Discover, rate, and discuss biology preprints.

The paper reanalyzes six mouse AD scRNA-seq datasets to identify a reproducible innate immune activation signature across studies.

YGEP provides a cloud platform for genomic evaluation and breeding in yaks, integrating pedigree reconstruction, genotype imputation, and genomic breeding value estimation with high accuracy.

The paper introduces a weighted pathway co-membership method for Reactome pathways, improving gene prioritization in cancer hallmarks by incorporating biological distances and hierarchical structure.

This paper introduces TIDGN, a deep learning method to encode protein dynamics into a transferable latent representation, achieving high AUROC in function prediction across different proteins.

CardamomOT improves gene regulatory network inference and trajectory reconstruction by integrating mechanistic models with optimal transport, using exact time labels and reducing hyperparameters.

The paper provides guidance on analyzing circular data in spatial omics, using case studies to illustrate key considerations and methods.

ASTRA enables zero-shot super-resolution of spatial transcriptomics across different capture geometries, improving accuracy and efficiency compared to existing methods.

STARIT converts spatial transcriptomics data into image tensors for deep learning analysis, enabling subcellular heterogeneity-based cell state identification.

This paper introduces Nagini3D, a 3D image segmentation method combining deep learning and active surfaces for improved shape analysis and consistency across 3D volumes.

The paper identifies improved hydroxymethylfurfural oxidases through iterative computational methods combining molecular simulation and machine learning.

The paper introduces pre-miRBench, a multispecies benchmark for pre-miRNA prediction, showing its model outperforms existing predictors in cross-species and cross-family tests.

PREpiBind evaluates ten protein representations for pMHC-II binding prediction across multiple datasets, showing varying performance depending on the task and evaluation method.

The paper develops likelihood ratios for forensic DNA mixtures from shotgun sequencing data, showing they can be unreliable and proposing a combined evidence score to improve accuracy.

PanRes is a curated database of antimicrobial resistance genes that uses structural clustering and HMMs to improve detection of resistance determinants in metagenomes.

The paper develops a proteomic aging clock using longitudinal plasma proteomics data to show that biological aging is dynamically influenced by modifiable risk factors.

HiFIseek identifies gene-specific enrichment of high-impact mutations in genomic regions associated with cancer and breast cancer risk SNPs, showing limited agreement across CRR-score combinations.

The paper characterizes cross-family conserved fragments, showing their structural and biophysical properties and their role in folding and stability.

The paper introduces digestome, a marker-gene panel for functional profiling of anaerobic digestion microbiomes, and benchmarks it against metagenome-assembled genomes and species representatives.

RGI-Toolkit enables controllable biomolecular structure prediction by integrating experimental restraints into diffusion models without retraining.