PROGRAM OF THE FIFTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE

RUSSIAN ACADEMY OF SCIENCES SIBERIAN BRANCH INSTITUTE OF CYTOLOGY AND GENETICS PROGRAM OF THE FIFTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE BGRS’2006 Novosibirsk, Russia July 16–22, 2006 Novosibirsk 2006 INTERNATIONAL PROGRAM COMMITTEE Nikolay Kolchanov Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia (Chairman of the Conference) Ralf Hofestaedt University of Bielefeld, Germany (Co-Chairman of the Conference) Dagmara Furman Institute of Cytology and Genetics SB RAS, Novosibirsk, (Conference Scientific Secretary) Dmitry Afonnikov Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Mikhail Gelfand GosNIIGenetika, Moscow, Russia Vadim Govorun Institute of Physicochemical Medicine, RAMS, Moscow, Russia Reinhart Heinrich Humboldt University Berlin, Berlin, Germany Charlie Hodgman Multidisciplinary Centre for Integrative Biology, School of Biosciences, University of Nottingham, UK Alexey Kochetov Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Eugene Koonin National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA Vassily Lyubetsky Institute for Informational Transmission Problems RAS, Moscow, Russia Luciano Milanesi National Research Council – Institute of Biomedical Technology, Italy Viatcheslav Mordvinov Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Yuriy Orlov Genome Institute of Singapore, Singapore Igor Rogozin Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Cenk Sahinalp Computing Science, Simon Fraser University, Burnaby, Canada Maria Samsonova St.Petersburg State Polytechnic University, St.Petersburg, Russia Akinori Sarai Kyushu Institute of Technology (KIT), Iizuka, Japan Konstantin Skryabin Centre "Bioengineering" RAS, Moscow, Russia Rustem Tchuraev Institute of Biology, Ufa Sci Centre RAS, Ufa, Russia Denis Thieffry ESIL-GBMA, Universite de la Mediterranee, Marseille, France Jennifer Trelewicz IBM Almaden Research Center, San Jose, California, USA Edgar Wingender UKG, University of Goettingen, Goettingen, Germany Lev Zhivotovsky Institute of General Genetics RAS, Moscow, Russia Jagath C Rajapakse School of Computer Engineering, Nanyang Technological University, Singapore LOCAL ORGANIZING COMMITTEE Sergey Lavryushev Institute of Cytology and Genetics, SB RAS, Novosibirsk (Chairperson) Ekaterina Denisova Institute of Cytology and Genetics, SB RAS, Novosibirsk Andrey Kharkevich Institute of Cytology and Genetics, SB RAS, Novosibirsk Galina Kiseleva Institute of Cytology and Genetics, SB RAS, Novosibirsk Anna Onchukova Institute of Cytology and Genetics, SB RAS, Novosibirsk Natalia Sournina Institute of Cytology and Genetics, SB RAS, Novosibirsk Our sponsors Organizers Laboratory of Theoretical Genetics of the Institute of Cytology and Genetics, SB RAS Institute of Cytology and Genetics, SB RAS Siberian Branch of the Russian Academy of Sciences В А В И Л О В С КО Е О Б Щ ЕС ТВ О ГЕНЕТИ КО В И СЕ ЛЕКЦ ИО Н ЕРО В Vavilov Society of Geneticists and Breeders Scientific Council on Bioinformatics, Siberian Branch of the Russian Academy of Sciences Chair of Informational Biology, Department of Natural Sciences, Novosibirsk State University Grants INTAS Grant Russian Foundation for Basic Research THE FIFTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2006) CONFERENCE PROGRAM SCHEDULE AT A GLANCE The Conference Sessions will be held in the Small Conference Hall and in Music Salon (room no 220) of the House of Scientists July 16, Sunday Foyer of the Small Conference Hall 10:00-14:00 Registration of the conference participants* *Participants who come later are welcome for registration in the Organizing Committee room (House of Scientists, room no.200) on any conference day 12:30-14:00 Lunch 14:00 Small Conference Hall Conference Opens: Welcome by Academician of the Russian Academy of Sciences Vladimir Shumny, Director of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences Greetings of Corresponding member of the Russian Academy of Sciences, Professor Nikolay Kolchanov and Professor Ralf Hofestaedt 14:30-18:00 PLENAR SESSION 16:00-16:30 Coffee break 19:00-23:00 Welcome party July 17, Monday Small Conference Hall 9:30-12:45 Morning Session COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICS 10:40-11:10 Coffee break 12:45-14:30 Lunch break 14:30-17:45 Evening Session COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICS 16:00-16:30 Coffee break Computer demos of this session will be available during the entire conference day July 18, Tuesday Small Conference Hall 9:30-12:50 Morning Session COMPUTATIONAL STRUCTURAL AND FUNCTIONAL PROTEOMICS 10:45-11:15 Coffee break 12:50 -14:30 Lunch break 14:30 -17:25 Evening Session COMPUTATIONAL STRUCTURAL AND FUNCTIONAL PROTEOMICS 16:05-16:35 Coffee break Computer demos of this session will be available during the entire conference day July 19, Wednesday Foyer of the Small Conference Hall 9:30-12:30 POSTER SESSION 10:45-11:15 Coffee break 12:30-14:00 Lunch break July 20, Thursday Small Conference Hall 9:30-12:55 Morning Session COMPARATIVE AND EVOLUTIONARY GENOMICS AND PROTEOMICS 10:45-11:15 Coffee break 12:55-14:30 Lunch break 14:30-18:10 Evening Session COMPARATIVE AND EVOLUTIONARY GENOMICS AND PROTEOMICS 16:00-16:30 Coffee break Computer demos of this session will be available during the entire conference day July 20, Thursday Music Salon (room no.220) 9:30-12:55 Morning Session NEW APPROACHES TO BIOMOLECULAR DATA AND PROCESSES ANALYSIS/MODELING 10:45-11:15 Coffee break 12:55-14:30 Lunch break 14:30-17:20 Evening Session NEW APPROACHES TO BIOMOLECULAR DATA AND PROCESSES ANALYSIS/MODELING 16:05-16:30 Coffee break July 21, Friday Small Conference Hall 9:30-12:55 Morning Session COMPUTATIONAL SYSTEMS BIOLOGY 10:45-11:15 Coffee break 12:50-14:30 Lunch break Computer demos of this session will be available during the entire conference day July 22, Saturday Small Conference Hall 9:30-12:50 Morning Session COMPUTATIONAL SYSTEMS BIOLOGY 10:45-11:15 Coffee break 12:50-14:30 Lunch break 14:30-16:40 Evening Session COMPUTATIONAL SYSTEMS BIOLOGY 15:20-15:50 Coffee break Computer demos of this session will be available during the entire conference day 16:40-17:20 Closing Ceremony; Comments of Session Chairpersons PLENAR SESSION July 16, Sunday House of Scientists, Small Conference Hall 14:30-18:00 Co-chairpersons: Prof Ralf Hofestaedt, Bielefeld University, AG Bioinformatics, Bielefeld, Germany Prof Nikolay Kolchanov, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia No Author(s) and Title of Talk Mazo I *, Sivachenko A., Yuryev A., Daraselia N Ariadne Genomics, Inc., Rockville, USA MOLECULAR NETWORKS IN MAMMALS: EXTRACTION FROM LITERATURE AND MICROARRAY Rodin S.N.1*, Rodin A.S.2 Beckman Research Institute of the City of Hope, Duarte, CA, USA Human Genetics Center, School of Public Health, University of Texas, Houston, TX, USA GENE DUPLICATIONS IN EVOLUTION: FROM ORIGIN OF THE GENETIC CODE TO THE HUMAN GENOME Timeline 14:3015:15 15:1516:00 Coffee/tea break 16:00-16:30 Ivanov A.S.*, Gnedenko O.V., Molnar A.A., Mezentsev Yu.V., Lisitsa A.V., Archakov A.I V.N.Orechovich Institute of Biomedical Chemistry RAMS, Moscow, Russia PROTEIN-PROTEIN INTERACTIONS AS NEW TARGETS FOR DRUG DESIGN: INTERACTIVE LINKS BETWEEN VIRTUAL AND EXPERIMENTAL APPROACHES Samsonova M.G.1, Reinitz J.2 St Petersburg State Polytechnical University, St Petersburg, Russia Stony Brook University, Stony Brook, New York, USA SYSTEMS BIOLOGY OF SEGMENT DETERMINATION 16:3017:15 17:1518:00 ORAL PRESENTATIONS Dear speakers, please, plan your presentation time including minutes for questions Only PowerPoint presentations made in Microsoft Office 2003 or earlier versions can be accepted Use embedded pictures and animations only; picture and animation links to the Internet or to other files will not be accessible Slide projectors or overhead projectors are NOT available during the BGRS'2006 Conference Please, take into account that it will not be possible for you to load your presentation during the session by yourselves Presentations are loaded on the main computer by the technician of the Organizing Committee only To ensure that the presentations are well prepared and compatible with the main presentation computer, we strongly advice you to bring your materials as PowerPoint files on USB device or CD disk to the Room no 200 at the House of Scientists and check the presentation with the technician of the Organizing Committee not later than 30 before the start time of the session where you are presenting This will prevent any confusion when loading the presentations on the main computer You may also bring your laptop for copying your presentation to the main presentation computer Use of your own laptop during your presentation is not recommended If you have any questions, please not hesitate to contact the Organizing Committee in Room no 200 at the House of Scientists July 17, Monday House of Scientists, Small Conference Hall Morning Session 9:30-12:45 COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICS AND TRANSCRIPTOMICS Co-chairpersons: Prof Andrey Mironov, Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Dr Georgii Bazykin, Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA No Author(s) and Title of Talk Timeline Seliverstov A.V.*, Lyubetsky V.A Institute for Information Transmission Problems RAS, Moscow, Russia GENE EXPRESSION REGULATION IN ACTINOBACTERIA AND CHLOROPLASTS Grosse I 1,2 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Bioinformatics Center Gatersleben-Halle, Gatersleben, Germany COMPUTATIONAL IDENTIFICATION OF TRANSCRIPTION FACTOR BINDING SITES WITH VARIABLE ORDER BAYESIAN NETWORKS Levitsky V.G.1,2*, Ignatieva E.V.1,2, Ananko E.A.1, Merkulova T.I.1 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia THE SITEGA AND PWM METHODS APPLICATION FOR TRANSCRIPTION FACTOR BINDING SITES RECOGNITION IN EPD PROMOTERS 9:309:55 9:5510:20 10:2010:40 Coffee/tea break 10:40-11:10 *1 Shelest E.S , Wingender E.1,2 Department of Bioinformatics, UKG, University of Göttingen, Göttingen, Germany BIOBASE GmbH, Wolfenbüttel, Germany PROMOTER MODELING APPROACHES APPLIED TO THE INVESTIGATION OF p63 UP- AND DOWNSTREAM PROMOTERS Vorobjev Y.N., Emelianov D.Y Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia MODELING OF DATA BASE OF CONTEXT-DEPENDENT CONFORMATIONAL PARAMETERS OF DNA DUPLEXES Kamzolova S.G., Osypov A.A.*, Dzhelyadin T.R., Beskaravainy P.M., Sorokin A.A Institute of Cell Biophysics of RAS, Pushchino, Moscow region, Russia CONTEXT-DEPENDENT EFFECTS OF UPSTREAM A-TRACTS ON PROMOTER ELECTROSTATIC PROPERTIES AND FUNCTION Vishnevsky O.V.1,2*, Konstantinov Yu.M.3 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia Siberian Institute of Plant Physiology and Biochemistry SB RAS, Irkutsk, Russia ANALYSIS OF THE NUCLEOTIDE CONTEXT OF HIGHER PLANT MITOCHONDRIAL mRNA EDITING SITES 11:1011:35 11:3512:00 12:0012:20 12:2012:45 12:45-14:30 Lunch break July 17, Monday House of Scientists, Small Conference Hall Evening Session 14:30-18:10 COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICS AND TRANSCRIPTOMICS Co-chairpersons: Prof Vasily Lyubetsky, Institute for Information Transmission Problems, the Russian Academy of Sciences, Moscow, Russia Dr Ivo Grosse, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) and Bioinformatics Center Gatersleben-Halle, Gatersleben, Germany No Author(s) and Title of Talk Omelianchuk N.A.1, Khomicheva I.V.1, Savinskaya S.A 1,2, Levitsky V.G.1,2, Vishnevsky O.V 1,2, Katokhin A.V.1,2, Ponomarenko M.P.1 , Kolchanov N.A.1,2 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk Russia REVEALING THE FUNCTIONAL-SPECIFIC TEXTUAL FEATURES OF THE microRNA SEQUENCES IN ARABIDOPSIS THALIANA Tutukina M.N., Masulis I.S., Ozoline O.N.* Institute of Cell Biophysics RAS, Pushchino, Moscow region, Russia TOWARDS THE IDENTIFICATION OF ANTISENSE RNA WITHIN GENES OF TRANSCRIPTION REGULATORS Orlov Yu.L.1, Zhou J.1, Lipovich L.1, Yong H.C.2, Li Yi2, Shahab A.2, Kuznetsov V.A.1* Genome Institute of Singapore, Singapore Bioinformatics Institute, Singapore A COMPREHENSIVE QUALITY ASSESSMENT OF THE AFFYMETRIX U133A/B PROBESETS BY AN INTEGRATED GENOMIC AND CLINICAL APPROACH Kuznetsov V.A.*, Zhou J., George J., Orlov Yu.L Genome Institute of Singapore, Singapore GENOME-WIDE CO-EXPRESSION PATTERNS OF HUMAN CIS-ANTISENSE GENE PAIRS Timeline 14:3014:55 14:5515:15 15:1515:35 15:3516:00 Coffee/tea break 16:00-16:30 1* Efimov V.M , Badratinov M.S.2, Katokhin A.V.2,3 Institute of Systematics and Ecology of Animals, SB RAS, Novosibirsk, Russia Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia INTERPRETATION OF RESULTS OF SOM ANALYSIS OF MICROARRAY DATA BY PRINCIPAL COMPONENTS Subkhankulova T., Livesey F.J Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 QN, UK HOW SIMILAR ARE PHENOTYPICALLY IDENTICAL CELLS AT THE TRANSCRIPTIONAL LEVEL Abhishek K.1*, Karnick H.1, Mitra P.2 Indian Institute of Technology Kanpur, Kanpur, India Indian Institute of Technology Kharagpur, Kharagpur, India A KNOWLEDGE AND DATA BASED HYBRID APPROACH TO GENE CLUSTERING 10 16:3016:55 16:5517:20 17:2017:45 COMPUTATIONAL STRUCTURAL AND FUNCTIONAL PROTEOMICS Afonnikov D.A.1,2, Morozov A.V.1 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia CONNP: THE PREDICTION OF THE CONTACT NUMBERS OF THE AMINO ACID RESIDUES IN PROTEINS USING NEURAL NETWORK REGRESSION Aman E.E *, Demenkov P.S., Ivanisenko V.A Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia ANALYSIS OF THE TERTIARY STRUCTURE OF THE PPAR AND RXR TRANSCRIPTIONAL FACTORS AND THEIR MUTANT VARIANTS Bakulina A.Yu.*1, Sineva E.V.2, Solonin A.S.2, Maksyutov A.Z.1 State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Novosibirsk region, Russia Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region, Russia MOLECULAR MODELING OF B CEREUS HEMOLYSIN II, A PORE-FORMING PROTEIN Baryshev P.B.1*, Afonnikov D.A.1,2, Nikolaev S.V.2 Novosibirsk State University, Novosibirsk, Russia Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia IDENTIFICATION AND STRUCTURE-FUNCTIONAL ANALYSIS OF THE SPECIFICITY DETERMINING RESIDUES OF THE ALPHA SUBUNITS OF THE PROTEOSOMAL COMPLEX Batsianovsy A.V.*, Vlasov P.K Engelhard Institute of Molecular Biology, RAS, Moscow, Russia *Moscow State University, Moscow, Russia CLUSTERING ANALYSIS OF CONFORMATIONAL STRUCTURES OF SHORT OLIGOPEPTIDES Chugunov A.O.1,2,*, Novoseletsky V.N.1,3, Efremov R.G.1 Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia Department of Bioengineering, Biological Faculty, M.V Lomonosov Moscow State University, Moscow, Russia Moscow Institute of Physics and Technology (State University), Moscow region, Russia A METHOD TO ASSESS CORRECT/MISFOLDED STRUCTURES OF TRANSMEMBRANE DOMAINS OF MEMBRANE PROTEINS Efimov A.V., Brazhnikov E.V., Kondratova M.S Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow region, Russia EFFECT OF THE STRUCTURAL CONTEXT ON SPECIFICITY OF INTRAAND INTERHELICAL INTERACTIONS IN PROTEINS Dulko V., Feranchuk S 31 United Institute of Informatics Problems of the National Academy of Sciences of Belarus,  Minsk, Belarus DYNAMIC PROGRAMMING ALGORITHM PARALLIZATION FOR PROTEIN FOLDING Gou Z., Hwang S., Kuznetsov I.B.* Gen*NY*sis Center for Excellence in Cancer Genomics, University at Albany, Rensselaer, USA SEQUENCE-BASED PREDICTION OF DNA-BINDING SITES ON DNA-BINDING PROTEINS Ivanisenko V.A.1,2*, Ivanisenko T.V.3, Sharonova I.V.2, Krestyanova M.A.2, Ivanisenko N.V.2, Grigorovich D.A.1 Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia Siberian State University of Telecommunications and Information Sciences, Novosibirsk, Russia PDBSite DATABASE AND PDBSiteScan TOOL: RECOGNITION OF FUNCTIONAL SITES IN PROTEIN 3d STRUCTURE AND TEMPLATE-BASED DOCKING Konshina A.G.*, Dubinnyi M.A., Efremov R.G Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia STRUCTURAL DETERMINANTS OF CARDIOTOXINS’ MEMBRANE BINDING: A MOLECULAR MODELING APPROACH Nizolenko L.Ph.1*, Bachinsky A.G 1, Yarygin A.A.1, Naumochkin A.N.1, Grigorovich D.A.2 SRC VB “Vector”, Koltsovo, Novosibirsk, Russia Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia PROF_PAT: THE UPDATED DATABASE OF PROTEIN FAMILY PATTERNS CURRENT STATUS Nyporko A.Yu.*, Blume Ya.B Institute of Cell Biology and Genetic Engineering of NAS of Ukraine, Kiev, Ukraine THE FEATURES OF STRUCTURAL DYNAMICS OF DIFFERENT TUBULIN SUBUNITS Polyansky A.A.*1,2, Aliper E.T.1,2, Volynsky P.E.1, Efremov R.G.1 M.M Shemyakin and Yu.A Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Moscow, Russia Biological Department, M.V.Lomonosov Moscow State University, Moscow, Russia ACTION OF MEMBRANE-ACTIVE PEPTIDES ON EXPLICIT LIPID BILAYERS ROLE OF SPECIFIC PEPTIDE-LIPID INTERACTIONS IN MEMBRANE DESTABILIZATION Pyrkov T.V.*1,2, Kosinsky Yu.A.1, Arseniev A.S.1, Priestle J.P.3, Jacoby E.3, Efremov R.G.1 M.M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia Moscow Institute of Physics and Technology, Moscow, Russia Novartis Institutes for Biomedical Research, Basel, Swizerland 32 COMBINING MOLECULAR DOCKING WITH RECEPTOR DOMAIN MOTIONS: SIMULATIONS OF BINDING OF ATP TO CA-ATPASE Shaytan A.K.*, Khokhlov A.R., Ivanov V.A Chair of Polymer and Crystal Physics, Physics Department, Moscow State University, Moscow, Russia PEPDITE DYNAMICS AT WATER MEMBRANE INTERFACE Slyadnikov E.E Informatization Problems Department of Tomsk Scientific Centre, SB RAS, Tomsk, Russia MICROSCOPIC MODEL OF CONFORMATION DEGREES OF FREEDOM CYTOSKELETON MICROTUBULE AND ITS STRUCTURAL ANALOG IN OPTICS Troshin P.V.1*, Papiz M.Z.1, Prince S.M.2, Daniel E.J.3, Morris C.3*, Griffiths S.L.4, Diprose J.M.5, Pilicheva K.5, Niekerk J.V.6, Pajon A.7 1* Membrane Protein Structure Initiative, CCLRC Daresbury Laboratory, UK Faculty of Life Sciences, University of Manchester, Sackville St., Manchester, UK Protein information Management System, CCLRC Daresbury Laboratory, UK York Structural Biology Laboratory, University of York, UK Oxford Protein Production Facility, Division of Structural Biology, University of Oxford, UK Scottish Structural Proteomics Facility, University of Dundee, UK European Bioinformatics Institute, Hinxton, UK LABORATORY INFORMATION MANAGEMENT SYSTEM FOR MEMBRANE PROTEIN STRUCTURE INITIATIVE Volkova O.A.1, Kochetov A.V.1* Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia AMINO ACID PREFERENCES AT THE N-TERMINAL PART OF EUKARYOTIC PROTEINS CORRELATING WITH A SPECIFIC CONTEXTUAL ORGANIZATION OF TRANSLATION INITIATION SIGNAL COMPARATIVE AND EVOLUTIONARY GENOMICS AND PROTEOMICS Babkin I.V.*, Shchelkunov S.N State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Novosibirsk region, Russia TIME SCALE OF POXVIRUS EVOLUTION Boeva V.A.*1, Makeev V.J.2 Moscow State University, Department of Bioengineering and Bioinformatics, Moscow, Russia GosNIIGenetika State Research Center, Moscow, Russia MICRO- AND MINISATELLITES IN HUMAN GENOME, TandemSWAN SOFTWARE IN USE Brinza D., Perelygin A., Brinton M., Zelikovsky A.* Georgia State University, Atlanta, USA SEARCH FOR MULTI-SNP DISEASE ASSOCIATION Bukin Y.S.*, Pudovkina T.A Limnological Institute of SB RAS, Irkutsk, Russia 33 THE MODELS OF POPULATION DYNAMICS AS TOOL FOR STUDYING OF GENETIC POLYMORPHISM OF BAIKALIAN POLYCHAETS Chumakov M.I., Mazilov S., Zotova T.V Institute of Symbiology RAS, Saratov, Russia SEARCHING FOR NUCLEOTIDE SEQUENCES LIKE AGROBACTERIAL T-DNA RIGHT BORDER IN PLANT GENOMES Golovnina K.*1, Blinov A.1, Chang L.-S.2 Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Center for Childhood Cancer, Children’s Research Institute, Children’s Hospital and Department of Pediatrics, The Ohio State University, USA EVOLUTION AND ORIGIN OF NEUROFIBROMIN, THE PRODUCT OF THE NEUROFIBROMATOSIS TYPE (NF1) TUMOR-SUPRESSOR GENE Gorbunov K.Yu.*, Lyubetsky V.A Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia INFERRING REGULATIORY SIGNAL PROFILES AND EVOLUTIONARY EVENTS Gunbin K.V., Morozov A.V., Afonnikov D.A Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia A METHOD FOR SEMIAUTOMATED ANALYSIS OF GENE EVOLUTION Guryev V.1*, Smits B.M.G.1, van de Belt J 1, Verheul M.1, Hubner N.2 , Cuppen E.1 Hubrecht Laboratorium, Utrecht, The Netherlands Max-Delbruck-Center for Molecular Medicine (MDC), Berlin-Buch, Germany HAPLOTYPE BLOCK STRUCTURE IS CONSERVED ACROSS MAMMALS Kabanova A1., Novikova O1., Gunbin K1., Fet V2., Blinov A.1* Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Marshall University, Huntington, WV, USA EVOLUTIONARY RELATIONSHIPS AND DISTRIBUTION OF THE DIFFERENT LTR RETROTRANSPOSON FAMILIES IN PLANTS Khan M 2, Jamil K.1, * Indo American Cancer Institute and Research Centre, Hyderabad, India School of Biotechnology, (MGNIRSA,) University of Mysore, Mysore, India THE PHYLOGENETIC ANALYSIS OF UBIQUITIN CONJUGATING ENZYMES OF CANCER METASIGNATURE Korostishevsky M.1*, Bonne’-Tamir B.1, Bentwich Z.2, Tsimanis A.2 Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Israel Institute of Clinical Immunology and AIDS, Kaplan Medical Center, Rehovot, Israel MULTI-SNP ANALYSIS OF CCR5-CCR2 GENES IN ETHIOPIAN JEWS: MICRO-EVOLUTION AND HIV-RESISTANCE IMPLICATIONS Kovaleva G.Yu.*1,2, Gelfand M.S.1,2 Moscow State University, Department of Bioengeneering and Bioinformatics, Moscow, Russia Institute for Information Transmission Problems RAS, Moscow, Russia TRANSCRIPTIONAL REGULATION OF THE METHIONINE BIOSYNTHESIS IN ACTINOBACTERIA AND STREPTOCOCCI 34 Kuznetsova A.Y.*1, Naumoff D.G.2 Moscow State University, Department of Bioengineering and Bioinformatics, Moscow, Russia State Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia PHYLOGENETIC ANALYSIS OF COG1649, A NEW FAMILY OF PREDICTED GLYCOSYL HYDROLASES Lashin S.A.*, Likhoshvai V.A., Kolchanov N.A, Matushkin Yu.G Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia EVOLUTIONARY CONSTRUCTOR: A PACKAGE FOR MODELING COEVOLUTION OF UNICELLULAR ORGANISMS Lashin S.A.*, Likhoshvai V.A., Kolchanov N.A., Matushkin Yu.G Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia MODELING OF HORIZONTAL GENE TRANSFER IN PROKARYOTIC POPULATIONS WITH THE “EVOLUTIONARY CONSTRUCTOR” PROGRAM PACKAGE Liventseva V.*, Kaygorodova I Limnological Institute, SB RAS, Irkutsk, Russia MOLECULES VERSUS MORPHOLOGY IN OLIGOCHAETA SYSTEMATICS Novikova O.*1, Fursov M.2, Blinov A.1 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Novosibirsk Center of Information Technologies “UniPro”, Novosibirsk, Russia NEW FAMILY OF LTR RETOTRANSPOSABLE ELEMENTS FROM FUNGI Peretolchina T.E.*, Bukin Yu.S., Sitnikova T.Ya., Sherbakov D.Yu Limnological Institute, SB RAS, Irkutsk, Russia POPULATION GENETIC POLYMORPHISM OF ENDEMIC MOLLUSCS BAICALIA CARINATA (MOLLUSCA: CAENOGASTROPODA) 35 Rotskaya U.N., Rogozin I.B., Vasyunina E.A., Kolosova N.G., Sinitsyna O.I * Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia THEORETICAL ANALYSIS OF THE MITOCHONDRIAL DNA SOMATIC MUTATION SPECTRA IN OXYS AND WISTAR RATS Rusin L.Y.*, Lyubetsky V.A Institute for Information Transmission Problems RAS, Moscow, Russia REFINEMENT OF PHYLOGENETIC SIGNAL IN MULTIPLE SEQUENCE ALIGNMENT: RESULTS OF SIMULATION STUDY Ryabinina O.M Vavilov Institute of General Genetics RAS, Moscow, Russia GENETIC DIVERSITY AND PHYLOGENETIC RELATIONSHIPS IN GROUPS OF ASIAN GUARDIAN, SIBERIAN HUNTING AND EUROPEAN SHEPHERD DOG BREEDS Yudin N.S.1*, Vasil’eva L.A.1, Kobzev V.F.1, Kuznetsova T.N.1, Ignatieva E.V.1, Oshchepkov D.Yu.1, Voevoda M.I.1,2, Romaschenko A.G.1 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Institute of Internal Medicine, SB RAMS, Novosibirsk, Russia ASSOCIATION STUDY OF SNP OF THE TNF-ALPHA GENE WITH BOVINE LEUKOSIS AND EVALUATION OF ITS FUNCTIONAL SIGNIFICANCE Zotov V.S.1, Punina N.V.1, Dorokhov D.B.1, Schaad N.W.2, Ignatov A.N.1* Centre “Bioengineering” RAS, Moscow, Russia FDWSRU, USDA-ARS, MD, USA PHYLOGENETIC CHANGES IN CHLOROPLAST GENOMES COMPUTATIONAL SYSTEMS BIOLOGY 4.1 Modeling of Molecular Genetic Systems and Processes in Bacterial Cell Khlebodarova T.M.1, Ananko E.A.1*, Nedosekina E.A.1, Podkolodnaya O.A.1, Poplavsky A.S.1, Smirnova O.G.1, Ibragimova S.S.1, Mishchenko E.L.1, Stepanenko I.L.1, Ignatieva E.V.1, Proskura A.L.1, Nishio Y.2, Imaizumi A.2, Usuda Y.2, Matsui K.2, Podkolodny N.L.1, Kolchanov N.A.1 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Institute of Life Sciences, Ajinomoto, Co., Inc., Kawasaki-city, Japan IN SILICO CELL II INFORMATION SOURCES FOR MODELING ESCHERICHIA COLI METABOLIC PATHWAYS Ratushny A.V.1*, Usuda Y.2, Matsui K.2, Podkolodnaya O.A.1 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Institute of Life Sciences, Ajinomoto, Co., Inc., Kawasaki, Japan MATHEMATICAL MODELING OF ELEMENTARY PROCESSES OF THE GENE NETWORK CONTROLLING HISTIDINE BIOSYNTHESIS IN ESCHERICHIA COLI Nedosekina E.A.1*, Usuda Y.2, Matsui K.2 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Institute of Life Sciences, Ajinomoto, Co., Inc., Kawasaki, Japan MODELING OF THE EFFECTS OF THREONINE, VALINE, ISOLEUCINE AND PYRIDOXAL 5'-MONOPHOSPHATE ON BIOSYNTHETIC THREONINE DEHYDRATASE REACTION 36 Ratushny A.V.*, Nedosekina E.A Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia REGULATION OF PYRIMIDINE BIOSYNTHESIS IN ESCHERICHIA COLI: GENE NETWORK RECONSTRUCTION AND MATHEMATICAL MODELING Ratushny A.V.1*, Smirnova O.G.1, Usuda Y.2, Matsui K.2 Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Institute of Life Sciences, Ajinomoto, Co., Inc., Kawasaki, Japan REGULATION OF THE PENTOSE PHOSPHATE PATHWAY IN ESCHERICHIA COLI: GENE NETWORK RECONSTRUCTION AND MATHEMATICAL MODELING OF METABOLIC REACTIONS Ananko E.A.1*, Ratushny A.V 1, Usuda Y.2, Matsui K.2 Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Institute of Life Sciences, Ajinomoto, Co., Inc., Kawasaki, Japan AROMATIC AMINO ACID BIOSYNTHESIS IN ESCHERICHIA COLI: GENERALIZED HILL FUNCTION MODEL OF THE TRYPTOPHAN-SENSITIVE 3-DEOXY-D-ARABINOHEPTULOSONATE-7-PHOSPHATE SYNTHASE REACTION DEMONSTRATE COMPLICATED MECHANISM Ratushny A.V.*, Khlebodarova T.M Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia MATHEMATICAL MODELING OF REGULATION OF cyоABCDE OPERON EXPRESSION IN ESCHERICHIA COLI Khlebodarova T.M.*, Lashin S.A., Apasieva N.V Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia GENE NETWORK RECONSTRUCTION AND MATHEMATICAL MODELING OF ESCHERICHIA COLI RESPIRATION: REGULATION OF F0F1-ATP SYNTHASE BY METAL IONS Nedosekina E.A Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia MATHEMATICAL MODELING OF REGULATION OF ESCHERICHIA COLI PURINE BIOSYNTHESIS PATHWAY ENZYMATIC REACTIONS Mishchenko E.L 1*, Lashin S.A.1, Usuda Y.2, Matsui K.2 Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Institute of Life Sciences, Ajinomoto, Co., Inc., Kawasaki, Japan RECONSTRUCTION AND MATHEMATICAL MODELING OF THE GENE NETWORK CONTROLLING CYSTEINE BIOSYNTHESIS IN ESCHERICHIA COLI: REGULATION OF SERINE ACETYLTRANSFERASE ACTIVITY Smirnova O.G.*, Ratushny A.V Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia GENE NETWORK RECONSTRUCTION AND MATHEMATICAL MODELING OF SALVAGE PATHWAYS: REGULATION OF ADENINE PHOSPHORIBOSYLTRANSFERASE ACTIVITY BY STRUCTURALLY SIMILAR SUBSTRATES 37 Turnaev I.I.1*, Ibragimova S.S.1, Usuda Y.2, Matsui K.2 Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Institute of Life Sciences, Ajinomoto, Co., Inc., Kawasaki, Japan MATHEMATICAL MODELING OF SERINE AND GLYCINE BIOSYNTHESIS REGULATION IN ESCHERICHIA COLI Turnaev I.I.*, Smirnova O.G Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia REGULATION OF PYRUVATE BIOSYNTHESIS IN ESCHERICHIA COLI: GENE NETWORK RECONSTRUCTION AND MATHEMATICAL MODELING OF ENZYMATIC REACTIONS OF THE PATHWAY Ibragimova S.S.*, Smirnova O.G., Grigorovich D.A., Khlebodarova T.M Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia BiotechPro: A DATABASE FOR MICROBIOLOGICALLY SYNTHESIZED PRODUCTS OF BIOTECHNOLOGICAL VALUE Peshkov I.M.1, Fadeev S.I.2 Novosibirsk State University, Novosibirsk, Russia Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia ABOUT RECONSTRUCTION OF REGULATORY MECHANISM OF GENE ELEMENTS’ EXPRESSION 4.2 Modeling of Molecular Genetic Systems and Processes in Multicellular Organisms Akberdin I.R.1*, Kashevarova N.A.2, Khlebodarova T.M.1, Bazhan S.I.3, Likhoshvai V.A.1 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia A MATHEMATICAL MODEL FOR THE INFLUENZA VIRUS LIFE CYCLE Bazhan S.I.1*, Schwartz Ya.Sh.2, Gainova I.A.3, Ananko E.A.4 State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia Institute of Internal Medicine, SB RAMS, Novosibirsk Institute of Mathematics, SB RAS, Novosibirsk Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia A MATHEMATICAL MODEL OF IMMUNE RESPONSE IN INFECTION INDUCED BY MYCOBACTERIA TUBERCULOSIS PREDICTION OF THE DISEASE COURSE AND OUTCOMES AT DIFFERENT TREATMENT REGIMENS Bezmaternikh K.D., Mishchenko E.L.*, Ratushny A.V., Likhoshvai V.A., Khlebodarova T.M., Ivanisenko V.A Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia A MINIMUM MATHEMATICAL MODEL FOR SUPPRESSION HCV RNA REPLICATION IN CELL CULTURE Fadeev S.I.1*, Shtokalo D.N.2, Likhosvai V.A.3 Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia MATRIX PROCESS MODELLING: STUDY OF A MODEL OF SYNTHESIS OF LINEAR BIOMOLECULES WITH REGARD TO REVERSIBILITY OF PROCESSES 38 Gursky V.V.1*, Samsonov A.M.1, Reinitz J.2 Ioffe Physico-Technical Institute of the Russian Academy of Sciences, St Petersburg, Russia Stony Brook University, Stony Brook, New York, USA APPROXIMATE STATIONARY ATTRACTORS IN DROSOPHILA GAP GENE CIRCUITS IN THE LIMIT OF STEEP-SIGMOID INTERACTIONS Kalashnikova E.V.1, Dymshits G M.1, Kolpakov F.A.2,3 Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia Institute of Systems Biology OOO, Novosibirsk, Russia SIGNAL TRANSDUCTION PATHWAYS INVOLVED IN TRANSCRIPTIONAL REGULATION OF TYROSINE HYDROXYLASE Mischenko E.L.1, Korotkov R.O.2, Ivanisenko V.A.1,2* Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia HCV-KINET DATABASE: KINETIC PARAMETER REACTIONS AND REGULATORY PROCESSES OF THE LIFE CYCLE OF THE HEPATITIS C VIRUS Ratushny A.V Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia MATHEMATICAL MODELING OF RECEPTOR MEDIATED ENDOCYTOSIS OF LOW-DENSITY LIPOPROTEINS AND THEIR DEGRADATION IN LYSOSOMES Ratushny A.V Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia MATHEMATICAL MODELING OF THE GENE NETWORK CONTROLLING HOMEOSTASIS OF INTRACELLULAR CHOLESTEROL Ratushny A.V.*, Bezmaternikh K.D Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia CONSERVED PROPERTIES OF ENZYMATIC SYSTEMS: PRENYLTRANSFERASE KINETICS Sharipov R.N.1,2,3,*, Kolpakova A.F.4 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia Institute of Systems Biology OOO, Novosibirsk, Russia State Research Institute for Medical Problems of the North, SB RAMS, Krasnoyarsk, Russia FORMAL DESCRIPTION OF NF-B PATHWAY, ITS ROLE IN INFLAMMATION, INHIBITION OF APOPTOSIS, CARCINOGENESIS, AND WAYS OF INACTIVATION FOR PREDICTION OF NEW TARGETS FOR ANTI-INFLAMMATORY AND ANTI-CANCER TREATMENT Stepanenko I.L1*., Podkolodnaya N.N.1, Paramonova N.V.1, Podkolodny N.L.1,2 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Institute of Computational Mathematics and Mathematical Geophysics SB RAS, Novosibirsk, Russia RECONSTRUCTION AND STRUCTURE ANALYSIS OF APOPTOSIS GENE NETWORK IN HEPATITIS C 39 4.3 Modeling of morphogenesis Bukharina T.A.1, Katokhin A.V.1,2, Furman D.P.1,2 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia THE GENE NETWORK DETERMINING DEVELOPMENT OF DROSOPHILA MELANOGASTER MECHANORECEPTORS Mironova V.V.1*, Poplavsky A.S.1, Ponomarev D.K.2, Omelianchuk N.A.1 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Institute of Informatics System, tait SB RAS, Novosibirsk, Russia ONTOLOGY OF ARABIDOPSIS GENE NET SUPPLEMENTARY DATABASE (AGNS), CROSS DATABASE REFERENCES TO TAIR ONTOLOGY Nikolaev S.V.1*, Fadeev S.I.2, Kogay V.V.2, Mjolsness E.3, Kolchanov N.A.1 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Institute of Mathematics SB RAS, Novosibirsk, Russia School of Information and Computer Science, and Institute for Genomics and Bioinformatics, University of California, Irvine, USA A ONE-DIMENSIONAL MODEL FOR THE REGULATION OF THE SIZE OF THE RENEWABLE ZONE IN BIOLOGICAL TISSUE Nikolaev S.V.1*, Penenko A.V.2, Belavskaya V.V.1, Mjolsness E.3, Kolchanov N.A.1 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Institute of Mathematics, SB RAS, Novosibirsk, Russia School of Information and Computer Science, and Institute for Genomics and Bioinformatics, University of California, Irvine, USA A SYSTEM FOR SIMULATION OF 2D PLANT TISSUE GROWTH AND DEVELOPMENT Ponomaryov D.1*, Omelianchuk N.2, Kolchanov N.2, Mjolsness E.3, Meyerowitz E.4 Institute of Informatics Systems, SB RAS, Novosibirsk, Russia Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Institute for Genomics and Bioinformatics, University of California, Irvine, USA Division of Biology, California Institute of Technology, Pasadena, CA, USA SEMANTICALLY RICH ONTOLOGY OF ANATOMICAL STRUCTURE AND DEVELOPMENT FOR ARABIDOPSIS THALIANA L 4.4 Gene networks theory: mathematical problems and software Aman E.E.*, Levitsky V.G., Ignatieva E.V Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia RECONSTRUCTION AND COMPUTER ANALYSIS OF THE GENE NETWORK OF FATTY ACID -OXIDATION REGULATED BY THE PPAR TRANSCRIPTIONAL FACTORS Demidenko G.V.1*, Khropova Yu.E.2 Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia 40 MATRIX PROCESS MODELLING: ON PROPERTIES OF SOLUTIONS OF ONE DELAY DIFFERENTIAL EQUATIONS Demidenko G.V.1*, Khropova Yu.E.2, Kotova T.V.2 Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia MATRIX PROCESS MODELLING: ON ONE CLASS OF INFINITE-ORDER SYSTEMS OF DIFFERENTIAL EQUATIONS AND ON DELAY DIFFERENTIAL EQUATIONS Demidenko G.V.1*, Mudrov A.V Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia MATRIX PROCESS MODELLING: ON A NEW METHOD OF APPROXIMATION OF SOLUTIONS OF DELAY DIFFERENTIAL EQUATIONS Fadeev S.I.*, Korolev V.K Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia PROGRAM PACKAGE HGNET FOR COMPUTATIONAL INVESTIGATION OF HYPOTHETICAL GENE NETWORKS Klishevich M.A.*, Kogai V.V., Fadeev S.I Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia RESEARCH OF CYCLIC GENE NETWORK CIRCUITS WITH NEGATIVE TYPE OF REGULATION Kolpakov F.1,2*, Sharipov R.3,1,2, Cheremushkina E.2, Kalashnikova E.3 Institute of Systems Biology OOO, Novosibirsk, Russia Design Technological Institute of Digital Techniques, SB RAS, Novosibirsk, Russia Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia BIOPATH – A NEW APPROACH TO FORMALIZED DESCRIPTION AND SIMULATION OF BIOLOGICAL SYSTEMS Komarov A.V.1*, Akberdin I R.2, Ozonov E A.1, Evdokimov A A.3 Novosibirsk State University, Novosibirsk, Russia Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia ON THE RECONSTRUCTION OF GENETIC AUTOMATE ON THE BASIS OF BOOLEAN DYNAMIC DATA Likhoshvai V.A.1*, Rudneva D.S.2, Fadeev S.I.3 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia OSCILLATIONS OF CHAOTIC TYPE IN SYMMETRIC GENE NETWORKS OF SMALL DIMENSION 41 Matveeva I.I 1, Popov A.M Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia MATRIX PROCESS MODELLING: DEPENDENCE OF SOLUTIONS OF A SYSTEM OF DIFFERENTIAL EQUATIONS ON PARAMETER Podkolodny N.L.1,2*, Podkolodnaya N.N.1, Miginsky D.S.1, Poplavsky A.S.1, Likhoshvai V.A.1, Compani B.3, Mjolsness E.3 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Institute of Computational Mathematics and Mathematical Geophysics, SB RAS, Novosibirsk, Russia Institute for Genomics and Bioinformatics, University of California, Irvine, USA AN INTEGRATION OF THE DESCRIPTIONS OF GENE NETWORKS AND THEIR MODELS PRESENTED IN SIGMOID (CELLERATOR) AND GENENET Tchuraev R.N Department of Physicochemical Biology and Epigenetics, Ufa Research Center, RAS, Ufa, Russia RESEARCH ON BEHAVIOR OF GOVERNING GENE/EPIGENE NETWORKS AS A PROBLEM OF CELLULAR AUTOMATA IDENTIFICATION NEW APPROACHES TO ANALYSIS/MODELING OF BIOMOLECULAR DATA AND PROCESSES Arrigo P.1*, Cardo P.P.2 CNR Institute for Macromolecular Studies, Genoa, Italy Department of Health Science, University of Genoa, Genoa, Italy INVESTIGATION OF NAMED ENTITY RECOGNITION IN MOLECULAR BIOLOGY BY DATA FUSION Axenovich M.A Department of Mathematics, Iowa State University, Ames, USA EDIT DISTANCE IN COMBINATORIAL STRUCTURES Axenovich T.I Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia GRAPH THEORY ALGORITHM FOR SOLUTION OF COMPUTATIONAL PROBLEMS OF GENE MAPPING Huang Shaoqing *, Cui Yini College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China UNEQUALLY SPACED SAMPLING MAPPING OF QTL Kolpakov F.1,2,*, Poroikov V.3, Sharipov R.4,2,1, Milanesi L.5, Kel A.6 Design Technological Institute of Digital Techniques, SB RAS, Novosibirsk, Russia Institute of Systems Biology, Novosibirsk OOO, Russia Institute of Biomedical Chemistry, RAMS, Moscow, Russia Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Institute of Biomedical Technologies, Segrate (MI), Italy BIOBASE GmbH, Wolfenbuettel, Germany Cyclonet — AN INTEGRATED DATABASE ON CELL CYCLE REGULATION AND CARCINOGENESIS 42 Miginsky D.S.1,3*, Sokolov S.A.2, Labuzhsky V.V.2, Nikitin A.G.2,3 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia A.P Ershov Institute of Informatics Systems SB RAS Novosibirsk State University, Novosibirsk, Russia OBJECT-ORIENTED APPROACH TO BIOINFORMATICS SOFTWARE RESOURCES INTEGRATION Sarsenbaev K.N Institute of Radiation Safety and Ecology, Kurchatov, Kazakhstan USE MOLECULAR MARKERS FOR DIFFERENTIATION POPULATIONS OF STIPA CAPILLATA GROWING IN THE REGIONS WITH HIGH CHRONICAL DOSES OF -RADIATION Suslov V.V1*, Sergeev M.G.2, Yurlova N.I.3, Miginsky D.S.1,2 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia Institute of Animal Systematics and Ecology, SB RAS, Novosibirsk, Russia THE ONTOLOGY OF ECOSYSTEMS 43 COMPUTER DEMONSTRATIONS (BY SECTIONS) Computer demos will be available during the entire conference day for the appropriate sections Munday, July 17 COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICS AND TRANSCRIPTOMICS Vishnevsky O.V.1,2*, Konstantinov Yu.M.3 Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia Siberian Institute of Plant Physiology and Biochemistry SB RAS, Irkutsk, Russia ANALYSIS OF THE NUCLEOTIDE CONTEXT OF HIGHER PLANT MITOCHONDRIAL mRNA EDITING SITES Thursday, July 20 COMPARATIVE AND EVOLUTIONARY GENOMICS AND PROTEOMICS Chupov V.S.*, Machs E.M Komarov Botanical institute RAS, St.Petersburg, Russia VARIATIONS IN NUCLEOTIDE COMPOSITION OF THE REGION ITS1-5.8S RDNA-ITS2 IN EVOLUTIONARY ADVANCED AND EVOLUTIONARY STATIC BRANCH OF THE MONOCOTYLEDONOUS PLANTS NEW APPROACHES TO ANALYSIS/MODELING OF BIOMOLECULAR DATA AND PROCESSES Kolpakov F.1,2,*, Poroikov V.3, Sharipov R.4,2,1, Milanesi L.5, Kel A.6 Design Technological Institute of Digital Techniques, SB RAS, Novosibirsk, Russia Institute of Systems Biology, Novosibirsk OOO, Russia Institute of Biomedical Chemistry, RAMS, Moscow, Russia Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Institute of Biomedical Technologies, Segrate (MI), Italy BIOBASE GmbH, Wolfenbuettel, Germany Cyclonet — AN INTEGRATED DATABASE ON CELL CYCLE REGULATION AND CARCINOGENESIS Kolpakov F.1,2*, Puzanov M.1,2, Koshukov A.1,2 Institute of Systems Biology OOO, Novosibirsk, Russia Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia 44 BioUML: VISUAL MODELING, AUTOMATED CODE GENERATION AND SIMULATION OF BIOLOGICAL SYSTEMS Friday, July 21 Saturday, July 22 COMPUTATIONAL SYSTEMS BIOLOGY Fadeev S.I.1*, Korolev V.K.1, Gainova I.A.2, Medvedev3A.E Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia Khristianovich Institute of Theoretical and Applied Mechanics SB RAS, Novosibirsk, Russia Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia THE PACKAGE STEP+ FOR NUMERICAL STUDY OF AUTONOMOUS SYSTEMS ARISING WHEN MODELING DYNAMICS OF GENETIC-MOLECULAR SYSTEMS Kolpakov F.1,2*, Sharipov R.3,1,2, Cheremushkina E.2, Kalashnikova E.3 Institute of Systems Biology OOO, Novosibirsk, Russia Design Technological Institute of Digital Techniques, SB RAS, Novosibirsk, Russia Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia BioPATH – A NEW APPROACH TO FORMALIZED DESCRIPTION AND SIMULATION OF BIOLOGICAL SYSTEMS Rudenko V.M.*, Korotkov E.V Center of Bioengineering RAS, Moscow, Russia CONSTRUCTION OF THE HCV-HEPATOCYTE SYSTEM MODEL Sharipov R.N.1,2,3*, Kolpakova A.F.4 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia Institute of Systems Biology OOO, Novosibirsk, Russia State Research Institute for Medical Problems of the North, SB RAMS, Krasnoyarsk, Russia FORMALIZED DESCRIPTION OF NF-B PATHWAY, ITS ROLE IN INFLAMMATION, INHIBITION OF APOPTOSIS, CARCINOGENESIS, AND WAYS OF INACTIVATION FOR PREDICTION OF NEW TARGETS FOR ANTI-INFLAMMATORY AND ANTI-CANCER TREATMENT 45 ... Foundation for Basic Research THE FIFTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2006) CONFERENCE PROGRAM SCHEDULE AT A GLANCE The Conference Sessions will... be held in the Small Conference Hall and in Music Salon (room no 220) of the House of Scientists July 16, Sunday Foyer of the Small Conference Hall 10:00-14:00 Registration of the conference participants*... the overall duration of the Conference A scheduled Poster Session, only one for all Conference sections, will be held on July 19 from 9:30 to 12:30 in the Small Conference Hall Foyer During the