Alexander Shlemov

Junior Research Fellow

Career

Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Junior Research Fellow, 2015–present time

Department of Statistical Modelling, Faculty of Mathematics and Mechanics, Saint Petersburg State University, Assistant Professor, 2012–2016

Molochniy Product, LTD, System Administrator, Programmer, 2011–2016

Education

Applied Mathematics, Faculty of Mathematics and Mechanics, Saint Petersburg State University, 2011–present time

Applied Mathematics, Faculty of Mathematics and Mechanics, Saint Petersburg State University, 2006–2011

Skills

  • Languages: Russian (native), English (fluent)
  • Programming languages: C++, Python, R
  • Parallel programming: C++ threads, OpenMP, MPI, SLURM, IBM LSF
  • Version control: git
  • Markup: LaTeX(+knitr), HTML, Microsoft Word

Scientific Interests

Probability theory, statistics, statistical learning, time series analysis, simulation, numeric methods

General bioinformatics algorithms and tools, genome assembly, immunoinformatics, mass-spectrometry, natural products discovery

Software

PathRacer
NPDtools
NPS
Dereplicator+
MetaMiner
VarQuest

Publications

  1. Mitchell AL, Almeida A, Beracochea M, Boland M, Burgin J, Cochrane G, Crusoe MR, Kale V, Potter SC, Richardson LJ, Sakharova E, Scheremetjew M, Korobeynikov A, Shlemov A, Kunyavskaya O, Lapidus A and Finn RD. MGnify: the microbiome analysis resource in 2020 Nucleic Acids Research, 2020
  3. Liu Cao, Alexey Gurevich , Kelsey L Alexander, C. Benjamin Naman, Tiago Leao, Evgenia Glukhov, Nathan A Moss, Tal Luzzatto Knaan, Fernando Vargas, Robby Quinn, Amina Bouslimani, Louis-Felix Nothias, Nitin K Singh, John G Sanders, Rodolfo A S Benitez, Luke R Thompson, Md-Nafiz Hamid, James T Morton, Alla Mikheenko , Alexander Shlemov ,  Anton Korobeynikov , Iddo Friedberg, Rob Knight, Kasthuri Venkateswaran, William Gerwick, Lena Gerwick, Peter C. Dorrestein, Pavel A. Pevzner , Hosein Mohimani MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities Cell Systems, 2019
  5. Tagirdzhanov A. , Shlemov A., Gurevich A. NPS: scoring and evaluating the statistical significance of peptidic natural product–spectrum matches (talk, poster), 2019
  6. Shlemov A., Korobeynikov A. PathRacer: racing profile HMM paths on assembly graph (poster), 2019
  7. Shlemov A., Korobeynikov A. PathRacer: racing profile HMM paths on assembly graph (talk), 2019
  8. Shlemov A. , Dvorkina T. , Antipov D. , Nurk S. , Korobeynikov A. Tools for assembly graph analysis via SPAdes toolbox and more (talk), 2019
  9. Antipov D. , Bushmanova E. , Dvorkina T. , Gurevich A. , Kunyavskaya O. , Shlemov A., Lapidus A. , Meleshko D. , Nurk S. , Prjibelski A. , Korobeynikov A. SPAdes Family of Tools for Genome Assembly and Analysis (poster), 2019
  11. Gurevich A. , Mikheenko A. , Shlemov A. , Korobeynikov A. , Pevzner P. A. Variable Identification and De Novo Sequencing of Cyclopeptides via Computational Processing of Tandem Mass Spectra (talk), 2018
  13. Bankevich S. , Shlemov A., Safonova Y., Bzikadze A. , Pevzner P. A. Reconstructing antibody repertoires from error-prone immunosequencing datasets (talk), 2017
  14. Shlemov A., Bankevich S. , Safonova Y., Bzikadze A. , Pevzner P. A. Identification of novel peptidic antibiotics via large scale scoring of mass spectra against natural products databases (poster), 2017
  15. Bzikadze A. , Shlemov A., Bankevich S. , Safonova Y., Pevzner P. A. AntEvolo: a novel approach for clonal analysis of antibody repertoires (poster), 2017
  16. Gurevich A. , Shlemov A., Mikheenko A. , Korobeynikov A. , Pevzner P. A. VarQuest: modification-tolerant identification of novel variants of peptidic antibiotics and other natural products. (poster), 2017
  17. Gurevich A. , Shlemov A., Mikheenko A. , Korobeynikov A. , Pevzner P. A. Identification of novel peptidic antibiotics via large scale scoring of mass spectra against natural products databases (poster), 2017
  18. Korobeynikov A. , Shlemov A., Bzikadze A. Accurate targeted assembly and variant calling from NanoString Hyb & Seq data (poster), 2017
  19. Shlemov A., Bzikadze A., Bankevich S., Safonova Y. IgReC 2.0: New algorithmic challenges of adaptive immune repertoire construction. Proceedings of RECOMB­Seq, 2016
  20. Safonova Y., Shlemov A., Bzikadze A., Bankevich S., Pevzner P. A. A novel toolkit for analysis of adaptive immune repertoires using immunosequencing and mass spectra data. Poster., 2016