Spis treści: Bioinformatics. Volume I, II

Preface, s. v
Contributors, s. ix
Contents of Volume II, s. xi

Contents of Volume I:

Section I: Data and Databases

1.    Managing Sequence Data / Ilene Karsch Mizrachi, s. 3

2.    RNA Structure Determination by NMR / Lincoln G. Scott and Mirko Hennig, s. 29

3.    Protein Structure Determination by X-Ray Crystallography / Andrea Ilari and Carmelinda Savino, s. 63

4.    Pre-Processing of Microarray Data and Analysis of Differential Expression / Stejfen Durinck, s. 89

5.    Developing an Ontology / Midori A. Harris, s. 111

6.    Genome Annotation / Hideya Kawaji and Yoshihide Hayashizaki, s. 125

Section II: Sequence Analysis

7.    Multiple Sequence Alignment / Walter Pirovano andjaap Heringa, s. 143

8.    Finding Genes in Genome Sequence / Alice Carolyn McHardy, s. 163

9.    Bioinformatics Detection of Alternative Splicing / Namshin Kim and Christopher Lee, s. 179

10.    Reconstruction of Full-Length Isoforms from Splice Graphs / Ti Xing and Christopher Lee, s. 199

11.    Sequence Segmentation / Jonathan M. Keith, s. 207

12.    Discovering Sequence Motifs / Timothy L. Bailey, s. 231

Section III: Phylogenetics and Evolution

13.    Modeling Sequence Evolution / Pietro Lid and Martin Bishop, s. 255

14.    Inferring Trees / Simon Whelan, s. 287

15.    Detecting the Presence and Location of Selection in Proteins / Tim Massingham, s. 311

16.    Phylogenetic Model Evaluation / Lars Sommer Jermiin, Vivek Jayaswal, Faisal Ababneh,and John Robinson, s. 331

17.    Inferring Ancestral Gene Order / Julian M. Catchen,John S. Conery, and John H. Postlethwait, s. 365

18.    Genome Rearrangement by the Double Cut and Join Operation / Richard Friedberg, Aaron E. Darling, and Sophia Tancopoulos, s. 385

19.    Inferring Ancestral Protein Interaction Networks / Jose M. Peregrin-Alvarez, s. 417

20.    Computational Tools for the Analysis of Rearrangements in Mammalian Genomes / Guillaume Bourque and Glenn Tester, s. 431

21.    Detecting Lateral Genetic Transfer: A Phylogenetic Approach / Robert G. Beiko and Mark A. Ragan, s. 457

22.    Detecting Genetic Recombination / Georg F. Weiller, s. 471

23.    Inferring Patterns of Migration / Paul M.E. Bunje and Thierry Wirth, s. 485

24.    Fixed-Parameter Algorithms in Phylogenetics / Jens Gramm, Arfst Nickelsen, and Till Tantau, s. 507

Index, s. 537
Evolution Index, s. 551

Contents of Volume II

Section I: Structures

1.    UNAFold: Software for Nucleic Acid Folding and Hybridization /  Nicholas R. Markham and Michael Zuker
2.    Protein Structure Prediction / Bissan Al-Lazikani, Emma E. Hill, and Veronica Morea
3.    An Introduction to Protein Contact Prediction / Nicholas Hamilton and Thomas Huber
4.    Analysis of Mass Spectrometry Data in Proteomics / Rune Matthiesen and Ole N. Jensen
5.    The Classification of Protein Domains / Russell L. Marsden and Christine A. Orengo

Section II: Inferring Function

6.     Inferring Function from Homology /  Richard D. Ernes
7.     The Rosetta Stone Method / Shailesh V. Date
8.     Inferring Functional Relationships from Conservation of Gene Order /  Gabriel Moreno-Hagelsieb
9.     Phylogenetic Profiling /  Shailesh V. Date and Jose M. Peregrin-Alvarez
10.    Phylogenetic Shadowing: Sequence Comparisons of Multiple Primate Species / Dario Bojfelli
11.    Prediction of Regulatory Elements /  Albin Sandelin
12.    Expression and Microarrays /  Joaquin Dopazo and Fdtima Al-Shahrour
13.    Identifying Components of Complexes /  Nicolas Gojfard and Georg Weiller
14.    Integrating Functional Genomics Data / Insuk Lee and Edward M. Marcotte

Section III: Applications and Disease

15.    Computational Diagnostics with Gene Expression Profiles / Claudio Lottaz, Dennis Kostka, Florian Markowetz, and Rainer Spang
16.    Analysis of Quantitative Trait Loci Mario Falchi
17.    Molecular Similarity Concepts and Search Calculations / Jens Auer and Jiirgen Bajorath
18.    Optimization of the MAD Algorithm for Virtual Screening /  Hanna Eckert and Jilrgen Bajorath
19.    Combinatorial Optimization Models for Finding Genetic Signatures from Gene Expression Datasets / Regina Berretta, Wagner Costa, and Pablo Moscato
20.    Genetic Signatures for a Rodent Model of Parkinson's Disease Using Combinatorial Optimization Methods / Mou'ath Hourani, Rejjina Berretta, Alexandre Mendes, and Pablo Moscato

Section IV: Analytical and Computational Methods

21.    Developing Fixed-Parameter Algorithms to Solve Combinatorially Explosive Biological Problems / Falk Hiiffner, RolfNiedermeier, and Sebastian Wernicke
22.    Clustering / Geoffrey J. McLachlan, Richard W. Bean, and Shu-Kay Ng
23.    Visualization / Falk Schreiber
24.    Constructing Computational Pipelines / Mark Halling-Brown and Adrian J. Shepherd
25.    Text Mining / Andrew B. Clegg and Adrian J. Shepherd


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