Subjects

Bioinformatics of Genome Regulation and Structure

Edited by Nikolay Kolchanov and Ralf Hofestaedt, Springer, 2005, pbk, Reprint, xv, 373 p, illus, ISBN : 8181283775, $50.00 (Includes free airmail shipping)

Contents: Preface. Foreword. I. Computational Genomics: 1. Nucleosomal DNA Organization: an integrated information system/V.G. Levitsky, A.V. Katokhin, O.A. Podkolodnaya and D.P. Furman. 2. Using change in local DNA sequence complexity as a pointer to the mechanism of mutagenesis in inherited disease/N.A. Chuzhanova and D.N. Cooper. 3. Properties of insertion regions of Drosophila LTR retrotransposons/D.P. Furman, D. Yu. Oshchepkov, M.A. Pozdnyakov and A.V. Katokhin. 4. Compositional asymmetries and predicated origins of replication of the Saccharomyces Cerevisiae Genome/J.O. Korbel, H.E. Assmus, S.M. Kielbasa and H. Herzel. 5. Revealing and functional analysis of RNA-like sequences in various genomes/F.E. Frenkel, M.B. Chaley, E.V. Korotkov and K.G. Skryabin. 6. Type-specific features of the structure of the tRNA gene promoters/Yu. V. Kondrakhin, I.B. Rogozin, T.M. Naykova, N.S. Yudin, M.I. Voevoda and A.G. Romashchenko. 7. Mathematical tools for regulatory signals extraction/M. Regnier. 8. Agro-viewer: a package for recognition and analysis of regulatory elements in eukaryotic genes/O.V. Vishnevsky, E.A. Ananko, E.V. Ignatieva, O.A. Podkolodnaya and I.L. Stepanenko. 9. Transcription Regulatory Regions Database (TRRD): description of transcription regulation and the main capabilities of the database/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 and N.A. Kolchanov. 10. Sitecon-a tool for analysis of DNA physicochemical and conformational properties: E2F/DP transcription factor binding site analysis and recognition/D. Yu. Oshchepkov, I.I. Turnaev, M.A. Pozdnyakov, L. Milanesi, E.E. Vityaev, and N.A. Kolchanov. 11. Local secondary structure may be a critical characteristic influencing translation of unicellular organisms mRNA/Yu G. Mutushkin, V.A. Likhoshvai and A.V. Kochetov. 12. Computer analysis of miRNA-mRNA duplexes and its application to predicting possible target mRNAS of arabidopsis/N.A. Omelyanchuk and D.G. Vorobiev. 13. Correlations between sequence features of yeast genes functional regions and the level of expression/A.G. Pichueva, A.V. Kochetov, L. Milanesi, Yu. V. Kondrakhin and N.A. Kolchanov. II. Computational Structural Biology: 1. Latent periodicity of many domains in protein sequences reflects their structure, function and evolution/A.A. Laskin, E.V. Korotkov and N.A. Kudryashov. 2. Logical analysis of data as a predictor of protein secondary structures/J. Btazewicz, P.L. Hammer and P. Lukasiak. 3. Structure-specificity relationship in protein-DNA recognition/H. Kono and A. Sarai. 4. Macromolecular modeling as a tool for expanding bioinformatics databases/Yu. N. Vorobjev. 5. Graphic representation of equilibrium and kinetics in oligopeptides: time-dependent free energy disconnectivity graphs/A.V. Gavrilov and S.F. Chekmarev. 6. Solvent electrostatic screening in protein simulations/S.M. Schwarzl, S. Fischer and J.C. Smith. 7. PDBSiteScan: a program searching for functional sites in protein 3D structures/V.A. Ivanisenko, S.S. Pintus, D.A. Grigorovich, L.N. Ivanisenko, V.A. Debelov and A.M. Matsokin. 8. A genetic algorithm for the inverse folding of RNA/I.I. Titov and A.Yu. Palyanov. 9. Signal transduction pathways initiated via cell surface receptor CD 150: in silico and in vitro analysis/S.P. Sidorenko, S.V. Mikhalap, L.M. Shlapatska, M.Y. Yurchenko, Y.M. Akimov and V.F. Chekhun. III. Computational Evolutionary Biology: 1. Study of the specific contextual features of translation initiation and termination sites in Saccharomyces cerevisiae/O.V. Vishnevsky, I.V. Avdeeva and A.V. Kochetov. 2. Contribution of coordinated substitutions to the constancy of physicochemical properties of ATP-binding loop in protein kinases/D.A. Afonnikov. 3. Sporadic emergence of latent phenotype during evolution/V.A. Likhoshvai and Yu.G. Matushkin. 4. Similarity analysis of inversion banding sequences in chromosomes of chironomus species (breakpoint phylogeny)/I.I. Kiknadze, L.I. Gunderina, A.G. Istomina, V.D. Gusev and L.A. Nemytikova. IV. System Computational Biology: 1. Integrative analysis of gene networks using dynamic process pattern modelling/A. Freier, M. Lange and R. Hofestaedt. 2. Development and analysis of models of genetic and metabolic networks and signal transduction pathways in the genenet system/E.A. Ananko, K.A. Loktev and N.L. Podkolodny. 3. Extension of cell cycle gene network description based on prediction of potential binding sites for E2F transcription factor/I.I. Turnaev, D. Yu. Oshchepkov and O.A. Podkolodnaya. 4. Mathematical simulation of dynamics of macrophage gene network activated by lipopolysacchrides and/or interferon-g/E.A. Nedosekina, E.A. Ananko, L. Milanesi, V.A. Likhoshvai and N.A. Kolchanov. 5. Computer dynamic modeling of the gene network controlling intracellular cholesterol homeostasis/A.V. Ratushny, E.V. Ignatieva and V.A. Likhoshvai. 6. An investigation of the structural stability of drosophila control gene subnetwork in computer experiments/A.V. Galimzyanov and R.N. Tchuraev. 7. Modeling plant development with gene regulation networks including signaling and cell division/H. Jonsson, B.E. Shapiro, E.M. Meyerowitz and E. Mjolsness. 8. The global operation modes of gene networks determined by the structure of negative feedbacks/V.A. Likhoshvai, S.I. Fadeev and Yu. G. Matushkin. 9. Statistical analysis of microarray data: identification and classification of yeast cell cycle genes/Yu. V. Kondrakhin, O.A. Podkolodnaya, A.V. Kochetov, G.N. Erokhin and N.A. Kolchanov. References. Index.

"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."

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