Discover, rate, and discuss biology preprints.

InVitroGap is an open-source tool for automated quantification of wound closure in scratch assays, showing strong agreement with commercial software.

ComplexDesign is a method for designing multichain protein complexes by optimizing sequences to fold proteins and form inter-chain interactions, achieving high success rates in designing dimers, trimers, and tetramers.

SEMFA infers the statistical significance of Mahalanobis similarity between multi-omics samples using multiple factor analysis, showing effectiveness in both Gaussian and non-Gaussian scenarios.

The paper trains a supervised VAE on bulk RNA-seq data to learn a unified tissue-aware representation, achieving high tissue classification accuracy and demonstrating the impact of dataset scale.

The paper introduces effect size-based methods to rank transcription factor binding motifs, showing they outperform p-value rankings under heterogeneous sample sizes.

This paper introduces NT-ABDiff, a diffusion model for antibody sequence-structure design that improves CDR recovery and structural accuracy using noisy and unreliable templates.

V3Cell predicts organoid responses to chemical perturbations using non-invasive bright-field microscopy, creating virtual 3D cell models that mimic real organoids in structure and developmental dynamics.

EnrichViz provides an interactive R Shiny tool for visualizing pathway enrichment results from omics data without requiring coding.

This study benchmarks tumor-naive ctDNA detection and quantification methods using WGS and methylation data from cancer patients, identifying performance trade-offs and optimal integration strategies.

trAIt uses large language models to retrieve species traits from scientific literature, achieving 47.1% accuracy in a case study, though expert curation remains more accurate.

fastQpick generates bootstrap replicates of FASTQ reads for uncertainty quantification in sequencing data.

Navigo models mouse embryogenesis to predict cell fates and disease by learning developmental trajectories from scRNA-seq data.

This paper introduces SIMBA, a transformer-based model that learns interpretable structural similarity from tandem mass spectra to improve small molecule analog discovery.

SPIRAL curates RNA-small molecule structures and identifies binding modes and predictors of affinity, aiding RNA-targeted therapeutic design.

The paper evaluates peptide-MHC generalization to unseen alleles and introduces a benchmark and model that improves prediction accuracy for rare HLA alleles.

HoloCell is a generative foundation model that integrates epigenomics, transcriptomics, and proteomics data across single-cell multi-omics modalities, demonstrating superior performance in representation learning and cross-modal generation.

This paper compares output-head designs for predicting diabetes and myocardial infarction complications, finding that symmetric CRF outperformed others in diabetes but no single method dominated in myocardial infarction.

FateLimit quantifies when future cell identities become predictable from current molecular states across multiple developmental systems.

OmniCell integrates single-cell and spatial transcriptomics to model tissue context, revealing how gene programs operate in different anatomical environments.

biomeStat automates genomic epidemiology analysis of 1,000 Dengue virus genomes, revealing immune escape sites and conserved drug targets in under 24 hours.