Participants are welcome to pass their demonstration material to the room № 200
of the House of Scientists to the Slide Manager Dmiry Oshchepkov in 30 minutes prior to the beginning of the Sessions.
August , 7, Monday
13:00-13:30 Opening Ceremony
Greetings for participants of the Conference:
N.A. Kolchanov and R. Hofestaedt
Speech of Welcome: L.L. Kisselev
13:30-17:55 Evening Session
Computer analysis of regulatory genomic sequences
Chairpersons: E. Wingender and A. Sarai
| Title
Authors Speaker’s affiliation |
Time |
Dur. |
| Discovery and modeling of transcriptional regulatory regions
J.W. Fickett and W.W. Wasserman SmithKline Beecham Pharmaceuticals, USA |
13:30 |
0:45 |
| Composite modules – the DNA blueprints of combinatorial transcriptional regulation in multicellular organisms
A.E. Kel, O.V. Kel-Margoulis, A.G. Romashchenko, E. Wingender, Institute of Cytology and Genetics SB RAS, Russia |
14:15 |
0:25 |
| Detection of cis-acting regulatory elements in plants: a Gibbs sampling approach
G. Thijs, S. Rombauts, M. Lescot, K. Marchal, B. De Moor, Y. Moreau, Katholieke Universiteit, Belgium |
14:40 |
0:25 |
| Nucleosome formation sites: coding, organization, and function
N.A. Kolchanov and V.G. Levitsky Institute of Cytology and Genetics SB RAS, Russia |
15:05 |
0:25 |
|
Coffee break |
15:30 |
0:20 |
August , 7, Monday
13:30-17:55 Evening Session
Computer analysis of regulatory genomic sequences
Chairpersons: E. Wingender and A. Sarai
| Title
Authors Speaker’s affiliation |
Time |
Dur. |
| Point mutations within 663-666 bp of intron 6 of the human TDO2 gene, associated with a number of psychiatric disorders, damage the YY-1 transcription factor binding site
T.I. Merkulova, G.V. Vasiliev, M.P. Ponomarenko, V.F. Kobzev, Institute of Cytology and Genetics SB RAS, Russia |
15:50 |
0:25 |
| The Bsp-repeats from Canidae contain a bidirectional promoter for the RNA polymerase III potentially capable of encoding double-stranded RNA
N.S. Yudin, T.M. Naykova, Yu.V. Kondrakhin, V.F. Kobzev, Institute of Cytology and Genetics SB RAS, Russia |
16:15 |
0:25 |
| Non-canonical sequence elements as additional signals in promoter recognition by E.coli RNA polymerase
O.N. Ozoline, A.A. Deev, I.V. Arkhipov Institute of Cell biophysics RAS, Russia |
16:40 |
0:25 |
| Finding transcription factor binding sites in coregulated genes by exhaustive sequence search
Sz.M. Kielbasa, J.O. Korbel, D. Beule, J. Schuchhardt H. Herzel Institute for Theoretical Biology, Germany |
17:05 |
0:25 |
| Computer analysis of 5’UTR regions of eukaryotic mRNAs
A.V. Kochetov Institute of Cytology and Genetics SB RAS, Russia |
17:30 |
0:25 |
August, 8, Tuesday
9:00-13:10 Morning Session
Bioinformatics of DNA, RNA and protein structure.
Structural genomics.
Chairpersons: A. Adzhubei and K. Nakata
| Title
Authors Speaker’s affiliation |
Time |
Dur. |
| Structure-based target prediction and structure-function relationship of transcription factors
A. Sarai RIKEN Tsukuba Life Science Center, Japan |
9:00 |
0:45 |
| An informational system FastProt on three-dimensional structures of DNA, RNA and proteins integrated with GeneExpress
D.A. Grigorovich, V.A. Ivanisenko Institute of Cytology and Genetics SB RAS, Russia |
9:45 |
0:25 |
| An approach to structural alignment with genetic algorithm
S.J. Park and M. Yamamura Tokyo Institute of Technology, Japan |
10:10 |
0:25 |
| The module organization of the A and B boxes in the tRNA intragenic promoter
I.B. Rogozin, Yu.I. Kondrakhin, T.M. Naykova, N.S. Yudin, M.I. Voevoda, A.G. Romashchenko Institute of Cytology and Genetics SB RAS, Russia |
10:35 |
0:25 |
|
Coffee break |
11:00 |
0:20 |
| Protein primary sequences as Markov chains
C.K. Mitra and A. Sen University of Hyderabad, Hyderabad,India |
11:20 |
0:25 |
| Structure codes of RNA
I.I. Titov Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia |
11:45 |
0:25 |
| CRASP: software package for analysis of physicochemical parameters of aligned sequences of protein families
D.A. Afonnikov Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia |
12:10 |
0:25 |
| Large scale protein modelling
M.C. Peitsch, A.Adzhubei Glaxo Wellcome Experimental Research, Plan-les-Ouates, Switzerland |
12:35 |
0:35 |
August, 8, Tuesday
15:00-19:20 Evening Session
INTAS Section
Introduction to the INTAS Section: Life sciences at INTAS
I. Schmidt ( 15:00-15:20 )
Chairpersons: I. Schmidt, G.A. Nevinsky, L.I. Korochkin
| Title
Authors Speaker’s affiliation |
Time |
Dur. |
| Theoretical Design of Effective Antisense Oligonucleotides
G.A. Sczakiel University of Lubeck, Germany |
15:20 |
0:20 |
| Xenotransplantation of drosophila embryonic nerve cells into mammals brain: molecular genetic and clinical aspects
L.I. Korochkin, M.A. Alexandrova, V.N. Bashkirov, Institute of GeneBiology, Russia |
15:40 |
0:20 |
| Heat shock knowledge base
I.L. Stepanenko, V.G. Levitsky, H.C. Schroeder Institute of Cytology and Genetics SB RAS, Russia |
16:00 |
0:20 |
| Detection of location and type of single nucleoitide replacement in any amplificated region of genome. Colorimertric test systems based on ligation of tandem of short oligonucleotides
G.M. Dymshits, M.R. Kabilov, V.P. Neischtadt, Institute of Cytology and Genetics SB RAS, Russia |
16:20 |
0:20 |
| Comparative characterization of the 5’-regions of the vole, human and mouse Xist gene: conserved and repetitive sequences
N.N. Kolesnikov, T.B. Nesterova, S.Ya. Slobodyanyuk, Institute of Cytology and Genetics SB RAS, Russia |
16:40 |
0:20 |
| Lawc – a new homeyotic mutation in Drosophila which influences on fly behavior
O.B. Simonova Institute of Gene Biology, Russia |
17:00 |
0:20 |
August, 8, Tuesday
15:00-19:20 Evening Session
INTAS Section
Chairpersons: I. Schmidt, G.A. Nevinsky, L.I. Korochkin
|
Coffee break |
17:00 |
0:20 |
| Title
Authors Speaker’s affiliation |
Time |
Dur. |
| tRNA database, its history and present developements
M. Sprinzl Universitat Bayreuth, Germany |
17:20 |
0:20 |
| How DNA repair enzymes recognize DNA
G.A. Nevinsky, N.L. Vasilenko, A.A. Ishchenko, Institute of Bioorganic Chemistry SB RAS, Russia |
17:40 |
0:20 |
| Identification of optimal target sites for antisense oligonucleotides in the a-sarcin loop region of E. coli 23S rRNA
V.A. Petyuk, M.A. Zenkova, V.V. Vlassov Institute of Bioorganic Chemistry SB RAS, Russia |
18:00 |
0:20 |
| Redox modulation of DNA topoisomerase I activity in plants
Yu.M. Konstantinov, V.I. Tarasenko, I.B. Rogosin Siberian Institute of Plant Physiology and Biochemistry SB RAS, Russia |
18:20 |
0:20 |
| Distribution of histones within defined band-interband region of Drosophila melanogaster polytene chromosomes
S.A. Demakov, Yu.B. Schwartz, H. Saumweber, V.F. Semeshin, I.F. Zhimulev Institute of Cytology and Genetics SB RAS, Russia |
18:40 |
0:20 |
| Computational biochemistry of hepatocyte
O.V. Demin A.N. Belozersky Institute of Physico-Chemical Biology, Russia |
19:00 |
0:20 |
August, 9, Wednesday
9:00-13:00 Morning Session
Databases on regulatory genomic sequences and regulatory proteins
Chairpersons: O.N. Ozoline and M.S. Gelfand
| Title
Authors Speaker’s affiliation |
Time |
Dur. |
| The transpath signal transduction database: a knowledge base on signal transduction networks
F. Schacherer, C. Choi, U. Gotze, M. Krull, E. Wingender. Gesellschaft fur Biotechnologische Forschung mbH, Braunschweig, Germany |
9:00 |
0:45 |
| Receptor Database (RDB) as an analytical tool for the drug design
K. Nakata, T. Takai, T. Nakano, T. Kaminuma National Institute of Health Sciences, Tokyo, Japan |
9:45 |
0:25 |
| Transcription Regulatory Regions Database (TRRD)
E.A. Ananko, O.A. Podkolodnaya, E.V. Ignatieva, Institute of Cytology and Genetics SB RAS, Russia |
10:10 |
0:25 |
| Activated databases on DNA sites, their structure, function and activity
J.V. Ponomarenko, G.V. Orlova, M.P. Ponomarenko, Institute of Cytology and Genetics SB RAS, Russia |
10:35 |
0:25 |
|
Coffee break |
11:00 |
0:20 |
August, 9, Wednesday
9:00-13:00 Morning Session
Databases on regulatory genomic sequences and regulatory proteins
Chairpersons: O.N. Ozoline and M.S. Gelfand
| Title
Authors Speaker’s affiliation |
Time |
Dur. |
| Database on composite regulatory elements in eukaryotic genes (COMPEL)
O.V. Kel-Margoulis, A.G. Romashchenko, I.V. Deineko, Institute of Cytology and Genetics SB RAS, Russia |
11:20 |
0:25 |
| PATHO DB – a database bridging the gap between the description of gene regulatory defects and clinical application
M. Pruess, T. Meinhardt, E. Wingender Biobase Biological Databases GmbH, Germany |
11:45 |
0:25 |
| TRANSTERM – a database of RNA components and motifs
G.H. Jacobs, P.A. Stockwell, C.M. Brown University of Otago, New Zealand |
12:10 |
0:25 |
| Genomics-aided drug development: population genomics ad informatics at work
R.S. Judson
Genaissance Pharmaceuticals, USA |
12:35 |
0:25 |
August, 10, Thursday
9:00-13:00 Morning Session
Comparative and evolutionary genomics
Chairpersons: V.A. Ratner and L. Milanezi
| Title
Authors Speaker’s affiliation |
Time |
Dur. |
| Comparative approach to analysis of bacterial regulatory patterns
M.S. Gelfand, M. Baitalyuk, E.V. Koonin, P. Novichkov, E. Novichkova, E. Panina, E. Permina, A.B. Rakhmaninova, D. Rodionov, A. Vitreschak, A.A. Mironov GosNIIGenetika, Russia |
9:00 |
0:45 |
| Comparative genomics:homology based gene identification and gene structure validation
T. Wiehe, S. Gebauer-Jung, J. Abril, R. Guigo Max Planck Institute for Chemical Ecology, Germany |
9:45 |
0:25 |
| INTERPRO as a new tool for whole genome analysis. A comparitive analysis of mycobacterium tuberculosis, bacillus subtilis and escherichia coli as a case study
N.J. Mulder, W. Fleischmann, R. Apweiler European Bioinformatics Institute, UK |
10:10 |
0:25 |
| No mystery of orfans in genomics – generation of orfans in the antisense of coding sequences
P. Mackiewicz, M. Kowalczuk, A. Gierlik, D. Szczepanik, A. Nowicka, M.R. Dudek, S. Cebrat University of Wroclaw, Poland |
10:35 |
0:25 |
|
Coffee break |
11:00 |
0:20 |
August, 10, Thursday
9:00-13:00 Morning Session
Comparative and evolutionary genomics
Chairpersons: V.A. Ratner and L. Milanezi
| Title
Authors Speaker’s affiliation |
Time |
Dur. |
| Pro-Gen: Prediction of the exon-intron structure by comparison of genomic sequences
P.S. Novichkov, M.S. Gelfand, A.A. Mironov GosNIIGenetika, Russia |
11:20 |
0:25 |
| Biological role categories for regulators and mechanisms of divergence of function
M. Riley Marine Biological Laboratory, Woods Hole, USA |
11:45 |
0:25 |
| In silico’ analysis of point mutation effects on the coding region of human beta globin gene
P. Arrigo, G. Ivaldi, P.P. Cardo C.N.R. Istituto Circuiti Elettronici, Italy |
12:10 |
0:25 |
| MIRs – family of the repeats common for primates, mammals and vertabrates
E.V. Korotkov Centre of Bioengineering RAS, Russia |
12:35 |
0:25 |
August, 10, Thursday
15:00-17:50 Evening Session
Comparative and evolutionary genomics
Chairpersons: A. Mironov and E. Trifonov
| Title
Authors Speaker’s affiliation |
Time |
Dur. |
| Evolution of the code and the earliest proteins. Reconstruction from modern sequences
E. Trifonov Weizmann Institute of Science, Israel |
15:00 |
0:45 |
| Computer modeling of evolution of the genetic diversity of interacting polygenic systems and patterns of mobile genetic elements in the course of selection for the quantitative character
V.A. Ratner, L.A. Vasilyeva, E.V. Bubenshchikova, Institute of Cytology and Genetics SB RAS, Russia |
15:45 |
0:25 |
| Molecular modelling of disease-causing single-nucleotide polymorphisms in collagen
Ju.V. Milchevsky, V.E. Ramensky, B.S.Zorov, N.G. Esipova, V.G.Tumanyan Engelhardt Institute of Molecular Biology RAS, Russia |
16:10 |
0:25 |
|
Coffee break |
16:35 |
0:25 |
| Analysis of mutational hotspots in human disease genes and mutational spectra
I.B. Rogozin, V.B. Berikov, G.V. Glazko Institute of Cytology and Genetics SB RAS, Russia |
17:00 |
0:25 |
| The evolution of regulatory families in Archea and Eubacteria: a common origin of transcriptional repressors
E. Perez-Rueda and J. Collado-Vides CIFN-UNAM, Cuernavaca, Mexico |
17:25 |
0:25 |
August, 11, Friday
9:00-13:05 Morning Session
Bioinformatics of gene networks and metabolic pathways
Chairpersons: J. Collado-Vides and J.W. Fickett
| Title Authors
Speaker’s affiliation |
Time |
Dur. |
| Gene circuits and fly segments: solving an inverse problem in Drosophila
J. Reinitz Mount Sinai School of Medicine, USA |
9:00 |
0:45 |
| Modelling of gene networks dynamics
V.A. Likhoshvai, Yu.G. Matushkin, E.V. Ignatieva, A.V. Ratushny, E.A. Ananko, O.A. Podkolodnaya Institute of Cytology and Genetics SB RAS, Russia |
9:45 |
0:25 |
| Metabolic engineering electronical infrastructure for the detection of inborn errors
R. Hofestaedt Otto-von-Guericke Universitat Magdeburg, Germany |
10:10 |
0:25 |
| Application of the method of generalized threshold models for the analysis of the eukaryotic control gene subnetworks
R.N. Tchuraev, A.V. Galimzyanov Institute of Biology of URC of the RAS, Russia |
10:35 |
0:25 |
|
Coffee break |
11:00 |
0:25 |
| GeneNet database: a technology for a formalized description of gene networks
E.A. Ananko, F.A. Kolpakov, N.A. Kolchanov Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia |
11:25 |
0:25 |
| Parallel simulated annealing algorithms for gene circuits analysis
Y. Deng SUNY-Stony Brook, USA |
11:50 |
0:25 |
| Modeling of molecular regulation networks with Meta-Model
J. Cai, X. Lu, Y. Li Bioinformatics Institute, School of Information Science and technology, Tsinghua University, P.R. China |
12:15 |
0:25 |
| Bioinformatics, electronic biology and a new functional model for biological cells
W.L. Zheng Institute of Molecular Biology, Liu Hua Qiao Hospital, P.R. China |
12:40 |
0:25 |
August, 11, Friday
15:00-18:40 Evening Session
Functional Genomics
Chairpersons: J. Reinitz and I. Rogozin
| Title Authors
Speaker’s affiliation |
Time |
Dur. |
| Functional genomics: an algorithmic perspective
A. Califano IBM Computational Biology Center, USA |
15:00 |
0:45 |
| Periodic patterns in sequence organization of replication origin of Escherichia coli k-12 chromosome
G.I. Kravatskaya, N.G. Esipova VA Engelhardt Institute of Molecular Biology, Russia |
15:45 |
0:25 |
| ESTMAP: a program for ESTs mapping on a genomic sequence
L. Milanesi, I.B. Rogozin CNR-ITBA, Italy |
16:10 |
0:25 |
| BASIO: a software system for segmentation of biological sequences into domains with homogenous composition
V.E. Ramensky, V.Ju. Makeev, M.A. Roytberg, VA Engelhardt Institute of Molecular Biology RAS, Russia |
16:35 |
0:25 |
|
Coffee break |
17:00 |
0:25 |
| Complexity measures of symbolic sequences and their application to DNA analysis
N. Chuzhanova, M. Krawczak, V.D. Gusev, L.A. Nemytikova, D.N. Cooper Department of Computer Science, University of Wales, UK |
17:25 |
0:25 |
| Functional gene networks – a data management approach for bioinformatics
O. Gabrielyan, J.C. Freytag Kelman GmbH, Berlin, Germany |
17:50 |
0:25 |
| Bioinformatic system identification
R.D. King, S.M. Garrett, G.M. Coghill Department of Computer Science, University of Wales, U.K. |
18:15 |
0:25 |