bioRxiv: Bioinformatics Preprints

MetaHarmonizer: robust biomedical metadata harmonization and a contamination control for inflated LLM performance on public benchmarks

biorxiv.org·

Posterior-calibrated multimodal motor states reveal longitudinal and imaging-associated heterogeneity in Parkinson's disease

biorxiv.org·

Correcting spatial transcriptomics data affected by a prevalent transcript leakage problem across platforms, species, and tissues

biorxiv.org·

In silico characterization of lysis and host-recognition modules in Staphylococcus aureus bacteriophage genomes

biorxiv.org·

An Integrated Framework for Transcriptomic Characterization and Lorentzian Hyperbolic Visualization of a High-Risk Topological Branch in Alzheimer's Disease

biorxiv.org·

Beyond phylogeny: Genome-wide DNA sequence patterns suggest DNA physical properties associated with thermal adaptation in extremophile microbes

biorxiv.org·

AutoZyme: An Autonomous Agentic Framework to Optimize Bioinformatics Software

biorxiv.org·

Phylogenetic tree inference using generative models

biorxiv.org·

DMcloud: Macromolecular Structure Modeling Using Local Structure Fitting for Medium to Low Resolution cryo-EM maps

biorxiv.org·

Orion: Towards Lab Automation with Computer-Using Agents

biorxiv.org·

Programmatic access to ICTV virus taxonomy through a public ontology API

biorxiv.org·

Evidence for recombination in dengue virus genomes

biorxiv.org·

Integrative Transfer Network: Deep Transfer Learning Across Populations and Prediction Targets

biorxiv.org·

cuBayes: GPU accelerated FreeBayes that achieves 1-minute whole-genome SNV calling while maintaining algorithmic semantics

biorxiv.org·

FlowBench: separating planning, fault recovery and interpretation in agentic bioinformatics

biorxiv.org·

Better data, better trees: GenBank-GISAID deduplication and source-specific artifact masking in viral genomics

biorxiv.org·

DNA-binding specificity recognition from predicted homologous protein-DNA structures

DesignMaster: A Multi-Conditional Diffusion Framework for Rational PROTAC Design

AMaNITA: an end-to-end workflow for native tRNA nanopore sequencing data analysis

MetaHarmonizer: robust biomedical metadata harmonization and a contamination control for inflated LLM performance on public benchmarks

Posterior-calibrated multimodal motor states reveal longitudinal and imaging-associated heterogeneity in Parkinson's disease

Correcting spatial transcriptomics data affected by a prevalent transcript leakage problem across platforms, species, and tissues

In silico characterization of lysis and host-recognition modules in Staphylococcus aureus bacteriophage genomes

An Integrated Framework for Transcriptomic Characterization and Lorentzian Hyperbolic Visualization of a High-Risk Topological Branch in Alzheimer's Disease

Beyond phylogeny: Genome-wide DNA sequence patterns suggest DNA physical properties associated with thermal adaptation in extremophile microbes

AutoZyme: An Autonomous Agentic Framework to Optimize Bioinformatics Software

Phylogenetic tree inference using generative models

DMcloud: Macromolecular Structure Modeling Using Local Structure Fitting for Medium to Low Resolution cryo-EM maps

Orion: Towards Lab Automation with Computer-Using Agents

Programmatic access to ICTV virus taxonomy through a public ontology API

Evidence for recombination in dengue virus genomes

Integrative Transfer Network: Deep Transfer Learning Across Populations and Prediction Targets

cuBayes: GPU accelerated FreeBayes that achieves 1-minute whole-genome SNV calling while maintaining algorithmic semantics

FlowBench: separating planning, fault recovery and interpretation in agentic bioinformatics

Better data, better trees: GenBank-GISAID deduplication and source-specific artifact masking in viral genomics

RetroMol: Parsing a shared encoding from natural products and their biosynthetic gene clusters