Conference program: a preliminary version

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

Beckman Research Institute of the City of Hope, Duarte, CA, USA

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.1

1Institute 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*

Institute of Thermophysics SB RAS, Novosibirsk, Russia

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

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

Institute of Cytology and Genetics RAS, Novosibirsk, Russia

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.

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
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

Bazykin G.A.1*, Dushoff J.1, Levin S.1, Kondrashov A.2

Department. of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA

National Center for Biotechnology Information, NIH, Bethesda, MD, USA

INSTANCES OF POSITIVE SELECTION AT CONSERVATIVE PROTEIN

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

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

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

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

Sabitha.K 1, 2Kaiser 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

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

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

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

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

Kapitonov V.V.*, Jurka J.

Genetic Information Research Institute, Mountain View, California, USA

NEW KIDS ON THE BLOCK: SELF-SYNTHESIZING DNA TRANSPOSONS

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

Golovnina K.1, Glushkov S.*1, Blinov A.1, Mayorov V.2, Adkison L., 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.

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

 

Mironov A.A.1,2,3

1Department 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

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

Hofestädt R.

Bielefeld University, AG Bioinformatics, Bielefeld, Germany

AN EXTENDED BACKUS-SYSTEM FOR THE REPRESENTATION AND ANALYSIS OF DNA SEQUENCES

Mjolsness E.

Institute for Genomics and Bioinformatics, and

Departments of Computer Science and Mathematics

University of California, Irvine, CA, USA
MODELING TRANSCRIPTIONAL REGULATION WITH EQUILIBRIUM MOLECULAR COMPLEX COMPOSITION

Tatarinova T.1, Schumitzky A.2

1Ceres, Inc. Thousand Oaks, California, USA

2University of Southern California, Los Angeles, USA

MULTIPLE COLLAPSE CLUSTERING

Litvinov I. I.1,3*, Finkelshtein A. V.2Roytberg 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

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

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

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
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

Ponomaryov D.1*, Omelianchuk N.2, Mironova V.2, Kolchanov N.2, Mjolsness E.3, Meyerowitz E.4

Institute of Informatics Systems SB RAS, Novosibirsk, Russia

Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

3 Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USA

Division of Biology, California Institute of Technology, Pasadena, CA, USA

A PROGRAM METHOD FOR INFERRING RELATIONSHIPS BETWEEN PHENOTYPIC ABNORMALITIES OF ARABIDOPSIS

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

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

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

Rudenko V.M.*, Korotkov E.V.

Center of Bioengineering RAS, Moscow, Russia

CONSTRUCTION OF THE HCV-HEPATOCYTE SYSTEM MODEL

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

Likhoshvai V.A.

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

MOLECULAR-GENETIC SYSTEMS: SYMMETRY OF STRUCTURE AND DYNAMIC CHAOS

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

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

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

Gunbin К.V.1*, Kogai V.V.2, Fadeev S.I.2Omelyanchuk 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

Galimzyanov A.V.

Department of Physicochemical Biology & Epigenetics, Ufa Research Center RAS, Ufa, Russia

GENE NETWORKS BEHAVIOR IN A SERIES OF SUCCESIVE CELL DIVISIONS

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

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

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

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

Kouznetsova T.N.1*, Ignatieva E.V.1, Oshchepkov D.Yu.1, Kondrakhin Y.V.1, Katokhin A.V.1,2, Shamanina M.Y.1Mordvinov 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

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

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.

 

  1. COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICSAND TRANSCRIPTOMICS

 

POSTER PRESENTATIONS

Abnizova I.1, Walter K.1, Rene te Boekhorst, 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

Institute of Cytology and Genetics RAS, Novosibirsk, Russia

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.
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

 

  1. 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

 

  1. 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

Moscow State University, Department of Bioengineering and Bioinformatics, Moscow, Russia

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

 

 

  1. 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., 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

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*

Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

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

Institute of Informatics Systems SB RAS, Novosibirsk, Russia

Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

3 Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USA

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

 

 

 

  1. 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

Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

2 A.P. Ershov Institute of Informatics Systems SB RAS

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

Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

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