Publications

• Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, and Glenn Tesler. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29(8) (2013), pp. 1072-1075. doi:10.1093/bioinformatics/btt086

• Son K. Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel A. Pevzner, and Max A. Alekseyev. Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly. Journal of Computational Biology 20(4) (2013), 359-371. doi:10.1089/cmb.2012.0098

• Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. Alekseyev, and Pavel A. Pevzner. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology 19(5) (2012), 455-477. doi:10.1089/cmb.2012.0021

RECOMB 2014 (Pittsburgh, USA, April 2-5, 2014)

Yana Safonova, Anton Bankevich, and Pavel Pevzner. dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.  In Sharan, Roded (eds.) RECOMB 2014, LNCS (8394). pp. 265-279. Springer, Heidelberg (2014)

The Annual DOE JGI User Meeting (Walnut Creek, USA, March 18-20, 2014)

RECOMB 2013   (Beijing, China, April 7-10, 2013)

• Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey Gurevich, Anton Korobeynikov, Alla Lapidus, Andrey Prjibelsky, Alexey Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Jeffrey McLean, Roger Lasken, Scott Clingenpeel, Tanja Woyke, Glenn Tesler, Max Alekseyev, and Pavel Pevzner. Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads. Lecture Notes in Computer Science 7821 (2013), pp. 158–170. doi:10.1007/978-3-642-37195-0_13
• posters:
  • Yana Safonova, Alexey Kondrashov, Maria Logacheva, Aleksey Penin, Anton Bankevich: NGS assembly of highly polymorphic diploid genomes.
  • Dmitry Antipov, Ksenia Krasheninnikova, and Pavel A. Pevzner: using uneven coverage depth in bacterial single-cell repeat resolution.
  • Alexey Gurevich, Vlad Saveliev, Nikolay Vyahhi, and Glenn Tesler: quality assessment of genome assemblies (web tool).

APBC 2013 (Vancouver, Canada, January 21-23, 2013)

• Sergey I. Nikolenko, Anton Korobeynikov, and Max A. Alekseyev. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics 14(Suppl 1) 2013, pp. S7. doi:10.1186/1471-2164-14-S1-S7

RECOMB-CG 2012 (Niterói, Brazil, October 17-19, 2012)

• Sergey Aganezov, Jr. and Max A. Alekseyev. On pairwise distances and median score of three genomes under DCJ. BMC Bioinformatics 13(Suppl 19) (2012), pp. S1. doi:10.1186/1471-2105-13-S19-S1

WABI 2012 (Ljubljana, Slovenia, September 10-12, 2012):

• Nikolay Vyahhi, Alexey Pyshkin, Son K. Pham, Pavel Pevzner. From de Bruijn Graphs to Rectangle Graphs for Genome Assembly, Lecture Notes in Bioinformatics 7534 (2012), pp. 249-261. doi:10.1007/978-3-642-33122-0_20
• Natalie E Castellana, Andrey Lushnikov, Piotr Rotkiewicz, Natasha Sefcovic, Pavel A. Pevzner, and Adam Godzik, Kira Vyatkina. MORPH-PRO: A Novel Algorithm and Web Server for Protein Morphing, Lecture Notes in Bioinformatics 7534 (2012), pp. 262-273. doi:10.1007/978-3-642-33122-0_21
• Ilya Minkin, Nikolay Vyahhi, Son Pham. "SyntenyFinder: A Synteny Blocks Generation and Genome Comparison Tool" (poster)
• Andrey D. Prjibelski, Tatiana Krivosheeva, Anton Bankevich, Sergey Nurk, Son Pham, Pavel A. Pevzner. "Path-Extend: An Approach for Repeat Resolution in de novo Genome Assembly" (poster)

   

8th Joint Meeting of AFERP, ASP, GA, PSE and SIF (New York City, July 28 - August 1, 2012):

• EA Monroe, H Choi, V Lesin, A Sirotkin, M Dvorkin, P Pevzner, WH Gerwick, L Gerwick. Genomic insights into secondary metabolism of the natural product-rich cyanobacterium Moorea bouillonii. Planta Med 78(11) (2012), pp. CL52. doi:10.1055/s-0032-1320287

CSR 2012 (Nizhni Novgorod, Russia, July 21-24, 2012)

• Max A. Alekseyev. Challenges in Comparative Genomics: from Biological Problems to Combinatorial Algorithms (and back). (talk)

• Yakov Sortkin, Xiaowen Liu, Maxim Gladkikh, Pavel A. Pevzner and Kira Vyatkina. Peptide Sequence Tags for Top-Down Spectra. (poster, session TP25) 

RECOMB 2012 (Barcelona, Spain, April 21-24, 2012):

• Yakov Sortkin, Xiaowen Liu, Maxim Gladkikh, Pavel A. Pevzner and Kira Vyatkina. Peptide Sequence Tags for Top-Down Spectra. (talk) 

POSTGENOME 2011 (Novosibirsk, Russia, November 14-17, 2011):

• Max Alekseyev. SPAdes: новый ассемблер геномов с поддержкой одноклеточного секвенирования. (talk)

ISMB 2011 (Vienna, Austria, July 15-19, 2011):

• Max Alekseyev, Pavel Pevzner. The Birth and Death of Fragile Regions in Human Genome (highlight track paper).

• Mikhail Dvorkin, Alexander Kulikov, Max Alekseyev. Earmark Graph Approach to de novo genome assembly (poster).

• Sergey Nikolenko, Max Alekseyev, Pavel Pevzner. Bayesian Evaluation of de novo Genome Assembly (poster).

• Nikolay Vyahhi, Sergey Nurk, Anton Bankevich, Max Alekseyev, Pavel Pevzner. Expandable de novo genome assembler for short-read sequence data (HiTSeq poster).

• Xiaowen Liu, Yakov Sirotkin, Yufeng Shen, Gordon Anderson, Yihsuan S. Tsai, Ying S. Ting, David R. Goodlett, Richard D. Smith, Vineet Bafna, Pavel A. Pevzner. Protein Identification Using Top-Down Spectra (poster).

G10K Genome Assembly Workshop 2011 (Santa Cruz, USA, March 14-16, 2011):

• Pavel A. Pevzner. How Will the Human Genome Evolve in the Next Million Years? (talk)