bioRxiv: Bioinformatics Preprints

Probabilistic coupling of cellular and microenvironmental heterogeneity by masked self-supervised learning

biorxiv.org·

Improving AlphaFold3 by Engineering MSA and Template Inputs

biorxiv.org·

PanVariants: Best Practice for Pangenome-based Variant Calling Pipeline and Framework

biorxiv.org·

Structural variation shapes regulatory and evolutionary diversity at the HLA locus

biorxiv.org·

Additive baselines furnish no evidence for epistasis learning by MULTI-evolve

biorxiv.org·

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

biorxiv.org·

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

biorxiv.org·

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

biorxiv.org·

HMCVelo: A Deterministic Model for Hydroxymethylation Velocity in Single Cells

biorxiv.org·

PEACE: Prototype-aware Effector Analysis via Contrastive Embeddings

biorxiv.org·

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

biorxiv.org·

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

biorxiv.org·

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

biorxiv.org·

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

biorxiv.org·

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

biorxiv.org·

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

biorxiv.org·

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

biorxiv.org·

AutoRNAseq: Automated Bulk RNA-seq Analysis Pipeline

scConcept enables concept-level exploration of single-cell transcriptomic data

Probabilistic coupling of cellular and microenvironmental heterogeneity by masked self-supervised learning

Improving AlphaFold3 by Engineering MSA and Template Inputs

PanVariants: Best Practice for Pangenome-based Variant Calling Pipeline and Framework

Structural variation shapes regulatory and evolutionary diversity at the HLA locus

Additive baselines furnish no evidence for epistasis learning by MULTI-evolve

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