Bioinformatics of Genome Regulation and Structure

by Kolchanov, Nikolay; Hofestadt, Ralf

• ISBN13: 9781402077357
• ISBN10: 1402077351
• Format: Hardcover
• Copyright: 2004-03-01
• Publisher: Kluwer Academic Pub

Summary

Bioinformatics of Genome Regulation and Structure covers: -regulatory genomic sequences: databases, knowledge bases, computer analysis, modeling, and recognition; -large-scale genome analysis and functional annotation; -gene structure detection and prediction; -comparative and evolutionary genomics; -computer analysis of genome polymorphism and evolution; computer analysis and modeling of transcription, splicing, and translation; structural computational biology: structure-function organization of genomic DNA, RNA, and proteins; -gene networks, signal transduction pathways, and genetically controlled metabolic pathways: principles of organization, operation, and evolution; -data warehousing, knowledge discovery and data mining; and, -analysis of basic patterns of genome operation, organization, and evolution. The data presented may be used while solving a wide range of problems, both basic and applied, in various directions of molecular biology, molecular genetics, biotechnology, pharmacogenetics, pharmacology, and adjacent fields of medicine, veterinary, and agrobiology.

Table of Contents

Contributing Authors	xi
Preface	xiii
Foreword	xv
Part 1. COMPUTATIONAL GENOMICS	1	(132)
Nucleosomal DNA Organization: An Integrated Information System	3	(10)
V.G. Levitsky
A.V. Katokhin
O.A. Podkolodnaya
D.P. Furman
Using Change in Local DNA Sequence Complexity as a Pointer to the Mechanism of Mutagenesis in Inherited Disease	13	(8)
N.A. Chuzhanova
D.N. Cooper
Properties of Insertion Regions of Drosophila LTR Retrotransposons	21	(12)
D.P. Furman
D. Yu. Oshchepkov
M.A. Pozdnyakov
A.V. Katokhin
Compositional Asymmetries and Predicted Origins of Replication of the Saccharomyces Cerevisiae Genome	33	(6)
J.O. Korbel
H.E. Assmus
S.M. Kielbasa
H. Herzel
Revealing and Functional Analysis of tRNA-Like Sequences in Various Genomes	39	(8)
F.E. Frenkel
M.B. Chaley
E.V. Korotkov
K.G. Skryabin
Type-Specific Features of the Structure of the tRNA Gene Promoters	47	(14)
Yu. V. Kondrakhin
I.B. Rogozin
T.M. Naykova
N.S. Yudin
M.I. Voevoda
A.G. Romaschenko
Mathematical Tools for Regulatory Signals Extraction	61	(10)
M. Regnier
Argo_Viewer: A Package for Recognition and Analysis of Regulatory Elements in Eukaryotic Genes	71	(10)
O.V. Vishnevsky
E.A. Ananko
E.V. Ignatieva
O.A. Podkolodnaya
I.L. Stepanenko
Transcription Regulatory Regions Database (TRRD): Description of Transcription Regulation and the Main Capabilities of the Database	81	(12)
E.V. Ignatieva
E.A. Ananko
O.A. Podkolodnaya
I.L. Stepanenko
T.M. Khlebodarova
T.I. Merkulova
M.A. Pozdnyakov
A.L. Proscura
D.A. Grigorovich
N.L. Podkolodny
A.N. Naumochkin
A.G. Romashchenko
N.A. Kolchanov
Sitecon---A Tool for Analysis of DNA Physicochemical and Conformational Properties: E2F/DP Transcription Factor Binding Site Analysis and Recognition	93	(10)
D. Yu. Oshchepkov
I.I. Turnaev
M.A. Pozdnyakov
L. Milanesi
E.E. Vityaev
N.A. Kolchanov
Local Secondary Structure May be a Critical Characteristic Influencing Translation of Unicellular Organisms mRNA	103	(12)
Yu. G. Matushkin
V.A. Likhoshvai
A.V. Kochetov
Computer Analysis of miRNA--mRNA Duplexes and its Application to Predicting Possible Target mRNAS of Arabidopsis	115	(10)
N.A. Omelyanchuk
D.G. Vorobiev
Correlations Between Sequence Features of Yeast Genes Functional Regions and the Level of Expression	125	(8)
A.G. Pichueva
A.V. Kochetov
L. Milanesi
Yu.V. Kondrakhin
N.A. Kolchanov
Part 2. COMPUTATIONAL STRUCTURAL BIOLOGY	133	(78)
Latent Periodicity of Many Domains in Protein Sequences Reflects Their Structure, Function, and Evolution	135	(10)
A.A. Laskin
E.V. Korotkov
N.A. Kudryashov
Logical Analysis of Data as a Predictor of Protein Secondary Structures	145	(10)
J. Blazewicz
P.L. Hammer
P. Lukasiak
Structure-Specificity Relationship in Protein-DNA Recognition	155	(8)
H. Kono
A. Sarai
Macromolecular Modeling as a Tool for Expanding Bioinformatics Databases	163	(8)
Yu. N. Vorobjev
Graphic Representation of Equilibrium and Kinetics in Oligopeptides: Time-Dependent Free Energy Disconnectivity Graphs	171	(8)
A.V. Gavrilov
S.F. Chekmarev
Solvent Electrostatic Screening in Protein Simulations	179	(6)
S.M. Schwarzl
S. Fischer
J.C. Smith
Pdbsitescan: A Program Searching for Functional Sites in Protein 3D Structures	185	(8)
V.A. Ivanisenko
S.S. Pintus
D.A. Grigorovich
L.N. Ivanisenko
V.A. Debelov
A.M. Matsokin
A Genetic Algorithm for the Inverse Folding of RNA	193	(10)
I.I. Titov
A.Yu. Palyanov
Signal Transduction Pathways Initiated Via Cell Surface Receptor CD150: In Silico and In Vitro Analysis	203	(8)
S.P. Sidorenko
S.V. Mikhalap
L.M. Shlapatska
M.Y. Yurchenko
Y.M. Akimov
V.F. Chekhun
Part 3. COMPUTATIONAL EVOLUTIONARY BIOLOGY	211	(44)
Study of the Specific Contextual Features of Translation Initiation and Termination Sites in Saccharomyces Cerevisiae	213	(10)
O.V. Vishnevsky
I.V. Avdeeva
A.V. Kochetov
Contribution of Coordinated Substitutions to the Constancy of Physicochemical Properties of ATP-Binding Loop in Protein Kinases	223	(8)
D.A. Afonnikov
Sporadic Emergence of Latent Phenotype During Evolution	231	(14)
V.A. Likhoshvai
Yu.G. Matushkin
Similarity Analysis of Inversion Banding Sequences in Chromosomes of Chironomus Species (Breakpoint Phylogeny)	245	(10)
I.I. Kiknadze
L.I. Gunderina
A.G. Istomina
V.D. Gusev
L.A. Nemytikova
Part 4. SYSTEM COMPUTATIONAL BIOLOGY	255	(88)
Integrative Analysis of Gene Networks Using Dynamic Process Pattern Modelling	257	(8)
A. Freier
M. Lange
R. Hofestaedt
Development and Analysis of Models of Genetic and Metabolic Networks and Signal Transduction Pathways in the Genenet System	265	(8)
E.A. Ananko
K.A. Loktev
N.L. Podkolodny
Extension of Cell Cycle Gene Network Description Based on Prediction of Potential Binding Sites for E2F Transcription Factor	273	(10)
I.I. Turnaev
D.Yu. Oshchepkov
O.A. Podkolodnaya
Mathematical Simulation of Dynamics of Macrophage Gene Network Activated by Lipopolysaccharides and/Or Interferon-G	283	(10)
E.A. Nedosekina
E.A. Ananko
L. Milanesi
V.A. Likhoshvai
N.A. Kolchanov
Computer Dynamic Modeling of the Gene Network Controlling Intracellular Cholesterol Homeostasis	293	(8)
A.V. Ratushny
E.V. Ignatieva
V.A. Likhoshvai
An Investigation of the Structural Stability of Drosophila Control Gene Subnetwork in Computer Experiments	301	(10)
A.V. Galimzyanov
R.N. Tchuraev
Modeling Plant Development with Gene Regulation Networks Including Signaling and Cell Division	311	(8)
H. Jonsson
B.E. Shapiro
E.M. Meyerowitz
E. Mjolsness
The Global Operation Modes of Gene Networks Determined by the Structure of Negative Feedbacks	319	(12)
V.A. Likhoshvai
S.I. Fadeev
Yu.G. Matushkin
Statistical Analysis of Microarray Data: Identification and Classification of Yeast Cell Cycle Genes	331	(12)
Yu.V. Kondrakhin
O.A. Podkolodnaya
A.V. Kochetov
G.N. Erokhin
N.A. Kolchanov
References	343	(28)
Index	371