bioRxiv: Bioinformatics Preprints · Scour

Integrated Multi-Omics Analysis for the Identification of Disease-Associated Variations and Prognostic Biomarkers in Triple-Negative Breast Cancer (TNBC)

Mitag4taxa: Extracting SSU rRNA Illumina reads from metagenomes for taxonomic classification

Learning the Language of the Microbiome with Transformers

Pharmacological proximities in the GPCR family discovered using contact-informed amino-acid and binding pocket similarities

PhenotypeToGeneDownloaderR: automated multi-source retrieval and validation of phenotype-associated genes

STAT: A multi-agent framework for integrated and interactive spatial transcriptomics analysis

Functional diversity across families of bacterial metalloregulators: what can we learn about specificity from sequence similarity?

Fast and Ultra-Capable Protein Design: Advancing the Frontier Through Atomistic SE(3)-Equivariance with Genie 3

First Survey of Publicly Available Metagenomic Sequencing Data Across 24 Middle Eastern and North African Countries: The MENA Microbiome Database

Tumor cell specific total mRNA expression informed neural networks predicts cancer progression

ArchaicSeeker 3.0: A deep-learning framework for scalable, haplotype-resolved inference of archaic introgression

Simple baselines rival protein language models in mutation-dense design tasks

Uncertainty-aware localization microscopy by variational diffusion

An LLM-driven pipeline for proteomics-based detection and structural modeling of post-translational modifications

MilliMap: interactive closed-loop analysis for spatial omics

UNKAI: A protein functional identity prediction model based on ESM-C latent representations and the attention mechanism

Bridging LLM Reasoning and Chemical Knowledge via an Evolutionary Multi-Agent Framework for Molecular Synthesis

Building computational benchmarks: an Omnibenchmark reimplementation of a single-cell preprocessing pipeline evaluation

DOMINO: Learning Domain Co-occurrence for Multidomain Protein Design

immuneKG: An Immune-Cell-Aware Knowledge Graph Framework for Target Discovery in Immune-Mediated Diseases

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