cfDNAanalyzer: a comprehensive toolkit for analyzing cell-free DNA genomic sequencing data in liquid biopsy biorxiv.org/content/10.110… #biorxiv_bioinfo

AbDesign: Database of point mutants of antibodies with associated structures reveals poor generalization of binding predictions from ... biorxiv.org/content/10.110… #biorxiv_bioinfo

Uncovering Functional Gene Regulatory Networks in Bulk and Single-Cell Data through Robust Transcription Factor Activity Estimation ... biorxiv.org/content/10.110… #biorxiv_bioinfo

HiFIseek: gene-specific enrichment of high-impact mutations in associated genomic regions biorxiv.org/content/10.110… #biorxiv_bioinfo

MitoDelta: identifying mitochondrial DNA deletions at cell-type resolution from single-cell RNA sequencing data biorxiv.org/content/10.110… #biorxiv_bioinfo

All-Atom Protein Sequence Design using Discrete Diffusion Models biorxiv.org/content/10.110… #biorxiv_bioinfo

Gene and cell line efficiency of CRISPR computed by tensor decomposition in genome-wide CRISPR-Cas9 knockout screens biorxiv.org/content/10.110… #biorxiv_bioinfo

Intratumoral heterogeneity in microsatellite instability status at single cell resolution biorxiv.org/content/10.110… #biorxiv_bioinfo

MLMarker: A machine learning framework for tissue inference and biomarker discovery biorxiv.org/content/10.110… #biorxiv_bioinfo

Simulating Iron Deficiency in Plant Plastids With a Flexible Physics-Informed Neural Network Approach biorxiv.org/content/10.110… #biorxiv_bioinfo

PHLAME: A benchmark for continuous evaluation of host phenotype prediction from shotgun metagenomic data biorxiv.org/content/10.110… #biorxiv_bioinfo

Unraveling cooperative and competitive interactions within protein triplets in the human interactome biorxiv.org/content/10.110… #biorxiv_bioinfo

A Functional Atlas of the Tardigrade Resistome Reveals a Diverse Molecular Toolkit for Extremotolerance biorxiv.org/content/10.110… #biorxiv_bioinfo

Applying Self-Supervised Tissue Patch Encoders to Enable Cellular Graph Encoding biorxiv.org/content/10.110… #biorxiv_bioinfo

Fetal sex is associated with the maternal gut microbiota composition and its metabolic function biorxiv.org/content/10.110… #biorxiv_bioinfo

CLUES2 Companion: Computational pipelines to estimate, visualize, and date selection on multi-locus sites biorxiv.org/content/10.110… #biorxiv_bioinfo

D-CoMEx: A Unified Approach to Identify Phenotype-specific miRNA Biomarkers Related to Diseases biorxiv.org/content/10.110… #biorxiv_bioinfo

ChemOrigins: A community curated database for origins of life chemistry biorxiv.org/content/10.110… #biorxiv_bioinfo

Protocol for GDT, Gene Dictionary Tool, to create and implement a gene dictionary across annotated genomes biorxiv.org/content/10.110… #biorxiv_bioinfo

S3Mirror: Making Genomic Data Transfers Fast, Reliable, and Observable with DBOS biorxiv.org/content/10.110… #biorxiv_bioinfo