Day 0. Monday, July 21st 

Moscow State University, Department of Bioengineering and Bioinformatics, 1st floor

15:00

19:00

REGISTRATION 

Day 1. Tuesday, July 22nd 

9:00

15:00

REGISTRATION (1st floor)

9:00

10:00

Morning coffee (2nd floor)

10:00

11:15

OPENING 2nd floor, room 221

10:00

10:30

SPEECHES

10:30

11:15

James W. Fickett (AstraZeneca, USA) Systems biology and drug discovery 

11:15

11:30

Coffee break (2nd floor)

11:30

13:00

Algorithms (Chairs: M. Regnier, N.A. Kolchanov) 2nd floor, room 221

11:30

12:15

Mark Borodovsky (Georgia Institute of Technology, USA) Are there better Markov and Hidden Markov models for gene discovery and function prediction?

12:15

13:00

Eleazar Eskin (Hebrew University, Israel) A unified framework for motif finding: finding position specific scoring matrices using patterns with mismatches

13:00

14:30

Lunch (Main University building, ground floor, dining room No. 1 (recommended))

14:30

16:45

Theory and applications (Chairs: J. Fickett, V.A. Lyubetsky) 2nd floor, room 221

14:30

15:00

Mireille Regnier (INRIA, France) Structured motifs statistics

15:00

15:30

Alexey G. Vitreschak (Institute for Problems of Information Transmission, Moscow) Identification of RNA 5'UTR regulatory elements and prediction of RNA riboswitch mechanism of regulation of vitamin biosynthetic and transport genes in bacteria

15:30

15:45

Coffee break (2nd floor)

15:45

16:15

N.A. Kolchanov (Institute of Cytology and Genetics, Novosibirsk) GeneNet Discovery: gene networks reconstruction, analysis and modeling

16:15

16:45

Maxim G. Barenboim (George Mason University, USA) A Laboratory Information Management System (LIMS) for a small-scale single nucleotide polymorphism detection

16:45

18:15

POSTERS 4th floor, room 406 and around

18:15

19:30

WELCOME RECEPTION (bad weather: 4th floor, room 403 and around; good weather: outside)

Day 2. Wednesday, July 23rd

9:00

9:30

Morning coffee (2nd floor)

9:30

11:00

Industry (Chairs: D. Frishman, A.A. Mironov) 2nd floor, room 221

9:30

10:15

Wanda Andreoni (IBM, Switherland) Computational Bioscience @ IBM Research

10:15

11:00

Azat Badretdinov (Accelrys Inc., USA) Informatics solutions for pharmacogenomics in a high throughput environment – Discovery Studio GeneAtlas(TM) and AtlasStore(TM)

11:00

11:30

Coffee break (2nd floor)

11:30

13:00

Regulation (Chair: E. Eskin, A. Kochetov) 2nd floor, room 221

11:30

12:00

M. Gelfand (GosNIIGenetika, Moscow) Comparative genomics of regulatory interactions in prokaryotes

12:00

12:30

V. Makeev (GosNIIGenetika, Moscow) Reconstruction of regulatory pathways in eukaryotes using clusters of transcription factor binding sites

12:30

13:00

M. Laessig (Universitat zu Koeln, Germany) Rapid evolution of gene regulation

13:00

14:30

Lunch (Main University building, ground floor, dining room No. 1 (recommended))

Wednesday, Track 2.I. EVOLUTION

14:30

16:00

Models and trees (Chair: M. Borodovsky, N.K. Yankovsky) 4th floor, room 403

14:30

15:00

Peter F. Arndt (Cologne University, Germany) Distinct changes of genomic biases in nucleotide substitution at the time of mammalian radiation

15:00

15:30

P. Novichkov (Moscow State University, Moscow) Detection of horizontal gene transfer events by testing hypothesis of molecular clock

15:30

16:00

Vladimir V. Vyugin (Institute for Information Transmission Problems, Moscow) Complex phylogenetic analysis of the evolutionary history for some prokaryotic gene families

16:00

16:30

Coffee break (4th floor, room 431, 442)

16:30

18:00

SNPs (Chairs: M. Barenboim, M. Samsonova) 4th floor, room 403

16:30

17:00

Fyodor A. Kondrashov (Nation Center for Biotechnology Information, USA) Genetics meets genomics: a question of dominance

17:00

17:30

N.K. Yankovsky (Institute of General Genetics, Moscow) Distribution of SNP density in human genome and its correlation with densities of other genomic elements

17:30

18:00

Svetlana Borinskaya (Institute of General Genetics, Moscow) A new approach to human populations study: comparative analysis of genetic diversity and ethno-cultural features

Wednesday, Track 2.II. GENOME STRUCTURES

14:30

16:00

Structure and function of nucleic acids (Chairs: A. Badretdinov, D. Rodionov) 2nd floor, room 221

14:30

15:00

Dmitri D. Pervouchine (Boston University, USA) Structure prediction for RNA-RNA complexes

15:00

15:15

Elena V. Lyubetskaya (Institute for Information Transmission Problems, Moscow) Algorithm for detecting alternative secondary RNA structures and mass analysis attenuator regulation in proteobac

15:15

15:30

D.Yu. Oschepkov (Institute of Cytology and Genetics, Novosibirsk) SITECON: a method for recognizing transcription factor binding sites basing on analysis of their cpnservative physicochamical and conformational properties

15:30

15:45

Valentina Boeva (Moscow State University, Moscow) Probability of tandem repeats in nucleotide sequences

15:45

16:00

E. Permina (GosNIIGenetika, Moscow) Heat shock regulons in eubacteria

16:00

16:30

Coffee break (4th floor, room 431, 442)

16:30

18:00

Genome structure (Chairs: G. Kucherov, A. Vitreschak) 2nd floor, room 221

16:30

17:00

M. Samsonova (St.Petersburg State Polytechnical University, St. Petersburg) Dynamics of segment determination in Drosophila

17:00

17:15

A.V. Kochetov (Institute of Cytology and Genetics, Novosibirsk) Sequence features of yeast mRNAs influencing recognition of the translation start site

17:15

17:30

I. Artamonova (Institute of Bioorganic Chemistry, Moscow) Endogenous retroviruses of the HERV-K family in the human genome

17:30

17:45

Alexei Paskhin (Moscow Institute of Physics and Technology, Moscow) Compositional properties of intergenic segments in eukaryotic genomes

17:45

18:00

E.V. Korotkov (Centre “Bioengineering”, Moscow) Information decomposition of symbolical sequences

Day 3. Thursday, July 24th

9:00

9:30

Morning coffee (2nd floor)

9:30

11:15

Comparative genomics (Chairs: S. Sunyaev, A. Laessig) 2nd floor, room 221

9:30

10:15

Inna Dubchak (Lawrence Berkeley National Laboratory, USA) Comparative genomics tools for biological discovery

10:15

10:45

Mikhail Roytberg (Institute of Mathematical Problems of Biology, Pushchino) Anchor-based alignment of sequences and profiles: accuracy and effectiveness

10:45

11:15

Dmitry Rodionov (GosNIIGenetika, Moscow) Comparative genomics of the vitamin B12 metabolism in bacteria

11:15

11:45

Coffee break (2nd floor)

11:45

13:15

Evolution (Chairs: I. Dibchak, M. Gelfand) 2nd floor, room 221

11:45

12:30

Shamil Sunyaev (Harward Universiy Medical School, USA) Structural and evolutionary analysis of human genetics variation

12:30

13:00

A. Mironov (Moscow State Universtity, Moscow) Why mouse is not human? Comparative analysis of alternative splicing

13:00

13:15

Georgii Bazykin (Princeton University, USA) Positive selection at sites of multiple amino acid replacements since mouse-rat divergence

13:15

14:45

Lunch (Main University building, ground floor, dining room No. 1 (recommended))

CULTURAL PROGRAMME

CONFERENCE DINNER

Day 4. Friday, July 25th

9:00

9:30

Morning coffee (2nd floor)

9:30

11:00

Protein function (Chairs: J. Heringa, A. Alexeevsky) 2nd floor, room 221

9:30

10:00

Alexander Kanapin (European Bioinformatics Institute, UK) Classification and annotation databases: applications for proteomes functional annotation

10:00

10:30

Olga Kalinina (Moscow State University, Moscow) Automated selection of specificity-determining positions in large protein families

10:30

11:00

Sergei Spirin (Moscow State University, Moscow) Geometrical core and classification of homeodomains

11:00

11:30

Coffee break (2nd floor)

11:30

13:00

Protein structure and interactions (Chairs: A. Kanapin, V.G. Tumanyan) 2nd floor, room 221

11:30

12:15

Dmitrij Frishman (Institute for Bioinformatics GSF, Germany) Bringing protein interactions into genomic context

12:15

13:00

Jaap Heringa (Free Univesity Amsterdam, The Netherlands) Integrating patterns in protein sequence and structure

13:00

14:30

Lunch (Main University building, ground floor, dining room No. 1 (recommended))

Friday, Track 4.I. PROTEINS

14:30

16:00

Protein structure and interactions (Chairs: A. Bockmayr, S.A. Spirin) 4th floor, room 403

14:30

15:00

Boris Galitsky (Russian State University for Humanities, Moscow) Where do the contact map areas shift under the point mutations of proteins

15:00

15:30

Andrei Alexeevski (Moscow State University, Moscow) A program for the determination of hydrophobic clusters in 3D structures of protein and protein – nucleic complexes

15:30

16:00

Andrey Gorin (Oak Ridge National Laboratory, USA) Computational challenges in rapid characterization of the protein-protein interactions by NMR-based methods

16:00

16:30

Coffee break (4th floor, room 431, 442)

16:30

18:00

Physics of proteins (Chairs: A. Gorin, V. Makeev) 4th floor, room 403

16:30

17:00

R.G. Efremov (Institute of Bioorganic Chemistry, Moscow) Peptides and proteins in membranes: what can we learn via computer simulations?

17:00

17:30

Alexander Bockmayr (Universite Henri Poincare, France) A Binary integer programming approach for the determination of structures of biological macromolecules

17:30

18:00

Alexey Onufriev (Scripps Research Institute, USA) Modeling real molecules in virtual water

Friday, Track 4.II. PROCESSES AND NETWORKS

14:30

16:00

Genome structure and cellular processes (Chairs: P. Arndt, M.A. Roytberg) 4th floor, room 406

14:30

15:00

Gregory Kucherov (Loria/INRIA-Lorraine, France) YASS: similarity search in DNA sequences

15:00

15:15

N.Y. Oparina (Institute for Molecular Biology, Moscow) Alpha-satellite DNAs in the human genomic sequences: centromeric markers outside of centromere

15:15

15:30

V.G. Levitsky (Institute of Cytology & Genetics, Novosibirsk) Periodic context features of human alpha satellite DNA related to its nucleosomal organization

15:30

15:45

A. Golubev (Research Institute of Experimental Medicine, St. Petersburg) Modeling of telomere length heterogeneity with regard to the Hayflick limit

15:45

16:00

Denis Tarasov (Kazan State University, Kazan) The model of biological molecular computational device and it’s application to automatic genome annotation

16:00

16:30

Coffee break (4th floor, room 431, 442)

16:30

18:00

Gene networks (Chairs: D. Oschepkov, P. Novichkov) 4th floor, room 406

16:30

17:00

V.V. Gursky (The Ioffe Physico-Technical Institute, St. Petersburg) Modelling segmentation gene network in Drosophila with continual diffusion

17:00

17:15

E.A. Nedosekina (Institute of Cytology and Genetics, Novosibirsk) Signaling in macrophage activation gene network: data accumulation and computer modeling

17:15

17:30

A.V. Ratushny (Institute of Cytology and Genetics, Novosibirsk) Computer analysis of mutations and evolution of gene networks

17:30

17:45

Deborah Weisser (Carnegie Mellon University, USA) Statistical Detection of Features in Protein Sequences

17:45

18:00

Klaus Prank (Bielefeld University, Germany) Bioformatics Education at Bielefeld University (1989 – 2003): From computer science in natural sciences to the International NRW Graduate School in Bioinformatics and Genome Research

18:00

18:15

CLOSING CEREMONY 2nd floor, room 221

Saturday-Sunday, July 26-27

POST-CONFERENCE TOUR