Sergey Koren

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

Verkko automates telomere-to-telomere diploid genome assembly using long-read sequencing and graph-based methods, achieving high accuracy in chromosome assembly.

The paper presents the first high-quality genome assembly of the house cricket and demonstrates genetic engineering techniques for improving its agricultural and industrial applications.

The paper evaluates sequencing and assembly methods to create high-quality diploid human genome assemblies, finding that long reads and haplotype sorting improve accuracy and completeness.

The paper identifies a family of immunoglobulin superfamily genes in the cnidarian Hydractinia symbiolongicarpus, showing they are homologous to vertebrate histocompatibility genes and suggest an ancient origin of V-set domains.

The paper presents a contiguous de novo genome assembly of sugar beet EL10 using long-read sequencing and scaffolding, showing high congruence with the reference genome and reduced gene copy number variation.

This paper introduces Winnowmap2, a long read mapping method that reduces allelic bias in repetitive sequences, improving variant calling accuracy in near-identical repeats.

The paper uses a complete human genome assembly to analyze epigenetic patterns in previously uncharacterized genomic regions, revealing methylation and chromatin accessibility features in satellite DNA and centromeres.

The paper improves a telomere-to-telomere human genome assembly by developing a repeat-aware polishing strategy, fixing 51% of errors and increasing assembly quality.

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

The paper presents a comprehensive analysis of fully assembled human centromeres, revealing their architecture, variation, and evolutionary dynamics at high resolution.

The T2T-CHM13 reference genome improves read mapping and variant calling across diverse samples, reducing false positives and enabling novel variant discovery.

The paper presents a comprehensive analysis of segmental duplications in a complete human genome, revealing their distribution, variation, and evolutionary significance.

Merfin improves variant filtering and polishing by using k-mer validation, enhancing precision and reducing errors in long-read assemblies.

The paper analyzes the whale shark genome to study vertebrate gene family evolution, finding patterns in immunity, gigantism, and cancer-related gene expansion.

The paper develops a pipeline for mitochondrial genome assembly and identifies errors and novel duplications in reference mitogenomes.

The paper summarizes methods and lessons from assembling 16 vertebrate genomes, highlights the importance of long-read sequencing, and introduces the Vertebrate Genomes Project to generate complete reference genomes for all vertebrate species.

FALCON-Phase uses long-read sequencing and Hi-C data to create phased diploid genome assemblies, achieving high accuracy in non-human species but lower accuracy in humans.

This paper completes the linear assembly of human chromosome 8, resolves long-standing gaps, and analyzes the evolutionary history of its centromeric regions across great apes.

Merqury estimates assembly consensus quality, k-mer completeness, and trio-based phasing from read k-mers alone, avoiding reference alignment; validated on Arabidopsis F1 hybrid and human NA12878 assemblies.

HiCanu improves genome assembly accuracy and haplotype resolution using HiFi long reads, achieving high contig size and consensus accuracy in human genomes.

The paper presents an improved genome assembly of Aedes albopictus, revealing new biological features and enabling population and developmental studies.

The paper presents a gapless, telomere-to-telomere assembly of the human X chromosome using ultra-long-read nanopore sequencing and complementary technologies.

The paper presents improved pig reference genomes using long-read sequencing, enhancing continuity and accuracy for pig genetics and genomics research.

This study evaluates the impact of sequence depth and read length on long-read assembly quality for the maize genome, finding that lower depths and shorter reads result in fragmented assemblies.

The paper presents an optimized PromethION nanopore sequencing method and new computational tools for efficient human genome assembly, achieving high accuracy and speed.

The paper introduces a weighted minimizer sampling algorithm to improve long-read mapping accuracy, particularly in repetitive regions, by reducing false positives while maintaining match guarantees.

The paper compares genome structure, sequence, and immunogenic potential of Plasmodium falciparum strains used in vaccine trials and finds significant differences affecting vaccine efficacy.

The paper improves Anopheles genome assemblies using comparative genomics methods and experimental data, resulting in more contiguous and chromosomally anchored assemblies.

The paper introduces a method to estimate genome containment in metagenomes and applies it to identify a novel polyomavirus.