Sergey Koren, PhD

Staff Scientist

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.



A fast and approximate long read mapper


A single molecule sequence assembler for genomes large and small


Fast genome and metagenome distance and containment estimation using MinHash


A probabilistic sequence overlap algorithm
News posts

Assembling the Cliveome

April 28, 2017

Assembly of a human genome from nanopore sequencing data

January 8, 2017
De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads
BMC Biology, January 11, 2018
Eccles D, Chandler J, Camberis M, Henrissat B, Koren S, Gros GL, Ewbank JJ
Analysis of the Aedes albopictus C6/36 genome provides insight into cell line adaptations to in vitro viral propagation
Gigascience, January 10, 2018
Miller JR, Koren S, Dilley KA, Puri V, Brown DM, Harkins DM, Thibaud-Nissen F, Rosen BD, Chen X, Tu Z, Sharakhov IV, Sharakhova MV, Sebra R, Stockwell TB, Bergman NH, Sutton GG, Phillippy AM, Piermarini PM, Shabman RS
Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control
bioRxiv, December 29, 2017
Matthews BJ … Koren SPhillippy AM, Vosshall LB
De novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
Plant Cell, October 13, 2017
Schmidt MHW, Vogel A, Denton AK, Istace B, Wormit A, Geest H, Bolger ME, Alseekh S, Maß J, Pfaff C, Schurr U, Chetelat RT, Maumus F, Aury JM, Koren S, Fernie AR, Zamir D, Bolger A, Usadel B