Discover, rate, and discuss biology preprints.

This study maps somatic mutations in B-cell subsets of SLE patients, finding high mutational burden in double-negative B cells linked to disease duration and therapy.

GT-Trio assembles haplotypes without parental sequencing by using genotype data, achieving high phasing accuracy and improved haplotype resolution.

This study uses scRNA-seq and immunophenotyping to analyze immune changes in RA patients on MTX, showing early restoration of naive T/B cells and reduced memory T cells, with plasmablasts as a potential biomarker.

The paper uses a novel 'liquidity' metric to analyze gene expression trajectories across lifespan, revealing delayed maturation and perinatal GABA switch in schizophrenia risk without detectable neuropathology.

The paper evaluates splicing models, identifies performance gaps, and introduces a cell-type-specific model for improved splice site prediction in human airway epithelial cells.

The paper introduces a pan-cell type chromatin state annotation that integrates all IHEC epigenomes using the epigenome-ssm method, avoiding cell type-specific annotations.

The paper analyzes CRISPR-Cas9 off-target mutations and translocations at single-cell and tissue-specific levels in mice, revealing context-dependent variability in editing outcomes.

This study recovers an 18th-century rhinovirus genome from ancient RNA isolated from human lung specimens, revealing insights into viral evolution.

The paper updates the RERconverge package with faster algorithms and new analysis features for studying convergent evolution at the genomic level.

The paper introduces circVDJ-seq for efficient T cell receptor profiling from single-cell and spatial multi-omics data, revealing distinct immune microenvironments and T cell clonality patterns in various clinical contexts.

The paper validates long-read sequencing methods for analyzing repeat expansions in DM2, identifying new repeat motifs and improving bioinformatic workflows.

CellBouncer demultiplexes and analyzes pooled single-cell data, revealing mitochondrial incompatibilities between humans and chimpanzees.

This study compares metagenomic pipelines for predicting methane emissions in sheep using functional and taxonomic features, finding COG-based functional features provide the highest accuracy.

The paper identifies genomic markers in Salmonella isolates that correlate with infection risk, showing lineage-specific associations and a conserved prophage marker in Salmonella Agona.

This study uses deep mutational scanning to analyze TYK2 variants and their impact on function and drug response, identifying novel therapeutic targets and degradation strategies.

This study compares cis-regulatory elements in immortalized liver cell lines to primary liver tissue using ATAC-seq, finding significant differences in transcription factor binding and gene regulation.

The paper introduces tRNAZAP, a deep learning method using nanopore ionic current signals to classify tRNA isodecoders, achieving better alignment results than BWA-MEM in E. coli and S. cerevisiae.

The paper identifies average polycomb CpG methylation as a hallmark of cellular aging using single-cell whole-genome methylation data, showing cell-to-cell variability and accelerated aging in faster proliferating cells.

This study examines how ceftiofur antibiotic treatment and E. coli inoculation affect the calf fecal microbiome using shotgun metagenomics and single-cell sequencing.