Publications and Conferences

Journal papers

2015 year

  1. Jha, A. K., Huang, S. C. C., Sergushichev, A., Lampropoulou, V., Ivanova, Y., Loginicheva, E., ... & Artyomov, M. N. Network Integration of Parallel Metabolic and Transcriptional Data Reveals Metabolic Modules that Regulate Macrophage Polarization // Immunity, 42(3), 419-430.

2013 year

  1. Kapun E., Tsarev F. On NP-Hardness of the Paired de Bruijn Sound Cycle Problem / Algorithms in Bioinformatics. Lecture Notes in Computer Science. Springer Berlin Heidelberg. Vol. 8126, pp. 59-69, doi: 10.1007/978-3-642-40453-5_6 http://link.springer.com/chapter/10.1007/978-3-642-40453-5_6# http://arxiv.org/pdf/1307.7806.pdf
  2. Keith R Bradnam, Joseph N Fass et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species // GigaScience 2013, 2:10 (22 July 2013), doi:10.1186/2047-217X-2-10. http://www.gigasciencejournal.com/content/2/1/10
  3. Kapun E., Tsarev F. De Bruijn Superwalk with Multiplicities Problem is NP-hard / BMC Bioinformatics.2013, 14(Suppl.5.Proceeding of the Third Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq 2013)): S7. http://www.biomedcentral.com/1471-2105/14/S5/S7

Papers in Russian journals (from the list of the higher attestation Commission of Russia)

2013 year

  1. Sergushichev A., Alexandrov A., Kazakov S., Tsarev F., Shalyto A. Combining de Bruijn graph, overlap graph and microassembly for de novo genome assembly // Izvestiya Saratovskogo Universiteta. New series. Series Mathematics. Mechanics. Informatics. 2013. № 2. Part 2, P. 51–57. Paper (in Russian)

2012 year

  1. Alexandrov A., Kazakov S., Melnikov S., Sergushichev A., Tsarev F. Contigs assembly method based on de Bruijn graph and overlap graph // Scientific and Technical Journal of Information Technologies, Mechanics and Optics. 2012. № 6 (82). P. 93-98. Paper (in Russian)

2011 year

  1. Alexandrov A., Kazakov S., Melnikov S., Sergushichev A., Tsarev F., Shalyto A. Base calling error correcting method. // Scientific and Technical Journal of Information Technologies, Mechanics and Optics. 2011. № 5, P. 81–84. Paper (in Russian)

Conference papers

2014 year

  1. A. Sergushichev, E. Pearce, M. Artyomov. GAM: a web-service for integrated transcriptional and metabolic network analysis / Metabolism and Immunity: A Rediscoverd Frontier 2014 (poster)
  2. S. Kazakov, A. Shalyto. Ovarlap graph simplification using edge reliability calculation / In Proceedings of the 8th International Conference on Intelligent Systems and Agents 2014 (ISA 2014). Lisbon, Portugal. 2014. pp. 222-226. Paper

2013 year

  1. Genome assembly algorithms for exaFLOPS systems. / Exhibition "The results the implementation of the federal program "Research and development on priority directions of scientific and technical complex of Russia for 2007-2013 years". Poster (in Russian)
  2. Akhi A., Sergushichev A., Tsarev F. Maximum Likelihood Scaffold Assembly / 17th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2013). Poster
  3. Kapun E., Tsarev F. De Bruijn Superwalk with Multiplicities Problem is NP-hard / Third Annual RECOMB Satellite Workshop On Massively Parallel Sequencing (RECOMB-SEQ 2013). Presentation
  4. Kapun E., Tsarev F. On NP-Hardness of the Paired de Bruijn Sound Cycle Problem / 13th Workshop on Algorithms in Bioinformatics
    (WABI 2013). Presentation

2012 year

  1. Alexandrov A., Kazakov S., Melnikov S., Sergushichev A., Tsarev F., Shalyto A. Combining de Bruijn graph, overlap graph and microassembly for de novo genome assembly. / Proc. of The Third International Scientific and Practical Conference "Postgenomic methods of analysis in biology, and laboratory and clinical medicine". P. 45–46. Abstract (in Russian)
  2. Akhi A., Nigmatullin N., Sergushichev A., Tsarev F. Contigs distance estimation method based on maximal likelihood method. / The Third International Scientific and Practical Conference "Postgenomic methods of analysis in biology, and laboratory and clinical medicine". Poster (in Russian)
  3. Alexandrov A., Kazakov S., Melnikov S., Sergushichev A., Tsarev F., Shalyto A. Contigs assembly method based on de Bruijn and overlap graphs. / Proc. of The International Symposium on Information Theory 2012. 2012. V. 3, p. 283-288. Paper (in Russian)
  4. Alexandrov A., Kazakov S., Melnikov S., Sergushichev A., Fedotov P., Tsarev F., Shalyto A. Parallel de novo genome assembly algorithm for MapReduce framework. / Proc. of The International Supercomputer Conference "Scientific service on the Internet: Searching for new solutions" and Conference of Young Scientists "Theory and Practice of parallel programming". 2012. P. 679-682. Paper (in Russian)
  5. Alexandrov A., Kazakov S., Melnikov S., Sergushichev A., Shalyto A., Tsarev F. Combining de Bruijn graph, overlap graph and microassembly for de novo genome assembly. / Proc. of «Bioinformatics 2012». Stockholm, 2012, p. 72. Abstract, Poster

2011 year

  1. Alexandrov A., Kazakov S., Melnikov S., Sergushichev A., Tsarev F. Genome assembly method based on de Bruijn and overlap graphs. The Second International Scientific and Practical Conference "Postgenomic methods of analysis in biology, and laboratory and clinical medicine". November 14-17, 2011. Novosibirsk. Conference program (in Russian)
  2. Alexandrov A. Development of an algorithm for assemble genome sequences from paired reads. The International Scientific and Proctical Conference "Modern information technologies and IT education". November 7–11, 2011. MIPT. Dolgoprudny. Conference program (in Russian)
  3. Tsarev F., Shalyto A. Extreme programming by contest teams for discrete mathematics problems on example of genome assembly. Central & Eastern European Software Engineering Conference in Russia 2011 (CEE-SECR 2011). Moscow. Paper announcement, Presentation (in Russian)
  4. Sergushichev A., Isenbaev V., Tsarev F., Prokhorchuk E., Shalyto A. Development of an algorithm for restoring genome fragments from paired reads. The second Interuniversity Scientific Informatics Conference 2011 (SPISOK – 2011). SPbSU, April 29, 2011. Section «Automata-based management, evolution algorithms, models verification». Paper (in Russian)
  5. Alexandrov A., Kazakov S., Melnikov S., Prokhorchuk E., Tsarev F., Shalyto A. Development of an algorithm for error correcting in genome reads. The second Interuniversity Scientific Informatics Conference 2011 (SPISOK – 2011). SPbSU, April 29, 2011. Section «Automata-based management, evolution algorithms, models verification». Paper (in reRussian)
  6. Alexandrov A., Kazakov S., Melnikov S., Sergushichev A., Isenbaev V., Tsarev F. Genome Assembly method based on restoring genome fragments from paired reads. The eighth All-Russian Interuniversity Conference of Young Scientists. SPbSU ITMO. April 12-15, 2011.
  7. Sergushichev A., Alexandrov A., Kazakov S., Melnikov S., Isenbaev V., Tsarev F. Combining "overlap-layout-consensus" and de Brujin graph approaches for de novo genome assembly. Sequence Mapping and Assembly Assessment Project workshop. Barcelona, April 5th, 2011. Presentation

Computer program registration certificates and patents

2012 year

  1. Alexandrov A., Kazakov S., Melnikov S., Sergushichev A., Fedotov P., Tsarev F. Software for assemble quasicontigs from paired reads // Computer program registration certificate № 2012614488. Registered at July 27, 2012. Certificate (in Russian)

2011 year

  1. Alexandrov A., Kazakov S., Melnikov S., Sergushichev A., Isenbaev V., Tsarev F. Software for error correcting in genome reads // Computer program registration certificate №2011614454. Registered at June 6, 2011. Certificate (in Russian)

Degree researches

2013 year

  1. Akhi А. Development of an algorithm for scaffold assembling using maximum-likelihood estimation. NRU ITMO. Master's thesis. 2013. Thesis (in Russian)
  2. Alexandrov А. Development of an algorithm for correcting indel errors in genome reads. NRU ITMO. Master's thesis. 2013. Thesis (in Russian)
  3. Sergushichev А. Development of an algorithm for restoring genome fragments from paired reads with indel errors. NRU ITMO. Master's thesis. 2013. Thesis (in Russian)
  4. Kazakov S. Development of an algorithm for overlap graph simplification. NRU ITMO. Master's thesis. 2013. Thesis (in Russian)

2012 year

  1. Melnikov S. Development of an algorithm for clustering paired reads for parallel restoring genome fragments. NRU ITMO. Bachelor's thesis. 2012. Thesis (in Russian)

2011 year

  1. Alexandrov A. Development of an algorithm for error correcting in genome reads. NRU ITMO. Bachelor's thesis. 2011. Thesis (in Russian)
  2. Sergushichev A. Development of an algorithm for restoring genome fragments from paired reads. NRU ITMO. Bachelor's thesis. 2011. Thesis (in Russian)

Awards

  1. Finalist diploma, Contest "BIT-north-west". Project "CloudGenomics - cloud service for processing and storing genome data". Diploma (in Russian)
  2. Participant diploma, Exhibition "The results the implementation of the federal program "Research and development on priority directions of scientific and technical complex of Russia for 2007-2013 years". Diploma (in Russian)

Miscellaneous

  1. Sergushichev A., Tsarev F. Genome assembly and MapReduce technology. // Journal «Supercomputers». 2012. № 12. P. 40-43. Paper (in Russian)
  2. Submitted to the journal "Nucleic Acids Research" article "The de novo Genome Assembly Assessment Project - dnGASP" (authors: Tyler Alioto, Andre Corvelo, Paolo Ribeca, Shaun Jackman, Rod Docking, Inanc Birol, Ruibang Luo, Zhenyu Li, Yinlong Xie, Binghang Liu, Yingrui Li, Jun Wang, Bryan R. Downie, Philipp Koch, Ekaterina E. Khrameeva, Egor B. Prokhortchouk, Zemin Ning, Jared T. Simpson, Richard Durbin, Alexey Sergushichev, Sergey Kazakov, Anton Alexandrov, Fedor Tsarev, Sergey Melnikov, Rayan Chikhi, Dominique Lavenier, Guillaume Chapuis, Delphine Naquin, Nicolas Maillet, Simon Heath, Ivo G. Gut).