Sergey Koren
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View article: The complete genome of a songbird
The complete genome of a songbird Open
Bird genomes are the smallest among amniotes, but remain challenging to assemble due to their structural complexity. This study presents the first fully phased, diploid, telomere-to-telomere (T2T) reference genome for the zebra finch ( Tae…
View article: Bighorn sheep T2T genome assembly reveals differences in immune genes: a potential cause of high morbidity due to respiratory pathogens
Bighorn sheep T2T genome assembly reveals differences in immune genes: a potential cause of high morbidity due to respiratory pathogens Open
The bighorn sheep ( Ovis canadensis ), despite its close relation to domestic sheep, suffer higher morbidity and mortality from respiratory disease complexes, likely due to genetic differences in immune responses. Unraveling highly repetit…
View article: Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet
Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet Open
SUMMARY High-quality genome assemblies are essential for understanding speciation, evolution, and for building reference genomes and pan-genomes. Despite major advances in long-read sequencing technologies and graph-based assembly algorith…
View article: Reference-guided assembly of metagenomes with MetaCompass
Reference-guided assembly of metagenomes with MetaCompass Open
Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used i…
View article: The formation and propagation of human Robertsonian chromosomes
The formation and propagation of human Robertsonian chromosomes Open
Robertsonian chromosomes are a type of variant chromosome that is commonly found in nature. Present in 1 in 800 humans, these chromosomes can underlie infertility, trisomies and increased cancer incidence1-5. They have been reco…
View article: A complete diploid human genome benchmark for personalized genomics
A complete diploid human genome benchmark for personalized genomics Open
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and structurally polymorphic regions of the…
View article: Analysis of a Novel Human Protein, ORF3, Encoded by Spacer rDNA
Analysis of a Novel Human Protein, ORF3, Encoded by Spacer rDNA Open
An open reading frame in the intergenic spacer of human ribosomal (r)DNA codes for a 190 amino acid, 22 kDa protein that we have named ORF3. It comprises a 5’AluSx repeat sequence encoding 96 amino acids followed by a stretch of 94 amino a…
View article: Author Correction: Complex genetic variation in nearly complete human genomes
Author Correction: Complex genetic variation in nearly complete human genomes Open
View article: Complex genetic variation in nearly complete human genomes
Complex genetic variation in nearly complete human genomes Open
Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (med…
View article: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding Open
The Telomere-to-Telomere Consortium recently finished the first truly complete sequence of a human genome. To resolve the most complex repeats, this project relied on the semimanual combination of long, accurate Pacific Biosciences (PacBio…
View article: Bighorn Sheep T2T Genome Assembly Reveals Differences in Immune Genes: A Potential Cause of High Morbidity Due to Respiratory Pathogens
Bighorn Sheep T2T Genome Assembly Reveals Differences in Immune Genes: A Potential Cause of High Morbidity Due to Respiratory Pathogens Open
View article: The Complete Genome of a Songbird
The Complete Genome of a Songbird Open
View article: Verkko2: Integrating proximity ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
Verkko2: Integrating proximity ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding Open
The Telomere-to-Telomere Consortium recently finished the first truly complete sequence of a human genome. To resolve the most complex repeats, this project relied on the semi-manual combination of long, accurate PacBio HiFi and ultra-long…
View article: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing Open
The combination of ultra-long (UL) Oxford Nanopore Technologies (ONT) sequencing reads with long, accurate Pacific Bioscience (PacBio) High Fidelity (HiFi) reads has enabled the completion of a human genome and spurred similar efforts to c…
View article: Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing
Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing Open
View article: Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content
Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content Open
Reference genomes of cattle and sheep have lacked contiguous assemblies of the sex-determining Y chromosome. Here, we assemble complete and gapless telomere to telomere (T2T) Y chromosomes for these species. We find that the pseudo-autosom…
View article: The formation and propagation of human Robertsonian chromosomes
The formation and propagation of human Robertsonian chromosomes Open
Robertsonian chromosomes are a type of variant chromosome found commonly in nature. Present in one in 800 humans, these chromosomes can underlie infertility, trisomies, and increased cancer incidence. Recognized cytogenetically for more th…
View article: Complex genetic variation in nearly complete human genomes
Complex genetic variation in nearly complete human genomes Open
Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here, we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (13…
View article: Whole-genome sequence of <i>Mucor velutinosus</i> NIH1002, a strain associated with disseminated disease
Whole-genome sequence of <i>Mucor velutinosus</i> NIH1002, a strain associated with disseminated disease Open
The draft genome of Mucor velutinosus NIH1002, a 2011 isolate from a case of disseminated disease, was sequenced using PacBio long-read and HiSeq short-read technologies. The genome has 43 contigs, an N50 of 2.65 Mb, and 13,295 protein-cod…
View article: The complete sequence and comparative analysis of ape sex chromosomes
The complete sequence and comparative analysis of ape sex chromosomes Open
View article: The reference genome of Macropodus opercularis (the paradise fish)
The reference genome of Macropodus opercularis (the paradise fish) Open
View article: Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph
Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph Open
View article: Phased nanopore assembly with Shasta and modular graph phasing with GFAse
Phased nanopore assembly with Shasta and modular graph phasing with GFAse Open
Reference-free genome phasing is vital for understanding allele inheritance and the impact of single-molecule DNA variation on phenotypes. To achieve thorough phasing across homozygous or repetitive regions of the genome, long-read sequenc…
View article: The variation and evolution of complete human centromeres
The variation and evolution of complete human centromeres Open
View article: The first complete T2T Assemblies of Cattle and Sheep Y-Chromosomes uncover remarkable divergence in structure and gene content
The first complete T2T Assemblies of Cattle and Sheep Y-Chromosomes uncover remarkable divergence in structure and gene content Open
View article: The genome of the colonial hydroid <i>Hydractinia</i> reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals
The genome of the colonial hydroid <i>Hydractinia</i> reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals Open
Hydractinia is a colonial marine hydroid that shows remarkable biological properties, including the capacity to regenerate its entire body throughout its lifetime, a process made possible by its adult migratory stem cells, known as i-cells…
View article: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing Open
The combination of ultra-long Oxford Nanopore (ONT) sequencing reads with long, accurate PacBio HiFi reads has enabled the completion of a human genome and spurred similar efforts to complete the genomes of many other species. However, thi…
View article: MetaCompass: Reference-guided Assembly of Metagenomes
MetaCompass: Reference-guided Assembly of Metagenomes Open
Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used i…
View article: Graph-based variant discovery reveals novel dynamics in the human microbiome
Graph-based variant discovery reveals novel dynamics in the human microbiome Open
Sequence differences between the strains of bacteria comprising host-associated and environmental microbiota may play a role in community assembly and influence the resilience of microbial communities to disturbances. Tools for characteriz…
View article: Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing
Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing Open
Haplotype information is crucial for biomedical and population genetics research. However, current strategies to produce de-novo haplotype-resolved assemblies often require either difficult-to-acquire parental data or an intermediate haplo…