bioRxiv SysBio
@biorxiv-sysbio.bsky.social
Characterizing spatial functional microniches with SpaceTravLR https://www.biorxiv.org/content/10.1101/2025.11.13.688264v1
November 15, 2025 at 1:03 AM
Characterizing spatial functional microniches with SpaceTravLR https://www.biorxiv.org/content/10.1101/2025.11.13.688264v1
Self-Organization Through Local Cell-Cell Communication Drives Intestinal Epithelial Zonation https://www.biorxiv.org/content/10.1101/2025.11.14.688372v1
November 14, 2025 at 10:02 PM
Self-Organization Through Local Cell-Cell Communication Drives Intestinal Epithelial Zonation https://www.biorxiv.org/content/10.1101/2025.11.14.688372v1
A Novel Prognostic Metric Resolves the MYCN enigma in Silico and Points to a Biosynthetic Regulatory Shift Driven by MYCN Amplification in Neuroblastoma https://www.biorxiv.org/content/10.1101/2025.11.13.688307v1
November 14, 2025 at 6:22 PM
A Novel Prognostic Metric Resolves the MYCN enigma in Silico and Points to a Biosynthetic Regulatory Shift Driven by MYCN Amplification in Neuroblastoma https://www.biorxiv.org/content/10.1101/2025.11.13.688307v1
Gut Microbiota-derived Adenosine Determines the Efficacy of Electroconvulsive Therapy for Depression https://www.biorxiv.org/content/10.1101/2025.11.13.688184v1
November 14, 2025 at 4:04 PM
Gut Microbiota-derived Adenosine Determines the Efficacy of Electroconvulsive Therapy for Depression https://www.biorxiv.org/content/10.1101/2025.11.13.688184v1
Analytical Solutions for the Time-Dependent Dynamics of Stochastic Gene Expression with mRNA-sRNA Interactions https://www.biorxiv.org/content/10.1101/2025.11.13.688103v1
November 14, 2025 at 4:04 PM
Analytical Solutions for the Time-Dependent Dynamics of Stochastic Gene Expression with mRNA-sRNA Interactions https://www.biorxiv.org/content/10.1101/2025.11.13.688103v1
Storing long-lived memories via molecular error correction: a minimal mathematical model of Crick's memory switch https://www.biorxiv.org/content/10.1101/2025.11.13.688304v1
November 14, 2025 at 8:08 AM
Storing long-lived memories via molecular error correction: a minimal mathematical model of Crick's memory switch https://www.biorxiv.org/content/10.1101/2025.11.13.688304v1
Microbial Cell-Adaptive Segmentation in Quantitative Phase Imaging https://www.biorxiv.org/content/10.1101/2025.11.13.688197v1
November 14, 2025 at 5:04 AM
Microbial Cell-Adaptive Segmentation in Quantitative Phase Imaging https://www.biorxiv.org/content/10.1101/2025.11.13.688197v1
Towards modeling in Large-Scale Genetic and Metabolic Networks https://www.biorxiv.org/content/10.1101/2025.11.11.687908v1
November 14, 2025 at 12:02 AM
Towards modeling in Large-Scale Genetic and Metabolic Networks https://www.biorxiv.org/content/10.1101/2025.11.11.687908v1
Using AI-MIDD for Mechanistic Erythropoietin Modeling: A Digital-Twin Framework for Optimizing ESA Therapies https://www.biorxiv.org/content/10.1101/2025.11.12.688044v1
November 13, 2025 at 10:07 PM
Using AI-MIDD for Mechanistic Erythropoietin Modeling: A Digital-Twin Framework for Optimizing ESA Therapies https://www.biorxiv.org/content/10.1101/2025.11.12.688044v1
Redefining Housekeeping Genes in the Context of Vertebrate Development https://www.biorxiv.org/content/10.1101/2025.11.12.687949v1
November 13, 2025 at 6:03 PM
Redefining Housekeeping Genes in the Context of Vertebrate Development https://www.biorxiv.org/content/10.1101/2025.11.12.687949v1
From plasmid sequence to process design: A computational analysis of metabolism in the context of plasmid DNA manufacturing https://www.biorxiv.org/content/10.1101/2025.11.12.687962v1
November 13, 2025 at 6:03 PM
From plasmid sequence to process design: A computational analysis of metabolism in the context of plasmid DNA manufacturing https://www.biorxiv.org/content/10.1101/2025.11.12.687962v1
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
November 12, 2025 at 8:05 PM
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
November 12, 2025 at 5:16 PM
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
November 11, 2025 at 10:18 PM
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
November 11, 2025 at 10:18 PM
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
November 11, 2025 at 6:05 PM
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
November 10, 2025 at 10:09 PM
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
November 10, 2025 at 10:09 PM
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
November 10, 2025 at 9:06 PM
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
November 10, 2025 at 4:08 AM
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
November 10, 2025 at 4:08 AM
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
November 8, 2025 at 4:09 PM
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
November 8, 2025 at 5:04 AM
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
November 8, 2025 at 2:04 AM
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
November 8, 2025 at 2:04 AM
Collective parameter estimation of related models with an initial stability constraint https://www.biorxiv.org/content/10.1101/2025.11.07.684636v1