Of the fifth international conference on bioinformatics
The Fifth International Conference
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The Fifth International Conference
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No. |
Author(s) and Title of Talk |
Timeline |
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1. |
Mazo I. *, Sivachenko A., Yuryev A., Daraselia N. Ariadne Genomics, Inc., Rockville, USA Molecular Networks in Mammals: Extraction from Literature and Microarray |
14:30-15:15 |
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2. |
Rodin S.N.1*, Rodin A.S.2 1 Beckman Research Institute of the City of Hope, Duarte, CA, USA 2 Human Genetics Center, School of Public Health, University of Texas, Houston, TX, USA Gene duplications in evolution: From origin of the genetic code to the human genome |
15:15-16:00 |
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Coffee/tea break 16:00-16:30 | ||
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3. |
Ivanov A.S.*, Gnedenko O.V., Molnar A.A., Mezentsev Yu.V., Lisitsa A.V., Archakov A.I. V.N.Orechovich Institute of Biomedical Chemistry RAMS, Moscow, Russia PROTEIN-PROTEIN INTERACTIONS AS NEW TARGETS FOR DRUG DESIGN: INTERACTIVE LINKS BETWEEN VIRTUAL
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16:30-17:15 |
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4. |
Samsonova M.G.1, Reinitz J.2 1St. Petersburg State Polytechnical University, St. Petersburg, Russia 2 Stony Brook University, Stony Brook, New York, USA Systems biology of segment determination |
17:15-18:00 |
oral presentations
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If you have any questions, please do not hesitate to contact the Organizing Committee in Room no. 200 at the House of Scientists.
July 17, Monday House of Scientists, Small Conference Hall
Morning Session
9:30-12:45
COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICS
and transcriptomics
Co-chairpersons:
Prof. Andrey Mironov, Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
Dr. Georgii Bazykin, Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
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No. |
Author(s) and Title of Talk |
Timeline |
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1. |
Seliverstov A.V.*, Lyubetsky V.A. Institute for Information Transmission Problems RAS, Moscow, Russia Gene expression regulation in Actinobacteria and Chloroplasts |
9:30- 9:55
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2. | Grosse I. 1,21Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) 2Bioinformatics Center Gatersleben-Halle, Gatersleben, Germany COMPUTATIONAL IDENTIFICATION OF TRANSCRIPTION FACTOR BINDING SITES WITH VARIABLE ORDER BAYESIAN NETWORKS |
9:55-10:20 |
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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 |
10:20-10:40 |
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Coffee/tea break 10:40-11:10 | ||
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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 |
11:10-11:35 |
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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 |
11:35-12:00 |
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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
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12:00-12:20 |
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7. |
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 |
12:20-12:45 |
12:45-14:30 Lunch break
July 17, Monday House of Scientists, Small Conference Hall
Evening Session
14:30-18:10
COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICS
and transcriptomics
Co-chairpersons:
Prof. Vasily Lyubetsky, Institute for Information Transmission Problems,
the Russian Academy of Sciences, Moscow, Russia
Dr. Ivo Grosse, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) and Bioinformatics Center Gatersleben-Halle, Gatersleben, Germany
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No. |
Author(s) and Title of Talk |
Timeline |
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1. | 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.1,21Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia 2 Novosibirsk State University, Novosibirsk Russia REVEALING THE FUNCTIONAL-SPECIFIC TEXTUAL FEATURES OF THE microRNA SEQUENCES IN ARABIDOPSIS THALIANA |
14:30-14:55 |
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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
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14:55-15:15 |
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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 A COMPREHENSIVE QUALITY ASSESSMENT OF THE AFFYMETRIX U133A/B PROBESETS BY AN INTEGRATED GENOMIC AND CLINICAL APPROACH |
15:15-15:35 |
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4. |
Kuznetsov V.A.*, Zhou J., George J., Orlov Yu.L. Genome Institute of Singapore, Singapore GENOME-WIDE CO-EXPRESSION PATTERNS OF HUMAN
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15:35-16:00 |
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Coffee/tea break 16:00-16:30 | ||
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5. |
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 |
16:30-16:55 |
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6. |
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 |
16:55-17:20 |
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7. |
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 |
17:20-17:45 |
July 18, Tuesday House of Scientists, Small Conference Hall
Morning Session
9:30-12:50
COMPUTATIONAL STRUCTURAL AND FUNCTIONAL PROTEOMICS
Co-chairpersons:
Dr. Kaiser Jamil, Indo American Cancer Institute and Research Center,
Hyderabad, India
Dr. Roman Efremov, M.M. Shemyakin and U.A.Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Moscow, Russia
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No. |
Author(s) and Title of Talk |
Timeline |
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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
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9:30- 9:55
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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 |
9:55-10:20 |
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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 and Chemical Biology, Harvard University, Cambridge, MA, USA “STRANGE KINETICS” of UBIQUITIN Folding: interpretation in terms of a simple KINETIC MODEL |
10:20-10:45 |
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Coffee/tea break 10:45-11:15 | ||
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4. |
Afonnikov D.A.1,2 1 Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia 2 Novosibirsk State University, Novosibirsk, Russia Residue-residue contact map prediction for proteins |
11:15-11:40 |
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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 |
11:40-12:05 |
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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 |
12:05-12:25 |
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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? |
12:25-12:50 |
12:50-14:30 Lunch break
July 18, Tuesday House of Scientists, Small Conference Hall
Evening Session
14:30-17:25
COMPUTATIONAL STRUCTURAL AND FUNCTIONAL PROTEOMICS
Co-chairpersons:
Dr. Vladimir Kuznetsov, Genome Institute of Singapore, Singapore
Prof. Sergei Chekmarev, Institute of Thermophysics Siberian Branch
of the Russian Academy of Sciences, Novosibirsk, Russia
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No. |
Author(s) and Title of Talk |
Timeline |
|
1. |
Ivanisenko V.A. 1, Demenkov P.S. 2, Fomin E.S. 1, Oshurkov I.S. 3, Korotkov R.O. 3, Aman E.E. 1, Pintus S.S. 1,3, Startcev K.S. 3, Tatarnikova L.Yu. 3, Panina I.I. 3, Sobolev A.A. 3, Seleznev I.V. 3, Elohov V.Yu. 3, Golovina A.N. 3, Aknazarov Z.I. 3, Sharonova I.V. 3, Krestianova M.A. 3, Mishchenko E.L. 1, Magdysuk A.V. 3, Nemiatov A.I. 3 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 |
14:30-14:55 |
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2. |
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 |
14:55-15:20 |
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3. |
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 |
15:20-15:40 |
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4. |
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 |
15:40-16:05 |
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Coffee/tea break 16:05-16:35 | ||
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5. |
Efremov R.G. Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia Computer simulations of peptides and proteins in membranes: perspectives in drug design |
16:35-17:00 |
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6. |
Nicklaus M. Center for Cancer Research, NCI/NIH, Frederick, USA New Developments at the NIH for Integration of Small-Molecule Databases and Bioinformatics Resources |
17:00-17:25 |
July 20, Thursday House of Scientists, Small Conference Hall
Morning Session
9:30-12:55
COMPARATIVE AND EVOLUTIONARY GENOMICS AND PROTEOMICS
Co-chairpersons:
Dr. Vladimir Kapitonov, Genetic Information Research Institute, Mountain View, California, USA
Dr. Igor Makunin, ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
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No. |
Author(s) and Title of Talk |
Timeline |
|
1. |
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 |
9:30- 9:55
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2. |
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 INSTANCES OF POSITIVE SELECTION AT CONSERVATIVE PROTEIN |
9:55-10:20 |
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3. |
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 |
10:20-10:45 |
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Coffee/tea break 10:45-11:15 | ||
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4. |
Kondrashov F.A.1*, Koonin E.V.2, Morgunov I.G.3, Finogenova T.V.3, Kondrashova M.N.4 1Section on Ecology, Behavior and Evolution, Division of Biological Sciences, University of California at San Diego, La Jolla, USA 2National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA 3Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Russia 4Institute of Theoretical and Experimental Biophysics RAS, Pushchino, Russia EVOLUTION OF THE GLYOXYLATE CYCLE ENZYMES IN THE METAZOA |
11:15-11:40 |
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5. |
Ramensky V.1*, Nurtdinov R.2, Neverov A.3, Mironov A. 2, Gelfand M. 2,4 1Engelhardt Institute of Molecular Biology RAS, 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 |
11:40-12:05 |
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6. |
Pintus S.S.1*, Fomin E.S.1, Oshurkov I.S.2, IvanisenkoV.A.1,2* 1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia 2Novosibirsk State University, Novosibirsk, Russia phylogenetic analysis of the p53 and p63/p73 gene families |
12:05-12:30 |
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7. |
Sabitha K. 1, 2, Jamil K.1, 2 * 1Genetics Department, Bhagawan Mahavir Hospital and Research Center, Hyderabad, India 2Indo American Cancer Institute and Research Center, Hyderabad, India ANALYSIS OF EGFR GENE MUTATIONS WHICH HAVE A RESPONSE TO QUINAZOLIN INHIBITORS |
12:30-12:55 |
12:55-14:30 Lunch break
July 20, Thursday House of Scientists, Small Conference Hall
Evening Session
14:30-18:10
COMPARATIVE AND EVOLUTIONARY GENOMICS AND PROTEOMICS
Co-chairpersons:
Dr. Sergei Rodin, Beckman Research Institute of the City of Hope, Duarte, USA
Dr. Vassily Ramensky, Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Moscow, Russia
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No. |
Author(s) and Title of Talk |
Timeline |
|
1. |
Ignatieva E.V.*, Oshchepkov D.Yu., Klimova N.V., Vasiliev G.V., Merkulova T.I. Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Analysis of regulatory regions of orthologous genes: prediction of SF1 binding sites with SITECON method proved by experimental verification and comparative genomics |
14:30-14:55 |
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2. |
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
|
14:55-15:20 |
|
3. |
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 |
15:20-15:35 |
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4. |
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 |
15:35-16:00 |
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Coffee/tea break 16:00-16:30 | ||
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5. |
Kapitonov V.V.*, Jurka J. Genetic Information Research Institute, Mountain View, California, USA NEW KIDS ON THE BLOCK: SELF-SYNTHEsizing DNA TRAnsposons
|
16:30-16:55 |
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6. |
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, Australia Transposon-free regions in mammalian genomes |
16:55-17:20 |
|
7. |
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. |
17:20-17:45 |
|
8. |
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 |
17:45-18:10 |
July 20, Thursday House of Scientists, Music Salon (room no. 200)
Morning Session
9:30-12:55
NEW APPROACHES TO BIOMOLECULAR DATA AND PROCESSES ANALYSIS/MODELING
Co-chairpersons:
Prof. Mikhail Lavrentiev, Jr., Novosibirsk State University, Novosibirsk, Russia
Prof. Vladimir Golubyatnikov, Institute of Mathematics, Siberian Branch
of the Russian Academy of Sciences, Novosibirsk, Russia
|
No. |
Author(s) and Title of Talk |
Timeline |
|
1. | Mironov A.A.1,2,31Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia 2Institite for Information Transmission Problems, RAS, Moscow, Russia 3State Scientific Center GosNIIGenetica, Russia Threshold selection using the rank statistics |
9:30- 9:55
|
|
2. |
Hofestaedt R. Bielefeld University, AG Bioinformatics, Bielefeld, Germany An Extended Backus-System for the representation and analysis of DNA sequences |
9:55-10:20 |
|
3. |
Mjolsness E. 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 |
10:20-10:45 |
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Coffee/tea break 10:45-11:15 | ||
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4. |
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 |
11:15-11:40 |
|
5. |
Tatarinova T.1, Schumitzky A.2 1Ceres, Inc. Thousand Oaks, California, USA 2University of Southern California, Los Angeles, USA MULTIPLE COLLAPSE CLUSTERING |
11:40-12:05 |
|
6. |
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 |
12:05-12:30 |
|
7. |
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 |
12:30-12:55 |
12:55-14:30 Lunch break
July 20, Thursday House of Scientists, Music Salon (room no. 200)
Evening Session
14:30-17:20
NEW APPROACHES TO BIOMOLECULAR DATA AND PROCESSES ANALYSIS/MODELING
Co-chairpersons:
Prof. Mikhail Roytberg, Institute of Mathematical Problems in Biology,
the Russian Academy of Sciences, Pushchino, Moscow Region, Russia
Dr. Andrei Zinovyev, Institute Curie, Bioinformatics Service, Paris, France
|
No. |
Author(s) and Title of Talk |
Timeline |
|
1. |
Demidenko G.V.*, Matveeva I.I. Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia ASYMPTOTIC PROPERTIES OF SOLUTIONS OF DIFFERENTIAL-DIFFERENCE EQUATIONS WITH PERIODIC COEFFICIENTS
|
14:30-14:55 |
|
2. |
Mateus D.*, Gallois J.P. CEA/LIST Saclay, F-91191 Gif sur Yvette Cedex, France Searching constraints in biological regulatory networks using symbolic analysis |
14:55-15:20 |
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3. |
Labarga A.*, Anderson M., Valentin F., Lopez R. European Bioinformatics Institute, Hinxton, United Kingdom WEB SERVICES AT THE EUROPEAN BIOINFORMATICS INSTITUTE
|
15:20-15:45 |
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4. |
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 |
15:45-16:05 |
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Coffee/tea break 16:05-16:30 | ||
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5. |
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 ARCHITECTURE OF SOFTWARE TOOLKIT FOR STORING AND OPERATNG WITH BIOSYSTEMS MODELS |
16:30-16:55 |
|
6. |
Lohmann M. Cologne University Bioinformatics Center (CUBIC), Cologne, Germany Metabolomics, Bioinformatics, Systems Biology — An overview of research and teaching activities at CUBIC |
16:55-17:20 |
July 21, Friday House of Scientists, Small Conference Hall
Morning Session
9:30-12:55
COMPUTATIONAL SYSTEMS BIOLOGY
Co-chairpersons:
Prof. Eric Mjolsness, Institute for Genomics and Bioinformatics and Departments
of Computer Science and Mathematics, University of California, Irvine, USA
Dr. Bjorn Olsson, School of Humanities and Informatics, University of Skövde, Sweden
|
No. |
Author(s) and Title of Talk |
Timeline |
|
1. |
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 |
9:30- 9:55
|
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2. |
Likhoshvai V.A. 1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Molecular-genetic systems: symmetry of structure and dynamic chaos |
9:55-10:20 |
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3. |
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 |
10:20-10:45 |
|
Coffee/tea break 10:45-11:15 | ||
|
4. |
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 |
11:15-11:40 |
|
5. |
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 |
11:40-12:05 |
|
6. |
Galimzyanov A.V. Department of Physicochemical Biology and Epigenetics, Ufa Research Center RAS, Ufa, RussiaGENE NETWORKS BEHAVIOR IN A SERIES OF SUCCESIVE CELL DIVISIONS |
12:05-12:30 |
|
7. |
Milanesi L.*, Alfieri R., Merelli I. CNR Institute of Biomedical Technologies, Milan, Italy HCCdb: Data Mining System for Human Cell Cycle Gene |
12:30-12:55 |
12:55-14:30 Lunch break
July 22, Saturday House of Scientists, Small Conference Hall
Morning Session
9:30-12:50
COMPUTATIONAL SYSTEMS BIOLOGY
Co-chairpersons:
Prof. Ralf Hofestaedt, Bielefeld University, AG Bioinformatics, Bielefeld, Germany
Dr. Vyatcheslav Mordvinov, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
|
No. |
Author(s) and Title of Talk |
Timeline |
|
1. |
Omelianchuk N.A.1*, Mironova V.V.1, Poplavsky A.S.1, Pavlov K.S.1, Savinskaya S.A.2, Podkolodny N.L.1, Mjolsness E.D.3, Meyerowitz E.M.4, Kolchanov N.A.1 1Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia 2 Novosibirsk State University, Novosibirsk, Russia 3Institute for Genomics and Bioinformatics; University of California, Irvine, USA 4Division of Biology, California Institute of Technology, Pasadena, USA AGNS (ARABIDOPSIS GENENET SUPPLEMENTARY DATABASE), RELEASE 3.0 |
9:30- 9:55
|
|
2. |
Ponomaryov D.1*, Omelianchuk N.2, Mironova V.2, Kolchanov N.2, Mjolsness E.3, Meyerowitz E.4 1Institute of Informatics Systems, SB RAS, Novosibirsk, Russia 2Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia 3Institute for Genomics and Bioinformatics, University of California, Irvine, USA 4Division of Biology, California Institute of Technology, Pasadena, USA A PROGRAM METHOD FOR INFERRING RELATIONSHIPS BETWEEN PHENOTYPIC ABNORMALITIES IN ARABIDOPSIS |
9:55-10:20 |
|
3. |
Akberdin R.*2, Ozonov E.A.1, Mironova V.V.2, Komarov A.V.1, Omelianchuk 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 IN ARABIDOPSIS THALIANA |
10:20-10:45 |
|
Coffee/tea break 10:45-11:15 | ||
|
4. |
Nikolaev S.V.1*, Fadeev S.I.2, Penenko A.V.2, Belavskaya V.V.1, Kogay V.V.2, Mjolsness E.3, Kolchanov N.A.1,4 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 CELLULAR-LEVEL MODELLING OF PLANT TISSUE GROWTH AND MORPHOGENESIS |
11:15-11:40 |
|
5. |
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 |
11:40-12:05 |
|
6. |
Rudenko V.M.*, Korotkov E.V. Center of Bioengineering RAS, Moscow, Russia CONSTRUCTION OF THE HCV-HEPATOCYTE SYSTEM MODEL |
12:05-12:25 |
|
7. |
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 |
12:25-12:50 |
12:50-14:30 Lunch break
July 22, Saturday House of Scientists, Small Conference Hall
Evening Session
14:30-16:40
COMPUTATIONAL SYSTEMS BIOLOGY
Co-chairpersons:
Dr. Luciano Milanesi, CNR Institute of Biomedical Technologies, Milan, Italy
Dr. Mark Lohmann, Cologne University Bioinformatics Center (CUBIC), Cologne, Germany
|
No. |
Author(s) and Title of Talk |
Timeline |
|
1. |
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 |
14:30-14:55 |
|
2. |
Kouznetsova T.N.1*, Ignatieva E.V.1, Oshchepkov D.Yu.1, Kondrakhin Y.V.1, Katokhin A.V.1,2, Shamanina M.Y.1, Mordvinov V.A.1 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, LXR AND PPAR |
14:55-15:20 |
|
Coffee/tea break 15:20-15:50 | ||
|
3. |
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 |
15:50-16:15 |
|
4. |
Kolchanov N.A.1*, Orlova G.V.1, Bachinsky A.G.2, Bazhan S.I.2, Shvarts Ya.Sh.3, Golomolzin V.V.1, Popov D.Yu.1, Efimov V.M.5, Tololo I.V.6, Ananko E.A.1, Podkolodnaya O.A.1, Il’ina E.N. 4, Rogov S.I. 4, Tretiakov V.E.4, Kubanova A.A.7, Govorun V.M.4 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 |
16:15-16:40 |
16:40- 17:20 Closing Ceremony. Summaries from session chairpersons
July 19, Wednesday House of Scientists, Small Conference Hall Foyer 9:30-12:30
POSTER SESSION
Poster Size: The maximum size allowed for each poster
is 0.7m wide 1.2m high.
Please note that this is a portrait (vertical) poster.
Authors must bring their posters printed and ready, as no facilities to produce posters at the Conference are available. Organizers will provide boards and push pins to display your posters. Posters should be readable from a distance of about two to three feet—for easy reading by several people at one time.
Presentations may be posted starting from 10:00 on July 17 in the Small Conference Hall Foyer.
The posters will be displayed for the overall duration of the Conference.
A scheduled Poster Session, only one for all Conference sections, will be held on July 19 from 9:30 to 12:30 in the Small Conference Hall Foyer.
During the allotted time, presenters are expected to remain at their individual displays to be available for questions and informal discussion of the poster content.
Material should be removed no later than 13.00 on July 22.
In the case the author(s) does not take away the presentation, it will be removed and destroyed by the BGRS’2006 Organizing Committee.
If you have any questions, please do not hesitate to contact the Organizing Committee
in Room no. 200 at the House of Scientists.
POSTER PRESENTATIONS (by sections)
1. COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICS
and transcriptomics
Abnizova I.1, Walter K.1, te Boekhorst R.2 , Gilks W.R.1
1Biostatistics Unit MRC, Institute of Public Health, Robinson Way, Cambridge, UK
2University of Hertfordshire, College Lane, Hatfield Campus,UK
NEW WAY TO OBTAIN A REGULATORY MOTIF REPRESENTATION DUE TO MOTIF ABUNDANCE LEVEL
Ananko E.A.*, Kondrakhin Yu.V., Merkulova T.I.
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
PREDICTION OF INTERFERON-INDUCIBLE GENES IN HUMAN GENOME
Apasyeva N.V. 1, Yudin N.S.1*, Ignatieva E.V.1, Voevoda M.I.1,2, Romashenko A.G.1
1Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2 Institute of Intrnal Medicine, SB RAMS, Novosibirsk, Russia
A DATABASE DESIGNED FOR THE POLYMORPHISMS OF THE HUMAN CCR2 GENE
Atambaeva S.A., Ivashchenko A.T.*, Khailenko V., Boldina G., Turmagambetova A.
al-Farabi Kazakh National University, Almaty, Kazakhstan
LENGTH OF EXONS AND INTRONS IN GENES OF SOME HUMAN CHROMOSOMES
Atambaeva S.A., Ivashchenko A.T.*
al-Farabi Kazakh National University, Almaty, Kazakhstan
THE EXONS AND INTRONS LENGTHS IN ARABIDOPSIS THALIANA
AND CAENORHABDITIS ELEGANS GENES
te Boekhorst R.1*, Walter K.2, Elgar G.3, Gilks W.R.2, Abnizova I.2
1University of Hertfordshire, College Lane, Hatfield Campus,UK
2MRC-BSU, Robinson Way, Cambridge, UK
3Queen’s Mary College, London, UK
Statistical characterization of conserved non-coding elements
in VERTEBRATES
Califano A.1, Margolin A.1, Fust A.1, Floratos A.1, Badii B.1, Daly E.1, Kim F.1, Ahmady H.1, Nemenman I.1,2, Watkinson J.1, Wang K.1, Smith K.1, Kustagi M.1, Hall M.1, Banerjee N.1, Morozov P.S.1, Hanasoge S.1, Zhang X.1, Wang X.1, Li Z.1
1Joint Centers for Systems Biology at Columbia University
2Los Alamos National Laboratory, Los Alamos, USA
geWorkbench: a Bioinformatic Platform for Integrated Genomics
Katyshev A.I.1, Rogozin I.B.2, Konstantinov Yu.M.1*
1Siberian Institute of Plant Physiology and Biochemistry, SB RAS, Irkutsk, Russia
2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
IDENTIFICATION OF NEW SUPEROXIDE DISMUTASE TRANSCRIPTS IN PLANTS
BY EST ANALYSIS: ALTERNATIVE POLYADENYLATION AND SPLICING EVENTS
Kayumov A.R.*, Kirillova J. M., Mikhailova E. O., Balaban N.P., Sharipova M.R.
Kazan State University, Kazan, Russia
The prediction of regulation of subtilisin-like proteinase gene from Bacillus intermedius through its regulatory sequence analysis
Khomicheva I.V.*, Levitsky V.G., Omelianchuk N.A., Ponomarenko M.P.
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
PATTERN OF LOCALLY POSITIONED DINUCLEOTIDES IN microRNA RELATES
TO ITS ACCUMULATION LEVELS
Khomicheva I.V.1, Levitsky V.G.1, Vishnevsky O.V.1, Savinskaya S.A.2, Omelianchuk N.A.1
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
Merkulov V.M.*, Merkulova T.I.
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
STRUCTURAL VARIANTS OF BINDING SITES FOR GLUCOCORTICOID RECEPTOR
AND THE MECHANISMS OF GLUCOCORTICOID REGULATION: ANALYSIS OF GR-TRRD DATABASE
Mitra C.K.
School of Life Sciences, University of Hyderabad, Hyderabad, India
STUDIES ON TRANSCRIPTIONAL REGULATION IN DNA
Morozov P.S.1, Morozova I.N.2, Pampou S.2, Shuman H.3, Kalachikov S.M.2
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, USA
2 Institute of Mathematical Problems in Biology, Pushchino, Moscow Region, Russia
2 Institute of Molecular Biology, Moscow, Russia
OWEN-SCRIPT – AN EXTENDED TOOL FOR PAIRWISE GENOME ALIGNMENT
Proskura A.L.1*, Levitsky V.G.1,2, Ignatieva E.V.1,2
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
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, Russia
2Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
ALTERNATIVE TRANSCRIPTION WITHIN PROCARYOTIC GENES PREDICTED
BY PROMOTER-SEARCH SOFTWARE
Smetanin D.V.*, Chumak N.M.
Krasnodar Research Institute of Agriculture, Krasnodar, Russia
A STEP BEYOND PLANT TRANSCRIPT`S POLYADENYLATION SITE
Smirnova O.G.*, Ibragimova S.S., Grigorovich D.A., Kochetov A.V.
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
TGP (TransGene Promoters): A DATABASE OF BIOTECHNOLOGICALLY IMPORTANT PLANT GENE PROMOTERS
Stavrovskaya E.D.1,2, *, Makeev V.J.3, Merkeev I.V.3, Mironov A.A.1,2,3
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
Taraskina A.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
1Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2Novosibirsk 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. *, Likhoshvai V.A., Matushkin Yu.G.
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
ROLES OF CODON BIASES AND POTENTIAL SECONDARY STRUCTURES
IN mRNA TRANSLATION OF UNICELLULAR ORGANISMS
Vladimirov N.V. *, Kochetov A.V., Grigorovich D.A., Matushkin Yu.G.
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
RSCU_COMPARER: A NEW STATISTICAL TOOL FOR PRACTICAL ANALYSIS
OF CODON USAGE
Vityaev Е.E.*1,2, Lapardin K.A.2, Khomicheva I.V.3, Levitsky V.G.2,3
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
Volod’ko V.B.1, Shuvaev R.Yu.1, Ulyashin A.V.1, Novikova O.S.2, Matushkin Yu.G.2,3
1Novosibirsk Center of Information Technologies "UniPro", Novosibirsk, Russia
2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
3Novosibirsk State University, Novosibirsk, Russia
GenomeBrowser – software for visual sequence analysis
Zagoruiko N.G. 1*, Kutnenko O.A. 1, Borisova I.A. 1, Kiselev A.N. 1, Ptitsyn A.A.2
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
2. COMPUTATIONAL STRUCTURAL AND FUNCTIONAL PROTEOMICS
Afonnikov D.A.1,2, Morozov A.V.1
1Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2Novosibirsk State University, Novosibirsk, Russia
CONNP: THE PREDICTION OF THE CONTACT NUMBERS OF THE AMINO ACID RESIDUES IN PROTEINS USING NEURAL NETWORK REGRESSION
Aman E.E. *, Demenkov P.S., Ivanisenko V.A.
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
ANALYSIS OF THE TERTIARY STRUCTURE OF THE PPAR AND RXR TRANSCRIPTIONAL FACTORS AND THEIR MUTANT VARIANTS
Bakulina A.Yu.*1, Sineva E.V.2, Solonin A.S.2, Maksyutov A.Z.1
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, SB RAS, Novosibirsk, Russia
Identification and structure-functional analysis of the specificity determining residues of the alpha subunits
of the proteosomal complex
Batsianovsy A.V.*, Vlasov P.K.
Engelhard Institute of Molecular Biology, RAS, Moscow, Russia
*Moscow State University, Moscow, Russia
Clustering analysis of conformational structures
of short oligopeptides
Chugunov A.O.1,2,*, Novoseletsky V.N.1,3, Efremov R.G.1
1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
2Department of Bioengineering, Biological Faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
3Moscow Institute of Physics and Technology (State University), Moscow region, Russia
A METHOD TO ASSESS CORRECT/MISFOLDED STRUCTURES OF TRANSMEMBRANE DOMAINS OF MEMBRANE PROTEINS
Efimov A.V., Brazhnikov E.V., Kondratova M.S.
Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow region, Russia
effect of the structural context on specificity of intra-
and interhelical interactions in proteins
Dulko V., Feranchuk S.
United Institute of Informatics Problems of the National Academy of Sciences of Belarus,
Minsk, Belarus
Dynamic Programming Algorithm Parallization For Protein Folding
Gou Z., Hwang S., Kuznetsov I.B.*
Gen*NY*sis Center for Excellence in Cancer Genomics, University at Albany, Rensselaer,
USA
SEQUENCE-BASED PREDICTION OF DNA-BINDING SITES ON DNA-BINDING PROTEINS
Ivanisenko V.A.1,2*, Ivanisenko T.V.3, Sharonova I.V.2, Krestyanova M.A.2, Ivanisenko N.V.2, Grigorovich D.A.1
1 Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2 Novosibirsk State University, Novosibirsk, Russia
3 Siberian State University of Telecommunications and Information Sciences, Novosibirsk, Russia
PDBSite DATABASE AND PDBSiteScan TOOL: RECOGNITION OF FUNCTIONAL SITES
IN PROTEIN 3d STRUCTURE AND TEMPLATE-BASED DOCKING
Konshina A.G.*, Dubinnyi M.A., Efremov R.G.
Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia
Structural determinants of cardiotoxins’ membrane binding:
a molecular modeling approach
Nizolenko L.Ph.1*, Bachinsky A.G. 1, Yarygin A.A.1, Naumochkin A.N.1, Grigorovich D.A.2
1SRC VB “Vector”, Koltsovo, Novosibirsk, Russia
2Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
PROF_PAT: THE UPDATED DATABASE OF PROTEIN FAMILY PATTERNS.
CURRENT STATUS
Nyporko A.Yu.*, Blume Ya.B.
Institute of Cell Biology and Genetic Engineering of NAS of Ukraine, Kiev, Ukraine
THE FEATURES OF STRUCTURAL DYNAMICS OF DIFFERENT TUBULIN SUBUNITS
Polyansky A.A.*1,2, Aliper E.T.1,2, Volynsky P.E.1, Efremov R.G.1
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
Action of membrane-active peptides on explicit lipid bilayers. Role
of specific peptide-lipid interactions in membrane destabilization
Pyrkov T.V.*1,2, Kosinsky Yu.A.1, Arseniev A.S.1, Priestle J.P.3, Jacoby E.3, Efremov R.G.1
1M.M. Shemyakin and 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
Slyadnikov E.E.
Informatization Problems Department of Tomsk Scientific Centre, SB RAS, Tomsk, Russia
Microscopic model of conformation degrees of freedom cytoskeleton microtubule and its structural analog in optics
Troshin P.V.1*, Papiz M.Z.1, Prince S.M.2, Daniel E.J.3, Morris C.3*, Griffiths S.L.4,
Diprose J.M.5, Pilicheva K.5, Niekerk J.V.6, Pajon A.7
1*Membrane Protein Structure Initiative, CCLRC Daresbury Laboratory, UK
2 Faculty of Life Sciences, University of Manchester, Sackville St., Manchester, UK
3 Protein information Management System, CCLRC Daresbury Laboratory, UK
4York Structural Biology Laboratory, University of York, UK
5Oxford Protein Production Facility, Division of Structural Biology, University of Oxford, UK
6Scottish Structural Proteomics Facility, University of Dundee, UK
7European 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, SB RAS, Novosibirsk, Russia
AMINO ACID PREFERENCES AT THE N-TERMINAL PART OF EUKARYOTIC PROTEINS CORRELATING WITH A SPECIFIC CONTEXTUAL ORGANIZATION OF TRANSLATION INITIATION SIGNAL
3. Comparative and evolutionary genomics AND PROTEOMICS
Babkin I.V.*, Shchelkunov S.N.
State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Novosibirsk region, Russia
Time Scale of Poxvirus Evolution
Boeva V.A.*1, Makeev V.J.2
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, USA
SEARCH FOR MULTI-SNP DISEASE ASSOCIATION
Bukin Y.S.*, Pudovkina T.A.
Limnological Institute of SB RAS, Irkutsk, Russia
The models of population dynamics as tool for studying
of genetic polymorphism of Baikalian polychaets
Chumakov M.I., Mazilov S., Zotova T.V.
Institute of Symbiology RAS, Saratov, Russia
Searching for nucleotide sequences like agrobacterial T-DNA right border in plant genomes
Golovnina K.*1, Blinov A.1, Chang L.-S.2
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
Guryev V.1*, Smits B.M.G.1, van de Belt J. 1, Verheul M.1, Hubner N.2 , Cuppen E.1
1 Hubrecht Laboratorium, Utrecht, The Netherlands
2 Max-Delbruck-Center for Molecular Medicine (MDC), Berlin-Buch, Germany
HAPLOTYPE BLOCK STRUCTURE IS CONSERVED ACROSS MAMMALS
Kabanova A1., Novikova O1., Gunbin K1., Fet V2., Blinov A.1*
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, Jamil K.1, 2 *
1Indo American Cancer Institute and Research Centre, Hyderabad, India
2 School of Biotechnology, (MGNIRSA,) University of Mysore, Mysore, India
The Phylogenetic Analysis of Ubiquitin Conjugating Enzymes
of Cancer Metasignature
Korostishevsky M.1*, Bonne’-Tamir B.1, Bentwich Z.2, Tsimanis A.2
1Department of Human Molecular Genetics and 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.*, Likhoshvai V.A., Kolchanov N.A, Matushkin Yu.G.
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
EVOLUTIONARY CONSTRUCTOR: A PACKAGE FOR MODELING COEVOLUTION
OF UNICELLULAR ORGANISMS
Lashin S.A.*, Likhoshvai V.A., Kolchanov N.A., Matushkin Yu.G.
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
MODELING OF HORIZONTAL GENE TRANSFER IN PROKARYOTIC POPULATIONS WITH THE “EVOLUTIONARY CONSTRUCTOR” PROGRAM PACKAGE
Liventseva V.*, Kaygorodova I.
Limnological Institute, SB RAS, Irkutsk, Russia
Molecules versus morphology in Oligochaeta systematics
Novikova O.*1, Fursov M.2, Blinov A.1
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 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
phylogenetic changes in chloroplast genomes
4. Computational systems biology
4.1 Modeling of Molecular Genetic Systems and Processes in Bacterial Cell
Khlebodarova T.M.1, Ananko E.A.1*, Nedosekina E.A.1, Podkolodnaya O.A.1, Poplavsky A.S.1, Smirnova O.G.1, Ibragimova S.S.1, Mishchenko E.L.1, Stepanenko I.L.1, Ignatieva E.V.1, Proskura A.L.1, Nishio Y.2, Imaizumi A.2, Usuda Y.2, Matsui K.2, Podkolodny N.L.1, Kolchanov N.A.1
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.2
1Novosibirsk State University, Novosibirsk, Russia
2Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia
ABOUT RECONSTRUCTION OF REGULATORY MECHANISM
OF GENE ELEMENTS’ EXPRESSION
4.2 Modeling of Molecular Genetic Systems and Processes in Multicellular Organisms
Akberdin I.R.1*, Kashevarova N.A.2, Khlebodarova T.M.1, Bazhan S.I.3, Likhoshvai V.A.1
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, Ananko E.A.4
1State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
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
2Stony Brook University, Stony Brook, New York, USA
APPROXIMATE STATIONARY ATTRACTORS IN DROSOPHILA GAP GENE CIRCUITS
IN THE LIMIT OF STEEP-SIGMOID INTERACTIONs
Kalashnikova E.V.1, Dymshits G. M.1, Kolpakov F.A.2,3
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
Mischenko E.L.1, Korotkov R.O.2, Ivanisenko V.A.1,2*
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2Novosibirsk State University, Novosibirsk, Russia
HCV-KINET DATABASE: KINETIC PARAMETER REACTIONS AND REGULATORY PROCESSES OF THE LIFE CYCLE OF THE HEPATITIS C VIRUS
Ratushny A.V.
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
MATHEMATICAL MODELING OF RECEPTOR MEDIATED ENDOCYTOSIS
OF LOW-DENSITY LIPOPROTEINS AND THEIR DEGRADATION IN LYSOSOMES
Ratushny A.V.
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
MATHEMATICAL MODELING OF THE GENE NETWORK CONTROLLING HOMEOSTASIS OF INTRACELLULAR CHOLESTEROL
Ratushny A.V.*, Bezmaternikh K.D
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
CONSERVED PROPERTIES OF ENZYMATIC SYSTEMS: PRENYLTRANSFERASE KINETICS
Sharipov R.N.1,2,3,*, Kolpakova A.F.4
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
Formal description of NF-B pathway, its role in inflammation, inhibition of apoptosis, carcinogenesis, and ways of inactivation
for prediction of new targets for anti-inflammatory and anti-cancer treatment
Stepanenko I.L1*., Podkolodnaya N.N.1, Paramonova N.V.1, Podkolodny N.L.1,2
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
4.3 Modeling of morphogenesis
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, Omelianchuk N.A.1
1Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2Institute of Informatics System,
tait SB RAS, Novosibirsk, Russia
ONTOLOGY OF ARABIDOPSIS GENE NET SUPPLEMENTARY DATABASE (AGNS), CROSS DATABASE REFERENCES TO TAIR ONTOLOGY
Nikolaev S.V.1*, Fadeev S.I.2, Kogay V.V.2, Mjolsness E.3, Kolchanov N.A.1
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
A SYSTEM FOR SIMULATION OF 2D PLANT TISSUE GROWTH AND DEVELOPMENT
Ponomaryov D.1*, Omelianchuk N.2, Kolchanov N.2, Mjolsness E.3, Meyerowitz E.4
1 Institute of Informatics Systems, SB RAS, Novosibirsk, Russia
2 Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
3 Institute for Genomics and Bioinformatics, University of California, Irvine, USA
4 Division of Biology, California Institute of Technology, Pasadena, CA, USA
Semantically rich ontology of anatomical structure
and development for Arabidopsis thaliana L.
4.4 Gene networks theory: mathematical problems and software
Aman E.E.*, Levitsky V.G., Ignatieva E.V.
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
RECONSTRUCTION AND COMPUTER ANALYSIS OF THE GENE NETWORK
OF FATTY ACID -OXIDATION REGULATED BY THE PPAR TRANSCRIPTIONAL FACTORS
Demidenko G.V.1*, Khropova Yu.E.2
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
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
Fadeev S.I.*, Korolev V.K.
Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia
PROGRAM PACKAGE HGNET FOR COMPUTATIONAL INVESTIGATION
OF HYPOTHETICAL GENE NETWORKS
Klishevich M.A.*, Kogai V.V., Fadeev S.I.
Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia
RESEARCH OF CYCLIC GENE NETWORK CIRCUITS WITH NEGATIVE TYPE
OF REGULATION
Kolpakov F.1,2*, Sharipov R.3,1,2, Cheremushkina E.2, Kalashnikova E.3
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
ON THE RECONSTRUCTION OF GENETIC AUTOMATE ON THE BASIS
OF BOOLEAN DYNAMIC DATA
Likhoshvai V.A.1*, Rudneva D.S.2, Fadeev S.I.3
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
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
Tchuraev R.N.
Department of Physicochemical Biology and Epigenetics, Ufa Research Center, RAS, Ufa, Russia
RESEARCH ON BEHAVIOR OF GOVERNING GENE/EPIGENE NETWORKS
AS A PROBLEM OF CELLULAR AUTOMATA IDENTIFICATION
5. NEW APPROACHES TO ANALYSIS/MODELING OF BIOMOLECULAR DATA
AND PROCESSES
Arrigo P.1*, Cardo P.P.2
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
Axenovich M.A.
Department of Mathematics, Iowa State University, Ames, USA
Edit distance in combinatorial structures
Axenovich T.I.
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
Graph theory algorithm for solution of computational problems
of gene mapping
Huang Shaoqing *, Cui Yini
College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
UNEQUALLY SPACED SAMPLING MAPPING OF QTL
Kolpakov F.1,2,*, Poroikov V.3, Sharipov R.4,2,1, Milanesi L.5, Kel A.6
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
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
Object-oriented approach to bioinformatics software resources integration
Sarsenbaev K.N.
Institute of Radiation Safety and Ecology, Kurchatov, Kazakhstan
Use molecular markers for differentiation populations of Stipa capillata growing in the regions with high chronical doses
of -radiation
Suslov V.V1*, Sergeev M.G.2, Yurlova N.I.3, Miginsky D.S.1,2
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 (by sections)
Computer demos will be available during the entire conference day
for the appropriate sections
Munday, July 17
COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICS
and transcriptomics
Vishnevsky O.V.1,2*, Konstantinov Yu.M.3
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
Thursday, July 20
Comparative and evolutionary genomics AND PROTEOMICS
Chupov V.S.*, Machs E.M.
Komarov Botanical institute RAS, St.Petersburg, Russia
Variations in nucleotide composition of the region ITS1-5.8S rDNA-ITS2
in evolutionary advanced and evolutionary static branch
of the Monocotyledonous plants
NEW APPROACHES TO ANALYSIS/MODELING OF BIOMOLECULAR DATA AND PROCESSES
Kolpakov F.1,2,*, Poroikov V.3, Sharipov R.4,2,1, Milanesi L.5, Kel A.6
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
Friday, July 21
Saturday, July 22
Computational systems biology
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
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
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-B pathway, its role in inflammation, inhibition of apoptosis, carcinogenesis, and ways of inactivation
for prediction of new targets for anti-inflammatory
and anti-cancer treatment
meeting -> Program description
meeting -> Iea shcp/pvps working Group on pv/t solar Systems
meeting -> Office of the collector: jagatsinghpur (st & sc development Section)
meeting -> World meteorological organization
meeting -> WG/hwsor action item summary (Current as of 28 Feb 2013)
meeting -> Review of the past hurricane season
meeting -> Review of the past hurricane season reports of hurricanes, tropical storms, tropical disturbances and related flooding during
meeting -> Town of seabrook island
meeting -> World meteorological organization
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