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PROCEEDINGS OF THE BGRS



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

BGRSĺ 2000
Novosibirsk, Russia
August 7 - 11, 2000

Volume 1

Volume 2

Volume 3, INTAS section



INTERNATIONAL PROGRAM COMMITTEE

LOCAL ORGANIZING COMMITTEE

INTRODUCTION

G. Christian Overton. 15.02.1948 . 1.06.2000


Volume 1

CONTENTS

SECTION 1. BIOINFORMATICS OF REGULATORY GENOMIC SEQUENCES

INTEGRATED SYSTEM ON GENE EXPRESSION REGULATION GENEEXPRESS - 2000
KOLCHANOV N.└., PODKOLODNY N.L., PONOMARENKO M.P., ANANKO E.A., IGNATIEVA E.V., KOLPAKOV F.└., LEVITSKY V.G., PODKOLODNAYA O.A., STEPANENKO I.L., MERKULOVA T.I., VOROBIEV D.G., LAVRYUSHEV S.V., GRIGOROVICH D.A., PONOMARENKO J.V., KOCHETOV A.V., ORLOVA G.V., KONDRAKHIN Y.V., TITOV I.I., VISHNEVSKY ╬.V.,ORLOV YU.L, VALUEV V.P., IVANISENKO V.A, OSCHEPKOV D.YU., OMELĺYANCHUK N.A., POZDNYAKOV M.A., KOSAREV P.S., GORYACHKOVSKAYA T. N., FOKIN O.N., KALINICHENKO L.A., KOTLYAROV YU.V.


TRANSCRIPTION REGULATORY REGIONS DATABASE (TRRD)
ANANKO E.A., PODKOLODNAYA O.A., IGNATIEVA E.V., KEL-MARGOULIS O.V., KEL A.E., MERKULOVA T.I., STEPANENKO I.L., GORYACHKOVSKAYA T.N., PODKOLODNY N.L., GRIGOROVICH D.A., NAUMOCHKIN A.N., KOROSTISHEVSKAYA I.M., LOKHOVA I.V., ROMASHCHENKO A.G., KOLCHANOV N.A.


DATABASES ON ENDOCRINE SYSTEM GENE EXPRESSION REGULATION: INFORMATIONAL CONTENT AND COMPUTER ANALYSIS
IGNATIEVA E.V., BUSYGINA T.V., ANANKO ┼.└., PODKOLODNAYA ╬.└., MERKULOVA T.I., SUSLOV V.V., POZDNYAKOV ╠.A.


ASDB: DATABASE OF ALTERNATIVE SPLICING
DRALYUK I., BRUDNO M., GELFAND M.S., ZORN M., DUBCHAK I.


CYCLE-TRRD: A DATABASE ON TRANSCRIPTIONAL REGULATION OF CELL CYCLE-DEPENDENT GENES
KEL-MARGOULIS O.V., KEL A.E.


LOCUS CONTROL REGIONS: DESCRIPTION IN A DATABASE
PODKOLODNAYA O.A. AND LEVITSKY V.G.


REPRESENTATION OF INFORMATION ON ERYTHROID GENE EXPRESSION REGULATION IN THE GENEEXPRESS SYSTEM
PODKOLODNAYA O.A. , STEPANENKO I.L., ANANKO E.A., VOROBIEV D.G.


SELEX_DB: AN ACTIVATED DATABASE ON DNA/RNA SEQUENCES OBTAINED IN SELEXEXPERIMENTS
PONOMARENKO J.V., ORLOVA G.V., PONOMARENKO M.P., LAVRYUSHEV S.V., ZYBOVA S.V., FROLOV A.S.


STEROIDOGENESIS-CONTROLLING GENE TRANSCRIPTION REGULATION: REPRESENTATION IN TRRD DATABASE
BUSYGINA T.V., IGNATIEVA E.V., OSADCHUK A.V.


DATABASE ON COMPOSITE REGULATORY ELEMENTS IN EUKARYOTIC GENES (COMPEL)
KEL-MARGOULIS O.V., ROMASCHENKO A.G., DEINEKO I.V., KOLCHANOV N.A., WINGENDER E., KEL A.E.


PATHO DB . A DATABASE BRIDGING THE GAP BETWEEN THE DESCRIPTION OF GENE REGULATORY DEFECTS AND CLINICAL APPLICATION
PRUESS M., ,MEINHARDT T., WINGENDER E.


THE TRANSPATH SIGNAL TRANSDUCTION DATABASE: A KNOWLEDGE BASE ON SIGNAL TRANSDUCTION NETWORKS
SCHACHERER F., CHOI C., GOTZE U., KRULL M., ,WINGENDER E.


GENOMICS-AIDED DRUG DEVELOPMENT: POPULATION GENOMICS AND INFORMATICS AT WORK
RICHARD SIDNEY JUDSON


KNOWLEDGE BASE ON MOLECULAR-GENETICAL FOUNDATIONS OF LIPID METABOLISM REGULATION: CURRENT STATE AND PERSPECTIVE
IGNATIEVA E.V., LIKHOSHVAI V.A., RATUSHNY A.V., KOSAREV P.S.


ACTIVITY: A DATABASE ON DNA REGULATORY SITES ACTIVITY, ADAPTED FOR ANALYSIS OF DNA-PROTEIN INTERACTIONS
PONOMARENKO J.V., FURMAN D.P., PONOMARENKO M.P., ORLOVA G.V., FROLOV └.S., PODKOLODNY N.L., SARAI A.


RECOGNITION GROUPS: A NEW METHOD FOR DESCRIPTION AND PREDICTION OF TRANSCRIPTION FACTOR BINDING SITES
KONDRAKHIN YU.V., MILANESI L., LAVRYUSHEV S.V., SCHUG J., KOLCHANOV N.A.


MD-CAVE . THE METABOLIC DISEASES DATABASE A SYSTEM FOR STORING INFORMATION ABOUT HUMAN INBORN ERRORS
A. FREIER, R. HOFESTADT, M. LANGE, U. SCHOLZ AND T. TOPEL


CONTEXTUAL FEATURES OF YEAST mRNA 5.UTRs POTENTIALLY IMPORTANT FOR THEIR TRANSLATIONAL ACTIVITY
KOCHETOV A.V., VOROBIEV D.G., ,SIRNIKO.A., KISSELEV L.L., KOLCHANOV N.A.


COMPOSITIONAL PROPERTIES OF PLANT mRNA 5.UNTRANSLATED REGIONS: THE PRESENCE OF ENHANCER-LIKE MOTIFS
KOCHETOV A.V., GLAZKO G.V., SIRNIK O.A., ROGOZIN I.B., TRIFONOVA E.A., KOMAROVA M.L., SHUMNY V.K.


TRANSLATIONAL FEATURES OF 5.UTR-LOCATED MINIORFS
KOCHETOV A.V., ,SIRNIK O.A., KOMAROVA M.L., TRIFONOVA E.A., KOLCHANOV N.A., SHUMNY V.K.


ASSOCIATED WITH REPEATED ELEMENTS STRUCTURAL DEFORMATION OF PROMOTER DNA UPON TRANSCRIPTION COMPLEX FORMATION
MASULIS I.S., CHASOV V.V., OZOLINE O.N.


TRRDEXTR: COMPUTER PROGRAM FOR EXTRACTION OF REGULATORY SEQUENCES DESCRIBED IN TRRD
KOSAREV P.S.


PERIODIC PATTERNS IN SEQUENCE ORGANIZATION OF REPLICATION ORIGIN OF ESCHERICHIA COLI K-12 CHROMOSOME
KRAVATSKAYA G.I., ESIPOVA N.G.


CHARACTERISTIC MODULAR PROMOTER STRUCTURE AND ITS APPLICATION TO DEVELOPMENT OF RECOGNITION PROGRAM SOFTWARE
LEVITSKY V.G. AND KATOKHIN A.V.


NUCLEOSOME ORGANIZATION OF CHROMATIN IN EUKARYOTIC GENES AND STRUCTUREFUNCTIONAL GENOME REGIONS
LEVITSKY V.G., KOLCHANOV N.A.


ANALYSIS OF RELATIONSHIPS BETWEEN NUCLEOSOME POSITIONING IN PROMOTER REGIONS AND GENE EXPRESSION PATTERN
LEVITSKY V.G., PODKOLODNAYA ╬.└.


COMMON B-DNA FEATURES OF A DEFINITE TRANSCRIPTION FACTOR BINDING SITES SUPERCLASS
PONOMARENKO J.V., PONOMARENKO M.P.


CONFORMATION OF TATA-PROMOTERS ┬-HELIX MAY GOVERN DIFFUSION OF TBP ALONG DNA TOWARDS -30 POSITION OF THESE PROMOTERS
PONOMARENKO J.V., POMONARENKO M.P., ZVOLSKY I.L.


THE MODULE ORGANIZATION OF THE A AND B BOXES IN THE tRNA INTRAGENIC PROMOTER
ROGOZIN I.B., KONDRAKHIN YU.V., NAYKOVA T.M., YUDIN N.S., VOEVODA M.I., ROMASCHENKO A.G.


B-DNA FEATURES CORRELATING WITH POINT MUTATIONS THAT INFLUENCE DNA/PROTEINBINDING FREE ENERGY
PONOMARENKO M.P., PONOMARENKO J.V., GORYACHKOVSKAYA T.N., ORLOVA G.V., SARAI A.


ANALYSIS OF CONTEXT DEPENDENCIES WITHIN REGULATORY GENE REGIONS IN EUKARYOTES
ORLOV YU.L., KOSAREV P.S., ORLOVA N.G., POTAPOV V.N.


DETECTION OF CIS-ACTING REGULATORY ELEMENTS IN PLANTS: A GIBBS SAMPLING APPROACH
THIJS G., ROMBAUTS S., LESCOT M., MARCHAL K., DE MOOR B., MOREAU Y., ROUZE P.


DISCOVERY AND MODELING OF TRANSCRIPTIONAL REGULATORY REGIONS
FICKETT J.W. AND WASSERMAN W.W.


COMPOSITE MODULES - THE DNA BLUEPRINTS OF COMBINATORIAL TRANSCRIPTIONAL REGULATION IN MULTICELLULAR ORGANISMS
KEL A.E., KEL-MARGOULIS O.V., ROMASCHENKO A.G., WINGENDER E., AND RATNER V.A.


FINDING TRANSCRIPTION FACTOR BINDING SITES IN COREGULATED GENES BY EXHAUSTIVE SEQUENCE SEARCH
KIELBASA SZ.M., KORBEL J.O., BEULE D., SCHUCHHARDT J., AND HERZEL H.


KERNEL METHOD FOR ESTIMATION OF FUNCTIONAL SITE LOCAL CONSENSI. CLASSIFICATION OF TRANSCRIPTION INITIATION SITES IN EUKARYOTIC GENES
TIKUNOV Y., KEL A.


ANALYSIS OF THE REGION OF INTRON 6 OF THE HUMAN TDO2 GENE IN THAT POINT MUTATIONS ASSOCIATED WITH PSYCHIATRIC DISORDERS ARE LOCATED WITH THE AID OF COMPUTER AND EXPERIMENTAL APPROACHES
MERKULOVA T.I., VASILIEV G.V., PONOMARENKO M.P., KOBZEV V.F., PODKOLODNAYA O.A., PONOMARENKO YU.V., KOLCHANOV N.A.


NON-CANONICAL SEQUENCE ELEMENTS AS ADDITIONAL SIGNALS IN PROMOTER RECOGNITION BY E.COLI RNA POLYMERASE
OZOLINE O.N., DEEV A.A., ARKHIPOV I.V.


BIOCHEMICAL AND COMPUTATIONAL ANALYSIS OF TYPE I COLLAGEN GENE REGULATORY ELEMENTS
BREINDL M., MIELKE C., BENHAM C.


COMPUTER ANALYSIS REVEALS A SET OF ADDITIONAL PROMOTER ELEMENTS UPSTREAM OF MAIZE PLASTID GENES
SHAHMURADOV I.A., AKBEROVA Y.YU., MUSTAFAYEV N.SH., ABDULAZIMOVA A.U., ALIYEV J.A.


A/T-TRACES IN THE INITIALLY TRANSCRIBED REGIONS OF BACTERIAL PROMOTERS. PUTATIVE FUNCTIONAL SIGNIFICANCE
CHASOV V.V., MASULIS I.S., OZOLINE O.N.


CONSTRUCTION OF THE MODULE STRUCTURE MODEL OF THE REGULATORY SITE ON THE BASE OF THE MULTIPLE RELATIONSHIPS BETWEEN SITE POSITIONS
KONDRAKHIN YU.V., ROGOZIN I.B., ROMASCHENKO A.G.


DETECTING PATTERNS OF STRUCTURE-FUNCTION ORGANIZATION OF REGULATORY GENOMIC SEQUENCES IN A FIRST ORDER LOGIC
VITYAEV E.E., PODKOLODNY N.L., VISHNEVSKY O.V., KOSAREV P.S., ANANKO E.A., IGNATIEVA E.V., PODKOLODNAYA O.A., KOLCHANOV N.A.


NUCLEOSOME CODE ANALYSIS BY ESTIMATING MARKOV DEPENDENCIES
ORLOV YU.L., LEVITSKY V.G.


CORRELATION ANALYSIS OF DNA CONFORMATIONAL CHARACTERISTICS OF HUMAN TOPOISOMERASE I CLEAVAGE SITES
OSHCHEPKOV D.YU., KUZIN F.E., AFONNIKOV D.A.


CORRELATION ANALYSIS OF HSF BINDING SITES CONFORMATIONAL PROPERTIES
OSHCHEPKOV D.YU., STEPANENKO I.L., AFONNIKOV D.A., SCHROEDER H.C.


SINGLE NUCLEOTIDE POLYMORPHISM IN THE REGION OF 288-296 BP OF INTRON 2 OF THE KRAS GENE, RELATED TO LUNG TUMOR SUSCEPTIBILITY, CAUSES ALTERATION IN THE SET OF PROTEINS BINDING TO THIS REGION
LEVASHOVA Z.B., KALEDIN V.I., PONOMARENKO M.P., KOBZEV V.F., VASILIEV G.V., PONOMARENKO J.V., PODKOLODNAYA O.A., MERKULOVA T.I., KOLCHANOV N.A.


REGULATORY GENOMIC SEQUENCES: CODING, ORGANIZATION, AND FUNCTION
KOLCHANOV N.A.


SECTION 2. BIOINFORMATICS OF GENE REGULATION, GENE NETWORKS AND METHABOLIC PATHWAYS

GeneNet DATABASE: A TECHNOLOGY FOR A FORMALIZED DESCRIPTION OF GENE NETWORKS
ANANKO E.A., KOLPAKOV F.A., KOLCHANOV N.A.


PathDB: A SECOND GENERATION METABOLIC DATABASE
MENDES P., BULMORE D.L., FARMER A.D., STEADMAN P.A., WAUGH M.E., WLODEK S.T.


GeneNet-BASED MODEL OF TWO-STAGE ALDOSTERONE EFFECT ON PRINCIPAL CELLS OF CORTICAL COLLECTING DUCTS
LOGVINENKO N.S., IGNATIEVA E.V., IVANOVA L.N.


DEVELOPMENT OF KNOWLEDGE BASE ON PLANT GENE EXPRESSION REGULATION
STEPANENKO I.L., GORYACHKOVSKY T.N., IBRAGIMOVA S.S., AXENOVICH A.V., OMELYANCHUK N.A., LAVRYUSHEV S.V., PODKOLODNY N.L.


FUNCTIONAL GENE NETWORKS . A DATA MANAGEMENT APPROACH FOR BIOINFORMATICS
GABRIELYAN O.R., FREYTAG J.C.


GENE NETWORK ON PLANT INTERACTION WITH PATHOGEN ORGANISMS
GORYACHKOVSKY T.N., ANANKO E.A., KOLPAKOV F.A.


PUMA/WIT -- A FAMILY OF INTEGRATED SYSTEMS FOR GENETIC SEQUENCE ANALYSIS AND METABOLIC RECONSTRUCTIONS
OVERBEEK R., SELKOV E., PUSCH G., DĺSOUZA M., MALTSEV N.


LATENT PHENOTYPE AS AN ADAPTATION RESERVE: A SIMPLEST MODEL OF CELL EVOLUTION
LIKHOSHVAI V.A., MATUSHKIN YU.G.


MATHEMATICAL MODEL OF CHOLESTEROL BIOSYNTHESIS REGULATION IN THE CELL
RATUSHNY A.V., IGNATIEVA E.V., MATUSHKIN YU.G., LIKHOSHVAI V.A.


MATHEMATICAL MODEL OF ERYTHROID CELL DIFFERENTIATION REGULATION
RATUSHNY A.V., PODKOLODNAYA O.A., ANANKO E.A., LIKHOSHVAI V.A.


GENE NETWORK OF REDOX REGULATION AND THE PROBLEM OF INTEGRATING LOCAL GENE NETWORKS
STEPANANKO I.L., SMIRNOVA O.G., KONSTANTINOV YU.M.


PARALLEL SIMULATED ANNEALING FOR LARGE-SCALE OPTIMIZATION APPLICATIONS
DENG Y.


BIOLOGICAL ROLE CATEGORIES FOR REGULATORS AND MECHANISMS OF DIVERGENCE OF FUNCTION
RILEY M.


METABOLIC ENGINEERING ELECTRONICAL INFRASTRUCTURE FOR THE DETECTION OF INBORN ERRORS
HOFESTADT R.


GENE CIRCUITS AND FLY SEGMENTS: SOLVING AN INVERSE PROBLEM IN DROSOPHILA
REINITZ J.B.


BIOINFORMATIC SYSTEM IDENTIFICATION
KING R.D., GARRETT S.M., COGHILL G.M.


APPLICATION OF THE METHOD OF GENERALIZED THRESHOLD MODELS FOR THE ANALYSIS OF THE EUKARYOTIC CONTROL GENE SUBNETWORKS
TCHURAEV R.N., GALIMZYANOV A.V.


THE BSP-REPEATS FROM CANIDAE CONTAIN A BIDIRECTIONAL PROMOTER FOR THE RNA POLYMERASE III POTENTIALLY CAPABLE OF ENCODING DOUBLE-STRANDED RNA
YUDIN N.S., NAYKOVA T.M., KONDRAKHIN YU.V., KOBZEV V.F., ROMASCHENKO A.G.


MODELING OF CELL CYCLE GENE REGULATORY NETWORK. A ROLE OF A POSITIVE FEEDBACK LOOP IMPLYING POTENTIAL E2F TARGET SITES IN THE REGULATORY REGIONS OF AP-1 GENES
DEINEKO I.V., KEL-MARGOULIS O.V., RATNER V.A., KEL A.E.


THE INTEGRATED TRANSFAC SYSTEM AS A BASIS FOR MODELING AND SIMULATION OF GENE REGULATION MECHANISMS
POTAPOV A., CHRISTENSEN M., DREWES V., SCHACHERER F., WINGENDER E.


SOFTWARE AUTOMATED PACKAGE FOR ANALYZING THE DYNAMICS OF CONTROL GENE NETWORKS
GALIMZYANOV A.V.


GENE NETWORK ON STORAGE MOBILIZATION IN SEED
AXENOVICH A.V., GORYACHKOVSKY T.N., ANANKO E.A., OMELYANCHUK N.A., STEPANENKO I.L.


SEED MATURATION IN HIGHER PLANTS: GENE NETWORKS ON ONTOGENESIS IN STORAGE TISSUES
GORYACHKOVSKY T.N., ANANKO E.A., KOLPAKOV F.A., STEPANENKO I.L.


NUMERICAL STUDY OF MATHEMATICAL MODELS DESCRIBED DYNAMICS OF GENE NETS FUNCTIONING: SOFTWARE PACKAGE STEP
BEREZIN A.YU., ,GAINOVAI.A., MATUSHKINYU.G.,LIKHOSHVAI V.A., FADEEV S.I.


THE RECONSTRUCTION OF THE DROSOPHILA SEGMENTATION MECHANISMS FROM EXPERIMENTAL DATA: PROCESSING AND ANALYSIS OF CONFOCAL IMAGES OF EXPRESSION PATTERNS
SPIROV A.V., TIMAKIN D.L., REINITZ J., KOSMAN D., SPIROVA O.A.



Volume 2

CONTENTS

SECTION 3. BIOINFORMATICS OF GENOME STRUCTURE AND EVOLUTION

AUTOMATED COMPARATIVE ANALYSIS OF REGULATORY PATTERNS: SUGAR METABOLISM AND TRANSPORT SYSTEMS IN GAMMA PURPLE BACTERIA
MIRONOV A.A., GELFAND M.S


PRO-FRAME: SIMILARITY-BASED GENE RECOGNITION IN EUKARYOTIC DNA SEQUENCES WITH ERRORS
MIRONOV A.A., GELFAND M.S


GENOMEEXPLORER: SOFTWARE FOR ANALYSIS OF COMPLETE BACTERIAL GENOMES
MIRONOV A.A., VINOKUROVA N.P., GELFAND M.S


COMPARATIVE APPROACH TO ANALYSIS OF REGULATION IN COMPLETE GENOMES: CATABOLITE REPRESSION IN GAMMA-PROTEOBACTERIA
NOVICHKOVA E.S., NOVICHKOV P.S., MIRONOV A.A., GELFAND M.S.


COMPARATIVE APPROACH TO ANALYSIS OF REGULATION IN COMPLETE GENOMES: SOS REPAIR IN BACILLUS SUBTILIS
PERMINA E.A., MIRONOV A.A., GELFAND M.S.


HrcA REGULATES NOT ONLY CHAPERONIN GENES
GELFAND M.S., MIRONOV A.A.


SOFTWARE FOR ORTHOLOGY ANALYSIS IN COMPLETE BACTERIAL GENOMES
BAITALYUK M.V., NOVICHKOV P.S., GELFAND M.S., MIRONOV A.A.


FUNCTIONAL GENOMICS: AN ALGORITHMIC PERSPECTIVE
CALIFANO A.


COMPARATIVE APPROACH TO ANALYSIS OF REGULATION IN COMPLETE GENOMES: TRANSCRIPTION REGULATORY SITES IN ARCHAEA
GELFAND M.S., KOONIN E.V., MIRONOV A.A.


InterPro AS A NEW TOOL FOR WHOLE GENOME ANALYSIS. A COMPARITIVE ANALYSIS OF MYCOBACTERIUM TUBERCULOSIS, BACILLUS SUBTILIS AND ESCHERICHIA COLI AS A CASE STUDY
MULDER N.J., FLEISCHMANN W., APWEILER R.


NO MYSTERY OF ORFans IN GENOMICS - GENERATION OF ORFans IN THE ANTISENSE OF CODING SEQUENCES
MACKIEWICZ P., KOWALCZUK M., GIERLIK A., SZCZEPANIK D., NOWICKA A., DUDEK M.R., CEBRAT S.


Pro-Gen: PREDICTION OF THE EXON-INTRON STRUCTURE BY COMPARISON OF GENOMIC SEQUENCES
NOVICHKOV P.S., GELFAND M.S., MIRONOV A.A.


COMPARATIVE GENOMICS: HOMOLOGY BASED GENE IDENTIFICATION AND GENE STRUCTURE VALIDATION
WIEHE T, GEBAUER-JUNG S., ABRIL J. AND GUIGĎ R.


MOUSE AQUAPORIN 4 GENE: PREDICTION OF A NEW EXON AND EXPERIMENTAL CONFIRMATION
BONDAR A.A., ALIKINA T.YU., ZELENIN S.M.


COMPARATIVE APPROACH TO ANALYSIS OF REGULATION IN COMPLETE GENOMES: MULTIDRUG RESISTANCE SYSTEMS IN GAMMA-PROTEOBACTERIA
RODIONOV D.A., GELFAND M.S., MIRONOV A.A. RAKHMANINOVA A.B.


REGULATION OF DAHP-SYNTHASES IN GAMMA-PROTEOBACTERIA: FEEDBACK INHIBITION AND REPRESSION OF TRANSCRIPTION
PANINA E.M., MIRONOV A.A., GELFAND M.S.


COMPARATIVE APPROACH TO ANALYSIS OF REGULATION IN COMPLETE GENOMES: ATTENUATORS OF AROMATIC AMINO ACID OPERONS OF GAMMA-PROTEOBACTERIA
VITRESCHAK A.G., GELFAND M.S.


AVOIDANCE OF PALINDROMES IN PROCARYOTIC GENOMES AND RESTRICTIONMODIFICATION SYSTEMS
PANINA E.M., GELFAND M.S.


ONE APPROACH FOR ANNOTATION AND CONFIRMATION OF DISCOVERIES OF ALTERNATIVE SPLICE EVENTS USING RECONSTRUCTED EXTENDED UNSPLICED TRANSCRIPTS FROM GENES ON CHROMOSOME 22
BABENKO V., VAN HEUSDEN P., HIDE W.


FAST SEARCH OF ALL TANDEM REPETITIONS IN NUCLEOTIDE SEQUENCES
GIRAUD M., KOLPAKOV R., KUCHEROV G.


RECONSTRUCTION OF THE OPEN READING FRAMES BY USING EST MULTIPLE ALIGNMENT AND DYNAMIC PROGRAMMING
VISHNEVSKY O.V., KATOKHIN A.V. BABENKO V.N.


ON RELATIONSHIPS BETWEEN GENE EXPRESSION EFFICIENCY AND NUCLEOTIDE CONTENT OF THE PROTEIN-CODING SEQUENCES
LIKHOSHVAI V.A. MATUSHKIN YU.G.


DETERMINING MARKOV MODEL OF GENETICAL TEXTS BY STOCHASTIC COMPLEXITY ESTIMATION
ORLOV YU.L., POTAPOV V.N.


NEW ALGORITHMS FOR LARGE-SCALE EST CLUSTERING
PTITSYN A., HIDE W.


PERIODIC PATTERNS IN SEQUENCE ORGANIZATION OF REPLICATION ORIGIN OF ESCHERICHIA COLI K-12 CHROMOSOME
KRAVATSKAYA G.I., ESIPOVA N.G.


ESTMAP: A PROGRAM FOR ESTs MAPPING ON A GENOMIC SEQUENCE
MILANESI L., ROGOZIN I.B.


COMPLEXITY MEASURES OF SYMBOLIC SEQUENCES AND THEIR APPLICATION TO DNA ANALYSIS
CHUZHANOVA N., KRAWCZAK M., GUSEV V.D., NEMYTIKOVA L.A., COOPER D.N.


ANALYSIS OF MUTATIONAL HOTSPOTS IN HUMAN DISEASE GENES AND MUTATIONAL SPECTRA
ROGOZIN I.B., 1BERIKOV V.B., GLAZKO G.V.


COMPARATIVE ANALYSIS OF FUNCTIONAL SITE MOTIFS OF MGE COPIA-GROUP RELATIVE TO THEIR POSSIBLE MOLECULAR FUNCTIONS
AMIKISHIEV V.G., RATNER V.A.


S/MARs AND SOME ELEMENTS FROM DIFFERENT REPETITIVE FAMILIES ARE COLOCALIZED IN HUMAN GENOME
GLAZKO G.V., KOCHETOV A.V., ROGOZIN I.B.


STUDYING CORRELATIONS OF COMPUTATIONALLY PREDICTED ORIGINS OF REPLICATION AND BASE SKEWS IN THE SACCHAROMYCES CEREVISIAE GENOME
KORBEL J.O., ASSMUS H., KIELBASA SZ.M., HERZEL H.


BASIO: A SOFTWARE SYSTEM FOR SEGMENTATION OF BIOLOGICAL SEQUENCES INTO DOMAINS WITH HOMOGENOUS COMPOSITION
RAMENSKY V.E., MAKEEV V.JU., ROYTBERG M.A., TUMANYAN V.G.


CAN GENETIC ALGORITHMS ASSIST IN GENOMIC RESEARCH?
WESTON P.S.


A DATABASE OF GENETIC TEXTS WITH LATENT PERIODICITY (LPD)
CHALEY M.B., KOROTKOV E.V.


DNA SEQUENCE ASSEMBLY ALGORITHMS BASED ON CLUSTERING APPROACHES
ELLOUMI M.


THE EVOLUTION OF REGULATORY FAMILIES IN ARCHEA AND EUBACTERIA: A COMMON ORIGIN OF TRANSCRIPTIONAL REPRESSORS
ERNESTO PEREZ-RUEDA, J. COLLADO-VIDES


USING LOCUS-SPECIFIC DATABASES OF HUMAN MUTATIONS FOR ESTIMATING PERNUCLEOTIDE RATE OF SPONTANEOUS MUTATION
KONDRASHOV A.S.


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
RATNER V.A. YUDANIN A.YA., EGOROVA A.V.


PATTERNS OF MOBILE GENETIC ELEMENTS (MGEs) GENOMIC LOCALIZATION: INDUCTION OF TRANSPOSITIONS BY STRESS FACTORS, RESPONSE TO SELECTION AND POSSIBLE EVOLUTIONARY CONSEQUENCES
RATNER V.A., VASILYEVA L.A., BUBENSHCHIKOVA E.V. ,ANTONENKO O.V.


EVOLUTION OF THE CODE AND THE EARLIEST PROTEINS. RECONSTRUCTION FROM PRESENTDAY SEQUENCES
TRIFONOV E.N.


EVOLUTION OF PLANT REGULATORY SEQUENCES
GOEBEL U., WIEHE T., MITCHELL-OLDS, T.


A NEW VERSION OF SYNAP COMPUTER PROGRAM FOR LOGICAL MODELING OF PHYLOGENY
BAIKOV K.S., ZVEREV A.A.


SECTION 4. BIOINFORMATICS OF DNA, RNA, AND PROTEIN STRUCTURE. STRUCTURAL GENOMICS

STRUCTURE AND FORMAT OF THE EnPDB DATABASE ACCUMULATING SPATIAL STRUCTURES OF DNA, RNA AND PROTEINS
GRIGOROVICH D.A.,IVANISENKO V.A., KOLCHANOV N.A.


MODEL OF PCR KINETICS
TITOV I.I.


INFORMATION SYSTEM ĹHIV VACCINE DEVELOPMENTĺ
BELOVA O.E., BAZHAN S.I.


RNA-POLYMERASE ľ PROMOTER RECOGNITION. SPECIFIC FEATURES OF ELECTROSTATIC POTENTIAL OF ôEARLYö T4 PHAGE DNA PROMOTERS
DZHELYADIN T.R., SOROKIN A.A., IVANOVA N.N., SIVOZHELEZOV V.S., KAMZOLOVA S.G., POLOZOV R.V.


STRUCTURE-BASED TARGET PREDICTION OF TRANSCRIPTION FACTORS
SARAI A., SELVARAJ S., PRABAKARAN P., KONO H.


REGIONS OF POTENTIAL INTERACTIONS IN RNA MOLECULES AS FOUND BY COMPUTER SEARCH
SHABALINA S.A.


STRUCTURAL FEATURES OF mRNA 5'UTRs OF EUKARYOTIC GENES EXPRESSED AT HIGH AND LOW LEVELS
VOROBIEV D.G., TITOV I.I., KOCHETOV A.V., KOLCHANOV N.A.


MASS ANALYSIS OF RNA SECONDARY STRUCTURES USING A GENETIC ALGORITHM
TITOV I.I., VOROBIEV D.G., KOLCHANOV N.A.


TRANSTERM - A DATABASE OF RNA COMPONENTS AND MOTIFS
JACOBS G.H., STOCKWELL P.A., BROWN C.M.


CRASP: SOFTWARE PACKAGE FOR ANALYSIS OF PHYSICOCHEMICAL PARAMETERS OF ALIGNED SEQUENCES OF PROTEIN FAMILIES
AFONNIKOV D.A.


NOVEL FUNCTIONAL FEATURES OF DNA-BINDING DOMAIN OF THE ôHOMEODOMAINö CLASS REVEALED BY ANALYSIS OF CORRELATIONS OF AMINO ACID SUBSTITUTIONS IN ITS POSITIONS
AFONNIKOV D.A.


ANALYSIS OF STRUCTURAL MOTIFS IN PROTEINS
JIANGHONG A.N., WAKO H., SARAI A.


ĹIN SILICOĺ ANALYSIS OF POINT MUTATION EFFECTS ON THE CODING REGION OF HUMAN BETA GLOBIN GENE.
ARRIGO P., IVALDI G., CARDO P.P.


DESIGN AND IMPLEMENTATION OF THERMODYNAMIC DATABASE FOR PROTEIN-NUCLEIC ACID INTERACTIONS
PRABAKARAN P., AN J., GROMIHA M.M., SELVARAJ S., UEDAIRA H., KONO H. AND SARAI A.


TOWARDS A STRUCTURAL BASIS OF HUMAN NON-SYNONYMOUS SINGLE NUCLEOTIDE POLYMORPHISMS
SUNYAEV S., RAMENSKY V., BORK P.


THE DATABASE ASPD ON EXPERIMENTS WITH APPLICATION OF PHAGE DISPLAY TECHNIQUE
VALUEV V. P., AFONNIKOV D.A., PETRENKO O., BEYLINA A.G., LOKHOVA I.V., GRIGOROVICH D.A., FOKIN O.N., IVANISENKO V.A.


3-DIMENSIONAL PROTEIN STRUCTURAL CLASS RECOGNITION
VALUEV V.P.


BLOCKWISE EVOLUTION OF HEMOSTASIS AND COMPLEMENT FUNCTIONAL SYSTEMS
ANANKO G.G.


PDBSite: A DATABASE ON BIOLOGICALLY ACTIVE SITES AND THEIR SPATIAL SURROUNDINGS IN PROTEINS WITH KNOWN TERTIARY STRUCTURE
IVANISENKO V.A., GRIGOROVICH D.A., KOLCHANOV N.A.


RECEPTOR DATABASE (RDB) AS AN ANALYTICAL TOOL FOR THE DRUG DESIGN
NAKATA K., TAKAI T., NAKANO T. AND KAMINUMA T.


PROTEIN PRIMARY SEQUENCES AS MARKOV CHAINS
MITRA CHANCHAL K, SEN ARUSHARKA


FROM GENOMES TO PROTEIN SPACE
PEITSCH MANUEL C., SCHWEDE TORSTEN, DIEMAND ALEXANDER. AND GUEX NICOLAS


DATABASE OF PATTERNS PROF_PAT, USED TO DETECT LOCAL SIMILARITIES
BACHINSKY A.G., GRIGOROVICH D.A., NAUMOCHKIN A.N., NIZOLENKO L.PH., YARIGIN A.A.


ESTIMATION OF THE ENTROPY CHANGE UPON H-BOND FORMATION IN PROTEINS
RAKHMANINOVA A.B., MIRONOV A.A.


THE SEARCH OF REGIONS IN HIV-1 PROTEINS THAT HAVE LOCAL SIMILARITIES WITH HUMAN PROTEINS
BAZHAN S.I., BACHINSKY A.G., MAKSYUTOV A.Z.


L-ZIP MOTIF AS A PROBABLE DIMERIZATION MOTIF OF LTB4 RECEPTOR
LUKASHEV V.A., LUKASHOVA V.V., ROLA-PLESZCZYNSKI M., STANKOVA J.


INVESTIGATION OF THE AMINO ACID SEQUENCES OF MYCOBACTERIUM TUBERCULOSIS COMPLETE GENOME WITH PROTEIN FAMILY PATTERNS BANK PROF_PAT 1.3
NIZOLENKO L.PH., KOZHINA E.M., YARIGIN A.A., BACHINSKY A.G.


EFFECT OF HUMAN NON-SYNONYMOUS SINGLE NUCLEOTIDE POLYMORPHISMS UPON A PROTEIN STRUCTURE
SUNYAEV S., RAMENSKY V., BORK P.


ANALYSIS OF HEPATITIS C VIRUS PROTEINS USING SEQUENCE AND PUBLISHED DATA
SOBOLEV B.N., POROIKOV V.V., MATVEEV I.V., OLENINA L.V., KOLESANOVA E.F., ARCHAKOV A.I.


AN APPROACH TO STRUCTURAL ALIGNMENT WITH GENETIC ALGORITHM
PARK S.-J., YAMAMURA M.


THEORETICAL MODEL OF INTERACTION: PLATELETE ACTIVATING FACTOR RECEPTOR (PAFR) AND TYROSINE KINASE TYK2.
LUKASHOVA V.V., LUKASHEV V.A., 2LUKASHEV V.V., ROLA-PLESZCZYNSKI M., STANKOVA J.


STABILITY OF PARTIAL CORRELATION COEFFICIENT ESTIMATES FOR RESIDUE CHARACTERISTICS AT DIFFERENT POSITIONS OF AMINO ACID SEQUENCES
D.A. AFONNIKOV


CONTEXT DEPENDENCIES IN AMINO ACID SEQUENCIES OF PROTEIN DOMAINS
ORLOV YU. L., IVANISENKO V.A., POTAPOV V.N.


HIERARCHICAL FEATURE DECOMPOSITION IN FUNCTIONAL DOMAINS
MURRAY D., HONIG B.H., CALIFANO A.1 .


SECTION 5.BIOINFORMATICS OF GENOME STRUCTURE AND EVOLUTION

MONO- AND BIVARIATE FLUORIMETRIC FLOW SORTING OF HUMAN CHROMOSOMES: QUANTITATIVE DATA ANALYSIS
KRAVATSKY YU.V., POLETAEV A.I.


EDUCATION ON THE BASIS OF THE GENEEXPRESS SYSTEM: BUSINESS GAME "REGULATORY SIGNALS"
PONOMARENKO M.P., PONOMARENKO J.V., LAVRYUSHEV S.V., VOROBIEV D.G., MININA A.V., IVASHIN S.A., MIKHAILOV YU.I.


COURSE ôINTRODUCTION TO BIOINFORMATICSö
VALUEV V.P., AFONNIKOV D.A.


BIOINFORMATICS: NOVEL PROFILE OF VOCATIONAL EDUCATION
1VALISHEV A.I., 2KOLCHANOV N.A., 2PODKOLODNY N.L., 1MELNIKOV V.N., 1ALSYNBAYEVA L.G., YAROSLAVTSEVA R.G., HAANS W.J.A.


MINK ENTERITIS VIRUS VP2 GENE FRAGMENTS ANALYSIS
TKACHEV S.E.


Volume 3, INTAS section

CONTENTS

INTAS SECTION

PREFACE

LIFE SCIENCES AT INTAS

REGULATION OF MDR1 GENE EXPRESSION BY ds-OLIGONUCLEOTIDES
SHATSKAYA N.V., BOZHENOK L.N., CHERNOLOVSKAYA E.L., VLASSOV V.V.


IDENTIFICATION OF OPTIMAL TARGET SITES FOR ANTISENSE OLIGONUCLEOTIDES IN THE â┐- SARCIN LOOP REGION OF E. Coli 23S rRNA
PETYUK V.A., ZENKOVA M.A., VLASSOV V.V.


DISTRIBUTION OF HISTONES WITHIN DEFINED BAND-INTERBAND REGION OF DROSOPHILA MELANOGASTER POLYTENE CHROMOSOMES
DEMAKOV S.A., SCHWARTZ YU.B., SAUMWEBER H., SEMESHIN V.F., ZHIMULEV I.F.


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
DYMSHITS G.M., KABILOV M.R., NEISCHTADT V.P., SKOBELTSYNA L.M. ZARYTOVA V.F., IVANOVA E.M., PYSHNYI D.V.


XENOTRANSPLANTATION OF DROSOPHILA EMBRYONIC NERVE CELLS INTO MAMMALS BRAIN: MOLECULAR GENETIC AND CLINICAL ASPECTS
KOROCHKIN L.I., ALEXANDROVA M.A., BASHKIROV V.N., DZITOEVA S.G., PAVLOVA G.V., TRUKHATCHEVA A.A., EVGENIEV M.B., MODESTOVA äE.R., GROSMAN A.A.


REDOX MODULATION OF DNA TOPOISOMERASE I ACTIVITY IN PLANTS
KONSTANTINOV Y.M., TARASENKO V.I., ROGOSIN I.B.


ARTIFICIAL RIBONUCLEASES: NOVEL TOOLS FOR INVESTIGATION OF RNA STRUCTURE IN SOLUTION
ZENKOVA M.A., KONEVETZ D.A., BELOGLAZOVA N.G., CHUMAKOVA N.A., VLASSOV V.V., SILüfNIKOV V.N.


BINDING OF OLIGONUCLEOTIDES WITH GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE INTERFERES WITH CELLULAR FUNCTIONS OF THE ENZYME
BRYKSIN A.V., LAKTIONOV P.P., VOLODĺKO N.V., GRIFFONI C., RYKOVA E.Y., SPISNI E., KRAFT R., TOMASI V., VLASSOV V.V.


THE MOLECULAR ANALYSIS OF MITOCHONDRIAL GENOME STRUCTURE OF WILD PERENNIAL CROP ELYMUS SIBIRICUS: EVOLUTIONARY CONSERVATION AND VARIATION OF COXI, COXIII, ATPA, RPS13 GENES
TAUSON E.L., ROGOZIN I.B., VERBITSKI D.S., KONSTANTINOV YU.M., ARZIEV A.SH., BASHALKHANOV S.I.


AGE-ASSOCIATED CHANGES IN 8-OXOGUANINE- AND HYPOXANTHINE-DNA-GLYCOSYLASE ACTIVITIES OF CELL.S EXTRACTS OF WISTAR AND OF RATS WITH INHERITED OVERGENERATION OF FREE RADICALS
ISHCHENKO A.A., SINITSYNA O.I., VASUNINA E.A., KRYSANOVA J.S., NEVINSKY G.A.


BISPYRENYLATED OLIGONUCLEOTIDE PROBES DISPLAYING HYBRIDIZAION INDUCED EXCIMER FLUORESCENCE
KOSTENKO E.V., DOBRIKOV M.I., KOMAROVA N.I., VLASSOV V.V., ZENKOVA M.A.


CHEMICAL CLEAVAGE OF PLASMID DNA BY ARENES IN THE PRESENCE OF CU(II) IONS
KOVAL O.A., OLEINIKOVA S.B., CHERNOLOVSKAYA E.L., LITVAK V.V., VLASSOV V.V.


BEHAVIORAL ANALYSIS OF HOMEOTIC LAWC-MUTANTS IN D. MELANOGASTER
SIMONOVA O., SUKHOVERKHOVA T., MODESTOVA E., KOROCHKIN L.


COMPLEX FORMATION OF Fpg PROTEIN WITH OLIGONUCLEOTIDES AND THEIR DERIVATIVES
ISHCHENKO A.A., NEVINSKY G.A.


EFFICIENT SITE-DIRECTED CLEAVAGE OF YAST tRNAPHE WITH OLIGONUCLEOTIDES CONJUGATED TO IMIDAZOLE CONSTRUCTS
BELOGLAZOVA N.G., POLUSHIN N.N., SIL.NIKOV V.N., ZENKOVA M.A., VLASSOV V.V.


COMPARATIVE CHARACTERIZATION OF THE 5'-REGIONS OF THE VOLE, HUMAN AND MOUSE XIST GENE: CONSERVED AND REPETITIVE SEQUENCES
KOLESNIKOV N.N., NESTEROVA T.B., SLOBODYANYUK S.Y., SHEVCHENKO A.V., PAVLOVA M.V., ROGOZIN I.B., ELISAPHENKO E.A., KEL A.E., LEVITSKY V.G., BROCKDORFF N., ZAKIAN S.M.


HEAT SHOCK KNOWLEDGE BASE
STEPANENKO I.L., LEVITSKY V.G., SCHROEDER H.C.


MODEL OF PHOSPHATE HIGH-AFFINITY TRANSPORT IN BACTERIA
TITOV I.I., KOLCHANOV N.A., SCHRODER H.C.


METHOD FOR PREDICTION OF TRANSCRIPTION FACTOR BINDING TO REGULATORY REGION, BASED ON CAUSED BY POINT MUTATION ALTERATIONS IN THE PATTERN OF THIS REGION INTERACTION WITH NUCLEAR PROTEINS
PONOMARENKO M.P., MERKULOVA T.I., POMONARENKO YU.V., ORLOVA G.V.


rSNP_GUIDE: A DATABASE DOCUMENTING INFLUENCE OF SUBSTITUTIONS IN REGULATORY GENE REGIONS ONTO THEIR INTERACTION WITH NUCLEAR PROTEINS AND PREDICTING PROTEIN BINDING SITES, DAMAGED OR APPEARED DE NOVO DUE TO THESE SUBSTITUTIONS
PONOMARENKO J.V., ORLOVA G.V., PONOMARENKO M.P., LAVRYUSHEV S.V., MERKULOVA T.I.


COMPUTATIONAL BIOCHEMISTRY OF HEPATOCYTE
,DEMIN O.V., KHOLODENKO B.N., RIZNICHENKO G.YU., LEBEDEVA G.


INTERACTION OF HUMAN MILK LACTOFERRIN WITH DNA IN CONTEXT OF IT.S POLYFUNCTIONAL BIOLOGICAL FUNCTIONS
KANYSHKOVA T.G., BABINA S.E., GAL'VITA A.V., NEVINSKY G.A.


SECTION 5

METHOD FOR SPATIAL REGISTRATION OF THE EXPRESSION PATTERNS OF DROSOPHILA SEGMENTATION GENES USING WAVELETS
KOZLOV K.N., MYASNIKOVA E.M., SAMSONOVA M.G., REINITZ J., KOSMAN D.


MOLECULAR-GENETICAL MECHANISMS OF THYROID SYSTEM REGULATION: DESCRIPTION IN TRRD AND GeneNet
DATABASES
SUSLOV V.V., IGNATIEVA E.V., OSADCHUK ä@.V.


COMPARISON OF MILK PROTEIN KINASE WITH SECRETORY IMMUNOGLOBULIN A POSSESSING PROTEIN KINASE ACTIVITY
AKIMZHANOV A.M., SEMENOV D.V., NEVINSKY G.A.


UNEXPECTED HIGH AFFINITY OF SOME VERY SHORT NONSPECIFIC OLIGONUCLEOTIDES FOR HUMAN DNA TOPOISOMERASE I
BUGREEV D.V, NEVINSKY G.A.


EFFECT OF DNA-HYDROLYZING ANTIBODIES ON CELL DIVISION AND IMMUNORESPONSE OF EXPERIMENTAL MICE
GAL.VITA A.V., KANYSHKOVA T.G., ISAEVA N. V., POLOSUKHINA D.I., NEVINSKY G.A.


PHYSICO-CHEMICAL CHARACTERISTICS OF THE FORMATION OF RecA-DNA NUCLEOFILAMENT
BUGREEVA I. P., BUGREEV D. V., SINITSYNA O. I., NEVINSKY G. A.


INFORMATIONAL SUPPORT OF ONTOLOGY FOR TRANSCRIPTION REGULATION (ISOTR)
IGNATIEVA E.V., PODKOLODNY N.L., KOLCHANOV N.A.


METHOD OF FUNCTIONAL SITES CLASSIFICATION BASED ON OLIGONUCLEOTIDE FREQUENCIES
NEDOSEKINA E.A., POZDNYAKOV M.A.


DROSOPHILA PROMOTER DATABASE EnDPD: PROJECT AND THE FIRST STEPS OF ITS REALIZATION
KATOKHIN A.V., LEVITSKY V.G.


EVOLUTIONARY DYNAMICS OF LOW COMPLEXITY DNA SEQUENCES IN CODING AND NON CODING REGIONS
CLAUDIA ACQUISTI, GIUSEPPE MERSI, MARCELLO BUIATTI, PATRIZIA BOGANI


THEORETICAL DESIGN OF EFFECTIVE ANTISENSE OLIGONUCLEOTIDES
SCZAKIEL G.


PERIODICITIES IN THE PRIMARY STRUCTURE OF E.COLI PROMOTERS
KRAVATSKAYA G.I., FRANK G.K., MAKEEV V.YU., POLOZOV R.V., ESIPOVA N.G.


MOLECULAR MODELLING OF DISEASE-CAUSING SINGLE-NUCLEOTIDE POLYMORPHISMS IN COLLAGEN
MILCHEVSKY JU.V., RAMENSKY V.E., ZOROV B.S., ESIPOVA N.G., TUMANYAN V.G.


ELUCIDATION OF THE STRUCTURE OF WHOLE PROTEIN: HUMAN COLLAGEN III
MILCHEVSKY JU.V., ZOROV B.S., ESIPOVA N.G., TUMANYAN V.G.











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IC&G  SB RAS,
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