variant calling

Cell recovery and DNA extraction methods skew relative abundance estimations of foodborne pathogens and spoilage organisms on stainless steel surfaces

Parallel evolution under constraint shapes echinocandin resistance in Candida auris

Across 681 matched isolates and 22,388 genomes, high-level micafungin resistance in Candida auris arises through recurrent FKS1 hotspot mutations amid strong purifying selection, and FKS2 appears dispensable.

Genetic diversity within and between polyploid sugarcane (Saccharum spp.) families obtained via caryopsis using microsatellite markers and multicategory model

The paper evaluates genetic diversity within and between sugarcane families using microsatellite markers and distances to account for polyploidy, finding most variation is within families.

Genomic consequences of admixture in an experimentally founded sand lizard population

The paper examines the genomic effects of genetic rescue in a sand lizard population, finding increased diversity and reduced genetic load after admixture.

OligoSeq: Rapid nanopore-sequencing of single-stranded oligonucleotides

OligoSeq enables accurate sequencing of single-stranded oligonucleotides using nanopore technology, offering a cost-effective alternative for quality control in oligonucleotide synthesis.

Response to divergent selection on meiotic recombination in Saccharomyces cerevisiae

The paper uses experimental evolution in yeast to study how recombination rates change under divergent selection, finding increased and decreased rates in selected lineages.

Joint ancestry inference reveals the landscape of archaic introgression in admixed populations

TRACTINATOR infers continental and archaic ancestry in admixed genomes using deep learning, revealing archaic introgression patterns in Latin American populations.

Optimizing DNA extraction from environmentally degraded bone samples for molecular identification of cetacean species

This paper presents an optimized DNA extraction protocol for degraded cetacean bone samples, successfully amplifying mitochondrial DNA from 55.6% of samples for species identification.

A rare deletion of IhUF3GT1 in the ivy-leaf morning glory eliminates anthocyanin-based pigmentation.

The paper identifies a rare deletion in IhUF3GT1 causing anthocyanin loss in ivy-leaf morning glory, confirming its role in pigmentation.

Recovering the pre-colonial population structure of Khoe-San descendant populations

The paper analyzes genetic ancestry in South African Coloured groups to reveal persistent Khoe-San ancestry and traces Indian Ocean slave trade signatures.

A sibling study of variation in parental mutation rates

The paper identifies de novo mutations in siblings and finds no differences in mutation rates by ancestry or smoking status, but links disruptions in REV1 and LIG1 to increased germline mutation rates.

Improved short nascent strand sequencing (iSNS-seq) enhances DNA replication origin detection and reduces non-origin biases

The paper improves the SNS-seq protocol to better detect DNA replication origins and reduce non-origin biases in yeast.

Design and Validation of New Primers for Specific and Sensitive Real-time PCR Detection and Quantification of Seven Botulinum Encoding Genes (Serotype A-G) of Clostridium botulinum

This study designs and validates new primers for specific and sensitive real-time PCR detection of seven Botulinum serotypes, achieving 10 copies/reaction sensitivity and eliminating carryover PCR products.

Cohesin promotes genomic stability by suppressing unequal sister chromatid exchange

This study shows cohesin suppresses unequal sister chromatid exchange by maintaining arm cohesion and limiting distal repeat interactions in yeast.

Conjugative serine recombinase engineering enables genome integration in transformation-resistant bacteria and bioproduction pathway prototyping

This paper introduces cSAGE, a conjugation-based genome engineering platform that enables site-specific integration in transformation-resistant bacteria, demonstrating its utility in bioproduction pathway prototyping.

Androgens mediate sexual dimorphism in Pilarowski-Bjornsson Syndrome

The paper investigates sex-specific penetrance in PILBOS, showing male overrepresentation and androgen-mediated sexual dimorphism through genetic and mouse model studies.

Ambrosia beetle invasions are structured by inbreeding, intraspecific hybridisation, and bridgeheads

The paper analyzes genomic data from ambrosia beetles to show that invasive populations experience inbreeding, hybridization, and genetic bottlenecks, with outbreeding helping purge deleterious mutations.

Evaluating rapid extraction methods for recovering ancient DNA from archaeological sediments

This paper evaluates rapid DNA extraction methods for ancient DNA recovery from sediments, finding that an Amicon-based method outperforms others in recovering short and modern-simulated aDNA from various sediment types.

On the sensitivity of qPCR diagnostics for the canola clubroot pathogen Plasmodiophora brassicae

This study evaluates three qPCR systems for detecting Plasmodiophora brassicae, finding one with high sensitivity suitable for routine diagnostics.

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV

AccuSNV is a deep learning tool for high-accuracy bacterial SNV calling that outperforms existing methods in simulated and real datasets.

Mutation timing, accumulation and selection in the male germline shape inheritance risk for developmental disorders

The paper investigates how mutation timing, accumulation, and selection in the male germline influence the risk of developmental disorders through de novo mutations.

JanusX: an integrated and high-performance platform for scalable genome-wide association studies and genomic selection

JanusX improves GWAS and genomic selection by reducing runtime and memory usage while maintaining accuracy across large datasets.

Deciphering the Genomic Landscape of Renal Cell Carcinoma Brain Metastases

The paper identifies recurrent copy-number alterations in RCC brain metastases and shows their association with poor prognosis and metastatic potential across multiple cancers.

Population genomics of the rice landrace Acuce reveals exceptional dynamics of immune receptors

The paper analyzes genomic diversity in the rice landrace Acuce to understand its resistance to pathogens and agricultural traits, finding high diversity and selection pressures in immunity genes.

Turnip mosaic virus-based gRNA delivery system for plant genome editing

This paper develops a turnip mosaic virus-based gRNA delivery system for plant genome editing, showing improved editing efficiency with Csy4-mediated processing and multiplex targeting capabilities.

Improving long-read somatic structural variant calling with pangenome and de novo personal genome assembly

This paper introduces a method for improving long-read somatic structural variant calling by integrating pangenome and de novo personal genome assembly, reducing false positives while maintaining sensitivity.

Structure-based design of soluble prefusion-stabilized herpes simplex virus type 2 glycoprotein B antigens

This study designs prefusion-stabilized HSV-2 gB antigens using structure-based methods and evaluates their immunogenicity, finding no improvement in neutralizing antibody titers compared to postfusion constructs.

T-Rex: Standardized Analysis of Germline Variants in Whole-Exome Sequencing Trios

T-Rex provides a standardized, no-programming-required tool for analyzing whole-exome sequencing trio data, achieving high precision and sensitivity in variant calling and filtering.

Optimizing genomic selection: A comparison of SNP selection strategies for reduced-density panels in beef cattle

This study compares SNP selection strategies for reduced-density panels in beef cattle to optimize computational efficiency while maintaining genomic prediction accuracy.

High-Molecular-Weight Genomic DNA Extraction from Recalcitrant Australian Plants: An Optimised CTAB Protocol for Anigozanthos

This paper develops an optimised CTAB protocol for extracting high-molecular-weight DNA from recalcitrant Australian plants, improving DNA purity and integrity for sequencing.