genome assembly

The paper develops a de novo assembly strategy using PacBio HiFi long-read sequencing to generate high-quality genomes of Malian Plasmodium falciparum field isolates, revealing natural variation in telomere structure and gene family diversity.

This study analyzes X-chromosomal STR diversity in the Vedda population, finding significant genetic differentiation from other South Asian groups and highlighting their unique genetic heritage.

The paper generates high-quality chromosome-level genomes for three Plasmodium species from natural infections, improving understanding of their biology and evolution.

SUMMIT improves heritability and genetic correlation estimation across diverse ancestries using LD scores and GWAS summary statistics, showing better accuracy in non-European populations.

This study develops a new cultivation method for Blastocystis, revealing that multiple strains can coexist within a single host.

This paper introduces an Oxford Nanopore sequencing framework for hantavirus genome assembly and variant analysis, revealing defective viral genomes as a new feature of hantavirus populations.

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.

The paper introduces sum-h2, a fast framework for evaluating genetic discovery from deep learning-derived phenotypes using heritability measures, and establishes a Genetic Discovery Arena for benchmarking.

This paper introduces LRQ, a long-read metagenomics method that enables absolute strain abundance measurement and resolves microbial evolution in a Crohn's disease patient over eight years.

This paper introduces Mikado, a method using sparse linear algebra to accelerate genotype representation graph computations, significantly improving speed over existing tools on large biobank datasets.

LongPhase-TO reconstructs somatic haplotypes from tumor-only long-read sequencing, improving variant calling accuracy and haplotype block size.

The paper uses whole genome sequencing to analyze the genetic structure of a Greek-speaking community in Southern Italy, finding no strong evidence for external origins and supporting a model of continuous gene flow.

The paper compares damage correction methods for ancient DNA libraries to assess their impact on imputation and kinship inference.

This study examines genetic correlations between reproduction and longevity in historical Dutch cohorts, finding weak or mixed evidence for a fertility-longevity trade-off.

This study conducts a multi-ancestry GWAS meta-analysis of 2.5 million participants to identify genetic variants associated with migraine and link them to biological pathways and therapeutic targets.

ECHO is a nanopore sequencing pipeline for comprehensive (epi)genetic analysis of the human repeatome, enabling haplotype-resolved and methylation-informative studies.

The paper uses optical genome mapping and long-read sequencing to resolve complex rearrangements at nucleotide resolution, revealing additional complexity and enabling accurate genotype-phenotype correlations.

This study analyzes ancient and present-day Central Eurasian genomes to assess archaic hominin introgression, finding stable levels of Neanderthal and Denisovan ancestry over time.

BLink-seq is a scalable Haplotagging method for generating phased haplotypes and detecting structural variants in non-model species using short-read sequencing.

The paper identifies a young, brain-regulatory subset of schizophrenia risk variants that concentrate heritability after accounting for age, frequency, and selection signals.

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

The paper introduces a support-based validation framework to correct assembly errors in diploid genomes using independent sequencing evidence.

The paper estimates human genetic load variation due to rare and ultra-rare deleterious mutations, showing significant ancestral fitness differences between individuals.

This paper develops molecular tools to overcome restriction-modification barriers in Staphylococcus haemolyticus, enabling genome editing and virulence gene targeting.

ImpuT2T patches gaps in HiFi assemblies using pangenomes, improving quality over existing methods.

Over 8,000 gapless human centromeres reveal population-stratified satellite-array, inversion and haplotype variation, multiple candidate kinetochore sites in 16.8% of centromeres, and single-base substitution rates comparable to flanking pericentromeres.

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

This paper introduces grapHiC, a contrastive learning framework for reference-free haplotype phasing in de novo genome assembly, achieving results comparable to state-of-the-art methods.

This study applies a modified natural vector method to mitochondrial genome data from the 1000 Genomes Project to evaluate population genetic characteristics beyond pairwise comparisons.