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Sergey Nurk

Hello, dear guest.

My name is Sergey Nurk and I live in Saint-Petersburg, Russia.

In 2011 I graduated with honors from SPbSU Department of Software Engineering

Currently I am a PhD student in Saint-Petersburg Academic University.

 

As you probably noticed, I work at Pavel Pevzner's Algorithmic Biology Lab on the development of SPAdes genome assembler and projects in the field of comparative genomics.

My interests include:

  • algorithms design
  • computational genomics
  • bioinformatics
  • software design
  • data analysis

Here is my detailed cv. If you decide to contact me, don't hesitate to write to sergeynurk at gmail dot com

 

Publications:

1. Sergey Nurk, Pavel A. Pevzner

SPArcle: Identifying Microbial Genome Variations with Colored de Bruijn Graphs”.

Manuscript in preparation

2. Yu Lin, Sergey Nurk and Pavel A. Pevzner

What is the difference between the breakpoint graph and the de Bruijn graph? ”.

S6 BMC Genomics Volume 15 Supplement 6, 2014: Proceedings of the Twelfth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics.

3. Gabriela I Guzman, Jose Utrilla, Sergey Nurk, Elizabeth Brunk, Jonathan M Monk, Ali Ebrahim, Bernhard Ø Palsson, Adam M. Feist

Model-driven discovery of underground metabolic functions in Escherichia coli”.

Accepted to PNAS

4. Andrey D. Prjibelski, Irina Vasilinetc, Anton Bankevich, Alexey Gurevich, Tatiana Krivosheeva, Sergey Nurk, Son Pham, Anton Korobeynikov, Alla Lapidus and Pavel A. Pevzner

ExSPAnder: a universal repeat resolver for DNA fragment assembly”.

Bioinformatics, 30(12), i293-i301, 2014

5. Sergey Nurk, Anton Bankevich ( equal contribution), Dmitry Antipov, Alexey A. Gurevich, Anton Korobeynikov, Alla Lapidus, Andrey D. Prjibelski, Alexey Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Scott R. Clingenpeel, Tanja Woyke, Jeffrey S. Mclean, Roger Lasken, Glenn Tesler, Max A. Alekseyev, and Pavel A. Pevzner

Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products”.

Journal of Computational Biology 20(10), 2013

6. Sergey Nurk, Anton Bankevich ( equal contribution), Dmitry Antipov, Alexey A. Gurevich, Anton Korobeynikov, Alla Lapidus, Andrey Prjibelsky, Alexey Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Jeffrey McLean, Roger Lasken, Scott R. Clingenpeel, Tanja Woyke, Glenn Tesler, Max A. Alekseyev, and Pavel A. Pevzner

Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads”.

Proceedings of the 17th Annual International Conference on Research in Computational Molecular Biology, Lecture Notes in Computer Science 7821 (2013).

7. Jeffrey S. McLean, Mary-Jane Lombardo, Michael G. Ziegler, Mark Novotny, Joyclyn Yee-Greenbaum, Jonathan H. Badger, Glenn Tesler, Sergey Nurk, Valery Lesin, Daniel Brami, Adam P. Hall, Anna Edlund, Lisa Z. Allen, Scott Durkin, Sharon Reed, Francesca Torriani, Kenneth H. Nealson, Pavel A. Pevzner, Robert Friedman, J. Craig Venter and Roger S. Lasken

Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single cell genomic platform”.

Genome research, 23(5), 867-877

8. Anton Bankevich, Sergey Nurk ( equal contribution), Dmitry Antipov, Alexey Gurevich, Mikhail Dvorkin, Alexander Kulikov, Valery Lesin, Sergey Nikolenko, Son Pham, Andrey Prjibelski, Alexey Pyshkin, Alexander Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max Alekseyev and Pavel Pevzner

SPAdes: a New Genome Assembler and its Applications to Single Cell Sequencing”.

Journal of Computational Biology 19(5), 2012

9. Sergey Nurk

An Upper Bound for Circuit SAT”.

PDMI preprint 10/2009, 2009