Discover, rate, and discuss biology preprints.

Wrap a genomic foundation model's inference methods once to score it on supervised and zero-shot GUE, VariantBenchmarks, BEND, TraitGym and ClinVar tasks; code is promised upon acceptance.

The paper presents two chromosome-scale assemblies of the Black bean aphid Aphis fabae using HiFi and Hi-C, revealing expanded UDP-glycosyltransferases linked to insecticide tolerance.

The paper identifies six novel immune-related genes in Nili-Ravi buffalo with selection signatures distinct from classical bovine tuberculosis candidate genes.

The paper reconstructs a transcript-resolved catalogue of human enhancer RNAs, identifies their splice junctions, and provides tools for further study.

This study identifies Bacteroides species as potential contributors to depression through metagenomic analysis of fecal samples, showing their association with nitric oxide synthesis and diagnostic accuracy.

This study uses phylogenomic and comparative genomic analyses of 104 Erwinia genomes to resolve evolutionary relationships, identify taxonomic inconsistencies, and uncover lineage-specific genomic features associated with virulence and ecological adaptation.

The paper describes the gene model for the DENR ortholog in Drosophila pseudoobscura using a specific gene annotation protocol.

The paper identifies a new transposable element, Tangerine, in the lichen fungus Xanthoria parietina, showing evidence of horizontal gene transfer and potential role in lichen genome evolution.

Open plastid orthogroup resource for algae: 496 named orthogroups from 893 genomes, 224 core profile hidden Markov models with calibrated cutoffs, alignments, predicted structures, 859-genome phylogeny, CheckM-compatible marker sets.

This paper presents the first chromosome-scale genome assembly of Colletotrichum cereale, revealing three large accessory chromosomes and a deeply structured genome with significant intraspecific divergence.

This paper introduces SCITO-Perturb-seq, a CRISPRa platform that maps surface protein regulation in CD4 T cells, finding 16% of activated genes alter surface protein expression.

The paper identifies chromosomal inversions in king scallops that contribute to genetic differentiation despite high gene flow, with associations to reproductive and physiological functions.

This study verifies nanopore sequencing for CRE surveillance by comparing it to routine diagnostics and determining required sequencing depths for various clinical tasks.

This study quantifies intrinsic dCas9-DNA recognition using TANGO, identifying key factors affecting gRNA performance and revealing new aspects of dCas9 specificity.

This study investigates genomic diversity of Bacillus anthracis in northern Tanzania using traditional and culture-free sequencing, finding high strain diversity and limited host-specific clustering.

This study identifies STRs associated with alternative splicing in human brain tissue and links some to disease-related GWAS signals.

Pan20, a Practical Haplotype Graph of 20 barley genomes, assigns sequences MorexV3 coordinates and imputes genotyping-by-sequencing (GBS) reads at 0.06% base-call error versus 0.32% for variant calling.

The paper introduces TIDEST, a framework that improves statistical inference in reconstructed spatial transcriptomes by correcting for prediction errors and spatial confounding, leading to more accurate biological interpretations.

This study uses spatial transcriptomics to analyze gene expression in heart transplant recipients during rejection, identifying distinct transcriptomic profiles associated with different rejection types and outcomes.

The paper presents a chromosome-level genome assembly of Thecaphora frezzii, the largest genome among true smut fungi, and compares it with 49 other smut fungi genomes to explore genomic traits and evolutionary adaptations.