Discover, rate, and discuss biology preprints.

PyiTOL provides reproducible Python workflows for iTOL annotation and taxonomic monophyly assessment, with accurate results on benchmark datasets.

Web resource offering predicted monomeric and oligomeric structures for 1,603 M. leprae proteins, with pockets, epitope scores, essentiality and a target priority ranking, plus a nanopore resistance-calling module.

Prot2Surf analyzes and predicts protein-surface binding modes by calculating key features like distances and orientations, enabling efficient characterization of interaction patterns.

fastCNV predicts copy number variations from spatial transcriptomics and scRNA-seq data, showing high accuracy and speed improvements over existing methods.

FuncSeek improves enzyme function prediction by using contrastive learning with multiple PLMs, outperforming existing methods on benchmark datasets.

nf_xpatial provides a standardized Nextflow pipeline for preprocessing and clustering Xenium spatial transcriptomics data, enabling reproducible analysis and parameter comparison.

FOCUS-3D segments cells in 3D fluorescence microscopy data across species and tissues, revealing phases of notochord morphogenesis in zebrafish.

Hi-Cformer models multi-scale chromatin contact maps from single-cell Hi-C data, improving cell type separation and imputation of 3D genome features.

This paper shows that ignoring gene-gene interactions in GWAS can lead to false positive results, highlighting the need for more complex models.

The paper tests if SMILES can be fragmented into ordered blocks for retrosynthetic analysis, finding that it improves physico-chemical property reproduction but degrades LLM performance.

scProtoTransformer provides a scalable reference mapping framework across molecular, cellular, and donor levels using a prototype-based Transformer model with improved interpretability and performance.

The paper shows label noise limits TCR-pMHC specificity prediction and improves performance using AlphaFold3 and denoising.

The paper introduces TOB-QMC, a method for scalable and accurate tree of blobs reconstruction under network multispecies coalescent, improving upon TINNiK in both speed and accuracy.

OmicsFM is a proteomics foundation model that matches transcriptomic models in performance, revealing complementary biology between proteomics and transcriptomics.

This paper develops a deep learning framework to infer gene expression from cell-free DNA, improving reliability and enabling functional genomics in precision oncology.

FigTreeKit provides a Python toolkit for programmatically styling and auditing phylogenetic trees, with scalability testing on large bacterial and archaeal datasets.

The paper evaluates how different model architectures, LD filtering thresholds, and variant prioritization methods affect gene-level eQTL score prediction quality using over 3 million models.

This study surveys public awareness of the gut-brain axis and compares microbial dysbiosis in depression, anxiety, schizophrenia, and ASD using the Disbiome database.

InsilicoCell predicts cellular functional profiles and enables multi-objective virtual drug screening by integrating diverse molecular data and tasks.

The paper introduces morphOTU, a framework using phenotypic data to create operational biodiversity units, achieving diversity estimates comparable to expert identifications.