whole-genome sequencing

Sorting S-phase cells by Cyclin A2 rather than DNA content exposes a uniform genome-wide delay after CDC7 inhibition and a broad replication timing advance in RIF1 knockout.

The paper develops a DNA-based T-cell infiltration score from whole-genome sequencing to predict immunotherapy response and survival.

The paper maps how local sequence context influences germline mutation rates using 1000 Genomes Project data, showing non-monotonic decay and higher-order interactions.

The paper develops EpiSignaLR, a resource for genome-wide episignature analysis using methylation-aware sequencing data, identifying DMRs and classifiers for three neurodevelopmental disorders.

Streamline CNV is a Nextflow pipeline for CNV analysis that simplifies processing, visualization, and interpretation of copy number data across various sequencing types and species.

This study uses ancient genomes to analyze adaptive evolution in East Asia, finding pre-Neolithic selection at key loci and a link between ADH1B*48His and wheat farming.

This paper describes two novel Corynebacterium species isolated from human nasal passages and skin, along with characteristics of two strains of a recently named species.

The paper characterizes the genome of Teratoramularia rumicicola, identifies functional genes and isolate-specific variations, and highlights potential virulence factors relevant to its use as a microbial herbicide.

The paper improves GWAS resolution in pearl millet by imputing missing genotypes using a whole-genome sequencing reference panel, leading to more localized association signals and candidate gene identification.

This paper introduces DSP as a reversible fixative for microbial cells that enables fluorescence imaging and DNA extraction, improving targeted microbial genomics.

The paper uses a genomic language model to cluster and annotate noncoding sequences in prokaryotic genomes, identifying structured RNAs and their potential functions.

Alignment-free pan-k-mer profiles track minimap2 similarity (whole-chromosome r^2 0.959-0.968), profile 605 vertebrate genomes in about a day on 40 cores, and nominate trait-linked loci across plants and animals.

This study shows that chromosomal instability (CIN) drives rapid genome changes in cancer cells, generating new copy number alterations each cell cycle and increasing genomic complexity.

The paper uses statistical analysis of mitochondrial genome data to identify convergent rearrangements in the WANCY region, suggesting it is a TDRL hotspot with higher convergence frequency than previously thought.

This study compares FST scans to a likelihood-based method using the joint site frequency spectrum to detect genomic regions of early divergence in Ostrinia nubilalis, finding the likelihood-based approach more effective for rare alleles.

The paper investigates the genetic and phenotypic changes associated with the loss of heterostyly in Primula boveana, revealing a disrupted CYP gene and developmental shifts leading to autonomous selfing.

G-ALN accelerates BWA-aln for ancient DNA analysis using GPU, achieving faster indexing and alignment speeds with identical output.

The paper identifies a specific mutation pattern in mismatch-repair-deficient cancers linked to DNA hole delocalization and oxidation, showing enrichment at 5' guanines and depletion at 3' guanines.

This study uses genome-scale CRISPR base editing in yeast to assess the functional effects of 308,461 variants, identifying 18,009 with significant growth impacts.

hvantk is a framework for variant annotation and analysis that integrates multi-omic data, improving the recovery of disease genes in case-control cohorts.

The paper introduces hEVO, a genomic foundation model trained on human haplotype sequences, achieving top performance in variant interpretation and functional annotation across multiple benchmarks.

The paper presents a chromosome-level genome assembly and transcriptome resource for the medicinal leech Hirudo verbana using PacBio and Hi-C data.

This study improves genome assemblies of Noccaea caerulescens accessions and identifies gene copy number variations linked to metal hyperaccumulation and adaptation.

This study identifies a CAG repeat expansion in EP400 as a novel cause of spinocerebellar ataxia in Serbian patients, with an inverse correlation between repeat number and age at onset.

The paper analyzes 328 Actinobacillus pleuropneumoniae genomes to explore relationships between genomic lineages, K:O antigen genotypes, and Apx toxin repertoires, finding strong associations between lineage and these traits.

The paper shows biosurfactant production in bacteria under cold-saline stress is strain-specific and not determined by phylogeny or biosynthetic gene content.

The paper shows a domesticated totivirus-like gene array in yeasts evolves faster than its exogenous relatives and undergoes interspecific transfer and asymmetric evolution.

This study shows that rare variant burden adds information beyond polygenic risk scores for breast cancer and is more strongly associated with earlier diagnosis.

This study shows how environmental factors like nutrients, pH, and oxygen affect the evolution of antibiotic resistance in Pseudomonas aeruginosa.

This study identifies de novo structural variants in individuals with orofacial clefts and finds they contribute to genetic risk, with some variants disrupting known risk genes and suggesting new candidate genes.