bioRxiv Subject Collection: Systems Biology
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This feed contains articles for bioRxiv Subject Collection "Systems Biology"
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Dynamic cancer dormancy and awakening emerge from tumor microenvironment feedback in a minimal theoretical model
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https://www.biorxiv.org/content/10.64898/2026.04.14.718509v1?rss=1
2026-04-17doi:10.64898/2026.04.14.718509Cold Spring Harbor Laboratory2026-04-17
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Serum protein profiling reveals hallmark-level aging trajectories and strain-specific resilience in CB6F1J and C57BL/6J male mice.
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https://www.biorxiv.org/content/10.64898/2026.04.14.718493v1?rss=1
2026-04-17doi:10.64898/2026.04.14.718493Cold Spring Harbor Laboratory2026-04-17
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Orchard management alters citrus root and rhizosphere microbiomes with functional consequences for plant performance
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https://www.biorxiv.org/content/10.64898/2026.04.14.717254v1?rss=1
2026-04-17doi:10.64898/2026.04.14.717254Cold Spring Harbor Laboratory2026-04-17
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SEC-seq reveals translation-focused metabolic strategies for high IgG productivity in clonal CHO cells
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https://www.biorxiv.org/content/10.64898/2026.04.14.718270v1?rss=1
2026-04-17doi:10.64898/2026.04.14.718270Cold Spring Harbor Laboratory2026-04-17
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A Modular Machine Learning Framework for Small-Molecule Drug Repurposing Based on Organ Permeability, Target Binding, and Biomarker Modulation
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https://www.biorxiv.org/content/10.64898/2026.04.14.718573v1?rss=1
2026-04-17doi:10.64898/2026.04.14.718573Cold Spring Harbor Laboratory2026-04-17
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Mapping kidney trait heritability to individual cells reals disease-specific remodeling of genetic risk architecture
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https://www.biorxiv.org/content/10.64898/2026.04.12.717976v1?rss=1
2026-04-16doi:10.64898/2026.04.12.717976Cold Spring Harbor Laboratory2026-04-16
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Opto-MDMi: a dual-lock optogenetic system for robust activation of endogenous p53
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https://www.biorxiv.org/content/10.64898/2026.04.13.718310v1?rss=1
2026-04-16doi:10.64898/2026.04.13.718310Cold Spring Harbor Laboratory2026-04-16
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EML4-ALK Fusion Rewires Transcriptomic, miRNA, and CAF-Associated Programs in Non-Small Cell Lung Cancer
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https://www.biorxiv.org/content/10.64898/2026.04.10.717853v1?rss=1
2026-04-16doi:10.64898/2026.04.10.717853Cold Spring Harbor Laboratory2026-04-16
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NovoGlyco: mapping protein glycosylation in prokaryotes
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https://www.biorxiv.org/content/10.64898/2026.04.15.718822v1?rss=1
2026-04-16doi:10.64898/2026.04.15.718822Cold Spring Harbor Laboratory2026-04-16
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Deep quantitative phosphoproteomics identifies non-canonical pH-sensitive yeast phosphorylation networks
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https://www.biorxiv.org/content/10.64898/2026.04.13.718172v1?rss=1
2026-04-15doi:10.64898/2026.04.13.718172Cold Spring Harbor Laboratory2026-04-15
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Tracing cell communication programs across conditions at single cell resolution with CCC-RISE
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https://www.biorxiv.org/content/10.64898/2026.04.14.718551v1?rss=1
2026-04-15doi:10.64898/2026.04.14.718551Cold Spring Harbor Laboratory2026-04-15
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Gene Expression Variability with Feedback Regulation Implemented via Protein-Dependent Cell Growth
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https://www.biorxiv.org/content/10.64898/2026.04.13.718123v1?rss=1
2026-04-15doi:10.64898/2026.04.13.718123Cold Spring Harbor Laboratory2026-04-15
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Targeting HIV at its core: A mathematical model for optimizing Tat Inhibitor-based therapies toward enhanced functional cure strategies
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https://www.biorxiv.org/content/10.64898/2026.04.13.718184v1?rss=1
1. Numerical simulations were performed to investigate therapy interactions, viral rebound following treatment interruption, and the impact of drug efficacy on viral set-points and latent reservoir dynamics.
To further explore therapy interactions, three-dimensional viral set-point surfaces and heat maps were generated to examine how combinations of infection inhibition, viral production inhibition, and transcriptional inhibition influence viral dynamics. The simulations reveal that Tat inhibition suppresses viral transcription, thereby reducing the transition of infected cells into productive infection and limiting viral propagation when combined with conventional ART mechanisms. The therapy parameter planes further demonstrate that strong transcriptional inhibition promotes the transition of infected cells into deep latency, supporting the emerging block-and-lock strategy for functional HIV cure. In addition, a three-dimensional eradication boundary surface and therapy cube were constructed to identify regions of parameter space where Re < 1, corresponding to successful viral control. These visualizations show that viral eradication is unlikely when therapies act independently but becomes achievable when multiple therapeutic mechanisms act simultaneously.
Overall, the results highlight the critical role of transcriptional inhibition through Tat-targeting therapies in complementing existing ART regimens. By simultaneously suppressing viral replication and promoting deep latency, Tat-based combination strategies may significantly reduce viral rebound and contribute to long-term functional control of HIV infection.
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iCNG99: a validated genome-scale metabolic model of Cryptococcus neoformans strain H99
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https://www.biorxiv.org/content/10.64898/2026.04.12.718001v1?rss=1
2026-04-15doi:10.64898/2026.04.12.718001Cold Spring Harbor Laboratory2026-04-15
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Equation-Based Integration of Flux Balance Analysis with Diffusion for Spatio-Temporal Simulation of Microbial Communities
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https://www.biorxiv.org/content/10.64898/2026.04.11.717857v1?rss=1
2026-04-14doi:10.64898/2026.04.11.717857Cold Spring Harbor Laboratory2026-04-14
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Hyperbolic stratification of protein intrinsic disorder and structure-mediated interactions in the human protein interactome
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https://www.biorxiv.org/content/10.64898/2026.04.10.717685v1?rss=1
2026-04-14doi:10.64898/2026.04.10.717685Cold Spring Harbor Laboratory2026-04-14
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Modeling and dissecting bidirectional feedback in gene-metabolite systems using the CausalFlux method
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https://www.biorxiv.org/content/10.64898/2026.04.10.717623v1?rss=1
2026-04-13doi:10.64898/2026.04.10.717623Cold Spring Harbor Laboratory2026-04-13
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Recently emerged Fusarium chemotypes reprogram wheat defence and detoxification networks during Fusarium head blight development
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https://www.biorxiv.org/content/10.64898/2026.04.09.717564v1?rss=1
2026-04-13doi:10.64898/2026.04.09.717564Cold Spring Harbor Laboratory2026-04-13
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Pushing the limits of SCP: bacSCP, a proof-of-concept study to investigate heterogeneity of bacteria by single cell proteomics.
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https://www.biorxiv.org/content/10.64898/2026.04.09.717485v1?rss=1
2026-04-13doi:10.64898/2026.04.09.717485Cold Spring Harbor Laboratory2026-04-13
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Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and Packages
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https://www.biorxiv.org/content/10.64898/2026.04.07.717118v1?rss=1
2026-04-10doi:10.64898/2026.04.07.717118Cold Spring Harbor Laboratory2026-04-10
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Cell-Type-Resolved Pseudobulk Classification Across Independent Cohorts Identifies Microglial PTPRG as a Transcriptional Hub in Alzheimer's Disease
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https://www.biorxiv.org/content/10.64898/2026.04.07.717029v1?rss=1
2026-04-10doi:10.64898/2026.04.07.717029Cold Spring Harbor Laboratory2026-04-10
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Rhythmic gene expression and behavioral plasticity in harvester and carpenter ants
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https://www.biorxiv.org/content/10.64898/2026.04.08.717309v1?rss=1
2026-04-10doi:10.64898/2026.04.08.717309Cold Spring Harbor Laboratory2026-04-10
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Interplay of the ribosome A and CAR sites
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https://www.biorxiv.org/content/10.64898/2026.04.07.714784v1?rss=1
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Nonlinear mixed-effect models and tailored parametrization schemes enables integration of single cell and bulk data
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https://www.biorxiv.org/content/10.64898/2026.04.06.716803v1?rss=1
2026-04-09doi:10.64898/2026.04.06.716803Cold Spring Harbor Laboratory2026-04-09
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Time-dependent memory of hypoxia exposure influences tumor invasion dynamics
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https://www.biorxiv.org/content/10.64898/2026.04.07.716866v1?rss=1
2026-04-09doi:10.64898/2026.04.07.716866Cold Spring Harbor Laboratory2026-04-09
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Improved inference of multiscale sequence statistics in generative protein models
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https://www.biorxiv.org/content/10.64898/2026.04.06.716859v1?rss=1
2026-04-09doi:10.64898/2026.04.06.716859Cold Spring Harbor Laboratory2026-04-09
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UQ-PhysiCell: An extensible Python framework for uncertainty quantification and model analysis in PhysiCell
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https://www.biorxiv.org/content/10.64898/2026.04.06.716692v1?rss=1
2026-04-08doi:10.64898/2026.04.06.716692Cold Spring Harbor Laboratory2026-04-08
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Quantification of domain-specific intrinsic capacity using mortality data
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https://www.biorxiv.org/content/10.64898/2026.04.06.714260v1?rss=1
2026-04-08doi:10.64898/2026.04.06.714260Cold Spring Harbor Laboratory2026-04-08
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An AI-Assisted Workflow for Reconstruction, Extension, and Calibration of Quantitative Systems Pharmacology Models.
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https://www.biorxiv.org/content/10.64898/2026.04.05.716273v1?rss=1
2026-04-07doi:10.64898/2026.04.05.716273Cold Spring Harbor Laboratory2026-04-07
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Kinome profiling allows examination and prediction of kinase inhibitor cardiotoxicity
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https://www.biorxiv.org/content/10.64898/2026.04.03.716310v1?rss=1
2026-04-07doi:10.64898/2026.04.03.716310Cold Spring Harbor Laboratory2026-04-07