Discover, rate, and discuss biology preprints.

PANDA analyzes targeted bisulfite amplicon sequencing data to assess methylation patterns and heterogeneity at the read level.

RKMR identifies predictive marker panels in spatial omics data using a scalable framework that integrates kernel modeling and spatial dependence.

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.

MIRCID improves drug mechanism modeling by integrating inferred hub miRNAs with gene expression and TF activity, showing better performance than TF activity alone.

The paper identifies the chromatoid body as a dynamic RNA sorting center in spermatogenesis, revealing its role in RNA surveillance and transcript regulation through sequence and structural features.

FourC identifies significant and differential contacts in 4C-seq data using a Bayesian model and Gaussian processes to address duplication and model spatial patterns.

The paper introduces REAL-SWIT, a generative framework for ultra-large virtual screening that efficiently explores chemical space by generating molecules with favorable docking scores.

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

The paper evaluates multi-view gene representations under a matched contract, showing condition-dependent fusion operator rankings across different view combinations and tasks.

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

The paper presents fifteen near T2T assemblies of Brazilian Fusarium graminearum isolates, revealing structural conservation and a core genome with implications for phenotypic variance.

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

The paper introduces baltic v1.0, a Python library for phylogenetic tree analysis and visualization, with new features for rooting, reticulate evolution, and composite figures.

The paper uses spatial transcriptomics to show that cardiac neural crest-derived glial cells are selectively lost in myocardial infarction, with metabolic failure and pyroptosis implicated as mechanisms.

The paper benchmarks uncertainty estimation and risk ranking in multi-task bioactivity prediction, introducing ICSR to improve reliability of kernel-based predictions.

The paper identifies artifacts in bacterial proteomes by analyzing cluster participation and protein length, finding that short proteins are often errors due to frame-shifts or termination codons.

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.

The paper introduces a new binary format and toolkit for efficient LC-MS data processing, enabling faster and more flexible feature detection.

DeepSCENIC uses transfer learning from sequence-to-function models to infer causal gene regulatory networks from single-cell multiome data.