Single-Islet Proteomics Maps Pseudo-Temporal Islet Immune Responses and Dysfunction in Stage 1 Type 1 Diabetes https://www.biorxiv.org/content/10.1101/2025.11.10.687674v1

Systematic structural and functional analysis of metal-binding sites in native proteomes https://www.biorxiv.org/content/10.1101/2025.11.10.687516v1

A Quantitative Design Guideline for Biomolecular Positive Feedback Systems https://www.biorxiv.org/content/10.1101/2025.11.09.687517v1

Computational Cellular Programming: In Silico Modeling of Direct and Reprogrammed Hepatic Lineage Induction via Gene Regulatory and Functional Dynamics https://www.biorxiv.org/content/10.1101/2025.11.09.687523v1

Scalable imaging-based profiling of CRISPR perturbations with protein barcodes https://www.biorxiv.org/content/10.1101/2025.11.11.687767v1

Androgen receptor activation stabilizes a hybrid epithelial/mesenchymal phenotype in presence of Notch-Jagged signaling https://www.biorxiv.org/content/10.1101/2025.11.09.687414v1

Ecological and Stochastic Determinants of the Growth and Persistence of the Oral Pathogen Porphyromonas gingivalis https://www.biorxiv.org/content/10.1101/2025.11.08.687400v1

Beyond synthetic lethality in large-scale metabolic and regulatory network models via genetic minimal intervention sets https://www.biorxiv.org/content/10.1101/2025.11.07.687323v1

Integrated Cross-Organ Transcriptomic Analysis Uncovers Conserved Gene Signatures Predictive of Allograft Rejection https://www.biorxiv.org/content/10.1101/2025.11.07.687316v1

A Deep Learning Framework for Quantifying Dynamic Self-Organization in Myxococcus xanthus https://www.biorxiv.org/content/10.1101/2025.11.07.686839v1

Attractors are less stable than their basins: Canalization creates a coherence gap in gene regulatory networks https://www.biorxiv.org/content/10.1101/2025.11.06.687062v1

Cell state plasticity emerging from co-regulated, competitive, and configurable interactions within the AP-1 network https://www.biorxiv.org/content/10.1101/2025.11.06.686987v1

The TEAIV model: Extending the standard TEIV model to account for viral budding ramp up https://www.biorxiv.org/content/10.1101/2025.11.07.687137v1

Collective parameter estimation of related models with an initial stability constraint https://www.biorxiv.org/content/10.1101/2025.11.07.684636v1

Multi-cohort, cross-species urinary proteomics reveals signatures of LRRK2 dysfunction in Parkinsons disease https://www.biorxiv.org/content/10.1101/2025.11.06.686787v1

Coupling mathematical modeling with a novel human intestinal stem cell system to understand feedback regulation during planar cell polarity https://www.biorxiv.org/content/10.1101/2025.11.05.686808v1

Integration of Hematopoietic and Thymus-like Niches in a Human iPSC-derived Bone Marrow Organoid https://www.biorxiv.org/content/10.1101/2025.11.04.686649v1

Bootstrap-based criteria for identifying differences between learned Bayesian networks https://www.biorxiv.org/content/10.1101/2025.11.04.686685v1

Integrated control of redox and energy metabolism by the membrane-bound and soluble transhydrogenases of Pseudomonas putida across metabolic regimes https://www.biorxiv.org/content/10.1101/2025.11.04.686620v1

Harnessing Interpretable Deep Learning to Predict Meropenem Resistance in Klebsiella pneumoniae https://www.biorxiv.org/content/10.1101/2025.11.04.686393v1

Inferring absolute counts from proportions by constraining multivariate normal distributions https://www.biorxiv.org/content/10.1101/2025.11.04.686543v1

BudFinder: A Masked Auto-Encoder Vision Transformer Framework for Yeast Budding Detection https://www.biorxiv.org/content/10.1101/2025.11.04.686463v1

Predicting strain-specific metabolic capabilities in the Genus Pseudomonas using a Flux-to-AI approach unravels hidden cell envelope properties. https://www.biorxiv.org/content/10.1101/2025.11.04.686459v1

CycleVI: Isolating cell cycle variation with an interpretable deep generative model https://www.biorxiv.org/content/10.1101/2025.11.04.686009v1

End-to-end high-throughput single-cell proteomics via SPRINT and dual-spray LC-MS https://www.biorxiv.org/content/10.1101/2025.11.03.686420v1

M4 drug discovery: human drug predictions from integrated pre-clinical insights exemplified with a GLP1-R agonist https://www.biorxiv.org/content/10.1101/2025.11.03.686224v1

Neuronal subtype-specific metabolic changes in neurodegenerative and neuropsychiatric diseases predicted via a systems biology-based approach https://www.biorxiv.org/content/10.1101/2025.11.03.686281v1

Phenotypic heterogeneity in lag reflects an evolutionarily stable bet-hedging strategy https://www.biorxiv.org/content/10.1101/2025.11.02.686100v1

Data-driven model reveals increased stability of CAG-expanded huntingtin RNA due to MID1 binding https://www.biorxiv.org/content/10.1101/2025.10.31.685889v1

Revisiting graph-based approaches for small protein analysis: Insights from anti-CRISPR protein networks https://www.biorxiv.org/content/10.1101/2025.10.31.685784v1

Glycolytic ATP production enables rapid mammalian cell growth https://www.biorxiv.org/content/10.1101/2025.10.30.685682v1

Decay in transcriptional information flow is a hallmark of cellular aging https://www.biorxiv.org/content/10.1101/2025.10.30.685689v1

STAT1 -- p53 Dynamics Program Cell Fate through p21 and PUMA https://www.biorxiv.org/content/10.1101/2025.10.28.685172v1

An Improved Systematic Method for Constructing ecGEMs using a Protein-Chemical Transformer https://www.biorxiv.org/content/10.1101/2025.10.29.684458v1

Integrative Network Analysis Reveals Organizational Principles of the Endocannabinoid System https://www.biorxiv.org/content/10.1101/2025.10.28.685143v1

Comparing Kinetic versus Stoichiometric Priorities in Hybrid Models of CHO Metabolism https://www.biorxiv.org/content/10.1101/2025.10.28.685134v1

Personalised whole-body modelling links gut microbiota to metabolic perturbations in Alzheimer's disease https://www.biorxiv.org/content/10.1101/2025.10.28.685084v1

Integrated tissue proteomics and lipidomics from ovine organs suggests novel functional implications for fatty acids and lipid mediators. https://www.biorxiv.org/content/10.1101/2025.10.28.685055v1

Elucidating a potential role of the infant gut microbiome on the bioavailability of L-tyrosine in phenylketonuria https://www.biorxiv.org/content/10.1101/2025.10.28.685037v1

Genome-scale metabolic model guided metabolic flux analysis in the endophyte Alternaria burnsii NCIM1409 https://www.biorxiv.org/content/10.1101/2025.10.28.685040v1

A structured evaluation and benchmarking of Boolean logical modelling tools https://www.biorxiv.org/content/10.1101/2025.10.28.684998v1

SPIN: Inkjet-Driven Nanowell Workflow for Scalable and Sensitive Single-Cell Proteomics https://www.biorxiv.org/content/10.1101/2025.10.27.684859v1

Sex differences in thyroid aging and their implications in thyroid disorders: insights from gene regulatory networks https://www.biorxiv.org/content/10.1101/2025.10.27.684890v1

Systems modeling of mitochondrial dynamics in different exercise regimes https://www.biorxiv.org/content/10.1101/2025.10.27.684912v1

Quantum Algorithm for Metabolic Network Analysis https://www.biorxiv.org/content/10.1101/2025.10.26.684702v1

Multiplexed embryo profiling links cellular state to zygotic genome activation in single cells https://www.biorxiv.org/content/10.1101/2025.10.27.684723v1

Unraveling the Mechanistic Links Between Blood Pressure Regulation and Calcium-Magnesium Homeostasis: Insights into Hypertension, Hyperparathyroidism, and Mineral Disorders https://www.biorxiv.org/content/10.1101/2025.10.26.684662v1

Rapid Parameter Inference for Spatiotemporal Stochastic Biological Models using Neural Posterior Estimation https://www.biorxiv.org/content/10.1101/2025.10.26.684706v1

A phenotype-structured PDE framework for investigating the role of hypoxic memory on tumor invasion under cyclic hypoxia https://www.biorxiv.org/content/10.1101/2025.10.26.684650v1

Design principles underlying nearly-homeostatic biological networks https://www.biorxiv.org/content/10.1101/2025.10.23.683559v1