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Roman Sutormin
rsutormin@gmail.com
Professional experience 11/2012, 05/2013 present: Lawrence Berkeley National Laboratory (Berkeley, CA, USA) Scientific Research Visitor Systematizing and developing the unified format for all structural types of TFBS profiles available in the RegPredict web server. Deep refactoring of the motif search engine implemented in RegPredict. Developing RegPrecise module to visualize genomescale regulatory cascades in bacteria. Improvement of Java type compiler using in language independent remote process calls in KBase project. 09/2011 present: Moscow State University, Dept. of Bioengineering and Bioinformatics (Russia) Scientific Research Java developer and lecturer Enhanced the CAMPS web resource (http://webclu.bio.wzw.tum.de/CAMPS2.0/) that enables multiple classification of transmembrane proteins. Optimized the speed of the HMMbased algorithm for classification of transmembrane proteins (10fold acceleration). Developed web based UI for visualization of a graph of transmembrane protein families. This project was supervised by Prof. Dmitrij Frishman. Participated in design of HMM model for identification of transcriptional regulatory regions in eukaryotes based on statistical rules (grammar) defining the architecture of the transcription factor binding sites (TFBS). Participated in the implementation of this model in the CORECLUST algorithm. See publications list. Currently developing the scalable pipeline for gene annotation of eukaryotic genomes to enable high performance distributed computing on 30 nodes cluster (24 cores on each node). The cluster is operated by Torque Resource Manager. The pipeline is currently using for gene annotation in the Fagopyrum Tataricum and Genlisea Margaretae. The genome Genlisea Margaretae annotated by the developed pipeline is submitted to NCBI GenBank. This project is supervised by Prof. Alex Kondrashov. Lecturer in Java Programming and Algorithms in Bioinformatics. 10/2009 08/2011: Astrum Nival (Moscow, Russia), Java developer Support and development of data warehouse (PostgreSQL) and administration web tool (JBoss + GWT) as parts of serverside of interactive social network. 06/2008 09/2009: Irbicon (Moscow/Dubna, Russia), Java developer Developed the plugin providing the credit scoring functionality for SAS Data Integration Studio tool. Developed web portlet for SAS Information Delivery Portal providing web interface for fulltext search in Subversion repositories. Developed web resource (GWT) for management of collection agency tasks related to a life cycle of payment debts based on SAS infrastructure. 09/2005 05/2008: Moscow State University, Dept. of Bioengineering and Bioinformatics (Russia) Scientific Research Java developer and lecturer Developed a web based UI module for identification and visualization of clusters of paralogous www.bioinf.fbb.msu.ru/~roman/

proteins in a bacterial genome. This module enables visualization of graph of paralogs based on protein domain similarity. Developed an algorithm for identification of linked (phylogenetically and by gene location) orthologous protein clusters in a group of bacterial genomes and the web module for visualization of the results. http://www.biomax.de/services/gencomp.php Developed an algorithm for the identification of syntenic regions between two bacterial genomes based on protein homology information and the web module for visualization.
http://www.biomax.de/products/pedantpro_scrsht.php

These modules were developed as a result of partnership between Moscow State University and Biomax AG, and supervised by Prof. Dmitrij Frishman

Developed the internal web resource for student term papers management based on JSP
(department order). Constructed the genomic data warehouse and ETLprocesses for data integration from different sources like Genbank, Uniprot, PDB and others. Lecturer in Java Programming and Algorithms in Bioinformatics.

03/2003 03/2005: Diasoft (Moscow, Russia), Java developer (part time while PhD student) Developed the visual tool for modeling metadata of data warehouse. Designed the unified script language to work with various dialects specific for different DBMSs such as: MSSQL, Sybase, DB2, Oracle. Developed the SQLquery parser and analysis tool for collecting column dependencies and SQLquery refactoring. 10/2002 08/2005: State Scientific Center GosNIIGenetika (Moscow, Russia), PhD Research Developed the BATMAS series of amino acid substitution matrices that are specific for transmembrane proteins (see publication list). Developed an algorithm for prediction of secondary structure of transmembrane proteins by analysis of multiple alignment. The algorithm is based on HMM forwardbackward posterior probability approach. 03/2002 02/2003: Integrated Genomics (Moscow office) Java developer (part time while undergraduate and PhD student) Developed the metabolic pathways editor software supervised by Prof. Andrey Mironov.
http://www.biomax.de/products/bioxm_scrsht.php

Bioinformatics expertise Dynamic programming on matrices and graphs, phylogenetic tree construction, functional optimization methods (gradients, genetic algorithm, annealing, Gibbs sampling), HMM construction, pairwise and multiple alignment algorithms development.

Software development expertise Languages: Java, C , C++, C#, Object Pascal, Perl, Groovy Database Management Systems: MSSQL, Sybase, DB2, Oracle, Mysql, Postgres, Access, JavaDB, HSQL Database technologies/dialects: JDBC, Hibernate, ANSI SQL, PL/SQL, PL/pgSQL, TransactSQL

Web development: JSP, Servelts, JavaScript, GWT, JQuery, Dojo, FreeMarker Application Servers: Tomcat, JBoss, Jetty Web services: SOAP, Jersey Clientserver development: sockets (clientserver TCP/IP, datagrams), RMI Other Java technologies: JavaCC (parser's compiler), multithreading, reflection, Swing, XML (DOM, SAX, XSLT), serialization, java code profiling, byte code decompilation, Android SDK Cluster computing: Torque Resource Manager IDEs: Eclipse, IntelliJ IDEA, Microsoft Visual Studio, Oracle JDeveloper Control Version Systems: CVS, Subversion, GIT

Education 19972002: Department of Mathematics and Mechanics, Moscow State University, Moscow, Russia. BS Mathematics and MS Computational Mathematics. 20022005: State Scientific Center GosNIIGenetika, Moscow, Russia. PhD Biophysics. 2008: Sun Certified Programmer for the Java 2 Platform, Standard Edition 5.0 certification.

Publications

Leushkin EV, Sutormin RA, Nabieva ER, Penin AA, Kondrashov AS, Logacheva MD. The miniature
genome of a carnivorous plant Genlisea aurea contains a low number of genes and short noncoding sequences. BMC Genomics. 2013 Jul 1514(1):476. Kurmangaliyev YZ, Sutormin RA, Naumenko SA, Bazykin GA, Gelfand MS. Functional implications of splicing polymorphisms in the human genome. Hum Mol Genet. 2013 Sep 122(17):344959. doi: 10.1093/hmg/ddt200. Epub 2013 May 2. Nikulova AA, Favorov AV, Sutormin RA, Makeev VJ, Mironov AA. CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation. Nucleic Acids Res. 2012 Jul 40(12):e93. Epub 2012 Mar 15. Sadovskaya NS, Sutormin RA, Gelfand MS. Recognition of transmembrane segments in proteins: review and consistencybased benchmarking of internet servers. J Bioinform. Comput. Biol. 2006 Oct 4(5):10331056. Sutormin RA, Mironov AA. Membrane probability profile construction based on amino acids sequences multiple alignment. Mol. Biol. (Mosk). 2006 MayJun40(3):541545. Sutormin RA, Rakhmaninova AB, Gelfand MS. BATMAS30: amino acid substitution matrix for alignment of bacterial transporters. Proteins. 2003 Apr 151(1):8595. Kalinina OV, Makeev VJ, Sutormin RA, Gelfand MS, Rakhmaninova AB. The channel in transporters is formed by residues that are rare in transmembrane helices. In Silico Biol. 20033(12):197204.