RUSSIAN ACADEMY OF SCIENCES
SIBERIAN BRANCH
INSTITUTE OF CYTOLOGY AND GENETICS
PROGRAM
OF THE FIFTH
INTERNATIONAL CONFERENCE
ON BIOINFORMATICS
OF GENOME REGULATION
AND STRUCTURE
BGRS’2006
Novosibirsk, Russia
July 16–22, 2006
Novosibirsk
2006
INTERNATIONAL PROGRAM COMMITTEE
Nikolay Kolchanov Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
(Chairman of the Conference)
Ralf Hofestaedt University of Bielefeld, Germany
(Co-Chairman of the Conference)
Dagmara Furman Institute of Cytology and Genetics SB RAS, Novosibirsk,
(Conference Scientific Secretary)
Dmitry Afonnikov Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Mikhail Gelfand GosNIIGenetika, Moscow, Russia
Vadim Govorun Institute of Physicochemical Medicine, RAMS, Moscow, Russia
Reinhart Heinrich Humboldt University Berlin, Berlin, Germany
Charlie Hodgman Multidisciplinary Centre for Integrative Biology,
School of Biosciences, University of Nottingham, UK
Alexey Kochetov Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Eugene Koonin National Center for Biotechnology Information,
National Library of Medicine, National Institutes of Health, Bethesda, USA
Vassily Lyubetsky Institute for Informational Transmission Problems RAS,
Moscow, Russia
Luciano Milanesi National Research Council – Institute of Biomedical Technology, Italy
Viatcheslav Mordvinov Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Yuriy Orlov Genome Institute of Singapore, Singapore
Igor Rogozin Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Cenk Sahinalp Computing Science, Simon Fraser University, Burnaby, Canada
Maria Samsonova St.Petersburg State Polytechnic University, St.Petersburg, Russia
Akinori Sarai Kyushu Institute of Technology (KIT), Iizuka, Japan
Konstantin Skryabin Centre "Bioengineering" RAS, Moscow, Russia
Rustem Tchuraev Institute of Biology, Ufa Sci. Centre RAS, Ufa, Russia
Denis Thieffry ESIL-GBMA, Universite de la Mediterranee, Marseille, France
Jennifer Trelewicz IBM Almaden Research Center, San Jose, California, USA
Edgar Wingender UKG, University of Goettingen, Goettingen, Germany
Lev Zhivotovsky Institute of General Genetics RAS, Moscow, Russia
Jagath C. Rajapakse School of Computer Engineering,
Nanyang Technological University, Singapore
LOCAL ORGANIZING COMMITTEE
Sergey Lavryushev Institute of Cytology and Genetics, SB RAS, Novosibirsk
(Chairperson)
Ekaterina Denisova Institute of Cytology and Genetics, SB RAS, Novosibirsk
Andrey Kharkevich Institute of Cytology and Genetics, SB RAS, Novosibirsk
Galina Kiseleva Institute of Cytology and Genetics, SB RAS, Novosibirsk
Anna Onchukova Institute of Cytology and Genetics, SB RAS, Novosibirsk
Natalia Sournina Institute of Cytology and Genetics, SB RAS, Novosibirsk
2
Our sponsors
Organizers
Laboratory of Theoretical Genetics
of the Institute of Cytology and Genetics, SB RAS
Institute of Cytology and Genetics, SB RAS
Siberian Branch of the Russian Academy
of Sciences
ВА В ИЛ О ВС КО Е О Б ЩЕС Т ВО
ГЕНЕТИКОВ И СЕЛЕКЦИОНЕРОВ
Vavilov Society of Geneticists and Breeders
Scientific Council on Bioinformatics,
Siberian Branch of the Russian Academy
of Sciences
Chair of Informational Biology,
Department of Natural Sciences,
Novosibirsk State University
Grants
INTAS Grant
Russian Foundation for Basic Research
3
THE FIFTH INTERNATIONAL CONFERENCE
ON BIOINFORMATICS OF GENOME REGULATION
AND STRUCTURE (BGRS'2006)
CONFERENCE PROGRAM
SCHEDULE AT A GLANCE
The Conference Sessions will be held in the Small Conference Hall and in Music Salon
(room no. 220) of the House of Scientists
July 16, Sunday Foyer of the Small Conference Hall
10:00-14:00 Registration of the conference participants*
*Participants who come later are welcome for registration in the Organizing
Committee room (House of Scientists, room no.200) on any conference day.
12:30-14:00 Lunch
14:00
Small Conference Hall
Conference Opens:
Welcome by
Academician of the Russian Academy of Sciences Vladimir Shumny,
Director of the Institute of Cytology and Genetics, Siberian Branch
of the Russian Academy of Sciences
Greetings of
Corresponding member of the Russian Academy of Sciences, Professor
Nikolay Kolchanov and Professor Ralf Hofestaedt
14:30-18:00 PLENAR SESSION
16:00-16:30 Coffee break
19:00-23:00 Welcome party
July 17, Monday Small Conference Hall
9:30-12:45
Morning Session
COMPUTATIONAL STRUCTURAL AND FUNCTIONAL
GENOMICS
10:40-11:10 Coffee break
12:45-14:30 Lunch break
14:30-17:45 Evening Session
COMPUTATIONAL STRUCTURAL AND FUNCTIONAL
GENOMICS
16:00-16:30 Coffee break
Computer demos of this session will be available during the entire conference day
July 18, Tuesday Small Conference Hall
9:30-12:50 Morning Session
COMPUTATIONAL STRUCTURAL AND FUNCTIONAL
PROTEOMICS
10:45-11:15 Coffee break
12:50 -14:30 Lunch break
4
14:30 -17:25 Evening Session
COMPUTATIONAL STRUCTURAL AND FUNCTIONAL
PROTEOMICS
16:05-16:35 Coffee break
Computer demos of this session will be available during the entire conference day
July 19, Wednesday Foyer of the Small Conference Hall
9:30-12:30 POSTER SESSION
10:45-11:15 Coffee break
12:30-14:00 Lunch break
July 20, Thursday Small Conference Hall
9:30-12:55
Morning Session
COMPARATIVE AND EVOLUTIONARY GENOMICS
AND PROTEOMICS
10:45-11:15 Coffee break
12:55-14:30 Lunch break
14:30-18:10 Evening Session
COMPARATIVE AND EVOLUTIONARY GENOMICS
AND PROTEOMICS
16:00-16:30 Coffee break
Computer demos of this session will be available during the entire conference day
July 20, Thursday Music Salon (room no.220)
9:30-12:55
Morning Session
NEW APPROACHES TO BIOMOLECULAR DATA
AND PROCESSES ANALYSIS/MODELING
10:45-11:15 Coffee break
12:55-14:30 Lunch break
14:30-17:20 Evening Session
NEW APPROACHES TO BIOMOLECULAR DATA
AND PROCESSES ANALYSIS/MODELING
16:05-16:30 Coffee break
July 21, Friday Small Conference Hall
9:30-12:55 Morning Session
COMPUTATIONAL SYSTEMS BIOLOGY
10:45-11:15 Coffee break
12:50-14:30 Lunch break
Computer demos of this session will be available during the entire conference day
5
July 22, Saturday Small Conference Hall
9:30-12:50
Morning Session
COMPUTATIONAL SYSTEMS BIOLOGY
10:45-11:15 Coffee break
12:50-14:30 Lunch break
14:30-16:40 Evening Session
COMPUTATIONAL SYSTEMS BIOLOGY
15:20-15:50 Coffee break
Computer demos of this session will be available during the entire conference day
16:40-17:20 Closing Ceremony; Comments of Session Chairpersons
PLENAR SESSION
July 16, Sunday House of Scientists, Small Conference Hall
14:30-18:00
Co-chairpersons:
Prof. Ralf Hofestaedt, Bielefeld University, AG Bioinformatics, Bielefeld, Germany
Prof. Nikolay Kolchanov, Institute of Cytology and Genetics, Siberian Branch
of the Russian Academy of Sciences, Novosibirsk, Russia
No.
1.
2.
Author(s) and Title of Talk
Mazo I. *, Sivachenko A., Yuryev A., Daraselia N.
Ariadne Genomics, Inc., Rockville, USA
MOLECULAR NETWORKS IN MAMMALS: EXTRACTION
FROM LITERATURE AND MICROARRAY
Rodin S.N.1*, Rodin A.S.2
1
Beckman Research Institute of the City of Hope, Duarte, CA, USA
2
Human Genetics Center, School of Public Health, University of Texas,
Houston, TX, USA
GENE DUPLICATIONS IN EVOLUTION: FROM ORIGIN
OF THE GENETIC CODE TO THE HUMAN GENOME
Timeline
14:3015:15
15:1516:00
Coffee/tea break 16:00-16:30
3.
4.
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
Samsonova M.G.1, Reinitz J.2
1
St. Petersburg State Polytechnical University, St. Petersburg, Russia
2
Stony Brook University, Stony Brook, New York, USA
SYSTEMS BIOLOGY OF SEGMENT DETERMINATION
6
16:3017:15
17:1518:00
ORAL PRESENTATIONS
Dear speakers, please, plan your presentation time including 5 minutes for questions.
Only PowerPoint presentations made in Microsoft Office 2003 or earlier versions can
be accepted. Use embedded pictures and animations only; picture and animation links
to the Internet or to other files will not be accessible.
Slide projectors or overhead projectors are NOT available during the BGRS'2006
Conference.
Please, take into account that it will not be possible for you to load your presentation
during the session by yourselves. Presentations are loaded on the main computer by
the technician of the Organizing Committee only.
To ensure that the presentations are well prepared and compatible with the main
presentation computer, we strongly advice you to bring your materials as PowerPoint
files on USB device or CD disk to the Room no. 200 at the House of Scientists and
check the presentation with the technician of the Organizing Committee not later
than 30 min before the start time of the session where you are presenting. This will
prevent any confusion when loading the presentations on the main computer.
You may also bring your laptop for copying your presentation to the main
presentation computer. Use of your own laptop during your presentation is not
recommended.
If you have any questions, please do not hesitate to contact the Organizing
Committee in Room no. 200 at the House of Scientists.
7
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
No.
1.
2.
3.
Author(s) and Title of Talk
Seliverstov A.V.*, Lyubetsky V.A.
Institute for Information Transmission Problems RAS, Moscow, Russia
GENE EXPRESSION REGULATION IN ACTINOBACTERIA
AND CHLOROPLASTS
Grosse I. 1,2
1
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
2
Bioinformatics Center Gatersleben-Halle, Gatersleben, Germany
COMPUTATIONAL IDENTIFICATION OF TRANSCRIPTION FACTOR
BINDING SITES WITH VARIABLE ORDER BAYESIAN NETWORKS
Levitsky V.G.1,2*, Ignatieva E.V.1,2, Ananko E.A.1, Merkulova T.I.1
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Novosibirsk State University, Novosibirsk, Russia
THE SITEGA AND PWM METHODS APPLICATION
FOR TRANSCRIPTION FACTOR BINDING SITES RECOGNITION
IN EPD PROMOTERS
Timeline
9:309:55
9:5510:20
10:2010:40
Coffee/tea break 10:40-11:10
4.
5.
6.
7.
Shelest E.S.*1, Wingender E.1,2
1
Department of Bioinformatics, UKG, University of Göttingen, Göttingen,
Germany
2
BIOBASE GmbH, Wolfenbüttel, Germany
PROMOTER MODELING APPROACHES APPLIED TO THE
INVESTIGATION OF p63 UP- AND DOWNSTREAM PROMOTERS
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
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
Vishnevsky O.V.1,2*, Konstantinov Yu.M.3
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Novosibirsk State University, Novosibirsk, Russia
3
Siberian Institute of Plant Physiology and Biochemistry SB RAS, Irkutsk, Russia
ANALYSIS OF THE NUCLEOTIDE CONTEXT OF HIGHER PLANT
MITOCHONDRIAL mRNA EDITING SITES
12:45-14:30 Lunch break
8
11:1011:35
11:3512:00
12:0012:20
12:2012:45
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
No.
1.
2.
3.
4.
Author(s) and Title of Talk
1
1
Timeline
1,2
1,2
Omelianchuk N.A. , Khomicheva I.V. , Savinskaya S.A. , Levitsky V.G. ,
Vishnevsky O.V. 1,2, Katokhin A.V.1,2, Ponomarenko M.P.1 , Kolchanov N.A.1,2
1
Institute 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
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
Orlov Yu.L.1, Zhou J.1, Lipovich L.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
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
14:3014:55
14:5515:15
15:1515:35
15:3516:00
Coffee/tea break 16:00-16:30
5.
6.
7.
Efimov V.M.1*, Badratinov M.S.2, Katokhin A.V.2,3
1
Institute of Systematics and Ecology of Animals, SB RAS, Novosibirsk, Russia
2
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
3
Novosibirsk State University, Novosibirsk, Russia
INTERPRETATION OF RESULTS OF SOM ANALYSIS
OF MICROARRAY DATA BY PRINCIPAL COMPONENTS
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
Abhishek K.1*, Karnick H.1, Mitra P.2
1
Indian Institute of Technology Kanpur, Kanpur, India
2
Indian Institute of Technology Kharagpur, Kharagpur, India
A KNOWLEDGE AND DATA BASED HYBRID APPROACH
TO GENE CLUSTERING
9
16:3016:55
16:5517:20
17:2017:45
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
No.
1.
2.
3.
Author(s) and Title of Talk
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
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
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
Timeline
9:309:55
9:5510:20
10:2010:45
Coffee/tea break 10:45-11:15
4.
5.
6.
7.
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
Aksianov E.1*, Zanegina O.2, Alexeevski A.3, Karyagina A.4,5, Spirin S.3
1
Virology Department, Biological Faculty, Moscow State University, Moscow,
Russia
2
Bioengineering and Bioinformatics Faculty, Moscow State University,
Moscow, Russia
3
Belozersky Institute, Moscow State University, Moscow, Russia
4
N.F.Gamaleya Research Institute of Epidemiology and Microbiology, Moscow,
Russia
5
Institute of Agricultural Biotechnology, Moscow, Russia
A TOOL FOR COMPARATIVE ANALYSIS OF SOLVENT MOLECULES
IN PDB STRUCTURES
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
Safro M.*1,Tworowski D.1, Feldman A.2
1
Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
2
EML Research gGmbH, Heidelberg, Germany
HOW ARE CHARGED RESIDUES DISTRIBUTED AMONG
FUNCTIONALLY DISTINCT STRUCTURAL DOMAINS
OF AMINOACYL-tRNA SYNTHETASES?
12:50-14:30 Lunch break
10
11:1511:40
11:4012:05
12:0512:25
12:2512:50
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
No.
1.
2.
3.
4.
Author(s) and Title of Talk
I.S. 3, Korotkov R.O. 3,
1
1,3
3
Aman E.E. , Pintus S.S. , Startcev K.S. , 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
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
Demenkov P.S.1*, Aman E.E.2, Ivanisenko V.A.2,3
1
Sobolev Institute of Mathematics of the SB RAS, Novosibirsk, Russia
2
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
3
Novosibirsk State University, Novosibirsk, Russia
PREDICTION IN CHANGES OF PROTEIN THERMODYNAMIC
STABILITY UPON SINGLE MUTATIONS
Kochetov A.V.1*, Sarai A.2, Kolchanov N.A.1
1
Institute of Cytology and Genetics, Novosibirsk, Russia
2
Kyushu Institute of Technology, Dept. Biochemical Engineering and Science,
Iizuka, Japan
THE CONTRIBUTION OF ALTERNATIVE TRANSLATION START
SITES TO HUMAN PROTEIN DIVERSITY
Timeline
Ivanisenko V.A. 1, Demenkov P.S. 2, Fomin E.S. 1, Oshurkov
14:3014:55
14:5515:20
15:2015:40
15:4016:05
Coffee/tea break 16:05-16:35
5.
6.
Efremov R.G.
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow,
Russia
COMPUTER SIMULATIONS OF PEPTIDES AND PROTEINS
IN MEMBRANES: PERSPECTIVES IN DRUG DESIGN
Nicklaus M.
Center for Cancer Research, NCI/NIH, Frederick, USA
NEW DEVELOPMENTS AT THE NIH FOR INTEGRATION OF SMALLMOLECULE DATABASES AND BIOINFORMATICS RESOURCES
11
16:3517:00
17:0017:25
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
No.
1.
2.
3.
Author(s) and Title of Talk
Vitreschak A.G.1*, Lyubetsky V.A.1, Gelfand M.S.1
1
Institute 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
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
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
Timeline
9:309:55
9:5510:20
10:2010:45
Coffee/tea break 10:45-11:15
4.
5.
6.
7.
Kondrashov F.A.1*, Koonin E.V.2, Morgunov I.G.3, Finogenova T.V.3,
Kondrashova M.N.4
1
Section on Ecology, Behavior and Evolution, Division of Biological Sciences,
University of California at San Diego, La Jolla, USA
2
National Center for Biotechnology Information, National Library
of Medicine, National Institutes of Health, Bethesda, USA
3
Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS,
Pushchino, Russia
4
Institute of Theoretical and Experimental Biophysics RAS, Pushchino, Russia
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
1
Engelhardt Institute of Molecular Biology RAS, Moscow, Russia
2
Department of Bioengineering and Bioinformatics, Moscow State University,
Moscow, Russia
3
State Scientific Center GosNIIGenetika, Russia
4
Institute 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*
1
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
Novosibirsk State University, Novosibirsk, Russia
PHYLOGENETIC ANALYSIS OF THE p53 AND P63/P73 GENE FAMILIES
Sabitha K. 1, 2, Jamil K.1, 2 *
1
Genetics Department, Bhagawan Mahavir Hospital and Research Center,
Hyderabad, India
2
Indo American Cancer Institute and Research Center, Hyderabad, India
ANALYSIS OF EGFR GENE MUTATIONS WHICH HAVE A RESPONSE
TO QUINAZOLIN INHIBITORS
12:55-14:30 Lunch break
12
11:1511:40
11:4012:05
12:0512:30
12:3012:55
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
No.
1.
2.
3.
4.
Author(s) and Title of Talk
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
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
Deyneko I.V.*1,2, Kalybaeva Y.M.1, Kel A.E. 3, Blöcker H.*1, Kauer G. 4
1
Department of Genome Analysis, GBF, Braunschweig, Germany
2
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
3
BIOBASE GmbH, Wolfenbüttel, Germany
4
University of Applied Sciences, Emden, Germany
HUMAN-CHIMPANZEE PROPERTY-DEPENDANT COMPARISONS
ON CHROMOSOMES 21
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
Timeline
14:3014:55
14:5515:20
15:2015:35
15:3516:00
Coffee/tea break 16:00-16:30
5.
6.
7.
8.
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, Australia
TRANSPOSON-FREE REGIONS IN MAMMALIAN GENOMES
Golovnina K.1, Glushkov S.*1, Blinov A.1, Mayorov V.2, Adkison L.2 ,
Goncharov N.1
1
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
Mercer 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
1
Institute 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
13
16:3016:55
16:5517:20
17:2017:45
17:4518:10
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.
1.
2.
3.
Author(s) and Title of Talk
Mironov A.A.1,2,3
1
Department of Bioengineering and Bioinformatics, Moscow State University,
Moscow, Russia
2
Institite for Information Transmission Problems, RAS, Moscow, Russia
3
State Scientific Center GosNIIGenetica, Russia
THRESHOLD SELECTION USING THE RANK STATISTICS
Hofestaedt 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, USA
MODELING TRANSCRIPTIONAL REGULATION WITH EQUILIBRIUM
MOLECULAR COMPLEX COMPOSITION
Timeline
9:309:55
9:5510:20
10:2010:45
Coffee/tea break 10:45-11:15
4.
5.
6.
7.
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
Tatarinova T.1, Schumitzky A.2
1
Ceres, Inc. Thousand Oaks, California, USA
2
University of Southern California, Los Angeles, USA
MULTIPLE COLLAPSE CLUSTERING
Litvinov I. I.1,3*, Finkelshtein A. V.2, Roytberg M. A.1,3*
1
Institute of Mathematical Problems in Biology, Russian Academy
of Sciences, Pushchino, Moscow region, Russia
2
Institute of Protein Research, Russian Academy of Sciences, Pushchino,
Moscow region, Russia
3
Pushchino 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
1
Department of Computational Biology, State Polytechnical University,
St.Petersburg, Russia
2
A.F. Ioffe Physico-technical Institute of the Russian Academy of Sciences,
St.Petersburg, Russia
NEW MIGRATION SCHEME FOR PARALLEL DIFFERENTIAL
EVOLUTION
12:55-14:30 Lunch break
14
11:1511:40
11:4012:05
12:0512:30
12:3012:55
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.
1.
2.
3.
4.
Author(s) and Title of Talk
Demidenko G.V.*, Matveeva I.I.
Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia
ASYMPTOTIC PROPERTIES OF SOLUTIONS OF DIFFERENTIALDIFFERENCE 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
Labarga A.*, Anderson M., Valentin F., Lopez R.
European Bioinformatics Institute, Hinxton, United Kingdom
WEB SERVICES AT THE EUROPEAN BIOINFORMATICS INSTITUTE
Kolpakov F.1,2*, Puzanov M.1,2, Koshukov A.1,2
1
Institute of Systems Biology OOO, Novosibirsk, Russia
2
Design Technological Institute of Digital Techniques SB RAS, Novosibirsk,
Russia
BioUML: VISUAL MODELING, AUTOMATED CODE GENERATION
AND SIMULATION OF BIOLOGICAL SYSTEMS
Timeline
14:3014:55
14:5515:20
15:2015:45
15:4516:05
Coffee/tea break 16:05-16:30
5.
6.
Miginsky D.S.1,2*, Suslov V.V.1, Rasskazov D.A.1,2, Podkolodny N.L.1,
Kolchanov N.A.1,2
1
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
Novosibirsk State University, Novosibirsk, Russia
ARCHITECTURE OF SOFTWARE TOOLKIT FOR STORING
AND OPERATNG WITH BIOSYSTEMS MODELS
Lohmann M.
Cologne University Bioinformatics Center (CUBIC), Cologne, Germany
METABOLOMICS, BIOINFORMATICS, SYSTEMS BIOLOGY —
AN OVERVIEW OF RESEARCH AND TEACHING ACTIVITIES
AT CUBIC
15
16:3016:55
16:5517:20
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.
1.
2.
3.
Author(s) and Title of Talk
Golubyatnikov
Gaidov Yu.A.2, Kleshchev A.G.1, Volokitin E.P.1
1
Institute of Mathematics, SB RAS, Novosibirsk, Russia
2
Novosibirsk State University, Novosibirsk, Russia
A GENE NETWORK MODEL WITH DIFFERENT TYPES
OF REGULATION
Likhoshvai V.A.
1
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
MOLECULAR-GENETIC SYSTEMS: SYMMETRY OF STRUCTURE
AND DYNAMIC CHAOS
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
Timeline
V.P.1*,
9:309:55
9:5510:20
10:2010:45
Coffee/tea break 10:45-11:15
4.
5.
6.
7.
1,2
Rapaport F. , Zinovyev A.1,3*, Barillot E.1, Vert J.-P.2
1
Institute Curie, Bioinformatics Service, Paris, France
2
Ecole des Mines de Paris, Center for Computational Biology,
Fontainebleau, France
3
Institute of Computational Modelling SB RAS, Krasnoyarsk, Russia
SPECTRAL ANALYSIS OF GENE EXPRESSION PROFILES USING
GENE NETWORKS
Gunbin К.V.1*, Kogai V.V.2, Fadeev S.I.2, Omelyanchuk L.V.1
1
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia
A MODEL FOR SENSING THE MORPHOGENE HEDGEHOG
CONCENTRATION GRADIENT
Galimzyanov A.V.
Department of Physicochemical Biology and Epigenetics, Ufa Research Center
RAS, Ufa, Russia
GENE NETWORKS BEHAVIOR IN A SERIES OF SUCCESIVE CELL
DIVISIONS
Milanesi L.*, Alfieri R., Merelli I.
CNR Institute of Biomedical Technologies, Milan, Italy
HCCDB: DATA MINING SYSTEM FOR HUMAN CELL CYCLE GENE
12:55-14:30 Lunch break
16
11:1511:40
11:4012:05
12:0512:30
12:3012:55
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.
1.
2.
3.
Author(s) and Title of 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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Novosibirsk State University, Novosibirsk, Russia
3
Institute for Genomics and Bioinformatics; University of California, Irvine, USA
4
Division of Biology, California Institute of Technology, Pasadena, 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
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, USA
A PROGRAM METHOD FOR INFERRING RELATIONSHIPS BETWEEN
PHENOTYPIC ABNORMALITIES IN ARABIDOPSIS
Akberdin R.*2, Ozonov E.A.1, Mironova V.V.2, Komarov A.V.1, Omelianchuk N.A.2
1
Novosibirsk State University, Novosibirsk, Russia
2
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
A CELLULAR AUTOMATON TO MODEL THE DEVELOPMENT
OF SHOOT MERISTEMS IN ARABIDOPSIS THALIANA
Timeline
9:309:55
9:5510:20
10:2010:45
Coffee/tea break 10:45-11:15
4.
5.
6.
7.
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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Institute of Mathematics, SB RAS, Novosibirsk, Russia
3
School of Information and Computer Science, and Institute for Genomics
and Bioinformatics, University of California, Irvine, USA
4
Novosibirsk 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
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
12:50-14:30 Lunch break
17
11:1511:40
11:4012:05
12:0512:25
12:2512:50
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.
1.
2.
Author(s) and Title of Talk
2
E.E.1,
3
Timeline
3
1
Aman
Demenkov P.S. , Pintus S.S. , Nemiatov A.I. , Apasieva N.V. ,
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
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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Novosibirsk State University, Novosibirsk, Russia
A GENE NETWORK OF ADIPOCYTE LIPID METABOLISM:
COORDINATED INTERACTIONS BETWEEN THE TRANSCRIPTION
FACTORS SREBP, LXR AND PPAR
14:3014:55
14:5515:20
Coffee/tea break 15:20-15:50
3.
4.
2*
Bezmaternykh K.D. , Nikulichev Yu.V.1, Likhoshvai V.A.2,
Matushkin Yu.G.2, Latipov A.F.1, Kolchanov N.A.2
1
Institute of Theoretical and Applied Mechanics SB RAS, Novosibirsk, Russia
2
Institute 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, 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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk
2
The State Research Center of Virology and Biotechnology “Vector”,
Novosibirsk
3
Institute of Internal Medicine SB RAMS, Novosibirsk
4
Institute of Physical and Chemical Medicine MZ RF, Moscow
5
Institute of Animal Taxonomy and Ecology, SB RAS, Novosibirsk
6
Institute of Automation and Electrometry, SB RAS, Novosibirsk
7
Central Research Institute of Dermatovenerology MZ RF, Moscow
EPI-GIS: GIS ASSISTED COMPUTER TOOLS FOR DATA
ACCUMULATION, COMPUTER ANALYSIS AND MODELING
IN MOLECULAR EPIDEMIOLOGY
16:40- 17:20 Closing Ceremony. Summaries from session chairpersons
18
15:5016:15
16:1516:40
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
1
Biostatistics Unit MRC, Institute of Public Health, Robinson Way, Cambridge, UK
2
University 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
1
Institute 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
19
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
1
University of Hertfordshire, College Lane, Hatfield Campus,UK
2
MRC-BSU, Robinson Way, Cambridge, UK
3
Queen’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
1
Joint Centers for Systems Biology at Columbia University
2
Los 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*
1
Siberian Institute of Plant Physiology and Biochemistry, SB RAS, Irkutsk, Russia
2
Institute 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
1
Institute 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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia
TRANSCRIPTION FACTOR BINDING SITES RECOGNITION BY THE ExpertDiscovery
SYSTEM BASED ON THE RECURSIVE COMPLEX SYGNALS
20
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
1
Joint Centers for Systems Biology, Columbia University, New York, USA
2
Columbia Genome Center, Columbia University, New York, USA
3
Department 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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Novosibirsk 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
21
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*
1
Institute of Cell Biophysics RAS, Pushchino, Moscow region, Russia
2
Institute 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
1
Institute for Information Transmission Problems RAS, Moscow, Russia
2
Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
3
State Scientific Center GosNIIGenetica, Moscow, Russia
TOOL FOR AUTOMATIC DETECTION OF CO-REGULATED GENES
Taraskina A.S. 1,3, Cheremushkin E.S.2,3
1
Mechanics and Mathematics Department, Novosibirsk State University, Novosibirsk, Russia
2
Biorainbow Group, Novosibirsk, Russia
3
Ershov 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, SB 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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Novosibirsk State University, Novosibirsk, Russia
A MODEL OF THE TRANSLATIONAL INHIBITION BY MIRISC COMPLEX DESCRIBES PROTEIN
SYNTHESIS VARIATIONS INDUCED BY MUTATIONS IN MAMMALIAN miRNA SITES
22
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
1
Institute of Mathematics, SB RAS, Novosibirsk, Russia
2
Novosibirsk State University, Novosibirsk, Russia
3
Institute 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
1
Novosibirsk Center of Information Technologies "UniPro", Novosibirsk, Russia
2
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
3
Novosibirsk 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
1
Institute 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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Novosibirsk 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
1
State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Novosibirsk region,
Russia
2
Institute 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
23
Baryshev P.B.1*, Afonnikov D.A.1,2, Nikolaev S.V.2
1
Novosibirsk State University, Novosibirsk, Russia
2
Institute 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
1
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences,
Moscow, Russia
2
Department of Bioengineering, Biological Faculty, M.V. Lomonosov Moscow State University,
Moscow, Russia
3
Moscow 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 INTRAAND 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
24
Nizolenko L.Ph.1*, Bachinsky A.G. 1, Yarygin A.A.1, Naumochkin A.N.1, Grigorovich D.A.2
1
SRC VB “Vector”, Koltsovo, Novosibirsk, Russia
2
Institute 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
1
M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry Russian Academy
of Sciences, Moscow, Russia
2
Biological 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
1
M.M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry RAS,
Moscow, Russia
2
Moscow Institute of Physics and Technology, Moscow, Russia
3
Novartis 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
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*
1
Institute 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
25
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
1
Moscow State University, Department of Bioengineering and Bioinformatics, Moscow, Russia
2
GosNIIGenetika 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
1
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
Center 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*
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Marshall University, Huntington, WV, USA
EVOLUTIONARY RELATIONSHIPS AND DISTRIBUTION OF THE DIFFERENT
LTR RETROTRANSPOSON FAMILIES IN PLANTS
26
Khan M. 2, Jamil K.1, 2 *
1
Indo 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
1
Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Israel
2
Institute 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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Novosibirsk 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)
27
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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Institute 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*
1
Centre “Bioengineering” RAS, Moscow, Russia
2
FDWSRU, 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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Institute 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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Institute 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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Institute 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
28
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
1
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
Institute 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
1
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
Institute 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-ARABINOHEPTULOSONATE-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
1
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
Institute 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
29
Turnaev I.I.1*, Ibragimova S.S.1, Usuda Y.2, Matsui K.2
1
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
Institute 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
1
Novosibirsk State University, Novosibirsk, Russia
2
Sobolev 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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Novosibirsk State University, Novosibirsk, Russia
3
State 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
1
State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
2
Institute of Internal Medicine, SB RAMS, Novosibirsk
3
Institute of Mathematics, SB RAS, Novosibirsk
4
Institute 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
1
Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia
2
Novosibirsk State University, Novosibirsk, Russia
3
Institute 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
30
Gursky V.V.1*, Samsonov A.M.1, Reinitz J.2
1
Ioffe Physico-Technical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
2
Stony 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
1
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia
3
Institute 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*
1
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
Novosibirsk State University, Novosibirsk, Russia
HCV-KINET DATABASE: KINETIC PARAMETER REACTIONS AND REGULATORY
PROCESSES OF THE LIFE CYCLE OF THE HEPATITIS C VIRUS
Ratushny A.V.
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
MATHEMATICAL MODELING OF RECEPTOR MEDIATED ENDOCYTOSIS
OF LOW-DENSITY LIPOPROTEINS AND THEIR DEGRADATION IN LYSOSOMES
Ratushny A.V.
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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia
3
Institute of Systems Biology OOO, Novosibirsk, Russia
4
State 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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Institute of Computational Mathematics and Mathematical Geophysics SB RAS,
Novosibirsk, Russia
RECONSTRUCTION AND STRUCTURE ANALYSIS OF APOPTOSIS GENE NETWORK
IN HEPATITIS C
31
4.3 Modeling of morphogenesis
Bukharina T.A.1, Katokhin A.V.1,2, Furman D.P.1,2
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Novosibirsk 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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Institute 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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Institute of Mathematics SB RAS, Novosibirsk, Russia
3
School 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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Institute of Mathematics, SB RAS, Novosibirsk, Russia
3
School 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
1
Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia
2
Novosibirsk State University, Novosibirsk, Russia
MATRIX PROCESS MODELLING: ON PROPERTIES OF SOLUTIONS
OF ONE DELAY DIFFERENTIAL EQUATIONS
32
Demidenko G.V.1*, Khropova Yu.E.2, Kotova T.V.2
1
Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia
2
Novosibirsk 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
1
Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia
2
Novosibirsk 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
1
Institute of Systems Biology OOO, Novosibirsk, Russia
2
Design Technological Institute of Digital Techniques, SB RAS, Novosibirsk, Russia
3
Institute 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
1
Novosibirsk State University, Novosibirsk, Russia
2
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
3
Sobolev 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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Novosibirsk State University, Novosibirsk, Russia
3
Sobolev 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.
1
Sobolev Institute of Mathematics, SB RAS, Novosibirsk, Russia
2
Novosibirsk State University, Novosibirsk, Russia
MATRIX PROCESS MODELLING: DEPENDENCE OF SOLUTIONS
OF A SYSTEM OF DIFFERENTIAL EQUATIONS ON PARAMETER
33
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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Institute of Computational Mathematics and Mathematical Geophysics, SB RAS,
Novosibirsk, Russia
3
Institute 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
1
CNR 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 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
1
Design Technological Institute of Digital Techniques, SB RAS, Novosibirsk, Russia
2
Institute of Systems Biology, Novosibirsk OOO, Russia
3
Institute of Biomedical Chemistry, RAMS, Moscow, Russia
4
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
5
Institute of Biomedical Technologies, Segrate (MI), Italy
6
BIOBASE GmbH, Wolfenbuettel, Germany
Cyclonet — AN INTEGRATED DATABASE ON CELL CYCLE REGULATION
AND CARCINOGENESIS
34
Miginsky D.S.1,3*, Sokolov S.A.2, Labuzhsky V.V.2, Nikitin A.G.2,3
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
A.P. Ershov Institute of Informatics Systems SB RAS
3
Novosibirsk State University, Novosibirsk, Russia
OBJECT-ORIENTED APPROACH TO BIOINFORMATICS SOFTWARE RESOURCES
INTEGRATION
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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Novosibirsk State University, Novosibirsk, Russia
3
Institute of Animal Systematics and Ecology, SB RAS, Novosibirsk, Russia
THE ONTOLOGY OF ECOSYSTEMS
35
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
1
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
2
Novosibirsk State University, Novosibirsk, Russia
3
Siberian 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
1
Design Technological Institute of Digital Techniques, SB RAS, Novosibirsk, Russia
2
Institute of Systems Biology, Novosibirsk OOO, Russia
3
Institute of Biomedical Chemistry, RAMS, Moscow, Russia
4
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
5
Institute of Biomedical Technologies, Segrate (MI), Italy
6
BIOBASE 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
1
Institute of Systems Biology OOO, Novosibirsk, Russia
2
Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia
BioUML: VISUAL MODELING, AUTOMATED CODE GENERATION AND SIMULATION
OF BIOLOGICAL SYSTEMS
36
Friday, July 21
Saturday, July 22
COMPUTATIONAL SYSTEMS BIOLOGY
Fadeev S.I.1*, Korolev V.K.1, Gainova I.A.2, Medvedev3A.E.
1
Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia
2
Khristianovich Institute of Theoretical and Applied Mechanics SB RAS, Novosibirsk, Russia
3
Institute 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
1
Institute of Systems Biology OOO, Novosibirsk, Russia
2
Design Technological Institute of Digital Techniques, SB RAS, Novosibirsk, Russia
3
Institute 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
1
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
2
Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia
3
Institute of Systems Biology OOO, Novosibirsk, Russia
4
State 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
37