variant calling

SLAFIT: Viral fitness inference and structural variant detection from TGS data

SLAFIT infers viral fitness and detects structural variants from third-generation sequencing data by analyzing linkage disequilibrium and haplotype frequencies.

Estimating self-fertilization rates from the diploid genotype spectrum

This paper introduces a method to estimate self-fertilization rates using diploid genotype spectra from population genomic data.

The Genetic Discovery (GeDi) resource: Deep characterization of a multi-ancestry panel of human reference iPSCs for functional genomic studies

A cold-adapted Cas9 nuclease from the deep ocean

This paper characterizes DO1Cas9, a cold-adapted Cas9 nuclease from the deep ocean, showing improved activity under cold conditions and broader organismal applicability.

Hidden introns and repeated gains shape the heavily interrupted tRNA genes of Asgard archaea

The paper identifies and corrects missed introns in tRNA genes of Asgard archaea, revealing repeated intron gains and their splicing motif preferences.

DIPLER: rapid k-mer-based locus identification

DIPLER identifies structurally complex loci using k-mer analysis and de novo assembly from low-coverage sequencing data.

DUMMEST: A simpler and faster model for frameshift-aware alignment of a DNA sequence to a protein family

DUMMEST improves frameshift-aware alignment of DNA sequences to protein families by combining simplicity and speed, outperforming existing methods in sensitivity and specificity.

Global signatures of Ribonucleotide Excision Repair deficiency and its therapeutic vulnerabilities

This study identifies RER deficiency as a new DNA repair defect in cancer, detectable through mutational signatures and linked to therapeutic vulnerabilities.

Population structure of human-infecting and environmental isolates of Coccidioides immitis, the fungus causing Valley fever

The paper analyzes genetic structure and diversity of Coccidioides immitis in environmental and human isolates to understand disease transmission and environmental distribution.

Pre-binning correction of chimeric contigs reduces reference-discordant gene annotations in near-complete metagenome-assembled genomes

The paper introduces DeepMM, a deep learning method to correct chimeric contigs in MAGs, improving gene annotation accuracy and reducing reference-discordant genes and virulence-factor calls.

Development, validation and clinical implementation of cellular swab materials for quality assurance of pharmacogenomic point-of-care testing

The paper develops and validates cell-based swab materials for pharmacogenomic point-of-care testing, demonstrating their effectiveness in quality assurance and external quality assessment.

Rye stem rust is a reservoir of diversity and virulence for wheat stem rust

The paper analyzes 385 Pg genomes to show Kazakhstan hosts a diverse sexual clade with many HD haplotypes, and Pgs contributes virulent alleles to wheat rust pathogens.

Lateral flow devices can fast-track rabies virus genomic surveillance

This paper demonstrates that lateral flow devices can be used for rabies virus genomic surveillance, enabling rapid and decentralized genome collection without additional sample collection.

LNP Delivery of Prime Editors Enables Durable Correction of PAH R408W in Phenylketonuria Models

This paper demonstrates the use of LNP-delivered prime editors to correct the PAH R408W mutation in PKU models, achieving ~50% correction efficiency.

IVA, a locally deployable Intelligent Variant Analyser based on a small language model for complete case-level and trio-based genomic interpretation.

IVA uses a small language model to perform local genomic variant interpretation, achieving high sensitivity but lower precision in identifying pathogenic variants.

PoLoCo: A reproducible pooled low-coverage workflow for draft genome assembly and allele frequency analysis from ethanol-preserved small non-model invertebrates

Using Polycistronic gRNAs and a tRNA Cleavage System in CRISPR-Based Genome Editing of Toxoplasma gondii

This paper improves CRISPR-based genome editing in Toxoplasma gondii by optimizing gRNA expression and introducing a tRNA-based polycistronic system for multiplexed editing.

Pangenome analyses uncover the scale and evolutionary consequences of structural variation in a wild mammal

This study constructs a pangenome for deer mice to reveal extensive structural variation and its evolutionary implications.

A silent intergenic locus for efficient and versatile transgene expression in Plasmodium falciparum

The paper identifies a silent intergenic locus in Plasmodium falciparum that allows stable transgene expression without disrupting native genes, enabling versatile genetic engineering.

A versatile set of computational tools for inference of genetic ancestry from human molecular data

The paper introduces RAIDS, a toolset for inferring genetic ancestry from various sequence data, including cancer and low-coverage scenarios.

Benchmarked sequencing methods reveal hidden mosaic variation in the human brain

The paper benchmarks sequencing methods to recover mosaic variants in human brain tissue and introduces RIVER to enhance variant detection across methods.

Biobank-scale genotyping of Robertsonian translocations reveals hidden structural variation on the human acrocentric chromosomes

Short-read genomes can flag Robertsonian translocation carriers by counting rDNA distal junction (DJ) copies (8 rather than 10); UK Biobank screening found 583 candidates, 1 in 841.

Long-read sequencing and benchmarking of saliva against blood for genomic variant detection in autism

This study benchmarks saliva-derived DNA against blood for long-read sequencing in autism, showing comparable variant detection despite nonhuman DNA contamination.

Proximity-mapped whole-genome sequencing for characterization of repeat expansions and variants in highly homologous genomic regions

This study evaluates TruPath Genome's ability to characterize repeat expansions and variants in complex genomic regions using archived DNA samples, showing consistent results with orthogonal methods.

Single-cell variant landscape of the human mitochondrial genome reveals cell type-specific functions and disease mechanisms

The paper presents scMOCHA, a tool to analyze mtDNA heteroplasmy from scRNA-seq data, revealing cell type-specific mtDNA variants and disease mechanisms in hematopoietic cells.

A national ecosystem for long-read genome sequencing: Integrating population genomics and rare disease diagnostics in Sweden

This paper evaluates the clinical use of long-read genome sequencing in Sweden, showing it provides molecular diagnoses and reduces diagnostic costs.

High-performance xenograft read-sorting for DNA methylation analysis

The paper improves a tool for sorting DNA reads in xenograft models, enhancing efficiency for epigenetic analysis.

High temperature ligation enables in vitro assembly of eukaryotic genes

This paper introduces High Temperature (HighT) assembly, a DNA assembly method that improves accuracy and yield by ligating DNA at higher temperatures, and demonstrates its application in constructing synthetic genes and genomic regions.

In silico subtractive genomics and reverse vaccinology approach reveal outer membrane proteins OMP47 and LptD as dual-purpose drug and vaccine targets in Pasteurella multocida Pm70

Scalable methylome-transcriptome profiling resolves clonal organization in human hematopoiesis

This paper introduces Droplet-MT, a method for joint methylome and transcriptome profiling, enabling clonal organization analysis in human hematopoiesis with high scalability and resolution.