Paul Medvedev 

PUBLICATIONS

Peer-Reviewed Conference Publications

  1. Paul Medvedev, Eric Scott, Boyko Kakaradov, and Pavel Pevzner, Error Correction of High-Throughput Sequencing Datasets with Non-Uniform Coverage, ISMB 2011, appears in Bioinformatics (2011) 27 (13): i137-i141.
  2. Paul Medvedev*, Son Pham*, Mark Chaisson, Glenn Tesler and Pavel Pevzner, Paired de Bruijn Graphs: a Novel Approach for Incorporating Mate Pair Information into Genome Assemblers, RECOMB 2011, LNCS 6577:238-251.
  3. Shortest Paths between Shortest Paths and Independent Sets, with Marcin Kaminski and Martin Milanic, International Workshop on Combinatorial Algorithms (IWOCA), 2010. (extended abstract, full version)
  4. Rearrangement Models and Single-Cut Operations, with Jens Stoye, RECOMB-CG, 2009. (conference version, journal version)
  5. On the Plane-Width of Graphs, with Marcin Kaminski and Martin Milanic, European Conference on Combinatorics, Graph Theory and Applications (EuroComb 2009), ENDM 34 (2009) 633-637. (extended abstract, journal version)
  6. Paul Medvedev and Michael Brudno, Ab Initio Whole Genome Shotgun Assembly With Mated Short Reads, RECOMB 2008, LNCS 4955:50-64. (conference version, journal version)
  7. Paul Medvedev, Konstaninos Georgiou, Gene Myers, and Michael Brudno, Computability of Models for Sequence Assembly, Algorithms in Bioinformatics, 7th International Workshop, WABI 2007, LNCS 4645:289-301.
  8. The Relative Worst Order Ratio Applied to Seat Reservation with Joan Boyar, Proceedings of the Ninth Scandinavian Workshop on Algorithm Theory, SWAT 2004, LNCS 3111:90-101. (conference version, journal version)
  9. Haiyun Luo, Paul Medvedev, Jerry Cheng and Songwu Lu, A Self-Coordinating Approach to Distributed Fair Queueing in Ad Hoc Wireless Networks, IEEE INFOCOM 2001, Anchorage, Alaska, Apr. 2001

    Peer-Reviewed Journal Publications

  10. Paul Medvedev*, Son Pham*, Mark Chaisson, Glenn Tesler and Pavel Pevzner, Paired de Bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers, Journal of Computational Biology, 18(11): 1625-1634, 2011.
  11. Shortest Paths between Shortest Paths, with Marcin Kaminski and Martin Milanic, Theoretical Computer Science, 412(39):5205-5210, 2011.
  12. The Plane-Width of Graphs, with Marcin Kaminski and Martin Milanic, Journal of Graph Theory, 68(3):229-245, 2011.
  13. Paul Medvedev, Marc Fiume, Misko Dzamba, Tim Smith, Michael Brudno, Detecting Copy Number Variation with Mated Short Reads, Genome Research, 20:1613-1622, 2010.
  14. Rearrangement Models and Single-Cut Operations, with Anne Bergeron and Jens Stoye, Journal of Computational Biology, 17(9):1213-1225, 2010.
  15. Paul Medvedev, Monica Stanciu, Michael Brudno, Computational Methods for Discovering Structural Variation with Next Generation Sequencing, Nature Methods, 6(11):S13-S20, 2009.
  16. Paul Medvedev and Michael Brudno, Maximum Likelihood Genome Assembly, Journal of Computational Biology, 16(8):1101-1116, 2009.
  17. The Relative Worst Order Ratio Applied to Seat Reservation, with Joan Boyar, ACM Transactions on Algorithms, 4(4):1-22, 2008.

    Other Publications/Manuscripts

  18. A Report on the 2009 SIG on Short Read Sequencing and Algorithms (Short-SIG), with Michael Brudno, Jens Stoye, and Fransisco M. de la Vega, Bioinformatics, 2009

    Joint first authors are indicated with (*).

    Please do not hesiitate to e-mail me for a copy of a paper if your institution does not provide you access.


Paul Medvedev 2011-12-05