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Episode | Date |
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Radiation necrosis after radiation therapy treatment of brain metastases: A computational approach
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Aug 03, 2023 |
Evaluation of Fendiline Treatment in VP40 System with Nucleation-Elongation Process: A Computational Model of Ebola Virus Matrix Protein Assembly
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Aug 03, 2023 |
Combined kinome inhibition states are predictive of cancer cell line sensitivity to kinase inhibitor combination therapies
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Aug 03, 2023 |
A Phosphoproteomics Data Resource for Systems-level Modeling of Kinase Signaling Networks
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Aug 03, 2023 |
Quantifying landscape-flux via single-cell transcriptomics uncovers the underlying mechanism of cell cycle
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Aug 03, 2023 |
Metabolic slowdown as the proximal cause of ageing and death
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Aug 03, 2023 |
Pathogenic mutations of human phosphorylation sites affect protein-protein interactions
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Aug 03, 2023 |
Body weight, gonadectomy, and other risk factors for diagnosis of osteoarthritis in companion dogs
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Aug 03, 2023 |
The axes of biology: a novel axes-based network embedding paradigm to decipher the functional mechanisms of the cell.
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Aug 02, 2023 |
Essential Gene Knockdowns Reveal Genetic Vulnerabilities and Antibiotic Sensitivities in Acinetobacter baumannii
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Aug 02, 2023 |
Density Physics-Informed Neural Network reveals sources of cell heterogeneity in signal transduction
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Aug 02, 2023 |
A demand-based framework explains prioritization strategies upon transient limitations of different amino acids.
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Aug 02, 2023 |
Identifying repurposed drugs with moderate anti-influenza virus activity through computational prioritization of drug-target pairs
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Aug 02, 2023 |
Pleiotropic effects of trisomy and pharmacologic modulation on structural, functional, molecular, and genetic systems in a Down syndrome mouse model
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Aug 01, 2023 |
Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML
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Jul 31, 2023 |
Computational prediction of protein interactions on single cells by proximity sequencing
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Jul 30, 2023 |
Correlations reveal the hierarchical organization of networks with latent binary variables
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Jul 30, 2023 |
The epigenetic response of mouse brown adipose tissue to cold stress: histone proteoform, DNA methylation, and RNA expression
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Jul 30, 2023 |
Multiple Receptor Tyrosine Kinases Regulate Dengue Infection of Hepatocytes
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Jul 30, 2023 |
Clinical prediction of wound re-epithelisation outcomes in non-severe burn injury using the plasma lipidome
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Jul 30, 2023 |
Genome scale metabolic network modelling for metabolic profile predictions
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Jul 29, 2023 |
Interpreting roles of mutations associated with the emergence of S. aureus USA300 strains using transcriptional regulatory network reconstruction
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Jul 29, 2023 |
Prediction of metabolites associated with somatic mutations in cancers by using genome-scale metabolic models and mutation data
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Jul 29, 2023 |
Automatic design of gene regulatory mechanisms for spatial pattern formation
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Jul 29, 2023 |
Enhanced cell segmentation with limited annotated data using generative adversarial networks
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Jul 28, 2023 |
Systematic exploration of prokaryotic form I rubisco maximal carboxylation rates
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Jul 27, 2023 |
Agent-based modeling of the prostate tumor microenvironment uncovers spatial tumor growth constraints and immunomodulatory properties
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Jul 27, 2023 |
Fecal Dysbiosis and Inflammation in Intestinal-Specific Cftr Knockout Mice on Regimens Preventing Intestinal Obstruction
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Jul 26, 2023 |
CURTAIN - A Unique Web-based tool for exploration and sharing of MS-based proteomics data
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Jul 25, 2023 |
Predictive Systems Biology Modeling: Unraveling Host Metabolic Disruptions and Potential Drug Targets in SARS-CoV-2 and Its Variants
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Jul 25, 2023 |
Prostate Cancer Reshapes the Secreted and Extracellular Vesicle Urinary Proteomes
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Jul 25, 2023 |
Transcriptomic signatures of progressive and regressive liver fibrosis and portal hypertension
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Jul 25, 2023 |
Spatial Metabolome Lipidome and Glycome from a Single brain Section
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Jul 25, 2023 |
Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis
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Jul 25, 2023 |
A comprehensive atlas of the aging vertebrate brain reveals signatures of progressive proteostasis dysfunction
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Jul 24, 2023 |
Metabolic Symbiosis between Oxygenated and Hypoxic Tumour Cells: An Agent-based Modelling Study
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Jul 24, 2023 |
Stochastic model of vesicular stomatitis virus replication reveals mutational effects on virion production
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Jul 24, 2023 |
Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon
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Jul 23, 2023 |
The timing of cellular events: a stochastic vs deterministic perspective
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Jul 21, 2023 |
An Automated Model Annotation System (AMAS) for SBML Models
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Jul 21, 2023 |
Better tree shape indices
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Jul 19, 2023 |
An aiHumanoid Simulation of Gram-Negative Sepsis: A Comprehensive Multi-Organoid Platform for Advanced Disease Modeling, Drug Discovery, and Personalized Medicine.
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Jul 19, 2023 |
Poisson representation: a bridge between discrete and continuous models of stochastic gene regulatory networks
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Jul 19, 2023 |
Positive and negative feedback regulation of the TGF-β1-SMAD4 axis explains two equilibrium states in human skin aging
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Jul 19, 2023 |
Biologically meaningful regulatory logic enhances the convergence rate in Boolean networks and bushiness of their state transition graph
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Jul 19, 2023 |
Deep spatial proteomic exploration of severe COVID-19-related pulmonary injury in post-mortem specimens
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Jul 17, 2023 |
Systems Age: A single blood methylation test to quantify aging heterogeneity across 11 physiological systems
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Jul 17, 2023 |
Systematic analysis of microorganisms' metabolism for selective targeting
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Jul 17, 2023 |
Fully automated and integrated proteomics sample preparation platform for high-throughput drug target identification
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Jul 16, 2023 |
Unveiling Hidden Connections in Omics Data via pyPARAGON: an Integrative Hybrid Approach for Disease Network Construction
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Jul 15, 2023 |
Amyloid β accelerates age-related proteome-wide protein insolubility.
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Jul 15, 2023 |
ReDirection: a numerically robust R-package to characterize every reaction of a user-defined biochemical network with the probable dissociation constant
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Jul 14, 2023 |
Liebig's law of the minimum in the TGF-β pathway
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Jul 14, 2023 |
The dominant role of post-transcriptional regulation in Yarrowia lipolytica to repeated O2 limitations
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Jul 13, 2023 |
Does enforcing glenohumeral joint stability matter? A new rapid muscle redundancy solver highlights the importance of non-superficial shoulder muscles
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Jul 12, 2023 |
Evaluation of single-sample network inference methods for precision oncology
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Jul 12, 2023 |
Proteome-wide copy-number estimation from transcriptomics
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Jul 11, 2023 |
The protein interactome of the citrus Huanglongbing pathogen Candidatus Liberibacter asiaticus
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Jul 11, 2023 |
Scaling, correlations, and artifacts in biological timeseries
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Jul 11, 2023 |
Quantifying mutational synergy using computational models predicts survival in haematological cancers
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Jul 11, 2023 |
Machine Learning identifies conserved traits that influence lifespan and healthspan responses to dietary restriction
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Jul 10, 2023 |
A systems-level analysis of the mutually antagonistic roles of RKIP and BACH1 in dynamics of cancer cell plasticity
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Jul 08, 2023 |
Maternal Under-Nutrition During Pregnancy Alters the Molecular Response to Over-Nutrition in Multiple Organs and Tissues in Juvenile Offspring
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Jul 07, 2023 |
Does ribosome composition maximize growth rate? The role of RNA instability
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Jul 07, 2023 |
Enhanced cellular longevity arising from environmental fluctuations
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Jul 07, 2023 |
Cross-regulation between proteome reallocation and metabolic flux redistribution governs bacterial growth transition kinetics
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Jul 07, 2023 |
Single transcript-level metabolic responsive landscape of human liver transcriptome
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Jul 06, 2023 |
The firing dynamics of replication origins affect their genome distribution
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Jul 05, 2023 |
Basal MET Phosphorylation is an Indicator of Hepatocyte Dysregulation in Liver Disease
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Jul 04, 2023 |
Modeling of the Network Mediated by IL-36 Involved inPsoriasis
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Jul 03, 2023 |
Pan-genome and Haplotype Map of Cultivars and Their Wild Ancestors Provides Insights into Adaptive Evolution of Cassava (Manihot esculenta Crantz)
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Jul 03, 2023 |
Optimal enzyme profiles in unbranched metabolic pathways
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Jul 03, 2023 |
Longitudinal hair cortisol in bipolar disorder and a mechanism based on HPA dynamics
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Jul 03, 2023 |
The PP2A-like phosphatase Ppg1 mediates assembly of the Far complex to balance gluconeogenic outputs and adapt to glucose depletion
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Jul 03, 2023 |
Inference for entomological semi-field experiments: Fitting a mathematical model assessing personal and community protection of vector-control interventions
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Jul 03, 2023 |
Independent component analysis reveals the transcriptional regulatory modules in Bradyrhizobium diazoefficiens USDA110
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Jul 02, 2023 |
Robustness of biomolecular networks suggests functional modules far from the edge of chaos
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Jul 02, 2023 |
Stochastic Model of Alzheimer's Disease Progression Using Two-State Markov Chains
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Jul 01, 2023 |
ISiCell: involving biologists in the design process of agent-based models in cell biology
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Jul 01, 2023 |
Disentangling gene expression burden identifies generalizable phenotypes induced by synthetic gene networks
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Jul 01, 2023 |
Integrative analysis of CAKUT multi-omics data
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Jul 01, 2023 |
Regulation of bacterial stringent response by an evolutionary conserved ribosomal protein L11 methylation
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Jun 30, 2023 |
Evaluating Study Design Rigor in Preclinical Cardiovascular Research: A Replication Study
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Jun 29, 2023 |
Simultaneous Multi-Omics Analysis by Direct Infusion Mass Spectrometry (SMAD-MS)
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Jun 29, 2023 |
The alternative sigma factor RpoD4 pulses at division and links the circadian clock and the cell cycle in Synechococcus elongatus
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Jun 28, 2023 |
Application of Coincidence Index in the Discovery of Co-Expressed Metabolic Pathways
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Jun 28, 2023 |
The metabolic role of vitamin D in children's neurodevelopment: a network study
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Jun 26, 2023 |
An integrated mechanistic and data-driven computational model predicts cell responses to high- and low-affinity EGFR ligands
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Jun 26, 2023 |
Parametric modeling of mechanical effects on circadian oscillators
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Jun 25, 2023 |
A fast method to distinguish between fermentative and respiratory metabolisms in single yeast cells
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Jun 24, 2023 |
Storm: Incorporating transient dynamics to infer the RNA velocity with metabolic labeling information
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Jun 23, 2023 |
Bayesian analysis dissects kinetic modulation during non-stationary gene expression
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Jun 23, 2023 |
A Systems Level Explanation for Gompertzian Mortality Patterns is provided by the "Multiple and Inter-dependent Component Cause Model"
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Jun 22, 2023 |
Dual proteomic signature of immune cells and Yersinia pestis upon blood infection
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Jun 22, 2023 |
The genetic and dietary landscape of the muscle insulin signalling network
|
Jun 22, 2023 |
Spatial connectivity and marine disease dispersal: missing links in aquaculture carrying capacity debates
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Jun 22, 2023 |
Comprehensive analysis of network reconstruction approaches based on correlation in metagenomic data
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Jun 22, 2023 |
Systematic biases in transcriptional parameters inferred from single-cell snapshot data
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Jun 21, 2023 |
Transcriptome of left ventricle and sinoatrial node in young and old C57 mice
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Jun 17, 2023 |
Using mixture density networks to emulate a stochastic within-host model of Francisella tularensis infection
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Jun 16, 2023 |
A scalable platform for efficient CRISPR-Cas9 chemical-genetic screens of DNA damage-inducing compounds
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Jun 16, 2023 |
JMnorm: a novel Joint Multi-feature normalization method for integrative and comparative epigenomics
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Jun 15, 2023 |
Regulatory properties of transcription factors with diverse mechanistic function
|
Jun 15, 2023 |
Development of an in situ cell-type specific proteome analysis method using antibody-mediated biotinylation
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Jun 14, 2023 |
The Size of Fields in Biomedical Sciences
|
Jun 14, 2023 |
AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor
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Jun 14, 2023 |
Impact of Bmal1 rescue and time-restricted feeding on liver and muscle proteomes during the active phase in mice
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Jun 13, 2023 |
Designing function-specific minimal microbiomes from large microbial communities
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Jun 12, 2023 |
Enhanced perfusion following exposure to radiotherapy: a theoretical investigation
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Jun 12, 2023 |
Repository of logically consistent real-world Boolean network models
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Jun 12, 2023 |
Dose optimization of an adjuvanted peptide-based personalized neoantigen melanoma vaccine
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Jun 11, 2023 |
Shared and distinct pathways and networks genetically linked to coronary artery disease between human and mouse
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Jun 11, 2023 |
Kinetic modeling of leucine-mediated signaling and protein metabolism in human skeletal muscle
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Jun 11, 2023 |
Senescent Subtypes Transition Model
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Jun 10, 2023 |
Information-theoretic analysis of a model of CAR-4-1BB-mediated NFκB activation
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Jun 10, 2023 |
Biological embedding of childhood adversity - a multi-omics perspective on stress regulation
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Jun 10, 2023 |
METABOLIC MODELLING AS A POWERFUL TOOL TO IDENTIFY CRITICAL COMPONENTS OF THE PNEUMOCYSTIS GROWTH MEDIUM
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Jun 09, 2023 |
Heritable epigenetic changes are constrained by the dynamics of regulatory architectures
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Jun 09, 2023 |
TMELand: An end-to-end pipeline for quantification and visualization of Waddington's epigenetic landscape based on gene regulatory network
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Jun 08, 2023 |
Classification of bacterial nanowire proteins using Machine Learning and Feature Engineering model
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May 05, 2023 |
Endothelial cells signaling and patterning under hypoxia: a mechanistic computational model
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May 05, 2023 |
Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells
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May 05, 2023 |
Nuclear export is a limiting factor in eukaryotic mRNA metabolism
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May 04, 2023 |
Excitable dynamics of flares and relapses in autoimmune diseases
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May 04, 2023 |
Drug Target Identification in Triple Negative Breast Cancer Stem Cell Pathways: a computational study of gene regulatory pathways using Boolean networks
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May 04, 2023 |
A provably convergent control closure scheme for the Method of Moments of the Chemical Master Equation
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May 03, 2023 |
A computational model of the DNA damage-induced IKK/ NF-κB pathway reveals a critical dependence on irradiation dose and PARP-1
|
May 02, 2023 |
Targeting metabolic fluxes reverts metastatic transitions in ovarian cancer
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May 02, 2023 |
Upregulation of steroidogenesis is associated with coma in human cerebral malaria
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May 02, 2023 |
Abolishing storage lipids induces protein misfolding and stress responses in Yarrowia lipolytica
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May 02, 2023 |
Evidence for conservation of a primordial 12-hour ultradian gene program in humans
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May 02, 2023 |
Particle-based simulations reveal two positive feedback loops allow relocation and stabilization of the polarity site during yeast mating
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May 01, 2023 |
Systematic Pan-cancer Functional Inference and Validation of Hyper, Hypo and Neomorphic Mutations
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Apr 30, 2023 |
SINGLE CELL RESOLUTION SPATIAL MAPPING OF HUMAN HEMATOPOIESIS REVEALS AGING-ASSOCIATED TOPOGRAPHIC REMODELING
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Apr 30, 2023 |
ISRES+: An improved evolutionary strategy for function minimization to estimate the free parameters of Systems Biology models
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Apr 30, 2023 |
Personalized Clostridioides difficile engraftment risk prediction and probiotic therapy assessment in the human gut.
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Apr 29, 2023 |
Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum
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Apr 29, 2023 |
Phenomenological modeling reveals the emergent simplicity of host-associated microbiomes
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Apr 29, 2023 |
Joint Distribution of Protein Concentration and Cell Volume Coupled by Feedback in Dilution
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Apr 29, 2023 |
Protein homeostasis from diffusion-dependent control of protein synthesis and degradation
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Apr 28, 2023 |
Statistical characterization of the dynamics of Glioblastoma Multiforme subtypes through parameters estimation of the epigenetic landscape
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Apr 28, 2023 |
Perfusion estimation using MRI-based measurements and a porous media flow model
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Apr 28, 2023 |
Metabolic consequences of non-severe burn injury are associated with increased plasma markers of inflammation and cardiovascular disease risk.
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Apr 28, 2023 |
Generating immunogenomic data-guided virtual patients using a QSP model to predict response of advanced NSCLC to PD-L1 inhibition
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Apr 28, 2023 |
Machine Learning Identifies Plasma Proteomic Signatures of Descending Thoracic Aortic Disease
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Apr 28, 2023 |
Epigenetically-regulated RNA-binding proteins signify malaria hypnozoite dormancy
|
Apr 26, 2023 |
BondGraphs.jl: Composable energy-based modelling in systems biology
|
Apr 25, 2023 |
Transcriptome Analysis Reveals Organ-Specific Effects of 2-Deoxyglucose Treatment in Healthy Mice
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Apr 25, 2023 |
Mycobacterium tuberculosis-Macrophage Interactome: Molecular Network Structure and Resilience against Antibiotics
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Apr 25, 2023 |
PEELing: an integrated and user-centric platform for cell-surface proteomics analysis
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Apr 25, 2023 |
Dynamics of cell type transition mediated by epigenetic modifications
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Apr 25, 2023 |
Analytical validation of the PROphet computational model for clinical benefit prediction and decision-making tool in metastatic NSCLC
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Apr 24, 2023 |
A mobile CRISPRi collection enables genetic interaction studies for the essential genes of Escherichia coli
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Apr 22, 2023 |
What controls carbon sequestration in plants under which conditions?
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Apr 21, 2023 |
A Logic-incorporated Gene Regulatory Network Deciphers Principles in Cell Fate Decisions
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Apr 21, 2023 |
A multi-scale digital twin for adiposity-driven insulin resistance in humans: diet and drug effects
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Apr 21, 2023 |
Age-dependent ventilator-induced lung injury: Mathematical modeling, experimental data, and statistical analysis
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Apr 21, 2023 |
Regulating microbiome metabolic stability for stable indigenous liquor fermentation
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Apr 21, 2023 |
BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale
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Apr 20, 2023 |
Flux Sampling in Genome-scale Metabolic Modeling of Microbial Communities
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Apr 20, 2023 |
Gene regulatory network inference with popInfer reveals dynamic regulation of hematopoietic stem cell quiescence upon diet restriction and aging
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Apr 20, 2023 |
In-silico modelling of the mitogen-activated kinase (MAPK) pathway in colorectal cancer: mutations and targeted therapy
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Apr 20, 2023 |
Proteomes Reveal Metabolic Capabilities of Yarrowia lipolytica for Biological Upcycling of Polyethylene into High-Value Chemicals
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Apr 18, 2023 |
Quantitative mechanistic model reveals key determinants of placental IgG transfer and informs prenatal immunization strategies
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Apr 18, 2023 |
Growth balance analysis models of cyanobacteria for understanding resource allocation strategies
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Apr 18, 2023 |
NFκB nuclear dynamics orchestrate inflammatory aging
|
Apr 18, 2023 |
Phenotype control techniques for Boolean gene regulatory networks
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Apr 18, 2023 |
Acute myeloid leukemia stratifies as two clinically relevant sphingolipidomic subtypes
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Apr 17, 2023 |
Neurodevelopmental disorders and cancer networks share pathways; but differ in mechanisms, signaling strength, and outcome
|
Apr 16, 2023 |
Efficient Fisher Information Computation and Policy Search in Sampled Stochastic Chemical Reaction Networks through Deep Learning
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Apr 14, 2023 |
Wide scope analysis of bioactive lipids, including steroids, bile acids, and polyunsaturated fatty acid metabolites, in human plasma by LC/MS/MS
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Apr 14, 2023 |
A physiologically based pharmacokinetic model for CYP2E1 phenotyping via chlorzoxazone
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Apr 14, 2023 |
Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors
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Apr 14, 2023 |
Fission yeast obeys a linear size law under nutrient titration
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Apr 13, 2023 |
Computational Screen for Sex-Specific Drug Effects in a Cardiac Fibroblast Network Model
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Apr 13, 2023 |
Sidestream bio-P and mainstream anammox in a BNR process with upstream carbon capture
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Apr 13, 2023 |
A calibration and uncertainty quantification analysis of classical, fractional and multiscale logistic models of tumour growth
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Apr 13, 2023 |
LabEmbryoCam: An opensource phenotyping system for developing aquatic animals
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Apr 12, 2023 |
An automated proximity proteomics pipeline for subcellular proteome and protein interaction mapping
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Apr 12, 2023 |
A benchmark of optimization solvers for genome-scale metabolic modeling
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Apr 12, 2023 |
Epistasis meets pleiotropy in shaping biophysical protein subspaces associated with antimicrobial resistance
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Apr 09, 2023 |
piTracer - Automatic reconstruction of molecular cascades for the identification of synergistic drug targets
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Apr 09, 2023 |
A statistical framework for quantifying the nuclear export rate of influenza viral mRNAs.
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Apr 08, 2023 |
Predictive power of non-identifiable models
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Apr 08, 2023 |
SynDISCO: A Mechanistic Modeling-Based Framework for Predictive Prioritization of Synergistic Drug Combinations Directed at Cell Signaling Networks
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Apr 08, 2023 |
Evolutionary druggability: leveraging low-dimensional fitness landscapes towards new metrics for antimicrobial applications
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Apr 08, 2023 |
Predictive links between petal color and pigment quantities in natural Penstemon hybrids
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Apr 08, 2023 |
Comparative analysis of noise-attenuation mechanisms in gene expression: From single cells to cell populations
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Apr 08, 2023 |
Logic-Based Modeling of Inflammatory Macrophage Crosstalk with Glomerular Endothelial Cells in Diabetic Kidney Disease
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Apr 06, 2023 |
Cellular energy regulates mRNA translation and degradation in a codon-specific manner
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Apr 06, 2023 |
Revealing the Grammar of Small RNA Secretion Using Interpretable Machine Learning
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Apr 06, 2023 |
Applications of Boolean modeling to study the dynamics of a complex disease and therapeutics responses
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Apr 06, 2023 |
μPhos: a scalable and sensitive platform for functional phosphoproteomics
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Apr 06, 2023 |
A diffusion-driven switch specifies rhizoid precursor cells in Marchantia polymorpha
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Apr 06, 2023 |
Sensitivity Analysis of Biochemical Systems Using Bond Graphs
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Apr 06, 2023 |
How Interactions During Viral-Viral Coinfection Can Shape Infection Kinetics
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Apr 05, 2023 |
A Mathematical Model of Glomerular Fibrosis in Diabetic Kidney Disease to Predict Therapeutic Efficacy
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Apr 04, 2023 |
A coarse-grained resource allocation model of carbon and nitrogen metabolism in unicellular microbes
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Apr 04, 2023 |
Extracellular Domains of CAR Reprogram T-Cell Metabolism Without Antigen Stimulation
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Apr 04, 2023 |
Mycobacterial Metabolic Model Development for Drug Target Identification
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Apr 03, 2023 |
Systems analysis of miR-199a/b-5p and multiple miR-199a/b-5p targets during chondrogenesis
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Apr 03, 2023 |
High-affinity biomolecular interactions are modulated by low-affinity binders
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Apr 03, 2023 |
Stochastic modeling of the dynamics of Salmonella infection of epithelial cells
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Apr 03, 2023 |
Data-driven structural analysis of Small Cell Lung Cancer transcription factor networksuggests potential subtype regulators and transition pathways
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Apr 03, 2023 |
A high-throughput approach reveals distinct peptide charging behaviors in electrospray ionization mass spectrometry
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Apr 03, 2023 |
Single-cell time-resolved multi-omics reveal apoptotic and ferroptotic heterogeneity during foam cell formation
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Apr 02, 2023 |
Evolution of the Telencephalon Anterior-Posterior Patterning by Core Endogenous Network Bifurcation
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Apr 02, 2023 |
Emergence of Bow-tie Architecture in Evolving Feedforward Networks
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Mar 29, 2023 |
The Road Less Traveled: Uncovering the Convergence Toward Specific Pleiotropic Phenotypes in Aging
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Mar 29, 2023 |
Tools and methods for high-throughput single-cell imaging with the mother machine
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Mar 29, 2023 |
Image-based temporal profiling of autophagy-related phenotypes
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Mar 28, 2023 |
Temporal perturbation of STAT1/2 activity reveals dynamic ligand discrimination of type I interferon signaling
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Mar 27, 2023 |
Predicting phenotype to mechanotype relationships in cells based on intra-cellular signaling network
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Mar 27, 2023 |
A multi-omics strategy for the study of microbial metabolism: application to the human skin's microbiome
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Mar 26, 2023 |
High versatility to meet conservation targets for biodiversity and hydrological services at the Riviera Maya, Quintana Roo, Mexico
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Mar 25, 2023 |
Genetic and dietary modulators of the inflammatory response in the gastro-intestinal tract of the BXD mouse genetic reference population
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Mar 25, 2023 |
Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models
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Mar 25, 2023 |
Mathematical models disentangle the role of IL-10 feedbacks in human monocytes upon proinflammatory activation
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Mar 25, 2023 |
Clonal differences underlie variable responses to sequential and prolonged treatment
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Mar 25, 2023 |
Gene-metabolite annotation with shortest reactional distance enhances metabolite genome-wide association studies results
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Mar 24, 2023 |
An improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells
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Mar 24, 2023 |
DIP-MS: A novel ultra-deep interaction proteomics for the deconvolution of protein complexes
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Mar 24, 2023 |
Geckopy 3.0: enzyme constraints, thermodynamics constraints and omics integration in python
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Mar 23, 2023 |
Learning Perturbation-specific Cell Representations for Prediction of Transcriptional Response across Cellular Contexts
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Mar 23, 2023 |
Compromised beta-cell identity in type 2 diabetes
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Mar 23, 2023 |
On the interactions of DNA replication and transcriptional regulation
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Mar 23, 2023 |
standard-GEM: standardization of open-source genome-scale metabolic models
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Mar 23, 2023 |
Using interactive platforms to encode, manage and explore immune-related adverse outcome pathways
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Mar 23, 2023 |
Modeling transcriptional regulation of the cell cycle using a novel cybernetic-inspired approach
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Mar 23, 2023 |
The intensities of canonical senescence biomarkers integrate the duration of cell-cycle withdrawal
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Mar 21, 2023 |
Emergence of power-law distributions in protein-protein interaction networks through study bias
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Mar 21, 2023 |
How total mRNA influences cell growth
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Mar 21, 2023 |
Modelling the dynamics of senescence spread
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Mar 20, 2023 |
MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes
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Mar 20, 2023 |
Ensemble and Iterative Engineering for Maximized Bioconversion to the Blue Pigment, Indigoidine from Non-Canonical Sustainable Carbon Sources
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Mar 20, 2023 |
Integrative proteomics and transcriptomics of human T-cells reveals temporal metabolic reprogramming following TCR-induced activation
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Mar 20, 2023 |
Exploring the noncanonical translatome using massively integrated coexpression analysis
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Mar 17, 2023 |
Identifying drug effects in a cardiac model of electrophysiology using kernel-based parameter estimation methods
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Mar 16, 2023 |
Guide-specific loss of efficiency and off-target reduction with Cas9 variants
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Mar 16, 2023 |
A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion
|
Mar 15, 2023 |
Comparative analysis between RNA-seq and single-molecule RNA FISH indicates that the pyrimidine nucleobase idoxuridine (IdU) globally amplifies transcriptional noise
|
Mar 15, 2023 |
Leveraging gene correlations in single cell transcriptomic data
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Mar 15, 2023 |
MolClustPy: A Python Package to Characterize Multivalent Biomolecular Clusters
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Mar 15, 2023 |
Leukemia core transcriptional circuitry is a sparsely interconnected hierarchy stabilized by incoherent feed-forward loops
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Mar 15, 2023 |
Distilling identifiable and interpretable dynamic models from biological data
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Mar 14, 2023 |
Cardiopulmonary structural, functional and immune-alterations in a Down syndrome mouse model and upon modulation of EGCG
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Mar 14, 2023 |
TimeTeller: a tool to probe the circadian clock as a multigene dynamical system
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Mar 14, 2023 |
In silico agent-based modeling approach to characterize multiple in vitro tuberculosis infection models
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Mar 14, 2023 |
Comparative assessment of mosquito size and receptiveness to P. falciparum infection of two rearing procedures for Anopheles mosquitoes
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Mar 12, 2023 |
OptEnvelope: a target point guided method for growth-coupled production using knockouts
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Mar 12, 2023 |
A systematic search for RNA structural switches across the human transcriptome
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Mar 12, 2023 |
A Consensus Model of Glucose-Stimulated Insulin Secretion in the Pancreatic beta-Cell
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Mar 12, 2023 |
Multidimensional proteomics identifies molecular trajectories of cellular aging and rejuvenation
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Mar 12, 2023 |
Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors
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Mar 12, 2023 |
2'-Fucosyllactose helps butyrate producers outgrow competitors in the infant gut
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Mar 11, 2023 |
Ensemble-based genome-scale modeling predicts metabolic differences between macrophage subtypes in colorectal cancer
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Mar 11, 2023 |
The ability to sense the environment is heterogeneously distributed in cell populations
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Mar 10, 2023 |
transomics2cytoscape: An automated software for interpretable 2.5-dimensional visualization of trans-omic networks
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Mar 10, 2023 |
An extension of the Walsh-Hadamard transform to calculate and model epistasis in genetic landscapes of arbitrary shape and complexity
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Mar 08, 2023 |
ENKIE: A package for predicting enzyme kinetic parameter values and their uncertainties
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Mar 08, 2023 |
A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology
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Mar 07, 2023 |
Beyond the Genetic Code: A Tissue Code?
|
Mar 06, 2023 |
Generally-healthy individuals with aberrant bowel movement frequencies show enrichment for microbially-derived blood metabolites associated with impaired kidney function.
|
Mar 06, 2023 |
Transcription factor interactions explain the context-dependent activity of CRX binding sites
|
Mar 05, 2023 |
Leveraging genetic diversity to identify small molecules that reverse mouse skeletal muscle insulin resistance
|
Mar 03, 2023 |
An integrated workflow for quantitative analysis of the newly synthesized proteome
|
Mar 03, 2023 |
The ups and downs of biological oscillators: A comparison of time-delayed negative feedback mechanisms
|
Mar 03, 2023 |
Inferring gene regulatory networks using transcriptional profiles as dynamical attractors
|
Mar 03, 2023 |
Logic-based mechanistic machine learning on high-content images reveals how drugs differentially regulate cardiac fibroblasts
|
Mar 02, 2023 |
Metabolomics investigation of post-mortem human pericardial fluid
|
Mar 01, 2023 |
An explainable artificial intelligence-based typification of chronic inflammatory responses enhances glioma prognosis
|
Mar 01, 2023 |
Systematic Identification of Post-Transcriptional Regulatory Modules
|
Mar 01, 2023 |
Efficient and scalable prediction of spatio-temporal stochastic gene expression in cells and tissues using graph neural networks
|
Mar 01, 2023 |
Bounds on the Ultrasensitivity of Biochemical ReactionCascades
|
Mar 01, 2023 |
Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut.
|
Mar 01, 2023 |
Data-Driven Screening to Infer Metabolic Modulators of the Cancer Epigenome
|
Feb 28, 2023 |
PrePPI: A structure informed proteome-wide database of protein-protein interactions
|
Feb 28, 2023 |
Methodology for inference of intercellular gene interactions
|
Feb 27, 2023 |
Multiscale networks in multiple sclerosis
|
Feb 27, 2023 |
A compact model for cold tolerance entrainment based on the ICE1-CBF-COR pathway in plants
|
Feb 24, 2023 |
Exploring tumor-normal cross-talk with TranNet: role of the environment in tumor progression
|
Feb 24, 2023 |
Multi-view learning to unravel the different levels underlying hepatitis B vaccine response
|
Feb 24, 2023 |
Transkingdom Network Analysis (TkNA): a systems approach inferring causal factors underlying host-microbiota interactions.
|
Feb 23, 2023 |
Comparative gene regulatory network analysis in Alzheimer's disease and major depressive disorder
|
Feb 23, 2023 |
Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease
|
Feb 23, 2023 |
Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states
|
Feb 22, 2023 |
Machine learning-assisted medium optimization revealed the discriminated strategies for improved production of the foreign and native metabolites
|
Feb 22, 2023 |
Oxygen intrusions sustain aerobic nitrite oxidation in anoxic marine zones
|
Feb 22, 2023 |
Ongoing HIV replication in lymph node sanctuary sites in treated patients contributes to the total latent HIV at a very slow rate.
|
Feb 21, 2023 |
Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches
|
Feb 21, 2023 |
FitMultiCell: Simulating and parameterizing computational models of multi-scale and multi-cellular processes
|
Feb 21, 2023 |
Population genomics-guided engineering of phenazine biosynthesis in Pseudomonas chlororaphis
|
Feb 18, 2023 |
Discovery of multi-state gene cluster switches determining the adaptive mitochondrial and metabolic landscape of breast cancer
|
Feb 18, 2023 |
Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics
|
Feb 18, 2023 |
Yeast cell responses and survival during periodic osmotic stress are controlled by glucose availability
|
Feb 17, 2023 |
Network-based elucidation of colon cancer drug resistance by phosphoproteomic time-series analysis
|
Feb 16, 2023 |
Enhanced protein secretion in reduced genome strains of Streptomyces lividans
|
Feb 16, 2023 |
Exploring the onset and progression of prostate cancer through a multicellular agent-based model
|
Feb 16, 2023 |
Out-of-equilibrium gene expression fluctuations in presence of extrinsic noise
|
Feb 15, 2023 |
Spectral methods for prediction uncertainty quantification in Systems Biology
|
Feb 15, 2023 |
Agricultural pesticides do not suppress infection of Biomphalaria (Gastropoda) by Schistosoma mansoni (Trematoda)
|
Feb 15, 2023 |
Identifying Spatial Co-occurrence in Healthy and InflAmed tissues (ISCHIA)
|
Feb 15, 2023 |
Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants
|
Feb 15, 2023 |
Multilevel Omics-Readouts of in vitro Perturbation Studies are Determined by Memory Effects from Subculture
|
Feb 14, 2023 |
Biphasic responses in cell signalling: A unified approach
|
Feb 14, 2023 |
CaV3.1 Channels Facilitate Calcium Wave Generation and Myogenic Tone Development in Mouse Mesenteric Arteries.
|
Feb 13, 2023 |
Utilizing high resolution ribosome profiling for the global investigation of gene expression in Chlamydomonas reinhardtii
|
Feb 13, 2023 |
CRISPR interference screens reveal tradeoffs between growth rate and robustness in Synechocystis sp. PCC 6803 across trophic conditions
|
Feb 13, 2023 |
Higher-order co-mutation interactions in mitochondrial genomes
|
Feb 13, 2023 |
Phosphoproteomics of cellular mechanosensing reveals NFATC4 as a regulator of myofibroblast activity
|
Feb 13, 2023 |
Coupling allows robust redox circadian rhythms despite heterogeneity and noise
|
Feb 13, 2023 |
The balance of acidic and hydrophobic residues predicts acidic transcriptional activation domains from protein sequence
|
Feb 11, 2023 |
Logistics of Bone Mineralization in the Chick Embryo Studied by 3D Cryo FIB-SEM Imaging
|
Feb 10, 2023 |
Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells
|
Feb 10, 2023 |
The impossible challenge of estimating non-existent moments of the Chemical Master Equation
|
Feb 09, 2023 |
Sensory diversity and precise adaptation enable independent bet-hedging strategies for multiple signals at the same time
|
Feb 09, 2023 |
A Structured Evaluation of Genome-Scale Constraint-Based Modeling Tools for Microbial Consortia
|
Feb 09, 2023 |
Pumping Iron: A Multi-omics Analysis of Two Extremophilic Algae Reveals Mechanisms of Iron Economy
|
Feb 09, 2023 |
Pgc-1α is an exercise-responsive regulator of myosteatosis in older individuals
|
Feb 08, 2023 |
RxRx3: Phenomics Map of Biology
|
Feb 08, 2023 |
Reconstructing cellular differentiation networks and identifying cell fate-determining features with CIBER
|
Feb 08, 2023 |
Unraveling codon usage of Escherichia coli using machine learning
|
Feb 07, 2023 |
Coupling Flux Balance Analysis with Reactive Transport Modeling through Machine Learning for Rapid and Stable Simulation of Microbial Metabolic Switching
|
Feb 07, 2023 |
Metabolic modeling of sex-specific tissue predicts mechanisms of differences in toxicological responses
|
Feb 07, 2023 |
From autopoiesis to self-optimization: Toward an enactive model of biological regulation
|
Feb 06, 2023 |
SingleCellGGM enables gene expression program identification from single-cell transcriptomes and facilitates universal cell label transfer
|
Feb 05, 2023 |
Mathematically mapping the network of cells in the tumor microenvironment
|
Feb 04, 2023 |
Extended fractional-polynomial generalizations of diffusion and Fisher-KPP equations on directed networks: Modeling neurodegenerative progression
|
Feb 04, 2023 |
Consensus tissue domain detection in spatial -omics data using MILWRM
|
Feb 03, 2023 |
Structure primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference
|
Feb 03, 2023 |
Systematic identification of structure-specific protein-protein interactions
|
Feb 03, 2023 |
Low dimensionality of phenotypic space as an emergent property of coordinated teams in biological regulatory networks
|
Feb 03, 2023 |
Climate, caribou and human needs linked by analysis of Indigenous and scientific knowledge
|
Feb 03, 2023 |
The unknown lipids project: harmonized methods improve compound identification and data reproducibility in an inter-laboratory untargeted lipidomics study
|
Feb 03, 2023 |
ENVIRONMENT MODULATES PROTEIN HETEROGENEITY THROUGH TRANSCRIPTIONAL AND TRANSLATIONAL STOP CODON MISCODING
|
Feb 03, 2023 |
Experiment-based Computational Model Predicts that IL-6 Trans-Signaling Plays a Dominant Role in IL-6 mediated signaling in Endothelial Cells
|
Feb 03, 2023 |
Computational biology predicts metabolic engineering targets for increased production of 102 valuable chemicals in yeast
|
Feb 03, 2023 |
Cell-free multi-omics analysis reveals tumor status-informative signatures in gastrointestinal cancer patients' plasma
|
Feb 03, 2023 |
The attractor landscape of duplicated networks
|
Feb 02, 2023 |
Single cell ATAC sequencing identifies sleepy macrophages during reciprocity of cytokines in L.major infection
|
Feb 01, 2023 |
Computational modeling of DLBCL predicts response to BH3-mimetics.
|
Feb 01, 2023 |
Distribution-modeling quantifies collective Th cell decision circuits in chronic inflammation
|
Jan 31, 2023 |
Elucidating Fibroblast Growth Factor-induced kinome dynamics using targeted mass spectrometry and dynamic modeling
|
Jan 28, 2023 |
scMINER: a mutual information-based framework for identifying hidden drivers from single-cell omics data
|
Jan 27, 2023 |
Top-down Proteomics of Myosin Light Chain Isoforms Define Chamber-Specific Expression in the Human Heart
|
Jan 27, 2023 |
Cell cycle oscillations driven by two interlinked bistable switches
|
Jan 27, 2023 |
The Spread of Interferon-γ in Melanomas is Highly Spatially Confined, Driving Non-Genetic Variability in Tumor Cells
|
Jan 27, 2023 |
Homeostasis at different backgrounds: The roles of overlayed feedback structures in vertebrate photoadaptation
|
Jan 26, 2023 |
Prevalence of Bovine Cysticercosis, Human Taeniasis and Associated Risk Factors in Selected Towns of Silte Zone, Southern Ethiopia
|
Jan 26, 2023 |
Using mechanistic models and machine learning to design single-color multiplexed Nascent Chain Tracking experiments
|
Jan 26, 2023 |
Network-based cytokine inference implicates Oncostatin M as a driver of knee osteoarthritis
|
Jan 25, 2023 |
The circadian clock is required for rhythmic lipid transport in the Drosophila hemolymph in interaction with diet, photic condition and feeding
|
Jan 25, 2023 |
Investigating the effect of changes in model parameters on optimal control policies, time to absorption, and mixing times
|
Jan 24, 2023 |
Topological design principle for the robustness of necroptosis biphasic, emergent, and coexistent (BEC) dynamics
|
Jan 24, 2023 |
Compressed Perturb-seq: highly efficient screens for regulatory circuits using random composite perturbations
|
Jan 23, 2023 |
Compressed phenotypic screens for complex multicellular models and high-content assays
|
Jan 23, 2023 |
Limits on Inferring Gene Regulatory Networks Subjected to Different Noise Mechanisms
|
Jan 23, 2023 |
High sensitivity proteome-scale search for crosslinked peptides using CRIMP 2.0
|
Jan 21, 2023 |
Glycoproteome remodelling and granule-specific N-glycosylation accompany neutrophil granulopoiesis
|
Jan 20, 2023 |
Gene expression of macaques infected with malaria species of zoonotic concern
|
Jan 20, 2023 |
A large-scale Boolean model of the Rheumatoid Arthritis Fibroblast-Like Synoviocytes predicts drug synergies in the arthritic joint
|
Jan 19, 2023 |
Apparent simplicity and emergent robustness in bacterial cell cycle control
|
Jan 19, 2023 |
Bromodomain-containing Protein 4 Regulates Innate Inflammation in Airway Epithelial Cells via Modulation of Alternative Splicing
|
Jan 19, 2023 |
Conic analysis of nonlinear metabolic networks
|
Jan 19, 2023 |
A workflow for incorporating cross-sectional data into the calibration of dynamic models
|
Jan 19, 2023 |
A 3-dimensional molecular cartography of human cerebral organoids revealed by double-barcoded spatial transcriptomics
|
Jan 19, 2023 |
N-terminal proteoforms may engage in different protein complexes
|
Jan 18, 2023 |
Self-supervised vision transformers accurately decode cellular state heterogeneity
|
Jan 18, 2023 |
Model-guided Design of Biological Controller for Septic Wound Healing Regulation
|
Jan 18, 2023 |
Simulated-to-real Benchmarking of Acquisition Methods in Metabolomics
|
Jan 15, 2023 |
SSI: A Statistical Sensitivity Index for Chemical Reaction Networks in cancer
|
Jan 15, 2023 |
Improving gene regulatory network inference and assessment: The importance of using network structure
|
Jan 15, 2023 |
Next-generation interaction proteomics for quantitative Jumbophage-bacteria interaction mapping
|
Jan 15, 2023 |
A Novel Algorithm to Calculate Elementary Modes: Analysis of Campylobacter jejuni Metabolism
|
Jan 15, 2023 |
Fitting agent-based models to tumor images using representation learning
|
Jan 14, 2023 |
Uncovering specific mechanisms across cell types in dynamical models
|
Jan 12, 2023 |
A human stomach cell type transcriptome atlas
|
Jan 11, 2023 |
Mathematical modeling indicates that regulatory inhibition of CD8+ T cell cytotoxicity can limit efficacy of IL-15 immunotherapy in cases of high pre-treatment SIV viral load
|
Jan 10, 2023 |
Integration of transcriptomics data into agent-based models of solid tumor metastasis
|
Jan 10, 2023 |
Ketocarotenoid production in tomato triggers metabolic reprogramming and cellular adaptation: The quest for homeostasis?
|
Jan 10, 2023 |
Missing data in amortized simulation-based neural posterior estimation
|
Jan 10, 2023 |
A tissue centric atlas of cell type transcriptome enrichment signatures
|
Jan 10, 2023 |
The arginine dihydrolase pathway shapes human gut microbial community assembly, functions, and mammalian host colonization
|
Jan 10, 2023 |
Curation of causal interactions mediated by genes associated to autism accelerates the understanding of gene-phenotype relationships underlying neurodevelopmental disorders
|
Jan 09, 2023 |
Insights into the metabolic specificities of pathogenic strains from the Ralstonia solanacearum species complex
|
Jan 09, 2023 |
A Multiscale Protein Abundance Structured Population Kinetic Model Systematically Explores the Design Space of Constitutive and Inducible CAR-T cells
|
Jan 09, 2023 |
Dynamical information enables inference of gene regulation at single-cell scale
|
Jan 08, 2023 |
Leveraging Developmental Landscapes for Model Selection in Boolean Gene Regulatory Networks
|
Jan 08, 2023 |
Realistic simulation of time-course measurements in systems biology
|
Jan 06, 2023 |
Identification and characterization of metabolic subtypes of endometrial cancer using systems-level approach
|
Jan 06, 2023 |
A Transcriptional Cofactor Regulatory Network for the C. elegans Intestine
|
Jan 06, 2023 |
Ultrasensitive Proteomics Depicted an In-depth Landscape for Mouse Embryo
|
Jan 06, 2023 |
Automated Enrichment of Phosphotyrosine Peptides for High-Throughput Proteomics
|
Jan 06, 2023 |
Critical assessment of E. coli genome-scale metabolic model with high-throughput mutant fitness data
|
Jan 05, 2023 |
Mapping the dynamic cell surface interactome of high-density lipoprotein reveals Aminopeptidase N as modulator of its endothelial uptake
|
Jan 03, 2023 |
Circuit to target approach defines an autocrine myofibroblast loop that drives cardiac fibrosis
|
Jan 03, 2023 |
Combined genome-scale fitness and paralog synthetic lethality screens with just 44k clones: the IN4MER CRISPR/Cas12a multiplex knockout platform
|
Jan 03, 2023 |
Integration of single-cell multiomic measurements across disease states with genetics identifies mechanisms of beta cell dysfunction in type 2 diabetes
|
Jan 02, 2023 |
Analysis of the genome-scale metabolic model of Bacillus subtilis to design novel in-silico strategies for native and recombinant L-asparaginase overproduction
|
Jan 02, 2023 |
MitoMouse is a model reconstruction of murine mitochondrial metabolism
|
Jan 02, 2023 |
Dynamic decomposition of transcriptome responses during plant effector-triggered immunity revealed conserved responses in two distinct cell populations
|
Dec 31, 2022 |
Temporal Regulation of Organelle Biogenesis
|
Dec 31, 2022 |
A basic model of calcium homeostasis in non-excitable cells
|
Dec 31, 2022 |
Insulin Effectiveness, a Measure Consisting of Insulin Sensitivity, Secretion, and Clearance, Captures Differences Between Diabetic and Nondiabetic States
|
Dec 30, 2022 |
Data-driven model of glycolysis identifies the role of allostery in maintaining ATP homeostasis
|
Dec 30, 2022 |
Accuracy of functional gene community detection in Saccharomyces cerevisiae by maximizing Generalized Modularity Density
|
Dec 30, 2022 |
Proteins with amino acid repeats constitute rapidly evolvable and human-specific essentialome
|
Dec 30, 2022 |
An updated end-to-end ecosystem model of the Northern California Current reflecting ecosystem changes due to recent marine heat waves
|
Dec 30, 2022 |
The Warburg Effect is the result of faster ATP production by glycolysis than respiration
|
Dec 29, 2022 |
Superinfection plays an important role in the acquisition of complex Plasmodium falciparum infections among female Anopheles mosquitoes
|
Dec 27, 2022 |
Reversibility of resistance in a fluctuation test experiment modifies the tail of the Luria-Delbrück distribution
|
Dec 27, 2022 |
Dysregulation of murine long non-coding single cell transcriptome in non-alcoholic steatohepatitis and liver fibrosis
|
Dec 27, 2022 |
Employing active learning in the optimization of culture medium for mammalian cells
|
Dec 25, 2022 |
Identification of Disease Modules Using Higher-Order Network Structure
|
Dec 25, 2022 |
Lab evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance
|
Dec 23, 2022 |
Peptide collision cross sections of 22 post-translational modifications
|
Dec 23, 2022 |
Antibody reliability influences observed mRNA-protein correlations in tumour samples
|
Dec 23, 2022 |
Integrating pharmacogenomics and cheminformatics with diverse disease phenotypes for cell type-guided drug discovery
|
Dec 22, 2022 |
A map of signaling responses in the human airway epithelium
|
Dec 22, 2022 |
Global analysis of the yeast knock-out phenome
|
Dec 22, 2022 |
Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection
|
Dec 22, 2022 |
A hierarchical model for external electrical control of an insect, accounting for inter-individual variation of muscle force properties
|
Dec 21, 2022 |
Analyzing postprandial metabolomics data using multiway models: A simulation study
|
Dec 20, 2022 |
RBAtools: a programming interface for Resource Balance Analysis modelling
|
Dec 20, 2022 |
Hybrid-DIA: Intelligent Data Acquisition for Simultaneous Targeted and Discovery Phosphoproteomics in Single Spheroids
|
Dec 20, 2022 |
Longitudinal flux balance analyses of a patient with Crohn's disease highlight microbiome metabolic alterations
|
Dec 20, 2022 |
MODELING POLARITY SITE MOVEMENT IN YEAST VIA CALCIUM-MEDIATED REGULATION OF GAP ACTIVITY
|
Dec 20, 2022 |
Systems Level Identification Of A Matrisome-Associated Macrophage Polarization State In Multi-Organ Fibrosis
|
Dec 20, 2022 |
A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms
|
Dec 19, 2022 |
High-Throughput Discovery and Characterization of Viral Transcriptional Effectors in Human Cells
|
Dec 19, 2022 |
Correlated protein modules reflecting functional coordination of interacting proteins are uncovered by single-cell proteomics
|
Dec 19, 2022 |
Fatecode: Cell fate regulator prediction using classification autoencoder perturbation
|
Dec 19, 2022 |
Homeostasis, injury and recovery dynamics at multiple scales in a self-organizing intestinal crypt
|
Dec 19, 2022 |
Backtracking: Improved methods for identifying the source of a deliberate release of Bacillus anthracis from the temporal and spatial distribution of cases
|
Dec 19, 2022 |
A microbial community growth model for dynamic phenotype predictions
|
Dec 18, 2022 |
Laboratory evolution of Mycobacterium smegmatis in the presence of a fluoroquinolone leads to extreme drug resistance phenotype through the over-expression of Msmeg_5659-61 efflux pump.
|
Dec 18, 2022 |
The protooncogene Ski regulates the neuron-glia switch during development of the mammalian cerebral cortex
|
Dec 16, 2022 |
A profile likelihood-based workflow for identifiability analysis, estimation, and prediction with mechanistic mathematical models
|
Dec 16, 2022 |
Mathematical modelling of brain mTOR activity identifies selective vulnerability of cell types and signalling pathways
|
Dec 15, 2022 |
Effective methods for bulk RNA-Seq deconvolution using scnRNA-Seq transcriptomes
|
Dec 15, 2022 |
Longevity and rejuvenation effects of cell reprogramming are decoupled from loss of somatic identity
|
Dec 14, 2022 |
Deciphering the determinants of recombinant protein yield across the human secretome
|
Dec 14, 2022 |
Logical modelling of myelofibrotic microenvironment predicts dysregulated progenitor stem cell crosstalk
|
Dec 14, 2022 |
In-silico and in-vitro morphometric analysis of intestinal organoids
|
Dec 13, 2022 |
Biochemical network motifs can transduce and process oscillatory information
|
Dec 13, 2022 |
Causal network inference based on cross-validation predictability
|
Dec 13, 2022 |
Cuticle development and underlying transcriptome-metabolome associations during early seedling establishment
|
Dec 12, 2022 |
BioNetGMMFit: a Parameter Estimation Tool for BioNetGen using Single-Cell Snapshot Data from Cell Populations Evolving over Time
|
Dec 12, 2022 |
The Holdup Multiplex, an assay for high-throughput measurement of protein-ligand affinity constants using a mass-spectrometry readout
|
Dec 12, 2022 |
Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification
|
Dec 12, 2022 |
Spateo: multidimensional spatiotemporal modeling of single-cell spatial transcriptomics
|
Dec 11, 2022 |
Homeostasis in Networks with Multiple Inputs
|
Dec 11, 2022 |
A framework for deriving analytic long-term behavior of biochemical reaction networks
|
Dec 11, 2022 |
Missense variant interaction scanning reveals a critical role of the FERM-F3 domain for tumor suppressor protein NF2 conformation and function
|
Dec 11, 2022 |
Large-scale changes of molecular network states explain complex traits
|
Dec 09, 2022 |
Design principles for perfect adaptation in biological networks with nonlinear dynamics
|
Dec 08, 2022 |
Guidelines for extracting biologically relevant context-specific metabolic models using gene expression data
|
Dec 07, 2022 |
Isobaric crosslinking mass spectrometry technology for studying conformational and structural changes in proteins and complexes
|
Dec 05, 2022 |
De novo linear phosphorylation site motifs for BCR-ABL kinase revealed by phospho-proteomics in yeast
|
Dec 05, 2022 |
Posterior marginalization accelerates Bayesian inference for dynamical systems
|
Dec 03, 2022 |
Phenotype-based single-cell transcriptomics reveal compensatory pathways involved in Golgi organization and associated transport.
|
Dec 03, 2022 |
Robust dimethyl-based multiplex-DIA workflow doubles single-cell proteome depth via a reference channel
|
Dec 03, 2022 |
Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome
|
Dec 03, 2022 |
Sfp1 integrates TORC1 and PKA activity towards yeast ribosome biogenesis
|
Dec 02, 2022 |
Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in severe COVID-19
|
Dec 02, 2022 |
Enhancing single-cell proteomics through tailored Data-Independent Acquisition and micropillar array-based chromatography
|
Nov 30, 2022 |
A general model-based causal inference overcomes the curse of synchrony and indirect effect
|
Nov 30, 2022 |
A Theoretical Framework for Relating Natural Movement to Length and Quality of Life in Human and Non-human Animals
|
Nov 30, 2022 |
A simple within-host, between-host model for a vector-transmitted disease
|
Nov 29, 2022 |
Global Endometrial DNA Multi-omics Analysis Reveals Insights into mQTL Regulation and Associated Endometriosis Disease Risk
|
Nov 28, 2022 |
The network structure of hematopoietic cancers
|
Nov 27, 2022 |
SLIDE: Significant Latent Factor Interaction Discovery and Exploration across biological domains
|
Nov 27, 2022 |
Flux analysis reveals specific regulatory modalities of gene expression
|
Nov 26, 2022 |
Statistical Inference of Enhancer-Gene Networks Reveals Pivotal Role of T-bet Expression Intensity for T Helper Cell Fate
|
Nov 25, 2022 |
Generating synthetic data with a mechanism-based Critical Illness Digital Twin: Demonstration for Post Traumatic Acute Respiratory Distress Syndrome
|
Nov 24, 2022 |
Expanding large-scale mechanistic models with machine learned associations and big datasets
|
Nov 24, 2022 |
Proteome mapping of the human pancreatic islet microenvironment reveals endocrine-exocrine signaling sphere of influence
|
Nov 24, 2022 |
Smurfness-based two-phase model of ageing helps deconvolve the ageing transcriptional signature
|
Nov 23, 2022 |
Organism-wide secretome mapping uncovers pathways of tissue crosstalk in exercise
|
Nov 23, 2022 |
A novel model of multicellular communication through extracellular matrix microstructure
|
Nov 22, 2022 |
Global connectivity and networks of marine reserves
|
Nov 20, 2022 |
Identifying Strong Modulators of Cellular Quiescence Depth Across Different Quiescent Cells and Conditions
|
Nov 20, 2022 |
Enzyme levels broadly influence flux throughout the metabolic network
|
Nov 18, 2022 |
In silico network-based screening reveals candidates for endothelial dysfunction therapy
|
Nov 18, 2022 |
SBMLKinetics: A Tool for Annotation Independent Data Driven Classification of Reaction Kinetics for SBML Models
|
Nov 18, 2022 |
Antagonism between viral infection and innate immunity at the single-cell level
|
Nov 18, 2022 |
Real-time library search increases cross-link identification depth across all levels of sample complexity
|
Nov 17, 2022 |
Binding Site-enhanced Sequence Pretraining and Out-of-cluster Meta-learning Predict Genome-Wide Chemical-Protein Interactions for Dark Proteins
|
Nov 17, 2022 |
CHRRT: boosting coordinate hit-and-run with rounding by thinning
|
Nov 17, 2022 |
Emergence of division of labor in tissues through cell interactions and spatial cues
|
Nov 17, 2022 |
Elevated energy costs of biomass production in mitochondrial-respiration deficient Saccharomyces cerevisiae
|
Nov 17, 2022 |
Identifying genes and pathways linking astrocyte regional specificity to Alzheimer's disease susceptibility
|
Nov 17, 2022 |
Assigning functionality to cysteines by base editing of cancer dependency genes
|
Nov 17, 2022 |
Brain energy metabolism is optimized to minimize the cost of enzyme synthesis and transport
|
Nov 16, 2022 |
Rational strain design with minimal phenotype perturbation
|
Nov 16, 2022 |
NRPreTo: A Machine Learning Based Nuclear Receptor and Subfamily Prediction Tool
|
Nov 15, 2022 |
Cerebrovascular damage caused by the gut microbe-derived uraemic toxin p-cresol sulfate isprevented by blockade of the epidermal growth factor receptor
|
Nov 15, 2022 |
Integrating a tailored recurrent neural network with Bayesian experimental design to optimize microbial community functions
|
Nov 15, 2022 |
Proteome efficiency of metabolic pathways in Escherichia coli increases along the nutrient flow
|
Nov 15, 2022 |
A physiologically based model of bile acid metabolism in mice
|
Nov 13, 2022 |
Role of multiple pericentromeric repeats on heterochromatin assembly
|
Nov 13, 2022 |
Physiological niche informs evolution of metabolic function and corresponding drug targets of pathobionts
|
Nov 13, 2022 |
Standardization of laboratory practices for the study of the human gut microbiome
|
Nov 10, 2022 |
Identification of a unique transcriptomic signature associated with islet amyloidosis
|
Nov 10, 2022 |
COMPUTATIONAL EVIDENCE FOR MULTI-LAYER CROSSTALK BETWEEN THE CADHERIN-11 AND PDGFR PATHWAYS
|
Nov 09, 2022 |
Systems-level transcriptional regulation of Caenorhabditis elegans metabolism
|
Nov 09, 2022 |
A gene essentiality signature for studying the mechanism of action of drugs
|
Nov 08, 2022 |
CellSighter - A neural network to classify cells in highly multiplexed images
|
Nov 08, 2022 |
Mathematical Modeling of Impacts of Patient Differences on COVID-19 Lung Fibrosis Outcomes
|
Nov 07, 2022 |
Identifying a developmental transition in honey bees using gene expression data
|
Nov 07, 2022 |
A rapid platform for 3D patient-derived cutaneous neurofibroma organoid establishment and screening
|
Nov 07, 2022 |
Proteomics and constraint-based modelling reveal enzyme kinetic properties of Chlamydomonas reinhardtii on a genome scale
|
Nov 06, 2022 |
Comparative proteome analysis of different Saccharomyces cerevisiae strains during growth on sucrose and glucose
|
Nov 05, 2022 |
Strategies for increasing the depth and throughput of protein analysis by plexDIA
|
Nov 05, 2022 |
Gene expression signatures predict circadian rhythms in oncogenic pathways
|
Nov 04, 2022 |
Towards Environmental Control of Microbiomes
|
Nov 04, 2022 |
Systematic analysis and optimization of early warning signals for critical transitions
|
Nov 04, 2022 |
Modeling the iron storage protein ferritin reveals how residual ferrihydrite iron determines initial ferritin iron sequestration kinetics
|
Nov 04, 2022 |
gMCStool: automated network-based tool to search for metabolic vulnerabilities in cancer
|
Nov 04, 2022 |
Quartet metabolite reference materials for assessing inter-laboratory reliability and data integration of metabolomic profiling
|
Nov 03, 2022 |
Identifying cross-lineage dependencies of cell-type specific regulators in gastruloids
|
Nov 02, 2022 |
Uncovering the principles coordinating systems-level organelle biogenesis with cellular growth
|
Nov 02, 2022 |
Single-cell bacterial sequencing of invertible loci reveals promoter inversion rates as a strong determinant of population heterogeneity
|
Nov 02, 2022 |
Integrated Multi-Omics Analysis of Brain Aging in Female Nonhuman Primates Reveals Altered Signaling Pathways Relevant to Age-Related Disorders
|
Nov 02, 2022 |
Model-driven optimal experimental design for calibrating cardiac electrophysiology models
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Nov 02, 2022 |
Genomic Characterization of Rare Earth Binding by Shewanella oneidensis
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Nov 02, 2022 |
Escape from the HER2-activated DCIS-like state is skewed by divergent nucleocytoplasmic transport
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Nov 01, 2022 |
A bistable autoregulatory module in the developing embryo commits cells to binary fates
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Nov 01, 2022 |
Kinetic Model With Feedback Cycle for Age-Dependent Beta Amyloid Accumulation in Mice
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Nov 01, 2022 |
Reversing gut microbiome-driven adipose tissue inflammation alleviates metabolic syndrome
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Oct 31, 2022 |
Affected cell types for hundreds of Mendelian diseases revealed by analysis of human and mouse single-cell data
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Oct 31, 2022 |
WEBNG: A templating tool for weighted ensemble sampling of rule-based models
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Oct 31, 2022 |
A scalable approach for solving chemical master equations based on modularization and filtering
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Oct 31, 2022 |
Deep model predictive control of gene expression in thousands of single cells
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Oct 31, 2022 |
Spatially coordinated collective phosphorylation filters spatiotemporal noises for precise circadian timekeeping
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Oct 28, 2022 |
SMbiot: A Shared Latent Model for Microbiomes and their Hosts
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Oct 28, 2022 |
Time of Sample Collection Critical for Microbiome Replicability
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Oct 28, 2022 |
Quantitative Relationship between Intracellular Metabolic Responses against Nutrient Conditions and Metabolic Inhibitions
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Oct 27, 2022 |
Metabolic modeling of Hermetia illucens larvae resource allocation for high-value fatty acid production
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Oct 27, 2022 |
Dissecting the effects of GTPase and kinase domain mutations on LRRK2 endosomal localization and activity
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Oct 27, 2022 |
Metabolic robustness to growth temperature of cold adapted bacterium
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Oct 26, 2022 |
Benchmarking of protein interaction databases for integration with manually reconstructed signaling network models
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Oct 26, 2022 |
Ratio-based quantitative multiomics profiling using universal reference materials empowers data integration
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Oct 26, 2022 |
Representation and quantification Of Module Activity from omics data with rROMA
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Oct 25, 2022 |
Functional Decomposition of Metabolism allows a system-level quantification of fluxes and protein allocation towards specific metabolic functions
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Oct 24, 2022 |
Therapy Induced Tumor Senescence Model
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Oct 24, 2022 |
Deep Reinforcement Learning for Stabilization of Large-scale Probabilistic Boolean Networks
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Oct 24, 2022 |
Patient-specific deep offline artificial pancreas for blood glucose regulation in type 1 diabetes
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Oct 24, 2022 |
The regulatory landscape of the yeast phosphoproteome
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Oct 24, 2022 |
Predicting yield traits of individual field-grown Brassica napus plants from rosette-stage leaf gene expression
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Oct 23, 2022 |
A quantitative model for the transcriptional landscape of the bacterial cell cycle
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Oct 23, 2022 |
Macrophage phenotype transitions in a stochasticgene-regulatory network model
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Oct 21, 2022 |
Global landscape of the host response to SARS-CoV-2 variants reveals viral evolutionary trajectories
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Oct 21, 2022 |
Filtered finite state projection method for the analysis andestimation of stochastic biochemical reaction networks
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Oct 21, 2022 |
Correcting batch effects in large-scale multiomic studies using a reference-material-based ratio method
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Oct 21, 2022 |
Dynamic genome-based metabolic modeling of the predominant cellulolytic rumen bacterium Fibrobacter succinogenes S85
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Oct 21, 2022 |
PMI estimation through metabolomics and potassium analysis on animal vitreous humour
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Oct 21, 2022 |
Microscopic Imaging of Epigenetic Age
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Oct 20, 2022 |
Damage dynamics in single E. coli and the role of chance in the timing of cell death
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Oct 17, 2022 |
Functionally annotating cysteine disulfides and metal binding sites in the plant kingdom using AlphaFold2 predicted structures
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Oct 17, 2022 |
Automatic mechanistic inference from large families of Boolean models generated by Monte Carlo Tree Search
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Oct 17, 2022 |
Investigating the unique ability of Trichodesmium to fix carbon and nitrogen simultaneously using MiMoSA
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Oct 17, 2022 |
Are under-studied proteins under-represented? How to fairly evaluate link prediction algorithms in network biology
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Oct 17, 2022 |
Computational Speed-Up of Large-Scale, Single-Cell Model Simulations Via a Fully-Integrated SBML-Based Format
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Oct 17, 2022 |
Predictive nonlinear modeling of malignant myelopoiesis and tyrosine kinase inhibitor therapy
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Oct 14, 2022 |
Dynamic map illuminates Hippo to cMyc module crosstalk driving cardiomyocyte proliferation
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Oct 14, 2022 |
An enhanced transcription factor repressilator that buffers stochasticity and entrains to an erratic external circadian signal
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Oct 13, 2022 |
Identifying Essential Genes in Genome-Scale Metabolic Models of Consensus Molecular Subtypes of Colorectal Cancer
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Oct 12, 2022 |
Signal integration by a bHLH circuit enables fate choice in neural stem cells
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Oct 11, 2022 |
Disturbed trophoblast transition links preeclampsia progression from placenta to the maternal syndrome
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Oct 11, 2022 |
Pytometry: Flow and mass cytometry analytics in Python
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Oct 11, 2022 |
Mechanisms underlying divergent relationships between Ca2+ and YAP/TAZ signaling
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Oct 07, 2022 |
Quantifying noise modulation from coupling of stochastic expression to cellular growth: An analytical approach
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Oct 07, 2022 |
High selectivity of frequency induced transcriptional responses
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Oct 07, 2022 |
Commitment in the Pink1/Parkin mitophagy decision circuit
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Oct 07, 2022 |
Continuity between ancient geochemistry and modern metabolism enabled by non-autocatalytic purine biosynthesis
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Oct 07, 2022 |
Novel Context-Specific Genome-Scale Modelling Explores the Potential of Chlamydomonas reinhardtii for Synthetic Biology Applications
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Oct 07, 2022 |
Tuning of cytokine signaling through imbalanced abundances of receptors and kinases
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Oct 07, 2022 |
Multi range ERK responses shape the proliferative trajectory of single cells following oncogene induced senescence
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Oct 07, 2022 |
Integrative Multi-Omics Approaches for Identifying Cervical Cancer Therapeutic Targets
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Oct 07, 2022 |
Predicting Anti-Cancer Drug Combination Responses with a Temporal Cell State Network Model
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Oct 07, 2022 |
Dynamic trade-offs between biomass accumulation and division determine bacterial cell size and proteome in fluctuating nutrient environments
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Oct 06, 2022 |
Machine learning on large-scale proteomics data identifies tissue- and cell type-specific proteins
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Oct 05, 2022 |
Beyond BRCA: Discovery of novel causes and consequences of homologous recombination deficiencies
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Oct 05, 2022 |
Evaluating the potential of marine invertebrate and insect protein hydrolysates to reduce fetal bovine serum in cell culture media for cultivated fish production
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Oct 05, 2022 |
Suppression of Betacellulin expression is a key mechanism for omega-3 fatty acid mediated attenuation of nonalcoholic steatohepatitis
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Oct 05, 2022 |
Minor intron containing genes: Achilles' heel of viruses?
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Oct 04, 2022 |
Trafficking dynamics of VEGFR1, VEGFR2, and NRP1 in human endothelial cells
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Oct 01, 2022 |
NHA1 is a cation/proton antiporter essential for the water-conserving functions of the rectal complex in Tribolium castaneum
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Oct 01, 2022 |
Electrophile scanning by chemical proteomics reveals a potent pan-active DUB probe for investigation of deubiquitinase activity in live cells
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Sep 30, 2022 |
Detecting and dissecting signaling crosstalk via the multilayer network integration of signaling and regulatory interactions
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Sep 30, 2022 |
Comprehensive analysis of intercellular communication in thermogenic adipose niche
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Sep 30, 2022 |
The trait coding rule in phenotype space
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Sep 30, 2022 |
Multi-scale spatial modeling of immune cell distributions enables survival prediction in primary central nervous system lymphoma
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Sep 28, 2022 |
The Quartet Data Portal: integration of community-wide resources for multiomics quality control
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Sep 28, 2022 |
A Genome Scale Transcriptional Regulatory Model of the Human Placenta
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Sep 28, 2022 |
A scalable screening platform for phenotypic subtyping of ALS patient-derived fibroblasts
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Sep 28, 2022 |
Nature of epigenetic aging from a single-cell perspective
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Sep 28, 2022 |
COVIDpro: Database for mining protein dysregulation in patients with COVID-19
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Sep 28, 2022 |
Identifying Genes with Location Dependent Noise Variance in Spatial Transcriptomics Data
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Sep 27, 2022 |
Comparative Study between In-silico and Clinical Works on the Control of Blood Glucose Level in People with Type 1 Diabetes using Improved Hovorka Equations
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Sep 26, 2022 |
On biological networks capable of robust adaptation in the presence of uncertainties: A systems-theoretic approach
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Sep 26, 2022 |
On the Geometry of Elementary Flux Modes
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Sep 26, 2022 |
Transcriptomics data integration for context-specific modeling of Atlantic salmon metabolism: functional evaluation of methods based on metabolic tasks
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Sep 24, 2022 |
Emergence of Supercoiling-Mediated Regulatory Networks through Bacterial Chromosome Rearrangements
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Sep 23, 2022 |
Proteome dynamics during transition from exponential to stationary phase under aerobic and anaerobic conditions in yeast
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Sep 23, 2022 |
A rapid protocol for ribosome profiling of low input samples
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Sep 23, 2022 |
Comprehensive characterization of multi-omic landscapes between gut-microbiota metabolites and the G-protein-coupled receptors in Alzheimer's disease
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Sep 22, 2022 |
Conserved coexpression at single cell resolution across primate brains
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Sep 22, 2022 |
RNA degradation heavily impacts mRNA co-expression
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Sep 22, 2022 |
Modeling Breast Cancer Proliferation, Drug Synergies, and Alternating Therapies
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Sep 22, 2022 |
Multi-omics biomarkers aid prostate cancer prognostication
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Sep 22, 2022 |
Alternative proteoforms and proteoform-dependent assemblies in humans and plants
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Sep 22, 2022 |
Development of muti-agent-simulation models for intercellular communication via cytokines and extracellular matrices
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Sep 22, 2022 |
From toxic waste to beneficial nutrient: acetate boosts Escherichia coli growth at low glycolytic flux
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Sep 21, 2022 |
Temporally resolved kinase regulatory networks control endothelial barrier integrity
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Sep 20, 2022 |
Evaluating proteome allocation of Saccharomyces cerevisiae phenotypes with resource balance analysis
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Sep 20, 2022 |
PrePCI: A structure- and chemical similarity-informed database of predicted protein compound interactions
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Sep 19, 2022 |
Secreted long non-coding RNAs Gadlor1 and Gadlor2 affect multiple cardiac cell types and aggravate cardiac remodeling during pressure overload
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Sep 19, 2022 |
Microbial interactions impact the growth response of Clostridioides difficile to antibiotics
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Sep 18, 2022 |
Evaluating the Robustness of Connectivity Methods to Noise for In Silico Drug Repurposing Studies
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Sep 17, 2022 |
Optimal energy and redox metabolism in the cyanobacterium Synechocystis sp. PCC 6803
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Sep 17, 2022 |
The magnitude of sex differences in host-microbe interactions are time-of-day dependent
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Sep 17, 2022 |