Discover, rate, and discuss biology preprints.

The paper identifies isomiR enrichment in extracellular vesicles and develops a model to link EVs to their cellular origins using miRNA and isomiR features.

The paper benchmarks normalization and differential expression methods for miRNA-seq using a realistic dataset, finding RPM normalization and edgeR perform best.

The paper identifies systematic regional bias in ChIP-seq data across multiple experiments and proposes metrics to improve data integration.

The paper introduces a de novo method for comparing RNA-seq data across species by analyzing protein domains rather than genes, and identifies species-specific domains in Selaginella species.

xNNPCD identifies regulators of programmed cell death by integrating CRISPR perturbation data with gene dependency profiles to predict therapeutic agents for apoptosis and ferroptosis.

The paper catalogs and analyzes CAZyme complements in Pectobacterium and Dickeya genomes, finding coevolution of CAZymes linked to host adaptation and tissue preference.

Figra enables publication-quality scientific visualization within Excel using ggplot2 via a WebAssembly-based add-in, eliminating the need for external software.

ClaroAI-Bench evaluates AI agents' ability to reproduce computational findings from biomedical papers by testing data findability, accessibility, code availability, environment reconstructability, and results reproducibility.

The paper fine-tunes a protein language model for PTM-site prediction and shows how model size, annotation depth, and modification chemistry affect PTM recognition.

This paper introduces REDIAL, an unsupervised framework to detect overparametrization in RNA language models, revealing inefficiencies and design flaws in current models.

MucOneUp generates MUC1-VNTR reference sequences and simulated sequencing reads to benchmark variant calling tools across platforms.

The paper quantifies amino acid side-chain insertion energetics in a POPC bilayer using unbiased molecular dynamics simulations and derives potentials of mean force to characterize bilayer partitioning.

StabCell integrates clustering and marker detection in scRNA-seq to improve robustness and reduce false positives by assessing stability across subsampled data.

The paper compares ARG detection pipelines and finds large discrepancies in reported ARG counts and composition across different habitats.

CardioSafe predicts blocker activity for cardiac ion channels using a multi-task neural network and identifies test-set contamination in existing benchmarks.

Dogcatcher2 improves detection of transcriptional readthrough and identifies Alu element enrichment in DoG regions across sequencing platforms.

SigBridgeR benchmarks phenotype-associated cell subpopulations across four cancer types using eight algorithms, providing standardized workflows and visualization tools for reproducible analysis.

This paper develops a pacemaker-driven human mini-heart using spatial multi-omics and stem-cell engineering to study cardiac conduction and drug discovery.

ProCAST is an R-based framework for analyzing protein corona proteomics data, enabling clustering, visualization, and functional interpretation of adsorbed proteins.

XtractPAV identifies presence-absence variations across genomes, showing improved precision and novel variation discovery compared to existing tools.