variant calling

Interpreting Short Tandem Repeat Variations with Genomic Foundation Models in Olive

The paper identifies STR variation in olive and evaluates how genomic language models respond to natural STR length changes, finding consistent embedding perturbations and prioritizing candidate loci linked to oil composition.

Optimisation and Validation of a UHPLC-MS/MS Assay Using Timed Post-Column Ammonium Fluoride Infusion for Sensitive Serum Steroids Quantitation

The paper develops and validates a UHPLC-MS/MS assay for quantifying 18 steroids in serum, showing improved sensitivity and applied it to healthy individuals.

Adaptive responses to antifungal selection depend on dose and drug combination in experimentally evolved yeast

This study shows that antifungal selection in yeast varies with drug dose and combination, leading to distinct genomic responses and resistance mechanisms.

Histone modifications define distinct nucleosome positions in cell-free DNA

This paper identifies histone modification-associated nucleosome positions in cfDNA that correlate with tumor fraction and cancer state across multiple cancers.

Integrating sequence-to-omics predictions and personal multi-omics for rare variant prioritization

The paper introduces Watershed-DL, a framework integrating sequence-to-omics predictions and multi-omics data to prioritize rare variants, finding it increases prioritized variants by 61.4% and identifies candidate disease alleles.

Genetic hallmarks of patients with congenital portosystemic shunts and portopulmonary hypertension: protocol for a multicentre exploratory study

This paper outlines a protocol to identify genetic variants associated with portopulmonary hypertension in congenital portosystemic shunt patients using whole-genome sequencing and family-based analyses.

High-resolution HLA and MICA/MICB typing of the 1000 Genomes panel: a resource for precision medicine

The paper provides high-resolution HLA and MICA/MICB typing for the 1000 Genomes panel, identifying population-specific variants and demonstrating the utility of HLA data for predicting MIC genotypes.

A cell-free system for mitotically-stimulated TMEJ

The paper develops a cell-free system using Xenopus egg extracts to study TMEJ, showing that Pol theta and Cyclin B-CDK1 are essential for efficient DNA joining.

Population-scale genome-wide prioritization of targets for allele-specific antisense oligonucleotide therapy design

This paper identifies population-scale SNV targets for allele-specific ASO therapy design, achieving high coverage across diverse ancestry groups and supporting clinical relevance.

Accurate calling of low-frequency somatic mutations by sample-specific modeling of error rates

This paper introduces BBQ, a tool that improves rare somatic variant calling by modeling sample-specific error rates using overlapping reads, reducing false positives compared to existing tools.

Long-read genome sequencing resolves complex structural variants in exome-negative developmental and epileptic encephalopathy

This study evaluates the diagnostic value of long-read genome sequencing in DEE patients, finding it particularly effective for resolving complex structural variants not detected by short-read sequencing.

Single-vector AAV delivery of En-ISPmu1 and donor DNA for in vivo targeted genome integration

The paper describes the development of En-ISPmu1, a modified TnpB nuclease, and demonstrates its ability to achieve targeted genome integration in mouse liver with a single AAV vector.

Development of a CRISPR-Cas9 genome editing system for the extremely thermophilic bacterium Anaerocellum bescii

This paper develops a CRISPR-Cas9 system for Anaerocellum bescii, enabling gene deletions and vector maintenance through thermostable Cas9.

VIPER-seq: Protein-mediated small RNA enrichment enhances plant virus detection at low viral abundance

VIPER-seq improves virus detection in plants by enriching viral small RNAs using protein-mediated methods, showing better sensitivity in low-titre infections.

Predicting clonal mutations from tumour spatial transcriptomics data using a graph convolutional neural network

This paper introduces SPOT-Mut, a graph convolutional neural network that predicts clonal mutations from spatial transcriptomics data, achieving high precision and recall for key driver genes.

Nutrient control enables metabolic reconstruction of L. rhamnosus GG and analysis of secretions

The paper presents the first curated genome-scale metabolic model for L. rhamnosus GG, validated using multiple approaches and provides insights into its nutrient requirements and secretions.

Stress-response regulators tune enterobacterial common antigen synthesis to support acid and reactive nitrogen species stress resistance

This study identifies regulators that control ECA biosynthesis in E. coli, showing ECA's role in acid and reactive nitrogen species stress resistance.

Rescued from extinction in two buckets: genomic consequences of an extreme bottleneck in the endangered Owens pupfish

The paper analyzes the genomic consequences of a severe bottleneck in Owens pupfish, finding reduced genetic diversity and a 17-fold contraction in effective population size, but low recent inbreeding due to population expansion.

OddCAPS: a simple, low-cost, universal technique for detecting single nucleotide variants

OddCAPS improves dCAPS by using three primers in one PCR reaction to detect SNVs with more engineered base changes and flexibility in restriction enzyme selection.

Reaction Norm Modeling of High-Dimensional Genomic and Environmental Data Improves Prediction Accuracy in Winter Wheat

This paper improves genomic prediction accuracy in winter wheat by integrating genotype-by-environment interactions and environmental covariates across multiple environments.

A specialized SUV3 RNA helicase is involved in plant mitochondrial DNA repair

This study identifies AtSUV3 as a mitochondrial RNA helicase involved in DNA repair and shows its role in mitigating DNA damage in Arabidopsis.

Beyond Delta Masses: MS Andrea Directly Resolves Combinatorial Peptide Modifications in Open Searches

MS Andrea, a tag-filtered open search engine, scores and localizes up to four Unimod modifications per peptide-spectrum match, with identification counts competitive with MSFragger and Sage.

U6 promoters in Ulva prolifera enable dual small-RNA/mRNA transcription and vector-based CRISPR-Cas9 genome editing

The paper identifies and characterizes U6 promoters in Ulva prolifera, showing their dual transcriptional activity and utility for CRISPR-Cas9 genome editing.

Application of the ORBIT Protocol for Targeted Gene Deletion to Mycobacterium abscessus

This paper optimizes the ORBIT protocol for efficient gene deletion in Mycobacterium abscessus, enabling precise genetic manipulation for studying its physiology and pathogenesis.

Whole genome-based Characterization of Virulence and Antimicrobial Resistance Determinants in Clinical Campylobacter jejuni Isolates from Minnesota, 2018-2021

This study uses whole-genome sequencing to analyze virulence and antimicrobial resistance in 2,783 Campylobacter jejuni isolates, finding high prevalence of resistance genes and strong correlation between genotypic and phenotypic resistance profiles.

Nutritional quality and genetic differences of five amaranth cultivars revealed by metabolome profiling and whole-genome sequencing

The paper profiles the metabolome and genomes of five amaranth cultivars to assess nutritional quality and genetic differences.

A gapless Landrace pig genome resolves centromeres and telomeres and highlights telomere repeat structures in different pig breeds

The paper presents a gapless Landrace pig genome assembly that improves resolution of repetitive regions and reveals breed-specific telomere repeat structures.

CRISPR-dPCR: A unified multiplex digital PCR framework for quantitative characterization of targeted knock-in

CRISPR-dPCR quantifies CRISPR knock-in by distinguishing integration from donor abundance and background, using multiplex digital PCR with orthogonal strategies.

Analysis of genome sequences of marine isolates of Saccharomyces cerevisiae

The paper reports the genome sequences of three marine Saccharomyces cerevisiae strains and assesses their salt and inhibitor tolerance compared to terrestrial strains.

Technology solutions for immune loci: integrated high-resolution KIR genotyping reveals allelic, structural, and KIR-HLA diversity across 24 human populations

This paper develops a high-resolution KIR genotyping system that accurately identifies allelic, structural, and KIR-HLA diversity across 24 human populations.