variant calling

Forecasting next-year change in antimicrobial resistance genes in Klebsiella pneumoniae and Acinetobacter baumannii from genomic surveillance data

The paper develops a model to forecast next-year changes in antimicrobial resistance genes in K. pneumoniae and A. baumannii using genomic surveillance data, showing better performance than baselines for both organisms.

Goat genome assemblies, nine breeds for pangenome contribution

The paper presents high-quality genome assemblies for nine goat breeds using long-read sequencing, contributing to pangenome construction and structural variant analysis.

BoNTax: a curated genome-based framework for taxonomic classification and characterization of Clostridium botulinum Group I and Clostridium sporogenes

BoNTax is a genomic framework for classifying and characterizing Clostridium botulinum Group I and C. sporogenes, resolving species relationships and providing toxin information.

CRISCross: Integration of Epigenetic Information for Deep-Learning-Based Prediction of CRISPR-Cas9 Off-Targets Across Cell Types

CRISCross improves CRISPR-Cas9 off-target prediction by integrating epigenetic features with sequence data across cell types, showing better performance than sequence-only models.

Exploiting Low-Rank Structure in Genomic Relationship Matrices for Computationally Efficient Optimum Contribution Selection

This paper introduces a method to accelerate optimum contribution selection by approximating genomic relationship matrices with low-rank structures, achieving significant speedups while maintaining accuracy.

THRESHER: A tool for evidence-based, phylogeny-corrected SNP thresholds for whole genome molecular epidemiology

THRESHER calculates data-driven SNP thresholds for bacterial genomes to improve strain classification compared to fixed cutoffs.

Genome assemblies and annotations of the poneroid ants Platythyrea mocquerysi (Ponerinae) and Stigmatomma oregonense (Amblyoponinae)

The paper presents draft genome assemblies for two ant species, analyzing genome size variation and gene family expansions related to brood management strategies.

The Genetic Landscape of Structural Variants in Aspergillus flavus using ONT and PacBio Sequencing

This study uses long-read sequencing to analyze structural variants in Aspergillus flavus, identifying homopolymer tracts and deletions that arise spontaneously.

RiboFlow v2: a configurable ribosome profiling pipeline reveals measurements sensitive to read-mapping methodology

RiboFlow v2 improves ribosome profiling analysis by incorporating genome alignment and configurable handling of multimapping reads, revealing gene-specific differences in coverage and translation efficiency.

Pooled progeny sequencing effectively estimates polyandry in species with large families

This paper develops a likelihood-based method to estimate polyandry using pooled progeny sequencing and applies it to Drosophila melanogaster, finding 57% of families were sired by a single male.

onsite: An Integrated Framework for Phosphosite Localization and False Localization Rate Estimation

The paper introduces onsite, a framework for estimating false localization rates in phosphoproteomics, showing pyLucXor achieves high accuracy and localization count.

Cheese adaptation beyond Penicillium: contrasting genomic trajectories in the distantly related Nectriaceae molds

This study compares genomic adaptations of cheese-associated Nectriaceae fungi, revealing contrasting evolutionary paths involving gene family expansions, reductions, and horizontal gene transfer.

Error correction of SARS-CoV-2 genomic sequences using a phylogenetic prior

This paper presents a statistical framework for correcting SARS-CoV-2 genomic sequences using phylogenetic priors, improving call rate and accuracy in challenging regions.

Strong correlations between mutation rates and selective constraint in the human genome?

The paper investigates the relationship between mutation rates and selective constraint in the human genome, finding higher mutation rates in protein-coding genes compared to non-coding regions.

Gene flux drives functional changes in an ancient supergene in Formica lemani

The paper identifies genetic elements within a supergene that influence queen number and body size in Formica lemani by analyzing haplotype-phenotype associations and gene flux.

HapSolo2: GPU-accelerated optimization for removing secondary haplotigs from diploid genome assemblies

HapSolo2 improves haplotig removal in diploid assemblies by optimizing performance and accuracy using GPU acceleration and updated ortholog datasets.

A novel analysis pipeline and experimental design for measuring expanded repeat instability

Delta plots from targeted long-read data separate repeat instability frequency, expansion bias and change size; a single-clone assay (SCIA) shows FAN1 knockout raises expansion frequency but shrinks expansions.

Genome-wide within-host evolution during prolonged SARS-CoV-2 infection in a person with advanced HIV infection

The paper tracks SARS-CoV-2 mutations over 90 days in an HIV-positive individual and tests their functional impact on viral entry and replication.

RASTRO: Branching Point Decision-Making in Unitig Graphs

RASTRO improves unitig graph path selection by using sequence-based models to identify read-supported branching points in HIV-1 and SARS-CoV-2 assemblies.

Unsupervised Clustering Enables Cohort-Specific Variant Recalibration in Crops

This paper develops an unsupervised machine learning framework for variant quality recalibration in crops, enabling high-quality variant discovery without reference datasets.

Selecting for lysis in a temperate phage population

This study shows that repeated selection for lytic replication in temperate phages drives rapid genomic adaptation, with mutations accumulating in lysis- and lysogeny-associated genes.

Approximate local alignment via chained MEM divergence estimation for detecting horizontal gene transfer

alamem and alasight are tools for fast and memory-efficient local alignment and horizontal gene transfer detection in bacterial genomes.

A Weighted Estimation Approach to Correct for Imperfect Mutation Detection Due to Intra-tumor Heterogeneity in Tumor Sequencing

The paper proposes a weighted estimation method to correct for imperfect mutation detection in tumor sequencing due to intra-tumor heterogeneity, reducing bias and type I error.

Insights from a mobile healthcare clinic in Madagascar: Diversity and dynamics of viruses from febrile individuals in rural subsistence communities

The paper characterizes viral diversity in febrile individuals in Madagascar using metagenomics, identifying both known and emerging viruses and highlighting associations with age and malaria.

Nation-scale recovery of complete environmental plasmids pushes the boundaries of plasmid diversity through long-read sequencing

The paper expands plasmid diversity by analyzing long-read metagenomes, identifying novel plasmid lineages and providing tools for plasmid discovery.

Distinct mechanisms of CNV formation at the human 15q13.3 locus

The paper identifies distinct mechanisms of CNV formation at the human 15q13.3 locus, showing that non-allelic homologous recombination is the primary mechanism, influenced by inversion polymorphisms and population-specific susceptibility.

Repurposing Shotgun Metagenomic Human Host Reads for Mitochondrial Heteroplasmy Detection

The paper uses shotgun metagenomic host reads to detect mitochondrial heteroplasmy at allele fractions ≥5% in human respiratory tract samples.

Origin and evolution of acrocentric chromosomes in human and great apes

The paper identifies evolutionary processes in acrocentric chromosomes of great apes, including repeat enrichment, inversion, and gene family amplification, with implications for human genomic instability.

Recomb-Mix Cloud: a cost-efficient and scalable cloud-friendly pipeline for local ancestry inference

On the All of Us workbench, a Recomb-Mix-based cloud pipeline runs whole-genome local ancestry inference for an estimated $0.01 per sample, versus $0.43 for FLARE and $4.58 for RFMix.

Long-read sequencing reveals genomic landscape of structural variants in a major disease vector

The paper uses long-read sequencing to identify structural variants in Culex quinquefasciatus, revealing their potential role in insecticide resistance and adaptation.