Discover, rate, and discuss biology preprints.

CADD-SV v2.0 improves variant prioritization by integrating coordinate- and sequence-based features, outperforming previous versions and other tools for structural variant deleteriousness scoring.

SOAAR improves cell-cell interaction inference in spatial transcriptomics by accounting for spatial autocorrelation, reducing false positives and identifying consistent immune signatures in cancer patients.

pylimma provides a Python port of the R limma package for differential expression analysis, validated across multiple datasets and showing high numerical agreement.

PANORAMA predicts and compares biological systems across species using pangenome graphs, demonstrating effectiveness on Pseudomonas and Enterobacteriaceae genomes.

AtlasLens enables interactive exploration and analysis of large scRNA-seq datasets using metadata-driven filtering and downstream analysis tools.

The paper evaluates weight-locking techniques to prevent fine-tuning of genomic foundation models, finding that naive attacks fail but informed attacks can partially bypass the lock.

MAERM predicts enzyme-reaction matching relationships using a mixed-attention model, outperforming baselines and enabling enzyme design.

Ribo-LENS detects RNA small-molecule binding sites using a geometric deep-learning framework, outperforming existing methods and enabling efficient virtual screening.

InstaNovo-P improves phosphorylated peptide detection and site localization in phosphoproteomics by using a transformer-based model fine-tuned on phosphoproteomics data.

The paper introduces CyCLOPS, a framework to deconvolve cell cycle chromatin occupancy in yeast, revealing dynamic chromatin and transcription patterns at high resolution.

This study models actin-tropomyosin interfaces using computational docking to analyze how filament length and isoform identity affect actin affinity across species.

GenCore uses Locally Consistent Parsing to sketch and estimate genomic distances between closely related large genomes, successfully reconstructing simulated progression trees and recapitulating primate phylogeny.

synpact improves PacBio HiFi read mapping accuracy while reducing memory usage and increasing speed compared to existing mappers.

This paper benchmarks PTIm-mAb, an AI-driven antibody design platform, against eleven FDA-approved bispecific antibodies, showing improvements in developability metrics without compromising other factors.

This paper introduces a semantic triage pipeline for systematic reviews in mutational signature analysis, achieving higher precision than keyword-only and model-based baselines.

scJET generates full-gene single-cell expression matrices using a patch-based Transformer model, preserving global and local transcriptomic features.

The paper introduces FlaPro, a tool to profile the human gut flagellome, revealing TLR5-related changes in IBD patients.

The paper identifies bimodal protein expression patterns in cancer proteomics, revealing 2401 tumor-associated bimodal proteins and their associations with key cancer pathways, with implications for biomarker discovery and precision oncology.

This paper develops k-mer-based estimators for substitution, insertion, and deletion mutation rates, showing improved accuracy when accounting for indels in mutation models.