Discover, rate, and discuss biology preprints.

BRIDGE prioritizes human-mouse gene correspondences using functional and disease evidence to improve gene selection for disease modeling and drug screening.

SpaNECT is a framework for characterizing cell niches from spatial multimodal and multi-omics data, outperforming existing methods in diverse biological contexts.

GatorDuo improves spatial domain identification in spatial transcriptomics by refining dual graphs with pseudo-label agreement and adaptive clustering.

RedNet improves protein binder design by incorporating side-chain information and contrastive decoding to enhance binding affinity, folding stability, and selectivity.

HAIRpred2 predicts antibody-interacting residues in human antigens using structural features, achieving an AUC of 0.78 on an independent test set.

This paper evaluates an extended data schema for integrating multi-assay entomological data across field, insectary, and lab workflows, achieving high-fidelity sample tracing and data linkage.

tugMedi simulates cancer-cell evolution using patient genomic data to predict drug responses and tumor dynamics.

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.