Discover, rate, and discuss biology preprints.

DeConveil extends differential gene expression analysis to account for genome aneuploidy by integrating CNV data, improving gene classification and biomarker discovery in cancer.

WayFindR converts pathway data into graph structures to analyze feedback loops, revealing their underrepresentation in curated databases.

This study compares Seurat and Scanpy, finding significant differences in their scRNA-seq analysis outputs, comparable to low sequencing depth or cell coverage.

TransBind improves TF binding site prediction by integrating DNA sequences with protein embeddings, achieving higher accuracy and generalizability for new TFs.

SAPTICoN provides a no-code pipeline for analyzing single-cell transcriptomics data across diverse species and tissues with limited genomic annotation.

The paper identifies NMD escape through alternative intronic polyadenylation by analyzing GTEx data and demonstrates tissue-specific isoform switches in several genes.

BaGPipe automates bacterial GWAS workflows, improving efficiency and reproducibility by integrating preprocessing, analysis, and visualization in a scalable pipeline.

GYDE provides an open-source platform for bench scientists to access AI tools for protein design and drug discovery through a collaborative interface.

The paper introduces markeR, an R package for evaluating gene sets as phenotypic markers, and demonstrates its application to senescence-related gene sets across multiple datasets.

The paper explains why phylogenetic compression works well by introducing a formal framework and showing that Neighbor Joining achieves near-optimal compression under the Infinite Sites Model.

TattleTail identifies pyocin-encoding gene clusters in Pseudomonas aeruginosa genomes, distinguishing them from prophages by lacking canonical phage features.

SuperSurv provides a unified R package for building, evaluating, and interpreting ensemble survival models with right-censored data, using SHAP values and IPCW Brier risk for weighting.

ColabPCR improves PCR success by optimizing primer design and reducing off-target binding through BLASTn analysis and Primer3 integration.

SpNeigh analyzes spatial transcriptomics data to detect neighborhood effects and differential expression, revealing tissue interface populations and spatial gene patterns in mouse brain, human breast cancer, and liver.

MEIsensor detects and classifies mobile element insertions from long-read sequencing data, outperforming existing tools in accuracy and efficiency, especially for complex insertions.

The paper identifies two distinct mechanisms of autoimmunity: altered antigen processing exposing cryptic self-antigens and breakdown of tolerance toward normally presented self-antigens.

TSProm identifies tissue-specific gene regulatory elements by training specialized DNA models and using explainable AI to analyze promoter sequences in human tissues.

Myloasm improves metagenome assembly using long reads, recovering more complete contigs and resolving antibiotic resistance genes.

MetaPepticon automates the discovery of anticancer peptides from microbial genomes and metagenomes, identifying 79,587 novel candidates including 13,149 high-confidence, non-toxic peptides.

ProTact improves protein-protein interaction prediction using a geometric graph neural network with physics-informed constraints, outperforming existing methods on benchmark datasets.