially resolved small intestine villi
|
Jun 26, 2023 |
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Optimizer's dilemma: optimization strongly influences model selection in transcriptomic prediction
|
Jun 26, 2023 |
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PepFlow: direct conformational sampling from peptide energy landscapes through hypernetwork-conditioned diffusion
|
Jun 26, 2023 |
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Small allelic variants are a source of ancestral bias in structural variant breakpoint placement
|
Jun 26, 2023 |
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Rapid and accurate multi-phenotype imputation for millions of individuals
|
Jun 26, 2023 |
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Twenty novel nsSNPs may affect FLT3 gene leading to Acute Myeloid Leukemia (AML) using in silico analysis
|
Jun 26, 2023 |
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BioLiP2: a database for biological unit-based protein-ligand interactions
|
Jun 26, 2023 |
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Rocket-miR, a Translational Launchpad for miRNA-based Antimicrobial Drug Development
|
Jun 25, 2023 |
|
Transcriptomic Enrichment of Ferroptosis-Related Gene ACSL4 in Advanced Hepatic Fibrosis/Cirrhosis: Bioinformatics Analysis and Experimental validation
|
Jun 25, 2023 |
|
wTSA-CRAFT : an open-access web server for rapid analysis of thermal shift assay experiments
|
Jun 25, 2023 |
|
Multi_CycGT: a DL-based multimodal model for membrane permeability prediction of cyclic peptides
|
Jun 24, 2023 |
|
Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching
|
Jun 24, 2023 |
|
RIBO-former: leveraging ribosome profiling information to improve the detection of translated open reading frames.
|
Jun 24, 2023 |
|
Trajectories of atherosclerotic cardiovascular disease risk scores as a predictor for incident chronic kidney disease
|
Jun 24, 2023 |
|
Brooklyn plots to identify co-expression dysregulation in single cell sequencing
|
Jun 24, 2023 |
|
A method for storing information in DNA with improved dropout tolerance
|
Jun 24, 2023 |
|
QuantUMS: uncertainty minimisation enables confident quantification in proteomics
|
Jun 24, 2023 |
|
Exact Sketch-Based Read Mapping
|
Jun 24, 2023 |
|
Co-linear Chaining on Pangenome Graphs
|
Jun 24, 2023 |
|
A Clear, Legible, Explainable, Transparent, and Elucidative (CLETE) Binary Classification Platform for Tabular Data
|
Jun 24, 2023 |
|
SEGMENTATION OF DYNAMIC TOTAL-BODY -FDG PET IMAGES USING UNSUPERVISED CLUSTERING
|
Jun 24, 2023 |
|
Pathway Centric Analysis for single-cell RNA-seq and Spatial Transcriptomics Data with GSDensity
|
Jun 24, 2023 |
|
FLOP: Tasks for Fitness Landscapes Of Protein wildtypes
|
Jun 24, 2023 |
|
ShinyMultiome.UiO: An interactive open-source framework utilizing Seurat Objects for visualizing single-cell Multiomes
|
Jun 24, 2023 |
|
Re-investigating the correctness of decoy-based false discovery rate control in proteomics tandem mass spectrometry
|
Jun 24, 2023 |
|
Rat Deconvolution as Knowledge Miner for Immune Cell Trafficking from Toxicogenomics Databases
|
Jun 24, 2023 |
|
The landscape of microRNA interactions annotation: analysis of three rare disorders as case study
|
Jun 24, 2023 |
|
DeepRank-GNN-esm: A Graph Neural Network for Scoring Protein-Protein Models using Protein Language Model
|
Jun 24, 2023 |
|
Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking
|
Jun 24, 2023 |
|
A mean-field to capture asynchronous irregular dynamics of conductance-based networks of adaptive quadratic integrate-and-fire neuron models
|
Jun 24, 2023 |
|
Vocabulary Matters: An Annotation Pipeline and Two Deep Learning Algorithms for Enzyme Named Entity Recognition
|
Jun 24, 2023 |
|
Bioinformatic Surveillance Leads to Discovery of Two Novel Putative Bunyaviruses Associated with Black Soldier Fly
|
Jun 24, 2023 |
|
MOCHA: Advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human disease cohorts
|
Jun 24, 2023 |
|
Fine-tuning Protein Embeddings for GeneralizableAnnotation Propagation
|
Jun 24, 2023 |
|
Peak-agnostic high-resolution cis-regulatory circuitry mapping using single cell multiome data
|
Jun 24, 2023 |
|
Language model-based B cell receptor sequence embeddings can effectively encode receptor specificity
|
Jun 23, 2023 |
|
Revisiting annotation of Schistosoma mansoni Micro-Exon Gene (MEG) family
|
Jun 23, 2023 |
|
GeNNius: An ultrafast drug-target interaction inference method based on graph neural networks
|
Jun 23, 2023 |
|
Deep learning, data ramping, and uncertainty estimation for detecting artifacts in large, imbalanced databases of MRI images
|
Jun 23, 2023 |
|
netMUG: a novel network-guided multi-view clustering workflow for dissecting genetic and facial heterogeneity
|
May 05, 2023 |
|
JLOH: Inferring Loss of Heterozygosity Blocks from Sequencing Data
|
May 05, 2023 |
|
Active and Allosteric Site Binding MOLECULAR MECHANICS-QUANTUM MECHANICS studies of STEVIOSIDE Derivative in PCSK9 Protein Intended to provide a safe Antilipidemic agent
|
May 05, 2023 |
|
ImSpiRE: Image feature-aided spatial resolution enhancement method
|
May 05, 2023 |
|
Diversity of the bacterial and viral communities in the tropical horse tick, Dermacentor nitens in Colombia
|
May 05, 2023 |
|
A Bayesian Noisy Logic Model for Inference of Transcription Factor Activity from Single Cell and Bulk Transcriptomic Data
|
May 05, 2023 |
|
Orphan Drugs and Rare Diseases: Unveiling Biological Patterns through Drug Repurposing
|
May 05, 2023 |
|
Worth the weight: Sub-Pocket EXplorer (SubPEx), a weighted-ensemble method to enhance binding-pocket conformational sampling
|
May 05, 2023 |
|
Protein Engineering for Thermostability through Deep Evolution
|
May 05, 2023 |
|
The evolution of splice site sequence preference is linked to the U6 snRNA m6A methyltransferase METTL16
|
May 05, 2023 |
|
Drug resistance prediction for Mycobacterium tuberculosis with reference graphs
|
May 04, 2023 |
|
Enhancing drug repurposing on graphs by integrating drug molecular structure as feature
|
May 04, 2023 |
|
Reverse Engineering DNA Origami Nanostructure Designs from Raw Scaffold and Staple Sequence Lists
|
May 04, 2023 |
|
A time-resolved meta-analysis of consensus gene expression profiles during human T-cell activation
|
May 04, 2023 |
|
HiPhase: Jointly phasing small and structural variants from HiFi sequencing
|
May 04, 2023 |
|
cellsnake: a user-friendly tool for single cell RNA sequencing analysis
|
May 04, 2023 |
|
GARSA: An integrative pipeline for genome wide association studies and polygenic risk score inference in admixed human populations
|
May 04, 2023 |
|
Single-cell Mayo Map (scMayoMap): an easy-to-use tool for cell type annotation in single-cell RNA-sequencing data analysis
|
May 04, 2023 |
|
ESKtides: a comprehensive database and mining method for ESKAPE-derived peptides
|
May 04, 2023 |
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Integrating gene mutation spectra from tumors and the general population with gene expression topological networks to identify novel cancer driver genes
|
May 03, 2023 |
|
Scalable Log-ratio Lasso Regression Enhances Microbiome Feature Selection for Predictive Models
|
May 03, 2023 |
|
Enzyme stability-activity trade-off: new insights from protein stability weaknesses and evolutionary conservation
|
May 03, 2023 |
|
Restrander: rapid orientation and QC of long-read cDNA data
|
May 03, 2023 |
|
Analysis of tandem mass spectrometry data with CONGA: Combining Open and Narrow searches with Group-wise Analysis
|
May 03, 2023 |
|
An image segmentation method based on the spatial correlation coefficient of Local Moran's I
|
May 02, 2023 |
|
memo-eQTL: DNA methylation modulated genetic variant effect on gene transcriptional regulation
|
May 02, 2023 |
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Automatic annotation of the bHLH gene family in plants
|
May 02, 2023 |
|
Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in Prokaryotic metagenome-assembled genome recovery
|
May 02, 2023 |
|
DrugMechDB: A Curated Database of Drug Mechanisms
|
May 02, 2023 |
|
An in-silico approach to study the molecular interaction of the PINK1 kinase domain with Parkin Ubl domain
|
May 02, 2023 |
|
A 2D convolutional neural network for taxonomic classification applied to viruses in the phylum Cressdnaviricota
|
May 02, 2023 |
|
scDisInFact: disentangled learning for integration and prediction of multi-batch multi-condition single-cell RNA-sequencing data
|
May 02, 2023 |
|
Molecule-Morphology Contrastive Pretraining for Transferable Molecular Representation
|
May 02, 2023 |
|
Variance Analysis of LC-MS Experimental Factors and Their Impact on Machine Learning
|
May 02, 2023 |
|
SAP: Synteny-aware gene function prediction for bacteria using protein embeddings
|
May 02, 2023 |
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Joint representation of molecular networks from multiple species improves gene classification
|
May 02, 2023 |
|
Syndecan-4 is the Key Proteoglycan Mediating LPS-induced Sepsis-associated Lung Injury
|
May 02, 2023 |
|
MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
|
May 02, 2023 |
|
Computational fitness estimates of SARS-CoV-2 mutations affecting spike protein binding to antibodies and ACE2
|
May 02, 2023 |
|
Building Trust in Deep Learning-based Immune Response Predictors with Interpretable Explanations
|
May 02, 2023 |
|
Building flexible and robust analysis frameworks for molecular subtyping of cancers
|
May 01, 2023 |
|
Only three principal components account for inter-embryo variability of the spindle length over time.
|
May 01, 2023 |
|
Automatic Classification of Normal and Abnormal Cell Division Using Deep Learning Analysis of Mitosis Videos
|
May 01, 2023 |
|
scGPT: Towards Building a Foundation Model for Single-Cell Multi-omics Using Generative AI
|
May 01, 2023 |
|
Automatic cell type harmonization and integration across Human Cell Atlas datasets
|
May 01, 2023 |
|
Improving AlphaFold2-based Protein Tertiary Structure Prediction with MULTICOM in CASP15
|
May 01, 2023 |
|
Annotation-free pathology images characterize tumor immune microenvironment in breast cancer by weakly supervised contrastive learning
|
Apr 30, 2023 |
|
Negligible effects of read trimming on the accuracy of germline short variant calling in the human genome
|
Apr 30, 2023 |
|
Exploring The Ability Of Machine Learning-Based Virtual Screening Models To Identify The Functional Groups Responsible For Binding
|
Apr 30, 2023 |
|
Semantic Representation of Neural Circuit Knowledge in Caenorhabditis elegans
|
Apr 30, 2023 |
|
Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples
|
Apr 30, 2023 |
|
Charting the alternative usage of protein repeated regions in evolution and its implication for protein interactions
|
Apr 30, 2023 |
|
Cell-attribute aware community detection improves differential abundance testing from single-cell RNA-Seq data
|
Apr 29, 2023 |
|
xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs
|
Apr 29, 2023 |
|
Identification of disease mechanisms and novel disease genes using clinical concept embeddings learned from massive amounts of biomedical data.
|
Apr 29, 2023 |
|
Network inference from temporal phosphoproteomics informed by protein-protein interactions
|
Apr 29, 2023 |
|
Integrated analysis of spatial multi-omics with SpatialGlue
|
Apr 29, 2023 |
|
Computational Insight into Anti-Obesity Effects of Combined Some Phytobiotics to GLP1R (Glucagon-Like Peptide 1 Receptor) Protein in Anas javanica
|
Apr 29, 2023 |
|
Improved Quality Metrics for Association and Reproducibility in Chromatin Accessibility Data Using Mutual Information
|
Apr 29, 2023 |
|
APOE-NOTCH Axis Governs Elastogenesis During Human Cardiac Valve Remodeling
|
Apr 29, 2023 |
|
TISSUE: uncertainty-calibrated prediction of single-cell spatial transcriptomics improves downstream analyses
|
Apr 29, 2023 |
|
Self-supervision advances morphological profiling by unlocking powerful image representations
|
Apr 29, 2023 |
|
Bacterial colony size growth estimation by deep learning
|
Apr 29, 2023 |
|
The Influence of Brain MRI Defacing Algorithms on Brain-Age Predictions via 3D Convolutional Neural Networks
|
Apr 29, 2023 |
|
Identification of transcription factor co-binding patterns with non-negative matrix factorization
|
Apr 29, 2023 |
|
scEpiTools: a database to comprehensively interrogate analytic tools for single-cell epigenomic data
|
Apr 29, 2023 |
|
MitoSort: robust demultiplexing of pooled single-cell genomics data using endogenous germline mitochondrial variants
|
Apr 28, 2023 |
|
MetPlast: an R package to evaluate Metabolic Plasticity using Information Theory statistical framework
|
Apr 28, 2023 |
|
Interpretable dimensionality reduction and classification of mass spectrometry imaging data in a visceral pain model via non-negative matrix factorization
|
Apr 28, 2023 |
|
VISTA: Visualizing the Spatial Transcriptome of the C. elegans Nervous System
|
Apr 28, 2023 |
|
Clade-Specific MPXV PCR Assays
|
Apr 28, 2023 |
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Learning the Language of Antibody Hypervariability
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Apr 28, 2023 |
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CcBHLA: pan-specific peptide-HLA class I binding prediction via Convolutional and BiLSTM features
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Apr 28, 2023 |
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RaptorX-Single: single-sequence protein structure prediction by integrating protein language models
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Apr 28, 2023 |
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A deep reinforcement learning approach to the optimization of epithelial sheets biofabrication
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Apr 28, 2023 |
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DEGAP: Dynamic Elongation of a Genome Assembly Path
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Apr 28, 2023 |
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EnGens: a computational framework for generation and analysis of representative protein conformational ensembles
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Apr 28, 2023 |
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Interfacial residues in protein-protein complexes are in the eyes of the beholder
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Apr 28, 2023 |
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Uncovering the hidden structure of dynamic T cell composition in peripheral blood during cancer immunotherapy: a topic modeling approach
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Apr 28, 2023 |
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Riboformer: A Deep Learning Framework for Predicting Context-Dependent Translation Dynamics
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Apr 28, 2023 |
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InterOpt: Improved gene expression quantification in qPCR experiments using weighted aggregation of reference genes
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Apr 28, 2023 |
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TIME-SERIES CLASSIFICATION FOR PATIENTS UNDER ACTIVE SURVEILLANCE AND SCREENING USING ECHO STATE NETWORK
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Apr 28, 2023 |
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Assessment of Total Oocyte Transcripts Representation through Single Ooplasm Biopsy in Bovine with High Reliability
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Apr 28, 2023 |
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Uncovering Co-regulatory Modules and Gene Regulatory Networks in the Heart through Machine Learning-based Analysis of Large-scale Epigenomic Data
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Apr 28, 2023 |
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KOunt - A reproducible KEGG orthologue abundance workflow
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Apr 28, 2023 |
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SeqImprove: Machine Learning Assisted Creation of Machine Readable Sequence Information
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Apr 28, 2023 |
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RNAvigate: Efficient exploration of RNA chemical probing datasets
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Apr 28, 2023 |
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A benchmark study on current GWAS models in admixed populations
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Apr 28, 2023 |
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Plasma-free samples for transcriptomic analysis: a potential alternative to whole blood samples
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Apr 28, 2023 |
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Benchmarking Bioinformatic Virus Identification Tools Using Real-World Metagenomic Data across Biomes
|
Apr 28, 2023 |
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Deep Learning for Protein Structure Prediction: Advancements in Structural Bioinformatics
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Apr 28, 2023 |
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STAPLER: Efficient learning of TCR-peptide specificity prediction from full-length TCR-peptide data
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Apr 28, 2023 |
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Surfaces: A software to quantify and visualize interactions within and between proteins and ligands
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Apr 28, 2023 |
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DeepUMQA3: a web server for model quality assessment of protein complexes
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Apr 28, 2023 |
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Supervised biological network alignment with graph neural networks
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Apr 28, 2023 |
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Genome-wide analysis of CRISPR perturbations indicates that enhancers act multiplicatively and without epistatic-like interactions
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Apr 27, 2023 |
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NextPolish2: a repeat-aware polishing tool for genomes assembled using HiFi long reads
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Apr 27, 2023 |
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De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep Learning Framework
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Apr 26, 2023 |
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VirtualFlow 2.0 - The Next Generation Drug Discovery Platform Enabling Adaptive Screens of 69 Billion Molecules
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Apr 26, 2023 |
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VODKA2: An accurate method to detect copy-back and deletion viral genomes from next-generation sequencing data
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Apr 25, 2023 |
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Automatic quantification of disgust taste reactivity in mice using machine learning
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Apr 25, 2023 |
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Representation Learning to Effectively Integrate and Interpret Omics Data
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Apr 25, 2023 |
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Chaotic aging: Intrinsically disordered proteins in aging-related processes
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Apr 25, 2023 |
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Histone methylation has a direct metabolic role in human cells
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Apr 25, 2023 |
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scDEED: a statistical method for detecting dubious 2D single-cell embeddings
|
Apr 25, 2023 |
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Comparative study of the mechanism of natural compounds with similar structures using docking and transcriptome data for improving in silico herbal medicine experimentations
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Apr 25, 2023 |
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AtlasXplore: a web platform for visualizing and sharing spatial epigenome data
|
Apr 25, 2023 |
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SurVIndel2: improving local CNVs calling from next-generation sequencing using novel hidden information
|
Apr 25, 2023 |
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Diagnostic Evidence Gauge of Spatial Transcriptomics (DEGAS): Using transfer learning to map clinical data to spatial transcriptomics in prostate cancer
|
Apr 25, 2023 |
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Model-based dimensionality reduction for single-cell RNA-seq using generalized bilinear models
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Apr 25, 2023 |
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CoSIA: an R Bioconductor package for CrOss Species Investigation and Analysis
|
Apr 25, 2023 |
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Molecular insight into the mechanism of action of some beneficial flavonoids for the treatment of Parkinson's Disease
|
Apr 25, 2023 |
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hipFG: High-throughput harmonization and integration pipeline for functional genomics data
|
Apr 25, 2023 |
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Accuracy and Reliability of a Suite of Digital Measures of Walking Generated Using a Wrist-worn Sensor: Performance Characterization Study
|
Apr 25, 2023 |
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Ranking Antibody Binding Epitopes and Proteins Across Samples from Whole Proteome Tiled Linear Peptides
|
Apr 25, 2023 |
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Capture-recapture for -omics data meta-analysis
|
Apr 25, 2023 |
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ORFeus: A Computational Method to Detect Programmed Ribosomal Frameshifts and Other Non-Canonical Translation Events
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Apr 25, 2023 |
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3D structural human interactome reveals proteome-wide perturbations by disease mutations
|
Apr 25, 2023 |
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Topology-Aware Focal Loss for 3D Image Segmentation
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Apr 24, 2023 |
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BEERS2: RNA-Seq simulation through high fidelity in silico modeling
|
Apr 24, 2023 |
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standR: a Bioconductor package for analysing transcriptomic Nanostring GeoMx DSP data
|
Apr 24, 2023 |
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Metabolic predictors of response to immune checkpoint blockade therapy
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Apr 21, 2023 |
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Protein family annotation for the Unified Human Gastrointestinal Proteome by DPCfam clustering
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Apr 21, 2023 |
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Reference-free and cost-effective automated cell type annotation with GPT-4 in single-cell RNA-seq analysis
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Apr 21, 2023 |
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Protein multiple conformations prediction using multi-objective evolution algorithm
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Apr 21, 2023 |
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Disruption of metazoan gene regulatory networks in cancer alters the balance of co-expression between genes of unicellular and multicellular origins
|
Apr 21, 2023 |
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Exploring the Landscape of Spatial Transcriptome Analysis: Introducing STASH, a Database of Spatial Transcriptome Tools
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Apr 21, 2023 |
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Alternative splicing impacts microRNA regulation within coding regions
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Apr 21, 2023 |
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Transcript Assembly and Annotations: Bias and Adjustment
|
Apr 21, 2023 |
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The Cell Subtypes Selection by Genes (CSSG) algorithm for discovering cell populations in high resolution
|
Apr 21, 2023 |
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GSR-DB: a manually curated and optimised taxonomical database for 16S rRNA amplicon analysis
|
Apr 21, 2023 |
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D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response
|
Apr 21, 2023 |
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Fibertools: fast and accurate DNA-m6A calling using single-molecule long-read sequencing
|
Apr 21, 2023 |
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Kronos: A computational tool to facilitate biological rhythmicity analysis
|
Apr 21, 2023 |
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TopoDoE: A Design of Experiment strategy for selection and refinement in ensembles of executable Gene Regulatory Networks
|
Apr 21, 2023 |
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Key common genes and pathways in ulcerative colitis and ankylosing spondylitis based on bioinformatics analysis
|
Apr 21, 2023 |
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The Promise and Pitfalls of Prophages
|
Apr 21, 2023 |
|
AI becomes a masterbrain scientist
|
Apr 21, 2023 |
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CellHeap: A scRNA-seq workflow for large-scalebioinformatics data analysis
|
Apr 21, 2023 |
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AbFold -- an AlphaFold Based Transfer Learning Model for Accurate Antibody Structure Prediction
|
Apr 21, 2023 |
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VoroIF-GNN: Voronoi tessellation-derived protein-protein interface assessment using a graph neural network
|
Apr 21, 2023 |
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Pathfinder: protein folding pathway prediction based on conformational sampling
|
Apr 21, 2023 |
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Scoary2: Rapid association of phenotypic multi-omics data with microbial pan-genomes
|
Apr 21, 2023 |
|
Impact of water models on structure and dynamics of ligand-transport tunnels in enzymes derived from molecular dynamics simulations
|
Apr 21, 2023 |
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Automatic recognition of complementary strands: Lessons regarding machine learning abilities in RNA folding
|
Apr 21, 2023 |
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Correcting 4sU induced quantification bias in nucleotide conversion RNA-seq data
|
Apr 21, 2023 |
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Machine learning detection of SARS-CoV-2 high-risk variants
|
Apr 20, 2023 |
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Contigs directed gene annotation (ConDiGA) for accurate protein sequence database construction in metaproteomics
|
Apr 20, 2023 |
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Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses
|
Apr 20, 2023 |
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Matrisome AnalyzeR: A suite of tools to annotate and quantify ECM molecules in big datasets across organisms
|
Apr 20, 2023 |
|
Efficient k-mer based curation of raw sequence data: application in Drosophila suzukii
|
Apr 20, 2023 |
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MACI: A machine learning-based approach to identify drug classes of antibiotic resistance genes from metagenomic data
|
Apr 20, 2023 |
|
A Comprehensive Benchmark Study on Biomedical Text Generation and Mining with ChatGPT
|
Apr 20, 2023 |
|
The covariance environment defines cellular niches for spatial inference
|
Apr 20, 2023 |
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Investigation of the usefulness of liver-specific deconvolution method toward legacy data utilization
|
Apr 20, 2023 |
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A novel Energy Landscape construction method incorporating the Latent Dirichlet Allocation topic model and the pairwise Maximum Entropy model, revealing the significant contribution of Bactericides to the development of Inflammatory Bowel Disease
|
Apr 20, 2023 |
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Exhaustive benchmarking of de novo assembly methods for eukaryotic genomes
|
Apr 20, 2023 |
|
YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample
|
Apr 20, 2023 |
|
Pyro: A Comprehensive Pipeline for Eukaryotic Genome Assembly
|
Apr 20, 2023 |
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Fine Tuning Rigid Body Docking Results Using the Dreiding Force Field: A Computational Study of 36 Known Nanobody-Protein Complexes
|
Apr 19, 2023 |
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Predicting Distant Recurrences in Invasive Breast Carcinoma Patients Using Clinicopathological Data: A cross-institutional and AI-based study
|
Apr 19, 2023 |
|
DeepCORE: An interpretable multi-view deep neural network model to detect co-operative regulatory elements
|
Apr 19, 2023 |
|
BrainTACO: An Explorable Multi-Scale Multi-Modal Brain Transcriptomic And Connectivity Data Resource
|
Apr 19, 2023 |
|
BREADR: An R Package for the Bayesian Estimation of Genetic Relatedness from Low-coverage Genotype Data
|
Apr 18, 2023 |
|
AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data
|
Apr 18, 2023 |
|
PaxDB 5.0: curated protein quantification data suggests adaptive proteome changes
|
Apr 18, 2023 |
|
The effect of removing repeat-induced overlaps in de novo assembly
|
Apr 18, 2023 |
|
An explainable graph neural framework to identify cancer-associated intratumoral microbial communities
|
Apr 18, 2023 |
|
Screening and identification of key biomarkers in diabetic kidney disease and its complications: Evidence from bioinformatics and next generation sequencing data analysis
|
Apr 18, 2023 |
|
mitoSpliter: a mitochondrial RNA variants-based method for single-cell RNA-seq analysis of multiplexed samples
|
Apr 18, 2023 |
|
CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data
|
Apr 18, 2023 |
|
An accurate and interpretable model to predict antimicrobial resistance in One Health settings
|
Apr 18, 2023 |
|
Transcriptome Complexity Disentangled: A Regulatory Elements Approach
|
Apr 18, 2023 |
|
NucleosomeDB - a database of 3D nucleosome structures and their complexes with comparative analysis toolkit
|
Apr 18, 2023 |
|
DESpace: spatially variable gene detection via differential expression testing of spatial clusters
|
Apr 18, 2023 |
|
Integrating Expert Knowledge with Deep Learning Improves QSAR Models for CADD Modeling
|
Apr 18, 2023 |
|
How AlphaFold shaped the structural coverage of the human transmembrane proteome
|
Apr 18, 2023 |
|
Rapid protein-protein interaction network creation from multiple sequence alignments with Deep Learning
|
Apr 17, 2023 |
|
SPADE: Spatial Deconvolution for Domain Specific Cell-type Estimation
|
Apr 17, 2023 |
|
Discovery of novel multi-functional peptides by using protein language models and graph-based deep learning
|
Apr 17, 2023 |
|
RNA covariation at helix-level resolution for the identification of evolutionarily conserved RNA structure
|
Apr 17, 2023 |
|
Assisting and Accelerating NMR Assignment with Restrainted Structure Prediction
|
Apr 17, 2023 |
|
GraphPart: Homology partitioning for biological sequence analysis
|
Apr 17, 2023 |
|
Assessing the quality of comparative genomics data and results with the cogeqc R/Bioconductor package
|
Apr 17, 2023 |
|
Mapping lineage-traced cells across time points with moslin
|
Apr 17, 2023 |
|
Reply to: The pitfalls of negative data bias for the T-cell epitope specificity challenge
|
Apr 17, 2023 |
|
Charting spatial ligand-target activity using Renoir
|
Apr 17, 2023 |
|
An Equivariant Generative Framework for Molecular Graph-Structure Co-Design
|
Apr 17, 2023 |
|
Weakly supervised contrastive learning infers molecular subtypes and recurrence risk of breast cancer from pathology images
|
Apr 17, 2023 |
|
Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression
|
Apr 16, 2023 |
|
Computational pathology infer clinically relevant protein levels and drug efficacy in breast cancer by weakly supervised contrastive learning
|
Apr 16, 2023 |
|
The Power of Two: integrating deep diffusion models and variational autoencoders for single-cell transcriptomics analysis
|
Apr 16, 2023 |
|
Single-Cell Transcriptomes and Immune Repertoires Reveal the Cell State and Molecular Changes in Pemphigus Vulgaris
|
Apr 14, 2023 |
|
Do NSm virulence factors in the Bunyavirales order originate from Gn gene duplication?
|
Apr 14, 2023 |
|
Context-Aware Amino Acid Embedding Advances Analysis of TCR-Epitope Interactions
|
Apr 14, 2023 |
|
A mouse-specific model to detect genes under selection in tumors
|
Apr 14, 2023 |
|
Identification of Mirror Repeats in Viral Genomes using FPCB Analysis
|
Apr 14, 2023 |
|
Surface-guided computing to analyze subcellular morphology and membrane-associated signals in 3D
|
Apr 14, 2023 |
|
PhenoCellPy: A Python package for biological cell behavior modeling
|
Apr 14, 2023 |
|
Linear and Neural Network Models for Predicting N-glycosylation in Chinese Hamster Ovary Cells Based on B4GALT Levels
|
Apr 14, 2023 |
|
Ultra-fast genotyping of SNPs and short indels using GPU acceleration
|
Apr 14, 2023 |
|
Ensembles for improved detection of invasive breast cancer in histological images
|
Apr 14, 2023 |
|
A comparison between Greengenes, SILVA, RDP, and NCBI reference databases in four published microbiota datasets
|
Apr 13, 2023 |
|
Barcode-free multiplex plasmid sequencing using Bayesian analysis and nanopore sequencing
|
Apr 13, 2023 |
|
PGSbuilder: An end-to-end platform for human genome association analysis and polygenic risk score predictions
|
Apr 13, 2023 |
|
LinRace: single cell lineage reconstruction using paired lineage barcode and gene expression data
|
Apr 13, 2023 |
|
Wearable-ome meets epigenome: A novel approach to measuring biological age with wearable devices.
|
Apr 13, 2023 |
|
SARS-CoV-2 selectively induces the expression of unproductive splicing isoforms of interferon, class I MHC and splicing machinery genes
|
Apr 13, 2023 |
|
Alignment of spatial transcriptomics data using diffeomorphic metric mapping
|
Apr 12, 2023 |
|
A zero-agnostic model for copy number evolution in cancer
|
Apr 12, 2023 |
|
WormSwin: Instance segmentation of C. elegans using vision transformer
|
Apr 12, 2023 |
|
acorn: an R package for de novo variant analysis
|
Apr 12, 2023 |
|
SpatialCTD: a large-scale TME spatial transcriptomic dataset to evaluate cell type deconvolution for immuno-oncology
|
Apr 12, 2023 |
|
Comparative Clustering (CompaCt) of eukaryote complexomes identifies novel interactions and sheds light on protein complex evolution
|
Apr 12, 2023 |
|
LOCC: a novel visualization and scoring of cutoffs for continuous variables
|
Apr 12, 2023 |
|
Programmed ribosomal frameshifts, and how to find them
|
Apr 12, 2023 |
|
Demultiplex2: robust sample demultiplexing for scRNA-seq
|
Apr 12, 2023 |
|
Accurate prediction of in vivo protein abundances by coupling constraint-based modeling and machine learning
|
Apr 12, 2023 |
|
G2GSnake: A Snakemake workflow for host-pathogen genomic association studies
|
Apr 12, 2023 |
|
Improved interpretability of bacterial genome-wide associations using gene cluster centric k-mers
|
Apr 12, 2023 |
|
Fecal metagenomics to identify biomarkers of food intake in healthy adults: Findings from randomized, controlled, nutrition trials
|
Apr 11, 2023 |
|
Deep Learning and Transfer Learning for Brain Tumor Detection and Classification
|
Apr 11, 2023 |
|
An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics
|
Apr 11, 2023 |
|
Estimating amino acid substitution models from genome datasets: A simulation study on the performance of estimated models
|
Apr 10, 2023 |
|
ReCom: A semi-supervised approach to ultra-tolerant database search for improved identification of modified peptides
|
Apr 10, 2023 |
|
GALBA: Genome Annotation with Miniprot and AUGUSTUS
|
Apr 10, 2023 |
|
A modular metagenomics analysis system for integrated multi-step data exploration
|
Apr 09, 2023 |
|
Predicting splicing patterns from the transcription factor binding sites in the promoter with deep learning
|
Apr 09, 2023 |
|
Evaluating proteomics imputation methods with improved criteria
|
Apr 08, 2023 |
|
scSPARKL: Apache Spark based parallel analytical framework for the downstream analysis of scRNA-seq data.
|
Apr 08, 2023 |
|
MOViDA: Multi-Omics Visible Drug Activity Prediction with a Biologically Informed Neural Network Model
|
Apr 08, 2023 |
|
Spatial-linked alignment tool (SLAT) for aligning heterogenous slices properly
|
Apr 08, 2023 |
|
Prediction of virus-host association using protein language models and multiple instance learning
|
Apr 08, 2023 |
|
scART: recognizing cell clusters and constructing trajectory from single-cell epigenomic data
|
Apr 08, 2023 |
|
Deep learning of genomic contexts predicts protein co-regulation and function
|
Apr 08, 2023 |
|
Salt corrections for RNA secondary structures in the ViennaRNA package
|
Apr 08, 2023 |
|
Determining the Statistical Significance of the Difference Between Arbitrary Curves: A Spreadsheet Approach
|
Apr 08, 2023 |
|
A Weighted Two-stage Sequence Alignment Framework to Identify DNA Motifs from ChIP-exo Data
|
Apr 08, 2023 |
|
Coding Sequence Insertions in Fungal Genomes are Intrinsically Disordered and can Impart Functionally-Important Properties on the Host Protein
|
Apr 07, 2023 |
|
HCV E1 influences the fitness landscape of E2 and may enhance escape from E2-specific antibodies
|
Apr 07, 2023 |
|
Binary classification machine-learning Unveils Sex-Dependent mutated gene Signatures in Melanoma
|
Apr 07, 2023 |
|
euka: Robust detection of eukaryotic taxa from modern and ancient environmental DNA using pangenomic reference graphs.
|
Apr 07, 2023 |
|
Benchmarking imputation methods for discrete biological data
|
Apr 07, 2023 |
|
A resampling-based approach to share reference panels
|
Apr 07, 2023 |
|
Integrating multiple single-cell multi-omics samples with Smmit
|
Apr 06, 2023 |
|
Building pangenome graphs
|
Apr 06, 2023 |
|
The pitfalls of negative data bias for the T-cell epitope specificity challenge
|
Apr 06, 2023 |
|
CT Multi-Task Learning with a Large Image-Text (LIT) Model
|
Apr 06, 2023 |
|
M-Ionic: Prediction of metal ion binding sites from sequence using residue embeddings
|
Apr 06, 2023 |
|
SFyNCS detects oncogenic fusions involving non-coding sequences in cancer
|
Apr 06, 2023 |
|
The ENCODE Uniform Analysis Pipelines
|
Apr 06, 2023 |
|
GEGVIC: A workflow to analyze Gene Expression, Genetic Variations and Immune cell Composition of tumor samples using Next Generation Sequencing data
|
Apr 06, 2023 |
|
PPIAT:Target mass spectrometry based Protein-Protein interaction analytics tool
|
Apr 06, 2023 |
|
GGoutlieR: an R package to identify and visualize unusual geo-genetic patterns of biological samples
|
Apr 06, 2023 |
|
Fast genome-based delimitation of Enterobacterales species
|
Apr 06, 2023 |
|
Characterization of proteoform post-translational modifications by top-down and bottom-up mass spectrometry in conjunction with UniProt annotations
|
Apr 06, 2023 |
|
GENI: a web server to identify gene set enrichments in tumor samples
|
Apr 06, 2023 |
|
tauFisher accurately predicts circadian time from a single sample of bulk and single-cell transcriptomic data
|
Apr 06, 2023 |
|
Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification.
|
Apr 06, 2023 |
|
Multiomics Approach to Understanding Olaparib Resistance and Predicting Drug Response
|
Apr 06, 2023 |
|
Meta-analysis of gene activity (MAGA) contributions and correlation with gene expression, through GAGAM.
|
Apr 06, 2023 |
|
THAPBI PICT - a fast, cautious, and accurate metabarcoding analysis pipeline
|
Apr 06, 2023 |
|
Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis
|
Apr 06, 2023 |
|
Assessment of the normal cell contamination impact on tumour samples analysed with SNP arrays: The signal confusion nightmare.
|
Apr 06, 2023 |
|
RSim: A Reference-Based Normalization Method via Rank Similarity
|
Apr 06, 2023 |
|
BetaBuddy: An end-to-end computer vision pipeline for the automated analysis of insulin secreting β-cells
|
Apr 06, 2023 |
|
XClone: detection of allele-specific subclonal copy number variations from single-cell transcriptomic data
|
Apr 05, 2023 |
|
TALLSorts: a T-cell acute lymphoblastic leukaemia subtype classifier using RNA-seq expression data
|
Apr 05, 2023 |
|
Improving deep models of protein-coding potential with a Fourier-transform architecture and machine translation task
|
Apr 05, 2023 |
|
Detecting Anomalous Proteins Using Deep Representations
|
Apr 05, 2023 |
|
Prediction of fast subcellular Ca2+ signals based on subcellular structures in label-free second harmonic generation microscopy measurements
|
Apr 05, 2023 |
|
Comparison of classification accuracy and feature selection between sparse and non-sparse modeling of metabolomics data
|
Apr 05, 2023 |
|
Cell Painting-based bioactivity prediction boosts high-throughput screening hit-rates and compound diversity
|
Apr 05, 2023 |
|
asmbPLS: Adaptive Sparse Multi-block Partial Least Square for Survival Prediction using Multi-Omics Data
|
Apr 05, 2023 |
|
Protein language model powers accurate and fast sequence search for remote homology
|
Apr 05, 2023 |
|
Reconstruction Set Test (RESET): a computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error
|
Apr 05, 2023 |
|
DrBERT: A Robust Pre-trained Model in French for Biomedical and Clinical domains
|
Apr 05, 2023 |
|
Coordination of host and endosymbiont gene expression governs endosymbiont growth and elimination in the cereal weevil Sitophilus spp.
|
Apr 05, 2023 |
|
SEQUENCE VS. STRUCTURE: DELVING DEEP INTO DATA DRIVEN PROTEIN FUNCTION PREDICTION
|
Apr 04, 2023 |
|
MANGEM - a web app for Multimodal Analysis of Neuronal Gene expression, Electrophysiology and Morphology
|
Apr 04, 2023 |
|
A hybrid single-cell demultiplexing strategy that increases both cell recovery rate and calling accuracy
|
Apr 04, 2023 |
|
Reconstruction of Gene Regulatory Networks using sparse graph recovery models
|
Apr 04, 2023 |
|
Dividing out quantification uncertainty allows efficient assessment of differential transcript expression
|
Apr 04, 2023 |
|
Phables: from fragmented assemblies to high-quality bacteriophage genomes
|
Apr 04, 2023 |
|
Using macromolecular electron densities to improve the enrichment of active compounds in virtual screening
|
Apr 04, 2023 |
|
Comparing chromatin contact maps at scale: methods and insights
|
Apr 04, 2023 |
|
The Functional RNA Identification (FRID) Pipeline: Identification of Potential Pseudoknot-Containing RNA Elements as Therapeutic Targets for SARS-CoV-2
|
Apr 04, 2023 |
|
Community structure and temporal dynamics of SARS-CoV-2 epistatic network allows for early detection of emerging variants with altered phenotypes
|
Apr 03, 2023 |
|
Protein language models can capture protein quaternary state
|
Apr 02, 2023 |
|
AI-based novel-chemotype GPCRs drugs: introducing ligand type classifiers and systems biology
|
Apr 02, 2023 |
|
TCR2vec: a deep representation learning framework of T-cell receptor sequence and function
|
Apr 02, 2023 |
|
Recombulator-X: a fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics
|
Apr 02, 2023 |
|
MOGAT: An Improved Multi-Omics Integration Framework Using Graph Attention Networks
|
Apr 02, 2023 |
|
A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing
|
Apr 02, 2023 |
|
CilioGenics: an integrated method and database for predicting novel ciliary genes
|
Apr 02, 2023 |
|
T9GPred: A Comprehensive Computational Tool for the Prediction of Type 9 Secretion System, Gliding Motility and the Associated Secreted Proteins
|
Apr 02, 2023 |
|
Determining epitope specificity of T-cell receptors with transformers
|
Apr 02, 2023 |
|
Deep Learning for Flexible and Site-Specific Protein Docking and Design
|
Apr 02, 2023 |
|
FLUTE: a Python GUI for interactive phasor analysis of FLIM data
|
Apr 02, 2023 |
|
CRD: a De novo Design algorithm for prediction of Cognate Protein Receptors for small molecule ligands
|
Apr 02, 2023 |
|
Connectivity-based Meta-Bands: A new approach for automatic frequency band identification in connectivity analyses
|
Apr 02, 2023 |
|
PanGraphViewer: A Versatile Tool to Visualize Pangenome Graphs
|
Apr 02, 2023 |
|
Discovering motifs and genomic patterns with SMT: a high-performance data structure for counting kmers
|
Apr 02, 2023 |
|
PanKmer: k-mer based and reference-free pangenome analysis
|
Apr 02, 2023 |
|
Spatially Resolved Transcriptomics Mining in 3D and Virtual Reality Environments with VR-Omics
|
Apr 02, 2023 |
|
Clinical Phenotype Prediction From Single-cell RNA-seq Data using Attention-Based Neural Networks
|
Apr 02, 2023 |
|
Assessing Random Forest self-reproducibility for optimal short biomarker signature discovery
|
Apr 01, 2023 |
|
Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities
|
Apr 01, 2023 |
|
Retention time and fragmentation predictors increase confidence in variant peptide identification
|
Apr 01, 2023 |
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Large-scale template-based structural modeling of T-cell receptors with known antigen specificity reveals complementarity features.
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Apr 01, 2023 |
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Stochastic modeling of a gene regulatory network driving B cell development in germinal centers
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Apr 01, 2023 |
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Model-based differential sequencing analysis
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Apr 01, 2023 |
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AutophagyNet: High-resolution data source for the analysis of autophagy and its regulation
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Mar 30, 2023 |
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Spatial Transcriptomics Analysis of Gene Expression Prediction using Exemplar Guided Graph Neural Network
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Mar 30, 2023 |
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Large-scale Annotation of Biochemically Relevant Pockets and Tunnels in Cognate Enzyme-Ligand Complexes
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Mar 30, 2023 |
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Sequencing accuracy and systematic errors in nanopore direct RNA sequencing
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Mar 30, 2023 |
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Modeling and predicting meat yield and growth performance using morphological features of narrow-clawed crayfish with machine learning techniques
|
Mar 29, 2023 |
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simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry
|
Mar 29, 2023 |
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Prediction of G4 formation in live cells with epigenetic data: a deep learning approach
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Mar 29, 2023 |
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3D Simulation of Tissue Mechanics with Cell Polarization
|
Mar 29, 2023 |
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A meta-analysis of liver microbiome in beef and dairy cattle using metatranscriptome sequencing reads
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Mar 29, 2023 |
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KGETCDA: an efficient representation learning framework based on knowledge graph encoder from transformer for predicting circRNA-disease associations
|
Mar 29, 2023 |
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Single-cell RNA-seq differential expression tests within a sample should use pseudo-bulk data of pseudo-replicates
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Mar 29, 2023 |
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Bayesian Multi-Study Non-Negative Matrix Factorization for Mutational Signatures
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Mar 29, 2023 |
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Machine learning-based gut microbiota pattern and response to fiber as a diagnostic tool for chronic inflammatory diseases
|
Mar 29, 2023 |
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The impact of FASTQ and alignment read order on structural variation calling from long-read sequencing data
|
Mar 29, 2023 |
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aPEAR: an R package for autonomous visualisation of pathway enrichment networks
|
Mar 29, 2023 |
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Structural characterization of a novel luciferase-like-monooxygenase from Pseudomonas meliae an in silico approach
|
Mar 29, 2023 |
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Scaling deep phylogenetic embedding to ultra-large reference trees: a tree-aware ensemble approach
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Mar 29, 2023 |
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Generating an Efficient Arginase Variant for Medical and Industrial Uses: in Silico Engineering
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Mar 28, 2023 |
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TemStaPro: protein thermostability prediction using sequence representations from protein language models
|
Mar 28, 2023 |
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i-stLearn: An interactive platform for spatial transcriptomics analysis
|
Mar 28, 2023 |
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Interpretable spatial cell learning enhances the characterization of patient tissue microenvironments with highly multiplexed imaging data
|
Mar 28, 2023 |
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AI-Designed, Mutation-Resistant Broad Neutralizing Antibodies Against Multiple SARS-CoV-2 Strains
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Mar 27, 2023 |
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AnimalGAN: A Generative Adversarial Network Model Alternative to Animal Studies for Clinical Pathology Assessment
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Mar 27, 2023 |
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In-silico Screening of Origanum vulgare Phytocompounds as Potential Drug Agents Against Vp35 Protein of the Ebola Virus
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Mar 27, 2023 |
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IDSL.GOA: Gene Ontology Analysis for Metabolomics
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Mar 27, 2023 |
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De novo Genome Assembly, Functional Annotation and SSR Mining of Citrus reticulata (Kinnow) from Pakistan
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Mar 27, 2023 |
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Flattening the curve - How to get better results with small deep-mutational-scanning datasets
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Mar 27, 2023 |
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Small molecule machine learning: All models are wrong, some may not even be useful
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Mar 27, 2023 |
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Artificial Intelligence Boosted Molecular Dynamics
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Mar 27, 2023 |
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A novel method to accurately estimate pathway activity in single cells for clustering and differential analysis
|
Mar 27, 2023 |
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exFINDER: identify external communication signals using single-cell transcriptomics data
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Mar 27, 2023 |
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Unravelling individual rhythmic abilities using machine learning
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Mar 26, 2023 |
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Clustering scRNA-seq data via qualitative and quantitative analysis
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Mar 26, 2023 |
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SMASH: Scalable Method for Analyzing Spatial Heterogeneity of genes in spatial transcriptomics data
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Mar 25, 2023 |
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Somatic small-variant calling methods in Illumina DRAGEN™ Secondary Analysis
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Mar 25, 2023 |
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Virtual screening of antimicrobial plant extracts by machine-learning classification of chemical compounds in semantic space
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Mar 25, 2023 |
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A fast algorithm for 3D volume reconstruction from light field microscopy datasets
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Mar 25, 2023 |
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Modelling Emergence of Wolbachia Toxin-Antidote Protein Functions with an Evolutionary Algorithm.
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Mar 25, 2023 |
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MutationExplorer - a webserver for mutation of proteins and 3D visualization of energetic impacts
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Mar 25, 2023 |
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Investigating Open Reading Frames in Known and Novel Transcripts using ORFanage
|
Mar 25, 2023 |
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Supervised learning of high-confidence phenotypic subpopulations from single-cell data
|
Mar 25, 2023 |
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MIDAS: a fast and simple simulator for realistic microbiome data
|
Mar 25, 2023 |
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xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data
|
Mar 25, 2023 |
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Mutafy: A webserver to identify high quality mutant protein structures in the Protein Data Bank
|
Mar 24, 2023 |
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Global effects of identity and aging on the human sperm methylome
|
Mar 24, 2023 |
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Dimension-agnostic and granularity-based spatially variable gene identification
|
Mar 24, 2023 |
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Spotless: a reproducible pipeline for benchmarking cell type deconvolution in spatial transcriptomics
|
Mar 24, 2023 |
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A Comprehensive Enumeration of the Human Proteostasis Network. 2. Components of the Autophagy-Lysosome Pathway
|
Mar 24, 2023 |
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Distances and their visualization in studies of spatial-temporal genetic variation using single nucleotide polymorphisms (SNPs)
|
Mar 24, 2023 |
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An explainable deep learning classifier of bovine mastitis based on whole genome sequence data - circumventing the p greater than greater than greater than n problem
|
Mar 24, 2023 |
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Estimation of a treatment effect based on a modified covariates method with L0 norm
|
Mar 24, 2023 |
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Integration of taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes
|
Mar 24, 2023 |
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A novel computational pipeline for var gene expression augments the discovery of changes in the Plasmodium falciparum transcriptome during transition from in vivo to short-term in vitro culture
|
Mar 24, 2023 |
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Epitranscriptome analysis of NAD-capped RNA by spike-in-based normalization
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Mar 24, 2023 |
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JUMP Cell Painting dataset: morphological impact of 136,000 chemical and genetic perturbations
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Mar 24, 2023 |
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Genetic structure and diversity of rfb locus of pathogenic species of genus Leptospira
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Mar 24, 2023 |
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Capturing Spatiotemporal Signaling Patterns in Cellular Data with Geometric Scattering Trajectory Homology
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Mar 24, 2023 |
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Uncovering Hidden Cancer Self-Dependencies through Analysis of shRNA-Level Dependency Scores
|
Mar 24, 2023 |
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LOCATOR: feature extraction and spatial analysis of the cancer tissue microenvironment using mass cytometry imaging technologies
|
Mar 24, 2023 |
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Ensemble-GNN: federated ensemble learning with graph neural networks for disease module discovery and classification
|
Mar 24, 2023 |
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An integrative framework for circular RNA quantitative trait locus discovery with application in human T cells
|
Mar 24, 2023 |
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A meta-analysis of immune cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes
|
Mar 23, 2023 |
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Accurate Flow Decomposition via Robust Integer Linear Programming
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Mar 23, 2023 |
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SpaceWalker: Interactive Gradient Exploration for Spatial Transcriptomics Data
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Mar 23, 2023 |
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Deep learning for rapid analysis of cell divisions in vivo during epithelial morphogenesis and repair
|
Mar 23, 2023 |
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Multi-Omics Integration For Disease Prediction Via Multi-Level Graph Attention Network And Adaptive Fusion
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Mar 23, 2023 |
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An Ensemble Learning Approach to perform Link Prediction on Large Scale Biomedical Knowledge Graphs for Drug Repurposing and Discovery
|
Mar 23, 2023 |
|
escheR: Unified multi-dimensional visualizations with Gestalt principles
|
Mar 23, 2023 |
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Artificial selection footprints in domestic chicken genomes
|
Mar 23, 2023 |
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FLONE: fully Lorentz network embedding for inferring novel drug targets
|
Mar 23, 2023 |
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HLA3DB: comprehensive annotation of peptide/HLA complexes enables blind structure prediction of T cell epitopes
|
Mar 23, 2023 |
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READRetro: Natural Product Biosynthesis Planning with Retrieval-Augmented Dual-View Retrosynthesis
|
Mar 23, 2023 |
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Inference of single cell profiles from histology stains with the Single-Cell omics from Histology Analysis Framework (SCHAF)
|
Mar 23, 2023 |
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Flexible parsing and preprocessing of technical sequences with splitcode
|
Mar 23, 2023 |
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DRPBind: prediction of DNA, RNA and protein binding residues in intrinsically disordered protein sequences
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Mar 23, 2023 |
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RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci
|
Mar 23, 2023 |
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MetaLLM: Residue-wise Metal ion Prediction UsingDeep Transformer Model
|
Mar 23, 2023 |
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Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment
|
Mar 22, 2023 |
|
High performance Legionella pneumophila source attribution using genomics-based machine learning classification
|
Mar 22, 2023 |
|
NOMAD2 provides ultra-efficient, scalable, and unsupervised discovery on raw sequencing reads
|
Mar 21, 2023 |
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aenmd: Annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants
|
Mar 21, 2023 |
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PAPET: a collection of performant algorithms to identify 5-methyl cytosine from PacBio SequelII data
|
Mar 21, 2023 |
|
A Video Segmentation Pipeline for Assessing changes in Pupil Response to Light After Cannabis Consumption
|
Mar 21, 2023 |
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Long read proteogenomics to connect disease-associated sQTLs to the protein isoform effectors of disease
|
Mar 21, 2023 |
|
PGAR-Zernike: an ultra-fast, accurate and fully open-sourcestructure retrieval toolkit for convenient structural database construction
|
Mar 21, 2023 |
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Identification of annotation artifacts concerning the CHALCONE SYNTHASE (CHS)
|
Mar 21, 2023 |
|
S3-CIMA: Supervised spatial single-cell image analysis for the identification of disease-associated cell type compositions in tissue
|
Mar 21, 2023 |
|
AB-Gen: Antibody Library Design with Generative Pre-trained Transformer and Deep Reinforcement Learning
|
Mar 21, 2023 |
|
A machine-readable specification for genomics assays
|
Mar 21, 2023 |
|
Statistical modeling and analysis of multiplexed imaging data
|
Mar 21, 2023 |
|
DeepBindGCN: Integrating Molecular Vector Representation with Graph Convolutional Neural Networks for Accurate Protein-Ligand Interaction Prediction
|
Mar 20, 2023 |
|
Accurate prediction of transcriptional activity of single missense variants in HIV Tat with deep learning
|
Mar 20, 2023 |
|
VariPred: Enhancing Pathogenicity Prediction of Missense Variants Using Protein Language Models
|
Mar 20, 2023 |
|
How far are we from personalized gene expression prediction using sequence-to-expression deep neural networks?
|
Mar 20, 2023 |
|
mosna reveals different types of cellular interactionspredictive of response to immunotherapies in cancer
|
Mar 20, 2023 |
|
ALaSCA: A novel in silico simulation platform to untangle biological pathway mechanisms, with a case study in Type 1 Diabetes progression
|
Mar 20, 2023 |
|
An interpretable, finite sample valid alternative to Pearson's X2 for scientific discovery
|
Mar 20, 2023 |
|
ITNR: Inversion Transformer-based Neural Ranking for Cancer Drug Recommendations
|
Mar 20, 2023 |
|
Rigid Scaffolds are Promising for Designing Macrocyclic Kinase Inhibitors
|
Mar 20, 2023 |
|
On quantum computing and geometry optimization
|
Mar 20, 2023 |
|
PhyloSophos: a high-throughput scientific name mapping algorithm augmented with explicit consideration of taxonomic science
|
Mar 20, 2023 |
|
Identification of selective sweeps in bacteria
|
Mar 19, 2023 |
|
compare_genomes: a comparative genomics workflow to streamline the analysis of evolutionary divergence across genomes
|
Mar 17, 2023 |
|
Magnipore: Prediction of differential single nucleotide changes in the Oxford Nanopore Technologies sequencing signal of SARS-CoV-2 samples
|
Mar 17, 2023 |
|
Standardizing and applying a mating-based whole-genome simulation approach reveals caution in using chromosome-level PCA and kinship estimates
|
Mar 16, 2023 |
|
Guiding the design of well-powered Hi-C experiments to detect differential loops
|
Mar 16, 2023 |
|
3DMolMS: Prediction of Tandem Mass Spectra from Three Dimensional Molecular Conformations
|
Mar 16, 2023 |
|
Accurate estimation of rare cell type fractions fromtissue omics data via hierarchical deconvolution
|
Mar 16, 2023 |
|
Uncovering the Hidden Gems of Psoriasis Literature: An Neural Language Model-Assisted Interactive Web Tool
|
Mar 16, 2023 |
|
NanoSquiggleVar: A method for direct analysis of targeted variants based on nanopore sequencing signals
|
Mar 16, 2023 |
|
Multiple sequence-alignment-based RNA language model and its application to structural inference
|
Mar 16, 2023 |
|
SafeMut: UMI-aware variant simulator incorporating allele-fraction overdispersion in read editing
|
Mar 15, 2023 |
|
SpatialScope: A unified approach for integrating spatial and single-cell transcriptomics data using deep generative models
|
Mar 15, 2023 |
|
Improved integration of single cell transcriptome data demonstrated on heart failure in mice and men
|
Mar 15, 2023 |
|
Library size confounds biology in spatial transcriptomics data
|
Mar 15, 2023 |
|
LEP-AD: Language Embedding of Proteins and Attention to Drugs predicts drug target interactions
|
Mar 15, 2023 |
|
Fast Approximate IsoRank for Scalable Global Alignment of Biological Networks
|
Mar 15, 2023 |
|
ChemEM: flexible docking of small molecules in Cryo-EM structures using difference maps
|
Mar 15, 2023 |
|
How much storage precision can be lost: Guidance for near-lossless compression of untargeted metabolomics mass spectrometry data
|
Mar 15, 2023 |
|
GenoPipe: identifying the genotype of origin within (epi)genomic datasets
|
Mar 15, 2023 |
|
BioConvert: a comprehensive format converter for life sciences
|
Mar 15, 2023 |
|
What is hidden in the darkness? Deep-learning assisted large-scale protein family curation uncovers novel protein families and folds
|
Mar 15, 2023 |
|
Development of QSAR Models to Identify Mycobacterium tuberculosis enoyl-ACP-reductase Enzyme Inhibitors
|
Mar 15, 2023 |
|
Testing nonparametrically for dependence between nonstationary time series with very few replicates
|
Mar 14, 2023 |
|
Spatially aware self-representation learning for tissue structure characterization and spatial functional genes identification
|
Mar 14, 2023 |
|
BQsupports: systematic assessment of the support and novelty of new biomedical associations
|
Mar 14, 2023 |
|
Analysis of RNA processing directly from spatial transcriptomics data reveals previously unknown regulation
|
Mar 14, 2023 |
|
InClust+: the multimodal version of inClust for multimodal data integration, imputation, and cross modal generation
|
Mar 14, 2023 |
|
The landscape of cancer rewired GPCR signaling axes
|
Mar 14, 2023 |
|
GeneTuring tests GPT models in genomics
|
Mar 13, 2023 |
|
Spectral detection of condition-specific biological pathways in single-cell gene expression data
|
Mar 13, 2023 |
|
eOmics: an R package for improved omics data analysis
|
Mar 13, 2023 |
|
PandoraRLO: DQN and Graph convolution based method for optimized ligand pose
|
Mar 13, 2023 |
|
An interpretable ML model to characterize patient-specific HLA-I antigen presentation
|
Mar 13, 2023 |
|
Improvements in the detection power of algorithms for analyzing next-generation sequencing based bulked segregant analysis data via estimating thresholds at the genomic region level
|
Mar 13, 2023 |
|
E2EGraph: An End-to-end Graph Learning Model for Interpretable Prediction of Pathlogical Stages in Prostate Cancer
|
Mar 12, 2023 |
|
Constraint-based modelling predicts metabolic signatures of low- and high-grade serous ovarian cancer
|
Mar 12, 2023 |
|
Impact and characterization of serial structural variations across humans and great apes
|
Mar 12, 2023 |
|
An efficient error correction and accurate assembly tool for noisy long reads
|
Mar 12, 2023 |
|
vcfdist: Accurately benchmarking phased small variant calls in human genomes
|
Mar 12, 2023 |
|
ZygosityPredictor
|
Mar 12, 2023 |
|
STdGCN: accurate cell-type deconvolution using graph convolutional networks in spatial transcriptomic data
|
Mar 12, 2023 |
|
Superposition of target structures enables design of bi-stable RNA molecules with deep learning
|
Mar 12, 2023 |
|
plasma: Partial LeAst Squares for Multiomics Analysis
|
Mar 12, 2023 |
|
Panpipes: a pipeline for multiomic single-cell data analysis.
|
Mar 12, 2023 |
|
The GlycoPaSER prototype as a real-time N-glycopeptide identification tool based on the PaSER parallel computing platform
|
Mar 12, 2023 |
|
Addressing Erroneous Scale Assumptions in Microbe and Gene Set Enrichment Analysis
|
Mar 12, 2023 |
|
Machine Learning to Identify Molecular Markers for Metabolic Disease Development Using Mouse Models
|
Mar 12, 2023 |
|
Proformer: a hybrid macaron transformer model predicts expression values from promoter sequences
|
Mar 12, 2023 |
|
Data-Driven Mathematical Approach for Removing Rare Features in Zero-Inflated Datasets
|
Mar 12, 2023 |
|
In-silico Discovery of Genetic Diversity in Cucumis sativus var. hardwickii: A Wild Relative of Cultivated Cucumber
|
Mar 12, 2023 |
|
Computational investigation of Scutellarein derivatives as an inhibitor against triple-negative breast cancer by Quantum calculation, and drug-designed approaches
|
Mar 08, 2023 |
|
Identification of mobile element insertion from whole genome sequencing data using deep neural network model
|
Mar 08, 2023 |
|
Prediction of protein assemblies by structure sampling followed by interface-focused scoring
|
Mar 08, 2023 |
|
Empowering Beginners in Bioinformatics with ChatGPT
|
Mar 08, 2023 |
|
Unraveling the Interactions between Human DPP4 Receptor, SARS-CoV-2 Variants, and MERS-CoV, converged for Pulmonary Disorders Integrating through Immunoinformatics and Molecular Dynamics
|
Mar 07, 2023 |
|
QuaC: A Pipeline Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Data
|
Mar 07, 2023 |
|
Quantum algorithm for position weight matrix matching
|
Mar 07, 2023 |
|
ELITE: Expression deconvoLution using lInear optimizaTion in bulk transcriptomics mixturEs
|
Mar 07, 2023 |
|
Morphine Re-arranges Chromatin Spatial Architecture of Primate Cortical Neurons
|
Mar 07, 2023 |
|
Application of fuzzy measures to move towards the cyber-taxonomy
|
Mar 07, 2023 |
|
Matrix and analysis metadata standards (MAMS) to facilitate harmonization and reproducibility of single-cell data
|
Mar 07, 2023 |
|
A bootstrap model comparison test for identifying genes with context-specific patterns of genetic regulation
|
Mar 07, 2023 |
|
SAKit: an all-in-one analysis pipeline for identifying novel protein caused by variant events at genomic and transcriptic level
|
Mar 07, 2023 |
|
Analysis of multi-condition single-cell data with latent embedding multivariate regression
|
Mar 07, 2023 |
|
optimalTAD: annotation of topologically associating domains based on chromatin marks enrichment
|
Mar 07, 2023 |
|
Modelling capture efficiency of single cell RNA-sequencing data improves inference of transcriptome-wide burst kinetics
|
Mar 07, 2023 |
|
You can move, but you can't hide: identification of mobile genetic elements with geNomad
|
Mar 06, 2023 |
|
Computational modeling and optimization of biofabrication in Tissue Engineering and Regenerative Medicine -- a literature review
|
Mar 06, 2023 |
|
PromoR and PromoS for E. coli promoter recognition and classification
|
Mar 06, 2023 |
|
Biological representation disentanglement of single-cell data
|
Mar 06, 2023 |
|
Cellos: High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology
|
Mar 06, 2023 |
|
Quantifying tumor specificity using Bayesian probabilistic modeling for drug target discovery and prioritization
|
Mar 06, 2023 |
|
LSTrAP-denovo: Automated Generation of Transcriptome Atlases for Eukaryotic Species Without Genomes
|
Mar 06, 2023 |
|
Novel crAssphage isolates exhibit conserved gene order and purifying selection of the host specificity protein
|
Mar 06, 2023 |
|
GPU-accelerated Dynamic Time Warping for SelectiveNanopore Sequencing
|
Mar 06, 2023 |
|
PAE Viewer: A webserver for the interactive visualization of the predicted aligned error for multimer structure predictions and crosslinks
|
Mar 06, 2023 |
|
Extraction of biological signals by factorization enables the reliable analysis of single-cell transcriptomics
|
Mar 04, 2023 |
|
JAMS - A framework for the taxonomic and functional exploration of microbiological genomic data
|
Mar 04, 2023 |
|
Underlying causes for prevalent false positives and false negatives in STARR-seq data
|
Mar 03, 2023 |
|
Feature selection followed by a residuals-based normalization simplifies and improves single-cell gene expression analysis
|
Mar 03, 2023 |
|
An econometric lens resolves cell-state parallax
|
Mar 03, 2023 |
|
Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation
|
Mar 03, 2023 |
|
Decoding Duchenne muscular dystrophy transcriptome to single nuclei level reveals clinical-genetic correlations
|
Mar 03, 2023 |
|
Fast and accurate DNASeq Variant Calling workflow composed of LUSH toolkit
|
Mar 02, 2023 |
|
Integrating weighted correlation network analysis and machine learning identifies common trajectories of prostate cancer
|
Mar 02, 2023 |
|
Gene essentiality in cancer is better predicted by mRNA abundance than by gene regulatory network-inferred activity
|
Mar 02, 2023 |
|
Molecular Adverse Outcome Pathways: towards the implementation of transcriptomics data in risk assessments
|
Mar 02, 2023 |
|
NMRQNet: a deep learning approach for automatic identification and quantification of metabolites using Nuclear Magnetic Resonance (NMR) in human plasma samples
|
Mar 02, 2023 |
|
Automatic Detection of Cell-cycle Stages using Recurrent Neural Networks
|
Mar 01, 2023 |
|
Evaluating Prompt Tuning for Conditional Protein Sequence Generation
|
Mar 01, 2023 |
|
PS4: a Next-Generation Dataset for Protein SingleSequence Secondary Structure Prediction
|
Mar 01, 2023 |
|
Rotamer Density Estimator is an Unsupervised Learner of the Effect of Mutations on Protein-Protein Interaction
|
Mar 01, 2023 |
|
StereoCell enables high accuracy single cell segmentation for spatial transcriptomic dataset
|
Mar 01, 2023 |
|
Triggering blood-lipid-profile by immunomodulatory and antimicrobial molecules for cross-evaluation of early detection of cancer
|
Mar 01, 2023 |
|
pyCapsid: Identifying dominant dynamics and quasi-rigid mechanical units in protein shells
|
Mar 01, 2023 |
|
Estimating the vertical ionization potential of single-stranded DNA molecules
|
Mar 01, 2023 |
|
ClockBase: a comprehensive platform for biological age profiling in human and mouse
|
Mar 01, 2023 |
|
Predicting CRISPR-Cas12a guide efficiency for targeting using Machine Learning
|
Mar 01, 2023 |
|
A data-efficient deep learning tool for scRNA-Seq label transfer in neuroscience
|
Mar 01, 2023 |
|
MEDIPIPE: an automated and comprehensive pipeline for cfMeDIP-seq data quality control and analysis
|
Mar 01, 2023 |
|
Directing Protein Design Choices by Per-Residue Energy Breakdown Analysis with an Interactive Web Application
|
Feb 28, 2023 |
|
Robustness of Felsenstein's versus Transfer Bootstrap Supports with respect to Taxon Sampling
|
Feb 28, 2023 |
|
A data-fusion approach to identifying developmental dyslexia from multi-omics datasets
|
Feb 28, 2023 |
|
Application of a Machine Learning Approach Towards the Targeted Identification of Phage Depolymerases
|
Feb 28, 2023 |
|
Automated quantification of lipophagy in Saccharomyces cerevisiae from fluorescence and cryo-soft X-ray microscopy data using deep learning
|
Feb 27, 2023 |
|
Protein embeddings improve phage-host interaction prediction
|
Feb 27, 2023 |
|
Repurposing of Anti-infectives for the Management of Onchocerciasis using Machine Learning and Protein Docking Studies
|
Feb 27, 2023 |
|
InjectionDesign: Plate Design with Optimized Stratified Block Randomization for Modern LC/GC-MS-Based Sample Preparation
|
Feb 27, 2023 |
|
Clonal phylogenies inferred from bulk, single cell, and spatial transcriptomic analysis of cancer
|
Feb 27, 2023 |
|
Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic models
|
Feb 27, 2023 |
|
An associative transcriptomics study on rice bean (Vigna umbellata) provides new insights into genetic basis and candidate genes governing flowering, maturity and seed weight
|
Feb 27, 2023 |
|
A global test of hybrid ancestry fromgenome-scale data
|
Feb 27, 2023 |
|
MsPBRsP: Multi-scale Protein Binding Residues Prediction Using Language Model
|
Feb 27, 2023 |
|
Influence of Demographic, Socio-economic, and Brain Structural Factors on Adolescent Neurocognition: A Correlation Analysis in the ABCD Initiative
|
Feb 27, 2023 |
|
EnCPdock: a web-interface for direct conjoint comparative analyses of complementarity and binding energetics in inter-protein associations
|
Feb 27, 2023 |
|
Advanced tensor decomposition-based integrated analysis of protein-protein interaction with cancer gene expression can improve coincidence with clinical labels
|
Feb 27, 2023 |
|
Microsnoop: a generalist tool for the unbiased representation of heterogeneous microscopy images
|
Feb 27, 2023 |
|
MDTOMO: Continuous conformational variability analysis in cryo electron subtomogram data using flexible fitting based on Molecular Dynamics simulations
|
Feb 27, 2023 |
|
PIFiA: Self-supervised Approach for Protein Functional Annotation from Single-Cell Imaging Data
|
Feb 27, 2023 |
|
Pan-cancer genetic analysis of disulfidptosis-related gene set
|
Feb 27, 2023 |
|
Cellograph: A Semi-supervised Approach to Analyzing Multi-condition Single-cell RNA-sequencing Data Using Graph Neural Networks
|
Feb 27, 2023 |
|
Benchmarking differential abundance methods for finding condition-specific prototypical cells in multi-sample single-cell datasets
|
Feb 27, 2023 |
|
A robust model for cell type-specific interindividual variation in single-cell RNA sequencing data
|
Feb 27, 2023 |
|
Adversarial and variational autoencoders improve metagenomic binning
|
Feb 27, 2023 |
|
Centrifuge+: improving metagenomic analysis upon Centrifuge
|
Feb 27, 2023 |
|
A generalizable Cas9/sgRNA prediction model using machine transfer learning with small high-quality datasets
|
Feb 26, 2023 |
|
Elucidation of Genome-wide Understudied Proteins targeted by PROTAC-induced degradation using Interpretable Machine Learning
|
Feb 24, 2023 |
|
GENEvaRX: A Novel AI-Driven Method and Web Tool Can Identify Critical Genes and Effective Drugs for Lichen Planus
|
Feb 24, 2023 |
|
Single cell and spatial alternative splicing analysis with long read sequencing
|
Feb 24, 2023 |
|
SEG: Segmentation Evaluation in absence of Ground truth labels
|
Feb 24, 2023 |
|
PhageDPO: Phage Depolymerase Finder
|
Feb 24, 2023 |
|
Themisto: a scalable colored k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes
|
Feb 24, 2023 |
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Predicting S. aureus antimicrobial resistance with interpretable genomic space maps
|
Feb 24, 2023 |
|
Ensemble deep learning of embeddings for clustering multimodal single-cell omics data
|
Feb 23, 2023 |
|
Retrieved Sequence Augmentation for Protein Representation Learning
|
Feb 23, 2023 |
|
Pacybara: Accurate long-read sequencing for barcoded mutagenized allelic libraries
|
Feb 23, 2023 |
|
A mechanistic simulation of molecular cell states over time
|
Feb 23, 2023 |
|
Dual-modality imaging of immunofluorescence and imaging mass cytometry for whole slide imaging with accurate single-cell segmentation
|
Feb 23, 2023 |
|
Genetic dependencies associated with transcription factor activities in human cancer cell lines
|
Feb 23, 2023 |
|
Utilizing Pre-trained Network Medicine Models for Generating Biomarkers, Targets, Re-purposing Drugs, and Personalized Therapeutic Regimes: COVID-19 Applications
|
Feb 22, 2023 |
|
CryoPPP: A Large Expert-Labelled Cryo-EM Image Dataset for Machine Learning Protein Particle Picking
|
Feb 22, 2023 |
|
choros: correction of sequence-based biases for accurate quantification of ribosome profiling data
|
Feb 22, 2023 |
|
Phased nanopore assembly with Shasta and modular graph phasing with GFAse
|
Feb 22, 2023 |
|
Reconstruction of TrkB complex assemblies and localizing an-tidepressant targets using Artificial Intelligence
|
Feb 22, 2023 |
|
Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources
|
Feb 22, 2023 |
|
Investigating racial disparities in carcinomas through TCGA transcriptomic and proteomic database
|
Feb 22, 2023 |
|
Dimensionality reduction methods for extracting functional networks from large-scale CRISPR screens
|
Feb 22, 2023 |
|
SPA-STOCSY: An Automated Tool for Identification of Annotated and Non-Annotated Metabolites in High-Throughput NMR Spectra
|
Feb 22, 2023 |
|
DR-BERT: A Protein Language Model to Annotate Disordered Regions
|
Feb 22, 2023 |
|
Fast Identification of Optimal Monotonic Classifiers
|
Feb 22, 2023 |
|
Identification of novel prognostic targets in coronary artery disease and related complications using bioinformatics and next generation sequencing data analysis
|
Feb 22, 2023 |
|
Europe PMC Annotated Full-text Corpus for Gene/Proteins, Diseases and Organisms
|
Feb 21, 2023 |
|
PANGEA: A New Gene Set Enrichment Tool for Drosophila and Common Research Organisms
|
Feb 21, 2023 |
|
LISTER: Semi-automatic metadata extraction from annotated experiment documentation in eLabFTW
|
Feb 21, 2023 |
|
Integrated analysis and annotation for T-cell receptor sequences using TCRosetta
|
Feb 21, 2023 |
|
Dual-wield NTPase: a novel protein family mined from AlphaFold DB
|
Feb 21, 2023 |
|
S1000: A better taxonomic name corpus for biomedical information extraction
|
Feb 21, 2023 |
|
DeepHeme: A generalizable, bone marrow classifierwith hematopathologist-level performance
|
Feb 21, 2023 |
|
Updating TCGA glioma classification through integration of molecular profiling data following the 2016 and 2021 WHO guidelines
|
Feb 21, 2023 |
|
Comprehensive codon usage analyses of the mutations in the Parkin protein leading to Parkinsonism
|
Feb 21, 2023 |
|
Merizo: A rapid and accurate domain segmentation method using invariant point attention
|
Feb 21, 2023 |
|
Structome: Exploring the structural neighbourhood of proteins
|
Feb 21, 2023 |
|
NTpred: A robust and precise machine learningframework for in-silico identification of Tyrosine nitration sites in protein sequences
|
Feb 21, 2023 |
|
Interpreting biologically informed neural networks for enhanced biomarker discovery and pathway analysis
|
Feb 21, 2023 |
|
A Simple Way to Incorporate Target Structural Information in Molecular Generative Models
|
Feb 21, 2023 |
|
OME-Zarr: a cloud-optimized bioimaging file format with international community support
|
Feb 21, 2023 |
|
Active mesh and neural network pipeline for cell aggregate segmentation
|
Feb 21, 2023 |
|
An integrated bioinformatics approach to identify candidate biomarkers and the evaluation of drugs for pheochromocytoma
|
Feb 21, 2023 |
|
OPTIMAL: An OPTimsed Imaging Mass cytometry AnaLysis framework for Segmentation and Data Exploration
|
Feb 21, 2023 |
|
Audit to Forget: A Unified Method to Revoke Patients' Private Data in Intelligent Healthcare
|
Feb 21, 2023 |
|
Cardinal v3 - a versatile open source software for mass spectrometry imaging analysis
|
Feb 21, 2023 |
|
A robust Platform for Integrative Spatial Multi-omics Analysis to Map Immune Responses to SARS-CoV-2 infection in Lung Tissues
|
Feb 20, 2023 |
|
Tracking and curating putative SARS-CoV-2 recombinants with RIVET
|
Feb 19, 2023 |
|
Accurate label-free quantification by directLFQ to compare unlimited numbers of proteomes
|
Feb 19, 2023 |
|
TRGdb: a universal resource for exploration of taxonomically restricted genes in bacteria
|
Feb 18, 2023 |
|
Computational prediction of human deep intronic variation
|
Feb 17, 2023 |
|
BinderSpace: A Package for Sequence Space Analyses for Datasets of Affinity-Selected Oligonucleotides and Peptide-Based Molecules
|
Feb 16, 2023 |
|
Toxoplasma gondii aspartic protease 5 (TgASP5): Understanding structural details and inhibition mechanism.
|
Feb 16, 2023 |
|
Virotest: a bioinformatics pipeline for virus identification in plants.
|
Feb 16, 2023 |
|
An attention network for predicting T cell receptor-peptide binding can associate attention with interpretable protein structural properties
|
Feb 16, 2023 |
|
BORD: A Biomedical Ontology based method for concept Recognition using Distant supervision: Application to Phenotypes and Diseases
|
Feb 16, 2023 |
|
Clustering rare diseases within an ontology-enriched knowledge graph
|
Feb 16, 2023 |
|
μ-PBWT: Enabling the Storage and Use of UK Biobank Data on a Commodity Laptop
|
Feb 16, 2023 |
|
Precise and ultrafast tandem repeat variant detection in massively parallel sequencing reads
|
Feb 16, 2023 |
|
Network Pharmacology and Bioinformatics Methods Reveal the Mechanism of Sishenwan in the Treatment of diabetic nephropathy
|
Feb 16, 2023 |
|
Benchmarking the Autoencoder Design for Imputing Single-Cell RNA Sequencing Data
|
Feb 16, 2023 |
|
Rational Prediction of PROTAC-compatible Protein-Protein Interfaces by Molecular Docking
|
Feb 16, 2023 |
|
Prediction and Design of Protease Enzyme Specificity Using a Structure-Aware Graph Convolutional Network
|
Feb 16, 2023 |
|
Automatic identification of scientific publications describing digital reconstructions of neural morphology
|
Feb 15, 2023 |
|
PIQLE: protein-protein interface quality estimation by deep graph learning of multimeric interaction geometries
|
Feb 15, 2023 |
|
A computational investigation on Rho-related GTP-binding protein RhoB through molecular modeling and molecular dynamics simulation study
|
Feb 15, 2023 |
|
BLINK: Ultrafast tandem mass spectrometry cosine similarity scoring
|
Feb 15, 2023 |
|
Uni-Fold MuSSe: De Novo Protein Complex Prediction with Protein Language Models
|
Feb 15, 2023 |
|
Classification of dog breeds using convolutional neural network models and support vector machine
|
Feb 15, 2023 |
|
Artificial Intelligence uncovers Evolutionarily Conserved Intracellular Allosteric Modulators of GPCR-Gα interface.
|
Feb 15, 2023 |
|
Multivariate Residualization in Medical Imaging Analysis
|
Feb 15, 2023 |
|
JUMP: statistical analysis of replicability across two studies
|
Feb 15, 2023 |
|
A Systematic Benchmark of Machine Learning Methods for Protein-RNA Interaction Prediction
|
Feb 15, 2023 |
|
SynEcoSys: a multifunctional platform of large-scale single-cell omics data analysis
|
Feb 15, 2023 |
|
Orthogonal outlier detection and dimension estimation for improved MDS embedding of biological datasets
|
Feb 15, 2023 |
|
DeepTAP: an RNN-based method of TAP-binding peptide prediction in the selection of tumor neoantigens
|
Feb 15, 2023 |
|
CellWalker: A user-friendly and modular computational pipeline for morphological analysis of microscopy images
|
Feb 15, 2023 |
|
Pairtools: from sequencing data to chromosome contacts
|
Feb 15, 2023 |
|
The HRA Organ Gallery Affords Immersive Superpowers for Building and Exploring the Human Reference Atlas with Virtual Reality
|
Feb 15, 2023 |
|
Vulture: Cloud-enabled scalable mining of microbial reads in public scRNA-seq data
|
Feb 15, 2023 |
|
NeoTCR: an immunoinformatic database of experimentally-supported functional neoantigen-specific TCR sequences
|
Feb 15, 2023 |
|
kakapo: Easy extraction and annotation of genes from raw RNA-seq reads
|
Feb 15, 2023 |
|
Single-cell transcriptomic analysis of mouse liver reveals nonparenchymal cells' intricate responses to PCB126 exposure
|
Feb 15, 2023 |
|
Pervasive, conserved secondary structure in highly charged protein regions
|
Feb 15, 2023 |
|
Genome-wide identification and characterization of major RNAi genes highlighting their regulatory factors in Cowpea (Vigna unguiculata (L.) Walp.)
|
Feb 15, 2023 |
|
Systematic analysis of disease-linked rare germline variants reveals new classes of cancer predisposing genes
|
Feb 15, 2023 |
|
NetSyn: genomic context exploration of protein families
|
Feb 15, 2023 |
|
Optimizing Xenium In Situ data utility by quality assessment and best practice analysis workflows
|
Feb 14, 2023 |
|
Cell type-specific Interaction Analysis using Doublets in scRNA-seq (CIcADA)
|
Feb 14, 2023 |
|
simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data
|
Feb 14, 2023 |
|
From Cell-Lines to Cancer Patients: Personalized Drug Synergy Prediction
|
Feb 14, 2023 |
|
A comparison of bioinformatics pipelines for compositional analysis of the human gut microbiome
|
Feb 14, 2023 |
|
Improved in situ Characterization of Proteome-wide Protein Complex Dynamics with Thermal Proximity Co-Aggregation
|
Feb 14, 2023 |
|
Gene-signatures for early detection of cancers
|
Feb 13, 2023 |
|
Olivar: fully automated and variant aware primer design for multiplex tiled amplicon sequencing of pathogen genomes
|
Feb 13, 2023 |
|
Petagraph: A large-scale unifying knowledge graph framework for integrating biomolecular and biomedical data
|
Feb 13, 2023 |
|
LEA: Latent Eigenvalue Analysis in application to high-throughput phenotypic profiling
|
Feb 13, 2023 |
|
Streamline unsupervised machine learning to survey and graph indel-based haplotypes from pan-genomes
|
Feb 13, 2023 |
|
Drug repurposing for Leishmaniasis with Hyperbolic Graph Neural Networks
|
Feb 13, 2023 |
|
Reply to: Caution Regarding the Specificities of Pan-Cancer Microbial Structure
|
Feb 13, 2023 |
|
Insight on physicochemical properties governing peptide MS1 response in HPLC-ESI-MS/MS proteomics: A deep learning approach
|
Feb 13, 2023 |
|
SeqScreen-Nano: a computational platform for rapid, in-field characterization of previously unseen pathogens.
|
Feb 13, 2023 |
|
Unraveling Spatial Gene Associations with SEAGAL: a Python Package for Spatial Transcriptomics Data Analysis and Visualization
|
Feb 13, 2023 |
|
Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale
|
Feb 12, 2023 |
|
Female gene networks are expressed in myofibroblast-like smooth muscle cells in vulnerable atherosclerotic plaques.
|
Feb 11, 2023 |
|
Protein Fitness Prediction is Impacted by the Interplay of Language Models, Ensemble Learning, and Sampling Methods
|
Feb 10, 2023 |
|
Prioritizing Complex Disease Genes from Heterogeneous Public Databases
|
Feb 10, 2023 |
|
PopTradeOff: a database for exploring population-specific trade-offs between adaptive evolution, disease susceptibility, and drug responsiveness
|
Feb 10, 2023 |
|
TidyGEO: Preparing analysis-ready datasets from Gene Expression Omnibus
|
Feb 10, 2023 |
|
IDSL.CSA: Composite Spectra Analysis for Chemical Annotation of Untargeted Metabolomics Datasets
|
Feb 10, 2023 |
|
Benchmarking Variational AutoEncoders on cancer transcriptomics data
|
Feb 10, 2023 |
|
ImmuneMirror: a Machine Learning-based Integrative Pipeline and Web Server for Neoantigen Prediction
|
Feb 10, 2023 |
|
Metaphor - A workflow for streamlined assembly and binning of metagenomes
|
Feb 10, 2023 |
|
Exploring the Knowledge of An Outstanding Protein to Protein Interaction Transformer
|
Feb 10, 2023 |
|
DRomics, a workflow to model and make sense of dose-response (multi-)omics data in (eco)toxicology
|
Feb 10, 2023 |
|
GENIUS: GEnome traNsformatIon and spatial representation of mUltiomicS data
|
Feb 10, 2023 |
|
An algorithm that combines machine learning ensemble modeling and network analysis to predict self-tolerant tumor-associated antigens for anti-cancer immunotherapy
|
Feb 10, 2023 |
|
HMMSTRTM: A hidden Markov model for local structure prediction in globular and membrane associated proteins
|
Feb 10, 2023 |
|
Unipept Desktop 2.0: construction of targeted reference protein databases for proteogenomics analyses
|
Feb 10, 2023 |
|
Adaptive Digital Tissue Deconvolution
|
Feb 10, 2023 |
|
Pharmacodynamic model of PARP1 inhibition and global sensitivity analyses can lead to cancer biomarker discovery
|
Feb 10, 2023 |
|
BioNAR: An Integrated Biological Network Analysis Package in Bioconductor
|
Feb 10, 2023 |
|
CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters
|
Feb 10, 2023 |
|
Identifying Mutational Hotspots using Differences in Atomic Fluctuations combined with Positional Variability
|
Feb 09, 2023 |
|
Does joint impedance improve dynamic leg simulations with explicit and implicit solvers?
|
Feb 09, 2023 |
|
Impact of experimental bias on compositional analysis of microbiome data
|
Feb 09, 2023 |
|
Proteome-wide comparison of tertiary protein structures reveal extensive molecular mimicry in Plasmodium-human interactions
|
Feb 09, 2023 |
|
Structural and functional classification of G-quadruplex families within the human genome
|
Feb 09, 2023 |
|
Spanve: an Effective Statistical Method to Detect Spatially Variable Genes in Large-scale Spatial Transcriptomics Data
|
Feb 08, 2023 |
|
Probabilistic cell/domain-type assignment of spatial transcriptomics data with SpatialAnno
|
Feb 08, 2023 |
|
GeneDART: Extending gene coverage in image-based spatial transcriptomics by deep learning-based domain adaptation with barcode-based RNA-sequencing data
|
Feb 08, 2023 |
|
Automatic quality control of single-cell and single-nucleus RNA-seq using valiDrops
|
Feb 08, 2023 |
|
Sex-specific declines in cholinergic-targeting tRNA fragments in the nucleus accumbens in Alzheimer's disease
|
Feb 08, 2023 |
|
aweMAGs: a fully automated workflow for quality assessment and annotation of eukaryotic genomes from metagenomes
|
Feb 08, 2023 |
|
CircSSNN: circRNA-binding site prediction via sequence self-attention neural networks with pre-normalization
|
Feb 07, 2023 |
|
Heuristics for the De Bruijn Graph Sequence Mapping Problem
|
Feb 07, 2023 |
|
Gaussian Mixture Modeling Extensions for Improved False Discovery Rate Estimation in GC-MS Metabolomics
|
Feb 07, 2023 |
|
IS-Seq: a bioinformatics pipeline for integration sites analysis with comprehensive abundance quantification methods
|
Feb 07, 2023 |
|
Accelerated nanopore basecalling with SLOW5 data format
|
Feb 07, 2023 |
|
Transcriptional profile of ribosome-associated quality control components and their associated phenotypes in mammalian cells
|
Feb 07, 2023 |
|
Clustering-independent estimation of cell abundances in bulk tissues using single-cell RNA-seq data
|
Feb 07, 2023 |
|
BiGPICC: a graph-based approach to identifying carcinogenic gene combinations from mutation data
|
Feb 07, 2023 |
|
Machine learning models for the prediction of enzyme properties should be tested on proteins not used for model training
|
Feb 07, 2023 |
|
xTrimoDock: Rigid Protein Docking via Cross-Modal Representation Learning and Spectral Algorithm
|
Feb 06, 2023 |
|
Taxonomical and ontological analysis of verified natural and laboratory human coronavirus hosts
|
Feb 06, 2023 |
|
Helixer--de novo Prediction of Primary Eukaryotic Gene Models Combining Deep Learning and a Hidden Markov Model.
|
Feb 06, 2023 |
|
Network-based molecular subtyping of acral melanoma
|
Feb 05, 2023 |
|
FarmGTEx TWAS-server: an interactive web server for customized TWAS analysis in both human and farm animals
|
Feb 05, 2023 |
|
MpoxRadar: a worldwide Mpox genomic surveillance dashboard
|
Feb 05, 2023 |
|
SoyOmics: A deeply integrated database on soybean multi omics
|
Feb 05, 2023 |
|
IQMMA: an efficient MS1 intensity extraction using multiple feature detection algorithms for DDA proteomics
|
Feb 04, 2023 |
|
Systematic Analysis of KRAS-ligand Interaction Modes and Flexibilities Reveals the Binding Characteristics
|
Feb 04, 2023 |
|
Gene panel selection for targeted spatial transcriptomics
|
Feb 04, 2023 |
|
Protein Sequence Design by Entropy-based Iterative Refinement
|
Feb 04, 2023 |
|
Correspondence between functional scores from deep mutational scans and predicted effects on protein stability
|
Feb 04, 2023 |
|
SIN3 gene regulatory activity is linked to RNA polymerase II pausing
|
Feb 04, 2023 |
|
Mammalian Milk Glycomes: Connecting the Dots between Evolutionary Conservation and Biosynthetic Pathways
|
Feb 04, 2023 |
|
Visualizing and exploring patterns of large mutational events with SigProfilerMatrixGenerator
|
Feb 04, 2023 |
|
IMPACT: a web server for exploring immunotherapeutic predictive and cancer prognostic biomarkers
|
Feb 03, 2023 |
|
A hybrid method for discovering interferon-gamma inducing peptides in human and mouse
|
Feb 03, 2023 |
|
SHARE-Topic: Bayesian Inerpretable Modelling of Single-Cell Multi-Omic Data
|
Feb 03, 2023 |
|
Towards Universal Cell Embeddings: Integrating Single-cell RNA-seq Datasets across Species with SATURN
|
Feb 03, 2023 |
|
LimoRhyde2: genomic analysis of biological rhythms based on effect sizes
|
Feb 03, 2023 |
|
Label-free tumor cells classification using deep learning and high-content imaging
|
Feb 03, 2023 |
|
Structure-informed Language Models Are Protein Designers
|
Feb 03, 2023 |
|
Construction of a 3D whole organism spatial atlas by joint modeling of multiple slices
|
Feb 03, 2023 |
|
Omicron's Intrinsic Gene-Gene Interactions Jumped Away from Earlier SARS-CoV-2 Variants and Gene Homologs between Humans and Animals
|
Feb 03, 2023 |
|
Paired single-cell multi-omics data integration with Mowgli
|
Feb 03, 2023 |
|
Novel integrated computational AMP discovery approaches highlight diversity in the helminth AMP repertoire
|
Feb 03, 2023 |
|
DandD: efficient measurement of sequence growth and similarity
|
Feb 03, 2023 |
|
Masked superstrings as a unified framework for textual ????-mer set representations
|
Feb 03, 2023 |
|
Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L2UniFrac
|
Feb 03, 2023 |
|
Data-driven filtering for denoising of TCRpMHC single-cell data: a benchmark
|
Feb 03, 2023 |
|
Development of attention-based robust deep learning model for tongue diagnosis by smartphone
|
Feb 03, 2023 |
|
Integrating AlphaFold and deep learning for atomistic interpretation of cryo-EM maps
|
Feb 03, 2023 |
|
sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data
|
Feb 03, 2023 |
|
Bioinformatic identification of ClpI, a distinct class of Clp unfoldases in Actinomycetota
|
Feb 03, 2023 |
|
The local topology of dynamical network models for biology
|
Feb 03, 2023 |
|
The Master Database of All Possible RNA Sequences and Its Integration with RNAcmap for RNA Homology Search
|
Feb 03, 2023 |
|
Benchmarking algorithms for joint integration of unpaired and paired single-cell RNA-seq and ATAC-seq data
|
Feb 03, 2023 |
|
Construction of a searchable database for gene expression changes in spinal cord injury experiments
|
Feb 03, 2023 |
|
Hmrbase2: A comprehensive database of hormones and their receptors
|
Feb 03, 2023 |
|
PlasmidHunter: Accurate and fast prediction of plasmid sequences using gene content profile and machine learning
|
Feb 03, 2023 |
|
PLANET: A Multi-Objective Graph Neural Network Model for Protein-Ligand Binding Affinity Prediction
|
Feb 03, 2023 |
|
Proteome encoded determinants of protein sorting into extracellular vesicles
|
Feb 03, 2023 |
|
stRainy: assembly-based metagenomic strain phasing using long reads
|
Feb 03, 2023 |
|
CATE: A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data.
|
Feb 03, 2023 |
|
Self-supervised learning on millions of pre-mRNA sequences improves sequence-based RNA splicing prediction
|
Feb 03, 2023 |
|
Analysis of AlphaFold and molecular dynamics structure predictions of mutations in serpins
|
Feb 03, 2023 |
|
scDecouple: Decoupling cellular response and infection bias in scCRISPR-seq
|
Feb 03, 2023 |
|
A statistical approach to identify regulatory DNA variations
|
Feb 03, 2023 |
|
ViWrap: A modular pipeline to identify, bin, classify, and predict viral-host relationships for viruses from metagenomes
|
Feb 02, 2023 |
|
The omnitig framework can improve genome assembly contiguity in practice
|
Feb 02, 2023 |
|
A random forest model for predicting exosomal proteins using evolutionary information and motifs
|
Feb 02, 2023 |
|
When sex scarce: A rapid approach to sexing individuals by RAD-seq using a reference genome
|
Feb 02, 2023 |
|
midiaPASEF maximizes information content in data-independent acquisition proteomics
|
Feb 02, 2023 |
|
BIRDMAn: A Bayesian differential abundance framework that enables robust inference of host-microbe associations
|
Feb 02, 2023 |
|
When do longer reads matter? A benchmark of long read de novo assembly tools for eukaryotic genomes
|
Feb 02, 2023 |
|
Self-supervised learning for DNA sequences with circular dilated convolutional networks
|
Feb 01, 2023 |
|
Cell type matching across species using protein embeddings and transfer learning
|
Feb 01, 2023 |
|
Learning to Generate 5' UTR Sequences for Optimized Ribosome Load and Gene Expression
|
Feb 01, 2023 |
|
BZINB model-based pathway analysis and module identification facilitates integration of microbiome and metabolome data
|
Feb 01, 2023 |
|
Characterizing transcriptomic responses to sediment stress across location and morphology in reef-building corals
|
Feb 01, 2023 |
|
Uncovering the Consequences of Batch-Effect Associated Missing Values in Omics Data Analysis
|
Jan 31, 2023 |
|
Charge-State-Dependent Collision-Induced Dissociation Behaviors of RNA Oligonucleotides via High-Resolution Mass Spectrometry
|
Jan 31, 2023 |
|
Differentiable Partition Function Calculation for RNA
|
Jan 31, 2023 |
|
Study on the expression of RAD51 in non-small cell lung cancer based on bioinformatics
|
Jan 31, 2023 |
|
MHCnvex: Likelihood-based model for calling the copy number variations and loss of heterozygosity in MHC class I and II locus
|
Jan 31, 2023 |
|
Scalable neighbour search and alignment with uvaia
|
Jan 31, 2023 |
|
Quantitative Annotations of T-Cell Repertoire Specificity
|
Jan 31, 2023 |
|
Normative Modeling of Brain Morphometry Across the Lifespan using CentileBrain: Algorithm Benchmarking and Model Optimization
|
Jan 31, 2023 |
|
Single-cell multi-omic topic embedding reveals cell-type-specific and COVID-19 severity-related immune signatures
|
Jan 31, 2023 |
|
HLAProphet: Personalized allele-level quantification of the HLA proteins
|
Jan 31, 2023 |
|
On Pre-trained Language Models for Antibody
|
Jan 31, 2023 |
|
Optimizing the design of spatial genomic studies
|
Jan 31, 2023 |
|
Single-cell RNA sequencing reveals dysregulated fibroblast subclusters in prurigo nodularis
|
Jan 31, 2023 |
|
Data-driven optimization of biomarker panels in highly multiplexed imaging
|
Jan 31, 2023 |
|
Crafting negative training datasets for a high-performance classification of bacterial proteins secreted via non-classical pathways
|
Jan 31, 2023 |
|
Explainable prediction of catalysing enzymes from reactions using multilayer perceptrons
|
Jan 30, 2023 |
|
A dual diffusion model enables 3D binding bioactive molecule generation and lead optimization given target pockets
|
Jan 30, 2023 |
|
Decontamination of ambient and margin noise in droplet-based single cell protein expression data with DecontPro
|
Jan 30, 2023 |
|
PPAD: A deep learning architecture to predict progression of Alzheimer's disease
|
Jan 30, 2023 |
|
Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments
|
Jan 29, 2023 |
|
demuxmix: Demultiplexing oligonucleotide-barcoded single-cell RNA sequencing data with regression mixture models
|
Jan 29, 2023 |
|
Motifs in SARS-CoV-2 evolution
|
Jan 29, 2023 |
|
Co-evolution integrated deep learning framework for variants generation and fitness prediction
|
Jan 29, 2023 |
|
A quantitative approach to measure and predict microbiome response to antibiotics
|
Jan 28, 2023 |
|
Efficient image analysis for large-scale next generation histopathology using pAPRica
|
Jan 28, 2023 |
|
scGREAT: Graph-based regulatory element analysis tool for single-cell multi-omics data
|
Jan 28, 2023 |
|
HAT: de novo variant calling for highly accurate short-read and long-read sequencing data
|
Jan 28, 2023 |
|
DeepERA: deep learning enables comprehensive identification of drug-target interactions via embedding of heterogeneous data
|
Jan 28, 2023 |
|
Efficient estimation of breakpoints in piecewise-linear mixed-effects models for longitudinal ophthalmic studies
|
Jan 28, 2023 |
|
N-of-one differential gene expression without control samples using a deep generative model
|
Jan 28, 2023 |
|
Efficiently Quantifying DNA Methylation for Bulk- and Single-cell Bisulfite Data
|
Jan 27, 2023 |
|
The Hidradenitis Suppurativa 'Omics Database (HS-OmicsDB)
|
Jan 27, 2023 |
|
Multi-omics data integration approach identifies potential biomarkers for Prostate cancer
|
Jan 27, 2023 |
|
Protein Representation Learning via Knowledge Enhanced Primary Structure Modeling
|
Jan 27, 2023 |
|
L0 segmentation enables data-driven concise representations of diverse epigenomic data
|
Jan 27, 2023 |
|
Assessing the functional impact of protein binding site definition
|
Jan 27, 2023 |
|
Evaluating Retention Index Score Assumptions to Refine GC-MS Metabolite Identification
|
Jan 27, 2023 |
|
GRN-VAE: A Simplified and Stabilized SEM Model for Gene Regulatory Network Inference
|
Jan 27, 2023 |
|
The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences
|
Jan 27, 2023 |
|
Building a Pangenome Alignment Index via Recursive Prefix-Free Parsing
|
Jan 27, 2023 |
|
macrosyntR : Drawing automatically ordered Oxford Grids from standard genomic files in R
|
Jan 27, 2023 |
|
Adaptation of Graph Convolutional Neural Networks and Graph Layer-wise Relevance Propagation to the Spektral library with application to gene expression data of Colorectal Cancer patients
|
Jan 27, 2023 |
|
PortPred: exploiting deep learning embeddings of amino acid sequences for the identification of transporter proteins and their substrates
|
Jan 27, 2023 |
|
SeqPanther: Sequence manipulation and mutation statistics toolset
|
Jan 27, 2023 |
|
Species-aware DNA language modeling
|
Jan 27, 2023 |
|
decOM: Similarity-based microbial source tracking of ancient oral samples using k-mer-based methods
|
Jan 27, 2023 |
|
Cleavable crosslinkers redefined by novel MS3-trigger algorithm
|
Jan 26, 2023 |
|
SPEAR: a Sparse Supervised Bayesian Factor Model for Multi-omic Integration
|
Jan 26, 2023 |
|
Strain Tracking with Uncertainty Quantification
|
Jan 26, 2023 |
|
A deep learning approach for the discovery of tumor-targeting small organic ligands from DNA-Encoded Chemical Libraries
|
Jan 26, 2023 |
|
Adjustments to the reference dataset design improves cell type label transfer
|
Jan 26, 2023 |
|
Quantum mechanical electronic and geometric parameters for DNA k-mers as features for machine learning
|
Jan 26, 2023 |
|
An intrinsically interpretable neural network architecture for sequence to function learning
|
Jan 26, 2023 |
|
RAMEN identifies effective indicators for severe COVID and Long COVID patients
|
Jan 25, 2023 |
|
DISCO: A deep learning ensemble for uncertainty-aware segmentation of acoustic signals
|
Jan 25, 2023 |
|
The Multi-State Epigenetic Pacemaker enables the identification of combinations of factors that influence DNA methylation
|
Jan 25, 2023 |
|
A Comparison of Lossless Compression Methods in Microscopy Data Storage Applications
|
Jan 25, 2023 |
|
Investigating the Complexity of Gene Co-expression Estimation for Single-cell Data
|
Jan 25, 2023 |
|
Leveraging genomic redundancy to improve inference and alignment of orthologous proteins
|
Jan 25, 2023 |
|
The Impact of Multiple Sequence Alignment Error on Phylogenetic Estimation under Variable-Across-Phylogeny Substitution Models
|
Jan 25, 2023 |
|
The Impact of Species Tree Estimation Error on Cophylogenetic Reconstruction
|
Jan 25, 2023 |
|
Delineating genotypes and phenotypes of individual cells from long-read single cell transcriptomes
|
Jan 25, 2023 |
|
Cell Instance Segmentation via Multi-Scale Non-local Correlation
|
Jan 25, 2023 |
|
A new web resource to predict the impact of missense variants at protein interfaces using 3D structural data: Missense3D-PPI
|
Jan 25, 2023 |
|
Towards Analyzing the Reclassification Dynamics of ClinVar Variants
|
Jan 25, 2023 |
|
The Evolution of Local Energetic Frustration in Protein Families
|
Jan 25, 2023 |
|
E2EDA: Protein domain assembly based on end-to-end deep learning
|
Jan 25, 2023 |
|
Unlocking the Power of R: A High-Accuracy Method for Measuring DAB Staining on Immunohistochemical Slides
|
Jan 25, 2023 |
|
{Theta}-Net: Achieving Enhanced Phase-Modulated Optical Nanoscopy in silico through a computational 'string of beads' architecture
|
Jan 25, 2023 |
|
Impact of cross-ancestry genetic architecture on GWAS in admixed populations
|
Jan 24, 2023 |
|
Explain-seq: an end-to-end pipeline from training to interpretation of sequence-based deep learning models
|
Jan 24, 2023 |
|
Utility of long-read sequencing for All of Us
|
Jan 24, 2023 |
|
Delineation of complex gene expression patterns in single cell RNA-seq data with ICARUS v2.0
|
Jan 24, 2023 |
|
PolyAMiner-Bulk: A Machine Learning Based Bioinformatics Algorithm to Infer and Decode Alternative Polyadenylation Dynamics from bulk RNA-seq data
|
Jan 24, 2023 |
|
Integrative ensemble modelling of cetuximab sensitivity in colorectal cancer PDXs
|
Jan 24, 2023 |
|
Accurate and fast graph-based pangenome annotation and clustering with ggCaller
|
Jan 24, 2023 |
|
NGS-enriched activated sludge modelling of an industrial wastewater treatment plant
|
Jan 24, 2023 |
|
Towards a reliable spatial analysis of missing features via spatially-regularized imputation
|
Jan 23, 2023 |
|
Assessing HLA imputation accuracy in a West African population
|
Jan 23, 2023 |
|
RawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals for Large Genomes
|
Jan 23, 2023 |
|
Accurate and interpretable gene expression imputation on scRNA-seq data using IGSimpute
|
Jan 23, 2023 |
|
Cont-ID:Detection of samples cross-contamination in viral metagenomic data
|
Jan 23, 2023 |
|
Novel Pipeline for Large-Scale Comparative Population Genetics
|
Jan 23, 2023 |
|
Minuteman - A versatile cloud computational platform for collaborative research
|
Jan 23, 2023 |
|
CompCorona: A Web Portal for Comparative Analysis of the Host Transcriptome of PBMC and Lung SARS-CoV-2, SARS-CoV, and MERS-CoV
|
Jan 23, 2023 |
|
In-silico Analysis of SARS-Cov2 Spike Proteins of Different Field Variants
|
Jan 23, 2023 |
|
Prediction of SARS-CoV-2 spike protein mutations using Sequence-to-Sequence and Transformer models
|
Jan 23, 2023 |
|
Pan-cancer Proteomics Analysis to Identify Tumor-Enriched and Highly Expressed Cell Surface Antigens as Potential Targets for Cancer Therapeutics
|
Jan 23, 2023 |
|
PC_sim: An integrated measure of protein sequence and structure similarity for improved alignments and evolutionary inference
|
Jan 22, 2023 |
|
Blind Assessment of Monomeric AlphaFold2 Protein Structure Models with Experimental NMR Data
|
Jan 22, 2023 |
|
Integrating disease genetics and drug bioassays to discover drug impacts on the human phenome
|
Jan 22, 2023 |
|
Gemini: Memory-efficient integration of hundreds of gene networks with high-order pooling
|
Jan 22, 2023 |
|
Accurate age prediction from blood using of small set of DNA methylation sites and a cohort-based machine learning algorithm
|
Jan 21, 2023 |
|
Prediction Analysis of Preterm Neonates Mortality using Machine Learning Algorithms via Python Programming
|
Jan 21, 2023 |
|
High tissue-specificity of lncRNAs maximises the prediction of tissue of origin of circulating DNA
|
Jan 21, 2023 |
|
TCGAnalyzeR: a web application for integrative visualization of molecular and clinical data of cancer patients for cohort discovery
|
Jan 21, 2023 |
|
VRPG: an interactive web viewer for reference pangenome graphs
|
Jan 21, 2023 |
|
Developing a robust technique for denoising and extracting speech and breath sounds in voice recordings from asthmatic patients
|
Jan 21, 2023 |
|
Structural Interaction Fingerprints and Machine Learning for predicting and explaining binding of small molecule ligands to RNA
|
Jan 15, 2023 |
|
Sensitive inference of alignment-safe intervalsfrom biodiverse protein sequence clusters usingEMERALD
|
Jan 15, 2023 |
|
Variational graph encoders: a surprisingly effective generalist algorithm for holistic computer-aided drug design
|
Jan 15, 2023 |
|
Cell segmentation for high-resolution spatial transcriptomics
|
Jan 15, 2023 |
|
Unveiling abundance-dependent metabolic phenotypes of microbial communities
|
Jan 15, 2023 |
|
Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation
|
Jan 15, 2023 |
|
Leveraging public transcriptome data with machine learning to infer pan-body age- and sex-specific molecular phenomena
|
Jan 15, 2023 |
|
GeneMark-ETP: Automatic Gene Finding in Eukaryotic Genomes in Consistence with Extrinsic Data
|
Jan 15, 2023 |
|
Deep-learning based bioactive peptides generation and screening against Xanthine oxidase
|
Jan 13, 2023 |
|
Mass spectrometry-based proteomics imputation using self supervised deep learning
|
Jan 13, 2023 |
|
Deep learning prediction boosts phosphoproteomics-based discoveries through improved phosphopeptide identification
|
Jan 12, 2023 |
|
nleval: A Python Toolkit for Generating Benchmarking Datasets for Machine Learning with Biological Networks
|
Jan 12, 2023 |
|
Identification of Cell-Type Specific Alternative Transcripts in the Multicellular Alga Volvox carteri
|
Jan 12, 2023 |
|
miRCurator: A rapid curation and analysis tool for plantmicroRNA studies
|
Jan 11, 2023 |
|
ODNA: Identification of Organellar DNA by Machine Learning
|
Jan 11, 2023 |
|
CellCharter: a scalable framework to chart and compare cell niches across multiple samples and spatial -omics technologies.
|
Jan 11, 2023 |
|
Benchmark and optimization of AlphaFold structures based virtual screening strategy
|
Jan 11, 2023 |
|
Origin Matters: Using a Local Reference Genome Improves Measures in Population Genomics
|
Jan 11, 2023 |
|
HOGVAX: Exploiting Peptide Overlaps to Maximize Population Coverage in Vaccine Design with Application to SARS-CoV-2
|
Jan 10, 2023 |
|
FastRecomb: Fast inference of genetic recombination rates in biobank scale data
|
Jan 10, 2023 |
|
BRDriver: Breast Cancer Driver Gene Predictor
|
Jan 10, 2023 |
|
CrossTx: Cross-cell line Transcriptomic Signature Predictions
|
Jan 10, 2023 |
|
Weakly-supervised temporal segmentation of cell-cycle stages with center-cell focus using Recurrent Neural Networks
|
Jan 09, 2023 |
|
Detection of circular RNAs and their potential as biomarkers predictive of drug response
|
Jan 09, 2023 |
|
Integration of chromatin accessibility and gene expression data with cisREAD reveals a switch from PU.1/SPIB-driven to AP-1-driven gene regulation during B cell activation
|
Jan 09, 2023 |
|
SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing
|
Jan 09, 2023 |
|
HQAlign: Aligning nanopore reads for SV detection using current-level modeling
|
Jan 09, 2023 |
|
Fluorescence Image Data with Sparse and Low-Rank Poisson Regression
|
Jan 08, 2023 |
|
Decoding CRISPR-Cas9 PAM recognition with UniDesign
|
Jan 08, 2023 |
|
Unsupervised Contrastive Peak Caller for ATAC-seq
|
Jan 08, 2023 |
|
Protein language model embedded geometric graphs power inter-protein contact prediction
|
Jan 08, 2023 |
|
Identification and Characterization of novel long non-coding RNAs in vascular smooth cells
|
Jan 08, 2023 |
|
DPHL v2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins.
|
Jan 08, 2023 |
|
EnsDTI-kinase: Web-server for Predicting Kinase-Inhibitor Interactions with Ensemble Computational Methods and Its Applications
|
Jan 08, 2023 |
|
PASTE2: Partial Alignment of Multi-slice Spatially Resolved Transcriptomics Data
|
Jan 08, 2023 |
|
Epileptic seizure suppression: a computational approach for identification and control using real data
|
Jan 08, 2023 |
|
Conformational changes in the AdeB transmembrane efflux pump protein by amphiphilic peptide Mastoparan-B, down-regulates expression of the adeB Gene and restores antibiotics Susceptibility.
|
Jan 07, 2023 |
|
HiDDEN: A machine learning label refinement method for detection of disease-relevant populations in case-control single-cell transcriptomics
|
Jan 07, 2023 |
|
Hetnet connectivity search provides rapid insights into how two biomedical entities are related
|
Jan 07, 2023 |
|
Minimal Positional Substring Cover: A Haplotype Threading Alternative to Li & Stephens Model
|
Jan 06, 2023 |
|
Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing
|
Jan 06, 2023 |
|
Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms
|
Jan 06, 2023 |
|
ChemGAPP; A Package for Chemical Genomics Analysis and Phenotypic Profiling.
|
Jan 06, 2023 |
|
CAT PETR: A Graphical User Interface for Differential Analysis of Phosphorylation Data
|
Jan 06, 2023 |
|
RabbitVar: ultra-fast and accurate somatic small-variant calling on multi-core architectures
|
Jan 06, 2023 |
|
ViralConsensus: A fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data
|
Jan 06, 2023 |
|
Heterogeneous pseudobulk simulation enables realistic benchmarking of cell-type deconvolution methods
|
Jan 06, 2023 |
|
ConDoR: Tumor phylogeny inference with a copy-number constrained mutation loss model
|
Jan 06, 2023 |
|
The probability of edge existence due to node degree: a baseline for network-based predictions
|
Jan 06, 2023 |
|
When Geometric Deep Learning Meets Pretrained Protein Language Models
|
Jan 06, 2023 |
|
The Use of Class Imbalanced Learning Methods on ULSAM Data to Predict the Case-Control Status in Genome-Wide Association Studies
|
Jan 06, 2023 |
|
The metagenomic analysis of viral diversity in Colorado potato beetle public NGS data
|
Jan 05, 2023 |
|
CRISPR-Cas-Docker: Web-based in silico docking and machine learning-based classification of crRNAs with Cas proteins
|
Jan 05, 2023 |
|
Understanding and evaluating ambiguity in single-cell and single-nucleus RNA-sequencing
|
Jan 04, 2023 |
|
Unravelling cell type specific response to Parkinson's Disease at single cell resolution
|
Jan 04, 2023 |
|
Bioinformatics Approaches to Determine the Effect of SARS-CoV-2 Infection on Patients with Intrahepatic Cholangiocarcinoma
|
Jan 04, 2023 |
|
HPC-Atlas: Computationally Constructing A Comprehensive Atlas of Human Protein Complexes
|
Jan 04, 2023 |
|
ASTK: a software for comprehensive analysis of alternative splicing
|
Jan 04, 2023 |
|
Human embryonic tanycyte: heterogeneity and developmental trajectory
|
Jan 04, 2023 |
|
EpiMix: an integrative tool for epigenomic subtyping using DNA methylation
|
Jan 04, 2023 |
|
IsoAnalytics: A Single-cell Proteomics Web Server
|
Jan 04, 2023 |
|
Computational mutagenesis by using AUTO-MUTE 2.0 to examine X-ray crystallography structures for p53 and the impact of its resolution on predictions
|
Jan 04, 2023 |
|
Niche differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions
|
Jan 04, 2023 |
|
PIsToN: Evaluating Protein Binding Interfaces with Transformer Networks
|
Jan 04, 2023 |
|
ElasticBLAST: Accelerating Sequence Search via Cloud Computing
|
Jan 04, 2023 |
|
Integrative proteogenomics using ProteomeGenerator2
|
Jan 04, 2023 |
|
Generalized tree structure to annotate untargeted metabolomics and stable isotope tracing data
|
Jan 04, 2023 |
|
MuLan-Methyl - Multiple Transformer-based Language Models for Accurate DNA Methylation Prediction
|
Jan 04, 2023 |
|
Reconstruction of 3-dimensional tissue organization at the single-cell resolution
|
Jan 04, 2023 |
|
How random is the review outcome? A systematic study of the impact of external factors on eLife peer review
|
Jan 04, 2023 |
|
AimSeg: a machine-learning-aided tool for axon, inner tongue and myelin segmentation
|
Jan 03, 2023 |
|
MASH Native: A Unified Solution for Native Top-Down Proteomics Data Processing
|
Jan 03, 2023 |
|
RNA-seq preprocessing and sample size considerations for gene network inference
|
Jan 03, 2023 |
|
DISCO+QR: Rooting Species Trees in the Presence of GDL and ILS
|
Jan 03, 2023 |
|
Scribe: next-generation library searching for DDA experiments
|
Jan 03, 2023 |
|
The Labbing Project: A database management application for neuroimaging research
|
Jan 03, 2023 |
|
Prediction of Polygenic Risk Score by Machine Learning and Deep Learning Methods in Genome-wide Association Studies
|
Jan 03, 2023 |
|
An RNA seq-based reference landscape of human normal and neoplastic brain
|
Jan 03, 2023 |
|
Sequence-to-sequence translation from mass spectra to peptides with a transformer model
|
Jan 03, 2023 |
|
In-silico monitoring of directed evolution convergence to unveil best performing variants with credibility score
|
Jan 03, 2023 |
|
Integrated Bioinformatics Analysis Reveals APEX1 as a Potential Biomarker for Septic Cardiomyopathy
|
Jan 03, 2023 |
|
On the correspondence between the transcriptomic response of a compound and its effects on its targets
|
Jan 02, 2023 |
|
RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data
|
Jan 02, 2023 |
|
The Identification of Key Genes and Biological Pathways in Polycystic Ovary Syndrome and its Complications by Next Generation Squancing (NGS) and Bioinformatics Analysis
|
Jan 02, 2023 |
|
The new mega dataset combined with a deep neural network makes progress in predicting the impact of single mutations on protein stability
|
Jan 02, 2023 |
|
Development of digital Hi-C assay
|
Jan 02, 2023 |
|
Brain Electrical Bioactivity Informational Specifics in Relation to Behavioural and Cognitive Functions in Children with Learning Difficulties
|
Dec 31, 2022 |
|
Annotating metabolite mass spectra with domain-inspired chemical formula transformers
|
Dec 31, 2022 |
|
SAMBA: Structure-Learning of Aquaculture Microbiomes Using a Bayesian-Network Approach
|
Dec 31, 2022 |
|
Differential Roles of positive and negative supercoiling in compacting the E. coli genome
|
Dec 31, 2022 |
|
Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data
|
Dec 30, 2022 |
|
Closing the Bio-Silicon Loop for Cellular Neural Prosthesis using FPGA-based Iono-Neuromorphic Models
|
Dec 30, 2022 |
|
FunGeneTyper: An Expandable Deep Learning-based Framework for Ultra-accurate Classification and Discovery of Functional Protein-Coding Genes
|
Dec 30, 2022 |
|
Alternative Polyadenylation alters UBASH3B-ZNF652 competition to involve in Triple-Negative Breast Cancer
|
Dec 30, 2022 |
|
Latent representation of single-cell transcriptomes enables algebraic operations on cellular phenotypes
|
Dec 30, 2022 |
|
Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction
|
Dec 30, 2022 |
|
A concerted increase in readthrough and intron retention drives transposon expression during aging and senescence
|
Dec 30, 2022 |
|
Residue communities reveal evolutionary signatures of γδ T-Cell receptor
|
Dec 30, 2022 |
|
The Standard Genetic Code Lacks Redundancy for Amino Acid Codons
|
Dec 30, 2022 |
|
Optimized MNase-seq pipeline reveals a novel gene regulation via differential nucleosome stability
|
Dec 30, 2022 |
|
A probabilistic view of protein stability, conformational specificity, and design
|
Dec 30, 2022 |
|
A robust deep learning platform to predict CD8+ T-cell epitopes
|
Dec 29, 2022 |
|
Evaluation of the molecular diversity of Brazilian strains of the B.1.1 variant of SARS-CoV-2 used in vaccines
|
Dec 27, 2022 |
|
Epitopes- Based Vaccine Design Against Foot and Mouth Disease SAT2 Serotype from Sudanese Isolate by Using Immunoinformatic Approaches
|
Dec 27, 2022 |
|
Simultaneous visualization of cells and marker genes from scRNA-seq studies
|
Dec 27, 2022 |
|
CoBeL-RL: A neuroscience-oriented simulation framework for complex behavior and learning
|
Dec 27, 2022 |
|
Refinement of AlphaFold-Multimer structures with single sequence input
|
Dec 27, 2022 |
|
Enhanced antibody-antigen structure predictionfrom molecular docking using AlphaFold2
|
Dec 27, 2022 |
|
PROSTATA: Protein Stability Assessment using Transformers
|
Dec 26, 2022 |
|
betAS: intuitive analysis and visualisation of differential alternative splicing using beta distributions
|
Dec 26, 2022 |
|
FCGRT, a cancer-derived immunoglobulin G binding protein, mediates the malignant phenotype of glioma
|
Dec 26, 2022 |
|
Integrating spatial transcriptomics data across different conditions, technologies, and developmental stages
|
Dec 26, 2022 |
|
DeepRTAlign: toward accurate retention time alignment for large cohort mass spectrometry data analysis
|
Dec 25, 2022 |
|
Best: A Tool for Characterizing Sequencing Errors
|
Dec 23, 2022 |
|
HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence
|
Dec 23, 2022 |
|
Combination of Expert Guidelines-based and MachineLearning-based Approaches Leads to Superior Accuracy ofAutomated Prediction of Clinical Effect of Copy Number Variations
|
Dec 23, 2022 |
|
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio High Fidelity reads
|
Dec 23, 2022 |
|
mapquik: Efficient low-divergence mapping of long reads in minimizer space
|
Dec 23, 2022 |
|
Guided-topic modelling of single-cell transcriptomes enables joint cell-type-specific and disease-subtype deconvolution of bulk transcriptomes with a focus on cancer studies
|
Dec 23, 2022 |
|
Inter-domain distance prediction based on deep learning for domain assembly
|
Dec 23, 2022 |
|
C-ToMExO: Learning Cancer Progression Dynamics from Clonal Composition of Tumors
|
Dec 23, 2022 |
|
plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets
|
Dec 23, 2022 |
|
Neural Networks beyond explainability: Selective inference for sequence motifs
|
Dec 23, 2022 |
|
Uncovering context-specific genetic-regulation of gene expression from single-cell RNA-sequencing using latent-factor models
|
Dec 23, 2022 |
|
Detection of A-to-I microRNA editing with miRmedon reveals widespread co-editing of mature microRNA in the human brain
|
Dec 23, 2022 |
|
voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues
|
Dec 23, 2022 |
|
LegNet: resetting the bar in deep learning for accurate prediction of promoter activity and variant effects from massive parallel reporter assays
|
Dec 23, 2022 |
|
16s rRNA gene sequence analysis of the microbial community on microplastic samples from the North Atlantic and Great Pacific Garbage Patches
|
Dec 22, 2022 |
|
Spatial transcriptomics deconvolution at single-cell resolution by Redeconve
|
Dec 22, 2022 |
|
Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas
|
Dec 22, 2022 |
|
HAPNEST: efficient, large-scale generation and evaluation of synthetic datasets for genotypes and phenotypes
|
Dec 22, 2022 |
|
Enhanced Viral Metagenomics with Lazypipe 2
|
Dec 22, 2022 |
|
CRAM compression: practical across-technologies considerations for large-scale sequencing projects
|
Dec 22, 2022 |
|
TrAGEDy: Trajectory Alignment of Gene Expression Dynamics
|
Dec 22, 2022 |
|
FERMO: a Dashboard for Streamlined Rationalized Prioritization of Molecular Features from Mass Spectrometry Data
|
Dec 22, 2022 |
|
Detection of horizontal sequence transfer in microorganisms in the genomic era
|
Dec 22, 2022 |
|
MetaPredict: A machine learning-based tool for predicting metabolic modules in incomplete bacterial genomes
|
Dec 22, 2022 |
|
PeptideForest: Semisupervised machine learning integrating multiple search engines for peptide identification
|
Dec 22, 2022 |
|
Diagnosis with Confidence: Deep Learning for Reliable Classification of Squamous Lesions of the Upper Aerodigestive Tract
|
Dec 22, 2022 |
|
A method for differential expression analysis and pseudo- temporal locating and ordering of genes in single-cell transcriptomic data
|
Dec 22, 2022 |
|
Liam tackles complex multimodal single-cell data integration challenges
|
Dec 22, 2022 |
|
BioNumPy: Fast and easy analysis of biological data with Python
|
Dec 22, 2022 |
|
CIRCUST: a novel methodology for reconstruction of temporal order of molecular rhythms; validation and application towards a human circadian gene expression atlas
|
Dec 22, 2022 |
|
motifNet: Functional motif interactions discovered in mRNA sequences with implicit neural representation learning
|
Dec 21, 2022 |
|
Supervised discovery of interpretable gene programs from single-cell data
|
Dec 21, 2022 |
|
STrack: A tool to Simply Track bacterial cells in microscopy time-lapse images
|
Dec 21, 2022 |
|
End-to-end protein-ligand complex structure generation with diffusion-based generative models
|
Dec 21, 2022 |
|
LuxHMM: DNA methylation analysis with genome segmentation via Hidden Markov Model
|
Dec 21, 2022 |
|
Multimodal learning of noncoding variant effects using genome sequence and chromatin structure
|
Dec 21, 2022 |
|
Benchmarking single-cell hashtag oligo demultiplexing methods
|
Dec 21, 2022 |
|
Dissecting Complexity: The Hidden Impact of Application Parameters on Bioinformatics Research
|
Dec 21, 2022 |
|
AIRRSHIP: simulating human B cell receptor repertoire sequences
|
Dec 21, 2022 |
|
CAbiNet: Joint visualization of cells and genes based on a gene-cell graph
|
Dec 21, 2022 |
|
QRATER: a collaborative and centralized imaging quality control web-based application.
|
Dec 21, 2022 |
|
CircPrime: a web-based platform for design of specific circular RNA primers
|
Dec 20, 2022 |
|
Greengenes2 enables a shared data universe for microbiome studies
|
Dec 20, 2022 |
|
Genomic Distance-based Rapid Uncovering of Microbial Population Structures (GRUMPS): a reference free genomic data cleaning methodology
|
Dec 20, 2022 |
|
Universal chromatin state annotation of the mouse genome
|
Dec 20, 2022 |
|
HBM-CITEseq: a uniform CITE-seq processing pipeline for the HuBMAP Consortium
|
Dec 20, 2022 |
|
Mabs, a suite of tools for gene-informed genome assembly
|
Dec 20, 2022 |
|
BUSZ: Compressed BUS files
|
Dec 20, 2022 |
|
Robust clustering of transcriptomes through multiple testing
|
Dec 20, 2022 |
|
SGCI (Smartwatch Gait Coordination Index): New Measure for Human Gait Utilizing Smartwatch Sensor
|
Dec 20, 2022 |
|
Utilizing co-abundances of antimicrobial resistance genes to identify potential co-selection in the resistome
|
Dec 20, 2022 |
|
Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin
|
Dec 20, 2022 |
|
AFsample: Improving Multimer Prediction with AlphaFold using Aggressive Sampling
|
Dec 20, 2022 |
|
Leveraging a Billion-Edge Knowledge Graph for Drug Re-purposing and Target Prioritization using Genomically-Informed Subgraphs
|
Dec 20, 2022 |
|
EPEK: creation and analysis of an Ectopic Pregnancy Expression Knowledgebase
|
Dec 20, 2022 |
|
A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution
|
Dec 20, 2022 |
|
Plant-PLMview: a database for identifying cis-regulatory sequences with preferential positions in gene-proximal regions of plants
|
Dec 20, 2022 |
|
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)
|
Dec 19, 2022 |
|
Codon language embeddings provide strong signals for protein engineering
|
Dec 19, 2022 |
|
Zero-shot reconstruction of mutant spatial transcriptomes
|
Dec 19, 2022 |
|
Handling ill-conditioned omics data with deep probabilistic models
|
Dec 19, 2022 |
|
novoRNABreak: local assembly for novel splice junction and fusion transcript detection from RNA-seq data
|
Dec 19, 2022 |
|
Varying molecular interactions explain crowder-dependent enzyme function of a viral protease
|
Dec 19, 2022 |
|
Structural characterizations of a unusual peptide CORO1C-47aa encoded by circRNA hsa-circ-0000437 associated with endometrial cancer
|
Dec 19, 2022 |
|
Finding the best cell lines across pan-cancer to use in pre-clinical research as a proxy for patient tumor samples considering immune cells, multi-omics, and cancer pathways
|
Dec 19, 2022 |
|
Filtering Methods for Asymmetric ODFs: Where and How Asymmetry Occurs in the White Matter
|
Dec 19, 2022 |
|
Hypergraphs and centrality measures identifying keyfeatures in gene expression data
|
Dec 19, 2022 |
|
Synthetic whole-slide image tile generation with gene expression profiles infused deep generative models
|
Dec 19, 2022 |
|
Tumor Segmentation using temporal Independent Component Analysis for DCE-MRI
|
Dec 19, 2022 |
|
MultiGML: Multimodal Graph Machine Learning for Prediction of Adverse Drug Events
|
Dec 19, 2022 |
|
De novo protein backbone generation based on diffusion with structured priors and adversarial training
|
Dec 19, 2022 |
|
Dashing Growth Curves - a web application for rapid and interactive analysis of microbial growth curves
|
Dec 19, 2022 |
|
Persistent spectral theory-guided protein engineering
|
Dec 19, 2022 |
|
SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data
|
Dec 19, 2022 |
|
Consistent typing of plasmids with the mge-cluster pipeline
|
Dec 19, 2022 |
|
Predicting transcription factor activity using prior biological information
|
Dec 19, 2022 |
|
DNA-protein quasi-mapping for rapid differential gene expression analysis in non-model organisms
|
Dec 19, 2022 |
|
The use of a graph database is a complementary approach to a classical similarity search for identifying commercially available fragment merges
|
Dec 19, 2022 |
|
Protein Language Model for Prediction of Subcellular Localization of Protein Sequences from Gram-negative bacteria (ProtLM.SCL)
|
Dec 19, 2022 |
|
Transformer-based tool recommendation system in Galaxy
|
Dec 19, 2022 |
|
Okapi-EM - a napari plugin for processing and analysing cryogenic serial FIB/SEM images
|
Dec 19, 2022 |
|
Accurate cell type deconvolution in spatial transcriptomics using a batch effect-free strategy
|
Dec 19, 2022 |
|
Assessing multiple evidence streams to decide on confidence for identification of post-translational modifications, within and across data sets
|
Dec 19, 2022 |
|
Estimating admixture pedigrees of recent hybrids without a contiguous reference genome
|
Dec 19, 2022 |
|
Detecting remote homolog using structure alignment algorithms and machine learning
|
Dec 19, 2022 |
|
Structure modeling and specificity of peptide-MHC class I interactions using geometric deep learning
|
Dec 19, 2022 |
|
Ot2Rec: A Semi-Automatic, Extensible, Multi-Software Tomographic Reconstruction Workflow
|
Dec 19, 2022 |
|
Startle: a star homoplasy approach for CRISPR-Cas9 lineage tracing
|
Dec 18, 2022 |
|
Evaluation of Mycobacterium Tuberculosis enrichment in metagenomic samples using ONT adaptive sequencing and amplicon sequencing for identification and variant calling
|
Dec 17, 2022 |
|
CAAStools, a toolbox to identify and test Convergent Amino Acid Substitutions.
|
Dec 16, 2022 |
|
Improving the prediction of white matter hyperintensities evolution in brain MRI of patients with small vessel disease using stroke lesions information
|
Dec 16, 2022 |
|
PyDESeq2: a python package for bulk RNA-seq differential expression analysis
|
Dec 16, 2022 |
|
Processing and evaluating the quality of genome-wide nascent transcription profiling libraries
|
Dec 16, 2022 |
|
BioASQ-QA: A manually curated corpus for Biomedical Question Answering
|
Dec 16, 2022 |
|
Unsupervized identification of prognostic copy-numberalterations using segmentation and lasso regularization
|
Dec 16, 2022 |
|
The necessity of considering enzymes as compartments in constraint-based genomescale metabolic models
|
Dec 16, 2022 |
|
Automated genome mining predicts combinatorial diversity and taxonomic distribution of peptide metallophore structures
|
Dec 16, 2022 |
|
Mirage2's high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms
|
Dec 16, 2022 |
|
E(3) equivariant graph neural networks for robust and accurate protein-protein interaction site prediction
|
Dec 16, 2022 |
|
Identifying indels from WGS short reads of haploid genomes distinguishes variant-calling algorithms
|
Dec 16, 2022 |
|
The impact of study design choices on significance and generalizability of canonical correlation analysis in neuroimaging studies
|
Dec 16, 2022 |
|
Integrating deep mutational scanning and low-throughput mutagenesis data to predict the impact of amino acid variants
|
Dec 16, 2022 |
|
Predicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networks
|
Dec 15, 2022 |
|
First fully-automated AI/ML virtual screening cascade implemented at a drug discovery centre in Africa
|
Dec 15, 2022 |
|
NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis
|
Dec 15, 2022 |
|
MIDAS: a deep generative model for mosaic integration and knowledge transfer of single-cell multimodal data
|
Dec 15, 2022 |
|
Exact Probability Distribution for the ROC Area Under Curve
|
Dec 15, 2022 |
|
Alignment-based protein mutational landscape prediction: doing more with less
|
Dec 15, 2022 |
|
GeneSegNet: A deep learning framework for cell segmentation by integrating gene expression and imaging
|
Dec 15, 2022 |
|
Cell-type-specific co-expression inference from single cell RNA-sequencing data
|
Dec 15, 2022 |
|
Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data
|
Dec 15, 2022 |
|
Single-nucleus co-expression networks of dopaminergic neurons support iron accumulation as a plausible explanation to their vulnerability in Parkinson's disease
|
Dec 15, 2022 |
|
A Versatile Deep Graph Contrastive Learning Framework for Single-cell Proteomics Embedding
|
Dec 15, 2022 |
|
Disentangling shared and group-specific variations in single-cell transcriptomics data with multiGroupVI
|
Dec 15, 2022 |
|
Merging short and stranded long reads improves transcript assembly
|
Dec 15, 2022 |
|
Enterotypes of the human gut mycobiome
|
Dec 15, 2022 |
|
De novo protein design by inversion of the AlphaFold structure prediction network
|
Dec 15, 2022 |
|
Crowdsourcing Temporal Transcriptomic Coronavirus Host Infection Data: resources, guide, and novel insights.
|
Dec 15, 2022 |
|
Embedding-based alignment: combining protein language models and alignment approaches to detect structural similarities in the twilight-zone
|
Dec 15, 2022 |
|
Mean Dimension of Generative Models for Protein Sequences
|
Dec 14, 2022 |
|
Proteome-wide structure-based accessibility analysis of ligandable and detectable cysteines in chemoproteomic datasets
|
Dec 14, 2022 |
|
COVID-19db linkage maps of cell surface proteins and transcription factors in immune cells
|
Dec 14, 2022 |
|
Genome-wide analysis of dry (Tamar) Date palm fruit color
|
Dec 14, 2022 |
|
Pan-cancer transcriptomic analysis reveals a tissue-specific loss of identity
|
Dec 14, 2022 |
|
FrustraPocket: A protein-ligand binding site predictor using energetic local frustration
|
Dec 14, 2022 |
|
Evaluation of a scalable approach to generate cell-type specific transcriptomic profiles of mesenchymal lineage cells
|
Dec 14, 2022 |
|
The ratio of adaptive to innate immune cells differs between genders and associates with improved prognosis and response to immunotherapy
|
Dec 14, 2022 |
|
Joint inference of transcription factor activity and context-specific regulatory networks
|
Dec 14, 2022 |
|
Application of Aligned-UMAP to longitudinal biomedical studies
|
Dec 14, 2022 |
|
Generalizing the isothermal efficiency by using Gaussian distributions
|
Dec 14, 2022 |
|
Mass Dynamics 2.0: An improved modular web-based platform for accelerated proteomics insight generation and decision making
|
Dec 14, 2022 |
|
Quantifying B-cell Clonal Diversity In Repertoire Data
|
Dec 14, 2022 |
|
PaleoProPhyler: a reproducible pipeline for phylogenetic inference using ancient proteins
|
Dec 13, 2022 |
|
PYPE: A Python pipeline for phenome-wide association (PheWAS) and mendelian randomization in investigator-driven phenotypes and genotypes of biobank data
|
Dec 13, 2022 |
|
Long COVID: G Protein-Coupled Receptors (GPCRs) responsible for persistent post-COVID symptoms
|
Dec 13, 2022 |
|
SpaGFT is a graph Fourier transform for tissue module identification from spatially resolved transcriptomics
|
Dec 13, 2022 |
|
Fibroblast Growth Factor 5 (FGF5) and Its Missense Mutant FGF5-Y174H Underlying Trichomegaly: A Molecular Dynamics Simulation Investigation
|
Dec 13, 2022 |
|
SWAMPy: Simulating SARS-CoV-2 Wastewater Amplicon Metagenomes with Python
|
Dec 12, 2022 |
|
Exploring B and T-cell epitopes for constructing a Novel Multiepitope vaccine to combat emerging Monkeypox infection: A Reverse Vaccinology approach
|
Dec 12, 2022 |
|
Structural Insights into Pink-eyed Dilution Protein (Oca2)
|
Dec 12, 2022 |
|
Origin, evolution and diversification of plant mechanosensitive channel of small conductance-like (MSL) proteins
|
Dec 12, 2022 |
|
Biological Cartography: Building and Benchmarking Representations of Life
|
Dec 12, 2022 |
|
Web-based Tool Validation for Antimicrobial Resistance Prediction: An Empirical Comparative Analysis
|
Dec 12, 2022 |
|
Identifying key residues in intrinsically disordered regions of proteins using machine learning
|
Dec 12, 2022 |
|
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering
|
Dec 12, 2022 |
|
Identification of a covert evolutionary pathway between two protein folds
|
Dec 12, 2022 |
|
3D multiplexed tissue imaging reconstruction and optimized region-of-interest (ROI) selection through deep learning model of channels embedding
|
Dec 12, 2022 |
|
Phantasus: web-application for visual and interactive gene expression analysis
|
Dec 12, 2022 |
|
Snakeobjects: an object-oriented workflow management system
|
Dec 12, 2022 |
|
Foldcomp: a library and format for compressing and indexing large protein structure sets
|
Dec 12, 2022 |
|
SpLitteR: Diploid genome assembly using linked TELL-Seq reads and assembly graphs
|
Dec 12, 2022 |
|
md_harmonize: a Python package for atom-level harmonization of public metabolic data-bases
|
Dec 12, 2022 |
|
Cell shape characterization, alignment and comparison using FlowShape
|
Dec 12, 2022 |
|
Towards a Clinically-based Common Coordinate Framework for the Human Gut Cell Atlas - The Gut Models
|
Dec 12, 2022 |
|
RNA-Chrom: a manually-curated analytical database of RNA-chromatin interactome
|
Dec 12, 2022 |
|
Learning orientation-invariant representations enables accurate and robust morphologic profiling of cells and organelles
|
Dec 12, 2022 |
|
Correction of transposase sequence bias in ATAC-seq data with rule ensemble modeling
|
Dec 12, 2022 |
|
Creating an Ignorance-Base: Exploring Known Unknowns in the Scientific Literature
|
Dec 12, 2022 |
|
SAINT-Angle: self-attention augmented inception-inside-inception network and transfer learning improve protein backbone torsion angle prediction
|
Dec 12, 2022 |
|
dgram2dmap: Extraction, visualisation and formatting of distance constraints from AlphaFold distograms
|
Dec 12, 2022 |
|
scTensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data
|
Dec 12, 2022 |
|
Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes
|
Dec 12, 2022 |
|
MAD HATTER correctly annotates 98% of small molecule tandem mass spectra searching in PubChem
|
Dec 12, 2022 |
|
IIIandMe: An Algorithm for Chromosome-scale Haplotype Determination Using Genome-wide Variants of Three Haploid Reproductive Cells
|
Dec 12, 2022 |
|
Cryo-EM map anisotropy can be attenuated by map post-processing and a new method for its estimation
|
Dec 12, 2022 |
|
Graph neural networks learn emergent tissue properties from spatial molecular profiles
|
Dec 11, 2022 |
|
Improving prediction of drug-target interactions based on fusing multiple features with data balancing and feature selection techniques
|
Dec 10, 2022 |
|
scEvoNet: a gradient boosting-based method for prediction of cell state evolution
|
Dec 10, 2022 |
|
Bayesian clustering with uncertain data
|
Dec 10, 2022 |
|
Integrated Single-Dose Kinome Profiling Data is Predictive of Cancer Cell Line Sensitivity to Kinase Inhibitors
|
Dec 10, 2022 |
|
AutoGater: A Weakly Supervised Neural Network Model to Gate Cells in Flow Cytometric Analyses
|
Dec 10, 2022 |
|
Points2regions: Fast Interactive Clustering Of In Situ Transcriptomics Data
|
Dec 10, 2022 |
|
Whole slide image representation in bone marrow cytology
|
Dec 10, 2022 |
|
Baseline Acute Myeloid Leukemia Prognosis Models using Transcriptomic and Clinical Profiles by Studying the Impacts of Dimensionality Reductions and Gene Signatures on Cox-Proportional Hazard
|
Dec 10, 2022 |
|
General stain deconvolution of histopathology images with physics-guided deep learning
|
Dec 10, 2022 |
|
Learning the Drug-Target Interaction Lexicon
|
Dec 10, 2022 |
|
metaDMG - A Fast and Accurate Ancient DNA Damage Toolkit for Metagenomic Data
|
Dec 09, 2022 |
|
ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models
|
Dec 09, 2022 |
|
Improvement of protein tertiary and quaternary structure predictions using the ReFOLD4 refinement method and the AlphaFold2 recycling process
|
Dec 09, 2022 |
|
Structural pre-training improves physical accuracy of antibody structure prediction using deep learning.
|
Dec 09, 2022 |
|
Identifying B-cell epitopes using AlphaFold2 predicted structures and pretrained language model
|
Dec 09, 2022 |
|
Discovering Haematoma-Stimulated Circuits for Secondary Brain Injury after Intraventricular Haemorrhage by Spatial Transcriptome Analysis
|
Dec 09, 2022 |
|
Learning the differences: a transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity
|
Dec 09, 2022 |
|
wastewaterSPAdes: SARS-CoV-2 strain deconvolution using SPAdes toolkit
|
Dec 09, 2022 |
|
From Multi-Allele Fish to Non-Standard Environments, How ZFIN Assigns Phenotypes, Human Disease Models, and Gene Expression Annotations to Genes
|
Dec 08, 2022 |
|
Dysfunctional analysis of the pre-training model on nucleotide sequences and the evaluation of different k-mer embeddings
|
Dec 08, 2022 |
|
NetGO 3.0: Protein Language Model Improves Large-scale Functional Annotations
|
Dec 08, 2022 |
|
Optimising a coordinate ascent algorithm for the meta-analysis of test accuracy studies
|
Dec 08, 2022 |
|
Fast and accurate protein function prediction from sequence through pretrained language model and homology-based label diffusion
|
Dec 08, 2022 |
|
Megan Server: facilitating interactive access to metagenomic data on a server
|
Dec 08, 2022 |
|
M-Band Wavelet-Based Imputation of scRNA-seq Matrix and Multi-view Clustering of Cell
|
Dec 08, 2022 |
|
A Meta-analysis of 2D vs. 3D Ovarian Cancer Cellular Models
|
Dec 08, 2022 |
|
Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2
|
Dec 08, 2022 |
|
Exploring the intricacies and pitfalls of the ATN framework: An assessment across cohorts and thresholding methodologies
|
Dec 08, 2022 |
|
BCLncRDB: A comprehensive database of LncRNAs associated with breast cancer
|
Dec 08, 2022 |
|
MembraneFold: Visualising transmembrane protein structure and topology
|
Dec 08, 2022 |
|
Discordant results among MHC binding affinity prediction tools
|
Dec 07, 2022 |
|
Deep Local Analysis deconstructs protein-protein interfaces and accurately estimates binding affinity changes upon mutation
|
Dec 07, 2022 |
|
Anti-correlated Feature Selection Prevents False Discovery of Subpopulations in scRNAseq
|
Dec 07, 2022 |
|
Monopogen: single nucleotide variant calling from single cell sequencing
|
Dec 07, 2022 |
|
Unsupervised reference-free inference reveals unrecognized regulated transcriptomic complexity in human single cells
|
Dec 07, 2022 |
|
The Inherited Rate Matrix algorithm for phylogenetic model selection for non-stationary Markov processes
|
Dec 07, 2022 |
|
rcCAE: a convolutional autoencoder based method for detecting tumor clones and copy number alterations from single-cell DNA sequencing data
|
Dec 07, 2022 |
|
Genome charaterization based on the Spike-614 and NS8-84 loci of SARS-CoV-2 reveals two major onsets of the COVID-19 pandemic
|
Dec 06, 2022 |
|
Sharing Massive Biomedical Data at Magnitudes Lower Bandwidth Using Implicit Neural Function
|
Dec 05, 2022 |
|
The PRALINE database: Protein and Rna humAn singLe nucleotIde variaNts in condEnsates
|
Dec 05, 2022 |
|
GDockScore: a graph-based protein-protein dockingscoring function
|
Dec 05, 2022 |
|
A knowledge-based system for personalised lifestyle recommendations: Design and simulation of potential effectiveness on the UK Biobank data
|
Dec 05, 2022 |
|
Covidscope: An atlas-scale COVID-19 resource for single-cell meta analysis at sample and cell levels
|
Dec 05, 2022 |
|
DiffDomain enables identification of structurally reorganized topologically associating domains
|
Dec 05, 2022 |
|
Performance of computational algorithms to deconvolve heterogeneous bulk tumor tissue depends on experimental factors
|
Dec 05, 2022 |
|
cazy_webscraper: local compilation and interrogation of comprehensive CAZyme datasets
|
Dec 03, 2022 |
|
Investigating graph neural network for RNA structural embedding
|
Dec 03, 2022 |
|
Evolutionary shortcuts via multi-nucleotide substitutions and their impact on natural selection analyses.
|
Dec 03, 2022 |
|
Finemap-MiXeR: A variational Bayesian approach for genetic finemapping
|
Dec 02, 2022 |
|
Statistical tests to detect differences between codon-specific Ramachandran plots
|
Dec 02, 2022 |
|
HTRX: an R package for learning non-contiguous haplotypes associated with a phenotype
|
Dec 02, 2022 |
|
Does Inter-Protein Contact Prediction Benefit from Multi-Modal Data and Auxiliary Tasks?
|
Dec 02, 2022 |
|
Improving Protein Subcellular Localization Prediction with Structural Prediction & Graph Neural Networks
|
Dec 02, 2022 |
|
Gene Set Scoring on the Nearest Neighbor Graph (gssnng) for Single Cell RNA-seq (scRNA-seq)
|
Dec 02, 2022 |
|
Contrastive learning of protein representations with graph neural networks for structural and functional annotations
|
Dec 02, 2022 |
|
TissUUmaps 3 Tools for Visualization & Quality Control in Large-scale Multiplex Tissue Analysis
|
Dec 02, 2022 |
|
Genetic fine-mapping from summary data using a non-local prior improves detection of multiple causal variants
|
Dec 02, 2022 |
|
CRMnet: a deep learning model for predicting gene expression from large regulatory sequence datasets
|
Dec 02, 2022 |
|
GOThresher: a program to remove annotation biases from protein function annotation datasets
|
Dec 02, 2022 |
|
Accurate quantification of single-nucleus and single-cell RNA-seq transcripts
|
Dec 02, 2022 |
|
Illuminating protein space with a programmable generative model
|
Dec 02, 2022 |
|
Annotation-agnostic discovery of associations between novel gene isoforms and phenotypes
|
Dec 02, 2022 |
|
MLcps: Machine Learning Cumulative Performance Score for classification problems
|
Dec 02, 2022 |
|
Secure and Federated Genome-Wide Association Studies for Biobank-Scale Datasets
|
Dec 02, 2022 |
|
Prediction and Curation of Missing Biomedical Identifier Mappings with Biomappings
|
Dec 02, 2022 |
|
WASCO: A Wasserstein-based statistical tool to compare conformational ensembles of intrinsically disordered proteins
|
Dec 02, 2022 |
|
Assessing the Nucleotide-Level Impact of Spaceflight Stress using RNA-Sequencing Data
|
Dec 02, 2022 |
|
PfaSTer: A ML-powered serotype caller for Streptococcus pneumoniae genomes
|
Dec 02, 2022 |
|
Chimeric U-Net - Modifying the standard U-Net towards Explainability
|
Dec 02, 2022 |
|
YOUNG PLASMA REJUVENATES BLOOD DNA METHYLATION PROFILE, PROLONGS MEAN LIFESPAN AND IMPROVES HEALTH IN OLD RATS
|
Dec 02, 2022 |
|
Predicting Drug Repurposing Candidates and Their Mechanisms from A Biomedical Knowledge Graph
|
Dec 02, 2022 |
|
Metacell projection for interpretable and quantitative use of transcriptional atlases
|
Dec 02, 2022 |
|
Effect of D128N mutation on OsSERK2 in Xa21 mediated immune complex: an in-silico study
|
Dec 02, 2022 |
|
Variational inference accelerates accurate DNA mixture deconvolution
|
Dec 02, 2022 |
|
Dynamic Data Independent Acquisition Mass Spectrometry with Real-Time Retrospective Alignment
|
Dec 02, 2022 |
|
TMvisDB: resource for transmembrane protein annotation and 3D visualization
|
Dec 02, 2022 |
|
Predicting Immune Escape with Pretrained Protein Language Model Embeddings
|
Dec 02, 2022 |
|
Proteomic profiling identifies biomarkers of COVID-19 severity
|
Nov 30, 2022 |
|
DAPTEV: Deep aptamer evolutionary modelling for COVID-19 drug design
|
Nov 30, 2022 |
|
Common gene signature model discovery and systematic validation for TB prognosis and response to treatment
|
Nov 30, 2022 |
|
predatoR: an R package for network-based mutation impact prediction
|
Nov 30, 2022 |
|
Methylmap: visualization of modified nucleotides for large cohort sizes
|
Nov 30, 2022 |
|
T-cell receptor specific protein language model for prediction and interpretation of epitope binding (ProtLM.TCR)
|
Nov 29, 2022 |
|
ARCHE: A HIERARCHICAL, EASY TO DOWNLOAD, FUNCTIONAL-OPTIMIZED ANNOTATOR FOR MICROBIAL META(GENOMES)
|
Nov 29, 2022 |
|
Rethinking bacterial relationships in light of their molecular abilities
|
Nov 29, 2022 |
|
Imputation of low-coverage sequencing data from 150,119 UK Biobank genomes
|
Nov 29, 2022 |
|
Computational deconvolution of fifteen leukocyte subtypes from DNA methylation microarrays trained on flow cytometry data in the Health and Retirement Study
|
Nov 29, 2022 |
|
Brewpitopes: a pipeline to refine B-cell epitope predictions during public health emergencies
|
Nov 29, 2022 |
|
NanoPack2: Population scale evaluation of long-read sequencing data
|
Nov 29, 2022 |
|
NanoTrans: an integrated computational framework for comprehensive transcriptome analyses with Nanopore direct-RNA sequencing
|
Nov 29, 2022 |
|
Real-time biochemical-free targeted sequencing of RNA species with RISER
|
Nov 29, 2022 |
|
Exploring Xylella fastidiosa's metabolic traits using a GSM model of the phytopathogenic bacterium
|
Nov 29, 2022 |
|
Multifaceted quality assessment of gene repertoire annotation with OMArk
|
Nov 28, 2022 |
|
CommonNNClustering--A Python package for generic common-nearest-neighbour clustering
|
Nov 28, 2022 |
|
PhosphoLingo: protein language models for phosphorylation site prediction
|
Nov 28, 2022 |
|
ViCloD, an interactive web tool for visualizing B cell repertoires and analyzing intra-clonal diversities: application to human B-cell tumors
|
Nov 28, 2022 |
|
CiliaMiner: an integrated database for Ciliopathy Genes and Ciliopathies
|
Nov 28, 2022 |
|
Fast protein structure searching using structure graph embeddings
|
Nov 28, 2022 |
|
SlideCNA: Spatial copy number alteration detection from Slide-seq-like spatial transcriptomics data
|
Nov 27, 2022 |
|
Deep Learning for Predicting 16S rRNA Copy Number
|
Nov 27, 2022 |
|
Identification of novel natural product inhibitors of BRD4 using high throughput virtual screening and MD simulation
|
Nov 27, 2022 |
|
A 3D genome atlas of genetic variants and their pathological effects
|
Nov 27, 2022 |
|
Inferring delays in partially observed gene regulatory networks
|
Nov 27, 2022 |
|
Deep Domain Adversarial Neural Network for the Deconvolution of Cell Type Mixtures in Tissue Proteome Profiling
|
Nov 25, 2022 |
|
scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data
|
Nov 25, 2022 |
|
Measuring cell-to-cell expression variability in single-cell RNA-sequencing data: a comparative analysis and applications to B cell ageing
|
Nov 25, 2022 |
|
Visualization of Incrementally Learned Projection Trajectories for Longitudinal Data
|
Nov 25, 2022 |
|
RNAlysis: analyze your RNA sequencing data without writing a single line of code
|
Nov 25, 2022 |
|
PRESGENE: A web server for PRediction of ESsential GENE using integrative machine learning strategies
|
Nov 25, 2022 |
|
Predicting and Interpreting Protein Developability via Transfer of Convolutional Sequence Representation
|
Nov 25, 2022 |
|
Developing best practices for genotyping-by-sequencing analysis using linkage maps as benchmarks
|
Nov 25, 2022 |
|
pLM-BLAST - distant homology detection based on direct comparison of sequence representations from protein language models
|
Nov 25, 2022 |
|
ADeS: a deep learning based Apoptosis Detection System for live cell imaging.
|
Nov 25, 2022 |
|
MAGE: Strain Level Profiling of MetagenomeSamples
|
Nov 25, 2022 |
|
Predicting Lung Cancer in Korean Never-Smokers with Polygenic Risk Scores
|
Nov 25, 2022 |
|
Dynamic Interaction Learning and MultimodalRepresentation for Drug Response Prediction
|
Nov 25, 2022 |
|
SCALA: A web application for multimodal analysis of single cell next generation sequencing data
|
Nov 25, 2022 |
|
Inhibiting a promiscuous GPCR: iterative discovery of bitter taste receptor ligands
|
Nov 25, 2022 |
|
Consensus Label Propagation with Graph Convolutional Networks for Single-Cell RNA Sequencing Cell Type Annotation
|
Nov 25, 2022 |
|
Re-implementation of an algorithm to integrate transcriptome and ChIP-seq data
|
Nov 25, 2022 |
|
Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine
|
Nov 25, 2022 |
|
Evaluating spatially variable gene detection methods for spatial transcriptomics data
|
Nov 25, 2022 |
|
Matrix prior for data transfer between single cell data types in latent Dirichlet allocation
|
Nov 25, 2022 |
|
MSdb: an integrated expression atlas of human musculoskeletal system
|
Nov 25, 2022 |
|
BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis
|
Nov 25, 2022 |
|
ExposomeX: Integrative Exposomic Platform Expediates Discovery of "Exposure-Biology-Disease" Nexus
|
Nov 25, 2022 |
|
CRISPRi-FGP: web-based genome-scale CRISPRi sgRNA design and validation tool in prokaryotes
|
Nov 25, 2022 |
|
Improving protein secondary structure prediction by deep language models and transformer networks
|
Nov 24, 2022 |
|
Interactive explainable AI platform for graph neural networks
|
Nov 24, 2022 |
|
Expression profiles of hypoxia-related genes of cancers originating from anatomically similar locations using TCGA database analysis
|
Nov 24, 2022 |
|
Optimization-Based Decoding of Imaging Spatial Transcriptomics Data
|
Nov 24, 2022 |
|
Peptide-MHC Structure Prediction With Mixed Residue and Atom Graph Neural Network
|
Nov 24, 2022 |
|
Terraces in Species Tree Inference from Gene Trees
|
Nov 24, 2022 |
|
A Novel Approach to Topological Network Analysis for the Identification of Metrics and Signatures in Non-Small Cell Lung Cancer
|
Nov 24, 2022 |
|
Node-degree aware edge sampling mitigates inflated classification performance in biomedical graph representation learning
|
Nov 24, 2022 |
|
Region- and variance-based DNA methylation analyses reveal novel disease genes and pathways for systemic lupus erythematosus
|
Nov 24, 2022 |
|
MerCat2: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from omics data
|
Nov 24, 2022 |
|
k2v: A Containerized Workflow for Creating VCF Files from Kintelligence Targeted Sequencing Data
|
Nov 24, 2022 |
|
Performance comparison of TCR-pMHC prediction tools reveals a strong data dependency
|
Nov 24, 2022 |
|
CASBERT: BERT-Based Retrieval for Compositely Annotated Biosimulation Model Entities
|
Nov 24, 2022 |
|
Multi-layer guilt-by-association-based drug repurposing by integrating clinical knowledge on biological heterogeneous networks
|
Nov 24, 2022 |
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Rapid Real-time Squiggle Classification for Read Until Using RawMap
|
Nov 24, 2022 |
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Evolution of drug resistance drives progressive destabilizations in functionally conserved molecular dynamics of the flap region of the HIV-1 protease
|
Nov 24, 2022 |
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gtexture: Haralick texture analysis for graphs and its application to biological networks
|
Nov 24, 2022 |
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excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies
|
Nov 24, 2022 |
|
Fragment-Based Hit Discovery via Unsupervised Learning of Fragment-Protein Complexes
|
Nov 24, 2022 |
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HAPPY: A deep learning pipeline for mapping cell-to-tissue graphs across placenta histology whole slide images
|
Nov 24, 2022 |
|
Starfysh reveals heterogeneous spatial dynamics in the breast tumor microenvironment
|
Nov 24, 2022 |
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RE2DC: a robust and efficient 2D classifier with visualization for processing massive and heterogeneous cryo-EM data
|
Nov 24, 2022 |
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Identifying Protein Haplotypes by Mass Spectrometry
|
Nov 24, 2022 |
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Database of recurrent mutations (DORM), a web tool to browse recurrent mutations in cancers
|
Nov 24, 2022 |
|
Quantitative assessment of association between noncoding variants and transcription factor binding
|
Nov 23, 2022 |
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Accuracy and completeness of long read metagenomic assemblies
|
Nov 23, 2022 |
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Computational investigations in inhibition of alcohol/aldehyde dehydrogenase in lignocellulosic hydrolysates
|
Nov 22, 2022 |
|
SUMO - In Silico Sequence Assessment Using Multiple Optimization Parameters
|
Nov 22, 2022 |
|
Plastid Genome Assembly Using Long-read Data (ptGAUL)
|
Nov 22, 2022 |
|
Does AlphaFold predict the spatial structure of a protein from physics or recognize it (its main parts and their association) using databases?
|
Nov 22, 2022 |
|
Computational Pipeline to Identify Gene signatures that Define Cancer Subtypes
|
Nov 22, 2022 |
|
OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization
|
Nov 22, 2022 |
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Identification of Key Genes and Underlying Mechanisms in Cystic fibrosis and its Associated Complications Based on Bioinformatics Analysis of Next Generation Sequencing Data Analysis
|
Nov 22, 2022 |
|
Predicting lifespan-extending chemical compounds with machine learning and biologically interpretable features
|
Nov 22, 2022 |
|
scFormer: A Universal Representation Learning Approach for Single-Cell Data Using Transformers
|
Nov 22, 2022 |
|
Updated benchmarking of variant effect predictors using deep mutational scanning
|
Nov 22, 2022 |
|
Single-Cell ATAC-seq analysis via Network Refinement with peaks location information
|
Nov 22, 2022 |
|
Polymorphic regions in BA.2.12.1, BA.4 and BA.5 likely implicated in immunological evasion of Omicron subvariant BQ.1.1
|
Nov 21, 2022 |
|
SARS-CoV-2 variant transition dynamics are associated with vaccination rates, number of co-circulating variants, and natural immunity
|
Nov 21, 2022 |
|
Decoding protein binding landscape on circular RNAs with base-resolution Transformer models
|
Nov 20, 2022 |
|
HoCoRT: Host contamination removal tool
|
Nov 20, 2022 |
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Network Based Identification of Holistic Drug Target for Parkinson Disease and Deep Learning assisted Drug Repurposing.
|
Nov 20, 2022 |
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SurvBoard: Standardised Benchmarking for Multi-omics Cancer Survival Models
|
Nov 20, 2022 |
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CAGEE: computational analysis of gene expression evolution
|
Nov 20, 2022 |
|
An Automatized Workflow to Study Mechanistic Indicators for Driver Gene Prediction with Moonlight
|
Nov 20, 2022 |
|
Running ahead of evolution - AI based simulation for predicting future high-risk SARS-CoV-2 variants
|
Nov 19, 2022 |
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Structural, functional and evolutionary analysis of wheat WRKY45 protein: A combined bioinformatics and MD simulation approach
|
Nov 19, 2022 |
|
A comparative study of neuroendocrine heterogeneity in SCLC and NBL
|
Nov 18, 2022 |
|
Cell-type annotation with accurate unseen cell-type identification using multiple references
|
Nov 18, 2022 |
|
Evaluating the analytical validity of mutation calling pipeline for tumor whole exome sequencing
|
Nov 18, 2022 |
|
Integrated single cell analysis reveals co-evolution of malignant B cells and the tumor microenvironment in transformed follicular lymphoma
|
Nov 18, 2022 |
|
TimiGP: inferring inter-cell functional interactions and clinical values in the tumor immune microenvironment through gene pairs
|
Nov 18, 2022 |
|
PlantTribes2: tools for comparative gene family analysis in plant genomics
|
Nov 18, 2022 |
|
Inferring ligand-receptor cellular networks from bulk and spatial transcriptomic datasets with BulkSignalR
|
Nov 18, 2022 |
|
CLOOME: a new search engine unlocks bioimaging databases for queries with chemical structures
|
Nov 18, 2022 |
|
Bioinformatic methods for stratification of obese patients and identification of cancer susceptibility biomarkers based on the analysis of the gut microbiome
|
Nov 18, 2022 |
|
Finding Consensus miRNAs Silencing KLF1 Expression as A Promising Therapeutic Option of Sickle Cell Anemia
|
Nov 18, 2022 |
|
Reference genome sequences of Mythimna separata (Lepidoptera: Noctuidae)
|
Nov 18, 2022 |
|
Analysis of spatial transcriptomics at varying resolution levels using the unified framework of SpaSEG
|
Nov 17, 2022 |
|
Inferring the distributions of fitness effects and proportions of strongly deleterious mutations
|
Nov 17, 2022 |
|
Purging genomes of contamination eliminates systematic bias from evolutionary analyses of ancestral genomes
|
Nov 17, 2022 |
|
Explainable Deep Generative Models, Ancestral Fragments, and Murky Regions of the Protein Structure Universe
|
Nov 17, 2022 |
|
Quality control for the target decoy approach for peptide identification
|
Nov 17, 2022 |
|
ECOLE: Learning to call copy number variants on whole exome sequencing data
|
Nov 17, 2022 |
|
Snapper: a high-sensitive algorithm to detect methylation motifs based on Oxford Nanopore reads
|
Nov 17, 2022 |
|
The effect of background noise and its removal on the analysis of single-cell expression data
|
Nov 17, 2022 |
|
MatchCLOT: Single-Cell Modality Matching with Contrastive Learning and Optimal Transport
|
Nov 17, 2022 |
|
KBPRNA: A novel method integrating bulk RNA-seq data and LINCS-L1000 gene signatures to predict kinase activity based on machine learning
|
Nov 17, 2022 |
|
gGN: learning to represent graph nodes as low-rank Gaussian distributions
|
Nov 17, 2022 |
|
Versatile detection of diverse selective sweeps with Flex-sweep
|
Nov 17, 2022 |
|
Conformational epistasis impairs AlphaFold structural predictions
|
Nov 17, 2022 |
|
ChromFormer: A transformer-based model for 3Dgenome structure prediction
|
Nov 17, 2022 |
|
Deep Representation Learning Determines Drug Mechanism of Action from Cell Painting Images
|
Nov 17, 2022 |
|
PSMC2 and CXCL8-Modulated Four Critical Gene Biomarkers and Druggable and Vaccinable Targets for Colorectal Cancer
|
Nov 17, 2022 |
|
DeepBryo: a web app for AI-assisted morphometric characterization of cheilostome bryozoans
|
Nov 17, 2022 |
|
Inferring a cell's capabilities from omics data with ImmCellFie
|
Nov 17, 2022 |
|
Genome-wide single-molecule analysis of long-read DNA methylation reveals heterogeneous patterns at heterochromatin
|
Nov 16, 2022 |
|
Revisiting pangenome openness with k-mers
|
Nov 16, 2022 |
|
A pan-cancer interrogation of intronic polyadenylation and its association with cancer characteristics
|
Nov 16, 2022 |
|
The repertoire of copy number alteration signatures in human cancer
|
Nov 16, 2022 |
|
Ultra-fast protein structure prediction to capture effects of sequence variation in mutation movies
|
Nov 16, 2022 |
|
CRitical Assessment of genomic COntamination detection at several Taxonomic ranks (CRACOT)
|
Nov 16, 2022 |
|
Application of a Latent Trait Modeling Method for Missing Data Across Datasets: Guidance on Appropriate Factor Structure
|
Nov 16, 2022 |
|
MOT: a Multi-Omics Transformer for multiclass classification tumour types predictions
|
Nov 16, 2022 |
|
Context-Aware Transcript Quantification from Long Read RNA-Seq data with Bambu
|
Nov 16, 2022 |
|
CREPE: A Shiny App for Transcription Factor Cataloguing
|
Nov 16, 2022 |
|
Deep-learning based bioactive therapeutic peptides generation and screening
|
Nov 16, 2022 |
|
Inflammation in the tumor-adjacent lung as a predictor of clinical outcome in lung adenocarcinoma
|
Nov 15, 2022 |
|
A Microfluidic Device to Simulate the Impact of Gut Microbiome in Cancer
|
Nov 15, 2022 |
|
Computational Design of a New Aflatoxin B1 Aptamer in lieu of SELEX Technique
|
Nov 15, 2022 |
|
A universal differential expression prediction tool for single-cell and spatial genomics data
|
Nov 15, 2022 |
|
AGouTI - flexible Annotation of Genomic and Transcriptomic Intervals
|
Nov 15, 2022 |
|
Using conditional Generative Adversarial Networks (GAN) to generate de novo synthetic cell nuclei for training machine learning-based image segmentation
|
Nov 15, 2022 |
|
FASSO: An AlphaFold based method to assign functional annotations by combining sequence and structure orthology
|
Nov 15, 2022 |
|
ACNN-6mA: Prediction of N6-Methyladenine Loci in Multiple Species Based on Rice Dataset Pre-training Model
|
Nov 15, 2022 |
|
A consensus score to combine inferences from multiple centres
|
Nov 14, 2022 |
|
VarSCAT: A computational tool for sequence context annotations of genomic variants
|
Nov 14, 2022 |
|
A Bioinformatic Study of the Distribution of Mn Oxidation Proteins in Sequenced Bacterial Genomes
|
Nov 14, 2022 |
|
Effect of Human microRNA on Dengue Virus Genome: a cross-specie approach
|
Nov 14, 2022 |
|
BeEM: fast and faithful conversion of mmCIF format structure files to PDB format
|
Nov 14, 2022 |
|
Rockfish: A Transformer-based Model for Accurate 5-Methylcytosine Prediction from Nanopore Sequencing
|
Nov 14, 2022 |
|
Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning
|
Nov 14, 2022 |
|
Generative modeling of short, disordered proteins with homogeneous sequence composition
|
Nov 14, 2022 |
|
Customized genomes for human and mouse ribosomal DNA mapping
|
Nov 14, 2022 |
|
Highly Realistic Whole Transcriptome Synthesis through Generative Adversarial Networks
|
Nov 14, 2022 |
|
Reconciliation and Evolution of Penicillium rubens Genome-Scale Metabolic Networks - What about Specialised Metabolism?
|
Nov 14, 2022 |
|
The usage of transcriptomics datasets as sources of Real-World Data for clinical trialling
|
Nov 13, 2022 |
|
STREAK: A Supervised Cell Surface Receptor Abundance Estimation Strategy for Single Cell RNA-Sequencing Data using Feature Selection and Thresholded Gene Set Scoring
|
Nov 13, 2022 |
|
Latch Verified Bulk-RNA Seq toolkit: a cloud-based suite of workflows for bulk RNA-seq quality control, analysis, and functional enrichment
|
Nov 13, 2022 |
|
DeepCCI: a deep learning framework for identifying cell-cell interactions from single-cell RNA sequencing data
|
Nov 13, 2022 |
|
GlyLES: Grammar-based Parsing of Glycans from IUPAC-condensed to SMILES
|
Nov 13, 2022 |
|
tFold-Ab: Fast and Accurate Antibody Structure Prediction without Sequence Homologs
|
Nov 13, 2022 |
|
INSIDER: Interpretable Sparse Matrix Decomposition for Bulk RNA Expression Data Analysis
|
Nov 13, 2022 |
|
Genebank genomics allows greatly improved taxonomic correction for Capsicum spp. accessions using a novel automated classification method
|
Nov 10, 2022 |
|
PAST: latent feature extraction with a Prior-based self-Attention framework for Spatial Transcriptomics
|
Nov 10, 2022 |
|
Massive proteogenomic reanalysis of publicly available proteomic datasets of human tissues in search for protein recoding via adenosine-to-inosine RNA editing
|
Nov 10, 2022 |
|
memento: Generalized differential expression analysis of single-cell RNA-seq with method of moments estimation and efficient resampling
|
Nov 10, 2022 |
|
Jointly aligning cells and genomic features of single-cell multi-omics data with co-optimal transport
|
Nov 10, 2022 |
|
Destin2: integrative and cross-modality analysis of single-cell chromatin accessibility data
|
Nov 10, 2022 |
|
Hybran: Hybrid Reference Transfer and ab initio Prokaryotic Genome Annotation
|
Nov 10, 2022 |
|
Accurate Detection of Incomplete Lineage Sorting via Supervised Machine Learning
|
Nov 10, 2022 |
|
Ibex: Variational autoencoder for single-cell BCR sequencing.
|
Nov 10, 2022 |
|
Reliable and accurate gene expression quantification with subpopulation structure-aware constraints for single-cell RNA sequencing
|
Nov 09, 2022 |
|
Pipeline for transferring annotations between proteins beyond globular domains
|
Nov 09, 2022 |
|
RBPamp: Quantitative Modeling of Protein-RNA Interactions in vitro Predicts in vivo Binding
|
Nov 09, 2022 |
|
dipwmsearch: a python package for searching di-PWM motifs
|
Nov 09, 2022 |
|
The Time-Course of Cancer Cachexia Onset Reveals Biphasic Transcriptional Disruptions in Female Skeletal Muscle Distinct from Males
|
Nov 09, 2022 |
|
Technical Note: STRATIS: A Cloud-enabled Software Toolbox for Radiotherapy and Imaging Analysis
|
Nov 09, 2022 |
|
PathExpSurv: Pathway Expansion for Explainable Survival Analysis and Disease Gene Discovery
|
Nov 09, 2022 |
|
Geneplot: a coordinate conversion approach for graphical representation of protein domain data on the exon-intron structure of a gene.
|
Nov 09, 2022 |
|
Combined promoter-capture Hi-C and Hi-C analysis reveals a fine-tuned regulation of 3D chromatin architecture in colorectal cancer
|
Nov 09, 2022 |
|
SSB toolkit: from molecular structure to subcellular signaling pathways.
|
Nov 09, 2022 |
|
scmTE: multivariate transfer entropy builds interpretable compact gene regulatory networks by reducing false predictions
|
Nov 09, 2022 |
|
Challenges in antibody structure prediction
|
Nov 09, 2022 |
|
Cerebellar granule neurons induce Cyclin D1 in an early stage of Huntington's disease
|
Nov 09, 2022 |
|
STAMarker: Determining spatial domain-specific variable genes with saliency maps in deep learning
|
Nov 08, 2022 |
|
Single-cell imaging based prognosis prediction identifies new breast cancer survival subtypes
|
Nov 08, 2022 |
|
scAN10: A reproducible and standardized pipeline for processing 10X single cell RNAseq data
|
Nov 08, 2022 |
|
Adversarial Attacks on Genotype Sequences
|
Nov 08, 2022 |
|
An Approach to Identify Expression Quantitative Super Enhancers Using Single-cell Multi-omic Data
|
Nov 08, 2022 |
|
Structured Joint Decomposition (SJD) identifies conserved molecular dynamics across collections of biologically related multi-omics data matrices
|
Nov 08, 2022 |
|
GIL: A Python package for designing custom indexing primers
|
Nov 08, 2022 |
|
eccDNA Atlas: a comprehensive resource of eccDNA catalog
|
Nov 08, 2022 |
|
A personal, reference quality, fully annotated genome from a Saudi individual
|
Nov 08, 2022 |
|
Linking Gene Expression to Clinical Outcomes in Pediatric Crohn's Disease Using Machine Learning
|
Nov 08, 2022 |
|
Normalized Semi-Covariance Co-Efficiency Analysis of Spike Proteins from SARS-CoV-2 variant Omicron and Other Coronaviruses for their Infectivity and Virulence
|
Nov 08, 2022 |
|
PIQUE: An ImageJ plugin for the quantification of toroidal nuclei in biological images
|
Nov 07, 2022 |
|
Enrichment of charge-absent regions in phase separated proteins
|
Nov 06, 2022 |
|
An integrated Bayesian framework for multi-omics prediction and classification
|
Nov 06, 2022 |
|
mimicINT: a workflow for microbe-host protein interaction inference
|
Nov 06, 2022 |
|
Identification of Potential DNA Gyrase Inhibitors: Virtual Screening, Extra-Precision Docking and Molecular Dynamics Simulation Study
|
Nov 06, 2022 |
|
Learning predictive models of tissue cellular neighborhoods from cell phenotypes with graph pooling
|
Nov 06, 2022 |
|
Deep unfolded convolutional dictionary learning for motif discovery
|
Nov 06, 2022 |
|
Transcriptome Data Analysis of Primary Cardiomyopathies Reveals Perturbations in Arachidonic Acid Metabolism
|
Nov 06, 2022 |
|
Deep Learning-based Feature Extraction with MRI Data in Neuroimaging Genetics for Alzheimer's Disease
|
Nov 05, 2022 |
|
MetaGraph-MLA: Label-guided alignment to variable-order De Bruijn graphs
|
Nov 05, 2022 |
|
Deciphering tumor ecosystems at super-resolution from spatial transcriptomics with TESLA
|
Nov 05, 2022 |
|
WarpSTR: Determining tandem repeat lengths using raw nanopore signals
|
Nov 05, 2022 |
|
MethylSeqLogo: DNA methylation smart sequence logos
|
Nov 05, 2022 |
|
Improving annotation propagation on molecular networks through random walks: Introducing ChemWalker
|
Nov 05, 2022 |
|
Decipher macrophage-fibroblast-cardiomyocyte signaling interactions associated with heart failure using deep graph neural network models and single-cell RNA-seq data
|
Nov 04, 2022 |
|
Contrasting drugs from decoys
|
Nov 04, 2022 |
|
Cellpanelr: identify predictive biomarkers from cell line panel response data
|
Nov 04, 2022 |
|
END-TO-END CLASSIFICATION OF CELL-CYCLE STAGES WITH CENTER-CELL FOCUS TRACKER USING RECURRENT NEURAL NETWORKS
|
Nov 04, 2022 |
|
A Web/Cloud based Digital Pathology Platform Framework for AI Development and Deployment
|
Nov 04, 2022 |
|
Evolution-inspired augmentations improve deep learning for regulatory genomics
|
Nov 04, 2022 |
|
Machine-learning based detection of adventitious microbes in T-cell therapy cultures using long read sequencing
|
Nov 04, 2022 |
|
Adapting protein language models for rapid DTI prediction
|
Nov 04, 2022 |
|
A graph clustering algorithm for detection and genotyping of structural variants from long reads
|
Nov 04, 2022 |
|
Ensemble Clustering Combined with Clustering Optimization: A Novel Workflow for Analyzing Metabolomics Data
|
Nov 04, 2022 |
|
TCR_Explore: a novel webtool for T cell receptor repertoire analysis
|
Nov 04, 2022 |
|
SEPepQuant enables comprehensive protein isoform characterization in shotgun proteomics
|
Nov 04, 2022 |
|
kegg_pull: a Software Package for the RESTful Access and Pulling from The Kyoto Encyclopedia of Gene and Genomes
|
Nov 04, 2022 |
|
ImmuneBuilder: Deep-Learning models for predicting the structures of immune proteins.
|
Nov 04, 2022 |
|
An immune-suppressing protein in human endogenous retroviruses
|
Nov 04, 2022 |
|
EukRibo: a manually curated eukaryotic 18S rDNA reference database to facilitate identification of new diversity
|
Nov 04, 2022 |
|
DeepOM: Single-molecule optical genome mapping via deep learning
|
Nov 04, 2022 |
|
Integrated analysis of single-cell transcriptome of liver cancer and cirrhosis reveals cell lineage similarity and prognostic-associated subpopulations
|
Nov 04, 2022 |
|
Improving the Quality of Co-evolution Intermolecular Contact Prediction with DisVis
|
Nov 04, 2022 |
|
Mutual Annotation-Based Prediction of Protein Domain Functions with Domain2GO
|
Nov 04, 2022 |
|
ASCARIS: Positional Feature Annotation and Protein Structure-Based Representation of Single Amino Acid Variations
|
Nov 04, 2022 |
|
Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance
|
Nov 03, 2022 |
|
IPLS-LDA: An Improved Partial Least Square Discriminant Analysis for Heterogeneous Transcriptomics and Metabolomics Data Analysis
|
Nov 03, 2022 |
|
TreeTerminus - Creating transcript trees using inferential replicate counts
|
Nov 03, 2022 |
|
Transcription is ubiquitously terminated in thousands of bidirectional termination zones in yeast
|
Nov 03, 2022 |
|
transmorph: a unifying computational framework for single-cell data integration
|
Nov 03, 2022 |
|
Sourmash Branchwater Enables Lightweight Petabyte-Scale Sequence Search
|
Nov 03, 2022 |
|
Sashimi.py: a flexible toolkit for combinatorial analysis of genomic data
|
Nov 03, 2022 |
|
Statistical analysis and simulation allowing simultaneously positive, negative, and no crossover interference in multilocus recombination data
|
Nov 03, 2022 |
|
Unraveling the coordinated dynamics of protein- and metabolite-mediated cell-cell communication
|
Nov 03, 2022 |
|
An information theoretic approach to detecting spatially varying genes
|
Nov 03, 2022 |
|
Gene model correction for PVRIG in single cell and bulk sequencing data enables accurate detection and study of its functional relevance
|
Nov 03, 2022 |
|
inMTSCCA: An Integrated Multi-task Sparse Canonical Correlation Analysis for Multi-omics Brain Imaging Genetics
|
Nov 02, 2022 |
|
Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods.
|
Nov 02, 2022 |
|
A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures
|
Nov 02, 2022 |
|
Singletrome: A method to analyze and enhance the transcriptome with long noncoding RNAs for single cell analysis
|
Nov 02, 2022 |
|
Filter inference: A scalable nonlinear mixed effects inference approach for snapshot time series data
|
Nov 02, 2022 |
|
HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes.
|
Nov 02, 2022 |
|
Drug prediction for reversing AD/PD transcriptional profiles using an aging of systems-centric approach
|
Nov 02, 2022 |
|
KA-Search: Rapid and exhaustive sequence identity search of known antibodies
|
Nov 02, 2022 |
|
Improving quantitative structure models of trees inspired by pipe and metabolic scaling theory
|
Nov 01, 2022 |
|
Developing an automated skeletal phenotyping pipeline to leverage biobank-level medical imaging databases
|
Nov 01, 2022 |
|
Hypothesis-driven modeling of the human lung-ventilator system for Acute Respiratory Distress Syndrome research
|
Nov 01, 2022 |
|
Negligible peptidome diversity of SARS-CoV-2 and its higher taxonomic ranks
|
Nov 01, 2022 |
|
Falign: An effective alignment tool for long noisy 3C data
|
Nov 01, 2022 |
|
STREAMLINE: Structural and TopologicalPerformance Analysis of Algorithms for the Inference of Gene Regulatory Networks from Single-Cell Transcriptomic Data
|
Nov 01, 2022 |
|
A representative Performance Assessment of Maximum Likelihood based Phylogenetic Inference Tools
|
Nov 01, 2022 |
|
Best Practices for Interpretable Machine Learning in Computational Biology
|
Nov 01, 2022 |
|
ALaSCA: a computational platform for quantifying the effect of proteins using Pearlian causal inference, with an example application in Alzheimer's disease
|
Nov 01, 2022 |
|
Cooltools: enabling high-resolution Hi-C analysis in Python
|
Nov 01, 2022 |
|
PointVS: A Machine Learning Scoring Function that Identifies Important Binding Interactions
|
Oct 31, 2022 |
|
Transformer-based deep learning integrates multi-omic data with cancer pathways
|
Oct 31, 2022 |
|
Toblerone: detecting exon deletion events in cancer using RNA-seq
|
Oct 31, 2022 |
|
Identifying endogenous peptide receptors bycombining structure and transmembrane topologyprediction
|
Oct 31, 2022 |
|
One-stop analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform
|
Oct 31, 2022 |
|
Expanding the stdpopsim species catalog, and lessons learned forrealistic genome simulations
|
Oct 31, 2022 |
|
Deep Learning vs Gradient Boosting in age prediction on immunology profile
|
Oct 31, 2022 |
|
Mining impactful discoveries from the biomedical literature
|
Oct 30, 2022 |
|
The BRAIN Initiative Cell Census Data Ecosystem: A User's Guide
|
Oct 30, 2022 |
|
Spectrum preserving tilings enable sparse and modular reference indexing
|
Oct 28, 2022 |
|
SalienceNet: an unsupervised Image-to-Image translation method for nuclei saliency enhancement in microscopy images
|
Oct 28, 2022 |
|
uORF4u: a tool for annotation of conserved upstream open reading frames
|
Oct 28, 2022 |
|
RecGraph: adding recombinations to sequence-to-graph alignments
|
Oct 28, 2022 |
|
Impact evaluation of score classes and annotation regions in deep learning-based dairy cow body condition prediction
|
Oct 28, 2022 |
|
Benchmarking solutions to the T-cell receptor epitope prediction problem: IMMREP22 workshop report
|
Oct 28, 2022 |
|
GENLIB: new function to simulate haplotype transmission in large complex genealogies
|
Oct 28, 2022 |
|
SEMPAI: a Self-Enhancing Multi-Photon Artificial Intelligence for prior-informed assessment of muscle function and pathology
|
Oct 28, 2022 |
|
Assessing the impacts of various factors related to identification, conservation, biogenesis, and function on circular RNA reliability
|
Oct 28, 2022 |
|
Quantitative analysis of cellular morphology during in vitro decidualization
|
Oct 28, 2022 |
|
Comparing 10x Genomics single-cell 3' and 5' assay in short-and long-read sequencing
|
Oct 28, 2022 |
|
Flux estimation analysis systematically characterizes the metabolic shifts of the central metabolism pathway in human cancer.
|
Oct 28, 2022 |
|
Identifying Neuropsychiatric Disorder Subtypes and Subtype-dependent Variation in Diagnostic Deep Learning Classifier Performance
|
Oct 28, 2022 |
|
Gait speed and individual characteristics can be used to predict specific gait metric magnitudes in neurotypical adults.
|
Oct 28, 2022 |
|
Modification of Seurat v4 for the development of a phase assignment tool able to distinguish between G2 and Mitotic cells
|
Oct 27, 2022 |
|
Statistical analysis supports pervasive RNA subcellular localization and alternative 3' UTR regulation
|
Oct 27, 2022 |
|
A Spectral Method for Assessing and Combining Multiple Data Visualizations
|
Oct 27, 2022 |
|
Hidden GPCR structural transitions addressed by multiple walker supervised molecular dynamics (mwSuMD)
|
Oct 27, 2022 |
|
BATCH-SCAMPP: Scaling phylogenetic placement methods to place many sequences
|
Oct 27, 2022 |
|
NanoBlot: A Simple Tool for Visualization of RNA Isoform Usage From Third Generation RNA-sequencing Data
|
Oct 27, 2022 |
|
A pan-cancer PDX histology image repository with genomic and pathological annotations for deep learning analysis
|
Oct 27, 2022 |
|
IntestLine: a Shiny-based application to map the rolled intestinal tissue onto a line
|
Oct 27, 2022 |
|
Aligning Distant Sequences to Graphs using Long Seed Sketches
|
Oct 27, 2022 |
|
Statistically Consistent Rooting of Species Trees under the Multi-Species Coalescent Model
|
Oct 27, 2022 |
|
A Robust Bayesian Approach to Bulk Gene Expression Deconvolution withNoisy Reference Signatures
|
Oct 27, 2022 |
|
AI-Enabled Classification of Head and Neck Tumors using Convolutional Neural Networks with Dynamic Optical Contrast Imaging
|
Oct 27, 2022 |
|
A Unified Modular Framework to Incorporate Structural Dependency in Spatial Omics Data
|
Oct 27, 2022 |
|
T1K: efficient and accurate KIR and HLA genotyping with next-generation sequencing data
|
Oct 27, 2022 |
|
Assessing SARS-CoV-2 evolution through the analysis of emerging mutations
|
Oct 26, 2022 |
|
PEGG: A computational pipeline for rapid design of prime editing guide RNAs and sensor libraries
|
Oct 26, 2022 |
|
Technical report on best practices for hybrid and long read de novo assembly of bacterial genomes utilizing Illumina and Oxford Nanopore Technologies reads
|
Oct 26, 2022 |
|
SurvivalML: an integrative platform for the discovery and exploration of prognostic models in multi-center cancer cohorts
|
Oct 26, 2022 |
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mutscan - a flexible R package for efficient end-to-end analysis of multiplexed assays of variant effect data
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Oct 26, 2022 |
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Ultra-fast joint-genotyping with SparkGOR
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Oct 26, 2022 |
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The geometry of hidden representations of protein language models
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Oct 26, 2022 |
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EUGENe: A Python toolkit for predictive analyses of regulatory sequences
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Oct 26, 2022 |
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Eliminate false positives in metagenomic profiling based on type IIB restriction sites
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Oct 25, 2022 |
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Cell Painting transfer increases screening hit rate
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Oct 25, 2022 |
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Regulation of cytoplasmic mRNA level by chromatin retention
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Oct 25, 2022 |
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meTCRs - Learning a metric for T-cell receptors
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Oct 25, 2022 |
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Transcriptome analyses using regulon, functional category, and operon information with GINtool
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Oct 25, 2022 |
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Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification
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Oct 25, 2022 |
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Fever temperatures modulate intraprotein dynamics and enhance the binding affinity between monoclonal antibodies and the Spike protein from SARS-CoV-2
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Oct 25, 2022 |
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ISPRED-SEQ: Deep neural networks and embeddings for predicting interaction sites in protein sequences.
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Oct 25, 2022 |
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NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange
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Oct 25, 2022 |
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Accurate de novo prediction of RNA 3D structure with transformer network
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Oct 25, 2022 |
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A scalable, reproducible and open-source pipeline for morphologically profiling image cytometry data
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Oct 25, 2022 |
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Adversarial Attacks on Protein Language Models
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Oct 25, 2022 |
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SDRAP for annotating scrambled or rearranged genomes
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Oct 25, 2022 |
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DeepSelectNet: Deep Neural Network Based Selective Sequencing for Oxford Nanopore Sequencing
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Oct 25, 2022 |
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Extremely-fast construction and querying of compacted and colored de Bruijn graphs with GGCAT
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Oct 25, 2022 |
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scifAI: Explainable machine learning for profiling the immunological synapse and functional characterization of therapeutic antibodies
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Oct 25, 2022 |
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Single-cell gene set enrichment analysis and transfer learning for functional annotation of scRNA-seq data
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Oct 25, 2022 |
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COOBoostR: an extreme gradient boosting-based tool for robust tissue or cell-of-origin prediction of tumors
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Oct 25, 2022 |
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The Molecular Signatures Database Revisited: Extending Support for Mouse Data
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Oct 25, 2022 |
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hgtseq: a standard pipeline to study horizontal gene transfer
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Oct 25, 2022 |
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MdrDB: Mutation-induced drug resistance DataBase
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Oct 24, 2022 |
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scCobra: Contrastive cell embedding learning with domain adaptation for single-cell data integration
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Oct 24, 2022 |
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MAVISp: Multi-layered Assessment of VarIants by Structure for proteins
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Oct 24, 2022 |
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Improving fine-mapping by modeling infinitesimal effects
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Oct 24, 2022 |
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Unsupervised Discovery of Ancestry Informative Markers and Genetic Admixture Proportions in Biobank-Scale Data Sets
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Oct 24, 2022 |
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Real-time detection of acute lymphoblastic leukemia cells using deep learning
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Oct 24, 2022 |
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Improving classification of correct and incorrect protein-protein docking models by augmenting the training set
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Oct 24, 2022 |
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SUsPECT: A pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant annotation
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Oct 24, 2022 |
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A positive statistical benchmark to assess network agreement
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Oct 24, 2022 |
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KBeagle: An Adaptive Strategy and Tool for Improvement of Imputation Accuracy and Computing Efficiency
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Oct 24, 2022 |
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Optimal microRNA sequencing depth to predict cancer patient survival with random forest and Cox models
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Oct 24, 2022 |
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GiRAFR improves gRNA detection and annotation in single cell CRISPR screens
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Oct 24, 2022 |
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ViReaDB: A user-friendly database for compactly storing viral sequence data and rapidly computing consensus genome sequences
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Oct 24, 2022 |
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Genome-wide identification and analysis of analysis of BURP genes in Triticum aestivum
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Oct 24, 2022 |
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ACDA: Implementation of an Augmented Drug Synergy Prediction Algorithm
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Oct 22, 2022 |
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MSBooster: Improving Peptide Identification Rates using Deep Learning-Based Features
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Oct 21, 2022 |
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Graph Regularized Probabilistic MatrixFactorization for Drug-Drug Interactions Prediction
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Oct 21, 2022 |
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DANCE: A Deep Learning Library and Benchmark for Single-Cell Analysis
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Oct 21, 2022 |
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MAW - The Reproducible Metabolome Annotation Workflow for Untargeted Tandem Mass Spectrometry
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Oct 21, 2022 |
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Discovery of gene-gene co-perturbation through big data
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Oct 21, 2022 |
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Towards Hierarchical Causal Representation Learning for Nonstationary Multi-Omics Data
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Oct 21, 2022 |
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DGH-GO: Dissecting the Genetic Heterogeneity of complex diseases using Gene Ontology
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Oct 21, 2022 |
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Census: accurate, automated, deep, fast, and hierarchical scRNA-seq cell-type annotation
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Oct 21, 2022 |
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TF-Prioritizer: a java pipeline to prioritize condition-specific transcription factors
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Oct 21, 2022 |
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Efficient minimizer orders for large values of k using minimum decycling sets
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Oct 21, 2022 |
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Vector-clustering Multiple Sequence Alignment: Aligning into the twilight zone of protein sequence similarity with protein language models
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Oct 21, 2022 |
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A Platform-Independent Framework for Phenotyping of Multiplex Tissue Imaging Data
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Oct 21, 2022 |
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Some Mendelian Disorders could be fixed with a pill? A Structural Bioinformatic investigation
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Oct 21, 2022 |
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Multi-histone ChIP-Seq Analysis with DecoDen
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Oct 21, 2022 |
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Prediction and scanning of IL-5 inducing peptides using alignment-free and alignment-based method
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Oct 21, 2022 |
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MorphNet Predicts Cell Morphology from Single-Cell Gene Expression
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Oct 21, 2022 |
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Insitutype: likelihood-based cell typing for single cell spatial transcriptomics
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Oct 21, 2022 |
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Pathway-informed deep learning model for survivalanalysis and pathological classification of gliomas
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Oct 21, 2022 |
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Performance Evaluation Of Prediction On Molecular Graphs With Graph Neural Networks
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Oct 21, 2022 |
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Identification of RNA-based cell-type markers for the stem cell manufacture system with a statistical scoring function
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Oct 21, 2022 |
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VStrains: De Novo Reconstruction of Viral Strains via Iterative Path Extraction From Assembly Graphs
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Oct 21, 2022 |
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Repurposing of Drugs against mutated strain of Eurasian Avian like H1N1 (EA H1N1) Swine flu, Genotype-4 (G4) virus
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Oct 21, 2022 |
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The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics .
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Oct 21, 2022 |
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NEMETEX: a Python software for the visualisation of the network of metabolic exchanges
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Oct 21, 2022 |
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Retention time prediction to facilitate molecularstructure identification with tandem mass spectrometry
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Oct 21, 2022 |
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Predicting individualized tissue gene expression profiles with multi-task learning
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Oct 21, 2022 |
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TEINet: a deep learning framework for prediction of TCR-epitope binding specificity
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Oct 21, 2022 |
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DeepChIA-PET: Accurately predicting ChIA-PET from Hi-C and ChIP-seq with deep dilated networks
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Oct 21, 2022 |
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GSearch: Ultra-Fast and Scalable Microbial Genome Search by combining Kmer Hashing with Hierarchical Navigable Small World Graphs
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Oct 21, 2022 |