Discover, rate, and discuss biology preprints.

This paper identifies hypoxia-related genes associated with prognosis in lung adenocarcinoma, finding DSG2, EIF6, and EXO1 as independent prognostic factors.

This study identifies protein domains under positive selection in tumor genomes, revealing convergent evolution in core cellular processes and regulatory functions.

This study compares age estimation models using DNA methylation data, finding that maximum likelihood estimation reduces bias compared to linear regression and random forest.

SpatioCell integrates histology and spatial transcriptomics to extract single-cell resolution cell type and expression information from ST data, revealing microenvironment features in triple negative breast cancer.

This paper develops AdventML, a model for predicting enzyme optimal temperature using transformer embeddings and resampling, achieving R2 ~0.64 and improved extreme temperature predictions.

AI-IDP predicts conformational ensembles of disordered proteins by combining deep learning with physical restraints, revealing common structural features across proteomes.

This study evaluates and improves low-frequency somatic mutation detection across multiple sequencing platforms using a simulated benchmark and a machine learning-based caller.

CodeCytos improves spatial molecular imaging analysis by enabling dynamic, programmable interaction with tissue data, outperforming baseline approaches in custom feature exploration.

CellClick is an interactive platform that improves cell type annotation accuracy in single-cell and spatial omics data through automated and user-guided tools.

QMAP evaluates antimicrobial peptide MIC and hemolytic activity prediction models using standardized, homology-constrained benchmarks, revealing limited progress and poor performance in high-potency predictions.

This paper introduces a top-down mass spectrometry workflow with DMTm technology and a new software platform to achieve deeper proteoform sequencing and improved sequence coverage.

The paper introduces the Reachability Preserving Minimum Edge Cut problem to model biological pathway interventions, showing when fast algorithms work and when exact methods are needed.

The paper introduces CCE, a framework to analyze transcriptomic coupling between intracellular compartments, revealing state transitions in single cells through information-geometric metrics.

This study identifies a Tinospora cordifolia compound as a potential inhibitor of ASFV B175L, restoring immune signaling through virtual screening and molecular dynamics.

The paper introduces SI-SimCLR, a self-supervised learning framework for reconstructing cellular phenotypic landscapes from microscopy data without segmentation or annotation, revealing substate organization and connections in astrocytes.

CpG Atlas integrates over 1.2 million CpG sites across multiple methylation arrays with 18 annotation layers and provides a query interface for epigenetic research.

This study compares the pangenome composition of ESBL-E. coli isolates from patients receiving selective digestive decontamination (SDD) and those receiving standard care, finding no major differences in overall pangenome but some antibiotic resistance gene associations.

The paper benchmarks variant calling tools in inbred mouse strains, finding tradeoffs between recall and precision and recommending ensemble approaches for optimal results.

sstar2 improves S*-based introgression detection by using quantile regression for better threshold calibration and compatibility with modern simulations.

The paper introduces two Bioconductor packages for multi-state QTL analysis, providing tools for data storage, analysis, and simulation.