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Episodes: 623

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Audio versions of bioRxiv and medRxiv paper abstracts

Episode Date
Radiation necrosis after radiation therapy treatment of brain metastases: A computational approach
Aug 03, 2023
Evaluation of Fendiline Treatment in VP40 System with Nucleation-Elongation Process: A Computational Model of Ebola Virus Matrix Protein Assembly
Aug 03, 2023
Combined kinome inhibition states are predictive of cancer cell line sensitivity to kinase inhibitor combination therapies
Aug 03, 2023
A Phosphoproteomics Data Resource for Systems-level Modeling of Kinase Signaling Networks
Aug 03, 2023
Quantifying landscape-flux via single-cell transcriptomics uncovers the underlying mechanism of cell cycle
Aug 03, 2023
Metabolic slowdown as the proximal cause of ageing and death
Aug 03, 2023
Pathogenic mutations of human phosphorylation sites affect protein-protein interactions
Aug 03, 2023
Body weight, gonadectomy, and other risk factors for diagnosis of osteoarthritis in companion dogs
Aug 03, 2023
The axes of biology: a novel axes-based network embedding paradigm to decipher the functional mechanisms of the cell.
Aug 02, 2023
Essential Gene Knockdowns Reveal Genetic Vulnerabilities and Antibiotic Sensitivities in Acinetobacter baumannii
Aug 02, 2023
Density Physics-Informed Neural Network reveals sources of cell heterogeneity in signal transduction
Aug 02, 2023
A demand-based framework explains prioritization strategies upon transient limitations of different amino acids.
Aug 02, 2023
Identifying repurposed drugs with moderate anti-influenza virus activity through computational prioritization of drug-target pairs
Aug 02, 2023
Pleiotropic effects of trisomy and pharmacologic modulation on structural, functional, molecular, and genetic systems in a Down syndrome mouse model
Aug 01, 2023
Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML
Jul 31, 2023
Computational prediction of protein interactions on single cells by proximity sequencing
Jul 30, 2023
Correlations reveal the hierarchical organization of networks with latent binary variables
Jul 30, 2023
The epigenetic response of mouse brown adipose tissue to cold stress: histone proteoform, DNA methylation, and RNA expression
Jul 30, 2023
Multiple Receptor Tyrosine Kinases Regulate Dengue Infection of Hepatocytes
Jul 30, 2023
Clinical prediction of wound re-epithelisation outcomes in non-severe burn injury using the plasma lipidome
Jul 30, 2023
Genome scale metabolic network modelling for metabolic profile predictions
Jul 29, 2023
Interpreting roles of mutations associated with the emergence of S. aureus USA300 strains using transcriptional regulatory network reconstruction
Jul 29, 2023
Prediction of metabolites associated with somatic mutations in cancers by using genome-scale metabolic models and mutation data
Jul 29, 2023
Automatic design of gene regulatory mechanisms for spatial pattern formation
Jul 29, 2023
Enhanced cell segmentation with limited annotated data using generative adversarial networks
Jul 28, 2023
Systematic exploration of prokaryotic form I rubisco maximal carboxylation rates
Jul 27, 2023
Agent-based modeling of the prostate tumor microenvironment uncovers spatial tumor growth constraints and immunomodulatory properties
Jul 27, 2023
Fecal Dysbiosis and Inflammation in Intestinal-Specific Cftr Knockout Mice on Regimens Preventing Intestinal Obstruction
Jul 26, 2023
CURTAIN - A Unique Web-based tool for exploration and sharing of MS-based proteomics data
Jul 25, 2023
Predictive Systems Biology Modeling: Unraveling Host Metabolic Disruptions and Potential Drug Targets in SARS-CoV-2 and Its Variants
Jul 25, 2023
Prostate Cancer Reshapes the Secreted and Extracellular Vesicle Urinary Proteomes
Jul 25, 2023
Transcriptomic signatures of progressive and regressive liver fibrosis and portal hypertension
Jul 25, 2023
Spatial Metabolome Lipidome and Glycome from a Single brain Section
Jul 25, 2023
Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis
Jul 25, 2023
A comprehensive atlas of the aging vertebrate brain reveals signatures of progressive proteostasis dysfunction
Jul 24, 2023
Metabolic Symbiosis between Oxygenated and Hypoxic Tumour Cells: An Agent-based Modelling Study
Jul 24, 2023
Stochastic model of vesicular stomatitis virus replication reveals mutational effects on virion production
Jul 24, 2023
Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon
Jul 23, 2023
The timing of cellular events: a stochastic vs deterministic perspective
Jul 21, 2023
An Automated Model Annotation System (AMAS) for SBML Models
Jul 21, 2023
Better tree shape indices
Jul 19, 2023
An aiHumanoid Simulation of Gram-Negative Sepsis: A Comprehensive Multi-Organoid Platform for Advanced Disease Modeling, Drug Discovery, and Personalized Medicine.
Jul 19, 2023
Poisson representation: a bridge between discrete and continuous models of stochastic gene regulatory networks
Jul 19, 2023
Positive and negative feedback regulation of the TGF-β1-SMAD4 axis explains two equilibrium states in human skin aging
Jul 19, 2023
Biologically meaningful regulatory logic enhances the convergence rate in Boolean networks and bushiness of their state transition graph
Jul 19, 2023
Deep spatial proteomic exploration of severe COVID-19-related pulmonary injury in post-mortem specimens
Jul 17, 2023
Systems Age: A single blood methylation test to quantify aging heterogeneity across 11 physiological systems
Jul 17, 2023
Systematic analysis of microorganisms' metabolism for selective targeting
Jul 17, 2023
Fully automated and integrated proteomics sample preparation platform for high-throughput drug target identification
Jul 16, 2023
Unveiling Hidden Connections in Omics Data via pyPARAGON: an Integrative Hybrid Approach for Disease Network Construction
Jul 15, 2023
Amyloid β accelerates age-related proteome-wide protein insolubility.
Jul 15, 2023
ReDirection: a numerically robust R-package to characterize every reaction of a user-defined biochemical network with the probable dissociation constant
Jul 14, 2023
Liebig's law of the minimum in the TGF-β pathway
Jul 14, 2023
The dominant role of post-transcriptional regulation in Yarrowia lipolytica to repeated O2 limitations
Jul 13, 2023
Does enforcing glenohumeral joint stability matter? A new rapid muscle redundancy solver highlights the importance of non-superficial shoulder muscles
Jul 12, 2023
Evaluation of single-sample network inference methods for precision oncology
Jul 12, 2023
Proteome-wide copy-number estimation from transcriptomics
Jul 11, 2023
The protein interactome of the citrus Huanglongbing pathogen Candidatus Liberibacter asiaticus
Jul 11, 2023
Scaling, correlations, and artifacts in biological timeseries
Jul 11, 2023
Quantifying mutational synergy using computational models predicts survival in haematological cancers
Jul 11, 2023
Machine Learning identifies conserved traits that influence lifespan and healthspan responses to dietary restriction
Jul 10, 2023
A systems-level analysis of the mutually antagonistic roles of RKIP and BACH1 in dynamics of cancer cell plasticity
Jul 08, 2023
Maternal Under-Nutrition During Pregnancy Alters the Molecular Response to Over-Nutrition in Multiple Organs and Tissues in Juvenile Offspring
Jul 07, 2023
Does ribosome composition maximize growth rate? The role of RNA instability
Jul 07, 2023
Enhanced cellular longevity arising from environmental fluctuations
Jul 07, 2023
Cross-regulation between proteome reallocation and metabolic flux redistribution governs bacterial growth transition kinetics
Jul 07, 2023
Single transcript-level metabolic responsive landscape of human liver transcriptome
Jul 06, 2023
The firing dynamics of replication origins affect their genome distribution
Jul 05, 2023
Basal MET Phosphorylation is an Indicator of Hepatocyte Dysregulation in Liver Disease
Jul 04, 2023
Modeling of the Network Mediated by IL-36 Involved inPsoriasis
Jul 03, 2023
Pan-genome and Haplotype Map of Cultivars and Their Wild Ancestors Provides Insights into Adaptive Evolution of Cassava (Manihot esculenta Crantz)
Jul 03, 2023
Optimal enzyme profiles in unbranched metabolic pathways
Jul 03, 2023
Longitudinal hair cortisol in bipolar disorder and a mechanism based on HPA dynamics
Jul 03, 2023
The PP2A-like phosphatase Ppg1 mediates assembly of the Far complex to balance gluconeogenic outputs and adapt to glucose depletion
Jul 03, 2023
Inference for entomological semi-field experiments: Fitting a mathematical model assessing personal and community protection of vector-control interventions
Jul 03, 2023
Independent component analysis reveals the transcriptional regulatory modules in Bradyrhizobium diazoefficiens USDA110
Jul 02, 2023
Robustness of biomolecular networks suggests functional modules far from the edge of chaos
Jul 02, 2023
Stochastic Model of Alzheimer's Disease Progression Using Two-State Markov Chains
Jul 01, 2023
ISiCell: involving biologists in the design process of agent-based models in cell biology
Jul 01, 2023
Disentangling gene expression burden identifies generalizable phenotypes induced by synthetic gene networks
Jul 01, 2023
Integrative analysis of CAKUT multi-omics data
Jul 01, 2023
Regulation of bacterial stringent response by an evolutionary conserved ribosomal protein L11 methylation
Jun 30, 2023
Evaluating Study Design Rigor in Preclinical Cardiovascular Research: A Replication Study
Jun 29, 2023
Simultaneous Multi-Omics Analysis by Direct Infusion Mass Spectrometry (SMAD-MS)
Jun 29, 2023
The alternative sigma factor RpoD4 pulses at division and links the circadian clock and the cell cycle in Synechococcus elongatus
Jun 28, 2023
Application of Coincidence Index in the Discovery of Co-Expressed Metabolic Pathways
Jun 28, 2023
The metabolic role of vitamin D in children's neurodevelopment: a network study
Jun 26, 2023
An integrated mechanistic and data-driven computational model predicts cell responses to high- and low-affinity EGFR ligands
Jun 26, 2023
Parametric modeling of mechanical effects on circadian oscillators
Jun 25, 2023
A fast method to distinguish between fermentative and respiratory metabolisms in single yeast cells
Jun 24, 2023
Storm: Incorporating transient dynamics to infer the RNA velocity with metabolic labeling information
Jun 23, 2023
Bayesian analysis dissects kinetic modulation during non-stationary gene expression
Jun 23, 2023
A Systems Level Explanation for Gompertzian Mortality Patterns is provided by the "Multiple and Inter-dependent Component Cause Model"
Jun 22, 2023
Dual proteomic signature of immune cells and Yersinia pestis upon blood infection
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
Jun 22, 2023
Comprehensive analysis of network reconstruction approaches based on correlation in metagenomic data
Jun 22, 2023
Systematic biases in transcriptional parameters inferred from single-cell snapshot data
Jun 21, 2023
Transcriptome of left ventricle and sinoatrial node in young and old C57 mice
Jun 17, 2023
Using mixture density networks to emulate a stochastic within-host model of Francisella tularensis infection
Jun 16, 2023
A scalable platform for efficient CRISPR-Cas9 chemical-genetic screens of DNA damage-inducing compounds
Jun 16, 2023
JMnorm: a novel Joint Multi-feature normalization method for integrative and comparative epigenomics
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
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
Jun 14, 2023
Impact of Bmal1 rescue and time-restricted feeding on liver and muscle proteomes during the active phase in mice
Jun 13, 2023
Designing function-specific minimal microbiomes from large microbial communities
Jun 12, 2023
Enhanced perfusion following exposure to radiotherapy: a theoretical investigation
Jun 12, 2023
Repository of logically consistent real-world Boolean network models
Jun 12, 2023
Dose optimization of an adjuvanted peptide-based personalized neoantigen melanoma vaccine
Jun 11, 2023
Shared and distinct pathways and networks genetically linked to coronary artery disease between human and mouse
Jun 11, 2023
Kinetic modeling of leucine-mediated signaling and protein metabolism in human skeletal muscle
Jun 11, 2023
Senescent Subtypes Transition Model
Jun 10, 2023
Information-theoretic analysis of a model of CAR-4-1BB-mediated NFκB activation
Jun 10, 2023
Biological embedding of childhood adversity - a multi-omics perspective on stress regulation
Jun 10, 2023
METABOLIC MODELLING AS A POWERFUL TOOL TO IDENTIFY CRITICAL COMPONENTS OF THE PNEUMOCYSTIS GROWTH MEDIUM
Jun 09, 2023
Heritable epigenetic changes are constrained by the dynamics of regulatory architectures
Jun 09, 2023
TMELand: An end-to-end pipeline for quantification and visualization of Waddington's epigenetic landscape based on gene regulatory network
Jun 08, 2023
Classification of bacterial nanowire proteins using Machine Learning and Feature Engineering model
May 05, 2023
Endothelial cells signaling and patterning under hypoxia: a mechanistic computational model
May 05, 2023
Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells
May 05, 2023
Nuclear export is a limiting factor in eukaryotic mRNA metabolism
May 04, 2023
Excitable dynamics of flares and relapses in autoimmune diseases
May 04, 2023
Drug Target Identification in Triple Negative Breast Cancer Stem Cell Pathways: a computational study of gene regulatory pathways using Boolean networks
May 04, 2023
A provably convergent control closure scheme for the Method of Moments of the Chemical Master Equation
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
May 02, 2023
Upregulation of steroidogenesis is associated with coma in human cerebral malaria
May 02, 2023
Abolishing storage lipids induces protein misfolding and stress responses in Yarrowia lipolytica
May 02, 2023
Evidence for conservation of a primordial 12-hour ultradian gene program in humans
May 02, 2023
Particle-based simulations reveal two positive feedback loops allow relocation and stabilization of the polarity site during yeast mating
May 01, 2023
Systematic Pan-cancer Functional Inference and Validation of Hyper, Hypo and Neomorphic Mutations
Apr 30, 2023
SINGLE CELL RESOLUTION SPATIAL MAPPING OF HUMAN HEMATOPOIESIS REVEALS AGING-ASSOCIATED TOPOGRAPHIC REMODELING
Apr 30, 2023
ISRES+: An improved evolutionary strategy for function minimization to estimate the free parameters of Systems Biology models
Apr 30, 2023
Personalized Clostridioides difficile engraftment risk prediction and probiotic therapy assessment in the human gut.
Apr 29, 2023
Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum
Apr 29, 2023
Phenomenological modeling reveals the emergent simplicity of host-associated microbiomes
Apr 29, 2023
Joint Distribution of Protein Concentration and Cell Volume Coupled by Feedback in Dilution
Apr 29, 2023
Protein homeostasis from diffusion-dependent control of protein synthesis and degradation
Apr 28, 2023
Statistical characterization of the dynamics of Glioblastoma Multiforme subtypes through parameters estimation of the epigenetic landscape
Apr 28, 2023
Perfusion estimation using MRI-based measurements and a porous media flow model
Apr 28, 2023
Metabolic consequences of non-severe burn injury are associated with increased plasma markers of inflammation and cardiovascular disease risk.
Apr 28, 2023
Generating immunogenomic data-guided virtual patients using a QSP model to predict response of advanced NSCLC to PD-L1 inhibition
Apr 28, 2023
Machine Learning Identifies Plasma Proteomic Signatures of Descending Thoracic Aortic Disease
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
Apr 25, 2023
Mycobacterium tuberculosis-Macrophage Interactome: Molecular Network Structure and Resilience against Antibiotics
Apr 25, 2023
PEELing: an integrated and user-centric platform for cell-surface proteomics analysis
Apr 25, 2023
Dynamics of cell type transition mediated by epigenetic modifications
Apr 25, 2023
Analytical validation of the PROphet computational model for clinical benefit prediction and decision-making tool in metastatic NSCLC
Apr 24, 2023
A mobile CRISPRi collection enables genetic interaction studies for the essential genes of Escherichia coli
Apr 22, 2023
What controls carbon sequestration in plants under which conditions?
Apr 21, 2023
A Logic-incorporated Gene Regulatory Network Deciphers Principles in Cell Fate Decisions
Apr 21, 2023
A multi-scale digital twin for adiposity-driven insulin resistance in humans: diet and drug effects
Apr 21, 2023
Age-dependent ventilator-induced lung injury: Mathematical modeling, experimental data, and statistical analysis
Apr 21, 2023
Regulating microbiome metabolic stability for stable indigenous liquor fermentation
Apr 21, 2023
BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale
Apr 20, 2023
Flux Sampling in Genome-scale Metabolic Modeling of Microbial Communities
Apr 20, 2023
Gene regulatory network inference with popInfer reveals dynamic regulation of hematopoietic stem cell quiescence upon diet restriction and aging
Apr 20, 2023
In-silico modelling of the mitogen-activated kinase (MAPK) pathway in colorectal cancer: mutations and targeted therapy
Apr 20, 2023
Proteomes Reveal Metabolic Capabilities of Yarrowia lipolytica for Biological Upcycling of Polyethylene into High-Value Chemicals
Apr 18, 2023
Quantitative mechanistic model reveals key determinants of placental IgG transfer and informs prenatal immunization strategies
Apr 18, 2023
Growth balance analysis models of cyanobacteria for understanding resource allocation strategies
Apr 18, 2023
NFκB nuclear dynamics orchestrate inflammatory aging
Apr 18, 2023
Phenotype control techniques for Boolean gene regulatory networks
Apr 18, 2023
Acute myeloid leukemia stratifies as two clinically relevant sphingolipidomic subtypes
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
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
Apr 14, 2023
A physiologically based pharmacokinetic model for CYP2E1 phenotyping via chlorzoxazone
Apr 14, 2023
Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors
Apr 14, 2023
Fission yeast obeys a linear size law under nutrient titration
Apr 13, 2023
Computational Screen for Sex-Specific Drug Effects in a Cardiac Fibroblast Network Model
Apr 13, 2023
Sidestream bio-P and mainstream anammox in a BNR process with upstream carbon capture
Apr 13, 2023
A calibration and uncertainty quantification analysis of classical, fractional and multiscale logistic models of tumour growth
Apr 13, 2023
LabEmbryoCam: An opensource phenotyping system for developing aquatic animals
Apr 12, 2023
An automated proximity proteomics pipeline for subcellular proteome and protein interaction mapping
Apr 12, 2023
A benchmark of optimization solvers for genome-scale metabolic modeling
Apr 12, 2023
Epistasis meets pleiotropy in shaping biophysical protein subspaces associated with antimicrobial resistance
Apr 09, 2023
piTracer - Automatic reconstruction of molecular cascades for the identification of synergistic drug targets
Apr 09, 2023
A statistical framework for quantifying the nuclear export rate of influenza viral mRNAs.
Apr 08, 2023
Predictive power of non-identifiable models
Apr 08, 2023
SynDISCO: A Mechanistic Modeling-Based Framework for Predictive Prioritization of Synergistic Drug Combinations Directed at Cell Signaling Networks
Apr 08, 2023
Evolutionary druggability: leveraging low-dimensional fitness landscapes towards new metrics for antimicrobial applications
Apr 08, 2023
Predictive links between petal color and pigment quantities in natural Penstemon hybrids
Apr 08, 2023
Comparative analysis of noise-attenuation mechanisms in gene expression: From single cells to cell populations
Apr 08, 2023
Logic-Based Modeling of Inflammatory Macrophage Crosstalk with Glomerular Endothelial Cells in Diabetic Kidney Disease
Apr 06, 2023
Cellular energy regulates mRNA translation and degradation in a codon-specific manner
Apr 06, 2023
Revealing the Grammar of Small RNA Secretion Using Interpretable Machine Learning
Apr 06, 2023
Applications of Boolean modeling to study the dynamics of a complex disease and therapeutics responses
Apr 06, 2023
μPhos: a scalable and sensitive platform for functional phosphoproteomics
Apr 06, 2023
A diffusion-driven switch specifies rhizoid precursor cells in Marchantia polymorpha
Apr 06, 2023
Sensitivity Analysis of Biochemical Systems Using Bond Graphs
Apr 06, 2023
How Interactions During Viral-Viral Coinfection Can Shape Infection Kinetics
Apr 05, 2023
A Mathematical Model of Glomerular Fibrosis in Diabetic Kidney Disease to Predict Therapeutic Efficacy
Apr 04, 2023
A coarse-grained resource allocation model of carbon and nitrogen metabolism in unicellular microbes
Apr 04, 2023
Extracellular Domains of CAR Reprogram T-Cell Metabolism Without Antigen Stimulation
Apr 04, 2023
Mycobacterial Metabolic Model Development for Drug Target Identification
Apr 03, 2023
Systems analysis of miR-199a/b-5p and multiple miR-199a/b-5p targets during chondrogenesis
Apr 03, 2023
High-affinity biomolecular interactions are modulated by low-affinity binders
Apr 03, 2023
Stochastic modeling of the dynamics of Salmonella infection of epithelial cells
Apr 03, 2023
Data-driven structural analysis of Small Cell Lung Cancer transcription factor networksuggests potential subtype regulators and transition pathways
Apr 03, 2023
A high-throughput approach reveals distinct peptide charging behaviors in electrospray ionization mass spectrometry
Apr 03, 2023
Single-cell time-resolved multi-omics reveal apoptotic and ferroptotic heterogeneity during foam cell formation
Apr 02, 2023
Evolution of the Telencephalon Anterior-Posterior Patterning by Core Endogenous Network Bifurcation
Apr 02, 2023
Emergence of Bow-tie Architecture in Evolving Feedforward Networks
Mar 29, 2023
The Road Less Traveled: Uncovering the Convergence Toward Specific Pleiotropic Phenotypes in Aging
Mar 29, 2023
Tools and methods for high-throughput single-cell imaging with the mother machine
Mar 29, 2023
Image-based temporal profiling of autophagy-related phenotypes
Mar 28, 2023
Temporal perturbation of STAT1/2 activity reveals dynamic ligand discrimination of type I interferon signaling
Mar 27, 2023
Predicting phenotype to mechanotype relationships in cells based on intra-cellular signaling network
Mar 27, 2023
A multi-omics strategy for the study of microbial metabolism: application to the human skin's microbiome
Mar 26, 2023
High versatility to meet conservation targets for biodiversity and hydrological services at the Riviera Maya, Quintana Roo, Mexico
Mar 25, 2023
Genetic and dietary modulators of the inflammatory response in the gastro-intestinal tract of the BXD mouse genetic reference population
Mar 25, 2023
Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models
Mar 25, 2023
Mathematical models disentangle the role of IL-10 feedbacks in human monocytes upon proinflammatory activation
Mar 25, 2023
Clonal differences underlie variable responses to sequential and prolonged treatment
Mar 25, 2023
Gene-metabolite annotation with shortest reactional distance enhances metabolite genome-wide association studies results
Mar 24, 2023
An improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells
Mar 24, 2023
DIP-MS: A novel ultra-deep interaction proteomics for the deconvolution of protein complexes
Mar 24, 2023
Geckopy 3.0: enzyme constraints, thermodynamics constraints and omics integration in python
Mar 23, 2023
Learning Perturbation-specific Cell Representations for Prediction of Transcriptional Response across Cellular Contexts
Mar 23, 2023
Compromised beta-cell identity in type 2 diabetes
Mar 23, 2023
On the interactions of DNA replication and transcriptional regulation
Mar 23, 2023
standard-GEM: standardization of open-source genome-scale metabolic models
Mar 23, 2023
Using interactive platforms to encode, manage and explore immune-related adverse outcome pathways
Mar 23, 2023
Modeling transcriptional regulation of the cell cycle using a novel cybernetic-inspired approach
Mar 23, 2023
The intensities of canonical senescence biomarkers integrate the duration of cell-cycle withdrawal
Mar 21, 2023
Emergence of power-law distributions in protein-protein interaction networks through study bias
Mar 21, 2023
How total mRNA influences cell growth
Mar 21, 2023
Modelling the dynamics of senescence spread
Mar 20, 2023
MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes
Mar 20, 2023
Ensemble and Iterative Engineering for Maximized Bioconversion to the Blue Pigment, Indigoidine from Non-Canonical Sustainable Carbon Sources
Mar 20, 2023
Integrative proteomics and transcriptomics of human T-cells reveals temporal metabolic reprogramming following TCR-induced activation
Mar 20, 2023
Exploring the noncanonical translatome using massively integrated coexpression analysis
Mar 17, 2023
Identifying drug effects in a cardiac model of electrophysiology using kernel-based parameter estimation methods
Mar 16, 2023
Guide-specific loss of efficiency and off-target reduction with Cas9 variants
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
Mar 15, 2023
MolClustPy: A Python Package to Characterize Multivalent Biomolecular Clusters
Mar 15, 2023
Leukemia core transcriptional circuitry is a sparsely interconnected hierarchy stabilized by incoherent feed-forward loops
Mar 15, 2023
Distilling identifiable and interpretable dynamic models from biological data
Mar 14, 2023
Cardiopulmonary structural, functional and immune-alterations in a Down syndrome mouse model and upon modulation of EGCG
Mar 14, 2023
TimeTeller: a tool to probe the circadian clock as a multigene dynamical system
Mar 14, 2023
In silico agent-based modeling approach to characterize multiple in vitro tuberculosis infection models
Mar 14, 2023
Comparative assessment of mosquito size and receptiveness to P. falciparum infection of two rearing procedures for Anopheles mosquitoes
Mar 12, 2023
OptEnvelope: a target point guided method for growth-coupled production using knockouts
Mar 12, 2023
A systematic search for RNA structural switches across the human transcriptome
Mar 12, 2023
A Consensus Model of Glucose-Stimulated Insulin Secretion in the Pancreatic beta-Cell
Mar 12, 2023
Multidimensional proteomics identifies molecular trajectories of cellular aging and rejuvenation
Mar 12, 2023
Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors
Mar 12, 2023
2'-Fucosyllactose helps butyrate producers outgrow competitors in the infant gut
Mar 11, 2023
Ensemble-based genome-scale modeling predicts metabolic differences between macrophage subtypes in colorectal cancer
Mar 11, 2023
The ability to sense the environment is heterogeneously distributed in cell populations
Mar 10, 2023
transomics2cytoscape: An automated software for interpretable 2.5-dimensional visualization of trans-omic networks
Mar 10, 2023
An extension of the Walsh-Hadamard transform to calculate and model epistasis in genetic landscapes of arbitrary shape and complexity
Mar 08, 2023
ENKIE: A package for predicting enzyme kinetic parameter values and their uncertainties
Mar 08, 2023
A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology
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
Nov 02, 2022
Genomic Characterization of Rare Earth Binding by Shewanella oneidensis
Nov 02, 2022
Escape from the HER2-activated DCIS-like state is skewed by divergent nucleocytoplasmic transport
Nov 01, 2022
A bistable autoregulatory module in the developing embryo commits cells to binary fates
Nov 01, 2022
Kinetic Model With Feedback Cycle for Age-Dependent Beta Amyloid Accumulation in Mice
Nov 01, 2022
Reversing gut microbiome-driven adipose tissue inflammation alleviates metabolic syndrome
Oct 31, 2022
Affected cell types for hundreds of Mendelian diseases revealed by analysis of human and mouse single-cell data
Oct 31, 2022
WEBNG: A templating tool for weighted ensemble sampling of rule-based models
Oct 31, 2022
A scalable approach for solving chemical master equations based on modularization and filtering
Oct 31, 2022
Deep model predictive control of gene expression in thousands of single cells
Oct 31, 2022
Spatially coordinated collective phosphorylation filters spatiotemporal noises for precise circadian timekeeping
Oct 28, 2022
SMbiot: A Shared Latent Model for Microbiomes and their Hosts
Oct 28, 2022
Time of Sample Collection Critical for Microbiome Replicability
Oct 28, 2022
Quantitative Relationship between Intracellular Metabolic Responses against Nutrient Conditions and Metabolic Inhibitions
Oct 27, 2022
Metabolic modeling of Hermetia illucens larvae resource allocation for high-value fatty acid production
Oct 27, 2022
Dissecting the effects of GTPase and kinase domain mutations on LRRK2 endosomal localization and activity
Oct 27, 2022
Metabolic robustness to growth temperature of cold adapted bacterium
Oct 26, 2022
Benchmarking of protein interaction databases for integration with manually reconstructed signaling network models
Oct 26, 2022
Ratio-based quantitative multiomics profiling using universal reference materials empowers data integration
Oct 26, 2022
Representation and quantification Of Module Activity from omics data with rROMA
Oct 25, 2022
Functional Decomposition of Metabolism allows a system-level quantification of fluxes and protein allocation towards specific metabolic functions
Oct 24, 2022
Therapy Induced Tumor Senescence Model
Oct 24, 2022
Deep Reinforcement Learning for Stabilization of Large-scale Probabilistic Boolean Networks
Oct 24, 2022
Patient-specific deep offline artificial pancreas for blood glucose regulation in type 1 diabetes
Oct 24, 2022
The regulatory landscape of the yeast phosphoproteome
Oct 24, 2022
Predicting yield traits of individual field-grown Brassica napus plants from rosette-stage leaf gene expression
Oct 23, 2022
A quantitative model for the transcriptional landscape of the bacterial cell cycle
Oct 23, 2022
Macrophage phenotype transitions in a stochasticgene-regulatory network model
Oct 21, 2022
Global landscape of the host response to SARS-CoV-2 variants reveals viral evolutionary trajectories
Oct 21, 2022
Filtered finite state projection method for the analysis andestimation of stochastic biochemical reaction networks
Oct 21, 2022
Correcting batch effects in large-scale multiomic studies using a reference-material-based ratio method
Oct 21, 2022
Dynamic genome-based metabolic modeling of the predominant cellulolytic rumen bacterium Fibrobacter succinogenes S85
Oct 21, 2022
PMI estimation through metabolomics and potassium analysis on animal vitreous humour
Oct 21, 2022
Microscopic Imaging of Epigenetic Age
Oct 20, 2022
Damage dynamics in single E. coli and the role of chance in the timing of cell death
Oct 17, 2022
Functionally annotating cysteine disulfides and metal binding sites in the plant kingdom using AlphaFold2 predicted structures
Oct 17, 2022
Automatic mechanistic inference from large families of Boolean models generated by Monte Carlo Tree Search
Oct 17, 2022
Investigating the unique ability of Trichodesmium to fix carbon and nitrogen simultaneously using MiMoSA
Oct 17, 2022
Are under-studied proteins under-represented? How to fairly evaluate link prediction algorithms in network biology
Oct 17, 2022
Computational Speed-Up of Large-Scale, Single-Cell Model Simulations Via a Fully-Integrated SBML-Based Format
Oct 17, 2022
Predictive nonlinear modeling of malignant myelopoiesis and tyrosine kinase inhibitor therapy
Oct 14, 2022
Dynamic map illuminates Hippo to cMyc module crosstalk driving cardiomyocyte proliferation
Oct 14, 2022
An enhanced transcription factor repressilator that buffers stochasticity and entrains to an erratic external circadian signal
Oct 13, 2022
Identifying Essential Genes in Genome-Scale Metabolic Models of Consensus Molecular Subtypes of Colorectal Cancer
Oct 12, 2022
Signal integration by a bHLH circuit enables fate choice in neural stem cells
Oct 11, 2022
Disturbed trophoblast transition links preeclampsia progression from placenta to the maternal syndrome
Oct 11, 2022
Pytometry: Flow and mass cytometry analytics in Python
Oct 11, 2022
Mechanisms underlying divergent relationships between Ca2+ and YAP/TAZ signaling
Oct 07, 2022
Quantifying noise modulation from coupling of stochastic expression to cellular growth: An analytical approach
Oct 07, 2022
High selectivity of frequency induced transcriptional responses
Oct 07, 2022
Commitment in the Pink1/Parkin mitophagy decision circuit
Oct 07, 2022
Continuity between ancient geochemistry and modern metabolism enabled by non-autocatalytic purine biosynthesis
Oct 07, 2022
Novel Context-Specific Genome-Scale Modelling Explores the Potential of Chlamydomonas reinhardtii for Synthetic Biology Applications
Oct 07, 2022
Tuning of cytokine signaling through imbalanced abundances of receptors and kinases
Oct 07, 2022
Multi range ERK responses shape the proliferative trajectory of single cells following oncogene induced senescence
Oct 07, 2022
Integrative Multi-Omics Approaches for Identifying Cervical Cancer Therapeutic Targets
Oct 07, 2022
Predicting Anti-Cancer Drug Combination Responses with a Temporal Cell State Network Model
Oct 07, 2022
Dynamic trade-offs between biomass accumulation and division determine bacterial cell size and proteome in fluctuating nutrient environments
Oct 06, 2022
Machine learning on large-scale proteomics data identifies tissue- and cell type-specific proteins
Oct 05, 2022
Beyond BRCA: Discovery of novel causes and consequences of homologous recombination deficiencies
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
Oct 05, 2022
Suppression of Betacellulin expression is a key mechanism for omega-3 fatty acid mediated attenuation of nonalcoholic steatohepatitis
Oct 05, 2022
Minor intron containing genes: Achilles' heel of viruses?
Oct 04, 2022
Trafficking dynamics of VEGFR1, VEGFR2, and NRP1 in human endothelial cells
Oct 01, 2022
NHA1 is a cation/proton antiporter essential for the water-conserving functions of the rectal complex in Tribolium castaneum
Oct 01, 2022
Electrophile scanning by chemical proteomics reveals a potent pan-active DUB probe for investigation of deubiquitinase activity in live cells
Sep 30, 2022
Detecting and dissecting signaling crosstalk via the multilayer network integration of signaling and regulatory interactions
Sep 30, 2022
Comprehensive analysis of intercellular communication in thermogenic adipose niche
Sep 30, 2022
The trait coding rule in phenotype space
Sep 30, 2022
Multi-scale spatial modeling of immune cell distributions enables survival prediction in primary central nervous system lymphoma
Sep 28, 2022
The Quartet Data Portal: integration of community-wide resources for multiomics quality control
Sep 28, 2022
A Genome Scale Transcriptional Regulatory Model of the Human Placenta
Sep 28, 2022
A scalable screening platform for phenotypic subtyping of ALS patient-derived fibroblasts
Sep 28, 2022
Nature of epigenetic aging from a single-cell perspective
Sep 28, 2022
COVIDpro: Database for mining protein dysregulation in patients with COVID-19
Sep 28, 2022
Identifying Genes with Location Dependent Noise Variance in Spatial Transcriptomics Data
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
Sep 26, 2022
On biological networks capable of robust adaptation in the presence of uncertainties: A systems-theoretic approach
Sep 26, 2022
On the Geometry of Elementary Flux Modes
Sep 26, 2022
Transcriptomics data integration for context-specific modeling of Atlantic salmon metabolism: functional evaluation of methods based on metabolic tasks
Sep 24, 2022
Emergence of Supercoiling-Mediated Regulatory Networks through Bacterial Chromosome Rearrangements
Sep 23, 2022
Proteome dynamics during transition from exponential to stationary phase under aerobic and anaerobic conditions in yeast
Sep 23, 2022
A rapid protocol for ribosome profiling of low input samples
Sep 23, 2022
Comprehensive characterization of multi-omic landscapes between gut-microbiota metabolites and the G-protein-coupled receptors in Alzheimer's disease
Sep 22, 2022
Conserved coexpression at single cell resolution across primate brains
Sep 22, 2022
RNA degradation heavily impacts mRNA co-expression
Sep 22, 2022
Modeling Breast Cancer Proliferation, Drug Synergies, and Alternating Therapies
Sep 22, 2022
Multi-omics biomarkers aid prostate cancer prognostication
Sep 22, 2022
Alternative proteoforms and proteoform-dependent assemblies in humans and plants
Sep 22, 2022
Development of muti-agent-simulation models for intercellular communication via cytokines and extracellular matrices
Sep 22, 2022
From toxic waste to beneficial nutrient: acetate boosts Escherichia coli growth at low glycolytic flux
Sep 21, 2022
Temporally resolved kinase regulatory networks control endothelial barrier integrity
Sep 20, 2022
Evaluating proteome allocation of Saccharomyces cerevisiae phenotypes with resource balance analysis
Sep 20, 2022
PrePCI: A structure- and chemical similarity-informed database of predicted protein compound interactions
Sep 19, 2022
Secreted long non-coding RNAs Gadlor1 and Gadlor2 affect multiple cardiac cell types and aggravate cardiac remodeling during pressure overload
Sep 19, 2022
Microbial interactions impact the growth response of Clostridioides difficile to antibiotics
Sep 18, 2022
Evaluating the Robustness of Connectivity Methods to Noise for In Silico Drug Repurposing Studies
Sep 17, 2022
Optimal energy and redox metabolism in the cyanobacterium Synechocystis sp. PCC 6803
Sep 17, 2022
The magnitude of sex differences in host-microbe interactions are time-of-day dependent
Sep 17, 2022