2006

2004

2002

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1998



PROCEEDINGS OF THE BGRS



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

BGRS’ 2004
Novosibirsk, Russia
July 25 - 30, 2004

Volume 1

Volume 2



INTERNATIONAL PROGRAM COMMITTEE

LOCAL ORGANIZING COMMITTEE

SPONSORS

INTRODUCTION


Volume 1

CONTENTS

COMPUTATIONAL STRUCTURAL AND FUNCTIONAL GENOMICS

SOME WAYS TO INFER A DNA FUNCTION FROM THE SEQUENCE INFORMATION
Abnizova I., te Boekhorts R., Gilks W.


AUTOMATIC LANE DETECTION AND SEPARATION IN ONE DIMENSIONAL DNA GEL IMAGES
Akbari A., Algregtsen A.


GpiMap, AN ENVIRONMENT FOR GENETIC/PHYSICAL MAP DATA MANAGEMENT, VISUALIZATION AND COMPARATIVE ANALYSIS
Albini G., Chetouani F., Rouille S., Karsenty E., Thomas B., Legeai F., Samson D., Pereira L., Arcade A., Joets J., Scala D., Viara E., Barillot E., Duclert A.


DATABASE OF LONG TERMINAL REPEATS IN HUMAN GENOME: STRUCTURE AND SYNCHRONIZATION WITH MAIN GENOME ARCHIVES
Alexeevski A.V., Lukina E.N., Salnikov A.N., Spirin S.A.


RECOGNITION OF CODING REGIONS IN GENOME ALIGNMENT
Astakhova T.V., Petrova S.V., Tsitovich I.I., Roytberg M.A.


ALGORITHM FOR SEARCHING FOR HIGHLY DIVERGENT TANDEM REPEATS IN DNA SEQUENCES, STATISTICAL TESTS, AND BIOLOGICAL APPLICATION IN DROSOPHILA MELANOGASTER GENOME
Boeva V.A., Regnier M., Makeev V.J.


NON-RANDOM DISTRIBUTION OF ALU ELEMENTS IN HUMAN: NOVEL INSIGHTS FROM ANALYSIS OF THE COMPLETE GENOME
Brahmachari S.K., Grover D., Majumder P.P., Mukerji M.


MAPPING OF POTENTIALLY TRANSCRIBED REGIONS IN THE GENOME OF E. COLI BY NEW PROMOTER-SEARCH ALGORITHM
Brok-Volchanski A.S., Purtov Yu.A., Lukyanov V.I., Kostyanicina E.G., Antipov S.S., Deev A.A., Ozoline O.N.


ACCURATE PREDICTION OF DNA OPENING PROFILES BY PEYRARD-BISHOP NONLINEAR DYNAMIC SIMULATIONS
Choi C.H., Kalosakas G., Rasmussen K.O., Bishop A.R., Usheva A.


DEVELOPMENT OF A METHOD FOR IN SILICO IDENTIFICATION OF DNA SEQUENCES PARTICIPATING IN MEIOTIC CHROMOSOME SYNAPSIS AND RECOMBINATION
Dadashev S.Ya., Grishaeva T.M., Bogdanov Yu.F.


CONSERVATION OF ALTERNATIVE SPLICING REGULATORY SIGNAL UGCAUG IN THE MOUSE AND HUMAN GENOMES
Denisov S.V., Gelfand M.S.


INFORMATIONAL ASPECTS OF THE LATENT TRIPLET PERIODICITY ANALYSIS
Frenkel F.E., Chaley M.B., Korotkov E.V., Skryabin K.G.


A PRACTICAL METHOD FOR MAXIMUM EXACT MATCHES IN LARGE GENOMES
Fursov M.Yu., Baksheyev D.G., Rodionov K.V., Golubitskii A.A., Saraev D.V., Denisov S.I., Blinov V.M.


DISTRIBUTION OF THE SF-1 BINDING SITES PREDICTED BY THE SITEGA METHOD IN THE GENOMIC SEQUENCES AND THEIR EXPERIMENTAL VERIFICATION
Ignatieva E.V. , Levitsky V.G., Vasiliev G.V., Klimova N.V., Busygina, T.V., Merkulova T.I.


COMPARISON OF THE RESULTS OF SEARCH FOR THE SF-1 BINDING SITES IN THE PROMOTER REGIONS OF THE STEROIDOGENIC GENES, USING THE SITEGA AND SITECON METHODS
Ignatieva E.V., Oshchepkov D.Yu., Levitsky V.G., Vasiliev G.V., Klimova N.V., Busygina T.V., Merkulova T.I.


A NEW ALGORITHM FOR RECOGNIZING THE OPERON STRUCTURE OF PROKARYOTES
Ishchukov I.M., Likhoshvai V.A., Matushkin Yu.G.


ANALYSIS OF OLIGONUCLEOTIDE COMPOSITION IN DNA OF E. COLI GENOME AND PROMOTER SITES
Kamzolova S.G., Sorokin A.A., Dzhelyadin T.R., Osypov A.A., Beskaravainy P.M.


ELECTROSTATIC PROPERTIES OF E. COLI GENOME DNA
Kamzolova S.G., Sorokin A.A., Dzhelyadin T.R., Beskaravainy P.M., Osypov A.A.


MOLECULAR PALEONTOLOGY OF DNA TRANSPOSONS IN EUKARYOTIC GENOMES
Kapitonov V.V., Jurka J.


ANALYSIS OF NUCLEOSOME FORMATION POTENTIAL AND CONFORMATIONAL PROPERTIES OF HUMAN J1-J2 TYPE ALPHA SATELLITE DNA
Katokhin A.V., Levitsky V.G., Oshchepkov D.Yu., Poplavsky A.S., Furman D.P.


BACTERIAL METAL RESISTANCE SYSTEMS REGULATED BY TRANSCRIPTION REGULATORS OF THE MERR FAMILY
Kazakov A.E., Kalinina O.V., Permina E.A., Gelfand M.S.


GENOME REVIEWS: INTEGRATED VIEWS OF COMPLETE GENOMES
Kersey P.J., Morris L., Faruque N., Kulikova T., Whitfield E., Apweiler R.


COMPARISON OF THE STRUCTURES OF IN VITRO SELECTED AND NATURAL BINDING SITES OF TRANSCRIPTION FACTORS
Khlebodarova T.M., Podkolodnaya O.A., Ananko E.A., Ignatieva E.V.


TRRD_ARTSITE DATABASE: STRUCTURES OF TRANSCRIPTION FACTOR BINDING SITES
Khlebodarova T.M., Podkolodnaya O.A., Ananko E.A., Stepanenko I.L., Ignatieva E.V., Podkolodny N.L., Pozdnyakov M.A., Proscura A.L.


TRANSLATIONAL POLYMORPHISM AS A POTENTIAL SOURCE OF EUKARYOTIC PROTEINS VARIETY
Kochetov A.V. , Sarai A., Kolchanov N.A.


ANALYSIS OF PLANT MITOCHONDRIAL GENOME ORGANIZATION: CHARACTERISTICS OF REPEATS AND SEQUENCE COMPLEXITY
Konstantinov Yu.M., Poplavsky A.S., Orlov Yu.L.


MANUAL CURATION OF EST LIBRARIES BY TISSUE SPECIFICITY AND CELL ORIGIN
Kosmodemiansky Il.A., Gelfand M.S., Mironov A.A.


DETECTION OF CLASSICAL ATTENUATION IN BACTERIAL GENOMES
Leontiev L.A., Shirshin M.A., Lyubetsky V.A.


ANALYSIS OF THE CONTEXT FEATURES OF SF-1 BINDING SITE AND DEVELOPMENT OF A CRITERION FOR SF-1 REGULATED GENE RECOGNITION BY THE SITEGA METHOD
Levitsky V.G., Ignatieva E.V., Busygina T.V., Merkulova T.I.


DNA NUCLEOSOME ORGANIZATION OF THE FUNCTIONAL GENES REGIONS AND ITS RELATION TO GENE EXPRESSION LEVEL
Levitsky V.G., Pichueva A.G., Kochetov A.V., Milanesi L.


ANALYSIS OF PERIODICITIES IN THE DINUCLEOTIDE CONTEXT OF NUCLEOSOMAL DNA USING THE METHOD PHASE
Levitsky V.G., Katokhin A.V., Furman D.P.


NUCLEOSOME FORMATION POTENTIAL OF THE GENE REGULATORY REGIONS
Levitsky V.G., Proscura A.P., Podkolodnaya O.A., Ignatieva E.V., Ananko E.A.


DISTANCE PREFERENCES IN DISTRIBUTION OF BINDING MOTIFS AND HIERARCHICAL LEVELS IN ORGANIZATION OF TRANSCRIPTION REGULATORY INFORMATION
Makeev V.J., Lifanov A.P., Nazina A.G., Papatsenko D.A.


EXTREMELY CONSERVED NON-CODING SEQUENCES IN VERTEBRATE GENOMES
Makunin I.V., Stephen S., Pheasant M., Bejerano G., Kent J.W., Haussler H., Mattick J.S.


COMPUTER-BASED ANALYSIS AND RECOGNITION OF POTENTIAL IRON-RESPONSIVE ELEMENTS IN 5’ AND 3’ UTR TRANSCRIPTS OF EUKARYOTIC GENES
Mishchenko E.L., Kondrakhin Yu.V., Podkolodnaya O.A.


THE NEW APPROACH OF BOTH NEW AND OLD SEGMENTAL DUPLICATIONS SEARCH: REPETITIVE DNA AS A MOLECULAR ARCHAEOLOGY TOOL
Oparina N., Rychkov A., Mashkova T.


NUCLEOSOME POSITIONING SIGNAL ANALYSIS
Orlov Yu.L., Levitsky V.G.


COMPUTER ANALYSIS OF GENOMIC SEQUENCE COMPLEXITY: NEW APPLICATIONS Orlov Yu.L., Potapov V.N., Poplavsky A.S.

CONTEXT FEATURES OF TRANSCRIPTION FACTOR BINDING SITE SEQUENCES: RELATION TO DNA-BINDING DOMAIN CLASSIFICATION
Orlov Yu.L., Proscura A.L., Vityaev E.E., Arrigo P.


SITECON: A TOOL FOR TRANSCRIPTION FACTOR BINDING SITE RECOGNITION
Oshchepkov D.Yu., Grigorovich D.A., Ignatieva E.V., Khlebodarova T.M.


A DATABASE ON DNA SEQUENCE/ACTIVITY RELATIONSHIPS: APPLICATION TO PHYLOGENETIC FOOTPRINTING
Ponomarenko M.P., Ponomarenko J.V.


ANALYSIS OF GENE REGULATORY SEQUENCES BY KNOWLEDGE DISCOVERY METHODS
Pozdnyakov M.A., Orlov Yu.L., Vishnevsky O.V., Proscura A.L., Vityaev E.E., Arrigo P.


SREBP BINDING SITES: CONTEXT FEATURES AND ANALYSIS OF GENOME DISTRIBUTION BY THE SITECON METHOD
Proskura A.L., Oshchepkov D.Yu., Pozdnyakov M.A., Ignatieva E.V.


APPLICATION OF TIME-FREQUENCY ANALYSIS IN EXON CLASSIFICATION
Renjun Yu., Eng Chong Tan


SEARCH FOR REGULATORY MOTIFS IN DROSOPHILA MELANOGASTER GENOME
Samsonova A., Dieterich C., Vingron M., Brazma A.


LONG SEGMENTAL REPEATS IN HUMAN GENOME: DENSITY, DISTRIBUTION, STRUCTURE
Saraev D.V., Dzhekshenbaeva G.K., Baksheyev D.G., Rodionov K.V., Golubitskii A.A., Fursov M.Yu., Golosov I.S., Kisselev L.L., Blinov V.M.


GENOME-SCALE PREDICTION OF TRANSCRIPTION FACTORS AND THEIR TARGETS
Sarai A., Ahmad Sh., Gromiha M.M., Kono H.


BINARY TREE FOR CLUSTERING OF REGULATORY SIGNALS
Stavrovskaya E.D., Mironov A.A.


THEORETICAL AND EXPERIMENTAL STUDY OF MUTATIONS INDUCED BY 8-OXOGUANINE
Vasyunina E.A., Rogozin I.B., Sinitsina O.I., Plaksina A.S., Rotskaya U.N.


THE ARGO_SITES: AN ANALYSIS AND RECOGNITION OF THE TRANSCRIPTION FACTOR BINDING SITES BASED ON SETS OF DEGENERATE OLIGONUCLEOTIDE MOTIFS
Vishnevsky O.V., Ignatieva E.V., Arrigo P.


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


USE OF AN INTEGRATED RULE SYSTEM FOR IDENTIFICATION OF THE TRANSCRIPTION FACTOR BINDING SITES FOR MCM1 AND FKH2 IN S. CEREVISIAE
Walker N.J., Sharrocks A.D., Attwood T.K.


A PECULIAR CODON USAGE PATTERN REVEALED AFTER REMOVING THE EFFECT OF DNA METHYLATION
Xuhua Xia


DEVELOPMENT OF METHOD FOR IN SILICO MAPPING OF QUANTITATIVE TRAIT LOCI
Zykovich A.S., Axenovich T.I.


COMPUTATIONAL STRUCTURAL AND FUNCTIONAL PROTEOMICS

PREDICTING CONTACT NUMBERS OF AMINO ACID RESIDUES USING A NEURAL NETWORK MODEL
Afonnikov D.A.


COMBINED APPROACH TO PROTEIN SECONDARY STRUCTURE PREDICTION
Amirova S.R., Machavariani M.A., Filatov I.V., Milchevsky Ju.V., Esipova N.G., Tumanyan V.G.


STRUCTURE AND POLYMORPHISM OF THE HIV-1 PRINCIPAL NEUTRALIZING EPITOPE
Andrianov A.M.


NEW APPROACHES TO ANALYSIS OF PROTEIN STRUCTURE AND FUNCTION
Bachinsky A.G., Solovyev V.V.


MOLECULAR MODELING AND COMPARATIVE ANALYSIS OF AMINO-TERMINAL DOMAIN OF NMDA IONOTROPIC GLUTAMATE RECEPTORS
Belenikin M.S.


KINETICS OF PROTEIN FOLDING: LATTICE SIMULATIONS AND ANALYTIC MODEL
Chekmarev S.F., Krivov S.V., Karplus M.


IDENTIFICATION AND ANALYSIS OF CELL SURFACE NUCLEIC ACIDS-BINDING PROTEINS
Chelobanov B.P., Ivanisenko V.A.1, Kharkova M.V., Laktionov P.P., Rykova E.Yu., Vlassov V.V.


EXPERIMENTAL AND COMPUTER EVALUATION OF THE ABILITY ssT-DNA-BINDING VirE2 PROTEIN TO INTERACT WITH LIPID MEMBRANES
Chumakov M.I., Burmatov A.V., Bogdanov V.I., Volokhina I.V.


MEMBRANE PROTEINS: THE NEW INSIGHTS via COMPUTATIONAL EXPERIMENTS
Efremov R.G., Volynsky P.E., Nolde D.E., Vereshaga Y.A., Konshina A.G., Simakov N.A., Arseniev A.S.


COMMON STRUCTURAL FEATURES OF HOMEODOMAINS AND HOMEODOMAIN-DNA COMPLEXES
Ershova A.S., Alexeevski A.V., Spirin S.A., Karyagina A.S.


COMPUTATION OF THE THREE DIMENSIONAL STRUCTURE OF THE HUMAN TYPE (III) COLLAGEN
Filatov I.V., Milchevsky Ju.V., Esipova N.G., Tumanyan V.G.


SEARCHING STRUCTURAL PROTEIN DATABASES FOR ENZYMATIC ACTIVE SITES BY 3D PATTERNS
Gariev I.A., Uporov I.V., Varfolomeev S.D.


A SYSTEM FOR COMPLEX ANALYSIS OF PROTEIN MACROMOLECULES SPATIAL STRUCTURES
Gribkov M.A., Korotkova M.A.


PDBSITE, PDBLIGAND AND PDBSITESCAN: A COMPUTATIONAL WORKBENCH FOR THE RECOGNITION OF THE STRUCTURAL AND FUNCTIONAL DETERMINANTS IN ROTEIN TERTIARY STRUCTURES COMBINED WITH PROTEIN DRAFT DOCKING
Ivanisenko V.A., Pintus S.S., Krestyanova M.A., Demenkov P.S., Znobisheva E.K., Ivanov E.E., Grigorovich D.A.


SDPPRED: A METHOD FOR PREDICTION OF AMINO ACID RESIDUES THAT DETERMINE DIFFERENCES IN FUNCTIONAL SPECIFICITY OF HOMOLOGOUS PROTEINS AND ITS APPLICATION TO THE MIP FAMILY OF MEMBRANE TRANSPORTERS
Kalinina O.V., Novichkov P.S., Mironov A.A., Gelfand M.S., Rakhmaninova A.B.


SYMMETRY AND SPATIAL STRUCTURE OF THE CANONICAL SET OF AMINO ACIDS
Karasev V.A., Luchinin V.V., Stefanov V.E.


STATISTICAL METRICS FOR PROTEIN ACTIVE SITE PREDICTION WITH THEMATICS
Ko J., Andre P., Murga L.F., Ondrechen M.J.


FROM PROTEIN SEQUENCE TO PROTEIN SPECIFICITY: COMPLETELY AUTOMATED DISCOVERY AND MAPPING OF SPECIFICITY DETERMINING RESIDUES
Kolesov G., Mirny L.A.


MOLECULAR MODELING OF THE NUCLEOTIDE-BINDING DOMAIN OF THE WILSON’ DISEASE PROTEIN: THE ATP-BINDING SITE AND DOMAIN DYNAMICS
Kosinsky Yu.A., Nolde D.E., Tsivkovskii R., Arseniev A.S., Lutsenko S., Efremov R.G.


ANALYSIS OF PROTEOME COMPEXITY BASED ON COUNTING DOMAIN-TO-PROTEIN LINKS
Kuznetsov V.A., Pickalov V.V., Knott G.D., Kanapin A.A.


VALIDATION OF RANDOM BIRTH-DEATH MODEL OF EVOLUTION OF PROTEOME COMPLEXITY
Kuznetsov V.A.


INFORMATION ABOUT SECONDARY STRUCTURE IMPROVES QUALITY OF PROTEIN ALIGNMENT
Litvinov I.I., Mironov A.A., Finkelstein A.V., Roytberg M.A.


AMINO ACID BIOSYNTHESIS ATTENUATION IN BACTERIA
Lyubetsky V.A., Seliverstov A.V.


REPRESENTATION AND MODELLING OF PROTEIN SURFACE DETERMINANTS
Milanesi L., Merelli I., Pattini L., Cerutti S.


THE ALPHA-GALACTOSIDASE SUPERFAMILY: SEQUENCE BASED CLASSIFICATION OF ALPHA-GALACTOSIDASES AND RELATED GLYCOSIDASES
Naumoff D.G.


INTER-SUBUNIT CONTACTS OF THE PROTEASOMAL ALPHA-SUBUNITS AS DETERMINANTS OF PARALOG GROUPS
Nikolaev S.V., Afonnikov D.A


PROTEIN FAMILY PATTERNS BANK PROF_PAT. CURRENT STATUS
Nizolenko L.Ph., Bachinsky A.G., Yarygin A.A., Naumochkin A.N., Grigorovich D.A.


PROTEIN FOLDING AND MISFOLDING: A BIFURCATION STUDY OF A LATTICE MODEL
Palyanov A.Yu., Krivov S.V., Titov I.I., Karplus M., Chekmarev S.F.


STRUCTURAL MEMORY OF A LATTICE PROTEIN
Palyanov A.Yu., Titov I.I.


COMPUTER SIMULATIONS OF ANIONIC UNSATURATED LIPID BILAYER: A BASE SYSTEM TO STUDY PEPTIDE-MEMBRANE INTERACTIONS
Polyansky A.A., Volynsky P.E., Efremov R.G.


ON AVERAGE ENERGY OF RANDOM WALKS WITH CONSTRAINTS AND GEOMETRICAL COMPLEXITY OF POLYMERS
Perevalov D.S., Davydov O.M., Tatur S.V., Lenskiy S.V.


A MOLECULAR MECHANISM FOR THE STRUCTURE-FUNCTIONAL ALTERATIONS IN MUTANT FORMS OF HUMAN P53 PROTEIN
Pintus S.S., Ivanisenko V.A.


PERIODICAL PATTERNS IN SEQUENCES OF SPIDROINS I AND II AND SECONDARY STRUCTURE PREDICTION
Ragulina L.E., Makeev V.Ju., Esipova N.G., Tumanyan V.G., Bogush V.G., Debabov V.G., Nikitin A.M., Vlasov P.K.


CONSTRUCTING DETAILED KNOWLEDGE-BASED ATOMIC POTENTIALS FOR WATER IN PROTEINS
Rahmanov S.V., Makeev V.Yu.


MINING FROM COMPLETE PROTEOMES TO IDENTIFY ADHESINS AND ADHESIN-LIKE PROTEINS: A RAPID AID TO EXPERIMENTAL RESEARCHERS
Ramachandran S., Jain P., Sachdeva G.


MUTANT PROTEIN STRUCTURES REVEAL MOLECULAR MECHANISMS OF INHERITED DISEASES
Ramensky V.E., Tumanyan V.G.


BENCHMARKING OF TRANSMEMBRANE HELIX PREDICTION SERVERS
Sadovskaya N.S.


MOLECULAR DYNAMICS SIMULATIONS FOR LARGE SERIES OF PEPTIDES (COMPARATIVE STUDY)
Shaitan K.V.


STRUCTURAL AND FUNCTIONAL ANALYSIS OF POORLY CHARACTERIZED PROTEIN FAMILIES AT THE ONTARIO CENTRE FOR STRUCTURAL PROTEOMICS
Skarina T., Evdokimova E., Yakunin A., Khachatryan A., Pennycooke M., Guido V., Guthrie J., Xu X., Semesi A., Gu J., Kudritska M., Egorova O., Gorodichtchenskaia E., Yee A., Savchenko A., Arrowsmith C.H., Edwards A.M.


A MARKOV MODEL FOR PROTEIN SEQUENCES
Surya pavan Y., Mitra Chanchal K.


MOLECULAR MODELING OF HUMAN MT1 AND MT2 MELATONIN RECEPTORS
Tchugunov A.O., Chavatte P., Efremov R.G.


LATENT PERIODICITY OF THE PROTEIN FAMILIES
Turutina V.P., Korotkov E.V., Laskin A.A.


Volume 2

CONTENTS

COMPUTATIONAL SYSTEMIC BIOLOGY

A SYSTEMIC APPROACH TO COMPLEX, MULTI-FACTOR AUTOIMMUNE DISEASES AIMED AT CREATION OF ADEQUATE MODELS OF PATHOLOGIES (e.g. PSORIASIS)
Abdeev R.M.


EBV INFECTION AND EBV TRANSFORMATION: RECONSTRUCTION OF GENE NETWORKS IN THE GeneNet SYSTEM AND SEARCHING FOR REGULATORY POINTS
Ananko E.A., Nedosekina E.A., Oshchepkov D.Yu., Lokhova I.V., Likhoshvai V.A.


FROM GRADIENTS TO STRIPES: A LOGICAL ANALYSIS OF THE GENETIC NETWORK CONTROLLING EARLY DROSOPHILA SEGMENTATION
Chaouiya C., Sanchez L., Thieffry D.


SIGNAL THEORY . AN ALTERNATIVE PERSPECTIVE OF PATTERN SIMILARITY SEARCH
Deyneko I.V., Kel A.E., Wingender E., Gossling F., Blocker H., Kauer G.


DETERMINATION OF STATIONARY SOLUTIONS IN GENE NETWORK MODELS BY HOMOTOPY METHOD
Fadeev S.I., Gainova I.A., Berezin A.Yu., Ratushny A.V., Matushkin Yu.G., Likhoshvai V.A.


ABOUT COMPUTATIONAL RESEARCH OF MATHEMATICAL MODELS OF HYPOTHETICAL GENE NETWORKS BY PARAMETER CONTINUATION
Fadeev S.I., Osokina V.A., Likhoshvai V.A.


ON ONE ALGORITHM FOR MODELING PASSIVE TRANSPORT IN CELL SETS OF ARBITRARY CONFIGURATION
Galimzyanov A.V.


CLOSED TRAJECTORIES IN THE GENE NETWORKS
Golubyatnikov V.P., Makarov E.V.


HOPF BIFURCATION IN THE GENE NETWORK MODELS
Golubyatnikov V.P., Volokitin E.P., Osipov A.F., Likhoshvai V.A.


A SOFTWARE ARCHITECTURE FOR DEVELOPMENTAL MODELING IN PLANTS: THE COMPUTABLE PLANT PROJECT
Gor V., Shapiro B.E., Jonsson H., Heisler M., Venugopala Reddy G., Meyerowitz E.M., Mjolsness E.


A MODEL OF TRYPTOPHAN BIOSYNTHESIS REGULATION
Gorbunov K.Yu., Lyubetsky V.A.


TWO GENE NETWORKS UNDERLYING THE FORMATION OF THE ANTERIOR-POSTERIOR AND DORSO-VENTRAL WING IMAGINAL DISC COMPARTMENT BOUNDARIES IN DROSOPHILA MELANOGASTER
Gunbin K.V., Omelyanchuk L.V., Ananko E.A.


COMBINED OPTIMIZATION TECHNIQUE FOR BIOLOGICAL DATA FITTING
Gursky V.V., Kozlov K.N., Samsonov A.M.


MATHEMATICAL MODEL OF THE GENE NETWORK OF TNFƒ¿-INDUCED NF-kappaB ACTIVATION
Guryeva Ya.P., Stepanenko I.L., Likhoshvai V.A.


METABOLIC PATHWAY PREDICTION/ALIGNMENT
Hofestaedt R., Chen M.


ABOUT NUMERICAL INVESTIGATION OF AUTO-OSCILLATIONS IN HYPOTHETICAL GENE NETWORKS
Kogai V.V., Fadeev S.I., Likhoshvai V.A.


BIOUML . OPEN SOURCE EXTENSIBLE WORKBENCH FOR SYSTEMS BIOLOGY
Kolpakov F.A.


EVOLUTIONARY ALGORITHMS FOR MATHEMATICAL MODELS OF GENE NETWORKS IDENTIFICATION
Lashin S.A. , Likhoshvai V.A.


EXPLICIT INTEGRAL METHOD FOR NONLINEAR DYNAMIC MATHEMATICAL MODELS IDENTIFICATION
Lashin S.A., Likhoshvai V.A.


EFFICIENT ALGORITHM FOR GENE SELECTION USING PLS-RLSC
Li Shen, Eng Chong Tan


ON THE STATIONARY POINTS OF REGULATORY CONTOURS OF GENE NETWORKS
Likhoshvai V.A.


MODELLING OF SUBSTANCE SYNTHESIS PROCESS WITHOUT BRANCHING BY THE DELAY EQUATION
Likhoshvai V.A., Demidenko G.V., Fadeev S.I.


GENE NETWORK OF THE ARABIDOPSIS DEVELOPING SHOOT MERISTEM AND ITS DESCRIPTION IN THE GENENET COMPUTER SYSTEM
Mironova V.V., Omelianchuk N.A.


COMPUTER MODELING OF THE FUNCTION OF TRANSCRIPTION FACTORS DURING MACROPHAGE ACTIVATION
Nedosekina E.A., Ananko E.A., Likhoshvai V.A.


COMPUTER ANALYSIS OF THE LABELED MITOSES CURVES
Nekrasov V., Chernyshev A., Omelyanchuk L.


A COHERENT KINETIC MODEL OF SENSING AND RESPONSE IN HALOBACTERIUM SALINARIUM PHOTOTAXIS BASED ON THE MECHANISM OF FLAGELLAR MOTOR SWITCHING
Nutsch T., Marwan W., Oesterhelt D., Gilles E.D.


AN ELEMENTARY MODULE RECOGNIZING MORPHOGENETIC GRADIENTS IN TISSUES
Omelyanchuk L.V., Gunbin K.V.


AGNS: ARABIDOPSIS GENENET SUPPLEMENTARY DATABASE
Omelianchuk N.A., Mironova V.V., Poplavsky A.S., Kukeeva Yu.A., Podkolodny N.L., Kolchanov N.A.


PROTEIN-PROTEIN INTERACTION NETWORK OF APOPTOSIS SIGNALING PATHWAYS AND ITS USAGE TO IDENTIFY APOPTOTIC REGULATORY ELEMENTS
Peng F., Pio F.


ON RESEARCH INTO HYPOTHETICAL NETWORKS OF ECOLOGICAL NATURE
Peshkov I.M., Likhoshvai V.A., Matushkin Yu.G., Fadeev S.I.


METHOD FOR INTEGRATION OF DATABASES WITH COMMON SUBJECT DOMAINS
Pisarev A., Blagov M., Samsonova M.


QUANTITATIVE APPROACH TO THE FUNCTIONAL GENOMICS OF DEVELOPMENT
Samsonova M. , Surkova S., Jaeger J., Reinitz J.


A SIMULATION MODEL OF EnvZ-OmpR TWO COMPONENT SYSTEM IN ESCHERICHIA COLI
Srividhya K.V., Krishnaswamy S.


TEMPORAL AND SPATIAL PRECISION IN FORMATION OF SEGMENTATION GENE
EXPRESSION DOMAINS IN DROSOPHILA Surkova S.Yu., Samsonova M.G.


A LANGUAGE FOR MODELING GENETIC REGULATION IN PROCARYOTES
Tarasov D.S., Leontiev A.Yu., Akberova N.I.


PRINCIPLES OF ORGANIZATION AND LAWS OF FUNCTIONING IN CONTROL GENE NETWORKS
Tchuraev R.N.


MODELING AND CONSTRUCTION OF MOLECULAR TRIGGER IN E. COLI
Vasilenko N.L., Balueva K.E., Likhoshvai V.A., Nevinsky G.A., Matushkin Yu.G.


STOCHASTIC MODEL OF TRANSLATION ELONGATION BASED ON CONTINUOUS TIME MONTE CARLO METHOD
Vladimirov N.V., Likhoshvai V.A.


RESTRICTION SITE TAGGED PASSPORTS AND MICROARRAYS FOR ANALYSIS OF COMPLEX BIOLOGICAL SYSTEMS
Zabarovsky E.R., Kashuba V.I., Li J., Kutsenko A.S., Protopopov A.I., Petrenko L., Wang F., Senchenko V.N., Kadyrova E., Zabarovska V.I., Muravenko O.V., Zelenin A.V., Kisselev L.L., Winberg G., Ernberg I., Braga E., Lerman M.I., Klein G.


MODELING OF NEURO-ENDOCRINE-IMMUNE NETWORK VIA SUBJECT ORIENTED LITERATURE MINING
Zhang C., Li S.


COMPUTATIONAL EVOLUTIONARY BIOLOGY

EVOLUTION OF GENE STRUCTURE IN EUKARYOTIC GENOMES
Babenko V.N., Sverdlov A., Rogozin I.B., Koonin E.V.


CHANGE IN CpG CONTEXT IS A LEADING CAUSE OF CORRELATION BETWEEN RATES OF NON-SYNONYMOUS AND SYNONYMOUS SUBSTITUTIONS IN RODENTS
Bazykin G.A., Ogurtsov A.Y. , Kondrashov A.S.


EVOLUTIONARY RELATIONSHIPS AND DISTRIBUTION OF NON-LTR RETROTRANSPOSONS IN EUKARYOTES
Beresikov E., Novikova O., Makarevich I., Lashina V., Plasterk R., Blinov A.


RELATIONSHIPS BETWEEN GENERAL CLASSIFICATION OF GENES’ LATENT TRIPLET PERIODICITY AND THE UNIVERSAL PHYLOGENETIC TREE
Chaley M.B., Frenkel F.E., Korotkov E.V., Skryabin K.G.


MCMC METHOD HAS FOUND THAT MULTIPLE SCLEROSIS IS ASSOCIATED WITH TWOTHREE GENES COMBINATIONS
Favorov A.V., Favorova O.O., Andreewski T.V., Sudomoina M.A., Alekseenkov A.D., Kulakova O.G., Boiko A.N., Gusev E.I., Parmigiani G., Ochs M.F.


EVOLUTION OF BACTERIAL REGULATORY SYSTEMS
Gelfand M.S.


COMPARATIVE GENOMIC ANALYSIS OF RESPIRATION SWITCH IN GAMMAPROTEOBACTERIA
Gerasimova A.V., Ravcheyev D.A., Gelfand M.S., Rakhmaninova A.B.


GENOME-WIDE IDENTIFICATION OF MITOCHONDRIAL DNA TOPOISOMERASE I IN ARABIDOPSIS
Katyshev A.I., Rogozin I.B., Konstantinov Y.M.


A SIMPLE TEST FOR LINKAGE DISEQUILIBRIUM BETWEEN A MARKER ALLELE AND A GENE MUTATION IN HETEROZYGOTE CARRIERS
Korostishevsky M., Bonne-Tamir B.


EVOLUTIONARY TREE RECONSTRUCTION AND TRAVELING SALESMAN PROBLEM: A POWERFUL ALGORITHM FOR SHAGGY TREES
Korostishevsky M., Burd A., Mester D., Bonnef-Tamir B., Nevo E., Korol A.


THE CONSERVATION OF TRANSCRIPTION FACTOR-BINDINS SITES IN SACCHAROMYCES GENOMES
Kovaleva G.Y., Mironov A.A., Gelfand M.S.


THE DISTANCE FUNCTION FOR COMPUTING THE CONTINUOUS DISTANCE OF BIOPOLYMER SEQUENCES
Margaryan T.V., Hakobyan G.O.


COMPARATIVE COMPLETE GENOME SEQUENCE ANALYSIS OF CORYNEBACTERIA
Nishio Y., Nakamura Y., Usuda Y., Kawarabayasi Y., Yamagishi A., Kimura E., Matsui K., Sugimoto S., Kikuchi H., Ikeo K., Gojobori T.


NEW LTR RETROTRANSPOSABLE ELEMENTS FROM THE EUKARYOTIC GENOMES
Novikova O., Fursov M., Beresikov E., Blinov A.


EVOLUTION OF DIPLOID PROGENITORS OF COMMON WHEAT AS SUGGESTED BY ANALYSIS OF RAPD AND SUBTELOMERIC REPEATS
Salina E.A., Adonina I.G., Lim Y.K., Shcherbanf A.B., Vatolina T.Yu., Leitch A.


COMPUTING LARGE PHYLOGENIES WITH STATISTICAL METHODS: PROBLEMS AND SOLUTIONS
Stamatakis A.P., Ludwig T., Meier H.


COUNTERING COORDINATED AMINO ACID SUBSTITUTIONS IN PHYLOGENETIC NALYSIS
Triboy T.I., Sherbakov D.Yu.


DOMINANT MODE IN PISUM DIVERSITY GENERATION: WHAT IS THE IMPACT OF TRANSPOSABLE ELEMENTS?
Vershinin A.V., Allnutt T.R., Knox M.R., Ambrose M.J., Ellis T.H.N.


EVOLUTION OF INTERLEUKIN-18 BINDING PROTEIN
Watanabe M., Goto N., Watanabe Y., Nishiguchi S., Shimada K., Yasunaga T., Yamanishi H.


SCANNING THE HUMAN GENOME FOR REGULATORY ISLANDS WITH PHYLOGENETIC FOOTPRINTING ALGORITHM
Wyrwicz L.S., Rychlewski L.


DATING POPULATION EXPANSION BASED ON STR VARIATION WITHIN Y-CHROMOSOME SNP-HAPLOGROUPS
Zhivotovsky L.A.


AN EVOLUTIONARY LINEAGE FOR INTRON LOSS/GAIN IN FIVE EUKARYOTIC GENOMES
Zhou Z., Kwoh C.K.


NEW APPROACHES TO ANALYSIS OF BIOMOLECULAR DATA AND PROCESSES

A FAST PROCEDURE FOR MODELING OF PROTEASOMAL PROTEIN DEGRADATION IN VITRO
Antyufeev V.S., Nikolaev S.V.


A SYSTEM FOR ON-LINE PROCESSING OF IMAGES OF GENE EXPRESSION PATTERNS
Blagov M.S., Poustelnikova E.G., Pisarev A.S., Myasnikova E.M., Samsonova M.G.


TOPICAL CLUSTERING OF BIOMEDICAL ABSTRACT BY SELF ORGANIZING MAPS
Fattore M., Arrigo P.


GIBBS SAMPLER FOR IDENTIFICATION OF SYMMETRICALLY STRUCTURED, SPACED DNA MOTIFS WITH IMPROVED ESTIMATION OF THE SIGNAL LENGTH AND ITS ALIDATION ON THE ArcA BINDING SITES
Favorov A.V., Gelfand M.S., Gerasimova A.V., Mironov A.A., Makeev V.J.


MATHEMATICAL MODELLING AND ANALYSIS OF THE FIXATION PROCESS OF DISCRETE GENETIC STRUCTURES IN A MENDELIAN ONE-LOCUS POPULATION OF DIPLOID ORGANISMS
Frisman E.Ya., Zhdanova O.L.


SEVEN CLUSTERS AND UNSUPERVISED GENE PREDICTION
Gorban A.N., Popova T.G., Zinovyev A.Yu.


MEASURING THE DISSIMILARITY BETWEEN GENE AND SPECIES TREES, THE QUALITY OF A COG
Lyubetsky V.A., Vfyugin V.V.


DETERMINATION OF THE DEVELOPMENTAL AGE OF A DROSOPHILA EMBRYO FROM CONFOCAL IMAGES OF ITS SEGMENTATION GENE EXPRESSION PATTERNS
Myasnikova E.M., Reinitz J.


YASS: ENHANCING THE SENSITIVITY OF DNA SIMILARITY SEARCH
Noe L., Kucherov G.


REVELATION AND CLASSIFICATION OF DINUCLEOTIDE PERIODICITY OF BACTERIAL GENOMES USING THE METHODS OF INFORMATION DECOMPOSITION AND MODIFIED PROFILE ANALYSIS
Shelenkov A.A., Chaley M.B., Korotkov E.V.


COMPUTER ANALYSIS OF MULTIPLE REPEATS IN BACTERIA
Vitreschak A., Noe L., Kucherov G.


BIOINFORMATICS AND EDUCATION

BIOINFORMATICS TEACHING IN MOSCOW ENGENEERING PHYSICS INSTITUTE (STATE UNIVERSITY)
Korotkova M.A.


RESEARCH AND TEACHING AT THE COLOGNE UNIVERSITY BIOINFORMATICS CENTER (CUBIC ) . MOLECULAR NETWORKS IN ORGANISMS
Lohmann M., Schomburg D.










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IC&G  SB RAS,
Laboratory of Theoretical Genetics