Public

Andrey Lushnikov

Personal

e-mail: aslushnikov@gmail.com

Education

Saint Petersburg State University, Department of Mathematics and Mechanics, 2007-2012

Scientific Interests
Computational Geometry, Data Structures, Software Engeneering
 

Hobbies
Sport, tourism

Alex Davydow

 

Contact Information:

adavydow@yandex.ru

Education:

  • St. Petersburg Academic University 2010...
  • Moscow Institue of Physucs and Technology 2006-2010    
  • Moscow State School #57 2003-2006
  • Moscow State School #547 1995-2003

Scinetific Interests:

Computer science, algorithms, math, tropical geometry.

Alex Pyshkin

Alexey Pyshkin

Personal:

e-mail: lexpyh@gmail.com

Education:

  • Saint Petersburg State University, expected degree: M.S. in mathematics , 2013

  • Lyceum "Physical-Technical High School"  of the Russian Academy of Sciences, 2004 – 2008 

Scientific Interests:

Discrete analysis, Functional analysis, CS

Hobbies:

Soccer, tourism

Maxim Gladkikh

Personal

E-mail (in hex): 6D 67 6E 61 72 67 40 67 6D 61 69 6C 2E 63 6F 6D

Scientific Interests

Algorithm and Data Structures, Complexity Theory, Computational Genomics and Proteomics

Career

Academic University Algorithmic Biology Lab, researcher intern (2011)

IntelliJ Labs, programmer intern (IDEA project 2008—2009)

Experience

CSR, St. Petersburg, Russia, participant (2011)

SPbSU Math-Mech Faculty Open School Programming Championship, science committee member (2009, 2011)

ADFOCS, Saarbruecken, Germany, participant (2010)

Education

St. Petersburg Academic University of the Russian Academy of Sciences, Russia (2011—present)

St. Petersburg State University, Russia, Specialist Degree in Math and Computer Science,  (2006—2011)

Lyceum "Physical-Technical High School", St. Petersburg, Russia (2003—2005)

Awards

Wide-Siberian Open Collegiate Programming Olympiad, Vice-champion (2008 with A. Smirnov and A. Bankevich), 8-th place (2007 with A. Smirnov and A. Sidorov)

ACM ICPC NEERC, 15-th place (2008 with A. Smirnov and A. Bankevich), 18-th place (2010 with A. Udalov and V. Samoylov); both times qualified for world finals, but scored lower than best university team

St. Petersburg State University Collegiate Programming Championship, Champion (2008 with A. Levin and A. Smirnov), Vice-Champion (8 times total with 7 other persons 2007—2011)

Russian Collegiate Olympiad in Informatics, High School, 3-rd place (2005 with A.Sidorov and O. Davydov)

Mariya Fomkina

Hello dear guest!

My name is Mariya Fomkina. I'm currently a student of SPb University of the RAS.

If you decide to contact me, don't hesitate to write mariyafomkina@gmail.com

 

Илья Макеев

Ilya Makeev

Personal

 E-mail: ilya.makeev@gmail.com

 

Education

B. Sc., M. Sc. student in Math and Computer Science, St. Petersburg State University of Information Technologies, Mechanics and Optics, St. Petersburg, Russia (2007—present)

Lyceum of Mathematics and Physics #239, St. Petersburg, Russia (2004—2007)

Scientific Interests

bioinformatics, computational geometry

 

Alexey Gurevich

Research Scientist at Center for Algorithmic Biotechnology, Saint Petersburg State University

 

Personal:

E-mail: gurevich@bioinf.spbau.ru

Birthday: 21 March 1989. Married, has a daughter (born in 2015).

 

Career:

Algorithmic Biology Lab/Center for Algorithmic Biotechnology, Research Scientist, 2011 -- present time

Algorithmic Biology Lab, Intern, 2011

St. Petersburg State Polytechnic University, Research Fellow, 2009-2010

 

Education:

Saint Petersburg Academic University of the Russian Academy of Sciences, PhD student in Bioinformatics, 2012 –  present time

Saint Petersburg Academic University of the Russian Academy of Sciences, MSc in Software Engineering (summa cum laude), 2010 – 2012

Saint Petersburg State Polytechnic University, BSc in Information Technologies (summa cum laude), 2006 – 2010

Lyceum "Physical-Technical High School" of the Russian Academy of Sciences, 2002 – 2006 

 

Projects:

Natural Products Discovery: Dereplicator and other projects (since 2015, ongoing)
Genome Assembly Evaluation: QUAST (since 2011, ongoing) and MetaQUAST (2015)
Genome Assembly: SPAdes (since 2011, ongoing)
Cancer Genomics: collaboration with AstraZeneca Oncology (2014-2015)
 

Publications

  • Alla Mikheenko, Gleb Valin, Andrey Prjibelski, Vladislav Saveliev, Alexey Gurevich. Icarus: visualizer for de novo assembly evaluation. Submitted.
  • Hosein Mohimani, Alexey Gurevich, Pieter C. Dorrestein, and Pavel A. Pevzner. In silico Identification of Peptidic Natural Products Through Database Search of Mass Spectra. Submitted.
  • Alla Mikheenko, Vladislav Saveliev, Alexey Gurevich. MetaQUAST: evaluation of metagenome assemblies, Bioinformatics (2015). doi: 10.1093/bioinformatics/btv697. First published online: November 26, 2015
  • Irina Vasilinetc, Andrey D. Prjibelski, Alexey Gurevich, Anton Korobeynikov and Pavel Pevzner. Assembling Short Reads from Jumping Libraries with Large Insert Sizes, Bioinformatics, 2015, 31 (12): pp. 3262-3268.
  • 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
  • Sergey Nurk, Anton Bankevich, 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, Pavel A Pevzner. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. Journal of Computational Biology 20(10) (2013), pp. 714-737.

  • 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

  • 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

 

Conferences

Translational Biomedicine, St. Petersburg, Russia, November 2015 (talk: Software pipeline for Oncology NGS data analysis)

CAMI evaluation meeting, Berlin, Germany, May 2015 (talk: metaQUAST: evaluating metagenome assemblies)

RECOMB & RECOMB-Seq, Beijing, China, April 2013 (poster: quality assessment of genome assemblies (web tool))

RECOMB-AB & RECOMB-BE, St. Petersburg, Russia, August 2012 

RECOMB & RECOMB-Seq, Barcelona, Spain, April 2012

 

Teaching

  • Informatics/Programming (Java/Python/Delphi) at Lyceum "Physical-Technical High School",  2012-2015

  • Linux for Beginners (MOOC at Stepic, in Russian), 2014

  • Journal Club in Algorithmic Bioinformatics at St. Petersburg Academic University, Fall 2014 

  • Scientific Software Design at St. Petersburg Academic University, Spring 2014

  • Python for Beginners, Bioinformatics Summer School 2013, Moscow, August 2013

 

 

Supervising:

  • Nikolay Kapralov, "Evaluating Quality and Enhancing Optical Chemical Structure Recognition Tools" (student of Bioinformatics Institute), Fall 2015
  • Alla Mikheenko, "MetaQUAST: Quality Assessment Tool for Metagenome Assemblies"  (Internship at the Lab), Summer 2015
  • Gleb Valin, "Interactive contig alignment browser" (St. Peterbsurg Academic University, first year Bachelor student), Spring 2015
  • Anna Lioznova, "Misassemblies detection without reference" (St. Peterbsurg Academic University, first year Master student), Spring 2014
  • Maxim Stepachev, "Interactive visualization of contig alignment" (student of Bioinformatics Institute), Spring 2013
  • Vlad Saveliev, "Web-interface for QUAST" (Internship at the Lab), Summer 2012

 

 

Scientific Interests:

Genome Assembly Evaluation, Antibiotics Sequencing, Software Engineering

Hobbies:

Soccer, snowboard

 


 

 


 

 

 

Andrey Prjibelski

Contact information

E-mail: ap (at) bioinf.spbau.ru

 

Education

  • St. Petersburg University of the Russian Academy of Sciences, expected degree: PhD, 2016

  • St. Petersburg University of the Russian Academy of Sciences, MSc in software engineering,  2010-2012

  • Academy of Modern Software Engineering, 2009 - 2011

  • St. Petersburg State Technical University, BSc in information technologies (magna cum laude), 2006 - 2010

  • Lyceum "Physical-Technical High School" of the Russian Academy of Sciences, 2004-2006

  • Giles School, Toronto, Canada, 2003-2004

 

Career

  • St. Petersburg University of the Russian Academy of Sciences, Teacher, 2012 - present time

  • Algorithmic Biology Lab, Researcher, 2011 - present time

  • Algorithmic Biology Lab, Intern, 2011

  • JetBrains, Part-time intern, 2010-2011

 

Publications

  • Elena Bushmanova, Dmitry Antipov, Alla Lapidus, Vladimir Suvorov and Andrey D. Prjibelski. rnaQUAST: a quality assessment tool for de novo transcriptome assemblies, Bioinformatics, 2016.
  • Irina Vasilinetc, Andrey D. Prjibelski, Alexey Gurevich, Anton Korobeynikov and Pavel Pevzner. Assembling Short Reads from Jumping Libraries with Large Insert Sizes, Bioinformatics, 2015,31 (12):.
  • 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.
  • Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey Gurevich, Anton Korobeynikov, Alla Lapidus, Andrey Prjibelski, Alexey Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Jeffrey McLean, Roger Lasken, Scott Clingenpeel, Tanja Woyke, Glenn Tesler, Max Alekseyev, and Pavel Pevzner. Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products. Journal of Computational Biology. October 2013, 20(10): 714-737. 
  • 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. 2013, 19(5), 455-477.
  • A.D. Prjiblelski, V.D. Miloslavskaya, D.O. Lebed and P.V. Trifonov. Usage of Field Extensions in Wiedemann Algorithm. Fundamental Research and Innovations in Technical Universities, 2009.

 

Talks & posters

  • Assembling Bacterial Genomes with SPAdes, Bioinformatics short course, St. Petersburg, Russia, April 2015

  • Assembling Bacterial Genomes with SPAdes, Working with Bacterial Genomes course, Helsinki, Finland, October 2014

  • Genome Assembly Future, Bioinformatics Summer School 2014, St. Petersburg, August 2014

  • ExSPAnder: a Universal Repeat Resolver for DNA Fragment Assembly, ISMB 2014, Boston, USA, July 2014

  • New Features in SPAdes Genome Assembler (Poster), ISMB 2014, Boston, USA, July 2014

  • New Frontiers of Genome Assembly with SPAdes 3.1, BOSC 2014, Boston, USA, July 2014

  • Introduction to NGS, Biological seminar, St. Petersburg State University, Russia, December 2013

  • Introduction to NGS, Bioinformatics Summer School 2013, Moscow, August 2013

  • Genome Draft Assembly Algorithms: From the Very Beginning till Present-day Problems, High-Throughput Sequencing in Genomics, Novosibirsk, Russia, July 2013

  • Introduction to Genome Assembly, System biology and Bioinformatics School, Novosibirsk, Russia, July 2013

  • Path-Extend: A New Approach for Repeat Resolution in Genome Assembly (Poster), WABI 2012, Ljubljana, Slovenia, August 2012

 

Awards

  • Ian Lawson Van Toch Memorial Award for Outstanding Student Paper, ISMB 2014, Boston, USA, July 2014

 

Teaching

  • NGS Data Analysis, Spring 2015

  • Algorithms in Bioinformatics, Fall 2014

  • Algorithms in Bioinformatics, Spring 2014

  • NGS Data Analysis, Fall 2013

  • NGS Data Analysis, Fall 2012

  • NGS Data Analysis, Spring 2012

 

Interests

Algorithms, bioinformatics, genomics, transcriptomics, genome assembly, software engineering

 

Hobbies

Volleyball, soccer, alpine skiing, cycling, water tourism, trekking

Publications

Journal Papers:

  • 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)

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)
 
 

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):

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):

  • 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)

Contacts

Address: St Petersburg, 199004, 6 linia V. O., 11d. (the house is marked as Bolshoy prospect V. O., 21 at Google maps.

 

Syndicate content