Discover, rate, and discuss biology preprints.

DNAharvester is a Nextflow pipeline designed to process highly degraded DNA from ancient specimens, improving authentic data recovery through modular workflows and contamination mitigation.

This study benchmarks Twist Genotyping-by-Sequencing against whole-genome sequencing in nuclear families, finding GxS slightly worse than GSA but still highly concordant with WGS.

StrainRefine improves strain-level metagenomic classification by refining read mappings using profile similarity, reducing false positives while maintaining accuracy.

CRISPR-VUS identifies rare variants linked to gene dependency in cancer cell lines, prioritizing potential drivers and therapeutic targets through functional validation.

The paper introduces viral_usher, a tool for scalable viral phylogenetics, and demonstrates that replication machinery explains most variance in viral mutation spectra.

SpectroVQ improves proteomics data compression and peptide identification by using a noise-aware vector-quantized autoencoder to retain useful signals and enhance library searches.

This paper compares chemical descriptors and deep learning embeddings for scoring de novo peptide designs, finding classical descriptors are effective and efficient for developability prediction.

Kintsugi improves spatial transcriptomics by letting data decide how much to borrow from neighbors and genes, showing it can identify epithelial programs and distinguish fibroblastic foci by composition rather than RNA amount.

CIDER detects gene regulatory network changes associated with continuous traits by modeling interactions between transcription factors and target genes, outperforming two-group methods in simulations and identifying trait-dependent regulatory relationships in human transcriptomes.

RAxML-NG 2.0 introduces new features for phylogenetic inference, including automatic model selection and faster branch support metrics, with significant speed improvements.

scOLAR annotates single-cell RNA-seq data using an ontology-guided framework to detect both known and novel cell types with high accuracy.

Merging CellAge, GenAge, SenMayo and Reactome senescence genes onto Ensembl IDs yields 1,250 provenance-tracked genes, most also annotated with mouse/zebrafish orthologs, tissue expression and STRING interactions.

BTEXgenie is a tool that uses profile HMMs to annotate BTEX degradation genes with higher sensitivity than existing methods, supporting pathway visualization and genomic analysis.

scPyviewer provides a Python-native interactive viewer for AnnData single-cell data, matching R Shiny tools' features and outperforming them in speed and memory efficiency.

The paper compares binding modes and thermodynamic properties of single domain and double domain antibodies using an integrated interface model.

Leverage-weighted sketching plus sparse spatial regularization deconvolves 1.6 million Visium HD bins in 153 seconds on commodity hardware, revealing tissue-specific resolution limits where cell-type co-localization can reverse sign.

The paper introduces a diploid genomic foundation model to represent diploid genotypes in genomic language models, improving variant discrimination in compound-heterozygous cases.

The paper presents a serverless cloud computing approach for scRNA-seq data processing, demonstrating significant speedup for large datasets.

MAP annotates mobilome elements and their functional cargo in prokaryotic (meta)genomic assemblies, enabling identification of composite elements like ARG-carrying integrons.

Geomosaic integrates read-, assembly-, and genome-resolved metagenomic analyses into a flexible, reproducible workflow for environmental studies.