Sergey Koren, Ph.D.

Bioinformatics Scientist, Genomics
National Biodefense Analysis and Countermeasures Center
Previously, J. Craig Venter Institute

Affiliations:

Center for Bioinformatics and Computational Biology
University of Maryland

Email: sergek[at]umd.edu

Research

I received my Ph.D. in Computer Science at the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park. My advisor was Mihai Pop.

My research interest is genomic assembly, specifically the aplication of graph analysis to metagenomes. I am also interested in the application of high-performance computing to genome assembly. I am a primary developer of the Bambus 2, pacBioToCA, and metAMOS projects. I am also a contributor to the Celera Assembler. Please look at the Graphs to Diversity project for more information.

I have developed or co-developed the following software tools:

  • metAMOS - a metagenomic assembly pipeline
  • pacBioToCA - a PacBio RS correction and assembly pipeline
  • Bambus 2 - a metagenomic standalone scaffolder, also applicable to single-cell and clonal projects
  • AMOS - shotgun sequence assembly infrastructure
  • Celera Assembler - a shotgun whole-genome assembler

Publications

PubMed, Google Scholar (⇔ denotes equal contribution)

  1. Complete Closed Genome Sequences of Mannheimia haemolytica Serotypes A1 and A6, Isolated from Cattle
    Harhay GP, Koren S, Phillippy AM, McVey DS, Kuszak J, Clawson ML, Harhay DM, Heaton MP, Chitko-McKown CG, Smith TPL. Genome Announcements May/June 2013.
  1. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.
    Treangen TJ ⇔ Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M. Genome Biology 14:R2 2013.
  1. Molecular epidemiologic investigation of an anthrax outbreak among heroin users, Europe.
    Price EP, Seymour ML, Sarovich DS, Latham J, Wolken R, Mason J, Vincent G, Drees KP, Beckstrom-Sternberg SM, Phillippy AM, Koren S, Okinaka RT, Chung W, Schupp JM, Wagner DM, Vipond R, Foster JT, Bergman NH, Burans J, Pearson T, Brooks T, Keim P. Emerging Infectious Diseases. 2012
  1. Hybrid error correction and de novo assembly of single-molecule sequencing reads.
    Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, and Phillippy AM. Nature Biotechnology 30(7):693-700 2012
  1. The bonobo genome compared with the chimpanzee and human genomes.
    Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, Higashino S, Hobolth A, Dutheil J, Karakoç E, Alkan C, Sajjadian S, Catacchio CR, Ventura M, Marques-Bonet T, Eichler EE, André C, Atencia R, Mugisha L, Junhold J, Patterson N, Siebauer M, Good JM, Fischer A, Ptak SE, Lachmann M, Symer DE, Mailund T, Schierup MH, Andrés AM, Kelso J, and Pääbo S. Nature Jun 28;486(7404):527-531 2012.
  1. Structure, function and diversity of the healthy human microbiome.
    Human Microbiome Project Consortium. Nature Jun 13;486(7402):207-14 2012.
  1. A framework for human microbiome research.
    Human Microbiome Project Consortium. Nature Jun 13;496(7402):215-21 2012.
  1. GAGE: A critical evaluation of genome assemblies and assembly algorithms.
    Salzberg SL, Phillippy AM, Zimin AV, Puiu D, Magoc T, Koren S, Treangen T, Schatz MC, Delcher AL, Roberts M, Marcais G, Pop M, Yorke JA. Genome Research 22:557-567 2012.
  1. Assemblathon 1: A competitive assessment of de novo short read assembly methods.
    Earl, DA et al. Genome Research Sep 16 2011.
  1. Bambus 2: Scaffolding Metagenomes.
    Koren S, Treangen TJ, Pop M. Bioinformatics 27(21): 2964-2971 2011.
  1. Next Generation Sequence Assembly with AMOS.
    Treangen, TJ, Sommer, DD, Angly, FE, Koren, S and Pop, M. Current Protocols in Bioinformatics. 33:11.8.1-11.8.18 2011.
  1. An algorithm for automated closure during assembly.
    Koren S, Miller JR, Walenz BP, Sutton G. BMC Bioinformatics 11:457 2010.
  1. Assembly algorithms for next-generation sequencing data.
    Miller JR, Koren S, Sutton G. Genomics Jun;95(6):315-27 2010.
  1. A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads.
    Rausch T, Koren S, Denisov G, Weese D, Emde A, Doring A, and Reinert K. Bioinformatics 25(9): 1118-1124 2009.
  1. Aggressive assembly of pyrosequencing reads with mates.
    Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, and Sutton G. Bioinformatics 24:2818-2824 2008.


Presentations

Talks (since 2009) (‡ denotes invited talk/seminar)

  1. "One-step bacterial genome closure with single-molecule hybrid assembly"‡ UC Davis, Davis, CA. November 2012.
  2. "One-step bacterial genome closure with single-molecule hybrid assembly"‡ Symposium on PacBio SMRT Sequencing. Sanford University, Stanford, CA. November 2012.
  3. "Hybrid Error Correction and De Novo Assembly of Single-Molecule Sequencing Reads."‡ NGS Leaders Webinar, August, 2012.
  4. "One Chromosome, One Contig: Towards Closed Bacterial Genomes using Single-Molecule Sequencing Reads." Sequencing, Finishing and Analysis in the Future, Santa Fe, NM, June 2012.
  5. "One Chromosome, One Contig : Hybrid Error Correction and de Novo Assembly of Single-Molecule Sequencing Reads."‡ Indiana University, Bloomington, May 2012.
  6. Ph.D. Thesis Defense, University of Maryland, March 2012.
  7. "Hybrid Error Correction and De Novo Assembly of Single-Molecule Sequencing Reads."‡ AGBT Pacific Biosciences User Group Meeting, February 2012.
  8. "Hands-on PacBio RS hybrid correction and assembly using the Celera Assembler."‡ Celera Assembler User Group Meeting, J. Craig Venter Institute, January 2012.
  9. "Metagenomic Assembly with metAMOS."‡ JGI Metagenomics Informatics Challenges Workshop, JGI Walnut Creek, October 2011.
  10. "Single-cell assembly workshop."‡ Bigelow Laboratory's redefining microbial genomics: The power of sequencing individual cells workshop, Bigelow Labs, September 2010.
  11. "Adapting Celera Assembler to Finishing Sequences." Sequencing, Finishing and Analysis in the Future, Santa Fe, NM, May 2009.

Posters (since 2009)

  1. "One-step bacterial genome closure with single-molecule hybrid assembly." Koren S, et al. Microbial Genomics. Lake Arrowhead, CA. September 2012.
  2. "Hybrid Error Correction and De Novo Assembly of Single-Molecule Sequencing Reads."
    Koren S, Schatz MC, Walenz BP, Martin J, Howard J, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, and Phillippy AM. AGBT, February 2012.
  3. "ScaffViz: Visualizing metagenomic assemblies."
    Koren S, Treangen TJ, and Pop M. Beyond the Genome, September, 2011.
  4. "MetAMOS: a metagenomic assembly and analysis pipeline for AMOS."
    Treangen TJ ⇔ Koren S, Astrovskaya I, Sommer D, Liu B, and Pop M. Beyond the Genome, September, 2011.
  5. "Separation of Propionibacterium acnes genomes HMP110/SK182."
    Koren S, Durkin S, Gillis M, Hostetler J, McCorrison J, Miller J, Perez-Perez G, Radune D, Tatz J, Torralba M, Blaser M, Sutton G and Nelson K. Sequencing, Finishing and Analysis in the Future, May, 2010.
  6. "Metagenomic assembly strategies."
    Koren S, Rusch D, Miller J, Sutton G and Pop, M. Sequencing, Finishing and Analysis in the Future, May 2010.
  7. "The Bonobo de novo genome assembly generated by CABOG."
    Miller J, Walenz B, Koren S and Sutton, G. International Conference on Intelligent Systems for Molecular Biology (ISMB), July 2010.
  8. "Shotgun assembly of a repetitive plant genome."
    Miller J, Koren S, Walenz B, and Sutton, G. Sequencing, Finishing and Analysis in the Future, May 2009.


Education