Sergey Nikolenko

Sergey Nikolenko

Main page

Books
Research papers
Talks and posters
Students
Popular science
Other stuff

   Research
CS and crypto
Bioinformatics
Machine learning
Algebraic geometry
Algebra
Bayesian networks
Earth sciences

   Teaching
 2014
ML, KFU
Game Theory, HSE
Mech. Design, HSE
ML, CSClub Kazan
Game theory, HSE
Math. logic, AU
Machine learning, STC
Machine learning, AU
 2013
Discrete math, HSE
Machine learning, STC
Math. logic, AU
Cryptography, AU
 2012
Machine learning, STC
Math. logic, AU
Machine learning II, AU
Machine learning, AU
Machine learning, EMC
 2011
Cryptography, AU
Math. logic, AU
Machine learning, AU
 2010
Math. logic, AU
Machine learning, AU
Cryptography, AU
 2009
Crypto in CS Club
Statistics
Machine learning, AU
Cryptography
 2008
Speech recognition
MD for CS Club
ML for CS Club
Mechanism design
 2007
Machine Learning
Probabilistic learning

  External links
Google Scholar profile
DBLP profile
LiveJournal account
userinfonikolenko (in Russian)

Bioinformatics

Starting in 2011, I've been working on bioinformatics as part of the Algorithmic Biology Lab at the St. Petersburg Academic University under the supervision of Prof. Pavel Pevzner.

Publications

  1. S.I. Nikolenko, A.I. Korobeynikov, M.A. Alekseyev. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics, vol. 14, Suppl. 1, S7, 2013 (open access).
  2. I.I. Chernyavsky, T. Alexandrov, P. Maass, S.I. Nikolenko. A Two-Step Soft Segmentation Procedure for MALDI Imaging Mass Spectrometry Data. Proceedings of the 18th German Conference in Bioinformatics (GCB-2012), OASIcs vol. 26, 2012, pp. 39–48. (.pdf, 2582kb)
  3. I.I. Chernyavsky, T. Alexandrov, S.I. Nikolenko. Segmentation of MALDI imaging results based on graphical models. SPIIRAS Proceedings, vol. 21, 2012, pp. 120–142. (.pdf, 1251kb, in Russian)
  4. A. Bankevich, S. Nurk, D. Antipov, A.A. Gurevich, M. Dvorkin, A.S. Kulikov, V.M. Lesin, S.I. Nikolenko, S. Pham, A.D. Prjibelski, A.V. Pyshkin, A.V. Sirotkin, N. Vyahhi, G. Tesler, M.A. Alekseyev, and P.A. Pevzner. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology, May 2012, vol. 19, no. 5, pp. 455–477. doi:10.1089/cmb.2012.0021.

Talks and posters

  1. S.I. Nikolenko. SPAdes: a new genome assembler for single-cell sequencing. RECOMB-AB, August 27, 2012, talk (slightly different from the previous one). (.pdf, 6232kb)
  2. S.I. Nikolenko. B4B Chapter Proposal: Evolutionary History of Repeats. RECOMB-BE, August 26, 2012, talk. (.pdf, 436kb)
  3. S.I. Nikolenko. SPAdes: a new genome assembler for single-cell sequencing. A symposium to launch the Theodosius Dobzhansky Center for Genome Informatics, April 28, 2012, talk. (.pdf, 5019kb)
  4. S.I. Nikolenko. Hammer 2.0: Bayesian error correction for non-uniform coverage. Moscow Conference on Computational Molecular Biology (MCCMB'11), July 24, 2011, talk.
  5. S.I. Nikolenko, M. Alekseyev, P. Pevzner. Bayesian Evaluation of de novo Genome Assembly. ISMB/ECCB 2011, poster.
  6. A. Krass, S.I. Nikolenko, E. Stepanov, Yu. Porozov. Protein conformational movements modeling based on the average action principle. ISMB/ECCB 2011, poster (F1000 link).
  7. M. Churakov, S.I. Nikolenko, Yu. Porozov. Predicting DNA Replication Origins with Machine Learning Techniques. ISMB/ECCB 2011, poster.