Sergey Koren, PhD

Associate Investigator

sergey.korennih.gov

Sergey received his PhD in computer science in 2012 under the supervision of Mihai Pop at the University of Maryland. He joined the National Bioforensics Analysis Center in 2011 and was appointed as an associate principal investigator in 2014. During this time, he pioneered the use of single-molecule sequencing for the reconstruction of complete genomes. In 2015, he joined the National Human Genome Research Institute as a founding member of the Genome Informatics Section. His research focuses on the efficient analysis of large-scale genomic datasets and new methods for metagenomic analysis and assembly of high-noise single-molecule sequencing data.

Software

Verkko

Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of long accurate (e.g. PacBio HiFi) and ultra-long (e.g. Oxford Nanopore UL) reads. Verkko is Finnish for net, mesh and graph.

Merqury

Evaluate genome assemblies with k-mers and more

Winnowmap

A long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences.

MetaMaps

Long-read metagenomic analysis
News posts

Human genome assemblies with nanopore, an update

May 23, 2018

Assembling the Cliveome

April 28, 2017

Assembly of a human genome from nanopore sequencing data

January 8, 2017
Publications
Recombination between heterologous human acrocentric chromosomes
Nature, May 10, 2023
Guarracino A, Buonaiuto S, de Lima LG, Potapova T, Rhie A, Koren S, Rubinstein B, Fischer C, Human Pangenome Reference Consortium, Gerton JL, Phillippy AM, Colonna V, Garrison E
Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions
BMC Biology, April 3, 2023
Waldbieser GC, Liu S, Yuan Z, Older CE, Gao D, Shi C, Bosworth BG, Li N, Bao L, Kirby MA, Jin Y, Wood ML, Scheffler B, Simpson S, Youngblood RC, Duke MV, Ballard L, Phillippy A, Koren S, Liu Z
Genome and genetic engineering of the house cricket (Acheta domesticus): a resource for sustainable agriculture
Biomolecules, March 24, 2023
Dossey AT, Oppert B, Chu FC, Lorenzen MD, Scheffler B, Simpson S, Koren S, Johnston JS, Kataoka K, Ide K