Automated Analysis of Interatomic Contacts in Proteins.
V Sobolev, A Sorokine, J Prilusky, E Abola, M Edelman, "Automated Analysis of Interatomic Contacts in Proteins.." Bioinformatics (Oxford, England), 1999.
CV
Education
- B.S. in Physics, Moscow Institute of Physics and Technology, 1993
- M.S. in Physics, Moscow Institute of Physics and Technology, 1995
- Ph.D in Biophysics, Institute of theoretical and experimental biophysics, 2000
Work experience
08.2022-now Senior Computational Biologist in Biological Systems Group in the Okinawa Institute of Science and Technology.
Analysis of multi-omics data from various environmental and host-related microbial communities. Development of new approaches for the mechanistic understanding of the principles guiding microbial community evolution.
11.2015-now Senior Researcher in the Laboratory of Molecular and Ion Physics in the Moscow Institute of Physics and Technology.
Development of computational infrastructure for collection, storage, retrieval and analysis of the brain tumor tissue fragments molecular profiles obtained with various ambient mass-spectrometry methods. Development new machine learning and AI approaches for the tumor boundary detection and estimation of the sample tumor cell percentage from the ambient mass-spectrometry spectra.
07.2019-07.2022 Researcher, School of Biochemistry, University of Liverpool.
07.2014-11.2019 Head of the laboratory of Mechanisms of genome functioning in the Institute of the cell biophysics RAS.
08.2013-06.2014 Lead researcher in the laboratory of Mechanisms of genome functioning in the Institute of the cell biophysics RAS.
04.2011-08.2013 Senior researcher in the laboratory of Mechanisms of genome functioning in the Institute of the cell biophysics RAS.
07.2009-03.2011 Senior software developer in BioMedCAD project, School of Informatics, The University of Edinburgh. Development of PRTR annotation workflow and text-mining backend.
05.2008-06.2009 Leading Informatics Researcher in ROBuST SABR project, School of Informatics, The University of Edinburgh.
Development of experimental data archive and datamart. Development of modeling pipeline.
09.2005-04.2008 Research fellow in Scottish Centre for Systems Biology and Edinburgh Centre for Bioinformatics School of Informatics The University of Edinburg.
Development of Edinburgh Pathway editor and related plug-ins, development of Edinburgh Chemical Ontology, development of biological network static properties analysis algorithm, analysis of human metabolic network, analysis of interferon signaling pathway. Coordination of SBGN activities in ECB with EPE development, development of Edinburgh Pathway notation. Development of parameter space exploration and fitting facility for SBSI. Students supervision.
08.2005-03.2011 Researcher in the laboratory of Mechanisms of genome functioning Institute of the cell biophysics RAS
Analysis of promoter-protein recognition on the basis of E.coli sigma-70 promoter database. Development of algorithm for fast electrostatic properties of long DNA fragments evaluation. Analysis of electrostatic profiles of promoter regions of chromosome of E. coli.
04.2002-08.2003 EMP Project Lead Software Developer
Development of web service and database for biochemical information for human metabolism reconstruction project.
09.1999-09.2000 EMP Project Software developer
Development module for statistical analysis of EMP database.
05.1998-08.2005 Junior researcher in the laboratory of Mechanisms of genome functioning Institute of the cell biophysics RAS
Analysis of promoter-protein recognition on the basis of E.coli sigma-70 promoter database. Development of algorithm for the fast evaluation of electrostatic properties of long DNA fragments. Analysis of electrostatic profiles of promoter regions of chromosome of E. coli.
02.1997-02.1998 Visiting student in the Plant Genetics Department, Weizmann Institute of Science
Analysis of ligand-protein contacts in the 3-D complexes (LPC software in any PDB mirror), analysis of influence of type of substitution on the structure of mutant protein modeling of the 3-D structure of the protein on the basis of sequence homology.
09.1995- 02.1997 Post-graduate student in the laboratory of The cell and tissue grow of the Institute of theoretical and experimental biophysics RAS.
Research: investigation of the rhythm of spontaneously beating cardiomyocytes in vitro.
Methods: on-line and off-line signal analysis, signal analysis on the basis of nonlinear dynamical and statistical methods.
Skills
- KNIME data processing, machine learning, cheminformatics, DB access, node development. Since 2020.
- Scala: data management, graph database access. Since 2013.
- Python: data management, graph analysis, nonlinear signal analysis, sensitivity analysis, statistical analysis. Since 2012.
- R/Bioconductor: data management, SQL-db connectivity, basic sequence analysis, Shiny applications, sensitivity analysis, statistical analysis, package development. Since 2008.
- Groovy: Graph analysis, chemoinformatics, Windows COM, general scripting. Since 2007
- Java: Web-services design on Servlet/JSP, Struts, non-visual server programming; since 2000. Eclipse plug-in and RCP application development; since 2005
- ANTLR: Domain-specific language development; since 2008
- C/C++: Normal usage, numerical algorithms, application development using GNU make. Development of code for parallel environments: BlueGene, MPI. Nonlinear analysis, ODE solving, Protein 3D structure analysis etc.; since 1992
- Fortran: Usage and modification of legacy software, application development using f77. MPI programming. Protein 3D structure analysis; since 1997
- Perl: CGI scripting since 1997
- Matlab: data modelling and analysis; since 1995
- Octave: data modelling and analysis; since 1995
- Misc Pascal, Basic
- Database programming: ANSI SQL(advanced),PostgreSQL(advanced, custom datatype development), Oracle PL/SQL(advanced), tSQLMS SQL Server(basic), MonetDB (basic)
- Database administration: PostgreSQL (base),Oracle (base), MS SQL Server(base), MonetDB (basic)
- Web design: HTML, CGI scripts, JavaScript
- OS: advanced user Windows, Irix6.1, Linux, MacOSX
Publications
Electrostatic Potentials of DNA. Comparative Analysis of Promoter and Nonpromoter Nucleotide Sequences.
R Polozov, T Dzhelyadin, Anatoly Sorokin, N Ivanova, V Sivozhelezov, S Kamzolova, "Electrostatic Potentials of DNA. Comparative Analysis of Promoter and Nonpromoter Nucleotide Sequences.." J. Biomol. Struct. Dyn., 1999.
Electrostatic Potentials of E.Coli Genome DNA
S Kamzolova, Anatoly Sorokin, T Dzhelyadin, P Beskaravainy, A Osypov, "Electrostatic Potentials of E.Coli Genome DNA." J. Biomol. Struct. Dyn., 2005.
Electrostatic Properties of Promoter Recognized by E. Coli RNA Polymerase Esigma70.
Anatoly Sorokin, Alexandr Osypov, Timur Dzhelyadin, Petr Beskaravainy, Svetlana Kamzolova, "Electrostatic Properties of Promoter Recognized by E. Coli RNA Polymerase Esigma70.." J. Bioinform. Comput. Biol., 2006.
The Edinburgh human metabolic network reconstruction and its functional analysis.
Hongwu Ma, Anatoly Sorokin, Alexander Mazein, Alex Selkov, Evgeni Selkov, Oleg Demin, and Igor I Goryanin. (2007). "The Edinburgh human metabolic network reconstruction and its functional analysis." Mol Syst Biol, vol. 3 p. 135.
ELECTROSTATIC PROPERTIES OF E. COLI GENOME DNA
S Kamzolova, Anatoly Sorokin, T Dzhelyadin, P Beskaravainy, A Osypov, "ELECTROSTATIC PROPERTIES OF E. COLI GENOME DNA." In the proceedings of BGRS 2004, 2008.
A Fragile Metabolic Network Adapted for Cooperation in the Symbiotic Bacterium Buchnera Aphidicola
Gavin Thomas, Jeremy Zucker, Sandy Macdonald, Anatoly Sorokin, Igor Goryanin, Angela Douglas, "A Fragile Metabolic Network Adapted for Cooperation in the Symbiotic Bacterium Buchnera Aphidicola." BMC Syst. Biol., 2009.
The systems biology graphical notation.
Nicolas Le Novère, Michael Hucka, Huaiyu Mi, Stuart Moodie, Falk Schreiber, Anatoly Sorokin, et al. (2009). "The systems biology graphical notation." Nat Biotechnol, vol. 27 (8) pp. 735-741.
Systems biology reveals new strategies for personalizing cancer medicine and confirms the role of PTEN in resistance to trastuzumab.
Dana Faratian, Alexey Goltsov, Galina Lebedeva, Anatoly Sorokin, Stuart Moodie, Peter Mullen, Charlene Kay, In Hwa Um, Simon Langdon, Igor I Goryanin, and David J Harrison. (2009). "Systems biology reveals new strategies for personalizing cancer medicine and confirms the role of PTEN in resistance to trastuzumab." Cancer Res, vol. 69 (16) pp. 6713-6720.
Chapter 13. Biomarkers of Exposure and Effect: Ionizing Radiation
A FUCIC, A Sorokin, "Chapter 13. Biomarkers of Exposure and Effect: Ionizing Radiation." In the proceedings of Biomarkers and Human Biomonitoring, 2011.
Electrostatic Properties of Bacteriophage T7 Early Promoters Recognized by E. Coli RNA Polymerase
S Kamzolova, P Beskaravainy, Anatoly Sorokin, "Electrostatic Properties of Bacteriophage T7 Early Promoters Recognized by E. Coli RNA Polymerase." J. Biomol. Struct. Dyn., 2011.
A User-Defined Data Type for the Storage of Time Series Data Allowing Efficient Similarity Screening
Anatoly Sorokin, Gene Selkov, Igor Goryanin, "A User-Defined Data Type for the Storage of Time Series Data Allowing Efficient Similarity Screening." Eur. J. Pharm. Sci., 2012.
A Community-Driven Global Reconstruction of Human Metabolism
Ines Thiele, Neil Swainston, Ronan Fleming, Andreas Hoppe, Swagatika Sahoo, Maike Aurich, Hulda Haraldsdottir, Monica Mo, Ottar Rolfsson, Miranda Stobbe, Stefan Thorleifsson, Rasmus Agren, Christian B{\"o}lling, Sergio Bordel, Arvind Chavali, Paul Dobson, Warwick Dunn, Lukas Endler, David Hala, Michael Hucka, Duncan Hull, Daniel Jameson, Neema Jamshidi, Jon Jonsson, Nick Juty, Sarah Keating, Intawat Nookaew, Nicolas Le, Naglis Malys, Alexander Mazein, Jason Papin, Nathan Price, Evgeni Selkov, Martin Sigurdsson, Evangelos Simeonidis, Nikolaus Sonnenschein, Kieran Smallbone, Anatoly Sorokin, Johannes {\noopsort{beek}}{van Beek}, Dieter Weichart, Igor Goryanin, Jens Nielsen, Hans Westerhoff, Douglas Kell, Pedro Mendes, Bernhard Palsson, "A Community-Driven Global Reconstruction of Human Metabolism." Nat. Biotechnol., 2013.
A Simulator for Spatially Extended Kappa Models.
Oksana Sorokina, Anatoly Sorokin, J Douglas, Vincent Danos, "A Simulator for Spatially Extended Kappa Models.." Bioinformatics (Oxford, England), 2013.
Electrostatic Map of T7 DNA: Comparative Analysis of Functional and Electrostatic Properties of T7 RNA Polymerase-Specific Promoters.
S Kamzolova, P Beskaravainy, A Osypov, T Dzhelyadin, E Temlyakova, Anatoly Sorokin, "Electrostatic Map of T7 DNA: Comparative Analysis of Functional and Electrostatic Properties of T7 RNA Polymerase-Specific Promoters.." J. Biomol. Struct. Dyn., 2014.
Dynamics of Elongation Factor 2 Kinase Regulation in Cortical Neurons in Response to Synaptic Activity.
Justin Kenney, Oksana Sorokina, Maja Genheden, Anatoly Sorokin, J Armstrong, Christopher Proud, "Dynamics of Elongation Factor 2 Kinase Regulation in Cortical Neurons in Response to Synaptic Activity.." J. Neurosci. Off. J. Soc. Neurosci., 2015.
Classification of E. Coli Promoters with DNA Open States Dynamic Characteristics
A Ryasik, Mikhail Orlov, E Temlyakova, Anatoly Sorokin, "Classification of E. Coli Promoters with DNA Open States Dynamic Characteristics." FEBS J., 2016.
Comparative Metagenomic Analysis of Electrogenic Microbial Communities in Differentially Inoculated Swine Wastewater-Fed Microbial Fuel Cells
Irina Khilyas, Anatoly Sorokin, Larisa Kiseleva, David Simpson, V Fedorovich, Margarita Sharipova, Mami Kainuma, Michael Cohen, Igor Goryanin, "Comparative Metagenomic Analysis of Electrogenic Microbial Communities in Differentially Inoculated Swine Wastewater-Fed Microbial Fuel Cells." Scientifica, 2017.
Feature Selection Algorithm for Spray-from-Tissue Mass Spectrometry
Anatoly Sorokin, Evgeny Zhvansky, Vsevolod Shurkhay, Konstantin Bocharov, Igor Popov, Nikita Levin, Dmitry Zubtsov, Denis Bormotov, Yury Kostyukevich, Alexander Potapov, Eugene Nikolaev, "Feature Selection Algorithm for Spray-from-Tissue Mass Spectrometry." Eur J Mass Spectrom Chichester, 2017.
High-Resolution Mass Spectra Processing for the Identification of Different Pathological Tissue Types of Brain Tumors
Evgeny Zhvansky, Anatoly Sorokin, Igor Popov, Vsevolod Shurkhay, Alexander Potapov, Eugene Nikolaev, "High-Resolution Mass Spectra Processing for the Identification of Different Pathological Tissue Types of Brain Tumors." Eur J Mass Spectrom Chichester, 2017.
Comparative Analysis of Mycoplasma Gallisepticum vlhA Promoters.
Mikhail Orlov, Irina Garanina, Gleb Fisunov, Anatoly Sorokin, "Comparative Analysis of Mycoplasma Gallisepticum vlhA Promoters.." Front. Genet., 2018.
Bacterial Promoter Prediction: Selection of Dynamic and Static Physical Properties of DNA for Reliable Sequence Classification.
Artem Ryasik, Mikhail Orlov, Evgenia Zykova, Timofei Ermak, Anatoly Sorokin, "Bacterial Promoter Prediction: Selection of Dynamic and Static Physical Properties of DNA for Reliable Sequence Classification.." J. Bioinform. Comput. Biol., 2018.
ASAR: Visual Analysis of Metagenomes in R.
Askarbek Orakov, Nazgul Sakenova, Anatoly Sorokin, Igor Goryanin, "ASAR: Visual Analysis of Metagenomes in R.." Bioinformatics (Oxford, England), 2018.
Inline Cartridge Extraction for Rapid Brain Tumor Tissue Identification by Molecular Profiling.
Stanislav Pekov, Vasily Eliferov, Anatoly Sorokin, Vsevolod Shurkhay, Evgeny Zhvansky, Alexander Vorobyev, Alexander Potapov, Eugene Nikolaev, Igor Popov, "Inline Cartridge Extraction for Rapid Brain Tumor Tissue Identification by Molecular Profiling.." Sci. Rep., 2019.
Evolutionary Dynamics of Microbial Communities in Bioelectrochemical Systems
Lukasz Szydlowski, Anatoly Sorokin, Olga Vasieva, Susan Boerner, Veyacheslav Feodorovich, Igor Goryanin, "Evolutionary Dynamics of Microbial Communities in Bioelectrochemical Systems." J. Comput. Sci. Syst. Biol., 2020.
Assessment of Variation of Inline Cartridge Extraction Mass Spectra.
Evgeny Zhvansky, Vasiliy Eliferov, Anatoly Sorokin, Vsevolod Shurkhay, Stanislav Pekov, Denis Bormotov, Daniil Ivanov, Denis Zavorotnyuk, Konstantin Bocharov, Iliyas Khaliullin, Maksim Belenikin, Aleksandr Potapov, Evgeny Nikolaev, Igor Popov, "Assessment of Variation of Inline Cartridge Extraction Mass Spectra.." J. Mass Spectrom., 2020.
Comparison of Dimensionality Reduction Methods in Mass Spectra of Astrocytoma and Glioblastoma Tissues.
Evgeny Zhvansky, Anatoly Sorokin, Vsevolod Shurkhay, Denis Zavorotnyuk, Denis Bormotov, Stanislav Pekov, Alexander Potapov, Evgeny Nikolaev, Igor Popov, "Comparison of Dimensionality Reduction Methods in Mass Spectra of Astrocytoma and Glioblastoma Tissues.." Mass Spectrom. Tokyo Jpn., 2021.
Changes in the Microbiome of Milk in Cows with Mastitis.
K Fursova, S Sokolov, M Shchannikova, D Nikanova, O Artem'eva, E Kolodina, A Sorokin, T Dzhelyadin, I Shulcheva, A Shepelyakovskaya, N Zinovieva, F Brovko, "Changes in the Microbiome of Milk in Cows with Mastitis.." Dokl. Biochem. Biophys., 2021.
Interactive Estimation of Heterogeneity from Mass Spectrometry Imaging.
Evgeny Zhvansky, Daniil Ivanov, Anatoly Sorokin, Anna Bugrova, Evgeny Nikolaev, Igor Popov, "Interactive Estimation of Heterogeneity from Mass Spectrometry Imaging.." Anal. Chem., 2021.
Comparative Analysis of Milk Microbiomes and Their Association with Bovine Mastitis in Two Farms in Central Russia.
Sergei Sokolov, Ksenia Fursova, Irina Shulcheva, Daria Nikanova, Olga Artyemieva, Evgenia Kolodina, Anatoly Sorokin, Timur Dzhelyadin, Margarita Shchannikova, Anna Shepelyakovskaya, Natalia Zinovieva, Fedor Brovko, "Comparative Analysis of Milk Microbiomes and Their Association with Bovine Mastitis in Two Farms in Central Russia.." Anim. Open Access J. MDPI, 2021.
Synaptome.db: A Bioconductor package for synaptic proteomics data.
Oksana Sorokina, Anatoly Sorokin, J Douglas Armstrong, "Synaptome.db: A Bioconductor package for synaptic proteomics data", Bioinformatics Advances, 2022, vbac086
Aggregation of Multimodal ICE-MS Data into Joint Classifier Increases Quality of Brain Cancer Tissue Classification.
Sorokin, Anatoly A., Denis S. Bormotov, Denis S. Zavorotnyuk, Vasily A. Eliferov, Konstantin V. Bocharov, Stanislav I. Pekov, Evgeny N. Nikolaev, and Igor A. Popov. 2023. "Aggregation of Multimodal ICE-MS Data into Joint Classifier Increases Quality of Brain Cancer Tissue Classification" Data 8, no. 1: 8. https://doi.org/10.3390/data8010008
FBA-PRCC. Partial Rank Correlation Coefficient (PRCC) Global Sensitivity Analysis (GSA) in Application to Constraint-Based Models.
Anatoly Sorokin, Igor Goryanin, "FBA-PRCC. Partial Rank Correlation Coefficient (PRCC) Global Sensitivity Analysis (GSA) in Application to Constraint-Based Models." Biomolecules 2023, 13(3), 500
BioNAR: an integrated biological network analysis package in bioconductor.
Colin McLean, Anatoly Sorokin, Thomas Ian Simpson, James Douglas Armstrong, Oksana Sorokina, BioNAR: an integrated biological network analysis package in bioconductor, Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad137
Computational Pipeline for Analysis of Biomedical Networks with BioNAR.
McLean, C., Sorokin, A., Armstrong, J. D., & Sorokina, O. (2023). Computational pipeline for analysis of biomedical networks with BioNAR. Current Protocols, 3, e940. doi: 10.1002/cpz1.940
Talks
Talk 1 on Relevant Topic in Your Field
Talk at UC San Francisco, Department of Testing, San Francisco, California
Tutorial 1 on Relevant Topic in Your Field
Tutorial at UC-Berkeley Institute for Testing Science, Berkeley CA, USA
Talk 2 on Relevant Topic in Your Field
Talk at London School of Testing, London, UK
Conference Proceeding talk 3 on Relevant Topic in Your Field
Conference proceedings talk at Testing Institute of America 2014 Annual Conference, Los Angeles, CA