bioRxiv Subject Collection: Systems Biology
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This feed contains articles for bioRxiv Subject Collection "Systems Biology"
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Supervised Learning of Phosphopeptide Sequence Constraints Enables Global Prediction of SH2 Domain Binding
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https://www.biorxiv.org/content/10.64898/2026.08.18.744962v1?rss=1
2026-08-19doi:10.64898/2026.08.18.744962Cold Spring Harbor Laboratory2026-08-19
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Evidence-constrained mechanistic synthesis for drug discovery
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https://www.biorxiv.org/content/10.64898/2026.08.17.745376v1?rss=1
2026-08-19doi:10.64898/2026.08.17.745376Cold Spring Harbor Laboratory2026-08-19
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Plantago lanceolata and Lolium perenne metabolite profiles, their impact on soil microbial community structures and soil biological nitrification inhibition.
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https://www.biorxiv.org/content/10.64898/2026.08.17.745343v1?rss=1
2026-08-18doi:10.64898/2026.08.17.745343Cold Spring Harbor Laboratory2026-08-18
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Circadian Oscillation Detection Analysis and Comparison (CODAC):a Multicriteria Method to Estimate and Compare Rhythmicity
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https://www.biorxiv.org/content/10.64898/2026.08.17.745071v1?rss=1
2026-08-18doi:10.64898/2026.08.17.745071Cold Spring Harbor Laboratory2026-08-18
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Small intestinal microbiota of undernourished women perturbs placentaldevelopment in mice
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https://www.biorxiv.org/content/10.64898/2026.08.17.745217v1?rss=1
2026-08-18doi:10.64898/2026.08.17.745217Cold Spring Harbor Laboratory2026-08-18
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Proteoform Barcode: An Intuitive Visualization Framework for Top-Down Proteomics
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https://www.biorxiv.org/content/10.64898/2026.08.17.745297v1?rss=1
2026-08-18doi:10.64898/2026.08.17.745297Cold Spring Harbor Laboratory2026-08-18
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Port of Protein-Protein Interactomes: An experiment-based protein-protein interactome database for rice
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https://www.biorxiv.org/content/10.64898/2026.08.16.744343v1?rss=1
2026-08-17doi:10.64898/2026.08.16.744343Cold Spring Harbor Laboratory2026-08-17
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A Structural Design Principle for Temperature Robustness in Biomolecular Circuits
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https://www.biorxiv.org/content/10.64898/2026.08.14.744825v1?rss=1
2026-08-17doi:10.64898/2026.08.14.744825Cold Spring Harbor Laboratory2026-08-17
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Integrated Clinical and Proteomic Precision Subgrouping for Severe Dengue Endotype Signature
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https://www.biorxiv.org/content/10.64898/2026.08.13.744720v1?rss=1
2026-08-17doi:10.64898/2026.08.13.744720Cold Spring Harbor Laboratory2026-08-17
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HI-JEPA: A World Model of Molecular Organization Learned from Measured Proximity
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https://www.biorxiv.org/content/10.64898/2026.08.14.744901v1?rss=1
2026-08-17doi:10.64898/2026.08.14.744901Cold Spring Harbor Laboratory2026-08-17
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Potential benefit of loss-of-function on bacterial fitness
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https://www.biorxiv.org/content/10.64898/2026.08.13.744710v1?rss=1
2026-08-15doi:10.64898/2026.08.13.744710Cold Spring Harbor Laboratory2026-08-15
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LIPOGRID: A HIGH-THROUGHPUT MULTI-OMICS PERTURBATION SCREEN DISSECTS THE GENETIC ARCHITECTURE OF LIPID METABOLISM
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https://www.biorxiv.org/content/10.64898/2026.08.12.744385v1?rss=1
2026-08-13doi:10.64898/2026.08.12.744385Cold Spring Harbor Laboratory2026-08-13
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Structural proteomics reveals a coagulation-complement accessibility signature of macrovascular invasion in hepatocellular carcinoma
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https://www.biorxiv.org/content/10.64898/2026.08.12.744566v1?rss=1
2026-08-13doi:10.64898/2026.08.12.744566Cold Spring Harbor Laboratory2026-08-13
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Metabolomic, lipidomic, and N-glycomic analyses of a human cell model of Krabbe disease reveal treatable deficits in glycosylation and serine-ceramide metabolism
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https://www.biorxiv.org/content/10.64898/2026.08.12.744295v1?rss=1
2026-08-13doi:10.64898/2026.08.12.744295Cold Spring Harbor Laboratory2026-08-13
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Differential routing of spectral light inputs separates circadian timing from energetic responsiveness
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https://www.biorxiv.org/content/10.64898/2026.08.07.743459v1?rss=1
2026-08-13doi:10.64898/2026.08.07.743459Cold Spring Harbor Laboratory2026-08-13
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A dysregulated stromal remodelling programme characterises prior anti-TNF failure in ulcerative colitis
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https://www.biorxiv.org/content/10.64898/2026.08.11.744139v1?rss=1
2026-08-12doi:10.64898/2026.08.11.744139Cold Spring Harbor Laboratory2026-08-12
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Decoding the role of microbial interspecies interactions on nitrogen fixation
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https://www.biorxiv.org/content/10.64898/2026.08.11.744197v1?rss=1
2026-08-12doi:10.64898/2026.08.11.744197Cold Spring Harbor Laboratory2026-08-12
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Cytokine interaction networks, not individual cytokines, drive anti-TNF response in Crohn's disease
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https://www.biorxiv.org/content/10.64898/2026.08.11.744137v1?rss=1
2026-08-11doi:10.64898/2026.08.11.744137Cold Spring Harbor Laboratory2026-08-11
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Solving High-Dimensional Population Balance Equations via Dynamics-Preserving Autoencoders
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https://www.biorxiv.org/content/10.64898/2026.08.09.743783v1?rss=1
2026-08-11doi:10.64898/2026.08.09.743783Cold Spring Harbor Laboratory2026-08-11
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Glucose repression of HXK1 is glucose flux-dependent via non-canonical regulation of Mig1
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https://www.biorxiv.org/content/10.64898/2026.08.09.743801v1?rss=1
2026-08-11doi:10.64898/2026.08.09.743801Cold Spring Harbor Laboratory2026-08-11
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Projection criteria and information risks forzero-dimensional biological dynamics across molecular,epidemic, and ecological systems
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https://www.biorxiv.org/content/10.64898/2026.08.05.743148v1?rss=1
2026-08-10doi:10.64898/2026.08.05.743148Cold Spring Harbor Laboratory2026-08-10
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Sample-specific protein-protein interaction networks inferred from transcriptomics and proteomics show high similarities
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https://www.biorxiv.org/content/10.64898/2026.08.09.743737v1?rss=1
2026-08-10doi:10.64898/2026.08.09.743737Cold Spring Harbor Laboratory2026-08-10
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Double Machine Learning with Multi-Gene Shared Backgroundfor Causal Inference in Single-Cell Data: Grouping Deviation Follows a Random Walk and the Accuracy-Compute Trade-Off
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https://www.biorxiv.org/content/10.64898/2026.08.08.743701v1?rss=1
2026-08-10doi:10.64898/2026.08.08.743701Cold Spring Harbor Laboratory2026-08-10
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LiverDCP: A Disease-Cell-Protein Framework for Multi-scale Modeling of Disease Biology
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https://www.biorxiv.org/content/10.64898/2026.08.07.743628v1?rss=1
2026-08-10doi:10.64898/2026.08.07.743628Cold Spring Harbor Laboratory2026-08-10
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scROMA: batch-aware pathway-activity inference and a ground-truth simulation framework for single-cell transcriptomics
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https://www.biorxiv.org/content/10.64898/2026.08.07.743516v1?rss=1
2026-08-10doi:10.64898/2026.08.07.743516Cold Spring Harbor Laboratory2026-08-10
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Improved Metabolic Flux Estimations through Compositional Data Analysis
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https://www.biorxiv.org/content/10.64898/2026.08.07.742769v1?rss=1
View larger version (34K):
org.highwire.dtl.DTLVardef@f8f1aborg.highwire.dtl.DTLVardef@1c22fccorg.highwire.dtl.DTLVardef@1d0118corg.highwire.dtl.DTLVardef@13012bf_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LINew compositional data approach improves metabolic flux estimation.
C_LIO_LIThis data transformation requires minimal changes to existing workflows.
C_LIO_LIThe new method reduced MSE of flux estimates by 42.6% in two examples tested.
C_LIO_LIThe confidence intervals of the estimated fluxes were substantially narrowed.
C_LIO_LIEstimation accuracy remained robust across a wide range of metabolic fluxes.
C_LI
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VariantFlux: A genotype-first modelling workflow for predicting the impact of genetic variations on human metabolism
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https://www.biorxiv.org/content/10.64898/2026.08.03.740213v1?rss=1
97% of models preserved baseline growth, indicating strong metabolic robustness. Yet individual genomes exhibited distinct flux-rewiring patterns, with frequent individual-specific gain-of-flux events and fewer shared loss-of-flux reactions. Limited ancestry clustering suggests metabolic responses are driven mainly by unique variant combinations. VariantFlux links human genomes to organ-level flux phenotypes, enabling precision medicine, pharmacogenomics, and disease risk prediction.
Conceptual advanceWe present VariantFlux, a genotype-first framework that integrates predicted variant effects directly into genome-scale metabolic networks to generate personalised, organ-specific flux phenotypes. Unlike association-based metabolomics studies, this bottom-up approach enables exploratory, mechanistic prediction of how naturally occurring genetic variation reshapes human metabolism.
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17α-Estradiol Confers Limited Protection Against APOE4 Phenotypes in Middle-Aged Female Mice
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https://www.biorxiv.org/content/10.64898/2026.08.06.743074v1?rss=1
2026-08-07doi:10.64898/2026.08.06.743074Cold Spring Harbor Laboratory2026-08-07
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A Spatiotemporal Atlas of Extranuclear Androgen Receptor Proximal Interaction Networks
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https://www.biorxiv.org/content/10.64898/2026.08.03.742469v1?rss=1
2026-08-06doi:10.64898/2026.08.03.742469Cold Spring Harbor Laboratory2026-08-06
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A Temporal Atlas of the Nuclear Androgen Receptor Proximal Interactome
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https://www.biorxiv.org/content/10.64898/2026.08.03.742470v1?rss=1
2026-08-06doi:10.64898/2026.08.03.742470Cold Spring Harbor Laboratory2026-08-06