variant calling

Variant effect predictors are shaping the ClinVar classifications used to train and evaluate them

The paper shows that variant effect predictors influence ClinVar classifications, creating circularity in variant classification and prediction.

Long-term experimental evolution of seasonal influenza A/H3N2 virus reveals diverse evolutionary potential

This study shows that A/H3N2 influenza virus evolves differently in independent human airway cultures, with limited parallelism and novel mutations, suggesting evolutionary paths are influenced by selective context rather than intrinsic constraints.

KmerSignificance Score: A discriminative and biologically-informed framework for viral k-mer prioritization

KmerSignificance Score (KSS) prioritizes viral k-mers by integrating strain-distinguishing capacity, mutation impact, and functional importance, achieving superior classification performance and cross-dataset comparability.

Robustness of the inference of the distribution of fitness effects to selective sweeps

This study evaluates how selective sweeps affect DFE inference using fitdadi, finding that performance declines at low recombination rates and with unfolded SFS, but remains largely unbiased with a flexible demographic model.

Correcting Multiple Scattering Enables Dynamical Electron Crystallography in Standard Workflows

GROND improves electron crystallography by correcting multiple scattering, enhancing refinement accuracy and revealing hidden structural details in various materials.

Collapsed Site Coalescent Facilitates Detection of Adaptive Divergences Between Segmental Duplicates

The paper introduces a method to analyze population genetics of segmental duplicates by modeling gene conversion events and detecting adaptive divergence.

A bistable type III secretion system is primed and loaded in Pseudomonas aeruginosa hypervirulent isolates with positively selected codon changes in exsA or exsD

The paper identifies positively selected codon changes in exsA or exsD that hyperactivate the T3SS in P. aeruginosa, leading to hypervirulence through increased T3SS activity and immunopathology.

Rare Genetic Mechanisms in Dyggve-Melchior-Clausen Disease

The paper identifies rare genetic variants in DYM causing Dyggve-Melchior-Clausen disease through reanalysis of whole-exome sequencing data from affected individuals.

Horizontal transfer of an antimicrobial peptide across insects

The paper identifies horizontal gene transfer of the Drosomycin antimicrobial peptide gene across insect species, suggesting HGT contributes to immune system novelty and defense capabilities.

CyriPanel for CYP2D6 Genotyping from Targeted Capture Panels Using Assay-Matched Diploid References

CyriPanel improves CYP2D6 genotyping accuracy using assay-matched diploid references and structural inference, achieving higher concordance than Aldy 4 in benchmark tests.

Insights Into The Early Diversification of blaNDM-1 Genetic Contexts Following its Emergence in Acinetobacter species and Spread to Enterobacterales

The paper analyzes early genetic contexts of blaNDM-1 in Acinetobacter and Enterobacterales isolates to understand its spread and resistance mechanisms.

Early Prenatal Cell-Free DNA Methylation Landscape Informs Epigenetic Purification of the Circulating Fetal Genome

The paper develops an epigenetic enrichment method for fetal cfDNA using a first-trimester methylome reference, increasing fetal fraction from 5.1% to 28.4%.

mobileRNA: a tool for efficient analysis of mobile RNA molecules in multiple genomes.

The paper introduces mobileRNA, an R package that efficiently identifies mobile RNA molecules in grafted plants using merged genome alignment and simulated datasets.

Differential k-mer distributions enable identification of tetrapod subterminal heterochromatin

The paper identifies subterminal heterochromatin in tetrapods using k-mer distributions, revealing ancient subgenome-specific repeats in Xenopus laevis.

ONT-LibQC: rapid quality control of chromatin assay libraries using shallow nanopore sequencing

ONT-LibQC uses shallow nanopore sequencing to rapidly assess chromatin assay library quality before deep sequencing, showing consistent results with Illumina sequencing.

Calibration of AlphaGenome Variant Impact and SpliceAI2 scores as PP3/BP4 evidence for missense, non-coding, and synonymous variants

The paper calibrates AlphaGenome Variant Impact (AVI) and SpliceAI2 scores for variant classification, showing their performance across different variant classes and comparison methods.

Phylogenomic screening reveals idsA2 loss conferring nitroimidazole cross-resistance in Mycobacterium tuberculosis

A length- and mutation-load-corrected homoplasy screen of 1,813 MDR-TB genomes flags idsA2; its loss raises pretomanid MIC fourfold, delamanid and ethambutol twofold, via isoprenoid flux redirection.

Purification of filamentous phage ssDNA genomes using Chaotropic salt/silica methods

The paper develops and optimizes two protocols for purifying ssDNA from filamentous phages using chaotropic salts and silica columns, achieving high recovery and purity comparable to commercial kits.

A heat-assisted ttLbCas12a workflow incorporating crRNA 3'-tailing enables efficient multiplex biallelic genome editing in hybrid poplar

Genotypic evidence of vector-mediated selection on Plasmodium falciparum in infected field-collected Anopheles mosquitoes

The paper analyzes parasite genotypes in sympatric mosquito species to show divergent selection on Plasmodium falciparum mediated by different vectors.

Tuning inhibitor susceptibility of human 4-hydroxyphenylpyruvate dioxygenase to rescue tyrosine catabolism in the presence of β-triketones

This study engineers HPD variants with enhanced NTBC tolerance to restore tyrosine metabolism while maintaining catalytic activity and MHC-II binding properties.

Micro-C-TALE: BAC-based targeted high-resolution measurement of 3D chromatin interactions

Micro-C-TALE provides a cost-effective method for high-resolution targeted chromatin interaction mapping with improved sensitivity and resolution compared to existing techniques.

Streamline CNV - A Handy Nextflow Pipeline for Chromosomal Copy Number Variation Analysis

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.

The Sensitivity of 13C-Metabolic Flux Analysis to Biomass Composition Underscores the Need for Accurate Biomass Formulation in Escherichia coli

This study shows that 13C-MFA in E. coli is sensitive to biomass composition, emphasizing the need for accurate biomass formulations in flux analysis.

Exome-based Preconception Carrier Screening for the Mexican Jewish Community; Yields and Implications

This study uses exome sequencing to identify genetic variants in the Mexican Jewish Community, finding higher rates of carrier status and novel alleles compared to standard panels.

Genome-wide conservation and locus-specific coding variation in Teratoramularia rumicicola, a candidate microbial herbicide for Rumex weeds

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.

Reversible fixation of microbial cells for targeted genomics

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

G-ALN: a GPU-accelerated BWA-aln algorithm for palaeogenomics

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

T2G: fast and accurate transcriptome to genome BAM liftover for short and long read RNA sequencing

T2G converts transcriptome-aligned BAM files to genome coordinates, improving specificity and splice junction accuracy across RNA sequencing technologies.

Delocalized DNA holes imprint mutation position in mismatch-repair-deficient cancers

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.