bioRxiv Subject Collection: Systems Biology https://biorxiv.org This feed contains articles for bioRxiv Subject Collection "Systems Biology" bioRxiv bioRxiv https://www.biorxiv.org/sites/default/files/bioRxiv_article.jpg https://www.biorxiv.org <![CDATA[ A kinetic-aware approach to infer metabolic variations and flux using transcriptomics and metabolomics data ]]> https://www.biorxiv.org/content/10.64898/2026.09.27.754711v1?rss=1 2026-10-02 doi:10.64898/2026.09.27.754711 Cold Spring Harbor Laboratory 2026-10-02 <![CDATA[ Multi-omics profiling identifies a metabolic and energetic signature associated with neuronal dENL/AF9 suppression in aged flies ]]> https://www.biorxiv.org/content/10.64898/2026.09.30.755827v1?rss=1 2026-10-02 doi:10.64898/2026.09.30.755827 Cold Spring Harbor Laboratory 2026-10-02 <![CDATA[ A global signature of microbiome resilience to climate stress ]]> https://www.biorxiv.org/content/10.64898/2026.09.30.755659v1?rss=1 2026-10-02 doi:10.64898/2026.09.30.755659 Cold Spring Harbor Laboratory 2026-10-02 <![CDATA[ Integrating CSF and EV Proteomes Enhances Biomarker Discovery by Capturing Shared Variation Across Compartments ]]> https://www.biorxiv.org/content/10.64898/2026.09.30.754912v1?rss=1 2026-10-02 doi:10.64898/2026.09.30.754912 Cold Spring Harbor Laboratory 2026-10-02 <![CDATA[ Population reweighting and reporter distortion obscure ribosome regulation during translation inhibition ]]> https://www.biorxiv.org/content/10.64898/2026.09.30.755718v1?rss=1 2026-10-02 doi:10.64898/2026.09.30.755718 Cold Spring Harbor Laboratory 2026-10-02 <![CDATA[ Dynamical stability and accuracy of moment closure approximations for bursty gene expression with nonlinear degradation ]]> https://www.biorxiv.org/content/10.64898/2026.09.30.755644v1?rss=1 2026-10-01 doi:10.64898/2026.09.30.755644 Cold Spring Harbor Laboratory 2026-10-01 <![CDATA[ From seven combination hypotheses to one testable interaction: a gated agentic AI QSP workflow applied to healthy ageing interventions ]]> https://www.biorxiv.org/content/10.64898/2026.09.29.755460v1?rss=1 2026-10-01 doi:10.64898/2026.09.29.755460 Cold Spring Harbor Laboratory 2026-10-01 <![CDATA[ The Metabolic Organ Clock: A Computable Framework Linking Cell-Lineage Architecture to Emergent Organ Bioenergetics ]]> https://www.biorxiv.org/content/10.64898/2026.09.29.755490v1?rss=1 2026-09-30 doi:10.64898/2026.09.29.755490 Cold Spring Harbor Laboratory 2026-09-30 <![CDATA[ Stress-recovery dynamics reveal a separatrix in transcriptomic landscapes across organs and aging ]]> https://www.biorxiv.org/content/10.64898/2026.09.29.755524v1?rss=1 2026-09-30 doi:10.64898/2026.09.29.755524 Cold Spring Harbor Laboratory 2026-09-30 <![CDATA[ A mechanistic, mortality-referenced biological age from routine blood tests: construction and temporal validation of IQN-BIOAGE-01 ]]> https://www.biorxiv.org/content/10.64898/2026.09.29.755448v1?rss=1 2026-09-30 doi:10.64898/2026.09.29.755448 Cold Spring Harbor Laboratory 2026-09-30 <![CDATA[ Cyclic uremia without kidney injury drives cardiovascular disease with rapid onset of immunosenescence and heart failure ]]> https://www.biorxiv.org/content/10.64898/2026.09.29.755324v1?rss=1 2026-09-30 doi:10.64898/2026.09.29.755324 Cold Spring Harbor Laboratory 2026-09-30 <![CDATA[ Reducing growth-medium complexity reveals nutrient-responsive programs in a near-minimal bacterium ]]> https://www.biorxiv.org/content/10.64898/2026.09.29.755377v1?rss=1 2026-09-30 doi:10.64898/2026.09.29.755377 Cold Spring Harbor Laboratory 2026-09-30 <![CDATA[ A Reduced Mechanistic Model for Aquatic Decomposition of a Human Body ]]> https://www.biorxiv.org/content/10.64898/2026.09.29.755382v1?rss=1 2026-09-30 doi:10.64898/2026.09.29.755382 Cold Spring Harbor Laboratory 2026-09-30 <![CDATA[ Mapping a genome-scale in vivo knockout screen to a mechanistic network model identifies VAV2, RASA1, and LEPR as regulators of cardiomyocyte hypertrophy ]]> https://www.biorxiv.org/content/10.64898/2026.09.24.754086v1?rss=1 2026-09-29 doi:10.64898/2026.09.24.754086 Cold Spring Harbor Laboratory 2026-09-29 <![CDATA[ Proteomic comparison of Marburg and Kasokero virus infection in natural host Egyptian rousette bat reveals distinct antiviral pathways ]]> https://www.biorxiv.org/content/10.64898/2026.09.28.755161v1?rss=1 2026-09-29 doi:10.64898/2026.09.28.755161 Cold Spring Harbor Laboratory 2026-09-29 <![CDATA[ SpaReg: sparsity-based 3D reconstruction of tissue microenvironments at native resolution across morphological and spatial molecular modalities ]]> https://www.biorxiv.org/content/10.64898/2026.09.28.754175v1?rss=1 2026-09-29 doi:10.64898/2026.09.28.754175 Cold Spring Harbor Laboratory 2026-09-29 <![CDATA[ TxCyto: A machine learning framework for estimating cytokine activity from whole transcriptome ]]> https://www.biorxiv.org/content/10.64898/2026.09.28.754405v1?rss=1 2026-09-29 doi:10.64898/2026.09.28.754405 Cold Spring Harbor Laboratory 2026-09-29 <![CDATA[ Integrative proteomic analysis and molecular dynamics simulations of ANKLE2 reveal mechanisms of microcephaly ]]> https://www.biorxiv.org/content/10.64898/2026.09.28.755110v1?rss=1 2026-09-29 doi:10.64898/2026.09.28.755110 Cold Spring Harbor Laboratory 2026-09-29 <![CDATA[ Interpretable machine learning coupled to gene regulatory networks uncovers subcircuits underlying cell fate decisions ]]> https://www.biorxiv.org/content/10.64898/2026.09.28.754797v1?rss=1 2026-09-29 doi:10.64898/2026.09.28.754797 Cold Spring Harbor Laboratory 2026-09-29 <![CDATA[ Comprehensive in silico analysis reveals candidate regulatory mechanisms underlying selective cerebellar vulnerability in pontocerebellar hypoplasia ]]> https://www.biorxiv.org/content/10.64898/2026.09.28.754951v1?rss=1 2026-09-29 doi:10.64898/2026.09.28.754951 Cold Spring Harbor Laboratory 2026-09-29 <![CDATA[ Quantifying Chemical Fluxes Underlying Gut Microbiota-Host Interactions ]]> https://www.biorxiv.org/content/10.64898/2026.09.27.754802v1?rss=1 2026-09-28 doi:10.64898/2026.09.27.754802 Cold Spring Harbor Laboratory 2026-09-28 <![CDATA[ GEMOT: Towards Mechanistic World Models for Biology ]]> https://www.biorxiv.org/content/10.64898/2026.09.26.754619v1?rss=1 2026-09-28 doi:10.64898/2026.09.26.754619 Cold Spring Harbor Laboratory 2026-09-28 <![CDATA[ Quantitative machine learning of protein interactions reveals the multiscale organization and molecular syntax of signaling networks ]]> https://www.biorxiv.org/content/10.64898/2026.09.25.754499v1?rss=1 2026-09-28 doi:10.64898/2026.09.25.754499 Cold Spring Harbor Laboratory 2026-09-28 <![CDATA[ A thermoregulatory design principle for transitions into hypometabolism ]]> https://www.biorxiv.org/content/10.64898/2026.09.25.754297v1?rss=1 2026-09-28 doi:10.64898/2026.09.25.754297 Cold Spring Harbor Laboratory 2026-09-28 <![CDATA[ Accessing Enzyme Kinetic Data and Prediction Methods at Scale ]]> https://www.biorxiv.org/content/10.64898/2026.09.25.751968v1?rss=1 2026-09-28 doi:10.64898/2026.09.25.751968 Cold Spring Harbor Laboratory 2026-09-28 <![CDATA[ Limit-pushing overexpression reveals constraints on protein abundance ]]> https://www.biorxiv.org/content/10.64898/2026.09.24.754258v1?rss=1 2026-09-28 doi:10.64898/2026.09.24.754258 Cold Spring Harbor Laboratory 2026-09-28 <![CDATA[ Concentration limits and localization of hydrogen peroxide in the extracellular space of solid tissues ]]> https://www.biorxiv.org/content/10.64898/2026.09.23.753516v1?rss=1 2026-09-25 doi:10.64898/2026.09.23.753516 Cold Spring Harbor Laboratory 2026-09-25 <![CDATA[ PyKappa: Rule-based modeling in Python ]]> https://www.biorxiv.org/content/10.64898/2026.09.18.752660v1?rss=1 2026-09-24 doi:10.64898/2026.09.18.752660 Cold Spring Harbor Laboratory 2026-09-24 <![CDATA[ Chaperone isoform and interactome mapping reveals functional diversification of DNAJA2-DNAJA4 complexes via stress-regulated isoforms ]]> https://www.biorxiv.org/content/10.64898/2026.09.23.753896v1?rss=1 2026-09-24 doi:10.64898/2026.09.23.753896 Cold Spring Harbor Laboratory 2026-09-24 <![CDATA[ Age-Related Remodeling of Cross-Tissue Transcriptional Coordination in the Human Motor System ]]> https://www.biorxiv.org/content/10.64898/2026.09.21.753254v1?rss=1 2026-09-24 doi:10.64898/2026.09.21.753254 Cold Spring Harbor Laboratory 2026-09-24