THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002)

July 14-20, 2002, Novosibirsk, Russia

Program of oral presentations

The Conference Sessions will be held in the Small Conference Hall and in Music Salon

(room ¹220) of the House of Scientists

Participants are welcome to pass their demonstration material to the room ¹ 200

of the House of Scientists in the 30 min prior to the beginning of the Sessions

July, 14, Sunday Foyer of the Small Conference Hall

12:30-19:00 Registration of the conference participants*

Lunch 14:30-15:30

*Participants who come later are welcome for registration in the Organizing Committee room (House of scientists room ¹200) on any conference day.

July, 15, Monday Small Conference Hall

9:00-9:30 Registration of the conference participants (Foyer of the Small Conference Hall)

9:30-10:00 Opening Ceremony

Speech of Welcome: Academician V.K. Shumny, Director of the Institute of Cytology & Genetics SB RAS;

Greetings for participants of the Conference: Prof.N.A.Kolchanov; Prof.R.Hofestadt

10:00-13:30 Morning Session

REGULATORY GENOMIC SEQUENCES

Chairpersons:

Dr. E. Wingender, German Research Centre for Biotechnology, Braunschweig, Germany

Dr. V. Makeev, State Scientific Centre NIIGenetika, Moscow, Russia

Reports

Timeline

Mizushima H., Ichikawa H., Ohki M.Center for Medical Genomics and Cancer Genomics Division, National Cancer Center Research Institute, Tokyo, Japan

ANALYSIS TOOL FOR FINDING TRANSCRIPTION REGULATORY ELEMENTS, USING TRANSCRIPTION FACTOR DATA BASE (TFDB)

10:00-10:30

Ignatieva E.V., Ananko E.A., Podkolodnaya O.A., Stepanenko I.L., Merkulova T.I., Pozdnyakov M.A., Podkolodny N.L., Naumochkin A.N., Romashchenko A.G.

Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

TRANSCRIPTION REGULATORY REGIONS DATABASE (TRRD): ITS STATUS IN 2002

10:30-11:00

Coffee-break

11:00-11:30

Frith M.C., Hansen U., Weng Z. Boston University, Boston, USA

A GIBBS SAMPLING ALGORITHM TO DETECT CLUSTERED CIS-ELEMENTS

11:30-12:00

1, 2 Wingender E., 1Kel A.E., 1Gößling E., 1Hornischer K., 1Lewicki-Potapov B., 1Tchekmenev D., 1Kel-Margoulis O.V.

1 BIOBASE GmbH, Wolfenbüttel, Germany; 2 GBF German Research Centre for Biotechnology, Braunschweig, Germany

ALL HUMAN GENOME ANALYSIS FOR REGULATORY SIGNALS

12:00-12:30

Lyubetsky V.A., Rubanov L.I.

Institute for Information Transmission Problems RAS, Moscow, Russia

PARALLEL ALGOTITHM FOR SEARCHING REGULATORY SIGNAL IN BACTERIAL GENOME

12:30-13:00

Oshchepkov D. Yu., Turnaev I.I.,Vityaev E.E.

Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

SITECON: A METHOD FOR RECOGNIZING TRANSCRIPTION FACTOR BINDING SITES BASING ON ANALYSIS OF THEIR CONSERVATIVE PHYSICOCHEMICAL AND CONFORMATIONAL PROPERTIES

13:00-13:30

Lunch 13:30-14:30

14:30-18:00 Evening Session

REGULATORY GENOMIC SEQUENCES

Chairpersons:

Prof. V. Lyubetsky, Institute for Information Transmission Problems RAS, Moscow, Russia

Dr. H. Mizushima, Center for Medical Genomics and Cancer Genomics Division, National Cancer Center Research Institute, Tokyo, Japan

Reports

Timeline

3Lifanov, A.P., 1Nazina, A.G., 2Makeev, V.J., 1Papatsenko, D.A., 4Regnier, M., 1Desplan.C.

1Department of Biology, New York University, New York, USA

2State Scientific Centre NIIGenetika, Moscow, Russia

3Institute of Chemical Physics, Russian Academy of Sciences, Moscow, Russia

4INRIA, Roquencour, France

COMPUTER IDENTIFICATION OF TRANSCRIPTION FACTOR BINDING SITES IN EARLY DEVELOPMENTAL ENHANCERS OF DROSOPHILA BASED ON REDUNDANT WORDS

14:30-15:00

Lockwood C R., Frayling T M

Department of Diabetes and Vascular Medicine, University of Exeter, United Kingdom

HNF1-ALPHA BINDING SITES IN A COMPUTER SEARCH

15:00-15:30

1Vityaev E.E., 2Pozdnyakov M.A.,2Orlov Yu.L., 2Vishnevsky O.V., 2Podkolodny N.L. 1Sobolev Institute of Mathematics, SB RAS, Novosibrisk, Russia

2Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia

GENE DISCOVERY COMPUTER SYSTEM FOR ANALYSIS OF REGULATORY REGIONS

15:30-16:00

Coffee break

16:00-16:30

Sarai A.

RIKEN Tsukuba Institute, Tsukuba 305-0074, Japan

STRUCTURE-SPECIFICITY RELATIONSHIP IN PROTEIN-DNA RECOGNITION

16:30-17:00

1,3Shelest E., 1Kel A.E., 1Gößling E., 1, 2Wingender E.

1 GBF German Research Centre for Biotechnology, Braunschweig, Germany;

2 BIOBASE GmbH, Wolfenbüttel, Germany;

3 permanent address: Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.

PREDICTION OF POTENTIAL C/EBP/NF-k B COMPOSITE ELEMENTS USING THE MATRIX-BASED SEARCH METHODS

17:00-17:30

Foyer of the Small Conference Hall

17:30 -18:30 1st Poster Session and Computer Demonstrations "REGULATORY GENOMIC SEQUENCES"

July, 16, Tuesday Small Confernce Hall

9:00-13:30 Morning Session

COMPARATIVE AND EVOLUTIONARY GENOMICS

Chairpersons:

Prof. L.Zhivotovsky, Institute of General Genetics RAS, Moscow, Russia

Dr. C. Watkins, University of London, Egham, Surrey, UK

Reports

Timeline

1 Vandenbogaert M., 2Makeev V.

1 INRIA Rocquencourt - LaBRI Bordeaux I, Le Chesnay, France and 2 State Scientific Centre 2"GosNIIGenetika", Moscow, Russia

ANALYSIS OF BACTERIAL RM-SYSTEMS THROUGH GENOME-SCALE ANALYSIS AND RELATED TAXONOMIC ISSUES

9:00-9:30

Permina E. A.

GosNII Genetika, Moscow, Russia

COMPARATIVE ANALYSIS OF REGULATORY INTERACTIONS IN BACTERIAL GENOMES

9:30-10:00

1Ramensky V.E., 2,3Bork P., 1,2Sunyaev S.R.

1Engelhardt Institute of Molecular Biology (EIMB), Vavilova 32, 119991 Moscow, Russia 2European Molecular Biology Laboratory (EMBL), Heidelberg, Germany, 3Max-Delbrueck Center for Molecular Medicine (MDC), Berlin, Germany

SURVEY OF HUMAN NON-SYNOMYMOUS SNPs

10:00-10:30

Zhivotovsky L.A.

Institute of General Genetics RAS, Moscow, Russia

COMPUTATIONAL BIOLOGY AND ANALYSIS OF HUMAN POPULATIONS WITH USE OF DNA MARKERS

10:30-11:00

Coffee break

11:00-11:30

Watkins C.

Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, UK

THE CHANNEL CAPACITY OF SELECTIVE BREEDING: LIMITS ON THE INFORMATION STORABLE IN GENETIC SYSTEMS

11:30-12:00

1 Yuryev A., 2Makeyev A.

1Orchid Biosciences Inc., Princeton, NJ USA

2InforMax Inc, Bethesda, MD USA

GENOTYPE CLASSIFICATION AND ALLELIC PATTERN RECOGNITION USING KOHONEN SELF-ORGANIZING MAPS

12:00-12:30

1Favorov A.V., 2Ochs M.F.

1State Scientific Centre "GosNIIGenetica" , Moscow, Russia

2Fox Chase Cancer Center, Philadelphia, USA.

MCMC METHOD FOR IDENTIFICATION OF ALLELIC PATTERNS IN DATA WITH QUANTITATIVELY DESCRIBABLE PHENOTYPIC FEATURES

12:30-13:00

Lyubetsky V.A., V’yugin V.V.

Institute for Information Transmission Problems RAS, Moscow, Russia

METHOD OF HORIZONTAL GENE TRANSFER DETERMINATION USING PHYLOGENETIC DATA

13:00-13:30

Lunch 13:30-14:30

Foyer of the Small Conference Hall

14:30-16:15 2nd Poster Session and Computer Demonstrations "GENOME STRUCTURE AND FUNCTION", "COMPARATIVE AND EVOLUTIONARY GENOMICS", "RNA COMPUTATIONAL BIOLOGY", "GENERAL PROBLEMS OF BIOINFORMATICS"

15:45-16:15 Coffee-break

July, 17, Wednesday Small Conference Hall

9:00-13:00 Morning Session

GENOME STRUCTURE AND FUNCTION

Chairperson:

Dr. M. Gelfand, GosNIIGenetika, Moscow, Russia

Reports

Timeline

1,2Chuzhanova N.A., 3Cooper D.N.

1 Department of Computer Science, Cardiff University, PO Box 916, Cardiff CF24 3XF, UK

2 Institute of Mathematics, Russian Academy of Science, 630090 Novosibirsk, Russia

3 Institute of Medical Genetics, University of Wales College of Medicine, Cardiff CF14 4XN UK

MECHANISMS OF MUTAGENESIS AND THE ROLE OF LOCAL DNA SEQUENCE COMPLEXITY

9:00-9:30

Korotkov E.V., Korotkova M.A. Kudryashov N.A.

Center of Bioengineering RAS, Moscow, Russia

Moscow Physical Engineering Institute, Moscow, Russia

INFORMATION CONCEPTION OF PERIODICITY OF SYMBOLIC TEXTS

9:30-10:00

Vorobjev Y. N.

Novosibirsk Institute of Bioorganic Chemistry RAS, Novosibirsk, Russia
A MACROMOLECULAR MODELING AS A TOOL TO EXPAND BIOINFORMATICS DATABASES

10:00-10:30

Oparina N.J., Lacroix M.-H., Mashkova T.D.

Engelhardt Institute of Molecular Biology RAS, Moscow, Russia

PERICENTROMERIC ALPHA SATELLITES: NON-RANDOM DISTRIBUTION OF STRUCTURAL REARRANGEMENTS AND INSERTIONS OF DISPERSED ELEMENTS ALONG THE MONOMER

10:30-11:00

Coffee-break

11:00-11:30

1Orlov Yu.L., 2Gusev V.D., 2Nemytikova L.A., 2Potapov V.N.

1 Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

2 Institute of Mathematics SB RAS, Novosibirsk, Russia

DECOMPOSITION OF GENOME SEQUENCES BY REPEAT FRAGMENTS

11:30-12:00

1Paskhin A.I. , 2Ramensky V.E., 3Gelfand M.S., 3Makeev V.J.

1 Moscow Institute of Physics and Technology, Moscow Region, Russia

2 Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia

3 GosNIIGenetika, Moscow, Russia

IDENTIFICATION OF CODING REGIONS IN GENOMES OF LOWER EUKARYOTES BY COMPOSITIONAL SEGMENTATION OF COMPLETE GENOMES

12:00-12:30

Regnier M.

INRIA Le Chesnay France

MATHEMATICAL TOOLS FOR REGULATORY SIGNALS EXTRACTION

12:30-13:00

Lunch 13:00 -14:00

14:00 -18:15 Evening Session

GENERAL PROBLEMS OF BIOINFORMATICS

Chairpersons:

Prof. N.Zagoruiko, Institute of Mathematics SB RAS, Novosibirsk, Russia

Dr. T.Hodgman, GlaxoSmithKline, Stevenage, UK

Plenary lecture 14:00-14:45

Ratner V.A.

Institute of Cytology and Genetics, SB RAS; Novosibirsk State University, Novosibirsk, Russia

VIRTUAL REALITY AND REGULATORY SYSTEMS

Reports

Timeline

1,2Heymann S., 2Gabrielyan O.R., 3Ghazaryan G.G., 3Danielyan E.A., 3Hakobyan G.G. , 3Hakobyan G.O.

1Humboldt-University Berlin, Institute of Computer Science, Berlin, Germany;

2Kelman GmbH, Berlin, Germany;

3Yerevan State University, Yerevan, Armenia

TOWARDS A METRICAL SPACE OF BIOLOGICAL SEQUENCES

14:45-15:15

Ivanov A.O. , Tuzhilin A.A.

Faculty of Mechanics and Mathematics, Moscow State University, Moscow, Russia

MINIMAL TREES IN PHYLOGENETIC SPACES

15:15-15:45

1Zagoruiko N.G., 1Pichueva A.G., 1Kutnenko O.A. , 2Borisova I.A. , 2Kochetov A.V.,

2Ivanisenko V.A., 2Nikolaev S.V., 2Likhoshvai V.A., 2 Ratushny A.V.

1Institute of Mathematics SB RAS, Novosibirsk, Russia

2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

APPLICATION OF THE METHODS OF INTELECTUAL DATA ANALYSIS TO SOLVING THE PROBLEMS OF BIOINFORMATICS

15:45-16:15

Coffee-break

16:15-16:45

1Yang Z.L., 1,2Liu G.R., 2,3 Lam K.Y.

1Center for Advanced Computations in Engineering Science (ACES) Department of Mechanical Engineering, National University of Singapore, Singapore

2 SMA Fellow, Singapore-MIT Alliance

3Institute of High Performance Computing (IHPC), Singapore

A MODIFIED GENETIC ALGORITHM WITH LOCAL AND GLOBAL SEARCH TECHNIQUES

16:45-17:15

1,2Vityaev E.E., 3Kovalerchuk B.

1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

2Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia

3Central Washington University (Ellensburg), USA

BIOINFORMATICS: KNOWLEDGE DISCOVERY AND DATA MINING

17:15-17:45

Hodgman T.C.

GlaxoSmithKline, Stevenage, United Kindom

THE IMPORTANCE OF GENOME REGULATION AND STRUCTURE TO THE PHARMACEUTICAL INDUSTRY

17:45-18:15

July, 18, Thursday Small Hall of the House of Scientists

9:00-13:30 Morning Session

RNA COMPUTATIONAL BIOLOGY

Chairperson:

Dr. A.Mironov, GosNIIGenetika, Moscow, Russia

 

Reports

Timeline

Gorbunov K.Yu., Lyubetsky V.A.

Institute for Information Transmission Problems RAS, Moscow, Russia

AN ALGORITHM FOR SEARCHING OF COMMON SECONDARY STRUCTURES IN A SET OF RNA SEQUENCES

9:00-9:30

Mironov A.

GosNIIGenetika, Moscow, Russia

REGULATION OF BACTERIAL GENE EXPRESSION ON THE RNA LEVEL

9:30-10:00

Pospisil H., Herrmann A., Pankow H., Reich J.

Max-Delbrueck-Center for Molecular Medicine, Berlin, Germany

A DATABASE ON ALTERNATIVE SPLICE FORMS ON THE INTEGRATED GENETIC MAP SERVICE (IGMS)

10:00-10:30
Gelfand M.

GosNIIGenetika, Moscow, Russia
EVOLUTION OF ALTERNATIVE SPLICING

10:30-11:00

Coffee-break

11:00-11:30

1Kochetov A.V., 2Sarai A.

1Institute of Cytology and Genetics SB RAS, Novosiborsk, Russia

2Tsukuba Institute, The Institute of Physical Chemical Research (RIKEN), Tsukuba, Japan

MRNA-LOCATED TRANSLATIONAL SIGNALS

11:30-12:00

Matushkin Yu.G., Likhoshvai V.A., Kochetov A.V.

Institute of Cytology and Genetics SB RAS, Novosiborsk, Russia

TRANSLATION ELONGATION STAGES AND STRUCTURAL FEATURES OF mRNA REGION AT THE TRANSLATION START SITE CRITICAL FOR THE EFFICIENCY OF GENE EXPRESSION IN UNICELLULAR ORGANISMS

12:00-12:30

1Vishnevsky O.V. , 2Avdeeva I.V. 

1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

2Novosibirsk State University, Novosibirsk, Russia

STUDY OF THE SPECIFIC CONTEXTUAL FEATURES OF TRANSLATION INITIATION AND TERMINATION REGIONS IN EUKARYOTES

12:30-13:00

Frenkel F.E, Korotkov E.V.

Center "Bioengineering" RAS, Moscow, Russia

REVEALING AND FUNCTIONAL ANALYSIS OF TRNA-LIKE SEQUENCES IN VARIOUS GENOMES

13:00-13:30

Lunch 13:30-14:30

 14:30 -16:30 3d Poster Session and Computer Demonstrations STRUCTURAL COMPUTATIONAL BIOLOGY", "SYSTEM COMPUTER BIOLOGY"
16:00 -16:30 Coffee-break

July, 18, Thursday Music Salon (room ¹220)

9:00-12:20 Morning Session

FUNDAMENTAL GENETIC PROCESSES AND MECHANISMS; INTAS SECTION

Chairpersons:

Prof. N.Yankovsky, Institute of General Genetics RAS, Moscow, Russia

Sidorenko S.P., Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology NASU, Kyiv, Ukraine

Reports

Timeline

Introductory remarks (Prof. G.Nevinsky)

9:00-9:05

1,2Sinyakov A.N., 3Arimondo P.B., 3Bailly C., 3Sun J-Sh., 3Garestier T., 3Boutorine A.S.,

1,2Ryabinin V.A., 3Hélène C.

1State Research Center for Virology and Biotechnology "Vector", Kol'tsovo, Novosibirsk Region, Russia,

2Institute of Bioorganic Chemistry, SB RAS, Novosibirsk, Russia,

3Laboratoire de Biophysique, INSERM UR 565, CNRS UMR 8646, Muséum National d'Histoire Naturelle, Paris, France

SYNTHESIS, PHYSICO-CHEMICAL AND BIOLOGICAL STUDIES OF SEQUENCE-SPECIFIC CONJUGATES AS THE AGENTS FOR REGULATION OF GENE EXPRESSION ON THE LEVEL OF DOUBLE-STRANDED DNA

9:05-9:30

1Nevinsky G.A. , 1Ishchenko A.A., 2Sinitsina O.I., 2Vasunina E.A., 1Koval V.V., 1Vasilenko N.L., 3Saparbaev M., 1Fedorova O.S.

1Novosibirsk Institute of Bioorganic Chemistry SB RAS, Novosibirsk, Russia

2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia;

3Group de Reparation des Lesions Radio et Chimio-Induites, Paris, France

REPAIR OF 8-OXOGUANINE IN DNA OF PROKARYOTES, WISTAR RATS AND OXYS RATS WITH OVERGENERATION OF FREE RADICALS

9:30-9:55

Allinson S. L., Dianov G. L.

MRC Radiation and Genome Stability Unit, Harwell, Oxfordshire, United Kingdom

CO-ORDINATION OF BASE EXCISION REPAIR

9:55-10:20

Chelobanov B.P., Laktionov P.P., Kharkova M.V., Rykova E.Yu., Pyshnyi D.V., Pyshnaya I.A., 1Kim A.A., 2Sczakiel G., Vlassov V.V.

Novosibirsk Institute of Bioorganic Chemistry SB RAS, Novosibirsk, Russia

1Institute of Nuclear Physics, Tashkent, Uzbekistan

2Institute of Molecular Medicine, Luebeck, Germany

ISOLATION AND IDENTIFICATION OF CELL SURFACE NUCLEIC ACIDS-BINDING PROTEINS

10:20-10:45

Coffee-break

10:45-11:00

Schröder H.C., Müller W.E.G.

Institut für Physiologische Chemie, Universität Mainz, Mainz, Germany and German Center of Excellence BIOTECmarin

MOLECULAR APPROACHES TO STUDY STRESS ADAPTATION, BIOACTIVITY, AND PHYLOGENETIC RELATIONSHIPS WITHIN THE PORIFERA

11:00-11:25

Sidorenko S.P., Mikhalap S.V., Shlapatska L.M., Yurchenko M.Yu., Akimov Yu.M., Chekhun V.F.

Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology National Academy of Sciences of Ukraine, Kyiv, Ukraine. 

SIGNAL TRANSDUCTION PATHWAYS INITIATED VIA CELL SURFACE RECEPTOR CD150

11:25-11:50

1,2Lebedeva N.A., 1Rechkunova N.I., 1Khodyreva S.N., 2Favre A. and 1,2Lavrik O.I.

1Novosibirsk Institute of Bioorganic Chemistry SB RAS, Novosibirsk, Russia

2Institut Jacques Monod (CNRS, Universite Paris 6, Universite Paris 7), Paris, France

BINARY SYSTEM OF PHOTOAFFINITY REAGENTS FOR SELECTIVE LABELLING OF DNA POLYMERASES IN NUCLEAR EXTRACT

11:50-12:10

Gruntenko N.E., Adonjeva N.V., Karpova E.K., Chentsova N.A., Faddeeva N.V., Rauschenbach I.Yu.

Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

DOPAMINE AND JUVENILE HORMONE IN THE CONTROL OF DROSOPHILA REPRODUCTION UNDER NORMAL CONDITIONS AND HEAT STRESS

12:10-12:30

Foyer of the Small Conference Hall

12:30-13:00 Poster Session "FUNDAMENTAL GENETIC PROCESSES AND MECHANISMS; INTAS SECTION"

Lunch 13:00 -14:00

14:00 -17:15 Evening Session

FUNDAMENTAL GENETIC PROCESSES AND MECHANISMS; INTAS SECTION

Chairpersons:

Dr. I.Schmidt (INTAS)

Prof. H. Schröder, Institut für Physiologische Chemie, Universität Mainz, Mainz, Germany

Prof. George Nevinsky, Novosibirsk Institute of Bioorganic Chemistry SB RAS, Novosibirsk, Russia 
supervisor of the INTAS Section at BGRS'2002

Reports

Timeline

Yurlova A.A., Belyakin S.N., Makunin I.V., Zhimulev I.F. Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

CLONING OF SUPPRESSOR OF UNDERREPLICATION GENE FROM D. ERECTA (REVEALS LOW SUBSTITUTION LEVEL FOR N-TERMINAL PART OF PROTEIN)

14:00-14:25

Adonina I., Vatolina T., Scherban A., Salina E.A.

The Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

THE GENOMIC ORGANIZATION AND EVOLUTION OF AEGILOPS SPELTOIDES SUBTELOMERIC REGIONS

14:25-14:50

1 Graphodatsky A., 1Perelman P., 1Alkalaeva E., 1Trifonov V., 1Shtukkert A., 1Serdukova N., 1Biltueva L., 1Vorobieva N., 2Ferguson-Smith M.A., 2Yang F., 2O’Brien P., 3Robinson T.J., 4Suwattana D., 5Sharipov I.K.

1Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia

2University of Cambridge, UK

3University of Stellenbosch, SAR

4Chulalongkorn University, Bangkok, Thailand

5Institute of Genetics and Cytology, Alma-Ata, Kazakhstan

KARYOTYPE EVOLUTION IN MAMMALS: A REAPPRAISAL BY COMPARATIVE CHROMOSOME PAINTING

14:50-15:15

1Khusnutdinova E., 1Bermisheva M., 1Victorova T.,1Korshunova T., 1Salimova A., 3Svyatova G., 2Tambets K., 2Willems R.

1Institute of Biochemistry and Genetics of the Ufa Scientific Center of RAS, Ufa, Russia

2Dept. Evolutionary Biology, Tartu University, Tartu, Estonia

3Republican centre of health of mother and child, Kazakhstan

PHYLOGEOGRAPHY OF MITOCHONDRIAL LINEAGES OF TURKIC AND URALIC - SPEAKING PEOPLE

15:15-15:40

1Borinskaya S.A., 2Korotaev A.B.

1 Vavilov Institute of General Genetics, Moscow, Russia

2 Russian State University for the Humanities, Moscow, Russia

CORRELATIONS BETWEEN GENETIC AND CULTURAL TRAITS IN POPULATIONS OF HUMANS

15:40-16:05

Coffee-break

16:05-16:30

Mazin A. V.

Department of Biochemistry, School of Medicine, MCP Hahnemann University, Philadelphia, USA

A COMBINATORIAL PRINCIPLE IN ORGANIZATION OF THE HOMOLOGOUS RECOMBINATION SYSTEM IN EUKARYOTES

16:30-16:55
Dr. I.Schmid

16:55-17:15

July, 19, Friday Small Hall of the House of Scientists

9:00-13:00 Morning Session

STRUCTURAL COMPUTATIONAL BIOLOGY

Chairpersons:

Prof. E.Korotkov, Center of Bioengineering RAS, Moscow, Russia

Dr. A.Sarai RIKEN Tsukuba Institute, Japan

Reports

Timeline

1Błażewicz J., 2Hammer P.L., 1Łukasiak P.

1 Institute of Computing Sciences, Poznan Univ. of Technology, Poznan, POLAND & Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, POLAND

2 Rutgers Center for Operations Research, Rutgers University, New Jersey, USA

LOGICAL ANALYSIS OF DATA APPROACH TO THE PREDICTION OF PROTEIN SECONDARY STRUCTURES

9:00-9:30

Bogdanov Yu.F., Dadashev S.Ya., Grishaeva T.M.

Vavilov Institute of General Genetics RAS, Moscow, Russia

DEVELOPMENT OF A STRATEGY FOR COMPUTER-ASSISSTED SEARCHING FOR FUNCTIONALLY SIMILAR PROTEINS IN EVOLUTIONARILY DISTANT ORGANISMS

9:30-10:00

Kuznetsov V.A., 1Pickalov V.V.

The Laboratory of Integrative and Medical Biophysics, National Institute of Child Health and Human Development, NIH, Bethesda, USA

1 Institute of Theoretical and Applied Mechanics SB RAS, Novosibirsk, Russia

THE NUMBERS OF PROTEIN DOMAIN SEQUENCES AND PROTEIN CODING GENES IN THE EVOLVED PROTEOMES

10:00-10:30

1,2 Ivanisenko V.A., 1 Grigorovich D.A.

1 Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

2 SRC VB "Vector", Koltsovo, Russia

PDBSITE – DATABASE ON PROTEIN ACTIVE SITES AND THEIR ENVIRONMENT

10:30-11:00

Coffee-break

11:00-11:30

Afonnikov D. A., Nikolaev S.V., Ivanisenko V.A.

Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

CLASSIFICATION OF LOCAL SPATIAL ENVIRONMENT OF AMINO ACID RESIDUES BY PHYSICOCHEMICAL CHARACTERISTICS: ANALYSIS OF TRANSCRIPTION FACTOR DNA-BINDING DOMAINS

11:30-12:00

Krivov S. V. 1, Chekmarev S. F. 3 and Karplus M. 1,2

1Laboratoire de Chimie Biophysique, ISIS, Université Louis Pasteur, Strasbourg, France

2Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts, USA

3Institute of Thermophysics, SB RAS, Novosibirsk, Russia

CONFINEMENT MOLECULAR DYNAMICS AND ITS APPLICATION TO THE STUDY OF POTENTIAL ENERGY SURFACES AND CONFORMATIONAL TRANSITIONS IN BIOMOLECULES

12:00-12:30

1Logvinenko T., 2Liu J.S.

1Statistics Department, Stanford University, Stanford, CA 94305, USA;

2Statistics Department, Harvard University, Cambridge, MA 02138, USA

SEQUENTIAL MONTE CARLO AND DIRICHLET MIXTURES FOR EXTRACTING PROTEIN ALIGNMENT MODELS

12:30-13:00

Lunch 13:00-14:00

14:00-17:30 Evening Session

STRUCTURAL COMPUTATIONAL BIOLOGY

Chairpersons:

Prof. Yu.Bogdanov, Vavilov Institute of General Genetics RAS, Moscow, Russia

Dr. V. Kuznetsov, National Institute of Child Health and Human Development, NIH, Bethesda, USA

Reports

Timeline

Vlasov P.K., Kilosanidze G.T., Ukrainskii D.L., Tumanyan V.G., Esipova N.G.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia

PREDOMINANT CONFORMATIONS OF OLIGOPEPTIDE FRAGMENTS OF GLOBULAR PROTEINS

14:00-14:30

1,2Sunyaev Sh.R., 1Bogopolsky G.A., 3,4Oleinikova N.V., 1,3Vlasov P.K., 5Finkelstein A.V., 4Roytberg M.A.

1 Institute of Molecular Biology RAS, Moscow, Russia

2 European Molecular Biology Laboratory (EMBL), Germany

3 Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia

4 Institute of Mathematical Problems in Biology, RAS, Pushchino, Moscow Region, Russia

5 Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia

ANCHOR-BASED ALIGNMENT METHOD FOR THE SEQUENCE VS. SEQUENCE AND PROFILE VS. SEQUENCE ALIGNMENT

14:30-15:00

Schwarzl S. M., Huang D., Smith J.C., Fischer S.

IWR Biocomputing, Heidelberg, Germany

CHARGE REPARAMETRIZATION FOR FAST ATOMIC-DETAIL CALCULATIONS IN PROTEINS

15:00-15:30

Novichkov P.S.

Integrated Genomics, Moscow, Russia

PROTEIN FAMILIES EVOLVE AT A CONSTANT RATE

15:30-16:00

Coffee-break

16:00-16:30

Sutormin R.A.

State Scientific Center GosNIIGenetica, Moscow, Russia

TRANSMEMBRANE SEGMENTS OF TRANSPORT PROTEINS: EVOLUTION, PREDICTION, ALIGNMENT

16:30-17:00

1 Titov I.I. , 2Pal'yanov A.Yu.
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

2Novosibirsk State University, Novosibirsk, Russia

THE INVERSE FOLDING OF BIOPOLYMERS

17:00-17:30

July, 20, Saturday Small Conference Hall

9:00-13:00 Morning Session

SYSTEM COMPUTER BIOLOGY

Chairpersons:

Dr. O.Ozoline, Institute of Cell Biophysics RAS, Pushchino, Moscow Region, Russia

Dr. L Milanesi, Institute of Biomedical Technology CNR-ITB, Milan, Italy

Reports

Timeline

1,2 Mjolsness E., 1Jonsson H., 2Shapiro B., 1Meyerowitz E.

1Division of Biology and 2Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA

MODELING PLANT DEVELOPMENT WITH GENE REGULATION NETWORKS INCLUDING SIGNALING AND CELL DIVISION

9:00-9:30

1Ratushny A.V., 1Nedosekina E.A., 1Ignatieva E.V., 1Ananko E.A., 1Podkolodnaya O.A., 1Podkolodny N.L., 2Fadeev S.I., 2Berezin A.Yu., 2Gainova I.A., 3Latypov A.F., 3Nikulichev Yu.V., 1Matushkin Yu.G., 1Likhoshvai V.A.
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2 Institute of Mathematics SB RAS, Novosibirsk, Russia
3 Institute of Theoretical and Applied Mechanics SB RAS, Novosibirsk, Russia
MODELING OF GENE NETWORKS BY USING GENERALIZED CHEMICAL KINETIC APPROACH

9:00-10:00

1Freier A., 1Hofestädt R., 2Lange M.

1 Bioinformatics Workgroup, Fakulty of Technology, Bielefeld University, Germany

2 Plant Genome and Resource Center, IPK Gatersleben, Germany

IIUDB: OBJECT-ORIENTED SYSTEM FOR MODELLING, INTEGRATION AND ANALYSIS OF GENE CONTROLLED METABOLIC NETWORKS

10:00-10:30

Kolchanov N.A., Stepanenko I.L., Podkolodnaya O.A., Ananko E.A., Ignatieva
E.V., Podkolodny N.L.

Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

GENE NETWORKS: PRINCIPLES OF ORGANIZATION AND MECHANISMS OF OPERATION AND INTEGRATION

10:30-11:00

Coffee-break

11:00-11:30

1Surkova S. Yu., 1Samsonova M.G., 1Myasnikova E.M.

1 St.Petersburg State Technical University, Russia ;

TEMPORAL CHANGES IN POSITION OF SEGMENTATION GENE EXPRESSION DOMAINS IN DROSOPHILA EARLY EMBRYO

11:30-12:00

Reinitz J. B.

Dept. Of Applied Math and Statistics, Stony Brook University, Stony Brook NY, USA

BIOINFORMATIC ANALYSIS OF A MORPHOGENETIC FIELD IN DROSOPHILA

12:00-12:30

1,2 Spirov A.V., 3Holloway D.

1State University of New York at Stony Brook, Stony Brook NY,USA

2The Sechenov Institute of Evolutionary Physiology and Biochemistry, St.Petersburg, Russia

3Mathematics/B.C.Institute of Technology/Burnaby, B.C. Canada

MEASUREMENTS OF PRECISION OF MOLECULAR MECHANISMS FOR EARLY DROSOPHILA EMBRYO SEGMENTATION

12:30-13:00

Lunch 13:00-14:00

14:00-17:00 Evening Session

SYSTEM COMPUTER BIOLOGY

Chairpersons:

Dr. M.Samsonova, St.Petersburg State Technical University, St.Petersburg, Russia

Dr. J. Reinitz, Stony Brook University, Stony Brook, USA

Reports

Timeline

1,2Ozoline O.N., 2Fujita N., 2,3Ishihama A.

1Institute of Cell Biophysics, RAS, Pushchino, Moscow Region, Russia

2National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan

3Nippon Institute for Biological Science, Ome, Tokyo 198-0024, Japan

Genome-wide expression profiling of Escherichia coli W3110: MICROARRAY AND STATISTIC ANALYSIS OF HEAT SHOCK REGULONS

14:00-14:30

Leyfer D., Funari V., Berwick R., Haverty P., Frith M., Tolan D.

Boston University, Boston, USA

A NOVEL ALGORITHM FOR IN-SILICO EST EXPRESSION PROFILING

14:30-15:00

Milanesi L., Rizzi R..

Institute of Biomedical Technology CNR-ITB, Milan, Italy

MICROARRAY IMAGING DATA READER SPOTVIEW

15:00-15:30

Coffee-break

15:30-16:00

1Likhoshvai V.A., 1Matushkin Yu.G., 2 Fadeev S.I.2, 3Klishevich M.A., 3Vernikovskaya E.V., 3Purtov A.V., 3Osokina V.A.
1 Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2 Mathematical Institute of SB RAS, Novosibirsk, Russia
3Novosibirsk State University, Novosibirsk, Russia
ON GLOBAL REGIMES OF A GENE NETWORK FUNCTIONING

16:00-16:30

Galimzyanov A.V., Tchuraev R.N.

Institute of Biology, Ufa Research Center, Russian Academy of Sciences, Ufa, Russia

STRUCTURAL STABILITY OF DROSOPHILA CONTROL GENE SUBNETWORK: COMPUTER EXPERIMENTS, QUANTITATIVE AND QUALITATIVE EVALUATION

16:30-17:00

17:00-17:30 Closing Ceremony; Comments of Chairpersons