Sergey Nikolenko

Main pageBooks'; print '
Research papers'; print '
Talks and posters'; print '
Students'; print '
Popular science'; print '
Other stuff'; print '

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

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

  External links'; print '
Google Scholar profile'; print '
DBLP profile'; print '
LiveJournal account
nikolenko (in Russian)

Bioinformatics

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 18^th 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.