2006

2004

2002

2000

1998



PROCEEDINGS OF THE BGRS



Proceedings of the Fifth International Conference
on Bioinformatics of Genome Regulation and Structure

BGRS' 2006
NOVOSIBIRSK, RUSSIA
JULY 16 - 22, 2006


Volume 1

Volume 2

Volume 3



INTERNATIONAL PROGRAM COMMITTEE

LOCAL ORGANIZING COMMITTEE

SPONSORS

INTRODUCTION


Volume 1

CONTENTS

PART 1. COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICS AND TRANSCRIPTOMICS

NEW WAY TO OBTAIN A REGULATORY MOTIF REPRESENTATION DUE TO MOTIF ABUNDANCE LEVEL
Abnizova I., Walter K., te Boekhorst R., Gilks W.R.


A KNOWLEDGE AND DATA BASED HYBRID APPROACH TO GENE CLUSTERING
Abhishek K., Karnick H., Mitra P.


PREDICTION OF INTERFERON-INDUCIBLE GENES IN HUMAN GENOME
Ananko E.A., Kondrakhin Yu.V., Merkulova T.I.


A DATABASE DESIGNED FOR THE POLYMORPHISMS OF THE HUMAN CCR2 GENE
Apasyeva N.V., Yudin N.S., Ignatieva E.V., Voevoda M.I., Romashenko A.G.


LENGTH OF EXONS AND INTRONS IN GENES OF SOME HUMAN CHROMOSOMES
Atambaeva S.A., Ivashchenko A.T., Khailenko V., Boldina G., Turmagambetova A.


THE EXON AND INTRON LENGTHS IN ARABIDOPSIS THALIANA AND CAENORHABDITIS ELEGANS GENES
Atambaeva S.A., Ivashchenko A.T.


STATISTICAL CHARACTERIZATION OF CONSERVED NON-CODING ELEMENTS IN VERTEBRATES
te Boekhorst R., Walter K., Elgar G., Gilks W.R., Abnizova I.


INTERPRETATION OF RESULTS OF SOM ANALYSIS OF MICROARRAY DATA BY PRINCIPAL COMPONENTS
Efimov V.M., Badratinov M.S., Katokhin A.V.


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


SITECON: A QUALITY TOOL FOR PREDICTION OF TRANSCRIPTION FACTOR BINDING SITES NOW HANDLES THOSE FOR SF-1. EXPERIMENTAL VERIFICATION AND ANALYSIS OF REGULATORY REGIONS OF ORTHOLOGOUS GENES
Ignatieva E.V., Oshchepkov D.Yu., Klimova N.V., Vasiliev G.V., Merkulova T.I.


CONTEXT-DEPENDENT EFFECTS OF UPSTREAM A-TRACTS ON PROMOTER ELECTROSTATIC PROPERTIES AND FUNCTION
Kamzolova S.G., Osypov A.A., Dzhelyadin T.R., Beskaravainy P.M., Sorokin A.A.


IDENTIFICATION OF NEW SUPEROXIDE DISMUTASE TRANSCRIPTS IN PLANTS BY EST ANALYSIS: ALTERNATIVE POLYADENYLATION AND SPLICING EVENTS
Katyshev A.I., Rogozin I.B., Konstantinov Yu.M.


THE PREDICTION OF REGULATION OF SUBTILISIN-LIKE PROTEINASE GENE FROM BACILLUS INTERMEDIUS THROUGH ITS REGULATORY SEQUENCE ANALYSIS
Kayumov A.R., Kirillova J.M., Mikhailova E.O., Balaban N.P., Sharipova M.R.


PATTERN OF LOCALLY POSITIONED DINUCLEOTIDES IN microRNA RELATES TO ITS ACCUMULATION LEVEL
Khomicheva I.V., Levitsky V.G., Omelianchuk N.A., Ponomarenko M.P.


IDENTIFICATION OF ARABIDOPSIS THALIANA microRNAS AMONG MPSS SIGNATURES
Khomicheva I.V., Levitsky V.G., Vishnevsky O.V., Savinskaya S.A., Omelianchuk N.A.


TRANSCRIPTION FACTOR BINDING SITES RECOGNITION BY THE ExpertDiscovery SYSTEM BASED ON THE RECURSIVE COMPLEX SIGNALS
Khomicheva I.V., Vityaev E.E., Shipilov T.I., Levitsky V.G.


TRRD: A DATABASE ON EXPERIMENTALLY IDENTIFIED TRANSCRIPTION REGULATORY REGIONS AND TRANSCRIPTION FACTOR BINDING SITES
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., Romashenko A.G.


METHODS FOR RECOGNITION OF INTERFERON-INDUCIBLE SITES, PROMOTERS, AND ENHANCERS
Kondrakhin Yu.V., Ananko E.A., Merkulova T.I.


GENOME-WIDE CO-EXPRESSION PATTERNS OF HUMAN CIS-ANTISENSE GENE PAIRS
Kuznetsov V.A., Zhou J.T., George J., Orlov Yu.L.


THE SITEGA AND PWM METHODS APPLICATION FOR TRANSCRIPTION FACTOR BINDING SITES RECOGNITION IN EPD PROMOTERS
Levitsky V.G., Ignatieva E.V., Ananko E.A., Merkulova T.I.


DETECTING HAIRPINS IN 3'-UNTRANSLATED REGIONS OF HIGHLY EXPRESSED GENES IN ACTINOBACTERIA
Lyubetskaya E.V., Seliverstov A.V., Lyubetsky V.A.


MODELING CLASSIC ATTENUATION REGULATION OF GENE EXPRESSION IN BACTERIA
Lyubetsky V.A., Seliverstov A.V.


STRUCTURAL VARIANTS OF BINDING SITES FOR GLUCOCORTICOID RECEPTOR AND THE MECHANISMS OF GLUCOCORTICOID REGULATION: ANALYSIS OF GR-TRRD DATABASE
Merkulov V.M., Merkulova T.I.


THRESHOLD SELECTION USING THE RANK STATISTICS
Mironov A.A.


STUDIES ON TRANSCRIPTIONAL REGULATION IN DNA
Mitra Ch.K.


MODELING TRANSCRIPTIONAL REGULATION WITH EQUILIBRIUM MOLECULAR COMPLEX COMPOSITION
Mjolsness E.


OWEN-SCRIPT . AN EXTENDED TOOL FOR PAIRWISE GENOME ALIGNMENT
Ogurtsov A.Yu., Vasilchenko A.N., Vlasov P.K., Shabalina S.A., Kondrashov A.S., Roytberg M.A.


A COMPREHENSIVE QUALITY ASSESSMENT OF THE AFFYMETRIX U133A&B PROBESETS BY AN INTEGRATIVE GENOMIC AND CLINICAL DATA ANALYSIS APPROACH
Orlov Yu.L., Zhou J.T., Lipovich L., Yong H.C., Li Yi, Shahab A., Kuznetsov V.A.


THE CONTENT OF miRNAS IN ARABIDOPSIS THALIANA CORRELATES WITH THE OCCURRENCE OF TETRAMERS WRHW AND DRYD
Ponomarenko M.P., Omelianchuk N.A., Katokhin A.V., Kolchanov N.A.


THE ANALYSIS OF SREBP BINDING SITES DISTRIBUTION IN GENE REGIONS BY COMBINED SITEGA AND PWM APPROACH
Proskura A.L., Levitsky V.G., Ignatieva E.V.


SIMPLE SEQUENCE (TG/CA)N REPEATS AS CIS MODULATORS OF GENE EXPRESSION
Ramachandran S., Sharma V.K., Sharma A., Brahmachari S.K.


IDENTIFICATION OF microRNAS ENCODED BY DROSOPHILA TRASPOSABLE ELEMENTS
Ryazansky S.S.


TRANSLATION REGULATION IN CHLOROPLASTS
Seliverstov A.V., Lyubetsky V.A.


ALTERNATIVE TRANSCRIPTION WITHIN PROCARYOTIC GENES PREDICTED BY PROMOTER-SEARCH SOFTWARE
Shavkunov K.S., Masulis I.S., Matushkin Yu.G., Ozoline O.N.


ANALYSIS OF REGULATORY REGION OF BACILLUS INTERMEDIUS GLUTAMYL ENDOPEPTIDASE GENE
Shagimardanova E.I., Shamsutdinov T.R., Chastuchina I.B., Sharipova M.R.


PROMOTER MODELING APPROACHES APPLIED TO THE INVESTIGATION OF p63 UPAND DOWNSTREAM PROMOTERS
Shelest E.S., Wingender E.


A STEP BEYOND PLANT TRANSCRIPT'S POLYADENYLATION SITE
Smetanin D.V., Chumak N.M.


TGP (TRANSGENE PROMOTERS): A DATABASE OF BIOTECHNOLOGICALLY IMPORTANT PLANT GENE PROMOTERS
Smirnova O.G., Ibragimova S.S., Grigorovich D.A., Kochetov A.V.


TOOL FOR AUTOMATIC DETECTION OF CO-REGULATED GENES
Stavrovskaya E.D., Makeev V.J., Merkeev I.V., Mironov A.A.


HOW SIMILAR ARE PHENOTYPICALLY IDENTICAL CELLS AT THE TRANSCRIPTIONAL LEVEL?
Subkhankulova T., Livesey F.J.


THE MODIFIED FUZZY C-MEANS METHOD FOR CLUSTERING OF MICROARRAY DATA
Taraskina A.S., Cheremushkin E.S.


MULTIPLE COLLAPSE CLUSTERING
Tatarinova T., Schumitzky A.


TOWARDS THE IDENTIFICATION OF ANTISENSE RNAS WITHIN GENES OF TRANSCRIPTION REGULATORS
Tutukina M.N., Masulis I.S., Ozoline O.N.


ANALYSIS OF THE NUCLEOTIDE CONTEXT OF HIGHER PLANT MITOCHONDRIAL mRNA EDITING SITES
Vishnevsky O.V., Konstantinov Yu.M.


TRANSCRIPTION FACTOR BINDING SITES RECOGNITION BY THE REGULARITIES MATRICES BASED ON THE NATURAL CLASSIFICATION METHOD
Vityaev E.E., Lapardin K.A., Khomicheva I.V., Levitsky V.G.


ROLES OF CODON BIASES AND POTENTIAL SECONDARY STRUCTURES IN mRNA TRANSLATION OF UNICELLULAR ORGANISMS
Vladimirov N.V., Likhoshvai V.A., Matushkin Yu.G.


MODELING OF DATA BASE OF CONTEXT-DEPENDENT CONFORMATIONAL PARAMETERS OF DNA DUPLEXES
Vorobjev Y.N., Emelianov D.Y.


SELECTION OF INFORMATIVE SUBSET OF GENE EXPRESSION PROFILES IN PROGNOSTIC ANALYSIS OF TYPE II DIABETES
Zagoruiko N.G., Kutnenko O.A., Borisova I.A., Kiselev A.N., Ptitsyn A.A.


PART 2. COMPUTATIONAL STRUCTURAL AND FUNCTIONAL PROTEOMICS

CONNP: THE PREDICTION OF THE CONTACT NUMBERS OF THE AMINO ACID RESIDUES IN PROTEINS USING NEURAL NETWORK REGRESSION
Afonnikov D.A., Morozov A.V.


A TOOL FOR COMPARATIVE ANALYSIS OF SOLVENT MOLECULES IN PDB STRUCTURES
Aksianov E., Zanegina O., Alexeevski A., Karyagina A., Spirin S.


ANALYSIS OF THE TERTIARY STRUCTURE OF THE PPAR AND RXR TRANSCRIPTIONAL FACTORS AND THEIR MUTANT VARIANTS
Aman E.E., Demenkov P.S., Ivanisenko V.A.


MOLECULAR MODELING OF B. CEREUS HEMOLYSIN II, A PORE-FORMING PROTEIN
Bakulina A.Yu., Sineva E.V., Solonin A.S., Maksyutov A.Z.


IDENTIFICATION AND STRUCTURE-FUNCTIONAL ANALYSIS OF THE SPECIFICITY DETERMINING RESIDUES OF THE ALPHA SUBUNITS OF THE PROTEOSOMAL COMPLEX
Baryshev P.B., Afonnikov D.A., Nikolaev S.V.


CLUSTERING ANALYSIS OF CONFORMATIONAL STATES OF SHORT OLIGOPEPTIDES
Batsianovsky A.V., Vlasov P.K.


“STRANGE KINETICS” OF UBIQUITIN FOLDING: INTERPRETATION IN TERMS OF A SIMPLE KINETIC MODEL
Chekmarev S.F., Krivov S.V., Karplus M.


A METHOD TO ASSESS CORRECT/MISFOLDED STRUCTURES OF TRANSMEMBRANE DOMAINS OF MEMBRANE PROTEINS
Chugunov A.O., Novoseletsky V.N., Efremov R.G.


DIRECT INFLUENCE OF UBIQUITYLATION ON A TARGET PROTEIN ACTIVITY: “LOSS-OF-FUNCTION” MECHANISM REVEALED BY COMPUTATIONAL ANALYSIS
Chernorudskiy A.L., Shorina A.S., Garcia A., Gainullin M.R.


PREDICTION IN CHANGES OF PROTEIN THERMODYNAMIC STABILITY UPON SINGLE MUTATIONS
Demenkov P.S., Ivanisenko V.A.


EFFECT OF THE STRUCTURAL CONTEXT ON SPECIFICITY OF INTRA- AND INTERHELICAL INTERACTIONS IN PROTEINS
Efimov A.V., Brazhnikov E.V., Kondratova M.S.


RISE OF NEW Zn2+ BINDING SITES CAN BE A MOLECULAR MECHANISM FOR IMPAIRED FUNCTION OF THE p53 MUTANTS
Fomin E.S., Oshurkov I.S., Ivanisenko V.A.


SEQUENCE-BASED PREDICTION OF DNA-BINDING SITES ON DNA-BINDING PROTEINS
Gou Z., Hwang S., Kuznetsov B.I.


PDBSite DATABASE AND PDBSiteScan TOOL: RECOGNITION OF FUNCTIONAL SITES IN PROTEIN 3d STRUCTURE AND TEMPLATE-BASED DOCKING
Ivanisenko V.A., Ivanisenko T.V., Sharonova I.V., Krestyanova M.A., Ivanisenko N.V., Grigorovich D.A.


PROTEIN-PROTEIN INTERACTIONS AS NEW TARGETS FOR DRUG DESIGN: INTERACTIVE LINKS BETWEEN VIRTUAL AND EXPERIMENTAL APPROACHES
Ivanov A.S., Gnedenko O.V., Molnar A.A., Mezentsev Yu.V., Lisitsa A.V., Archakov A.I.


THE CONTRIBUTION OF ALTERNATIVE TRANSLATION START SITES TO HUMAN PROTEIN DIVERSITY
Kochetov A.V., Sarai A., Kolchanov N.A.


STRUCTURAL DETERMINANTS OF CARDIOTOXINS MEMBRANE BINDING: A MOLECULAR MODELING APPROACH
Konshina A.G., Dubinnyi M.A., Efremov R.G.


OPTIMIZATION OF ACCURACY AND CONFIDENCE FOR ALIGNMENT ALGORITHMS EXPLOITING DATA ON SECONDARY STRUCTURE
Litvinov I.I., Finkelshtein A.V., Roytberg M.A.


DEVELOPMENT OF A HIERARCHICAL CLASSIFICATION OF THE TIM-BARREL TYPE GLYCOSIDE HYDROLASES
Naumoff D.G.


PROF_PAT: THE UPDATED DATABASE OF PROTEIN FAMILY PATTERNS. CURRENT STATUS
Nizolenko L.Ph., Bachinsky A.G., Yarygin A.A., Naumochkin A.N., Grigorovich D.A.


ACTION OF MEMBRANE-ACTIVE PEPTIDES ON EXPLICIT LIPID BILAYERS. ROLE OF SPECIFIC PEPTIDE-LIPID INTERACTIONS IN MEMBRANE DESTABILIZATION
Polyansky A.A., Aliper E.T., Volynsky P.E., Efremov R.G.


COMBINING MOLECULAR DOCKING WITH RECEPTOR DOMAIN MOTIONS: SIMULATIONS OF BINDING OF ATP TO CA-ATPase
Pyrkov T.V, Kosinsky Yu.A., Arseniev A.S., Priestle J.P., Jacoby E., Efremov R.G.


HOW ARE CHARGED RESIDUES DISTRIBUTED AMONG FUNCTIONALLY DISTINCT STRUCTURAL DOMAINS OF AMINOACYL-tRNA SYNTHETASES?
Safro M., Tworowski D., Feldman A.


MOLECULAR DYNAMICS AND DESIGN OF TRANSMEMBRANE ION CHANNELS
Shaitan K.V., Tereshkina K.B., Levtsova O.V.


PEPTIDE DYNAMICS AT WATER-MEMBRANE INTERFACE
Shaytan A.K., Khokhlov A.R., Ivanov V.A.


CONFORMATION PROPERTIES OF SHORT OLIGOPEPTIDES AND PREDICTION OF PROTEIN CHAIN CONFORMATION
Vlasov P.K., Esipova N.G., Tumanyan V.G.


AMINO ACID PREFERENCES AT THE N-TERMINAL PART OF EUKARYOTIC PROTEINS CORRELATING WITH A SPECIFIC CONTEXTUAL ORGANIZATION OF TRANSLATION INITIATION SIGNAL
Volkova O.A., Kochetov A.V.


PROBING DIMERIZATION OF TRANSMEMBRANE PEPTIDES VIA MOLECULAR DYNAMICS IN EXPLICIT BILAYERS
Volynsky P.E., Vereshaga Ya.A., Nolde D.E., Efremov R.G.


Volume 2

CONTENTS

PART 3. COMPUTATIONAL SYSTEMS BIOLOGY

3.1. MODELLING OF MOLECULAR GENETIC SYSTEMS AND PROCESSES IN BACTERIAL CELL

IN SILICO CELL I. HIERARCHICAL APPROACH AND GENERALIZED HILL FUNCTIONS IN MODELING ENZYMATIC REACTIONS AND GENE EXPRESSION REGULATION
Likhoshvai V.A., Ratushny A.V.


IN SILICO CELL II. INFORMATION SOURCES FOR MODELING ESCHERICHIA COLI METABOLIC PATHWAYS
Khlebodarova T.M., Ananko E.A., Nedosekina E.A., Podkolodnaya O.A., Poplavsky A.S., Smirnova O.G., Ibragimova S.S., Mishchenko E.L., Stepanenko I.L., Ignatieva E.V., Proskura A.L., Nishio Y., Imaizumi A., Usuda Y., Matsui K., Podkolodny N.L., Kolchanov N.A.


MATHEMATICAL MODELING OF ELEMENTARY PROCESSES OF THE GENE NETWORK CONTROLLING HISTIDINE BIOSYNTHESIS IN ESCHERICHIA COLI
Ratushny A.V., Usuda Y., Matsui K., Podkolodnaya O.A.


MODELING OF THE EFFECTS OF THREONINE, VALINE, ISOLEUCINE AND PYRIDOXAL 5'-MONOPHOSPHATE ON BIOSYNTHETIC THREONINE DEHYDRATASE REACTION
Nedosekina E.A., Usuda Y., Matsui K.


REGULATION OF PYRIMIDINE BIOSYNTHESIS IN ESCHERICHIA COLI: GENE NETWORK RECONSTRUCTION AND MATHEMATICAL MODELING
Ratushny A.V., Nedosekina E.A.


REGULATION OF THE PENTOSE PHOSPHATE PATHWAY IN ESCHERICHIA COLI: GENE NETWORK RECONSTRUCTION AND MATHEMATICAL MODELING OF METABOLIC REACTIONS
Ratushny A.V., Smirnova O.G., Usuda Y., Matsui K.


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
Ananko E.A., Ratushny A.V., Usuda Y., Matsui K.


MATHEMATICAL MODELING OF REGULATION OF cy§àABCDE OPERON EXPRESSION IN ESCHERICHIA COLI
Ratushny A.V., Khlebodarova T.M.


GENE NETWORK RECONSTRUCTION AND MATHEMATICAL MODELING OF E. COLI RESPIRATION: REGULATION OF F0F1-ATP SYNTHASE BY METAL IONS
Khlebodarova T.M., Lashin S.A., Apasieva N.V.


ATHEMATICAL MODELING OF REGULATION OF ESCHERICHIA COLI PURINE BIOSYNTHESIS PATHWAY ENZYMATIC REACTIONS
Nedosekina E.A.


RECONSTRUCTION AND MATHEMATICAL MODELING OF THE GENE NETWORK CONTROLLING CYSTEINE BIOSYNTHESIS IN ESCHERICHIA COLI: REGULATION OF SERINE ACETYLTRANSFERASE ACTIVITY
Mishchenko E.L., Lashin S.A., Usuda Y., Matsui K.


GENE NETWORK RECONSTRUCTION AND MATHEMATICAL MODELING OF SALVAGE PATHWAYS: REGULATION OF ADENINE PHOSPHORIBOSYLTRANSFERASE ACTIVITY BY STRUCTURALLY SIMILAR SUBSTRATES
Smirnova O.G., Ratushny A.V.


MATHEMATICAL MODELING OF SERINE AND GLYCINE BIOSYNTHESIS REGULATION IN ESCHERICHIA COLI
Turnaev I.I., Ibragimova S.S., Usuda Y., Matsui K.


REGULATION OF PYRUVATE BIOSYNTHESIS IN ESCHERICHIA COLI: GENE NETWORK RECONSTRUCTION AND MATHEMATICAL MODELING OF ENZYMATIC REACTIONS OF THE PATHWAY
Turnaev I.I., Smirnova O.G.


BiotechPro: A DATABASE FOR MICROBIOLOGICALLY SYNTHESIZED PRODUCTS OF BIOTECHNOLOGICAL VALUE
Ibragimova S.S., Smirnova O.G., Grigorovich D.A., Khlebodarova T.M.


DATABASE GenSensor AS INFORMATIONAL SOURCE FOR DESIGN OF BIOSENSORS. EXPERIMENTAL DEVELOPMENT OF BIOSENSOR BASED ON yfiA GENE
Khlebodarova T.M., Kachko A.V., Stepanenko I.L., Tikunova N.V.


ABOUT RECONSTRACTION OF REGULATORY MECHANISM OF GENE ELEMENTS’ EXPRESSION
Peshkov I.M., Fadeev S.I.


3.2. MODELLING OF MOLECULAR GENETIC SYSTEMS AND PROCESSES IN MULTICELLULAR ORGANISMS

A MATHEMATICAL MODEL FOR THE INFLUENZA VIRUS LIFE CYCLE
Akberdin I.R., Kashevarova N.A., Khlebodarova T.M., Bazhan S.I., Likhoshvai V.A.


A MINIMUM MATHEMATICAL MODEL FOR SUPPRESSION HCV RNA REPLICATION IN CELL CULTURE
Bezmaternikh K.D., Mishchenko E.L., Likhoshvai V.A., Khlebodarova T.M., Ivanisenko V.A.


A MATHEMATICAL MODEL OF IMMUNE RESPONSE IN INFECTION INDUCED BY MYCOBACTERIA TUBERCULOSIS. PREDICTION OF THE DISEASE COURSE AND OUTCOMES AT DIFFERENT TREATMENT REGIMENS
Bazhan S.I., Schwartz Ya.Sh., Gainova I.A., Ananko E.A.


THE PACKAGE STEP+ FOR NUMERICAL STUDY OF AUTONOMOUS SYSTEMS ARISING WHEN MODELING DYNAMICS OF GENETIC-MOLECULAR SYSTEMS
Fadeev S.I., Korolev V.K., Gainova I.A., Medvedev A.E.


MATRIX PROCESS MODELING: STUDY OF A MODEL OF SYNTHESIS OF LINEAR BIOMOLECULES WITH REGARD TO REVERSIBILITY OF PROCESSES
Fadeev S.I., Shtokalo D.N., Likhoshvai V.A.


APPROXIMATE STATIONARY ATTRACTORS IN DROSOPHILA GAP GENE CIRCUITS IN THE LIMIT OF STEEP-SIGMOID INTERACTIONS
Gursky V.V., Samsonov A.M., Reinitz J.


SIGNAL TRANSDUCTION PATHWAYS INVOLVED IN TRANSCRIPTIONAL REGULATION OF TYROSINE HYDROXYLASE
Kalashnikova E.V., Dymshits G.M., Kolpakov F.A.


Cyclonet – AN INTEGRATED DATABASE ON CELL CYCLE REGULATION AND CARCINOGENESIS
Kolpakov F., Poroikov V., Sharipov R., Milanesi L., Kel A.


A GENE NETWORK OF ADIPOCYTE LIPID METABOLISM: COORDINATED INTERACTIONS BETWEEN THE TRANSCRIPTION FACTORS SREBP, LXRa AND PPARy
Kouznetsova T.N., Ignatieva E.V., Oshchepkov D.Yu., Kondrakhin Y.V., Katokhin A.V., Shamanina M.Y., Mordvinov V.A.


NEW MIGRATION SCHEME FOR PARALLEL DIFFERENTIAL EVOLUTION
Kozlov K.N., Samsonov A.M.


HCCDB: DATA MINING SYSTEM FOR HUMAN CELL CYCLE GENE
Milanesi L., Alfieri R., Merelli I.


HCV-KINET DATABASE: KINETIC PARAMETER REACTIONS AND REGULATORY PROCESSES OF THE LIFE CYCLE OF THE HEPATITIS C VIRUS
Mishchenko E.L., Korotkov R.Î., IvanisenkoV.A.


MATHEMATICAL MODELING OF RECEPTOR MEDIATED ENDOCYTOSIS OF LOW-DENSITY LIPOPROTEINS AND THEIR DEGRADATION IN LYSOSOMES
Ratushny A.V.


CONSERVED PROPERTIES OF ENZYMATIC SYSTEMS: PRENYLTRANSFERASE KINETICS
Ratushny A.V., Bezmaternikh K.D.


MATHEMATICAL MODELING OF THE GENE NETWORK CONTROLLING HOMEOSTASIS OF INTRACELLULAR CHOLESTEROL
Ratushny A.V.


CONSTRUCTION OF THE HCV-HEPATOCYTE SYSTEM MODEL
Rudenko V.M., Korotkov E.V.


FORMAL DESCRIPTION OF NF-¦ÊB 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
Sharipov R.N., Kolpakova A.F.


RECONSTRUCTION AND STRUCTURE ANALYSIS OF APOPTOSIS GENE NETWORK IN HEPATITIS C
Stepanenko I.L., Podkolodnaya N.N., Paramonova N.V., Podkolodny N.L.


DYNAMIC FILTRATION OF VARIABILITY WITHIN EXPRESSION PATTERNS OF ZYGOTIC SEGMENTATION GENES IN DROSOPHILA
Surkova S.Yu., Samsonova M.G.


3.3. MODELLING OF MORPHOGENESIS

A CELLULAR AUTOMATON TO MODEL THE DEVELOPMENT OF SHOOT MERISTEMS OF ARABIDOPSIS THALIANA
Akberdin I.R., Ozonov E.A., Mironova V.V., Komarov A.V., Omelianchuk N.A.


THE GENE NETWORK DETERMINING DEVELOPMENT OF DROSOPHILA MELANOGASTER MECHANORECEPTORS
Bukharina T.A., Katokhin A.V., Furman D.P.


A MODEL FOR SENSING THE MORPHOGEN HEDGEHOG CONCENTRATION GRADIENT I: A NUMERICAL STUDY
Kogai V.V., Gunbin Ê.V., Omelyanchuk L.V., Fadeev S.I.


A MODEL FOR SENSING THE HEDGEHOG CONCENTRATION GRADIENT II: A CHECK FOR ADEQUACY
Gunbin Ê.V., Kogai V.V., Fadeev S.I., Omelyanchuk L.V.


METHODOLOGY FOR BUILDING OF COMPLEX WORKFLOWS WITH PROSTAK PACKAGE AND ISIMBIOS
Matveeva A., Kozlov K., Samsonova M.


ONTOLOGY OF ARABIDOPSIS GENE NET SUPPLEMENTARY DATABASE (AGNS), CROSS DATABASE REFERENCES TO TAIR ONTOLOGY
Mironova V.V., Poplavsky A.S., Ponomarev D.K., Omelianchuk N.A.


A ONE-DIMENSIONAL MODEL FOR THE REGULATION OF THE SIZE OF THE RENEWABLE ZONE IN BIOLOGICAL TISSUE
Nikolaev S.V., Fadeev S.I., Kogay V.V., Mjolsness E., Kolchanov N.A.


A SYSTEM FOR SIMULATION OF 2D PLANT TISSUE GROWTH AND DEVELOPMENT
Nikolaev S.V., Penenko A.V., Belavskaya V.V., Mjolsness E., Kolchanov N.A.


AGNS (ARABIDOPSIS GeneNet SUPPLEMENTARY DATABASE), RELEASE 3.0
Omelianchuk N.A., Mironova V.V., Poplavsky A.S., Pavlov K.S., Savinskaya S.A., Podkolodny N.L., Mjolsness E.D., Meyerowitz E.M., Kolchanov N.A.


SEMANTICALLY RICH ONTOLOGY OF ANATOMICAL STRUCTURE AND DEVELOPMENT FOR ARABIDOPSIS THALIANA L.
Ponomaryov D., Omelianchuk N., Kolchanov N., Mjolsness E., Meyerowitz E.


A PROGRAM METHOD OF CONSTRUCTING ONTOLOGY OF PHENOTYPIC ABNORMALITIES FOR ARABIDOPSIS THALIANA
Ponomaryov D., Omelianchuk N., Mironova V., Kolchanov N., Mjolsness E., Meyerowitz E.


Volume 3

CONTENTS

PART 4. GENE NETWORKS THEORY: MATHEMATICAL PROBLEMS AND SOFTWARE

DEVELOPMENT OF A COMPUTER SYSTEM FOR THE AUTOMATED RECONSTRUCTION OF MOLECULAR-GENETIC INTERACTION NETWORKS
Aman E.E., Demenkov P.S., Pintus S.S., Nemiatov A.I., Apasieva N.V., Dubovenko E.A., Ignatieva E.V., Podkolodny N.L., Ivanisenko V.A.


RECONSTRUCTION AND COMPUTER ANALYSIS OF THE FATTY ACID b-OXIDATION GENE NETWORK REGULATED BY THE PPAR TRANSCRIPTION FACTORS
Aman E.E., Levitsky V.G., Ignatieva E.V.


OPTIMAL CONTROL TASKS IN TERMS OF THE GENE NETWORK MODELS
Bezmaternykh K.D., Nikulichev Yu.V., Likhoshvai V.A., Matushkin Yu.G., Latipov A.F., Kolchanov N.A.


MATRIX PROCESS MODELLING: ON ONE CLASS OF INFINITE-ORDER SYSTEMS OF DIFFERENTIAL EQUATIONS AND ON DELAY DIFFERENTIAL EQUATIONS
Demidenko G.V., Khropova Yu.E., Kotova T.V.


MATRIX PROCESS MODELLING: ON A NEW METHOD OF APPROXIMATION OF SOLUTIONS OF DELAY DIFFERENTIAL EQUATIONS
Demidenko G.V., Mudrov A.V.


MATRIX PROCESS MODELLING: ON PROPERTIES OF SOLUTIONS OF ONE DELAY DIFFERENTIAL EQUATIONS
Demidenko G.V., Khropova Yu.E.


ASYMPTOTIC PROPERTIES OF SOLUTIONS OF DIFFERENTIAL-DIFFERENCE EQUATIONS WITH PERIODIC COEFFICIENTS IN LINEAR TERMS
Demidenko G.V., Matveeva I.I.


PROGRAM PACKAGE HGNET FOR COMPUTATIONAL STUDIES OF HYPOTHETICAL GENE NETWORKS Fadeev S.I., Korolev V.K.

GENE NETWORKS BEHAVIOR IN A SERIES OF SUCCESIVE CELL DIVISIONS
Galimzyanov A.V.


ASYMMETRIC MODELS OF THE GENE NETWORKS
Golubyatnikov V.P., Gaidov Yu.A., Kleshchev A.G.


GENE NETWORK MODELS WITH DIFFERENT TYPES OF REGULATION
Golubyatnikov V.P., Gaidov Yu.A., Kleshchev A.G., Volokitin E.P.


RESEARCH OF CYCLIC GENE NETWORK CIRCUITS WITH NEGATIVE TYPE OF REGULATION
Klishevich M.A., Kogai V.V., Fadeev S.I.


ON THE RECONSTRUCTION OF A GENETIC AUTOMATON ON THE BASIS OF BOOLEAN DYNAMIC DATA
Komarov A.V., Akberdin I.R., Ozonov E.A., Evdokimov A.A.


OSCILLATIONS OF CHAOTIC TYPE IN SYMMETRIC GENE NETWORKS OF SMALL DIMENSION
Likhoshvai V.A., Rudneva D.S., Fadeev S.I.


SEARCHING CONSTRAINTS IN BIOLOGICAL REGULATORY NETWORKS USING SYMBOLIC ANALYSIS
Mateus D., Gallois J.P.


MATRIX PROCESS MODELLING: DEPENDENCE OF SOLUTIONS OF A SYSTEM OF DIFFERENTIAL EQUATIONS ON PARAMETER
Matveeva I.I., Popov A.M.


AN INTEGRATION OF THE DESCRIPTIONS OF GENE NETWORKS AND THEIR MODELS PRESENTED IN SIGMOID (CELLERATOR) AND GENENET
Podkolodny N.L., Podkolodnaya N.N., Miginsky D.S., Poplavsky A.S., Likhoshvai V.A., Compani B., Mjolsness E.


SPECTRAL ANALYSIS OF GENE EXPRESSION PROFILES USING GENE NETWORKS
Rapaport F., ZinovyevA., Barillot E., Vert J.-P.


BIOPATH . A NEW APPROACH TO FORMALIZED DESCRIPTION AND SIMULATION OF BIOLOGICAL SYSTEMS
Kolpakov F., Sharipov R., Cheremushkina E., Kalashnikova E.


RESEARCH ON BEHAVIOR OF GOVERNING GENE/EPIGENE NETWORKS AS A PROBLEM OF CELLULAR AUTOMATA IDENTIFICATION
Tchuraev R.N.


PART 5. COMPARATIVE AND EVOLUTIONARY GENOMICS AND PROTEOMICS

TIME SCALE OF POXVIRUS EVOLUTION
Babkin I.V., Shchelkunov S.N.


BURSTS OF NON-SYNONYMOUS SUBSTITUTIONS IN HIV-1 PHYLOGENETIC TREE REVEAL INSTANCES OF POSITIVE SELECTION AT CONSERVATIVE PROTEIN SITES
Bazykin G.A., Dushoff J., Levin S., Kondrashov A.


MICRO- AND MINISATELLITES IN HUMAN GENOME, TANDEMSWAN SOFTWARE IN USE
Boeva V.A., Makeev V.J.


SEARCH FOR MULTI-SNP DISEASE ASSOCIATION
Brinza D., Perelygin A., Brinton M., Zelikovsky A.


THE MODELS OF POPULATION DYNAMICS AS TOOL FOR STUDYING OF GENETIC POLYMORPHISM OF BAIKALIAN POLYCHAETS
Bukin Yu.S., Pudovkina T.A.


SEARCHING FOR AGROBACTERIAL T-DNA FRAGMENTS IN PLANT GENOMES
Chumakov M.I., Mazilov S.I., Zotova T.V.


VARIATIONS IN NUCLEOTIDE COMPOSITION OF THE REGION ITS1-5.8S RDNA-ITS2 IN EVOLUTIONARY ADVANCED AND EVOLUTIONARY STATIC BRANCHES OF THE MONOCOTYLEDONOUS PLANTS
Chupov V.S., Machs E.M.


HUMAN-CHIMPANZEE PROPERTY-DEPENDANT COMPARISONS ON CHROMOSOMES 21
Deyneko I.V., Kalybaeva Y.M., Kel A.E., Blocker H., Kauer G.


EVOLUTION AND ORIGIN OF NEUROFIBROMIN, THE PRODUCT OF THE NEUROFIBROMATOSIS TYPE 1 (NF1) TUMOR-SUPRESSOR GENE
Golovnina K., Blinov A., Chang L.-S.


MOLECULAR PHYLOGENY OF THE GENUS TRITICUM L.
Golovnina K., Glushkov S., Blinov A., Mayorov V., Adkison L., Goncharov N.


INFERRING REGULATIORY SIGNAL PROFILES AND EVOLUTIONARY EVENTS
Gorbunov K.Yu., Lyubetsky V.A.


A METHOD FOR SEMIAUTOMATED ANALYSIS OF GENE EVOLUTION
Gunbin K.V., Morozov A.V., Afonnikov D.A.


AROMORPHOSES AND ADAPTIVE MOLECULAR EVOLUTION: MORPHOGENS AND SIGNALING CASCADE GENES
Gunbin K.V.


EVOLUTIONARY RELATIONSHIPS AND DISTRIBUTION OF THE DIFFERENT LTR RETROTRANSPOSON FAMILIES IN PLANTS
Kabanova A., Novikova O., Gunbin K., Fet V., Blinov A.


NEW KIDS ON THE BLOCK: SELF-SYNTHESIZING DNA TRANSPOSONS
Kapitonov V.V., Jurka J.


MULTI-SNP ANALYSIS OF CCR5-CCR2 GENES IN ETHIOPIAN JEWS: MICRO-EVOLUTION AND HIV-RESISTANCE IMPLICATIONS
Korostishevsky M., Bonne’-Tamir B., Bentwich Z., Tsimanis A.


TRANSCRIPTIONAL REGULATION OF THE METHIONINE BIOSYNTHESIS IN ACTINOBACTERIA AND STREPTOCOCCI
Kovaleva G.Yu., Gelfand M.S.


PHYLOGENETIC ANALYSIS OF COG1649, A NEW FAMILY OF PREDICTED GLYCOSYL HYDROLASES
Kuznetsova A.Y., Naumoff D.G.


EVOLUTIONARY CONSTRUCTOR: A PACKAGE FOR MODELING COEVOLUTION OF UNICELLULAR ORGANISMS
Lashin S.A., Likhoshvai V.A., Kolchanov N.A., Matushkin Yu.G.


MODELING OF HORIZONTAL GENE TRANSFER IN PROKARYOTIC POPULATIONS WITH THE ¡°EVOLUTIONARY CONSTRUCTOR¡± PROGRAM PACKAGE
Lashin S.A., Likhoshvai V.A., Kolchanov N.A., Matushkin Yu.G.


MOLECULES VERSUS MORPHOLOGY IN OLIGOCHAETA SYSTEMATICS
Liventseva V., Kaygorodova I.


NEW FAMILY OF LTR RETROTRANSPOSABLE ELEMENTS FROM FUNGI
Novikova O., Fursov M., Blinov A.


CONCERTED EVOLUTION OF PARALOGOUS OAS1 GENES IN RODENTIA AND CETARTIODACTYLA
Perelygin A.A., Zharkikh A.A., Brinton M.A.


POPULATION GENETIC POLYMORPHISM OF ENDEMIC MOLLUSCS BAICALIA CARINATA (MOLLUSCA: CAENOGASTROPODA)
Peretolchina T.E., Bukin Yu.S., Sitnikova T.Ya., Sherbakov D.Yu.


PHYLOGENETIC ANALYSIS OF THE p53 AND p63/p73 GENE FAMILIES
Pintus S.S., Ivanisenko V.A.


HUMAN GENOME POLYMORPHISM AND ALTERNATIVE SPLICING
Ramensky V., Nurtdinov R., Neverov A., Mironov A., Gelfand M.


PRIMORDIAL TRANSLATION OF BOTH COMPLEMENTARY STRANDS MIGHT DIRECT THE EARLY EVOLUTION OF THE GENETIC CODE
Rodin S.N., Rodin A.S.


THEORETICAL ANALYSIS OF MITOCHONDRIAL DNA SOMATIC MUTATION SPECTRA IN OXYS AND WISTAR RATS
Rotskaya U.N., Rogozin I.B., Vasyunina E.A., Kolosova N.G., Sinitsyna O.I.


REFINEMENT OF PHYLOGENETIC SIGNAL IN MULTIPLE SEQUENCE ALIGNMENT: RESULTS OF SIMULATION STUDY
Rusin L.Y., Lyubetsky V.A.


GENETIC DIVERSITY AND PHYLOGENETIC RELATIONSHIPS IN GROUPS OF ASIAN GUARDIAN, SIBERIAN HUNTING AND EUROPEAN SHEPHERD DOG BREEDS
Ryabinina O.M.


ANALYSIS OF EGFR GENE MUTATIONS WHICH HAVE A RESPONSE TO QUINAZOLIN INHIBITORS
Sabitha K., Kaiser J.


TRANSPOSON-FREE REGIONS IN MAMMALIAN GENOMES
Simons C., Pheasant M., Makunin I.V., Mattick J.S.


EVOLUTIONAL AND FUNCTIONAL ANALYSIS OF T-BOX REGULON IN BACTERIA: IDENTIFICATION OF NEW GENES INVOLVED IN AMINO ACID METABOLISM
Vitreschak A.G., Lyubetsky V.A., Gelfand M.S.


RSCU_COMPARER: A NEW STATISTICAL TOOL FOR PRACTICAL ANALYSIS OF CODON USAGE
Vladimirov N.V., Kochetov A.V., Grigorovich D.A., Matushkin Yu.G.


ASSOCIATION STUDY OF SNP OF THE TNF-ALPHA GENE WITH BOVINE LEUKOSIS AND EVALUATION OF ITS FUNCTIONAL SIGNIFICANCE
Yudin N.S., Vasil'eva L.A., Kobzev V.F., Kuznetsova T.N., Ignatieva E.V., Oshchepkov D.Yu., Voevoda M.I., Romaschenko A.G.


PHYLOGENETIC CHANGES IN CHLOROPLAST GENOMES
Zotov V.S., Punina N.V., Dorokhov D.B., Schaad N.W., Ignatov A.N.


PART 6. OTHER TOPICS RELATED WITH BIOINFORMATICS

INVESTIGATION OF NAMED ENTITY RECOGNITION IN MOLECULAR BIOLOGY BY DATA FUSION
Arrigo P., Cardo P.P.


GRAPH THEORY ALGORITHM FOR SOLUTION OF COMPUTATIONAL PROBLEMS OF GENE MAPPING
Axenovich T.I.


BIOINFORMATICS EDUCATION IN THE INSTITUTE OF BIOMEDICAL CHEMISTRY RAMS: COURSE «BIOINFORMATICS – THE WAY FROM GENE TO DRUG» AND SPECIAL COURSE «BIOINFORMATICS AND COMPUTER-AIDED DRUG DESIGN»
Ivanov A.S., Poroikov V.V., Archakov A.I.


IN SEARCH OF GENETIC SIGNATURE FOR THE EXPANSION OF IRRIGATION SYSTEMS IN BALI
Karafet T.M., Lansing, J.S., Hammer M.F.


EPI-GIS: GIS ASSISTED COMPUTER TOOLS FOR DATA ACCUMULATION, COMPUTER ANALYSIS AND MODELING IN MOLECULAR EPIDEMIOLOGY
Kolchanov N.A., Orlova G.V., Bachinsky A.G., Bazhan S.I., Shvarts Ya.Sh., Golomolzin V.V., Popov D.Yu., Efimov V.M., Tololo I.V., Ananko E.A., Podkolodnaya O.A., Il'ina E.N., Rogov S.I., Tretiakov V.E., Kubanova A.A., Govorun V.M.


EVOLUTION OF THE STRUCTURE OF THE XIST LOCUS IN MAMMALS
Kolesnikov N.N., Elisafenko E.A., Zakian S.M.


BioUML: VISUAL MODELING, AUTOMATED CODE GENERATION AND SIMULATION OF BIOLOGICAL SYSTEMS
Kolpakov F., Puzanov M., Koshukov A.


WEB SERVICES AT THE EUROPEAN BIOINFORMATICS INSTITUTE
Labarga A., Anderson M., Valentin F., Lopez R.


OBJECT-ORIENTED APPROACH TO BIOINFORMATICS SOFTWARE RESOURCES INTEGRATION
Miginsky D.S., Sokolov S.A., Labuzhsky V.V., Nikitin A.G., Tarancev I.G.


ARCHITECTURE OF SOFTWARE TOOLKIT FOR STORING AND OPERATING WITH BIOSYSTEMS MODELS
Miginsky D.S., Suslov V.V., Rasskazov D.A., Podkolodny N.L., Kolchanov N.A.


AUTOMATED TEXT ANALYSIS OF BIOMEDICAL ABSTRACTS APPLIED TO THE EXTRACTION OF SIGNALING PATHWAYS INVOLVED IN PLANT COLD-ADAPTATION
Olsson B., Gawronska B., Erlendsson B., Lindlof A., Dura E.


THE ONTOLOGY OF ECOSYSTEMS
Suslov V.V., Sergeev M.G., Yurlova N.I., Miginsky D.S.


THE GArna TOOLBOX FOR RNA STRUCTURE ANALYSIS: THE 2006 STATE OF THE ART
Titov I.I.


A MODEL OF THE TRANSLATIONAL INHIBITION BY MIRISC COMPLEX DESCRIBES PROTEIN SYNTHESIS VARIATIONS INDUCED BY MUTATIONS IN MAMMALIAN miRNA SITES
Titov I.I., Ivanisenko A.Yu.


PART 7. SHORT ABSTRACTS

DETERMINATION OF NATIVELY UNFOLDED REGIONS OF SUPEROXIDE DISMUTASE FROM PACIFASTACUS LENIUSCULUS
Cavas L., Cavas C.K.


DYNAMIC PROGRAMMING ALGORITHM PARALLIZATION FOR PROTEIN FOLDING
Dulko V., Feranchuk S.


COMPUTATIONAL IDENTIFICATION OF TRANSCRIPTION FACTOR BINDING SITES WITH VARIABLE ORDER BAYESIAN NETWORKS
Grosse Ivo


HAPLOTYPE BLOCK STRUCTURE IS CONSERVED ACROSS MAMMALS
Guryev V., Smits B.M.G., van de Belt J., Verheul M., Hubner N., Cuppen E.


USING BIOLOGICAL KNOWLEDGE IN COMPUTATIONAL METHODS TO DISCOVER MECHANISMS OF TRANSCRIPTION REGULATION
Martin D., Portales-Casamar E., Kirov S., Lim J., Brumm J., Snoddy J., Wasserman W.W.


MOLECULAR NETWORKS IN MAMMALS: EXTRACTION FROM LITERATURE AND MICROARRAY ANALYSIS
Mazo I., Sivachenko A., Yuryev A., Daraselia N.


THE FEATURES OF STRUCTURAL DYNAMICS OF DIFFERENT TUBULIN SUBUNITS
Nyporko A.Yu., Blume Ya.B.


RegulonDB: GOING BEYOND TRANSCRIPTIONAL REGULATION
Penaloza-Spinola M.I., Peralta-Gil M., Gama-Castro S.*, Contreras-Moreira B., Santos-Zavaleta A., Martinez-Flores I., Collado-Vides J.


RegulonDB. THE MOST IMPORTANT DATABASE IN TRANSCRIPTIONAL REGULATORY NETWORK, OPERON ORGANIZATION, AND GROWTH CONDITIONS OF ESCHERICHIA COLI K12
Santos-Zavaleta A., Salgado H., Gama-Castro S., Peralta-Gil M., Contreras-Moreira B., Penaloza-Spinola M.I., Collado-Vides J.


USE MOLECULAR MARKERS FOR DIFFERENTIATION POPULATIONS OF STIPA CAPILLATA GROWING IN THE REGIONS WITH HIGH CHRONICAL DOSES OF y-RADIATION
Sarsenbaev K.N.


UNEQUALLY SPACED SAMPLING MAPPING OF QTL
Shaoqing Huang, Yini Cui


LABORATORY INFORMATION MANAGEMENT SYSTEM FOR MEMBRANE PROTEIN STRUCTURE INITIATIVE
Troshin P.V., Papiz M.Z., Prince S.M., Daniel E.J., Morris C., Griffiths S.L., Diprose J.M., Pilicheva K., v. Niekerk J., Pajon A.











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IC&G  SB RAS,
Laboratory of Theoretical Genetics