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The Fifth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2006)
CONFERENCE PROGRAM
Small Conference Hall
Computer demos of this session will be available during the entire conference day
Computer demos of this session will be available during the entire conference day
Computer demos of this session will be available during the entire conference day
Computer demos of this session will be available during the entire conference day
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
Samsonova M.G.1, Reinitz J.2
COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICS and transcriptomics
Seliverstov A.V.*, Lyubetsky V.A.
ANALYSIS OF THE NUCLEOTIDE CONTEXT OF HIGHER PLANT MITOCHONDRIAL mRNA EDITING SITES
COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICS and transcriptomics
Omelianchuk N.A.1, Khomicheva I.V.1, Savinskaya S.A. 1,2, Levitsky V.G.1,2, Vishnevsky O.V. 1,2, Katokhin A.V.1,2, Ponomarenko M.P.1 , Kolchanov N.A.1,2
Tutukina M.N., Masulis I.S., Ozoline O.N.*
Institute of Cell Biophysics RAS, Pushchino, Moscow region, Russia
Towards the identification of ANTISENSE RNA WITHIN GENES OF TRANSCRIPTION REGULATORS
3.
Orlov Yu.L.1, Zhou J.1, Lipovich L.1, Yong H.C.2, Li Yi2, Shahab A.2, Kuznetsov V.A.1*
1Genome Institute of Singapore, Singapore
2Bioinformatics Institute, Singapore
Kuznetsov V.A.*, Zhou J., George J., Orlov Yu.L.
Genome Institute of Singapore, Singapore
Efimov V.M.1*, Badratinov M.S.2, Katokhin A.V.2,3
1Institute of Systematics and Ecology of Animals, SB RAS, Novosibirsk, Russia
2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
3Novosibirsk State University, Novosibirsk, Russia
INTERPRETATION OF RESULTS OF SOM ANALYSIS OF MICROARRAY DATA BY PRINCIPAL COMPONENTS
Abhishek K.1*, Karnick H.1, Mitra P.2
1Indian Institute of Technology Kanpur, Kanpur, India
2Indian Institute of Technology Kharagpur, Kharagpur, India
A KNOWLEDGE AND DATA BASED HYBRID APPROACH TO GENE CLUSTERING
Vlasov P.K.*, Esipova N.G., Tumanyan V.G.
Chekmarev S.F.1*, Krivov S.V.2, Karplus M.2,3*
Afonnikov D.A.1,2
1 Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2 Novosibirsk State University, Novosibirsk, Russia
How are charged residues distributed among functionally distinct structural domains of aminoacyl-tRNA synthetases?
Dr. Vladimir Kuznetsov, Genome Institute of Singapore, Singapore
Prof. Sergei Chekmarev, Institute of Thermophysics Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
1 Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2 Institute of Mathematics SB RAS, Novosibirsk, Russia
2.
Chernorudskiy A.L., Shorina A.S., Garcia A., Gainullin M.R.*
Demenkov P.S.1*, Aman E.E.2, Ivanisenko V.A.2,3
1Sobolev Institute of Mathematics of the SB RAS, Novosibirsk, Russia
2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Kochetov A.V.1*, Sarai A.2, Kolchanov N.A.1
1Institute of Cytology and Genetics, Novosibirsk, Russia
Bazykin G.A.1*, Dushoff J.1, Levin S.1, Kondrashov A.2
1 Department. of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
2 National Center for Biotechnology Information, NIH, Bethesda, USA
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
AROMORPHOSES AND ADAPTIVE MOLECULAR EVOLUTION: MORPHOGENS AND SIGNALING CASCADE GENES
Ignatieva E.V.*, Oshchepkov D.Yu., Klimova N.V., Vasiliev G.V., Merkulova T.I.
2.
Kolesnikov N.N.*, Elisafenko E.A., Zakian S.M.
Deyneko I.V.*1,2, Kalybaeva Y.M.1, Kel A.E. 3, Blöcker H.*1, Kauer G. 4
1Department of Genome Analysis, GBF, Braunschweig, Germany
2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
3BIOBASE GmbH, Wolfenbüttel, Germany
4University of Applied Sciences, Emden, Germany
Perelygin A.A.*1, Zharkikh A.A.2, Brinton M.A.1
1 Biology Department, Georgia State University, Atlanta, GA, USA
MOLECULAR PHYLOGENY OF THE GENUS TRITICUM L.
Mironov A.A.1,2,3
Hofestaedt R.
Institute for Genomics and Bioinformatics and Departments of Computer Science and Mathematics, University of California, Irvine, USA MODELING TRANSCRIPTIONAL REGULATION WITH EQUILIBRIUM MOLECULAR COMPLEX COMPOSITION
1Department of computational biology, State Polytechnical University, St.Petersburg, Russia
Demidenko G.V.*, Matveeva I.I.
2.
Mateus D.*, Gallois J.P.
Labarga A.*, Anderson M., Valentin F., Lopez R.
BioUML: visual modeling, automated code generation and simulation of biological systems
Miginsky D.S.1,2*, Suslov V.V.1, Rasskazov D.A.1,2, Podkolodny N.L.1, Kolchanov N.A.1,2
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Novosibirsk State University, Novosibirsk, Russia
Dr. Bjorn Olsson, School of Humanities and Informatics, University of Skövde, Sweden
Golubyatnikov V.P.1*, Gaidov Yu.A.2, Kleshchev A.G.1, Volokitin E.P.1
1Institute of Mathematics, SB RAS, Novosibirsk, Russia
2Novosibirsk State University, Novosibirsk, Russia
Likhoshvai V.A.
DATABASE GenSensor AS INFORMATIONAL SOURCE FOR DESIGN OF BIOSENSORS. EXPERIMENTAL DEVELOPMENT OF BIOSENSOR BASED ON YfiA GENE
Rapaport F.1,2, Zinovyev A.1,3*, Barillot E.1, Vert J.-P.2
1Institute Curie, Bioinformatics Service, Paris, France
2Ecole des Mines de Paris, Center for Computational Biology, Fontainebleau, France
3Institute of Computational Modelling SB RAS, Krasnoyarsk, Russia
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia
Department of Physicochemical Biology and Epigenetics, Ufa Research Center RAS, Ufa, Russia
Prof. Ralf Hofestaedt, Bielefeld University, AG Bioinformatics, Bielefeld, Germany
1Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2 Novosibirsk State University, Novosibirsk, Russia
4Division of Biology, California Institute of Technology, Pasadena, USA
A CELLULAR AUTOMATON TO MODEL THE DEVELOPMENT OF SHOOT MERISTEMS IN ARABIDOPSIS THALIANA
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
1Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2Institute of Mathematics, SB RAS, Novosibirsk, Russia
3School of Information and Computer Science, and Institute for Genomics and Bioinformatics, University of California, Irvine, USA
4Novosibirsk State University, Novosibirsk, Russia
Olsson B.*, Gawronska B., Erlendsson B., Lindlöf A., Dura E.
School of Humanities and Informatics, University of Skövde, Sweden
1 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2 Institute of Mathematics, SB RAS, Novosibirsk, Russia
3 Novosibirsk State University, Novosibirsk, Russia
2.
1Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
1Institute of Theoretical and Applied Mechanics SB RAS, Novosibirsk, Russia
2Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
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
2Los Alamos National Laboratory, Los Alamos, USA
geWorkbench: a Bioinformatic Platform for Integrated Genomics
Kayumov A.R.*, Kirillova J. M., Mikhailova E. O., Balaban N.P., Sharipova M.R.
Khomicheva I.V.*, Levitsky V.G., Omelianchuk N.A., Ponomarenko M.P.
PATTERN OF LOCALLY POSITIONED DINUCLEOTIDES IN microRNA RELATES TO ITS ACCUMULATION LEVELS
2 Novosibirsk State University, Novosibirsk, Russia
Lyubetskaya E.V., Seliverstov A.V.*, Lyubetsky V.A.
DETECTING HAiRPINS IN 3’-UNTRANSLATED REGIONS OF HIGHLY EXPRESSED GENES IN ACTINOBACTERIA
STUDIES ON TRANSCRIPTIONAL REGULATION IN DNA
THE ANALYSIS OF SREBP BINDING SITES DISTRIBUTION IN GENE REGIONS BY COMBINED SITEGA AND PWM APPROACH
Institute for Information Transmission Problems RAS, Moscow, Russia
TRANSLATION REGULATION IN CHLOROPLASTS
2. COMPUTATIONAL STRUCTURAL AND FUNCTIONAL PROTEOMICS
CONNP: THE PREDICTION OF THE CONTACT NUMBERS OF THE AMINO ACID RESIDUES IN PROTEINS USING NEURAL NETWORK REGRESSION
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
Baryshev P.B.1*, Afonnikov D.A.1,2, Nikolaev S.V.2
1Novosibirsk State University, Novosibirsk, Russia
2Institute 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
A METHOD TO ASSESS CORRECT/MISFOLDED STRUCTURES OF TRANSMEMBRANE DOMAINS OF MEMBRANE PROTEINS
Efimov A.V., Brazhnikov E.V., Kondratova M.S.
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
Konshina A.G.*, Dubinnyi M.A., Efremov R.G.
1M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Moscow, Russia
2Biological Department, M.V.Lomonosov Moscow State University, Moscow, Russia
1M.M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
2Moscow Institute of Physics and Technology, Moscow, Russia
COMBINING MOLECULAR DOCKING WITH RECEPTOR DOMAIN MotIONS: SIMULATIONS OF BINDING OF ATP TO CA-ATPASE
Micro- and Minisatellites in Human genome, Tandemswan software in use
Brinza D., Perelygin A., Brinton M., Zelikovsky A.*
Georgia State University, Atlanta, USA
The models of population dynamics as tool for studying of genetic polymorphism of Baikalian polychaets
Chumakov M.I., Mazilov S., Zotova T.V.
inferring regulatiory signal profiles and evolutionary events
HAPLOTYPE BLOCK STRUCTURE IS CONSERVED ACROSS MAMMALS
The Phylogenetic Analysis of Ubiquitin Conjugating Enzymes of Cancer Metasignature
1Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Israel
2Institute of Clinical Immunology and AIDS, Kaplan Medical Center, Rehovot, Israel
2 State Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia
Molecules versus morphology in Oligochaeta systematics
Ryabinina O.M.
GENETIC DIVERSITY AND PHYLOGENETIC RELATIONSHIPS IN GROUPS OF ASIAN GUARDIAN, SIBERIAN HUNTING AND EUROPEAN SHEPHERD DOG BREEDS
Zotov V.S.1, Punina N.V.1, Dorokhov D.B.1, Schaad N.W.2, Ignatov A.N.1*
1Centre “Bioengineering” RAS, Moscow, Russia
2FDWSRU, USDA-ARS, MD, USA
phylogenetic changes in chloroplast genomes
Peshkov I.M.1, Fadeev S.I.2
A MATHEMATICAL MODEL FOR THE INFLUENZA VIRUS LIFE CYCLE
1Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia
2Novosibirsk State University, Novosibirsk, Russia
3Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Gursky V.V.1*, Samsonov A.M.1, Reinitz J.2
1Ioffe Physico-Technical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
2Stony Brook University, Stony Brook, New York, USA
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Mironova V.V.1*, Poplavsky A.S.1, Ponomarev D.K.2, Omelianchuk N.A.1
1Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2Institute of Informatics System,
tait SB RAS, Novosibirsk, Russia
Nikolaev S.V.1*, Fadeev S.I.2, Kogay V.V.2, Mjolsness E.3, Kolchanov N.A.1
1Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2Institute of Mathematics SB RAS, Novosibirsk, Russia
3School 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
1Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2Institute of Mathematics, SB RAS, Novosibirsk, Russia
3School of Information and Computer Science, and Institute for Genomics and Bioinformatics, University of California, Irvine, USA
Semantically rich ontology of anatomical structure and development for Arabidopsis thaliana L.
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
1Novosibirsk State University, Novosibirsk, Russia
2Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
3Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia
1Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2Novosibirsk State University, Novosibirsk, Russia
3Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia
Matveeva I.I. 1, Popov A.M.
1Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia
2Novosibirsk State University, Novosibirsk, Russia
matrix process modelling: Dependence of solutions of a system of DIFferential equations on parameter
Podkolodny N.L.1,2*, Podkolodnaya N.N.1, Miginsky D.S.1, Poplavsky A.S.1, Likhoshvai V.A.1, Compani B.3, Mjolsness E.3
1Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2Institute of Computational Mathematics and Mathematical Geophysics, SB RAS, Novosibirsk, Russia
3Institute 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
Department of Physicochemical Biology and Epigenetics, Ufa Research Center, RAS, Ufa, Russia
Arrigo P.1*, Cardo P.P.2
1CNR Institute for Macromolecular Studies, Genoa, Italy
2Department of Health Science, University of Genoa, Genoa, Italy
Investigation of Named entity recognition in molecular biology by data fusion
Graph theory algorithm for solution of computational problems of gene mapping
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
2A.P. Ershov Institute of Informatics Systems SB RAS
3Novosibirsk State University, Novosibirsk, Russia
THE ONTOLOGY OF ECOSYSTEMS
1Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia
2Khristianovich Institute of Theoretical and Applied Mechanics SB RAS, Novosibirsk, Russia
3Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia