High-throughput cell-free profiling of SARS-CoV-2 RBD variants enables rapid and quantitative in vitro affinity landscape mapping https://www.biorxiv.org/content/10.1101/2025.09.23.678000v1

scPortrait integrates single-cell images into multimodal modeling https://www.biorxiv.org/content/10.1101/2025.09.22.677590v1

Designing signaling environments to modulate neural progenitor cell differentiation with regulatory network models https://www.biorxiv.org/content/10.1101/2025.09.20.677552v1

Ultrasensitive proteomics uncovers nociceptor diversity and novel pain targets https://www.biorxiv.org/content/10.1101/2025.09.20.677124v1

Interpretable biophysical neural networks of transcriptional activation domains separate roles of protein abundance and coactivator binding https://www.biorxiv.org/content/10.1101/2025.09.19.677413v1

Deciphering Global Patterns of Marine Microbial Community Assembly and Network Stability https://www.biorxiv.org/content/10.1101/2025.09.19.677047v1

Dynamic Gene Regulatory Network Inference with Interpretable, Biophysically-Motivated Neural ODEs https://www.biorxiv.org/content/10.1101/2025.09.19.676870v1

Partially-functional exhausted CD8+ T cells can contribute to short-term viral suppression: a computational prediction for children with perinatal HIV https://www.biorxiv.org/content/10.1101/2025.09.18.677001v1

Cryo-mtscATAC-seq for single-cell mitochondrial DNA genotyping and clonal tracing in archived human tissues https://www.biorxiv.org/content/10.1101/2025.09.17.675534v1

Revealing Transcriptomic Responses in Escherichia coli During Early Antibiotic Exposure https://www.biorxiv.org/content/10.1101/2025.09.17.676618v1

Principles of protein abundance regulation across single cells in a mammalian tissue https://www.biorxiv.org/content/10.1101/2025.09.17.676955v1

Integrative Analysis of Left Ventricle and Epicardial Adipose Tissue Identifies SDHA and OGDH as Candidate Targets for Ischemic Heart Disease https://www.biorxiv.org/content/10.1101/2025.09.17.676232v1

Personalized Metabolite Biomarker Predictions Reveal Heterogeneous Characteristics of Parkinson's Disease https://www.biorxiv.org/content/10.1101/2025.09.16.676636v1

Autofluorescence-based Label-free Cell Counting Method in Suspension Culture with Microcarriers https://www.biorxiv.org/content/10.1101/2025.09.16.676704v1

Systems-level feedback loops maintain gene expression homeostasis following RNA polymerase II dosage perturbation https://www.biorxiv.org/content/10.1101/2025.09.18.677100v1

Tissue-level division of labor is coordinated across organs through universal programs and context-specific adaptations https://www.biorxiv.org/content/10.1101/2025.09.16.676484v1

Rethinking the Estrogen Receptor Beta Dominance Hypothesis in Endometriosis: Insights from Single Cell RNA Sequencing Meta-analysis https://www.biorxiv.org/content/10.1101/2025.09.15.676330v1

Generative semantic multiplexing (SemaPlex) for accessible and scalable multiplexed fluorescence imaging https://www.biorxiv.org/content/10.1101/2025.09.15.676186v1

Mathematical modeling for primitive form of habituation in an amoeba https://www.biorxiv.org/content/10.1101/2025.09.15.675989v1

Inverse modeling unveils governing law of mechano-chemical dynamics of epithelial migration https://www.biorxiv.org/content/10.1101/2025.09.17.676715v1

Mistranslating tRNA variants impact the proteome and phosphoproteome of Saccharomyces cerevisiae https://www.biorxiv.org/content/10.1101/2025.09.15.676438v1

Control of a Bi-Stable Genetic System via Parallelized Reinforcement Learning https://www.biorxiv.org/content/10.1101/2025.09.14.676149v1

Integrative Spatial Omics for Systems-Level Mapping of Pathological Niches https://www.biorxiv.org/content/10.1101/2025.09.12.675904v1

Exploring the multifactorial causes and therapeutic strategies for anabolic resistance in sarcopenia: A systems modeling study https://www.biorxiv.org/content/10.1101/2025.09.12.675977v1

Application of evolutionary algorithms to optimization of Boolean models in biomedicine https://www.biorxiv.org/content/10.1101/2025.09.12.675817v1

METABOLOMIC SIGNATURES OF EXTREME OLD AGE: FINDINGS FROM THE NEW ENGLAND CENTENARIAN STUDY https://www.biorxiv.org/content/10.1101/2025.09.10.675341v1

Double-CRISPR Knockout Simulation (DKOsim): A Monte-Carlo Randomization System to Model Cell Growth Behavior and Infer the Optimal Library Design for Growth-Based Double Knockout Screens https://www.biorxiv.org/content/10.1101/2025.09.11.675497v1

Modification of RNAs in natural rG4 (MoRNiNG), A Database of RNA Modification Sites Associated with the Dynamics of RNA Secondary Structures https://www.biorxiv.org/content/10.1101/2025.09.11.675469v1

Systematic Mapping of Protein Interactions Underlying IL-2 Secretion in Human T Cells https://www.biorxiv.org/content/10.1101/2025.09.09.675165v1

Computational Approaches in Chemical Space Exploration for Carbon Fixation Pathways https://www.biorxiv.org/content/10.1101/2025.09.13.671265v1

The SjD Map: An interactive pathway tour into Sjogren's disease signalling mechanisms https://www.biorxiv.org/content/10.1101/2025.09.08.674876v1

Proteomics profiling of serum and liver in GSD Ia and Ib patients: insights into complication mechanisms and circulation biomarkers https://www.biorxiv.org/content/10.1101/2025.09.08.674441v1

Integrative Thermodynamics Strategies in Microbial Metabolism https://www.biorxiv.org/content/10.1101/2025.09.09.672066v1

Guided multi-agent AI invents highly accurate, uncertainty-aware transcriptomic aging clocks https://www.biorxiv.org/content/10.1101/2025.09.08.674588v1

Proliferation to suppress neoplasia: a general model and a first test in the moon jelly https://www.biorxiv.org/content/10.1101/2025.09.07.674745v1

Climatic Influence on COVID-19: Investigating the Role of Temperature and Humidity in the Spread of the Omicron Variant https://www.biorxiv.org/content/10.1101/2025.09.11.675496v1

Ribosome biogenesis mediates the translational increase of non-optimal codon transcripts during IFN stimulation https://www.biorxiv.org/content/10.1101/2025.09.05.673799v1

Multiblock Integration and Modeling of Localized Microbiome, Metabolome, and Clinical Metadata to Identify Biomarkers Predictive of Outcome in Veterans with Non-Healing Wounds https://www.biorxiv.org/content/10.1101/2025.09.07.674782v1

Subcellular mRNA localization patterns across tissues resolved with spatial transcriptomics https://www.biorxiv.org/content/10.1101/2025.09.07.674688v1

Translating clinical gene sequencing into a foundational representation of tumor subtype https://www.biorxiv.org/content/10.1101/2025.09.08.674723v1

Universal principles of protein resource allocation among cellular organelles revealed by yeast large-scale absolute quantitative proteomics https://www.biorxiv.org/content/10.1101/2025.09.04.674116v1

A dominant role of cell death in limiting Chandipura virus propagation at cell-saturating high multiplicity of infection https://www.biorxiv.org/content/10.1101/2025.09.04.673995v1

Proteomic Signatures of Hepatitis B Virus Mutations Reveal Genotype-Specific Host Responses and Biomarker Candidates https://www.biorxiv.org/content/10.1101/2025.09.04.674240v1

Biomarker Discovery via Integrative Multi-omics for Children exposed to Humidifier Disinfectant https://www.biorxiv.org/content/10.1101/2025.09.04.674118v1

TurboID proximity interactome mapping reveals NR2E3 association with AP-1 and retinal developmental complexes https://www.biorxiv.org/content/10.1101/2025.09.04.674188v1

Decoupling between activation time and steady-state level in input-output responses https://www.biorxiv.org/content/10.1101/2025.09.03.673941v1

Modeling and Tracking of Heterogeneous Cell Populations via Open Multi-Agent Systems https://www.biorxiv.org/content/10.1101/2025.09.02.673711v1

BOGO: A Proteome-Wide Gene Overexpression Platform for Discovering Rational Cancer Combination Therapies https://www.biorxiv.org/content/10.1101/2025.09.02.673780v1

Genome-scale modeling reveals regulation of human metabolism by the histone deacetylase SIRT1 https://www.biorxiv.org/content/10.1101/2025.09.03.673976v1

Differences between in vivo and ex vivo hematopoietic model systems modulate the outcomes of genetic perturbations. https://www.biorxiv.org/content/10.1101/2025.09.02.673692v1