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					       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




                                                 2
                                 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



ВА В ИЛ О ВС КО Е О Б ЩЕС Т ВО
ГЕНЕТИКОВ И СЕЛЕКЦИОНЕРОВ
                                 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




                                           3
     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
                    Small Conference Hall
    14:00           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

                                                 4
    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




                                               5
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                             Timeline
 1.      Mazo I. *, Sivachenko A., Yuryev A., Daraselia N.
         Ariadne Genomics, Inc., Rockville, USA                                             14:30-
         MOLECULAR NETWORKS IN MAMMALS: EXTRACTION                                          15:15
         FROM LITERATURE AND MICROARRAY
  2.     Rodin S.N.1*, Rodin A.S.2
         1
           Beckman Research Institute of the City of Hope, Duarte, CA, USA
         2
           Human Genetics Center, School of Public Health, University of Texas,             15:15-
           Houston, TX, USA                                                                 16:00
         GENE DUPLICATIONS IN EVOLUTION: FROM ORIGIN
         OF THE GENETIC CODE TO THE HUMAN GENOME
                                   Coffee/tea break 16:00-16:30
  3.     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              16:30-
         PROTEIN-PROTEIN INTERACTIONS AS NEW TARGETS FOR DRUG                               17:15
         DESIGN: INTERACTIVE LINKS BETWEEN VIRTUAL
         AND EXPERIMENTAL APPROACHES
  4.     Samsonova M.G.1, Reinitz J.2
         1
           St. Petersburg State Polytechnical University, St. Petersburg, Russia            17:15-
         2
           Stony Brook University, Stony Brook, New York, USA                               18:00
         SYSTEMS BIOLOGY OF SEGMENT DETERMINATION




                                                  6
                              ORAL PRESENTATIONS
Dear speakers, please, plan your presentation time including 5 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 min 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 do not hesitate to contact the Organizing
Committee in Room no. 200 at the House of Scientists.




                                           7
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
 1.    Seliverstov A.V.*, Lyubetsky V.A.
       Institute for Information Transmission Problems RAS, Moscow, Russia                9:30-
       GENE EXPRESSION REGULATION IN ACTINOBACTERIA                                       9:55
       AND CHLOROPLASTS
  2.   Grosse I. 1,2
       1
         Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
       2                                                                                   9:55-
         Bioinformatics Center Gatersleben-Halle, Gatersleben, Germany
                                                                                          10:20
       COMPUTATIONAL IDENTIFICATION OF TRANSCRIPTION FACTOR
       BINDING SITES WITH VARIABLE ORDER BAYESIAN NETWORKS
  3.   Levitsky V.G.1,2*, Ignatieva E.V.1,2, Ananko E.A.1, Merkulova T.I.1
       1
         Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
       2
         Novosibirsk State University, Novosibirsk, Russia                                10:20-
       THE SITEGA AND PWM METHODS APPLICATION                                             10:40
       FOR TRANSCRIPTION FACTOR BINDING SITES RECOGNITION
       IN EPD PROMOTERS
                                Coffee/tea break 10:40-11:10
  4.   Shelest E.S.*1, Wingender E.1,2
       1
         Department of Bioinformatics, UKG, University of Göttingen, Göttingen,
       Germany                                                                            11:10-
       2
         BIOBASE GmbH, Wolfenbüttel, Germany                                              11:35
       PROMOTER MODELING APPROACHES APPLIED TO THE
       INVESTIGATION OF p63 UP- AND DOWNSTREAM PROMOTERS
  5.   Vorobjev Y.N., Emelianov D.Y.
       Institute of Chemical Biology and Fundamental Medicine, SB RAS,
                                                                                          11:35-
       Novosibirsk, Russia
                                                                                          12:00
       MODELING OF DATA BASE OF CONTEXT-DEPENDENT
       CONFORMATIONAL PARAMETERS OF DNA DUPLEXES
  6.   Kamzolova S.G., Osypov A.A.*, Dzhelyadin T.R., Beskaravainy P.M.,
       Sorokin A.A.
                                                                                          12:00-
       Institute of Cell Biophysics of RAS, Pushchino, Moscow region, Russia
                                                                                          12:20
       CONTEXT-DEPENDENT EFFECTS OF UPSTREAM A-TRACTS
       ON PROMOTER ELECTROSTATIC PROPERTIES AND FUNCTION
  7.   Vishnevsky O.V.1,2*, Konstantinov Yu.M.3
       1
         Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
       2
         Novosibirsk State University, Novosibirsk, Russia                                12:20-
       3
        Siberian Institute of Plant Physiology and Biochemistry SB RAS, Irkutsk, Russia   12:45
       ANALYSIS OF THE NUCLEOTIDE CONTEXT OF HIGHER PLANT
       MITOCHONDRIAL mRNA EDITING SITES
12:45-14:30 Lunch break

                                                8
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                          Timeline
                         1                   1                  1,2            1,2
 1.    Omelianchuk N.A. , Khomicheva I.V. , Savinskaya S.A. , Levitsky V.G. ,
       Vishnevsky O.V. 1,2, Katokhin A.V.1,2, Ponomarenko M.P.1 , Kolchanov N.A.1,2
       1
         Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia               14:30-
       2
          Novosibirsk State University, Novosibirsk Russia                             14:55
       REVEALING THE FUNCTIONAL-SPECIFIC TEXTUAL FEATURES
       OF THE microRNA SEQUENCES IN ARABIDOPSIS THALIANA
  2.   Tutukina M.N., Masulis I.S., Ozoline O.N.*
       Institute of Cell Biophysics RAS, Pushchino, Moscow region, Russia              14:55-
       TOWARDS THE IDENTIFICATION OF ANTISENSE RNA                                     15:15
       WITHIN GENES OF TRANSCRIPTION REGULATORS
  3.   Orlov Yu.L.1, Zhou J.1, Lipovich L.1, Yong H.C.2, Li Yi2, Shahab A.2,
       Kuznetsov V.A.1*
       1
         Genome Institute of Singapore, Singapore
       2                                                                               15:15-
         Bioinformatics Institute, Singapore
                                                                                       15:35
       A COMPREHENSIVE QUALITY ASSESSMENT OF THE AFFYMETRIX
       U133A/B PROBESETS BY AN INTEGRATED GENOMIC
       AND CLINICAL APPROACH
  4.   Kuznetsov V.A.*, Zhou J., George J., Orlov Yu.L.
       Genome Institute of Singapore, Singapore                                        15:35-
       GENOME-WIDE CO-EXPRESSION PATTERNS OF HUMAN                                     16:00
       CIS-ANTISENSE GENE PAIRS
                                Coffee/tea break 16:00-16:30
  5.   Efimov V.M.1*, Badratinov M.S.2, Katokhin A.V.2,3
       1
        Institute of Systematics and Ecology of Animals, SB RAS, Novosibirsk, Russia
       2
         Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia                16:30-
       3
         Novosibirsk State University, Novosibirsk, Russia                             16:55
       INTERPRETATION OF RESULTS OF SOM ANALYSIS
       OF MICROARRAY DATA BY PRINCIPAL COMPONENTS
  6.   Subkhankulova T., Livesey F.J.
       Gurdon Institute and Department of Biochemistry, University of Cambridge,
                                                                                       16:55-
       Tennis Court Road, Cambridge, CB2 1 QN, UK
                                                                                       17:20
       HOW SIMILAR ARE PHENOTYPICALLY IDENTICAL CELLS
       AT THE TRANSCRIPTIONAL LEVEL
  7.   Abhishek K.1*, Karnick H.1, Mitra P.2
       1
         Indian Institute of Technology Kanpur, Kanpur, India
       2                                                                               17:20-
         Indian Institute of Technology Kharagpur, Kharagpur, India
                                                                                       17:45
       A KNOWLEDGE AND DATA BASED HYBRID APPROACH
       TO GENE CLUSTERING




                                                 9
July 18, Tuesday            House of Scientists, Small Conference Hall
                                                                                Morning Session
                                                                                     9:30-12:50
COMPUTATIONAL STRUCTURAL AND FUNCTIONAL PROTEOMICS
Co-chairpersons:
Dr. Kaiser Jamil, Indo American Cancer Institute and Research Center,
            Hyderabad, India
Dr. Roman Efremov, M.M. Shemyakin and U.A.Ovchinnikov Institute of Bioorganic
            Chemistry, the Russian Academy of Sciences, Moscow, Russia
 No.                              Author(s) and Title of Talk                              Timeline
 1.    Vlasov P.K.*, Esipova N.G., Tumanyan V.G.
       Engelhardt Institute of Molecular Biology, Russian Academy of Sciences,             9:30-
       Moscow, Russia                                                                      9:55
       CONFORMATION PROPERTIES OF SHORT OLIGOPEPTIDES
       AND PREDICTION OF PROTEIN CHAIN CONFORMATION
  2.   Volynsky P.E.*, Vereshaga Ya. A., Nolde D.E., Efremov R.G.
       M.M.Shemyakin and Yu.A.Ovchinnikov Institute of Bioorganic Chemistry                 9:55-
       RAS, Moscow, Russia                                                                 10:20
       PROBING DIMERIZATION OF TRANSMEMBRANE PEPTIDES
       VIA MOLECULAR DYNAMICS IN EXPLICIT BILAYERS
  3.   Chekmarev S.F.1*, Krivov S.V.2, Karplus M.2,3*
       1
         Institute of Thermophysics SB RAS, Novosibirsk, Russia
       2
         Laboratoire de Chimie Biophysique, ISIS, Université Louis Pasteur,
       Strasbourg, France                                                                  10:20-
       3
         Department of Chemistry and Chemical Biology, Harvard University,                 10:45
         Cambridge, MA, USA
       ―STRANGE KINETICS‖ OF UBIQUITIN FOLDING: INTERPRETATION
       IN TERMS OF A SIMPLE KINETIC MODEL
                                 Coffee/tea break 10:45-11:15
  4.   Afonnikov D.A.1,2
       1
          Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia                   11:15-
       2
          Novosibirsk State University, Novosibirsk, Russia                                11:40
       RESIDUE-RESIDUE CONTACT MAP PREDICTION FOR PROTEINS
  5.   Aksianov E.1*, Zanegina O.2, Alexeevski A.3, Karyagina A.4,5, Spirin S.3
       1
         Virology Department, Biological Faculty, Moscow State University, Moscow,
          Russia
       2
         Bioengineering and Bioinformatics Faculty, Moscow State University,
          Moscow, Russia                                                                   11:40-
       3
         Belozersky Institute, Moscow State University, Moscow, Russia                     12:05
       4
         N.F.Gamaleya Research Institute of Epidemiology and Microbiology, Moscow,
          Russia
       5
         Institute of Agricultural Biotechnology, Moscow, Russia
       A TOOL FOR COMPARATIVE ANALYSIS OF SOLVENT MOLECULES
       IN PDB STRUCTURES
  6.   Naumoff D.G.
       State Institute for Genetics and Selection of Industrial Microorganisms,            12:05-
       Moscow, Russia                                                                      12:25
       DEVELOPMENT OF A HIERARCHICAL CLASSIFICATION
       OF THE TIM-BARREL TYPE GLYCOSIDE HYDROLASES
  7.   Safro M.*1,Tworowski D.1, Feldman A.2
       1
        Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
       2
         EML Research gGmbH, Heidelberg, Germany                                           12:25-
       HOW ARE CHARGED RESIDUES DISTRIBUTED AMONG                                          12:50
       FUNCTIONALLY DISTINCT STRUCTURAL DOMAINS
       OF AMINOACYL-tRNA SYNTHETASES?
12:50-14:30 Lunch break


                                                10
July 18, Tuesday             House of Scientists, Small Conference Hall
                                                                                   Evening Session
                                                                                      14:30-17:25
COMPUTATIONAL STRUCTURAL AND FUNCTIONAL PROTEOMICS

Co-chairpersons:
Dr. Vladimir Kuznetsov, Genome Institute of Singapore, Singapore
Prof. Sergei Chekmarev, Institute of Thermophysics Siberian Branch
         of the Russian Academy of Sciences, Novosibirsk, Russia
 No.                               Author(s) and Title of Talk                               Timeline
 1.                     1
       Ivanisenko V.A. , Demenkov P.S. 2, Fomin E.S. 1, Oshurkov I.S. 3, Korotkov R.O. 3,
       Aman E.E. 1, Pintus S.S. 1,3, Startcev K.S. 3, Tatarnikova L.Yu. 3, Panina I.I. 3,
       Sobolev A.A. 3, Seleznev I.V. 3, Elohov V.Yu. 3, Golovina A.N. 3, Aknazarov Z.I. 3,
       Sharonova I.V. 3, Krestianova M.A. 3, Mishchenko E.L. 1, Magdysuk A.V. 3,
       Nemiatov A.I. 3                                                                       14:30-
       1
          Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia                     14:55
       2
          Institute of Mathematics SB RAS, Novosibirsk, Russia
       3
          Novosibirsk State University, Novosibirsk, Russia
       FASTPROT: A COMPUTATIONAL WORKBENCH FOR ANALYSIS
       OF FUNCTION, ACTIVITY AND STRUCTURE OF PROTEINS
  2.   Chernorudskiy A.L., Shorina A.S., Garcia A., Gainullin M.R.*
       Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
                                                                                             14:55-
       DIRECT INFLUENCE OF UBIQUITYLATION ON A TARGET PROTEIN
                                                                                             15:20
       ACTIVITY: ―LOSS-OF-FUNCTION‖ MECHANISM REVEALED
       BY COMPUTATIONAL ANALYSIS
  3.   Demenkov P.S.1*, Aman E.E.2, Ivanisenko V.A.2,3
       1
         Sobolev Institute of Mathematics of the SB RAS, Novosibirsk, Russia
       2
         Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia                      15:20-
       3
         Novosibirsk State University, Novosibirsk, Russia                                   15:40
       PREDICTION IN CHANGES OF PROTEIN THERMODYNAMIC
       STABILITY UPON SINGLE MUTATIONS
  4.   Kochetov A.V.1*, Sarai A.2, Kolchanov N.A.1
       1
         Institute of Cytology and Genetics, Novosibirsk, Russia
       2
         Kyushu Institute of Technology, Dept. Biochemical Engineering and Science,          15:40-
       Iizuka, Japan                                                                         16:05
       THE CONTRIBUTION OF ALTERNATIVE TRANSLATION START
       SITES TO HUMAN PROTEIN DIVERSITY
                                  Coffee/tea break 16:05-16:35
  5.   Efremov R.G.
       Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow,
                                                                                             16:35-
       Russia
                                                                                             17:00
       COMPUTER SIMULATIONS OF PEPTIDES AND PROTEINS
       IN MEMBRANES: PERSPECTIVES IN DRUG DESIGN
  6.   Nicklaus M.
       Center for Cancer Research, NCI/NIH, Frederick, USA                                   17:00-
       NEW DEVELOPMENTS AT THE NIH FOR INTEGRATION OF SMALL-                                 17:25
       MOLECULE DATABASES AND BIOINFORMATICS RESOURCES




                                                 11
July 20, Thursday          House of Scientists, Small Conference Hall
                                                                              Morning Session
                                                                                   9:30-12:55
COMPARATIVE AND EVOLUTIONARY GENOMICS AND PROTEOMICS
Co-chairpersons:
Dr. Vladimir Kapitonov, Genetic Information Research Institute, Mountain View,
         California, USA
Dr. Igor Makunin, ARC Special Research Centre for Functional and Applied
         Genomics, Institute for Molecular Bioscience, University of Queensland,
         Brisbane, Australia
 No.                             Author(s) and Title of Talk                            Timeline
 1.    Vitreschak A.G.1*, Lyubetsky V.A.1, Gelfand M.S.1
       1
         Institute for Information Transmission Problems of RAS, Moscow, Russia         9:30-
       EVOLUTIONAL AND FUNCTIONAL ANALYSIS OF T-BOX REGULON                             9:55
       IN BACTERIA. IDENTIFICATION AND CHARACTERIZATION
       OF NEW GENES INVOLVED IN AMINO ACID METABOLISM
  2.   Bazykin G.A.1*, Dushoff J.1, Levin S.1, Kondrashov A.2
       1
          Department. of Ecology and Evolutionary Biology, Princeton University,         9:55-
       Princeton, NJ, USA
       2                                                                                10:20
          National Center for Biotechnology Information, NIH, Bethesda, USA
       INSTANCES OF POSITIVE SELECTION AT CONSERVATIVE PROTEIN
  3.   Gunbin K.V., Suslov V.V., Kolchanov N.A.*
       Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia                  10:20-
       AROMORPHOSES AND ADAPTIVE MOLECULAR EVOLUTION:                                   10:45
       MORPHOGENS AND SIGNALING CASCADE GENES
                                Coffee/tea break 10:45-11:15
  4.   Kondrashov F.A.1*, Koonin E.V.2, Morgunov I.G.3, Finogenova T.V.3,
       Kondrashova M.N.4
       1
         Section on Ecology, Behavior and Evolution, Division of Biological Sciences,
       University of California at San Diego, La Jolla, USA
       2
         National Center for Biotechnology Information, National Library                11:15-
       of Medicine, National Institutes of Health, Bethesda, USA
       3                                                                                11:40
         Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS,
       Pushchino, Russia
       4
         Institute of Theoretical and Experimental Biophysics RAS, Pushchino, Russia
       EVOLUTION OF THE GLYOXYLATE CYCLE ENZYMES IN THE
       METAZOA 1*
  5.   Ramensky V. , Nurtdinov R.2, Neverov A.3, Mironov A. 2, Gelfand M. 2,4
       1
       2
         Engelhardt Institute of Molecular Biology RAS, Moscow, Russia
         Department of Bioengineering and Bioinformatics, Moscow State University,      11:40-
       Moscow, Russia
       3                                                                                12:05
       4
         State Scientific Center GosNIIGenetika, Russia
         Institute for Information Transmission Problems, RAS, Moscow, Russia
       HUMAN GENOME POLYMORPHISM AND ALTERNATIVE SPLICING
  6.   Pintus S.S.1*, Fomin E.S.1, Oshurkov I.S.2, IvanisenkoV.A.1,2*
       1
       2
         Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia                 12:05-
         Novosibirsk State University, Novosibirsk, Russia                              12:30
       PHYLOGENETIC ANALYSIS OF THE p53 AND P63/P73 GENE FAMILIES
  7.   Sabitha K. 1, 2, Jamil K.1, 2 *
       1
         Genetics Department, Bhagawan Mahavir Hospital and Research Center,
       Hyderabad, India
       2
                                                                                        12:30-
         Indo American Cancer Institute and Research Center, Hyderabad, India           12:55
       ANALYSIS OF EGFR GENE MUTATIONS WHICH HAVE A RESPONSE
       TO QUINAZOLIN INHIBITORS
12:55-14:30 Lunch break




                                               12
July 20, Thursday          House of Scientists, Small Conference Hall
                                                                              Evening Session
                                                                                 14:30-18:10
COMPARATIVE AND EVOLUTIONARY GENOMICS AND PROTEOMICS
Co-chairpersons:
Dr. Sergei Rodin, Beckman Research Institute of the City of Hope, Duarte, USA
Dr. Vassily Ramensky, Engelhardt Institute of Molecular Biology, the Russian
         Academy of Sciences, Moscow, Russia
 No.                             Author(s) and Title of Talk                            Timeline
 1.    Ignatieva E.V.*, Oshchepkov D.Yu., Klimova N.V., Vasiliev G.V., Merkulova T.I.
       Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
       ANALYSIS OF REGULATORY REGIONS OF ORTHOLOGOUS GENES:                             14:30-
       PREDICTION OF SF1 BINDING SITES WITH SITECON METHOD                              14:55
       PROVED BY EXPERIMENTAL VERIFICATION AND COMPARATIVE
       GENOMICS
  2.   Kolesnikov N.N.*, Elisafenko E.A., Zakian S.M.
       Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia                   14:55-
       EVOLUTION OF THE STRUCTURE OF THE XIST LOCUS                                     15:20
       IN MAMMALS
  3.   Deyneko I.V.*1,2, Kalybaeva Y.M.1, Kel A.E. 3, Blöcker H.*1, Kauer G. 4
       1
         Department of Genome Analysis, GBF, Braunschweig, Germany
       2
         Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
       3                                                                                15:20-
         BIOBASE GmbH, Wolfenbüttel, Germany
       4                                                                                15:35
         University of Applied Sciences, Emden, Germany
       HUMAN-CHIMPANZEE PROPERTY-DEPENDANT COMPARISONS
       ON CHROMOSOMES 21
  4.   Perelygin A.A.*1, Zharkikh A.A.2, Brinton M.A.1
       1
          Biology Department, Georgia State University, Atlanta, GA, USA
       2                                                                                15:35-
          Bioinformatics Department, Myriad Genetics, Inc., Salt Lake City, UT, USA
                                                                                        16:00
       CONCERTED EVOLUTION OF PARALOGOUS Oas1 GENES
       IN RODENTIA AND CETARTIODACTYLA
                                Coffee/tea break 16:00-16:30
  5.   Kapitonov V.V.*, Jurka J.
       Genetic Information Research Institute, Mountain View, California, USA           16:30-
       NEW KIDS ON THE BLOCK: SELF-SYNTHESIZING DNA                                     16:55
       TRANSPOSONS
  6.   Simons C., Pheasant M., Makunin I.V., Mattick J.S.*
       ARC Special Research Centre for Functional and Applied Genomics, Institute       16:55-
       for Molecular Bioscience, University of Queensland, Brisbane, Australia          17:20
       TRANSPOSON-FREE REGIONS IN MAMMALIAN GENOMES
  7.   Golovnina K.1, Glushkov S.*1, Blinov A.1, Mayorov V.2, Adkison L.2 ,
       Goncharov N.1
       1                                                                                17:20-
         Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
       2                                                                                17:45
         Mercer University School of Medicine, Macon, USA
       MOLECULAR PHYLOGENY OF THE GENUS TRITICUM L.
  8.   Karafet T. M.1,2*, Lansing J.S.2, Hammer M.F.2
       1
         Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
       2                                                                                17:45-
          University of Arizona, Tucson, USA
                                                                                        18:10
       IN SEARCH OF GENETIC SIGNATURE FOR THE EXPANSION
       OF IRRIGATION SYSTEMS IN BALI




                                               13
July 20, Thursday          House of Scientists, Music Salon (room no. 200)
                                                                               Morning Session
                                                                                    9:30-12:55
NEW APPROACHES TO BIOMOLECULAR DATA AND PROCESSES
ANALYSIS/MODELING
Co-chairpersons:
Prof. Mikhail Lavrentiev, Jr., Novosibirsk State University, Novosibirsk, Russia
Prof. Vladimir Golubyatnikov, Institute of Mathematics, Siberian Branch
         of the Russian Academy of Sciences, Novosibirsk, Russia
 No.                              Author(s) and Title of Talk                         Timeline
 1.    Mironov A.A.1,2,3
       1
         Department of Bioengineering and Bioinformatics, Moscow State University,
       Moscow, Russia                                                                 9:30-
       2
         Institite for Information Transmission Problems, RAS, Moscow, Russia         9:55
       3
         State Scientific Center GosNIIGenetica, Russia
       THRESHOLD SELECTION USING THE RANK STATISTICS
  2.   Hofestaedt R.
       Bielefeld University, AG Bioinformatics, Bielefeld, Germany                     9:55-
       AN EXTENDED BACKUS-SYSTEM FOR THE REPRESENTATION                               10:20
       AND ANALYSIS OF DNA SEQUENCES
  3.   Mjolsness E.
       Institute for Genomics and Bioinformatics and Departments of Computer
                                                                                      10:20-
       Science and Mathematics, University of California, Irvine, USA
                                                                                      10:45
       MODELING TRANSCRIPTIONAL REGULATION WITH EQUILIBRIUM
       MOLECULAR COMPLEX COMPOSITION
                                Coffee/tea break 10:45-11:15
  4.   Matveeva A.*, Kozlov K., Samsonova M.G.
       Department of Computational Biology, Center for Advanced Studies
                                                                                      11:15-
       St. Petersburg State Polytechnical University, St. Petersburg, Russia
                                                                                      11:40
       METHODOLOGY FOR BUILDING OF COMPLEX WORKFLOWS
       WITH PROSTAK PACKAGE AND ISIMBIOS
  5.   Tatarinova T.1, Schumitzky A.2
       1
         Ceres, Inc. Thousand Oaks, California, USA                                   11:40-
       2
         University of Southern California, Los Angeles, USA                          12:05
       MULTIPLE COLLAPSE CLUSTERING
  6.   Litvinov I. I.1,3*, Finkelshtein A. V.2, Roytberg M. A.1,3*
       1
         Institute of Mathematical Problems in Biology, Russian Academy
       of Sciences, Pushchino, Moscow region, Russia
       2
         Institute of Protein Research, Russian Academy of Sciences, Pushchino,       12:05-
       Moscow region, Russia                                                          12:30
       3
         Pushchino State University, Pushchino, Moscow region, Russia
       OPTIMIZATION OF ACCURACY AND CONFIDENCE FOR ALIGNMENT
       ALGORITHMS EXPLOITING DATA ON SECONDARY STRUCTURE
  7.   Kozlov K.N.*1, Samsonov A.M.2
       1
         Department of Computational Biology, State Polytechnical University,
       St.Petersburg, Russia
       2                                                                              12:30-
         A.F. Ioffe Physico-technical Institute of the Russian Academy of Sciences,
                                                                                      12:55
       St.Petersburg, Russia
       NEW MIGRATION SCHEME FOR PARALLEL DIFFERENTIAL
       EVOLUTION
12:55-14:30 Lunch break

                                                14
July 20, Thursday          House of Scientists, Music Salon (room no. 200)
                                                                             Evening Session
                                                                                14:30-17:20
NEW APPROACHES TO BIOMOLECULAR DATA AND PROCESSES
ANALYSIS/MODELING

Co-chairpersons:
Prof. Mikhail Roytberg, Institute of Mathematical Problems in Biology,
         the Russian Academy of Sciences, Pushchino, Moscow Region, Russia
Dr. Andrei Zinovyev, Institute Curie, Bioinformatics Service, Paris, France
 No.                             Author(s) and Title of Talk                         Timeline
 1.    Demidenko G.V.*, Matveeva I.I.
       Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia
                                                                                     14:30-
       ASYMPTOTIC PROPERTIES OF SOLUTIONS OF DIFFERENTIAL-
                                                                                     14:55
       DIFFERENCE EQUATIONS WITH PERIODIC COEFFICIENTS
       IN LINEAR TERMS
  2.   Mateus D.*, Gallois J.P.
       CEA/LIST Saclay, F-91191 Gif sur Yvette Cedex, France                         14:55-
       SEARCHING CONSTRAINTS IN BIOLOGICAL REGULATORY                                15:20
       NETWORKS USING SYMBOLIC ANALYSIS
  3.   Labarga A.*, Anderson M., Valentin F., Lopez R.
                                                                                     15:20-
       European Bioinformatics Institute, Hinxton, United Kingdom
                                                                                     15:45
       WEB SERVICES AT THE EUROPEAN BIOINFORMATICS INSTITUTE
  4.   Kolpakov F.1,2*, Puzanov M.1,2, Koshukov A.1,2
       1
         Institute of Systems Biology OOO, Novosibirsk, Russia
       2
         Design Technological Institute of Digital Techniques SB RAS, Novosibirsk,   15:45-
       Russia                                                                        16:05
       BioUML: VISUAL MODELING, AUTOMATED CODE GENERATION
       AND SIMULATION OF BIOLOGICAL SYSTEMS
                               Coffee/tea break 16:05-16:30
  5.   Miginsky D.S.1,2*, Suslov V.V.1, Rasskazov D.A.1,2, Podkolodny N.L.1,
       Kolchanov N.A.1,2
       1
         Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia              16:30-
       2
         Novosibirsk State University, Novosibirsk, Russia                           16:55
       ARCHITECTURE OF SOFTWARE TOOLKIT FOR STORING
       AND OPERATNG WITH BIOSYSTEMS MODELS
  6.   Lohmann M.
       Cologne University Bioinformatics Center (CUBIC), Cologne, Germany
                                                                                     16:55-
       METABOLOMICS, BIOINFORMATICS, SYSTEMS BIOLOGY —
                                                                                     17:20
       AN OVERVIEW OF RESEARCH AND TEACHING ACTIVITIES
       AT CUBIC




                                               15
July 21, Friday           House of Scientists, Small Conference Hall
                                                                          Morning Session
                                                                               9:30-12:55
COMPUTATIONAL SYSTEMS BIOLOGY

Co-chairpersons:
Prof. Eric Mjolsness, Institute for Genomics and Bioinformatics and Departments
          of Computer Science and Mathematics, University of California, Irvine, USA
Dr. Bjorn Olsson, School of Humanities and Informatics, University of Skövde,
          Sweden
 No.                            Author(s) and Title of Talk                         Timeline
 1.                       1
       Golubyatnikov V.P. *, Gaidov Yu.A.2, Kleshchev A.G.1, Volokitin E.P.1
       1
         Institute of Mathematics, SB RAS, Novosibirsk, Russia
       2                                                                            9:30-
         Novosibirsk State University, Novosibirsk, Russia
                                                                                    9:55
       A GENE NETWORK MODEL WITH DIFFERENT TYPES
       OF REGULATION
  2.   Likhoshvai V.A.
       1
         Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia              9:55-
       MOLECULAR-GENETIC SYSTEMS: SYMMETRY OF STRUCTURE                             10:20
       AND DYNAMIC CHAOS
  3.   Khlebodarova T.M.*, Kachko A.V., Stepanenko I.L., Tikunova N.V.
       Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
                                                                                    10:20-
       DATABASE GenSensor AS INFORMATIONAL SOURCE FOR DESIGN
                                                                                    10:45
       OF BIOSENSORS. EXPERIMENTAL DEVELOPMENT OF BIOSENSOR
       BASED ON YfiA GENE
                               Coffee/tea break 10:45-11:15
  4.              1,2
       Rapaport F. , Zinovyev A.1,3*, Barillot E.1, Vert J.-P.2
       1
         Institute Curie, Bioinformatics Service, Paris, France
       2
         Ecole des Mines de Paris, Center for Computational Biology,
                                                                                    11:15-
       Fontainebleau, France
       3                                                                            11:40
         Institute of Computational Modelling SB RAS, Krasnoyarsk, Russia
       SPECTRAL ANALYSIS OF GENE EXPRESSION PROFILES USING
       GENE NETWORKS
  5.   Gunbin К.V.1*, Kogai V.V.2, Fadeev S.I.2, Omelyanchuk L.V.1
       1
         Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
       2                                                                            11:40-
         Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia
                                                                                    12:05
       A MODEL FOR SENSING THE MORPHOGENE HEDGEHOG
       CONCENTRATION GRADIENT
  6.   Galimzyanov A.V.
       Department of Physicochemical Biology and Epigenetics, Ufa Research Center
                                                                                    12:05-
       RAS, Ufa, Russia
                                                                                    12:30
       GENE NETWORKS BEHAVIOR IN A SERIES OF SUCCESIVE CELL
       DIVISIONS
  7.   Milanesi L.*, Alfieri R., Merelli I.
                                                                                    12:30-
       CNR Institute of Biomedical Technologies, Milan, Italy
                                                                                    12:55
       HCCDB: DATA MINING SYSTEM FOR HUMAN CELL CYCLE GENE

12:55-14:30 Lunch break


                                              16
July 22, Saturday           House of Scientists, Small Conference Hall
                                                                                  Morning Session
                                                                                       9:30-12:50
COMPUTATIONAL SYSTEMS BIOLOGY
Co-chairpersons:
Prof. Ralf Hofestaedt, Bielefeld University, AG Bioinformatics, Bielefeld, Germany
Dr. Vyatcheslav Mordvinov, Institute of Cytology and Genetics SB RAS,
         Novosibirsk, Russia
 No.                                Author(s) and Title of Talk                            Timeline
 1.    Omelianchuk N.A.1*, Mironova V.V.1, Poplavsky A.S.1, Pavlov K.S.1,
       Savinskaya S.A.2, Podkolodny N.L.1, Mjolsness E.D.3, Meyerowitz E.M.4,
       Kolchanov N.A.1
       1
        Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
       2                                                                                   9:30-
         Novosibirsk State University, Novosibirsk, Russia
       3                                                                                   9:55
        Institute for Genomics and Bioinformatics; University of California, Irvine, USA
       4
        Division of Biology, California Institute of Technology, Pasadena, USA
       AGNS (ARABIDOPSIS GENENET SUPPLEMENTARY DATABASE),
       RELEASE 3.0
  2.   Ponomaryov D.1*, Omelianchuk N.2, Mironova V.2, Kolchanov N.2,
       Mjolsness E.3, Meyerowitz E.4
       1
        Institute of Informatics Systems, SB RAS, Novosibirsk, Russia
       2
        Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia                     9:55-
       3
        Institute for Genomics and Bioinformatics, University of California, Irvine, USA   10:20
       4
        Division of Biology, California Institute of Technology, Pasadena, USA
       A PROGRAM METHOD FOR INFERRING RELATIONSHIPS BETWEEN
       PHENOTYPIC ABNORMALITIES IN ARABIDOPSIS
  3.   Akberdin R.*2, Ozonov E.A.1, Mironova V.V.2, Komarov A.V.1, Omelianchuk N.A.2
       1
        Novosibirsk State University, Novosibirsk, Russia
       2                                                                                   10:20-
        Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia                     10:45
       A CELLULAR AUTOMATON TO MODEL THE DEVELOPMENT
       OF SHOOT MERISTEMS IN ARABIDOPSIS THALIANA
                                  Coffee/tea break 10:45-11:15
  4.   Nikolaev S.V.1*, Fadeev S.I.2, Penenko A.V.2, Belavskaya V.V.1, Kogay V.V.2,
       Mjolsness E.3, Kolchanov N.A.1,4
       1
        Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
       2
        Institute of Mathematics, SB RAS, Novosibirsk, Russia
       3                                                                                   11:15-
        School of Information and Computer Science, and Institute for Genomics             11:40
       and Bioinformatics, University of California, Irvine, USA
       4
        Novosibirsk State University, Novosibirsk, Russia
       CELLULAR-LEVEL MODELLING OF PLANT TISSUE GROWTH
       AND MORPHOGENESIS
  5.   Ratushny A.V.
       Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia                     11:40-
       IN SILICO CELL: HIERARCHICAL APPROACH AND GENERALIZED HILL                          12:05
       FUNCTION METHOD FOR GENETIC SYSTEMS AND METABOLIC
       PATHWAYS MODELING
  6.   Rudenko V.M.*, Korotkov E.V.
                                                                                           12:05-
       Center of Bioengineering RAS, Moscow, Russia                                        12:25
       CONSTRUCTION OF THE HCV-HEPATOCYTE SYSTEM MODEL
  7.   Olsson B.*, Gawronska B., Erlendsson B., Lindlöf A., Dura E.
       School of Humanities and Informatics, University of Skövde, Sweden                  12:25-
       AUTOMATED TEXT ANALYSIS OF BIOMEDICAL ABSTRACTS APPLIED                             12:50
       TO THE EXTRACTION OF SIGNALING PATHWAYS INVOLVED
       IN PLANT COLD-ADAPTATION
12:50-14:30 Lunch break


                                                  17
July 22, Saturday          House of Scientists, Small Conference Hall
                                                                            Evening Session
                                                                               14:30-16:40
COMPUTATIONAL SYSTEMS BIOLOGY

Co-chairpersons:
Dr. Luciano Milanesi, CNR Institute of Biomedical Technologies, Milan, Italy
Dr. Mark Lohmann, Cologne University Bioinformatics Center (CUBIC), Cologne,
Germany
 No.                             Author(s) and Title of Talk                          Timeline
                  1                2                3          3               1
 1.    Aman E.E. , Demenkov P.S. , Pintus S.S. , Nemiatov A.I. , Apasieva N.V. ,
       Korotkov R.O. 3, Ignatieva E.V.1, Podkolodny N.L.1, Ivanisenko V.A.*1
       1
          Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
       2                                                                              14:30-
          Institute of Mathematics, SB RAS, Novosibirsk, Russia
       3                                                                              14:55
          Novosibirsk State University, Novosibirsk, Russia
       A COMPUTER SYSTEM FOR THE AUTOMATED RECONSTRUCTION
       OF MOLECULAR-GENETIC INTERACTION NETWORKS
  2.   Kouznetsova T.N.1*, Ignatieva E.V.1, Oshchepkov D.Yu.1, Kondrakhin Y.V.1,
       Katokhin A.V.1,2, Shamanina M.Y.1, Mordvinov V.A.1
       1
         Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
       2                                                                              14:55-
         Novosibirsk State University, Novosibirsk, Russia
                                                                                      15:20
       A GENE NETWORK OF ADIPOCYTE LIPID METABOLISM:
       COORDINATED INTERACTIONS BETWEEN THE TRANSCRIPTION
       FACTORS SREBP, LXR AND PPAR
                                Coffee/tea break 15:20-15:50
  3.                       2*
       Bezmaternykh K.D. , Nikulichev Yu.V.1, Likhoshvai V.A.2,
       Matushkin Yu.G.2, Latipov A.F.1, Kolchanov N.A.2
       1
         Institute of Theoretical and Applied Mechanics SB RAS, Novosibirsk, Russia   15:50-
       2
         Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia              16:15
       OPTIMAL CONTROL TASKS IN TERMS OF THE GENE NETWORK
       MODELS
  4.   Kolchanov N.A.1*, Orlova G.V.1, Bachinsky A.G.2, Bazhan S.I.2,
       Shvarts Ya.Sh.3, Golomolzin V.V.1, Popov D.Yu.1, Efimov V.M.5,
       Tololo I.V.6, Ananko E.A.1, Podkolodnaya O.A.1, Il’ina E.N. 4, Rogov S.I. 4,
       Tretiakov V.E.4, Kubanova A.A.7, Govorun V.M.4
       1
         Institute of Cytology and Genetics, SB RAS, Novosibirsk
       2
         The State Research Center of Virology and Biotechnology ―Vector‖,
       Novosibirsk
       3                                                                              16:15-
         Institute of Internal Medicine SB RAMS, Novosibirsk
       4                                                                              16:40
         Institute of Physical and Chemical Medicine MZ RF, Moscow
       5
         Institute of Animal Taxonomy and Ecology, SB RAS, Novosibirsk
       6
         Institute of Automation and Electrometry, SB RAS, Novosibirsk
       7
         Central Research Institute of Dermatovenerology MZ RF, Moscow
       EPI-GIS: GIS ASSISTED COMPUTER TOOLS FOR DATA
       ACCUMULATION, COMPUTER ANALYSIS AND MODELING
       IN MOLECULAR EPIDEMIOLOGY

16:40- 17:20 Closing Ceremony. Summaries from session chairpersons


                                               18
July 19, Wednesday            House of Scientists, Small Conference Hall Foyer 9:30-12:30

                                    POSTER SESSION

            Poster Size: The maximum size allowed for each poster
                             is 0.7m wide  1.2m high.
               Please note that this is a portrait (vertical) poster.

   Authors must bring their posters printed and ready, as no facilities to produce posters at the
   Conference are available. Organizers will provide boards and push pins to display your posters.
   Posters should be readable from a distance of about two to three feet—for easy reading by
   several people at one time.
   Presentations may be posted starting from 10:00 on July 17 in the Small Conference Hall
   Foyer.
   The posters will be displayed for 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 allotted time, presenters are expected to remain at their individual displays to be
   available for questions and informal discussion of the poster content.

   Material should be removed no later than 13.00 on July 22.
   In the case the author(s) does not take away the presentation, it will be removed and destroyed
   by the BGRS’2006 Organizing Committee.

   If you have any questions, please do not hesitate to contact the Organizing Committee
   in Room no. 200 at the House of Scientists.



POSTER PRESENTATIONS (BY SECTIONS)

1. COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICS
   AND TRANSCRIPTOMICS

Abnizova I.1, Walter K.1, te Boekhorst R.2 , Gilks W.R.1
1
  Biostatistics Unit MRC, Institute of Public Health, Robinson Way, Cambridge, UK
2
  University of Hertfordshire, College Lane, Hatfield Campus,UK
NEW WAY TO OBTAIN A REGULATORY MOTIF REPRESENTATION DUE TO MOTIF
ABUNDANCE LEVEL

Ananko E.A.*, Kondrakhin Yu.V., Merkulova T.I.
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
PREDICTION OF INTERFERON-INDUCIBLE GENES IN HUMAN GENOME

Apasyeva N.V. 1, Yudin N.S.1*, Ignatieva E.V.1, Voevoda M.I.1,2, Romashenko A.G.1
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
   Institute of Intrnal Medicine, SB RAMS, Novosibirsk, Russia
A DATABASE DESIGNED FOR THE POLYMORPHISMS OF THE HUMAN CCR2 GENE


                                                 19
Atambaeva S.A., Ivashchenko A.T.*, Khailenko V., Boldina G., Turmagambetova A.
al-Farabi Kazakh National University, Almaty, Kazakhstan
LENGTH OF EXONS AND INTRONS IN GENES OF SOME HUMAN CHROMOSOMES

Atambaeva S.A., Ivashchenko A.T.*
al-Farabi Kazakh National University, Almaty, Kazakhstan
THE EXONS AND INTRONS LENGTHS IN ARABIDOPSIS THALIANA
AND CAENORHABDITIS ELEGANS GENES

te Boekhorst R.1*, Walter K.2, Elgar G.3, Gilks W.R.2, Abnizova I.2
1
  University of Hertfordshire, College Lane, Hatfield Campus,UK
2
  MRC-BSU, Robinson Way, Cambridge, UK
3
  Queen’s Mary College, London, UK
STATISTICAL CHARACTERIZATION OF CONSERVED NON-CODING ELEMENTS
IN VERTEBRATES

Califano A.1, Margolin A.1, Fust A.1, Floratos A.1, Badii B.1, Daly E.1, Kim F.1, Ahmady H.1,
Nemenman I.1,2, Watkinson J.1, Wang K.1, Smith K.1, Kustagi M.1, Hall M.1, Banerjee N.1,
Morozov P.S.1, Hanasoge S.1, Zhang X.1, Wang X.1, Li Z.1
1
 Joint Centers for Systems Biology at Columbia University
2
  Los Alamos National Laboratory, Los Alamos, USA
GEWORKBENCH: A BIOINFORMATIC PLATFORM FOR INTEGRATED GENOMICS

Katyshev A.I.1, Rogozin I.B.2, Konstantinov Yu.M.1*
1
  Siberian Institute of Plant Physiology and Biochemistry, SB RAS, Irkutsk, Russia
2
  Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
IDENTIFICATION OF NEW SUPEROXIDE DISMUTASE TRANSCRIPTS IN PLANTS
BY EST ANALYSIS: ALTERNATIVE POLYADENYLATION AND SPLICING EVENTS

Kayumov A.R.*, Kirillova J. M., Mikhailova E. O., Balaban N.P., Sharipova M.R.
Kazan State University, Kazan, Russia
THE PREDICTION OF REGULATION OF SUBTILISIN-LIKE PROTEINASE GENE FROM
BACILLUS INTERMEDIUS THROUGH ITS REGULATORY SEQUENCE ANALYSIS

Khomicheva I.V.*, Levitsky V.G., Omelianchuk N.A., Ponomarenko M.P.
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
PATTERN OF LOCALLY POSITIONED DINUCLEOTIDES IN microRNA RELATES
TO ITS ACCUMULATION LEVELS

Khomicheva I.V.1, Levitsky V.G.1, Vishnevsky O.V.1, Savinskaya S.A.2, Omelianchuk N.A.1
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
   Novosibirsk State University, Novosibirsk, Russia
IDENTIFICATION OF ARABIDOPSIS THALIANA microRNAs AMONG MPSS SIGNATURES

Khomicheva I.V.*1,2, Vityaev E.E.2, Shipilov T.I.2, Levitsky V.G.1
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia
TRANSCRIPTION FACTOR BINDING SITES RECOGNITION BY THE ExpertDiscovery
SYSTEM BASED ON THE RECURSIVE COMPLEX SYGNALS




                                              20
Kolchanov N.A.*, Podkolodnaya O.A., Ananko E.A., Ignatieva E.V., Stepanenko I.L.,
Khlebodarova T.M., Merkulov V.M., Merkulova T.I., Podkolodny N.L., Romashchenko A.G.
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
TRRD: A DATABASE ON EXPERIMENTALLY IDENTIFIED TRANSCRIPTION
REGULATORY REGIONS AND TRANSCRIPTION FACTOR BINDING SITES

Kondrakhin Yu.V.*, Ananko E.A., Merkulova T.I.
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
METHODS FOR RECOGNITION OF INTERFERON-INDUCIBLE SITES, PROMOTERS,
AND ENHANCERS

Lyubetskaya E.V., Seliverstov A.V.*, Lyubetsky V.A.
Institute for Information Transmission Problems RAS, Moscow, Russia
DETECTING HAIRPINS IN 3’-UNTRANSLATED REGIONS OF HIGHLY EXPRESSED
GENES IN ACTINOBACTERIA

Merkulov V.M.*, Merkulova T.I.
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
STRUCTURAL VARIANTS OF BINDING SITES FOR GLUCOCORTICOID RECEPTOR
AND THE MECHANISMS OF GLUCOCORTICOID REGULATION: ANALYSIS OF GR-TRRD
DATABASE

Mitra C.K.
School of Life Sciences, University of Hyderabad, Hyderabad, India
STUDIES ON TRANSCRIPTIONAL REGULATION IN DNA

Morozov P.S.1, Morozova I.N.2, Pampou S.2, Shuman H.3, Kalachikov S.M.2
1
 Joint Centers for Systems Biology, Columbia University, New York, USA
2
  Columbia Genome Center, Columbia University, New York, USA
3
  Department of Microbiology, Columbia University, New York, USA
UNIQUE OLIGOTIDE BASED MICROARRAY DESIGN FOR THE STUDY OF GENE
EXPRESSION OF THE ACCIDENTAL HUMAN PATHOGEN LEGIONELLA PNEUMOPHILA

Ogurtsov A.Yu.1*, Vasilchenko A.S.2, Vlasov P.K.3, Shabalina S.A.1, Kondrashov A.S.1,
Roytberg M.A.2*
1
  National Center for Biotechnology Information, NIH, Bethesda, USA
2
  Institute of Mathematical Problems in Biology, Pushchino, Moscow Region, Russia
2
  Institute of Molecular Biology, Moscow, Russia
OWEN-SCRIPT – AN EXTENDED TOOL FOR PAIRWISE GENOME ALIGNMENT

Proskura A.L.1*, Levitsky V.G.1,2, Ignatieva E.V.1,2
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  Novosibirsk State University, Novosibirsk, Russia
THE ANALYSIS OF SREBP BINDING SITES DISTRIBUTION IN GENE REGIONS
BY COMBINED SITEGA AND PWM APPROACH

Ryazansky S.S.
Institute of Molecular Genetics RAS, Moscow, Russia
IDENTIFICATION OF microRNAs ENCODED BY DROSOPHILA TRASPOSABLE
ELEMENTS




                                               21
Seliverstov A.V.*, Lyubetsky V.A.
Institute for Information Transmission Problems RAS, Moscow, Russia
TRANSLATION REGULATION IN CHLOROPLASTS

Shagimardanova E.I.*, Shamsutdinov T.R., Chastuchina I.B., Sharipova M.R.
Kazan State University, Kazan, Russia
ANALYSIS OF REGULATORY REGION OF BACILLUS INTERMEDIUS GLUTAMYL
ENDOPEPTIDASE GENE

Shavkunov K.S. 1, Masulis I.S. 1, Matushkin Yu.G.2, Ozoline O.N.1*
1
  Institute of Cell Biophysics RAS, Pushchino, Moscow region, Russia
2
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
ALTERNATIVE TRANSCRIPTION WITHIN PROCARYOTIC GENES PREDICTED
BY PROMOTER-SEARCH SOFTWARE

Smetanin D.V.*, Chumak N.M.
Krasnodar Research Institute of Agriculture, Krasnodar, Russia
A STEP BEYOND PLANT TRANSCRIPT`S POLYADENYLATION SITE

Smirnova O.G.*, Ibragimova S.S., Grigorovich D.A., Kochetov A.V.
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
TGP (TransGene Promoters): A DATABASE OF BIOTECHNOLOGICALLY IMPORTANT
PLANT GENE PROMOTERS

Stavrovskaya E.D.1,2, *, Makeev V.J.3, Merkeev I.V.3, Mironov A.A.1,2,3
1
  Institute for Information Transmission Problems RAS, Moscow, Russia
2
  Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
3
  State Scientific Center GosNIIGenetica, Moscow, Russia
TOOL FOR AUTOMATIC DETECTION OF CO-REGULATED GENES

Taraskina A.S. 1,3, Cheremushkin E.S.2,3
1
  Mechanics and Mathematics Department, Novosibirsk State University, Novosibirsk, Russia
2
  Biorainbow Group, Novosibirsk, Russia
3
  Ershov Institute of Informatics Systems, Novosibirsk, Russia
THE MODIFIED FUZZY C- MEANS METHOD FOR CLUSTERING
OF MICROARRAY DATA

Titov I.I.1,2
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  Novosibirsk State University, Russia
THE GArna TOOLBOX FOR RNA STRUCTURE ANALYSIS: THE 2006 STATE
OF THE ART

Titov I.I.1,2*, Ivanisenko A.Yu.2
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  Novosibirsk State University, Novosibirsk, Russia
A MODEL OF THE TRANSLATIONAL INHIBITION BY MIRISC COMPLEX DESCRIBES PROTEIN
SYNTHESIS VARIATIONS INDUCED BY MUTATIONS IN MAMMALIAN miRNA SITES




                                              22
Vladimirov N.V. *, Likhoshvai V.A., Matushkin Yu.G.
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
ROLES OF CODON BIASES AND POTENTIAL SECONDARY STRUCTURES
IN mRNA TRANSLATION OF UNICELLULAR ORGANISMS

Vladimirov N.V. *, Kochetov A.V., Grigorovich D.A., Matushkin Yu.G.
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
RSCU_COMPARER: A NEW STATISTICAL TOOL FOR PRACTICAL ANALYSIS
OF CODON USAGE

Vityaev Е.E.*1,2, Lapardin K.A.2, Khomicheva I.V.3, Levitsky V.G.2,3
1
  Institute of Mathematics, SB RAS, Novosibirsk, Russia
2
  Novosibirsk State University, Novosibirsk, Russia
3
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
TRANSCRIPTION FACTOR BINDING SITES RECOGNITION BY THE REGULARITIES
MATRICES BASED ON THE NATURAL CLASSIFICATION METHOD

Volod’ko V.B.1, Shuvaev R.Yu.1, Ulyashin A.V.1, Novikova O.S.2, Matushkin Yu.G.2,3
1
  Novosibirsk Center of Information Technologies "UniPro", Novosibirsk, Russia
2
  Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
3
  Novosibirsk State University, Novosibirsk, Russia
GENOMEBROWSER – SOFTWARE FOR VISUAL SEQUENCE ANALYSIS

Zagoruiko N.G. 1*, Kutnenko O.A. 1, Borisova I.A. 1, Kiselev A.N. 1, Ptitsyn A.A.2
1
  Institute of Mathematics, SB RAS, Novosibirsk, Russia
2
   Pennington Biomedical Research Center, Baton Rouge LA 70808, USA
SELECTION OF INFORMATIVE SUBSET OF GENE EXPRESSION PROFILES
IN PROGNOSTIC ANALYSIS OF TYPE II DIABETES


2. COMPUTATIONAL STRUCTURAL AND FUNCTIONAL PROTEOMICS


Afonnikov D.A.1,2, Morozov A.V.1
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  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
1
  State Research Center of Virology and Biotechnology ―Vector‖, Koltsovo, Novosibirsk region,
Russia
2
  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




                                               23
Baryshev P.B.1*, Afonnikov D.A.1,2, Nikolaev S.V.2
1
  Novosibirsk State University, Novosibirsk, Russia
2
  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
1
  Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences,
Moscow, Russia
2
  Department of Bioengineering, Biological Faculty, M.V. Lomonosov Moscow State University,
Moscow, Russia
3
  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 INTRA-
AND INTERHELICAL INTERACTIONS IN PROTEINS

Dulko V., Feranchuk S.
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
1
  Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
  Novosibirsk State University, Novosibirsk, Russia
3
  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




                                               24
Nizolenko L.Ph.1*, Bachinsky A.G. 1, Yarygin A.A.1, Naumochkin A.N.1, Grigorovich D.A.2
1
  SRC VB ―Vector‖, Koltsovo, Novosibirsk, Russia
2
  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
1
  M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry Russian Academy
of Sciences, Moscow, Russia
2
  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
1
  M.M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry RAS,
Moscow, Russia
2
  Moscow Institute of Physics and Technology, Moscow, Russia
3
  Novartis Institutes for Biomedical Research, Basel, Swizerland
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
2
  Faculty of Life Sciences, University of Manchester, Sackville St., Manchester, UK
3
  Protein information Management System, CCLRC Daresbury Laboratory, UK
4
  York Structural Biology Laboratory, University of York, UK
5
  Oxford Protein Production Facility, Division of Structural Biology, University of Oxford, UK
6
  Scottish Structural Proteomics Facility, University of Dundee, UK
7
  European Bioinformatics Institute, Hinxton, UK
LABORATORY INFORMATION MANAGEMENT SYSTEM FOR MEMBRANE PROTEIN
STRUCTURE INITIATIVE

Volkova O.A.1, Kochetov A.V.1*
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


                                                25
3. 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
1
  Moscow State University, Department of Bioengineering and Bioinformatics, Moscow, Russia
2
  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
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
1
  Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
  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 1 (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
1
  Hubrecht Laboratorium, Utrecht, The Netherlands
2
  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*
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  Marshall University, Huntington, WV, USA
EVOLUTIONARY RELATIONSHIPS AND DISTRIBUTION OF THE DIFFERENT
LTR RETROTRANSPOSON FAMILIES IN PLANTS


                                                26
Khan M. 2, Jamil K.1, 2 *
1
  Indo American Cancer Institute and Research Centre, Hyderabad, India
2
   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
1
  Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Israel
2
  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
1
  Moscow State University, Department of Bioengeneering and Bioinformatics, Moscow, Russia
2
  Institute for Information Transmission Problems RAS, Moscow, Russia
TRANSCRIPTIONAL REGULATION OF THE METHIONINE BIOSYNTHESIS
IN ACTINOBACTERIA AND STREPTOCOCCI

Kuznetsova A.Y.*1, Naumoff D.G.2
1
  Moscow State University, Department of Bioengineering and Bioinformatics, Moscow, Russia
2
  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
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  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)




                                               27
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
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  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*
1
  Centre ―Bioengineering‖ RAS, Moscow, Russia
2
  FDWSRU, USDA-ARS, MD, USA
PHYLOGENETIC CHANGES IN CHLOROPLAST GENOMES


4. 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
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  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
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  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
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  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

                                             28
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
1
  Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
  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
1
  Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
  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-ARABINO-
HEPTULOSONATE-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
1
  Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
  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




                                    29
Turnaev I.I.1*, Ibragimova S.S.1, Usuda Y.2, Matsui K.2
1
  Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
  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
1
  Novosibirsk State University, Novosibirsk, Russia
2
  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
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  Novosibirsk State University, Novosibirsk, Russia
3
  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
1
  State Research Center of Virology and Biotechnology ―Vector‖, Koltsovo, Russia
2
  Institute of Internal Medicine, SB RAMS, Novosibirsk
3
  Institute of Mathematics, SB RAS, Novosibirsk
4
  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
1
  Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia
2
  Novosibirsk State University, Novosibirsk, Russia
3
  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


                                            30
Gursky V.V.1*, Samsonov A.M.1, Reinitz J.2
1
  Ioffe Physico-Technical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
2
  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
1
  Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
  Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia
3
  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*
1
  Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
  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
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia
3
  Institute of Systems Biology OOO, Novosibirsk, Russia
4
  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
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  Institute of Computational Mathematics and Mathematical Geophysics SB RAS,
Novosibirsk, Russia
RECONSTRUCTION AND STRUCTURE ANALYSIS OF APOPTOSIS GENE NETWORK
IN HEPATITIS C




                                                31
4.3 Modeling of morphogenesis

Bukharina T.A.1, Katokhin A.V.1,2, Furman D.P.1,2
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  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
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  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
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  Institute of Mathematics SB RAS, Novosibirsk, Russia
3
  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
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  Institute of Mathematics, SB RAS, Novosibirsk, Russia
3
  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
1
  Institute of Informatics Systems, SB RAS, Novosibirsk, Russia
2
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
3
  Institute for Genomics and Bioinformatics, University of California, Irvine, USA
4
  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
1
  Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia
2
  Novosibirsk State University, Novosibirsk, Russia
MATRIX PROCESS MODELLING: ON PROPERTIES OF SOLUTIONS
OF ONE DELAY DIFFERENTIAL EQUATIONS


                                               32
Demidenko G.V.1*, Khropova Yu.E.2, Kotova T.V.2
1
  Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia
2
  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. 2
1
  Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia
2
  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
1
  Institute of Systems Biology OOO, Novosibirsk, Russia
2
  Design Technological Institute of Digital Techniques, SB RAS, Novosibirsk, Russia
3
  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
1
  Novosibirsk State University, Novosibirsk, Russia
2
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
3
  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
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  Novosibirsk State University, Novosibirsk, Russia
3
  Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia
OSCILLATIONS OF CHAOTIC TYPE IN SYMMETRIC GENE NETWORKS
OF SMALL DIMENSION

Matveeva I.I. 1, Popov A.M.
1
  Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia
2
  Novosibirsk State University, Novosibirsk, Russia
MATRIX PROCESS MODELLING: DEPENDENCE OF SOLUTIONS
OF A SYSTEM OF DIFFERENTIAL EQUATIONS ON PARAMETER




                                          33
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
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  Institute of Computational Mathematics and Mathematical Geophysics, SB RAS,
   Novosibirsk, Russia
3
  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


5. NEW APPROACHES TO ANALYSIS/MODELING OF BIOMOLECULAR DATA
   AND PROCESSES

Arrigo P.1*, Cardo P.P.2
1
  CNR Institute for Macromolecular Studies, Genoa, Italy
2
  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
1
  Design Technological Institute of Digital Techniques, SB RAS, Novosibirsk, Russia
2
  Institute of Systems Biology, Novosibirsk OOO, Russia
3
  Institute of Biomedical Chemistry, RAMS, Moscow, Russia
4
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
5
  Institute of Biomedical Technologies, Segrate (MI), Italy
6
  BIOBASE GmbH, Wolfenbuettel, Germany
Cyclonet — AN INTEGRATED DATABASE ON CELL CYCLE REGULATION
AND CARCINOGENESIS




                                               34
Miginsky D.S.1,3*, Sokolov S.A.2, Labuzhsky V.V.2, Nikitin A.G.2,3
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  A.P. Ershov Institute of Informatics Systems SB RAS
3
  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
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  Novosibirsk State University, Novosibirsk, Russia
3
  Institute of Animal Systematics and Ecology, SB RAS, Novosibirsk, Russia
THE ONTOLOGY OF ECOSYSTEMS




                                               35
           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
1
  Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
  Novosibirsk State University, Novosibirsk, Russia
3
  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
1
  Design Technological Institute of Digital Techniques, SB RAS, Novosibirsk, Russia
2
  Institute of Systems Biology, Novosibirsk OOO, Russia
3
  Institute of Biomedical Chemistry, RAMS, Moscow, Russia
4
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
5
  Institute of Biomedical Technologies, Segrate (MI), Italy
6
  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
1
  Institute of Systems Biology OOO, Novosibirsk, Russia
2
  Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia
BioUML: VISUAL MODELING, AUTOMATED CODE GENERATION AND SIMULATION
OF BIOLOGICAL SYSTEMS



                                               36
Friday, July 21
Saturday, July 22

                     COMPUTATIONAL SYSTEMS BIOLOGY
Fadeev S.I.1*, Korolev V.K.1, Gainova I.A.2, Medvedev3A.E.
1
  Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia
2
  Khristianovich Institute of Theoretical and Applied Mechanics SB RAS, Novosibirsk, Russia
3
  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
1
  Institute of Systems Biology OOO, Novosibirsk, Russia
2
  Design Technological Institute of Digital Techniques, SB RAS, Novosibirsk, Russia
3
  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
1
  Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
  Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia
3
  Institute of Systems Biology OOO, Novosibirsk, Russia
4
  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




                                               37

				
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