Discover, rate, and discuss biology preprints.

The paper benchmarks full-length ITS metabarcoding across Illumina, PacBio, and Oxford Nanopore platforms using mock and soil communities, finding PacBio has the lowest error rate and recommends standard pipelines for biodiversity assessments.

ParaDISM improves read placement and variant calling accuracy in highly homologous genomic regions by reducing misalignment artifacts.

RANKOR ranks candidate drugs from transcriptomic signatures using a machine learning framework, outperforming existing methods in bulk and single-cell data.

This study uses multimodal single-cell analysis to identify transcription factor networks involved in T-cell aging.

geneML improves fungal gene prediction accuracy and recall using deep learning, outperforming existing tools and enabling faster, more comprehensive genome annotation.

This paper introduces a method to recover cell-type and systems architecture from bulk and single-cell RNA-seq data using spectral unfolding, revealing new gene expression signatures in human hair follicles.

GIRAFI improves sparse single-cell proteomics by imputing missing values and revealing cell states using graph-informed statistical learning, outperforming existing methods and recovering biological structure.

resLens improves antibiotic resistance gene detection by using genomic language models trained on curated datasets, outperforming reference-based methods in varied scenarios.

MirMachine 2 annotates microRNAs across thousands of animal genomes, revealing methodological biases in apparent microRNA absence.

The paper predicts gene-rare disease associations using a network-based algorithm to improve variant prioritization and guide functional validation.

DNAS-Bench evaluates Biosecurity Screening Software by testing its ability to detect malicious sequences in synthetic DNA, finding that simple sequence manipulations can bypass many systems.

This paper improves mRNA stability prediction by incorporating fine-scale structural metrics into a regression model, achieving better accuracy than existing methods.

DGAT imputes spatial protein expression from transcriptomics-only data, revealing cell states and tissue organization not visible from RNA alone.

This study characterizes age-related immune dynamics through multi-layer transcriptomic analysis, revealing non-linear transcriptional reprogramming and novel regulatory elements associated with immune aging.

This paper presents a framework for peptide identification using commercial nanopore sequencing platforms, achieving single-amino-acid resolution and reliable performance across sequencing runs.

The paper introduces BioRAG-DRAG, a local-first multimodal retrieval system for biomedical agents, combining neural retrieval, BLAST verification, and graph-based evidence packaging.

The paper introduces MolCodon, a codon-based molecular language that provides high-fidelity, interpretable, and alignment-compatible sequence representations for small molecules, outperforming existing methods in various tasks.

This study examines tissue-specific transcriptional responses to cold stress in Drosophila, finding distinct gene expression patterns across tissues.

sxLaep is a fast and accurate enzyme predictor for metagenomic sequences, achieving high accuracy and speed compared to existing tools.