Публикации

 

Статьи в журналах:

  •  Kira Vyatkina, Si Wu, Lennard J. M. Dekker, Martijn M. Vanduijn, Xiaowen Liu, Nikola Tolić, Mikhail Dvorkin, Sonya Alexandrova, Theo M. Luider, Ljiljana Paša-Tolić, and Pavel A. Pevzner. De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra. Journal of Proteome Research, DOI: 10.1021/pr501244v, September 28, 2015. [Epub ahead of Print.]
  • Xiaowen Liu, Lennard J. M. Dekker, Si Wu, Martijn M. Vanduijn, Theo M. Luider, Nikola Tolić, Qiang Kou, Mikhail Dvorkin, Sonya Alexandrova, Kira Vyatkina, Ljiljana Paša-Tolić, and Pavel A. Pevzner. De Novo Protein Sequencing by Combining Top-Down and Bottom-Up Tandem Mass Spectra. Journal of Proteome Research, 13(7):3241-3248, 2014. 

  • 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 (2014) 30 (12): i293-i301. doi: 10.1093/bioinformatics/btu266

  • Ivan Terterov, Kira Vyatkina, Vitali Boitsov, Sergey Vyazmin, Igor Popov, Alexey Kononikhin, Eugene Nikolaev, Pavel Pevzner, and Michael Dubina. Application of de novo sequencing tools to study abiogenic peptides formation by MS/MS. The case of homo-peptides from glutamic acid complicated by substitutions of hydrogen by sodium or potassium atoms. Rapid Communications in Mass Spectrometry, 28(1):33-41, 15 Jan. 2014.

  • Natalie Castellana, Andrey Lushnikov, Piotr Rotkiewicz, Natasha Sefcovic, Pavel A. Pevzner, and Adam Gozdik, Kira Vyatkina. MORPH-PRO: a novel algorithm and web server for protein morphing. Algorithms for Molecular Biology 8: 19 (2013) (invited paper following WABI 2012) doi:10.1186/1748-7188-8-19

  • Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, and Glenn Tesler. QUAST: Quality Assessment Tool for Genome Asssemblies. Bioinformatics (2013). doi:10.1093/bioinformatics/btt086

  • 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

  • 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 (2012). doi:10.1089/cmb.2012.0098

  • 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 2012; 78 - CL52 doi:10.1055/s-0032-1320287

 

International Scientific Conference "Science of the Future" (St Petersburg, Russia, September 17-20, 2014): 

  • Pavel Pevzner.  SPAdes Genome Assembler or How to Build a World-Class Laboratory in Russia in Just 12 Months. (abstract and talk)
  • Vitalii Demianiuk, Si Wu, Lennard Dekker, Martijn Vanduijn, Xiaowen Liu, Nikola Tolić, Theo Luider, Ljiljana Paša-Tolić, Pavel Pevzner and Kira Vyatkina. De Novo Sequencing of Proteins from Top-Down Tandem Mass Spectra. (abstract and talk) 

 

WABI 2014 (Wroclav, Poland, September 8-10, 2014):

  • Vitalii Demianiuk, Si Wu, Lennard Dekker, Martijn Vanduijn, Xiaowen Liu, Nikola Tolić, Theo Luider, Ljiljana Paša-Tolić, Pavel Pevzner and Kira Vyatkina. De Novo Sequencing of Proteins from Top-Down Tandem Mass Spectra. (poster) 

 

The 62nd ASMS Annual Conference on Mass Spectrometry and Allied Topics (Baltimore, MD, USA, June 15-19, 2014):

  • Kira Vyatkina, Lennard Dekker, Si Wu, Martijn Vanduijn, Vitalii Demianiuk, Xiaowen Liu, Nikola Tolić, Mikhail Dvorkin, Sonya Alexandrova, Theo Luider, Ljiljana Paša-Tolić, and Pavel Pevzner. A Top-Down Driven Approach to De Novo Sequencing of Proteins. (poster)

  • Xiaowen Liu, Lennard Dekker, Si Wu, Martijn Vanduijn, Theo Luider, Nikola Tolić, Mikhail Dvorkin, Sonya Alexandrova, Kira Vyatkina, Ljiljana Paša-Tolić, and Pavel Pevzner. De novo protein sequencing by combining-top-down and bottom-up tandem mass spectra. (poster)

 

International Conference "Towards Therapies of the Future" (Skolkovo Innovation Center, Moscow, Russia, May 26-28, 2014):

  • Kira Vyatkina, Lennard Dekker, Si Wu, Martijn Vanduijn, Vitalii Demianiuk, Xiaowen Liu, Nikola Tolić, Mikhail Dvorkin, Sonya Alexandrova, Theo Luider, Ljiljana Paša-Tolić, and Pavel Pevzner. A Top-Down Driven Approach to De Novo Sequencing of Proteins. (poster)

 

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)

Alla Lapidus, Dmitry Antipov, Anton Bankevich, Alexey Gurevich, Anton Korobeynikov, Sergey Nurk, Andrey D. Prjibelski, Yana Safonova, Irina Vasilinetc, and Pavel Pevzner. New Frontiers of Genome Assembly with SPAdes 3.0. (poster)
 
 

  • Mikhail Dvorkin, Sonya Alexandrova, Xiaowen Liu, Si Wu, Ljiljana Paša-Tolić, Nikola Tolić, Lennard Dekker, Martijn Vanduijn, Theo Luider, Pavel Pevzner, and Kira Vyatkina. Sequencing antibodies from top-down spectra. (poster)

  • Ivan Terterov, Kira Vyatkina, Vitali Boitsov, Sergey Vyazmin, Igor Popov, Alexey Kononikhin, Eugene Nikolaev, Pavel Pevzner, and Michael Dubina. Application of de novo sequencing tools to study abiogenic oligo-peptides. (poster)

 

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

 

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

 

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

 

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

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):

  • Son K. Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel Pevzner, and Max A. Alekseyev. Pathset Graphs: A Novel Approach for Comprehensive Utilization of Mate-Pairs in Genome Assembly. Lecture Notes in Computer Science 7262 (2012), pp. 200-212. doi:10.1007/978-3-642-29627-7_21

 

RECOMB CP 2012 (San Diego, CA, USA, April 6-8, 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)

 

MCCMB 2011 (Moscow, Russia, July 21-24, 2011):

 

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

 

RECOMB 2011 (Vancouver, Canada, March 28-31, 2011):

  • Hosein Mohimani, Wei Ting Liu, Yu Liang Yang, Susana Gaudencio, William Fenical, Pieter Dorrestein, and Pavel Pevzner. Multiplex De Novo Sequencing of Peptide Antibiotics. (paper, talk)

  • Julio Ng, Amihood Amir, and Pavel Pevzner. Blocked Pattern Matching Problem and its Applications in Proteomics. (paper, talk)

  • 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. (paper, talk)

  • Shuai Jiang and Max Alekseyev. Weighted genomic distance can hardly impose a bound on the proportion of transpositions. (paper, talk)

 

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)