whole-genome sequencing

The paper analyzes whole genome data from Plasmodium falciparum isolates in Ethiopia to identify adaptive trajectories of antimalarial resistance evolution.

The paper uses genomic data from sea lions to investigate sex-biased dispersal and reproductive skew, finding male-biased migration and varying levels of polygyny between species.

The paper uses sequence-to-function models to show that long-range regulatory information in vertebrate genomes stops being shared before local sequence information, with a phylogenetic boundary around 320-435 Mya.

CPDD adapts an autoregressive DNA language model for bidirectional phage genome modeling, achieving higher random-mask restoration accuracy and supporting fitness prediction and classification.

This study identifies sex-determining genes and links them to self-incompatibility in an androdioecious plant species.

Genomes2Genes converts Progressive Cactus alignments into validated gene-level alignments, identifying de novo genes and enabling evolutionary analysis.

The paper examines how Drosophila simulans adapts to three new transposable element invasions through piRNA cluster insertions and finds that resistance evolves independently in different strains.

This paper improves SBWT-based k-mer indexes by making them faster and smaller through batching, prefetching, and orientation optimization, outperforming SSHash in speed and space efficiency.

The paper identifies a Y-specific translocated gsdf copy as the master sex-determining gene in common dab through genome sequencing and comparative analysis.

This study analyzes genomic changes in a 50-year dairy cattle selection experiment, finding increased inbreeding and localized genetic differentiation in the selected line.

The paper quantifies T6SS prevalence in Gram-negative bacteria using genome analysis and finds it is present in 41% of well-sampled genera.

This study analyzes phylogenetic resolution differences among Oropouche virus genome segments and identifies sampling biases in publicly available sequences.

This study re-sequences Solenogastres genomes to analyze biomineralization gene evolution, finding reduced SMP gene families and structural proteins in Solenogastres compared to other molluscs.

This paper introduces a variant filtering framework called SMART filtering to improve diagnostic outcomes in genome sequencing by prioritizing non-coding and regulatory variants.

The paper presents chromosome-level genome assemblies for two Brazilian soybean cultivars with contrasting stink bug resistance and identifies divergent gene isoforms between them.

The paper characterizes genetic variation in the bovine sialic acid network across European and South African cattle breeds, identifying 15 prioritized protein-altering variants and highlighting population differences.

This study shows that reduced swimming motility accompanies B-lactam antibiotic resistance in E. coli through efflux mechanisms, with motility recovery after antibiotic removal.

TurboANI is a fast, homology-aware ANI estimator with up to ~40,000x speedup over alignment-based methods and better accuracy than FastANI and skani.

TideCluster is a pipeline for clustering and classifying tandem repeats across genomes, demonstrated on Arabidopsis and Solanum species.

The paper shows that the source of annotation data significantly affects the quality of automatically reconstructed genome-scale metabolic models.

The paper generates the first chromosome-scale genome and methylome for the tiger shark, revealing genomic and epigenomic features of shark evolution and population decline.

This study estimates mutation and recombination rates in polar bears using whole-genome sequencing, finding species-specific values that improve demographic inference for conservation.

mFrag improves lung cancer early detection using fragmentomics by integrating DNA methylation data and combining two models to enhance prediction accuracy.

This study evaluates genomic prediction methods for growth traits in black soldier fly larvae across different diets and generations, finding that dominance effects and SNP density significantly impact predictive ability.

Ok-k-mer selects optimal k-mer length ensembles to improve genomic distance estimation by maximizing correlation with phylogenetic branch distances.

This paper introduces efficient methods to update colored k-mer indexes without rebuilding them from scratch, enabling dynamic maintenance of large genomic collections.

MELD predicts SNV functional effects by directly training on wild-type versus mutant differences, outperforming post-hoc in-silico mutagenesis methods with fewer parameters.

This study identifies TilR, a MarR-family regulator in Klebsiella oxytoca, as a repressor of tilimycin biosynthesis and links it to metabolic and virulence-related gene expression.