About Me

I'm a Ph.D. Student student in CS at the CBCB.
I am currently working at BNBI on assembly. I used to work on the Celera Assembler at the JCVI.
My adviser is Mihai Pop.


Research

My research interest is in genomic assembly, specifically the aplication of graph analysis to metagenomes. Please look at the Graphs to Diversity project for more information.

I'm also interested in the application of high-performance computing to assembly. My code is available though the AMOS and CA projects. For more details, see Bambus2. I am also participating in the metAMOS project.


Selected Publications

  1. 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. GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Research 2011.
  2. Koren S., Treangen TJ, Pop M. Bambus 2: Scaffolding Metagenomes. Bioinformatics 27(21): 2964-2971 2011.
  3. Treangen, T. J., Sommer, D. D., Angly, F. E., Koren, S. and Pop, M. 2011. Next Generation Sequence Assembly with AMOS. Current Protocols in Bioinformatics. 33:11.8.1-11.8.18.
  4. Koren S., Miller J.R., Walenz B.P., Suttion G. An algorithm for automated closure during assembly. BMC Bioinformatics 11:457 2010.
  5. Miller J.R., Koren S., Sutton G. Assembly algorithms for next-generation sequencing data. Genomics Jun;95(6):315-27 2010. 1.
  6. Rausch T., Koren S., Denisov G., Weese D., Emde A., Doring A., and Reinert K. A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. Bioinformatics 25:1118-1124 2009.
  7. Miller J.R., Delcher A.L., Koren S., Venter E., Walenz B.P., Brownley A., Johnson J., Li K., Mobarry C., and Sutton G. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 24:2818-2824 2008.
Full list is available through PubMed.


Presentations

  1. PacBio RS hybrid correction and assembly using Celera Assembler at the CAUG 2012, January 2012.
  2. Metagenomic Assembly with metAMOS at the JGI Metagenomics Informatics Challenges Workshop, October, 2011.
  3. Single-cell assembly workshop at the Bigelow Laboratory Redefining microbial genomics: The power of sequencing individual cells Workshop, September 2010.


Contact Me

  1. UMD - sergek AT umd.edu