July 16: Registration from 10:00
Opening Ceremony at 14:00
Plenar Session 14:30-18:00
A PRELIMINARY WORKING SCHEDULE BY SECTIONS:
July 17: COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICS;
July 18: COMPUTATIONAL STRUCTURAL AND FUNCTIONAL PROTEOMICS;
July 19: POSTER SESSION
July 20: COMPUTATIONAL EVOLUTIONARY BIOLOGY;
NEW APPROACHES TO BIOMOLECULAR DATA AND PROCESSES ANALYSIS/MODELING;
July 21-22: COMPUTATIONAL SYSTEMS BIOLOGY
July 22: Closing Ceremony at 17:30
JULY 16
PLENAR SESSION
Mazo I. *, Sivachenko A., Yuryev A., Daraselia N.
Ariadne Genomics, Inc., Rockville MD 20850б, USA
MOLECULAR NETWORKS IN MAMMALS: EXTRACTION FROM LITERATURE AND MICROARRAY
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, Houston, TX, USA
GENE DUPLICATIONS IN EVOLUTION: FROM ORIGIN OF THE GENETIC CODE TO THE HUMAN GENOME
Ivanov A.S.*, Gnedenko O.V., Molnar A.A., Mezentsev Yu.V., Lisitsa A.V., Archakov A.I.
V.N.Orechovich Institute of Biomedical Chemistry RAMS, Moscow, Russia
PROTEIN-PROTEIN INTERACTIONS AS NEW TARGETS FOR DRUG DESIGN: INTERACTIVE LINKS BETWEEN VIRTUAL AND EXPERIMENTAL APPROACHES
Surkova S.Yu.*, Samsonova M.G.
St. Petersburg State Polytechnical University, St. Petersburg, Russia
SYSTEMS BIOLOGY OF SEGMENT DETERMINATION
JULY 17
COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICS AND TRANSCRIPTOMICS
ORAL PRESENTATIONS
| № № | AUTHOR (S ) AND TITLE OF A TALK |
| 1. | Seliverstov A.V.*, Lyubetsky V.A.
Institute for Information Transmission Problems RAS, Moscow, Russia GENE EXPRESSION REGULATION IN CHLOROPLASTS AND BACTERIA |
| 2. | te Boekhorst R.1*, Walter K.2, Elgar G.3, Gilks W.R.2, Abnizova I.2
1University of Hertfordshire, College Lane, Hatfield, UK 1MRC-BSU, Robinson Way, Cambridge, UK STATISTICAL INFORMATION CHARACTERIZATION OF CONSERVED NON-CODING ELEMENTS IN VERTEBRATES |
| 3. | Levitsky V.G.1,2*, Ignatieva E.V.1,2, Ananko E.A.1., Merkulova T.I.1
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia 2Novosibirsk State University, Novosibirsk, Russia THE SITEGA AND PWM METHODS APPLICATION FOR TRANSCRIPTION FACTOR BINDING SITES RECOGNITION IN EPD PROMOTERS |
| 4. | Shelest E.S.*1, Wingender E.1,2
1Department of Bioinformatics, UKG, University of Göttingen, Göttingen, Germany 2BIOBASE GmbH, Wolfenbüttel, Germany 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, Novosibirsk, Russia 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.
Institute of Cell Biophysics of RAS, Pushchino, Moscow region, Russia. CONTEXT-DEPENDENT EFFECTS OF UPSTREAM A-TRACTS ON PROMOTER ELECTROSTATIC PROPERTIES AND FUNCTION |
| 7. |
Grosse I.Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) and Bioinformatics Center Gatersleben-Halle, Gatersleben, Germany COMPUTATIONAL IDENTIFICATION OF TRANSCRIPTION FACTOR BINDING SITES WITH VARIABLE ORDER BAYESIAN NETWORKS |
| 8. | Orlov Yu.L.1, Lipovich L.1, Zhou J.1, Yong H.C.2, Li Yi2, Shahab A.2, Kuznetsov V.A.1*
1 Genome Institute of Singapore, Singapore 2 Bioinformatics Institute, Singapore A COMPREHENSIVE QUALITY ASSESSMENT OF THE AFFYMETRIX U133A/B PROBESETS BY AN INTEGRATED GENOMIC AND CLINICAL APPROACH |
| 9. | Kuznetsov V.A.*, Zhou J., George J., Orlov Yu.L.
Genome Institute of Singapore, Singapore GENOME-WIDE CO-EXPRESSION PATTERNS OF HUMAN CIS-ANTISENSE GENE PAIRS |
| 10. | 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 |
| 11. |
Ponomarenko M.P.1*, Omelyanchuk N.A.1, Katokhin A.V.1, Kolchanov N.A.11Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia THE CONTENT OF miRNAs IN ARABIDOPSIS THALIANA CORRELATES WITH THE OCCURRENCE OF WRHW AND DRYD |
| 12. | Vishnevsky O.V.1,2*, Konstantinov Yu.M.3
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia 2Novosibirsk State University, Novosibirsk, Russia 3Siberian Institute of Plant Physiology and Biochemistry SB RAS, Irkutsk, Russia ANALYSIS OF THE NUCLEOTIDE CONTEXT OF HIGHER PLANT MITOCHONDRIAL mRNA EDITING SITES |
| 13. | 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 |
| 14. | 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 |
| 15. | Subkhankulova T., Livesey F.J.
Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1 QN, UK HOW SIMILAR ARE PHENOTYPICALLY IDENTICAL CELLS AT THE TRANSCRIPTIONAL LEVEL? |
JULY 18
COMPUTATIONAL STRUCTURAL AND FUNCTIONAL PROTEOMICS
ORAL PRESENTATIONS
| № № | AUTHOR (S ) AND TITLE OF A TALK |
| 1. | Vlasov P.K.*, Esipova N.G., Tumanyan V.G.
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia 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 RAS, Moscow, Russia 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 3 Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA “STRANGE KINETICS” OF UBIQUITIN FOLDING: INTERPRETATION IN TERMS OF A SIMPLE KINETIC MODEL |
| 4. | Afonnikov D.A.1,2
1 Institute of Cytology and Genetics RAS, Novosibirsk, Russia 2 Novosibirsk State University, Novosibirsk, Russia RESIDUE-RESIDUE CONTACT MAP PREDICTION FOR PROTEINS |
| 5. | Aksianov E.1*, Zanegina O.2, Alexeevski A.3, Karyagina A.4,5, Spirin S.3
1Virology department, Biological faculty, Moscow State University, Moscow, Russia 2Bioengineering and Bioinformatics faculty, Moscow State University, Moscow, Russia 3Belozersky Institute, Moscow State University, Moscow Russia 4N.F. Gamaleya Research Institute of Epidemiology and Microbiology, Moscow, Russia 5Institute 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, Moscow, Russia DEVELOPMENT OF A HIERARCHICAL CLASSIFICATION OF THE TIM-BARREL TYPE GLYCOSIDE HYDROLASES |
| 7. | Safro M.*1,Tworowski D.1, Feldman A.2
1Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel; 2EML Research gGmbH, Heidelberg, Germany HOW ARE CHARGED RESIDUES DISTRIBUTED AMONG FUNCTIONALLY DISTINCT STRUCTURAL DOMAINS OF AMINOACYL-TRNA SYNTHETASES? |
| 8. | Ivanisenko1 V.A., Demenkov2 P.S., Fomin1 E.S., Oshurkov3 I.S., Korotkov3 R.O., Aman1 E.E., Pintus1,3 S.S., Startcev3 K.S., Tatarnikova3 L.Yu., Panina3 I.I., Sobolev3 A.A., Seleznev3 I.V., Elohov3 V.Yu., Golovina3 A.N., Aknazarov3 Z.I., Sharonova3 I.V., Krestianova3 M.A., Mishchenko1 E.L., Magdysuk3 A.V., Nemiatov3 A.I.
1 Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia 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 |
| 9. | Chernorudskiy A.L., Shorina A.S., Garcia A., Gainullin M.R*
Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia DIRECT INFLUENCE OF UBIQUITYLATION ON A TARGET PROTEIN ACTIVITY: “LOSS-OF-FUNCTION” MECHANISM REVEALED BY COMPUTATIONAL ANALYSIS |
| 10. | 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 3Novosibirsk State University, Novosibirsk, Russia PREDICTION IN CHANGES OF PROTEIN THERMODYNAMIC STABILITY UPON SINGLE MUTATIONS |
| 11. | Kochetov A.V.1*, Sarai A.2, Kolchanov N.A.1
1Institute of Cytology and Genetics, Novosibirsk, Russia 2Kyushu Institute of Technology, Dept. Biochemical Engineering and Science, Iizuka, Japan THE CONTRIBUTION OF ALTERNATIVE TRANSLATION START SITES TO HUMAN PROTEIN DIVERSITY |
| 12. | Efremov R.G.
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia COMPUTER SIMULATIONS OF PEPTIDES AND PROTEINS IN MEMBRANES: PERSPECTIVES IN DRUG DESIGN |
| 13. | Shaitan K.V., Tereshkina K.B., Levtsova O.V.
Department of Bioengineering, Faculty of Biology, M.V.Lomonosov Moscow state University, Moscow, Russia MOLECULAR DYNAMICS AND DESIGN OF TRANSMEMBRANE ION CHANNELS |
| 14. | Nicklaus M.
Center for Cancer Research, NCI/NIH, Frederick, MD, USA NEW DEVELOPMENTS AT THE NIH FOR INTEGRATION OF SMALL-MOLECULE DATABASES AND BIOINFORMATICS RESOURCES |
JULY 20
COMPARATIVE AND EVOLUTIONARY GENOMICS AND PROTEOMICS
ORAL PRESENTATIONS
| № № | AUTHOR (S ) AND TITLE OF A TALK |
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Vitreschak A.G.1*, Lyubetsky V.A.1, Gelfand M.S.1
1Institute for Information Transmission Problems of RAS, Moscow, Russia EVOLUTIONAL AND FUNCTIONAL ANALYSIS OF T-BOX REGULON IN BACTERIA. IDENTIFICATION AND CHARACTERIZATION OF NEW GENES INVOLVED IN AMINO ACID METABOLISM |
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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, MD, USA INSTANCES OF POSITIVE SELECTION AT CONSERVATIVE PROTEIN |
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Gunbin K.V., Suslov V.V., Kolchanov N.A.*
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia AROMORPHOSES AND ADAPTIVE MOLECULAR EVOLUTION: MORPHOGENS AND SIGNALING CASCADE GENES |
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Kondrashov F.A.
Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093 USA EVOLUTION OF THE GLYOXYLATE CYCLE ENZYMES IN THE METAZOA |
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Ramensky V.1*, Nurtdinov R.2, Neverov A.3, Mironov A. 2, Gelfand M. 2,4
1Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, Russia, 2Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia., 3State Scientific Center GosNIIGenetika, Russia, 4Institute for Information Transmission Problems, RAS, Moscow, Russia HUMAN GENOME POLYMORPHISM AND ALTERNATIVE SPLICING |
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Pintus S.S.1*, Fomin E.S.1, Oshurkov I.S.2, IvanisenkoV.A.1,2*
1Institute of Cytology and Genetics RAN SB, Novosibirsk, Russia 2Novosibirsk State University, Novosibirsk, Russia PHYLOGENETIC ANALYSIS OF THE P53 AND P63/P73 GENE FAMILIES |
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Sabitha.K 1, 2, Kaiser J.1, 2 *
1Genetics Department, Bhagawan Mahavir Hospital & Research Center, Masab tank, Hyderabad, India 2,* Indo American Cancer Institute & Research Center, Banjara Hills, Hyderabad, India ANALYSIS OF EGFR GENE MUTATIONS WHICH HAVE A RESPONSE TO QUINAZOLIN INHIBITORS |
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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 HUMAN-CHIMPANZEE PROPERTY-DEPENDANT COMPARISONS ON CHROMOSOMES 21 |
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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 ORTHOLGOUS GENES: PREDICTION OF SF1 BINDING SITES WITH SITECON METHOD PROVED BY EXPERIMENTAL VERIFICATION AND COMPARATIVE GENOMICS |
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Kolesnikov N.N.*, Elisafenko E.A,.Zakian S.M
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia EVOLUTION OF THE STRUCTURE OF THE XIST LOCUS IN MAMMALS |
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Perelygin A.A.*1, Zharkikh A.A.2, Brinton M.A.1
1 Biology Department, Georgia State University, Atlanta, GA, USA 2 Bioinformatics Department, Myriad Genetics, Inc., Salt Lake City, UT, USA CONCERTED EVOLUTION OF PARALOGOUS OAS1 GENES IN RODENTIA AND CETARTIODACTYLA |
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Kapitonov V.V.*, Jurka J.
Genetic Information Research Institute, Mountain View, California, USA NEW KIDS ON THE BLOCK: SELF-SYNTHESIZING DNA TRANSPOSONS |
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Simons C., Pheasant M., Makunin I.V., Mattick J.S.*
ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia. TRANSPOSON-FREE REGIONS IN MAMMALIAN GENOMES |
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Golovnina K.1, Glushkov S.*1, Blinov A.1, Mayorov V.2, Adkison L.2 , Goncharov N.1
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia; 2Mercer University School of Medicine, Macon, USA MOLECULAR PHYLOGENY OF THE GENUS TRITICUM L. |
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Karafet T. M.1,2*, Lansing J.S.2, Hammer M.F.2
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia; 2 University of Arizona, Tucson, USA IN SEARCH OF GENETIC SIGNATURE FOR THE EXPANSION OF IRRIGATION SYSTEMS IN BALI |
JULY 20
NEW APPROACHES TO BIOMOLECULAR DATA AND PROCESSES ANALYSIS/MODELING
ORAL PRESENTATIONS
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Mironov A.A.1,2,31Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia. 2Institite for Information Transmission Problems, RAS, Moscow, Russia 3State Scientific Center GosNIIGenetica, 1st Dorozhny pr., 1, Moscow, 113545, Russia; THRESHOLD SELECTION USING THE RANK STATISTICS |
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Kolpakov F.1,2*, Puzanov M.1,2, Koshukov A.1,2
1Institute of Systems Biology OOO, Novosibirsk, Russia 2Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia BIOUML: VISUAL MODELING, AUTOMATED CODE GENERATION AND SIMULATION OF BIOLOGICAL SYSTEMS |
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Hofestädt R.
Bielefeld University, AG Bioinformatics, Bielefeld, Germany AN EXTENDED BACKUS-SYSTEM FOR THE REPRESENTATION AND ANALYSIS OF DNA SEQUENCES |
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Mjolsness E.
Institute for Genomics and Bioinformatics, and Departments of Computer Science and Mathematics University of California, Irvine, CA, USA |
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Tatarinova T.1, Schumitzky A.2
1Ceres, Inc. Thousand Oaks, California, USA 2University of Southern California, Los Angeles, USA MULTIPLE COLLAPSE CLUSTERING |
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Litvinov I. I.1,3*, Finkelshtein A. V.2, Roytberg M. A.1,3*
1Institute of Mathematical Problems in Biology, Russian Academy of Sciences, Pushchino, Moscow Region, Russia; 2Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia 3Pushchino State University, Pushchino, Moscow Region, Russia OPTIMIZATION OF ACCURACY AND CONFIDENCE FOR ALIGNMENT ALGORITHMS EXPLOITING DATA ON SECONDARY STRUCTURE |
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Kozlov K.N.*1, Samsonov A.M.2
1Department of Computational Biology, State Polytechnical University, St.Petersburg, Russia 2A.F. Ioffe Physico-technical Institute of the Russian Academy of Sciences, St.Petersburg, Russia NEW MIGRATION SCHEME FOR PARALLEL DIFFERENTIAL EVOLUTION |
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Demidenko G.V.*, Matveeva I.I.
Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia ASYMPTOTIC PROPERTIES OF SOLUTIONS OF DIFFERENTIAL-DIFFERENCE EQUATIONS WITH PERIODIC COEFFICIENTS IN LINEAR TERMS |
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Mateus D.*, Gallois J.P.
CEA/LIST Saclay, F-91191 Gif sur Yvette Cedex, France SEARCHING CONSTRAINTS IN BIOLOGICAL REGULATORY NETWORKS USING SYMBOLIC ANALYSIS |
JULY 21-22
COMPUTATIONAL SYSTEMS BIOLOGY
ORAL PRESENTATIONS
| № № | AUTHOR (S ) AND TITLE OF A TALK |
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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
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia 2 Novosibirsk State University, Novosibirsk, Russia 3Institute for Genomics and Bioinformatics; University of California, Irvine, CA, USA 4Division of Biology, California Institute of Technology, Pasadena, CA, USA AGNS (ARABIDOPSIS GENENET SUPPLEMENTARY DATABASE), RELEASE 3.0 |
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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 3 Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USA 4 Division of Biology, California Institute of Technology, Pasadena, CA, USA A PROGRAM METHOD FOR INFERRING RELATIONSHIPS BETWEEN PHENOTYPIC ABNORMALITIES OF ARABIDOPSIS |
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Akberdin R.*2, Ozonov E. A.1, Mironova V.V.2, Komarov A.V.1, Omelyanchuk N. A.2
1Novosibirsk State University, Novosibirsk, Russia 2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia A CELLULAR AUTOMATON TO MODEL THE DEVELOPMENT OF SHOOT MERISTEMS OF ARABIDOPSIS THALIANA |
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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, CA, USA 4Novosibirsk State University, Novosibirsk, Russia CELLULAR-LEVEL MODELLING OF PLANT TISSUE GROWTH AND MORPHOGENESIS |
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Ratushny A.V.
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia IN SILICO CELL: HIERARCHICAL APPROACH AND GENERALIZED HILL FUNCTION METHOD FOR GENETIC SYSTEMS AND METABOLIC PATHWAYS MODELING |
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Rudenko V.M.*, Korotkov E.V.
Center of Bioengineering RAS, Moscow, Russia CONSTRUCTION OF THE HCV-HEPATOCYTE SYSTEM MODEL |
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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 SPECTRAL ANALYSIS OF GENE EXPRESSION PROFILES USING GENE NETWORKS |
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Likhoshvai V.A.
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia MOLECULAR-GENETIC SYSTEMS: SYMMETRY OF STRUCTURE AND DYNAMIC CHAOS |
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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 A GENE NETWORK MODEL WITH DIFFERENT TYPES OF REGULATION |
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Khlebodarova T.M.*, Kachko A.V., Stepanenko I.L., Tikunova N.V.
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia DATABASE GenSensor AS INFORMATIONAL SOURCE FOR DESIGN OF BIOSENSORS. EXPERIMENTAL DEVELOPMENT OF BIOSENSOR BASED ON YfiA GENE |
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Matveeva A.*, Kozlov K., Samsonova M.G.
Department of Computational Biology, Center for Advanced Studies, St. Petersburg State Polytechnical University, St. Petersburg, Russia METHODOLOGY FOR BUILDING OF COMPLEX WORKFLOWS WITH PROSTAK PACKAGE AND ISIMBIOS |
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Gunbin К.V.1*, Kogai V.V.2, Fadeev S.I.2, Omelyanchuk L.V.1
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia 2Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia A MODEL FOR SENSING THE MORPHOGENE HEDGEHOG CONCENTRATION GRADIENT |
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Galimzyanov A.V.
Department of Physicochemical Biology & Epigenetics, Ufa Research Center RAS, Ufa, RussiaGENE NETWORKS BEHAVIOR IN A SERIES OF SUCCESIVE CELL DIVISIONS |
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Milanesi L.1*, Alfieri R.1, Merelli I.1
1CNR Institute of Biomedical Technologies, Milan, Italy HCCDB: DATA MINING SYSTEM FOR HUMAN CELL CYCLE GENE |
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Olsson B.*, Gawronska B., Erlendsson B., Lindlöf A., Dura E.
School of Humanities and Informatics, University of Skövde, Sweden AUTOMATED TEXT ANALYSIS OF BIOMEDICAL ABSTRACTS APPLIED TO THE EXTRACTION OF SIGNALING PATHWAYS INVOLVED IN PLANT COLD-ADAPTATION |
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Aman E.E.1, Demenkov P.S.2, Pintus S.S.3, Nemiatov A.I.3, Apasieva N.V.1, 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 Institute of Mathematics SB RAS, Novosibirsk, Russia 3 Novosibirsk State University, Novosibirsk, Russia A COMPUTER SYSTEM FOR THE AUTOMATED RECONSTRUCTION OF MOLECULAR-GENETIC INTERACTION NETWORKS |
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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
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia 2Novosibirsk State University, Novosibirsk, Russia A GENE NETWORK OF ADIPOCYTE LIPID METABOLISM: COORDINATED INTERACTIONS BETWEEN THE TRANSCRIPTION FACTORS SREBP, LXRa AND PPARg |
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Bezmaternykh K.D.2*, Nikulichev Yu.V.1, Likhoshvai V.A.2, Matushkin Yu.G.2, Latipov A.F.1, Kolchanov N.A.2
1Institute of Theoretical and Applied Mechanics SB RAS, Novosibirsk, Russia 2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia OPTIMAL CONTROL TASKS IN TERMS OF THE GENE NETWORK MODELS |
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Kolchanov N.A.1*, Orlova G.V.1, Bachinsky A.G.2, Bajan 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
1Institute of Cytology and Genetics SB RAS, Novosibirsk; 2The State Research Center of Virology and Biotechnology VECTOR, Novosibirsk; 3Institute of Internal Medicine SB RAMS, Novosibirsk; 4Institute of Physical and Chemical Medicine MZ RF, Moscow; 5Institute of Animal Taxonomy and Ecology SB RAS, Novosibirsk; 6Institute of Automation and Electrometry SB RAS, Novosibirsk; 7Central Research Institute of Dermatovenerology MZ RF, Moscow EPI-GIS: GIS ASSISTED COMPUTER TOOLS FOR DATA ACCUMULATION, COMPUTER ANALYSIS AND MODELING IN MOLECULAR EPIDEMIOLOGY |
JULY 19
PROGRAM OF POSTER PRESENTATIONS AND COMPUTER DEMONSTRATIONS
Poster Size: The maximum size allowed for each poster
is 0.7m wide X 1.2m high.
Please note that this is a portrait (vertical) poster.
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COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICSAND TRANSCRIPTOMICS
POSTER PRESENTATIONS
Abnizova I.1, Walter K.1, Rene te Boekhorst2 , Gilks W.R.1
1Biostatistics Unit MRC, Institute of Public Health, Robinson Way, Cambridge, 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.авуьшвутлщ1, Voevoda M.I.1,2, Romashenko A.G.1
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia;
2 Institute of Therapeutics SB RAMS, Novosibirsk, Russia
A DATABASE DESIGNED FOR THE POLYMORPHISMS OF THE HUMAN CCR2 GENE.
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 LENGTH OF EXONS AND INTRONS IN GENES OF ARABIDOPSIS THALIANA AND CAENORHABDITIS ELEGANS
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
1Joint Centers for Systems Biology at Columbia University
2Los Alamos National Laboratory, Los Alamos, USA
geWorkbench: a Bioinformatic Platform for Integrated Genomics
Cheremushkin E.1,2, Konovalova T.1,3, Valeev T.1,2, Shtokalo D.1,4*, Taraskina A.1,4
1Biorainbow Group, Novosibirsk, Russia,
2Ershov Institute of Informatics Systems, Novosibirsk, Russia;
3Institute Of Cytology And Genetics, Novosibirsk, Russia;
4Mechanics and Mathematics Department, Novosibirsk State University, Novosibirsk, Russia
CISSEARCH: SOFTWARE PACKAGE FOR ANALYSIS OF GENE REGULATORY SEQUENCES
Katyshev A.I.1, Rogozin I.B.2, Konstantinov Yu.M.1*
1Siberian Institute of Plant Physiology and Biochemistry SB RAS, Irkutsk, Russia
2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
EST ANALYSIS ALLOWS TO IDENTIFY NEW SUPEROXIDE DISMUTASE GENE TRANSCRIPTS IN PLANTS AND TO ESTIMATE ALTERNATIVE POLYADENILATION AND ALTERNATIVE SPLICING EVENTS IN SOD GENE TRANSCRIPTS
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 RELATES TO MICRORNA EXPRESSION LEVELS
Khomicheva I.V.1, Levitsky V.G.1, Vishnevsky O.V.1, Savinskaya S.A.2 Omelyanchuk N.A.1
1Institute 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
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia,
2Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia
TRANSCRIPTION FACTOR BINDING SITES RECOGNITION BY THE EXPERTDISCOVERY SYSTEM BASED ON THE RECURSIVE COMPLEX SYGNALS
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
Martin D.1, Portales-Casamar E.1, Kirov S.2, Lim J.1, Brumm J.1, Snoddy J.2, Wasserman W.W.1*
1Centre for Molecular Medicine and Therapeutics, CFRI, University of British Columbia, Vancouver, BC, CANADA
2Biomedical Informatics Dept, Vanderbilt University School of Medicine, Nashville, TN, USA
* Corresponding author : wyeth@cmmt.ubc.ca
USING BIOLOGICAL KNOWLEDGE IN COMPUTATIONAL METHODS TO DISCOVER MECHANISMS OF TRANSCRIPTION REGULATION
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, Pompu S.2, Shuman H.3, Kalachikov S.M.2
1Joint Centers for Systems Biology, Columbia University, New York, USA
2Columbia Genome Center, Columbia University, New York, USA
3Department 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, MD, 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.V1,2.
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Novosibirsk State University, Novosibirsk, Russia
THE ANALYSIS OF SREBP BINDING SITES DISTRIBUTION IN GENE REGIONS BY COMBINED SITEGA AND PWM APPROACH
Ramachandran S.*, Vineet Kumar Sharma, Anu Sharma, Samir K. Brahmachari
G.N. Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Delhi, India
SIMPLE SEQUENCE (TG/CA)n REPEATS AS CIS MODULATORS OF GENE EXPRESSION
Ryazansky S.S.*
Institute of Molecular Genetics RAS, Moscow, Russia
IDENTIFICATION OF microRNAs ENCODED BY DROSOPHILA TRASPOSABLE ELEMENTS
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*
1Institute of Cell Biophysics RAS, Pushchino, Moscow region, Russian Federation
2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
Alternative transcription within PROCaryotic genes
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, Novosibirsk, Russia
*Corresponding author: planta@bionet.nsc.ru
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
1Institute for Information Transmission Problems RAS, Moscow, Russia
2Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
3State Scientific Center GosNIIGenetica, Moscow, Russia
TOOL FOR AUTOMATIC DETECTION OF CO-REGULATED GENES
TaraskinaA.S. 1,3, Cheremushkin E.S.2,3
1Mechanics and Mathematics Department, Novosibirsk State University, Novosibirsk, Russia
2Biorainbow Group, Novosibirsk, Russia
3Ershov 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 SD 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
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Novosibirsk State University, Novosibirsk, Russia
A MODEL OF THE TRANSLATIONAL INHIBITION BY MIRISC COMPLEX DESCRIBES PROTEIN SYNTHESIS VARIATIONS INDUCED BY MUTATIONS IN MAMMALIAN MIRNA SITES
Vladimirov N.V.1*, Likhoshvai V.A.1, Matushkin Yu.G.1
1Institute 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.1*, Kochetov A.V.1, Grigorovich D.A.1, Matushkin Yu.G.1
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
RSCU_COMPARER: A NEW STATISTICAL TOOL FOR PRACTICAL CODON USAGE ANALYSIS
Vityaev Е.E.*1,2, Lapardin K.A.2, Khomicheva I.V.3, Levitsky V.G.2,3
1Institute of Mathematics SB RAS, Novosibirsk, Russia
2Novosibirsk state university, Novosibirsk, Russia
3Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
TRANSCRIPTION FACTOR BINDING SITES RECOGNITION BY THE REGULARITIES MATRICES BASED ON THE NATURAL CLASSIFICATION METHOD
Zagoruiko N.G. 1*, Kutnenko O.A. 1, I.A. Borisova V.A. 1, Kiselev A.N. 1, Ptitsyn A.A.2
1Institute 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
COMPUTER DEMONSTRATIONS
Vishnevsky O.V.1,2*, Konstantinov Yu.M.3
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Novosibirsk State University, Novosibirsk, Russia
3Siberian Institute of Plant Physiology and Biochemistry SB RAS, Irkutsk, Russia
ANALYSIS OF THE NUCLEOTIDE CONTEXT OF HIGHER PLANT MITOCHONDRIAL mRNA EDITING SITES
2. COMPUTATIONAL STRUCTURAL AND FUNCTIONAL PROTEOMICS
POSTER PRESENTATIONS
Afonnikov D.A.1,2, Morozov A.V.1
1 Institute of Cytology and Genetics RAS, Novosibirsk, Russia
2 Novosibirsk State University, Novosibirsk, Russia
CONNP: WWW SERVER for the prediction of the contact numbers of the amino acid residues in proteins
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
1State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Novosibirsk
region, Russia.
2Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
MOLECULAR MODELING OF B. CEREUS HEMOLYSIN II, A PORE-FORMING PROTEIN
Baryshev P.B.1*, Afonnikov D.A.1,2, Nikolaev S.V.2
1Novosibirsk State University, Novosibirsk, Russia
2Institute of Cytology and Genetics 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, Russian Academy of Sciences, Moscow, Russia;
*Moscow State University, Vorob’evy Gory, Moscow, Russia;
CLUSTERING ANALYSIS OF CONFORMATIONAL STRUCTURES OF SHORT OLIGOPEPTIDES
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, NY, 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 RAN, 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
NizolenkoL. Ph.1*, Bachinsky A.G. 1, YaryginA. A.1, Naumochkin A.N.1, Grigorovich D.A.2
1SRC VB “Vector”, Koltsovo, Novosibirsk, Russia.
2 Institute of Cytology and Genetics, 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
dfnalex@univ.kiev.ua
THE FEATURES OF STRUCTURAL DYNAMICS OF DIFFERENT TUBULIN SUBUNITS
Pyrkov T.V.*1,2, Kosinsky Yu.A.1, Arseniev A.S.1, Priestle J.P.3, Jacoby E.3, Efremov R.G.1
1M.M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
2Moscow Institute of Physics and Technology, Moscow, Russia
3Novartis 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
P.V.Troshin1*, M.Z. Papiz1, S.M. Prince2, E. J. Daniel3, C. Morris3*, S.L.Griffiths4, J. M. Diprose5, K. Pilicheva5, J. v. Niekerk6, A. Pajon7
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*
1Institute of Cytology and Genetics, Novosibirsk, Russia
AMINO ACID PREFERENCES AT THE N-TERMINAL PART OF EUKARYOTIC PROTEINS CORRELATING WITH A SPECIFIC CONTEXTUAL ORGANIZATION OF TRANSLATION INITIATION SIGNAL
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COMPARATIVE AND EVOLUTIONARY GENOMICS AND PROTEOMICS
POSTER PRESENTATIONS
Babkin I.V.*, Shchelkunov S.N.
State Research Center of Virology and Biotechnology Vector, Koltsovo, Novosibirsk oblast, Russia
TIME SCALE OF POXVIRUS EVOLUTION
Boeva V.A.*1, Makeev V.J.2
1Moscow State University, Department of bioengineering and bioinformatics, Moscow, Russia
2GosNIIGenetika 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, GA, 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, Russian Academy of Sciences, 13 Prospekt Entuziastov, Saratov 410049, Russia
SEARCHING FOR NUCLEOTIDE SEQUENCES LIKE AGROBACTERIAL T-DNA RIGHT BORDER IN PLANT GENOMES
Golovnina K.*1, Blinov A.1, Chang L.-S.2
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia;
2Center 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
- Guryev1*, B.M.G. Smits1, J. van de Belt1, M. Verheul1, N. Hubner2and E. Cuppen1
1 Hubrecht Laboratorium, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
2 Max-Delbruck-Center for Molecular Medicine (MDC), Robert-Rossle-Str. 10, 13092, Berlin-Buch, Germany.
HAPLOTYPE BLOCK STRUCTURE IS CONSERVED ACROSS MAMMALS
Kabanova A1., Novikova O1., Gunbin K1., Fet V2., Blinov A1*.
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
2Marshall University, Huntington, WV, USA.
EVOLUTIONARY RELATIONSHIPS AND DISTRIBUTION OF THE DIFFERENT LTR RETROTRANSPOSON FAMILIES IN PLANTS
Khan M. 2, Kaiser Jamil1, 2 *
1Genetics Department, Bhagwan Mahavir Hospital and Research Center, and Research Director IACI & RC, Hyderabad, A.P, India
2School of Biotechnology, MGNIRSA (Affiliated to University of Mysore), Hyderabad, A.P, India
The Phylogenetic Analysis of Ubiquitin Conjugating Enzymes of Cancer Metasignature
Korostishevsky M.1*, Bonne’-Tamir B.1, Bentwich Z.2, Tsimanis A.2
1Department of Human Molecular Genetics & Biochemistry, Tel Aviv University, Israel
2Institute 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.*1, Likhoshvai V.A.1, Kolchanov N.A1, Matushkin Yu.G.1
1Institute 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 of SB RAS, Irkutsk, Russia
MOLECULES VERSUS MORPHOLOGY IN OLIGOCHAETA SYSTEMATICS
Novikova O.*1, Fursov M.2, Blinov A.1
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Novosibirsk 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)
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 of the 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
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Institute 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*
1Centre “Bioengineering” RAS, Moscow, Russia
2FDWSRU, USDA-ARS, MD, USA
ADAPTIVE and phylogenetic changes in chloroplast genomes
COMPUTER DEMONSTRATIONS
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
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COMPUTATIONAL SYSTEMS BIOLOGY
4.1 Modeling of Molecular Genetic Systems and Processes in Bacterial Cell
POSTER PRESENTATIONS
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
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Institute 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
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Institute 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
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Institute 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
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
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Institute 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
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Institute 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
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Institute 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
Turnaev I.I.1*, Ibragimova S.S.1, Usuda Y.2, Matsui K.2
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Institute 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.3
1Novosibirsk State University, Novosibirsk, Russia
2Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia
ABOUT RECONSTRUCTION OF REGULATORY MECHANISM OF GENE ELEMENTS’ EXPRESSION
Peñaloza-Spínola M.I., Peralta-Gil M.*, Gama-Castro S.*, Contreras-Moreira B., Santos-Zavaleta A., Martínez-Flores I. and Collado-Vides J.
Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (Center of Genomic Sciences, UNAM) Cuernavaca, Morelos; México.
REGULONDB: GOING BEYOND TRANSCRIPTIONAL REGULATION
Santos-Zavaleta A., Salgado H*., Gama-Castro S., Peralta-Gil M., Contreras-Moreira B., Peñaloza-Spínola M. I., Collado-Vides J.
Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (Center of Genomic Sciences, UNAM). Cuernavaca, Morelos; México.
REGULONDB. THE MOST IMPORTANT DATABASE IN TRANSCRIPTIONAL REGULATORY NETWORK, OPERON ORGANIZATION, AND GROWTH CONDITIONS OF ESCHERICHIA COLI K-12
4.2 Modeling of Molecular Genetic Systems and Processes in Multicellular Organisms
POSTER PRESENTATIONS
Akberdin I.R.1*, Kashevarova N.A.2, Khlebodarova T.M.1, Bazhan S.I.3, Likhoshvai V.A.1
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Novosibirsk State University, Novosibirsk, Russia
3State 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, E.A. Ananko E.A.4
1SRC VB Vector, Novosibirsk
2Institute of Internal Medicine SB RAMS, Novosibirsk
3Institute of Mathematics, SB RAS, Novosibirsk
4Institute 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
1Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia;
2Novosibirsk State University, Novosibirsk, Russia
3Institute 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
Gursky V.V.1*, Samsonov A.M.1, Reinitz J.2
1Ioffe Physico-Technical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
2 Stony Brook University, Stony Brook, New York, U.S.A.
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
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia;
3Institute of Systems Biology OOO, Novosibirsk, Russia
SIGNAL TRANSDUCTION PATHWAYS INVOLVED IN TRANSCRIPTIONAL REGULATION OF TYROSINE HYDROXYLASE.
MischenkoE.L.1, KorotkovR.O.2, IvanisenkoV.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.*, Bezmaternikh K.D
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
CONSERVED PROPERTIES OF ENZYMATIC SYSTEMS: PRENYLTRANSFERASE KINETICS
Ratushny A.V
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
MATHEMATICAL MODELING OF THE GENE NETWORK CONTROLLING HOMEOSTASIS OF INTRACELLULAR CHOLESTEROL
Sharipov R.N.1,2,3,*, Kolpakova A.F.4
1Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia;
2Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia;
3Institute of Systems Biology OOO, Novosibirsk, Russia;
4State Research Institute for Medical Problems of the North, SB RAMS, Krasnoyarsk, Russia
FORMALIZED DESCRIPTION OF NF-ΚB 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
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Institute of Computational Mathematics and Mathematical Geophysics SB RAS, Novosibirsk, Russia
RECONSTRUCTION AND STRUCTURE ANALYSIS OF APOPTOSIS GENE NETWORK IN HEPATITIS C
COMPUTER DEMONSTRATION
Fadeev S.I.1*, Korolev V.K.1, Gainova I.A.2, Medvedev3A.E.
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
THE PACKAGE STEP+ FOR NUMERICAL STUDY OF AUTONOMOUS SYSTEMS ARISING WHEN MODELING DYNAMICS OF GENETIC-MOLECULAR SYSTEMS
4.3 Modeling of Morphogenesis
POSTER PRESENTATIONS
Bukharina T.A.1, Katokhin A.V.1,2, Furman D.P.1,2
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Novosibirsk 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, Omelyanchuk N.A.1
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Institute of Informatics System SB RAS, Novosibirsk, Russia
ONTOLOGY OF ARABIDOPSIS GENE NET SUPPLEMENTARY DATABASE (AGNS), CROSS DATABASE REFERENCES TO TAIR ONTOLOGY
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, CA, 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
POSTER PRESENTATIONS
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 Β OXIDATION REGULATED BY THE PPAR TRANSCRIPTIONAL FACTORS
Demidenko G.V.1*, Khropova Yu.E.2, Kotova T.V.2
1Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia;
2Novosibirsk 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
1Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia;
2Novosibirsk State University, Novosibirsk, Russia;
matrix process modelling: On a new method of approximation of solutions of delay differential equations
Demidenko G.V.1*, Khropova Yu.E.2
1Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia
2Novosibirsk State University, Novosibirsk, Russia
matrix process modelling: ON PROPERTIES OF SOLUTIONS OF ONE DELAY DIFFERENTIAL EQUATIONS
Fadeev S.I.1*, Korolev V.K.1
1Sobolev 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
1Institute of Systems Biology OOO, Novosibirsk, Russia; 2Design Technological Institute of Digital Techniques, SB RAS, Novosibirsk, Russia; 3Institute 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
1Novosibirsk State University, Novosibirsk, Russia;
2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia;
3Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia;
ABOUT RECONSTRUCTION OF GENETIC AUTOMATE ON BASIS OF BOOLEAN DYNAMIC DATA
Likhosvai V.A.1*, Rudneva D.S.2, Fadeev S.I.3
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia;
2Novosibirsk State University, Novosibirsk, Russia;
3Sobolev 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.
1Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia;
2Novosibirsk State University, Novosibirsk, Russia
3Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
matrix process modelling: Dependence of solutions of a system of DIFferential equations on parameter
Podkolodnyy N.L1,2.*, 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
COMPUTER DEMONSTRATIONS
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
1Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia;
2Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia;
3Institute of Systems Biology OOO, Novosibirsk, Russia;
4State Research Institute for Medical Problems of the North, SB RAMS, Krasnoyarsk, Russia
FORMALIZED DESCRIPTION OF NF-ΚB 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
Kolpakov F.1,2*, Sharipov R.3,1,2, Cheremushkina E.2, Kalashnikova E.3
1Institute of Systems Biology OOO, Novosibirsk, Russia; 2Design Technological Institute of Digital Techniques, SB RAS, Novosibirsk, Russia; 3Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
BIOPATH – A NEW APPROACH TO FORMALIZED DESCRIPTION AND SIMULATION OF BIOLOGICAL SYSTEMS
-
NEW APPROACHES TO ANALYSIS/MODELING OF BIOMOLECULAR DATA AND PROCESSES
POSTER PRESENTATIONS
Arrigo P.1*, CardoP.P.2
1CNR 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 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 & 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
1Design Technological Institute of Digital Techniques, SB RAS, Novosibirsk, Russia;
2Institute of Systems Biology, Novosibirsk OOO, Russia;
3Institute of Biomedical Chemistry, RAMS, Moscow, Russia;
4Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia;
5Institute of Biomedical Technologies, Segrate (MI), Italy;
6BIOBASE GmbH, Wolfenbuettel, Germany
CYCLONET – AN INTEGRATED DATABASE ON CELL CYCLE REGULATION AND CARCINOGENESIS
Labarga A.*, Anderson M., Valentin F., Lopez R.
European Bioinformatics Institute, Hinxton, United Kingdom
e-mail: alabarga@ebi.ac.uk
*Corresponding author
WEB SERVICES AT THE EUROPEAN BIOINFORMATICS INSTITUTE
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
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
2 Novosibirsk State University, Novosibirsk, Russia
ARCHITECTURE OF SOFTWARE TOOLKIT FOR STORING AND OPERATNG WITH BIOSYSTEMS MODELS
K.N.Sarsenbaev
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 γ-RADIATION
Suslov V.V1*, Sergeev M.G.2, Yurlova N.I.3, Miginsky D.S.1,2
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Novosibirsk State University, Novosibirsk, Russia
3Institute of Animal Systematics and Ecology, SB RAS, Novosibirsk, Russia
THE ONTOLOGY OF ECOSYSTEMS
COMPUTER DEMONSTRATIONS
Kolpakov F.1,2,*, Poroikov V.3, Sharipov R.4,2,1, Milanesi L.5, Kel A.6
1Design Technological Institute of Digital Techniques, SB RAS, Novosibirsk, Russia;
2Institute of Systems Biology, Novosibirsk OOO, Russia;
3Institute of Biomedical Chemistry, RAMS, Moscow, Russia;
4Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia;
5Institute of Biomedical Technologies, Segrate (MI), Italy;
6BIOBASE 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
1Institute of Systems Biology OOO, Novosibirsk, Russia
2Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia
BIOUML: VISUAL MODELING, AUTOMATED CODE GENERATION AND SIMULATION OF BIOLOGICAL SYSTEMS