Discover, rate, and discuss biology preprints.

Crumblr is a statistical method for analyzing changes in cell type composition across studies, showing increased power over existing methods in simulations and applied to multiple single-cell RNA-seq datasets.

AptViralDB is a manually curated database of 1,768 experimentally validated antiviral aptamers against 40 viruses and 104 targets, offering annotations, predicted structures, and search tools.

The paper compares single-cell and aggregated morphological profiling to identify programmed cell death mechanisms, finding aggregated data performs better in supervised models.

This paper introduces Leff, a spectral measure to quantify effective information in multiple sequence alignments, showing evolutionary constraints reduce sequence diversity in RNA and proteins.

This study uses spatial transcriptomics and snRNA-seq to identify 25 forebrain regions and characterize dynamic changes in the human fetal cortex and striatum during late first and early second trimesters.

This paper proposes a structurally constrained message-passing framework for brain decoding on small datasets, achieving competitive performance while maintaining interpretability.

DesignMaster improves PROTAC design by incorporating linker length and physicochemical constraints through a diffusion framework, achieving better validity and recovery than existing methods.

OT-knn aligns spatial transcriptomics data by integrating local neighborhood information within an optimal transport framework, achieving accurate alignment across diverse datasets and conditions.

EZSolver predicts polar enzymatic mechanisms without templates using flow matching and beam search, achieving 60% accuracy on unseen reactions.

ViTAMIn-O is an open DL model for organoid differentiation prediction, outperforming existing models and adaptable to various datasets and imaging modalities.

Songbird is a single cell whole genome sequencing copy number caller that detects whole genome duplication and outperforms existing tools in breakpoints identification and true copy number detection.

This paper introduces a counterfactual explanation algorithm for graph neural networks to explain patient outcome predictions in patient similarity networks.

SVPG improves structural variant detection using pangenome references and accelerates pangenome graph construction from long-read data.

Precomputed PPanGGOLiN pangenomes for over 4,600 prokaryotic species (Genome Taxonomy Database clusters), with plasticity regions and modules, downloadable via web, API and command line for projection onto new genomes.

Poly Pipeline is a spatial transcriptomics workflow validated across polyploid and diploid organisms, demonstrating effectiveness in clustering and co-expression network analysis.

This paper introduces a machine learning framework to classify phylogenetic patterns in interkingdom horizontal gene transfer, achieving high accuracy and outperforming existing methods.

The paper introduces decemedip, a Bayesian hierarchical model for cell type deconvolution of MeDIP-seq data, showing its accuracy and utility in identifying methylation signatures.

The paper classifies archaeal proteomes at the domain level, revealing that structural diversity is conserved across archaea and that unclassified proteins are due to classification limitations, not structural novelty.

LazypipeX improves virus discovery in mNGS data by offering customizable and efficient annotation strategies that reduce execution time while maintaining accuracy.

fDOG-Assembly identifies orthologs in unannotated genomes, outperforming traditional methods by not relying on pre-annotated proteomes and recovering missed orthologs.