bioRxiv: Bioinformatics Preprints · Scour

Housekeeping Gene Expression Normalization in Transcriptomics Mitigates Data Leakage in Machine Learning Models

MVCBench: A Multimodal Benchmark for Drug-induced Virtual Cell Phenotypes

RNABag: A Generalizable Transcriptome Foundation Model for Precision Oncology across Biopsy Modalities

HMCVelo: A Deterministic Model for Hydroxymethylation Velocity in Single Cells

PEACE: Prototype-aware Effector Analysis via Contrastive Embeddings

Systematic Benchmarking of Kinase Bioactivity Models Across Splitting Strategies and Protein Representations

Mechanotransduction-Aware Causal Omics on Tissue Scaffolds: A Controlled Mechanochemical Framework for Identifying Disease Genes Beyond Pure Omics Analysis

SPaCeD: Spatial Point Process Distances for Pairing the Heavy and Light Chains of B Cell Receptors from Spatial BCR-seq

Structure-aware graph attention based hierarchical transformer framework for drug-target binding affinity prediction

BioEngine: scalable execution and adaptation of bioimage AI through agent-readable interfaces

Scalable, Generalizable, and Uncertainty-Aware Integration of Spatial Multi-Omics Across Diverse Modalities and Platforms with SCIGMA

Human-supervised Agentic AI for Hypothesis Generation and Experimental Assistance in Drug Repurposing

Protein inverse folding through joint modeling of surface and backbone geometry

CHORD: a framework for cross-species single-cell integration across gene, cell and cell-type levels

Agent-Guided Ranking Policy Improvement for Peptide Drug Candidate Prioritization

A Unified Agent-Enabled Platform for Drug Repurposing across Molecular, Phenotypic, and Clinical Scales

Network-based integration of cross-dataset proteomic profiles using fold-change directionality

Expanding P-NET, a multi-purpose biologically informed deep learning framework

GeomMotif: A Benchmark for Arbitrary Geometric Preservation in Protein Generation

Comparative benchmarking of single-cell transcriptomes and immune repertoires across technologies

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