Sergey Koren

GBZ-base and GAF-base: Indexed pangenome file formats

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

Biobank-scale genotyping of Robertsonian translocations reveals hidden structural variation on the human acrocentric chromosomes

Short-read genomes can flag Robertsonian translocation carriers by counting rDNA distal junction (DJ) copies (8 rather than 10); UK Biobank screening found 583 candidates, 1 in 841.

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.

Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures

The paper presents a population-scale Y chromosome reference panel with 142 assemblies, revealing structural and epigenetic variation across 180,000 years of evolution.

Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet

The paper introduces Verkko-Fillet, a tool for refining genome assemblies, and applies it to produce a telomere-to-telomere giraffe genome.

The complete genome of a songbird

This paper presents the first fully phased, diploid, telomere-to-telomere genome of the zebra finch, revealing new genes and structural features.

A complete diploid human genome benchmark for personalized genomics

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 Vertebrate Genomes Project Phase I: A global reference genome resource

The Vertebrate Genomes Project Phase I provides high-quality reference genomes for 816 species, enabling evolutionary and conservation insights across vertebrates.

A near-complete human pancreatic cancer genome

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

Germline sequence variation within the ribosomal DNA is associated with human complex traits

The paper identifies rDNA sequence variants associated with human traits using UK Biobank data, finding enrichment in body size traits within the 28S rRNA Expansion Segment 15L region.

The complete genome of the KOLF2.1J reference iPSC line

The paper generates and characterizes a custom genome assembly for the KOLF2.1J iPSC line to improve genomic analysis accuracy compared to standard references.

Automatic Generation of Model Sequences for Complex Regions in Assembly Graphs

The paper introduces TTT, an algorithm that resolves assembly graph tangles in genomes, improving the accuracy of complex regions in reference assemblies.

Fully Phased Telomere-to-Telomere Assemblies for Thoroughbred Horse and Donkey Haplotypes derived from a Mule Illuminate the Peculiar Evolution of Equid Centromeres

The paper presents telomere-to-telomere genome assemblies of a Thoroughbred horse and donkey derived from a mule, revealing insights into equid centromere evolution and plasticity.

Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance

The paper presents T2T reference genomes from a multi-generational pedigree to study genetic and epigenetic inheritance across the complete genome.

Complete de novo assembly and re-annotation of the zebrafish genome

The paper presents a new zebrafish genome assembly with increased sequence coverage and improved annotation, along with a pangenome resource for variant analysis.

Bighorn sheep T2T genome assembly reveals differences in immune genes: a potential cause of high morbidity due to respiratory pathogens

This paper presents a telomere-to-telomere genome assembly of bighorn sheep, revealing immune gene differences that may explain their susceptibility to respiratory pathogens.

The formation and propagation of human Robertsonian chromosomes

This study assembles human Robertsonian chromosomes, identifies a common breakpoint and centromere epigenetic changes, and explores structural features enabling their formation.

Complex genetic variation in nearly complete human genomes

Hybrid HiFi/ultra-long ONT assemblies of 65 diverse humans yield 130 haplotypes, 1,246 complete centromeres, and a pangenome panel enabling short-read genome inference at median QV 45.

Verkko2: Integrating proximity ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding

Verkko2 improves genome assembly by integrating proximity ligation data with long-read De Bruijn graphs, enabling complete telomere-to-telomere assemblies for diploid human genomes.

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing

This paper demonstrates that ONT Duplex sequencing combined with Pore-C data can assemble complete, high-quality human and plant chromosomes with base accuracy over 99.999%.

Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing

Graphasing uses Strand-seq and assembly graphs to produce chromosome-scale haplotypes without parental data or intermediate steps.

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes

The paper produces gapless assemblies of ape sex chromosomes for five great apes and a lesser ape, revealing divergence in Y chromosomes and evolutionary dynamics.

Phased nanopore assembly with Shasta and modular graph phasing with GFAse

The paper introduces methods for haplotype-resolved de novo assembly using Shasta and GFAse, showing improved assembly quality with newer Oxford Nanopore reads.

The variation and evolution of complete human centromeres

A second complete human centromere set (CHM1) plus 31 nonhuman primate centromeres reveals extensive α-satellite higher-order repeat variation, kinetochore repositioning, and saltatory emergence of new repeats.

The genome of the colonial hydroid Hydractinia reveals their stem cells use a toolkit of genes shared with all animals

This study characterizes the genome and single-cell transcriptome of Hydractinia, revealing that its stem cells use a conserved gene toolkit shared with all animals.

Improved sequence mapping using a complete reference genome and lift-over

The paper introduces levioSAM2, a method for accurate lift-over between genome assemblies, improving variant calling accuracy when mapping to older references.

The complete sequence of a human Y chromosome

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

The reference genome of the paradise fish (Macropodus opercularis)

The paper reports the reference genome of the paradise fish (Macropodus opercularis) using long-read sequencing, identifying 20,157 protein-coding genes and demonstrating high completeness.

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

A Draft Human Pangenome Reference

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.