2^nd Moscow Conference in Computational Molecular Biology (MCCMB'05)

Moscow State University, July 18–21, 2005

Monday, 18/07

8.30

10.00

registration, coffee (Building "B", 1st floor)

10.00

11.00

official talks

11.00

12.30

Proteins: structure, evolution and interactions

30

D.L. Hatfield

Identification and characterization of the system involved in selenocysteine biosynthesis, insertion into protein and regulation of expression by comparative functional genomics

30

Yao Chen

30

Janusz M. Bujnicki

Low-resolution structural genomics and phylogeny of restriction enzymes and related nucleases (EMBO Young Investigator Lecture)

12.30

14.00

lunch

14.00

15.30

Large-scale analyses

45

Alexei Kondrashov

Strength of selection against amino acid replacements in human proteins

45

Michael Ochs

Identifying Changes in Signaling from High-Throughput Data

15.30

16.00

break

16.00

17.30

Genomics

45

Maxim Frank-Kamenetsky

Fluctuational opening of base pairs in DNA

45

W.Hide

Exhaustive cross-platform ontology mapping provides evidence of Cancer Testis genes expression during mammalian development

evening

DINNER

Tuesday, 19/07

8.40

9.00

coffee (Building "B", 1st floor and near room 221)

a

9.00

10.20

Regulation / Genomes

20

F. Kolpakov

BioUML: visual modeling, automated code generation and simulation of biological systems

20

Rene Te Boekhorst

An adaptive sliding window technique for inferring dna functionality from sequence information

20

V.Boeva

Search for degenerate tandem repeats in nucleotide sequences. Their possible role in regulation of gene expression

20

G.Yagil

Binary dna tracts are promoter elements

b

9.00

10.30

Genome structure

20

S.L. Nikolajewa

Purine-Pyrimidine Patterns in the Genetic Code and in Restriction Enzyme Recognition Sequences

20

Yu.L. Orlov

Prediction of Nucleosome Formation Sites in Gene Regulatory Regions

20

Simon Kogan

The sequence structure of human nucleosome DNA

30

V. Makeev

Compositional segmentation of H.sapiens genome (and correlation of features with local composition)

10.30

11.00

break

a

11.00

12.30

Regulation

20

Natalia Polouliakh

Comparative genomic analysis of transcription regulation elements involved in the human MAP kinase G-protein coupling pathway

20

Levitsky V.G.

The sitega tool for transcription factor binding sites recognition and context analysis exemplified by SF-1 binding site

20

Ruye Wang

Network inference based on differential equation model

20

A.V. Ratushny

Molecular-genetic mechanisms of prokaryotic cell respiration: gene network reconstruction and mathematical modeling

b

11.00

12.30

Systems biology

30

A.Gerasimova, D.Ravcheev

How gamma-proteobacteria switch the mode of respiration: A comparative genomic analysis

30

E. J. Alm

Operon Formation is Driven by Co-regulation and Not by Horizontal Gene Transfer

30

Vladimir V. Poroikov

12.30

14.00

lunch

a

14.00

15.40

Regulation

30

Sudhir Kumar

Automating discovery of gene interactions by in silico analysis of in situ gene expression patterns in fruit fly embryos

30

D. Papatsenko

Early steps in Drosophila development: From binding site arrangements to spatial gene expression patterns

20

D.A. Rodionov

A universal regulatory system of ribonucleotide reductase genes in bacterial genomes

20

M. Troukhan

Statistical approach to identify cis-elements in promoter sequences using microarray data

b

14.00

15.40

Systems and structure

30

Vadim Gladyshev

Redox Networks in Eukaryotes

30

Andrei V. Alexeevski

The Role of Water in DNA-protein Interaction

20

Osypov A.A.

Electrostatic properties of promoters recognized by RNA polymerase Es70. New promoter determinants

20

M. Nikitin

Evolution of ribosomal protein S5 gene introns

15.40

17.40

POSTERS (see the list of posters)

Wednesday, 20/07

8.40

9.00

coffee (Building "B", 1st floor and near room 221)

a

9.00

10.30

Comparative genomics and proteomics

40

Dmitry Frishman

Comparative proteomics in silico: software and applications

40

Andrei Osterman

BIOINFORMATICS-DRIVEN WET LAB: Úmapping the Molecular Machinery of Life

b

9.00

10.30

Algorithms

40

Mireille Regnier

Comparison of statistical significance criteria

30

Gregory Kucherov

Estimating seed sensitivity for DNA similarity search: general framework and an efficient application

20

Oleg Rokhlenko

A New Tool for the Alignment of Metabolic Pathways

10.30

11.00

break

a

11.00

12.30

Genes and alternatives

30

M.S.Gelfand

Evolution of alternative splicing

20

Kangueane P.

An untold story on single exon genes (SEG) in eukaryotes

20

Alex V. Kochetov

The role of alternative translation start sites in generation of human protein diversity

20

V. Ramensky

Human SNPs and alternative splicing

b

11.00

12.20

Algorithms for regulation

30

Eugene Fratkin

Motif-finding in DNA Sequences Using Maximum Density Subgraphs

30

A.A. Mironov

An effective algorithm for identification of clustered regulatory sites

20

Irina Abnizova

Using short memory Markov models to detect regulatory elements

12.30

14.00

lunch

a

14.00

15.30

Annotation

30

L. Clarke

The Ensembl Annotation System

30

Ana Tereza de Vasconcelos

SABIA: A software for genome annotation and its use on the Brazilian genomes

30

Dmitry Kuznetsov

BRAIN — an integrated environment to generate and evaluate gene lists from heterogeneous biological criteria

b

14.00

15.30

Algorthims

30

Inna Dubchak

Glocal (global/local) alignment methods for comparison of DNA sequences and whole-genome assemblies utilized in VISTA tools

20

N. PerdigÖo

Hybrids Evolutive Algorithms for Multiple Sequence Alignment

20

Nikolay Zagoruiko

Algorithm GRAD for selection of informative genetic characteristics

20

Paul Horton

Optimization of S-system models for quantitative time-developing gene networks

15.30

16.00

break

a

16.00

17.40

Annotation and large-scale analyses

20

Irena I. Artamonova

Application of the association rules mining to the correction of annotation errors

20

Evgenia V. Kriventseva

Transcriptome analysis of A. gambiae suggests higher number of genes

30

E.M. Zdobnov

Whole genome comparative analysis of higher animals

30

I. Grigoriev

Genome Annotation: Going Beyond Human Genome

b

16.00

17.30

Algorithms

20

A. Favorov

A Markov Chain Monte Carlo Technique for Identification of Combinations of Allelic Variants Underlying Complex Diseases and Its Applications

20

Sang Jun Kim

LD-based Haplotype Reconstruction System

30

M.A. Roytberg

RNA secondary structure and internal loops

20

Tariq Alsheddi

Small Interference (si) RNAs with High Specificity to the Target: a Systematic Approach to Design

Thursday, 21/07

8.40

9.00

coffee (Building "B", 1st floor and near room 221)

a

9.00

10.30

Proteins / structure and function

20

Fomenko A.E.

Prediction of enzyme specificity based on structural MNA descriptors

20

Sergei Rahmanov

Knowledge-based protein hydration potentials

20

Artem Cherkasov

Selective Targeting of Indel - Inferred Differences in Spatial Structures of Highly Homologous Proteins

30

O. Kalinina

Intersubunit contacts are often facilitated by specificity-determining positions

b

9.00

10.30

Evolution

20

Roman L. Tatusov

Rank-based clustering of the complete proteomes

20

Julian Mintseris

Distinguishing Structural, Functional, and Evolutionary Properties of Transient and Obligate Protein Interactions

20

Dmitry Klimov

Regions of low SNP density cover 20% of the human genome

30

Vladimir V. Kapitonov

Transib transposons and origin of V(D)J recombination

10.30

11.00

break

a

11.00

12.30

Proteins / structure and function

20

A.N. Nekrasov

An informational structures approach to the identification of structural and functional features of proteins

20

S.F. Chekmarev

Folding and Stability of a Prion-Like Lattice Protein

30

Alexei V. Finkelstein

Prediction of Protein Folding Rates

20

Oxana V. Galzitskaya

Prediction of unfolded and amyloidogenic regions in protein chains

b

11.00

12.30

Evolution of regulation

40

Michael Galperin

A genomic view at prokaryotic signal transduction networks: bacterial IQ, extroverts and introverts

30

Mustonen and Laessig

Evolutionary population genetics of promoters: Predicting binding sites and their functional histories

20

G. Kryukov

Genetic Variation in Conserved Non-coding Regions: a story of thousands deleterious mutations in each and every human genome

12.30

14.00

lunch

a

14.00

15.40

Proteins / evolution

20

Sergey Pintus

Computer analysis of structure and evolution of functional sites of the DNA-binding domain of human p53 protein

20

Daniil G. Naumoff

Phylogenetic analysis of GH97 family of glycoside hydrolases

20

F. Kondrashov

Prediction of pathogenic mutations in mitochondrial tRNAs

20

Georgii Bazykin

Amino acid volatility: amino acid composition of viral and bacterial genomes is influenced by selection regime

20

K. Popadin

Effectively-neutral evolution of mitochondrial genes of mammals

b

14.00

15.40

Regulation

30

Leonid Mirny

Biological implications of protein-DNA sliding

30

O.N. Ozoline

Promoter-Search Software as a Tool Predicting Antisense Transcription within Bacterial Genes

20

Florian Sohler

Inference of Developmental Transcription Factor Activities in Drosophila Melanogaster

20

Alexey Vitreschak

Computer prediction of H-NS regulon in Escherichia coli. Comparative analysis of regulation of rrn operons in proteobacteria

15.40

16.00

break

a

16.00

17.40

Proteomes

30

Andrei Grigoriev

Mobile Protein Domains and Proteome Evolution

30

Boris E. Shakhnovich

Protein Structure and Evolutionary History Determine Sequence Space Topology

20

Elena Nabieva

Inferring protein function via graph-theoretic analysis of physical and integrated interaction maps

20

M. Raffinot

Domain teams: high level comparative genomics using domain proximity

b

16.00

17.40

Evolution

30

Sudhir Kumar

Placing confidence limits on the molecular age of the human-chimpanzee divergence

30

V.A. Lyubetsky

Algorithms to reduce phylogenetic noise and infer gene evolution events from protein families

20

Gordana M. Pavlović-Lažetić

Bioinformatics study of SARS CoV genome polymorphism

20

A. Melkikh

Deterministic mechanism of molecular evolution

17.40

Closing the conference