Compiled by Aik Choon TAN

The list was updated on 26th January 2004

No.

Author(s)

Title

TOC

Price

ISBN

1

Andreas D. Baxevanis and B. F. Francis Ouellette (Eds)

Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition

·         Bioinformatics and the Internet (A. Baxevanis).

·         The NCBI Data Model (J. Ostell, et al.).

·         The GenBank Sequence Database (I. Karsch-Mizrachi & B. Ouellette).

·         Submitting DNA Sequences to the Databases (J. Kans & B. Ouellette).

·         Structure Databases (C. Hogue).

·         Genomic Mapping and Mapping Databases (P. White & T. Matise).

·         Information Retrieval from Biological Databases (A. Baxevanis).

·         Sequence Alignment and Database Searching (G. Schuler).

·         Creation and Analysis of Protein Multiple Sequence Alignments (G. Barton).

·         Predictive Methods Using DNA Sequences (A. Baxevanis).

·         Predictive Methods Using Protein Sequences (S. Banerjee-Basu & A. Baxevanis).

·         Expressed Sequence Tags (ESTs) (T. Wolfsberg & D. Landsman).

·         Sequence Assembly and Finishing Methods (R. Staden, et al.).

·         Phylogenetic Analysis (F. Brinkman & D. Leipe).

·         Comparative Genome Analysis (M. Galperin & E. Koonin).

·         Large-Scale Genome Analysis (P. Meltzer).

·         Using Perl to Facilitate Biological Analysis (L. Stein).

·         Glossary.

·         Index.

Paper

488 Pages                                            May 2001

2nd Edition

£51.95 /

$69.95/

 €82.30

 

·         Willey&Sons

 

·         www

ISBN: 0-471-38391-0

2

David W. Mount

Bioinformatics: Sequence and Genome Analysis

·         Chapter 1: Historical Introduction and Overview

·         Chapter 2: Collecting and Storing Sequences in the Laboratory

·         Chapter 3: Alignment of Pairs of Sequences

·         Chapter 4: Multiple Sequence Alignment

·         Chapter 5: Prediction of RNA Secondary Structure

·         Chapter 6: Phylogenetic Prediction

·         Chapter 7: Database Searching for Similar Sequences

·         Chapter 8: Gene Prediction

·         Chapter 9: Protein Classification and Structure Prediction

·         Chapter 10: Genome Analysis

Paperback

564 pages

1st edition (March 15, 2001)

 Dimensions (in inches): 1.15 x 11.02 x 8.08

·         Cold Spring Harbor Laboratory

 

·         www

ISBN: 0879696087

3

Gregory R. Grant, Warren J. Ewens

Statistical Methods in Bioinformatics: An Introduction

·         An Introduction to Probability Theory: One Random Variable

·         An Introduction to Probability Theory: Many Random Variables Statistics: An Introduction to Statistical Inference

·         Stochastic Processes: An Introduction to Poisson Processes and Markov Chains

·         The Analysis of DNA Sequence Patterns: One sequence

·         The Analysis of DNA Sequences: Multiple sequences

·         Stochastic Processes: Random Walks

·         Statistics: Classical Estimation and Hypothesis Testing

·         BLAST

·         Stochastic Processes: Markov Chains

·         Hidden Markov Models

·         Computationally intensive methods

·         Evolutionary models

·         Phylogenetica tree estimation

Hardcover

476 pages

1st edition

(June 2001)

 

$79.95

 

·         Springer Verlag

 

Dimensions (in inches): 1.07 x 9.55 x 6.40

ISBN: 0387952292

4

H.-W. Mewes,

B. Weiss,

H. Seidel,

Bioinformatics and Genome Analysis

·         Human Genetics

·         Genotyping.

·         Bioinformatics of Membrane Proteins.

·         SNAPping up Functionally Related Genes Based on Context Information.

·         Promoter Analysis.

·         Cluster Analysis and its Applications to Gene Expression Data.

·         Statistical Methods for Analyzing Gene Expression Data for Cancer Research.

·         Structural Genomics.

·         Computational Structural Proteomics.

·         Proteomics in Biological Research.

·         The Challenge to Make Proteins Speak.

·         Construction and Prediction of Protein-Protein Interaction Maps.

·         Bioinformatics, Cellular Flows, and Simulation.

·         Graph-based Analysis of Metabolic Networks.

·         Orphan Protein Function and its Relation to Glycosylation.

$85.00

 320 pages 75 illus., hardcover

Availability: Not yet published; expected release date:07/16/2002

 

·         Springer Verlag

ISBN: 3-540-42893-3, published 2002

5

Lecture Notes in Computer Science, Vol. 2066

Computational Biology

 

Price: $45.00

165 pages paperback

ISBN: 3-540-42242-0, published 2001

6

Cynthia Gibas, Per Jambeck

Developing Bioinformatics Computer Skills

I. Introduction

1. Biology in the Computer Age 

2. Computational  Approaches to Biological Questions 

II. The Bioinformatics Workstation

3. Setting Up Your Workstation 

4. Files and Directories in Unix 

5. Working on a Unix System 

III. Tools for Bioinformatics

6. Biological Research on the Web 

7. Sequence Analysis, Pairwise Alignment, and Database Searching 

8. Multiple Sequence Alignments, Trees, and Profiles 

9. Visualizing Protein Structures and Computing Structural Properties 

10. Predicting Protein Structure and Function from Sequence 

11. Tools for Genomics and Proteomics 

IV. Databases and Visualization

12. Automating Data Analysis with Perl 

13. Building Biological Databases 

14. Visualization and Data Mining 

Bibliography  

Index  

April 2001 

1-56592-664-1, Order Number: 6641

                                        446 pages, $34.95 US $51.95 CA £24.95 UK

 

·         O'Reilly

7

James Tisdall

Beginning Perl for Bioinformatics

Preface

1. Biology and Computer Science

2. Getting Started with Perl

3. The Art of Programming

4. Sequences and Strings

5. Motifs and Loops

6. Subroutines and Bugs

7. Mutations and Randomization

8. The Genetic Code

9. Restriction Maps and Regular Expressions

10. GenBank

11. Protein Data Bank

12. BLAST

13. Further Topics

A. Resources

B. Perl Summary

Index

 

 

 

October 2001 

0-596-00080-4, Order Number: 0804

                                        384 pages, $39.95 US $59.95 CA £28.50 UK

 

·         O'Reilly

 

8

Cathy H. Wu, Jerry W. McLarty

Neural Networks and Genome Informatics

PART I. OVERVIEW.

Chapter 1. Neural Networks for Genome Informatics.

PART II. Neural Network Foundations.

Chapter 2. Neural Network Basics.

Chapter 3. Perceptrons and Multilayer Perceptrons.

Chapter 4. Other Common Architectures.

Chapter 5. Training of Neural Networks.

PART III. Genome Informatics Applications.

Chapter 6. Design Issues - Feature Presentation.

Chapter 7. Design Issues - Data Encoding.

Chapter 8. Design Issues - Neural Networks.

Chapter 9. Applications - Nucleic Acid Sequence Analysis.

Chapter 10. Applications - Protein Structure Prediction.

Chapter 11. Applications - Protein Sequence Analysis.

PART IV. Open Problems and Future Directions.

Chapter 12. Integration of Statistical Methods into Neural Network Applications.

Chapter 13. Future of Genome Informatics Applications.

Glossary.

Author Index.

Subject Index.

Hardcover - 220 pages (September 2000)

Price: Order form

          USD 91

          EUR 91

·         Elsevier Science;

ISBN: 0080428002

9

P.Baldi and S. Brunak

Bioinformatics: The Machine Learning Approach

1.  Introduction

2.   Machine-Learning Foundations: The Probabilistic Framework 

3.   Probabilistic Modeling & Inference: Examples

4.   Machine Learning Algorithms  

5. Neural Networks: The Theory

6.   Neural Networks: Applications     

7.  Hidden Markov Models: The Theory

8.  Hidden Markov Models: Applications  

9.  Probabilistic Graphical Models in Bioinformatics

10.  Probabilistic Models of Evolution: Phylogenetic

11.  Stochastic Grammars & Linguistics

12.  Microarrays & Gene Expression

13.  Internet Resources & Public Databases

A.   Statistics     

B.   Information Theory, Entropy, & Relative

C.   Probabilistic Graphical Models

D.   HMM Technicalities, Scaling, Periodic

E.   Gaussian Processes, Kernel Methods, and Support Vector Machines

F.   Symbols and Abbreviations 

References  Index

August 2001

ISBN 0-262-02506-X

400 pp.

                           $49.95/£34.95 (CLOTH)

 

·         MIT Press

 

10

J. Leszczynski

Computational Molecular Biology

Chapter 1. Hybrid potentials for large molecular systems

(P. Amara, M.J. Field).

2. Proton transfer in models biomolecules

(S. Scheiner).

3. Computational approaches to the studies of the interactions of nucleic acid bases

(J Sponer, P. Hobza, J. Leszczynski).

4. Nucleic acid bases in solution

(M. Orozco, E. Cubero, X. Barril, C. Colominas, F.J. Luque).

5. Current trends in modeling interactions of DNA fragments with polar solvents

(L. Gorb, J. Leszczynski).

6. Radiation-induced DNA damage and repair: An approach from ab initio MO method

(M. Aida, M. Kaneko, M. Dupuis).

7.  Application of molecular orbital theory to elucidation of radical processes induced by radiation damage to DNA

(A.-O. Colson, M.D. Sevilla).

8. Exploring the structural repertoire of Guanine-rich DNA sequences: Computer modeling studies

(M. Bansal, M. Ravikiran, S. Chowdhury).

9. The calculation of relative binding thermodynamics of molecular associations in aqueous environments

(G.J. Tawa, I.A. Topol, S.K. Burt).

10. Theoretical tools for analysis and modeling electrostatic effects in biomolecules

(W.A. Sokalski, P. Kedierski, J. Grembecka, P. Dziedonski, K. Strasburger).

11. Application of reduced models to protein structure prediction

(J. Skolnick, A. Kolinski, A.R. Ortiz).

12. Modeling DNA-protein interactions

(K. Zakrzewska, R. Lavery).

13. Interactions of small molecules and peptides with membranes

(A. Pohorille, M.A. Wilson, C. Chipot, M.H. New, K. Schwieghofer).

14. Modeling of antifreeze proteins

(J.D. Madura, A. Wierzbicki).

15. The role of computational techniques in retrometabolic drug design strategies

(N. Bodor, P. Buchwald, M.-J. Huang).

16. Computational aspects of neural membrane biophysics

(R. Wallace).

Year 1999  

 

Hardbound

 

662 pages

Price: Order form

          USD 305.50

          EUR 305.50

 

·         Elsevier Science

ISBN: 0-444-50030-8

11

S.L. Salzberg, D.B. Searls, S. Kasif,

Computational Methods in Molecular Biology

1. Grand challenges in computational biology (D.B. Searls).

2. A tutorial introduction to computation for biologists (S.L. Salzberg).

3. An introduction to biological sequence analysis (K.H. Fasman, S.L. Salzberg).

4. An introduction to hidden Markov models for biological sequences (A. Krogh).

5. Case-based reasoning driven gene annotation (G.C. Overton, J. Haas).

6.  Classification-based molecular sequence analysis (D.J. States, W.C. Reisdorf, Jr.) 7. Computational gene prediction using neural networks and similarity search (Y. Xu, E.C. Uberbacher).

8. Modeling dependencies in pre-mRNA splicing signals (C.B. Burge).

9.  Evolutionary approaches to computational biology (R.J. Parsons).

10. Decision trees and Markov chains for gene finding (S.L. Salzberg).

11. Statistical analysis of protein structures: using environmental features for multiple purposes (L. Wei, J.T. Chang, R.B. Altman).

12. Analysis and algorithms for protein sequence-structure alignment (R.H. Lathrop et al.).

13. THREADER: protein sequence threading by double dynamic programming (D. Jones).

14. From computer vision to protein structure and association (H.J. Wolfson, R. Nussinov).

15. Modeling biological data and structure with probabilistic networks (S. Kasif, A.L. Delcher).

Appendix A: Software and databases for computational biology on the Internet.

Appendix B: Suggestions for further reading in computational biology.

Year 1998   Hardbound , Paperback

 

Hardbound

 

ISBN: 0-444-82875-3

     398 pages

     Please contact your Regional Sales Office for a discount offer for larger orders.

     Price: Order form

          USD 174.50

          EUR 174.50

 

Paperback

 

     ISBN: 0-444-50204-1

     Price: Order form

          USD 52.50

          EUR 52.50

 

·         Elsevier Science

12

Teresa Attwood, David Parry-Smith

Introduction to Bioinformatics

 

Paperback - 240 pages 1st edition (March 8, 1999)

·         Prentice Hall;

ISBN: 0582327881

 

13

Des Higgins (Editor), Willie Taylor (Editor)

Bioinformatics : Sequence, Structure, and Databanks : A Practical Approach (Practical Approach

Series (Paper))

Threading Methods for Protein Structure Prediction

Comparison of Protein Three-Dimensional Structure

Multiple Alignments for Structural, Functional or Phylolgenetic Analyses of Homologous Sequences

Hidden Markov Models for Data Base Similarity Searches

Protein Family-Based methods for Homology Detection and Analysis

Predicting Secondary Structure from Protein Sequences

Methods for Discovering Conserved Patterns in Protein Sequences and Structures

Comparison of Protein Sequences and Practical Database Searching

Networking for the Biologist

SRS - Access to Molecular Biological Databanks and Integrated Data Analysis

Price: £32.50 (Paperback )

                                                                         0-19-963790-3

                                                                         Publication date: 14 September

                                                                         2000

                                                                         270 pages, numerous line figures

 

·         OUP

14

Minoru Kanehisa

Post-genome Informatics

Preface

Blueprint of life

Molecular biology databases - Historical background, Informatics technologies,

New generation of molecular biology databases

Sequence analysis of nucleic acids and proteins - Similarity search, Prediction of structures and functions

Network analysis of molecular interactions - Network representation and computation, Principles of biochemical networks

References and further reading

Price: £21.95 (Paperback )

                                                                        0-19-850326-1

                                                                        Publication date: 20 January 2000

                                                                        158 pages, numerous line figures,

                                                                        234mm x 156mm

 

·         OUP

15

Jason T. L. Wang, Bruce A. Shapiro, and Dennis Shasha

Pattern Discovery in Biomolecular Data -

Tools, Techniques, and Applications

Part I. Finding Patterns in Sequences

1. Discovering Patterns in DNA Sequences by the Algorithmic

Significance Method, Aleksandar Milosavljevic

2. Assembling Blocks, Jorja G. Henikoff

3. MEME, MAST, and Meta-MEME: New Tools for Motif Discovery in Protein Sequences, Timothy L. Bailey et al.

4. Pattern Discovery and Classification in Biosequences, Jason T. L. Wang et al.

Part II. Finding Patterns in 3D Structures

5. Motif Discovery in Protein Structure Databases, Janice Glasgow, Evan Steeg, and Suzanne Fortier

6. Systematic Detection of Protein Structural Motifs, Kentaro Tomii and Minoru Kanehisa

7. Representation and Matching of Small Flexible Molecules in Large Databases of 3D Molecular Information, Isidore Rigoutsos et al.

Part III. System Components for Discovery

8.  A Framework for Biological Pattern Discovery on Networks of Workstations, Bin Li, Dennis Shasha, and Jason T. L. Wang

9. Discovering Concepts in Structural Data, Diane J. Cook, Lawrence B. Holder, and Gehad Galal

10. Overview: A System for Tracking and Managing the Results from Sequence Comparison Programs, David P. Yee et al.

11. RNA Structure Analysis: A Multifaceted Approach, Bruce A.

Shapiro et al.

Glossary

References

Index

Price: £49.50 (Hardback )                                                        0-19-511940-1

Publication date: 2 December 1999                                                         OUP USA 272 pages, numerous halftones and line

figures, 234mm x 156mm

 

16

Hooman H. Rashidi, Lukas K. Buehler

Bioinformatics Basics Applications in Biological Science and Medicine

INTRODUCTION

DATABASES AND SEARCH TOOLS

PROTEOME ANALYSIS

COMPUTER REVOLUTION IN NEUROBIOLOGY

APPENDIX

Hardcover - 200 pages (December 15, 1999)

·         CRC Press;

·         ISBN: 0849323754

 

17

Michael S Waterman

Introduction to Computational Biology: Maps, Sequences and Genomes

·         Introduction

·         Some Molecular Biology

·         Restriction Maps

·         Multiple Maps

·         Algorithms for DDP

·         Cloning and Clone Libraries

·         Physical Genome Maps: Oceans, Islands, and Anchors

·         Sequence Assembly

·         Databases and Rapid Sequence Analysis

·         Dynamic Programming Alignment of Two Sequences

·         Multiple Sequence Alignment

·         Probability and Statistics for Sequence Alignment

·         Probability and Statistics for Sequence Patterns

·         RNA Secondary Structure

·         Trees and Sequences

·         Sources and Perspectives

·         References

·         Problem Solutions and Hints

·         Mathematical Notation

·         Algorithm Index

·         Author Index

·         Subject Index

List Price: $62.95

                                                      Cat. #: C9391

                                                      ISBN: 0412993910

                                                      Publication Date: 6/1/1995

                                                      Number of Pages: 448

·         Chapman & Hall / CRC

18

Thomas Lengauer

Bioinformatics: From Genomes to Drugs

VOLUME I.

·         From Genomes to Drugs with Bioinformatics - An Overview.

·         Sequence Analysis.

·         Structure, Properties and Computer Identification of Eukaryotic Genes.

·         Analyzing Regulatory Regions in Genomes.

·         Homology Modeling in Biology and Medicine.

·         Protein Structure Prediction.

·         Protein-Ligand Docking in Drug Design.

·         Modelling Protein-Protein and Protein-DNA Docking.

·         Appendix: Algorithmic Methods in Bioinformatics.

 

VOLUME II.

·         Integrating and Accessing Molecular Biology Resources.

·         Bioinformatics Support of Genome Sequencing Projects.

·         Analysis of Sequence Variations.

·         Proteome Analysis.

·         Target Finding in Genomes and Proteomes.

·         Screening of Drug Databases.

·         Future Trends.

Hardcover - 648 pages 2nd edition Vol 2.s (July 25, 2001)

·         John Wiley & Sons

Dimensions (in inches): 1.71 x 8.94 x 7.64

ISBN: 3527299882

19

Luke Alphey

DNA Sequencing: From Experimental Methods to Bioinformatics

 

Paperback - 206 pages 1st edition (January 15, 1997)

·         Springer Verlag

Dimensions (in inches): 0.52 x 9.12 x 6.07

ISBN: 0387915095

 

20

S. Schulze Kremer (Editor), S. Schulze-Kremer (Editor)

Advances in Molecular Bioinformatics

 

Paperback - 268 pages Vol 22 FAIA (January 1, 1994)

·         IOS Press;

US$79/EUR87/£55

 

ISBN: 905199172X

21

Dietmar Schomburg (Editor), Uta Lessel (Editor)

Bioinformatics: From Nucleic Acids and Proteins to Cell Metabolism

·         BIOLOGICAL DATA BASES.

·         An Integrated Service Approach to Biological Sequence Databases (K. Heumann, et al.).

·         DNA AND RNA.

·         Statistical Analysis of DNA Sequences (H. Herzel, et al.).

·         A Consensus Match Scoring System that is Correlated with Biological Functionality (K. Quandt, et al.).

·         PROTEIN SEQUENCES AND STRUCTURES.

·         Statistical Significance of Local Alignments with Gaps (M. Vingron & M. Waterman).

·         An Algorithm for the Protein Docking Problem (H.-P. Lenhof).

·         FROM MOLECULES TO CELL METABOLISM.

·         Force Field Minimization: Domain Decomposition, Positive Definite Functions, and Wavelets (E. Schmitt).

·         Simulation and Animation of Intracellular Diffusion (H.-G. Lipinski).

Paperback - 196 pages (November 1995)

·         John Wiley & Sons;

£60.00 / €99.00

ISBN: 3527300724

22

James M. Bower and Hamid Bolouri

Computational Modeling of Genetic and Biochemical Networks

 

This book provides specific examples, across a wide range of molecular and cellular systems, of how modeling techniques can be used to explore functionally relevant molecular and cellular relationships. The modeling techniques covered are applicable to cell, developmental, structural, and mathematical biology; genetics; and computational neuroscience. The book, intended as a primer for both theoretical and experimental biologists, is organized in two parts: models of gene activity and models of interactions among gene products. Modeling examples are provided at several scales for each subject. Each chapter includes an overview of the biological system in question and extensive references to important work in the area.

January 2001

 390 pp., 126 illus.

$59.95/£41.95 (CLOTH)

·         MIT Press

ISBN 0-262-02481-0

23

Tao Jiang, Ying Xu and Michael Q. Zhang

Current Topics in Computational Molecular Biology

This survey of computational molecular biology covers traditional topics such as protein structure modeling and sequence alignment, and more recent ones such as expression data analysis and comparative genomics. It combines algorithmic, statistical, database, and AI-based methods for studying biological problems. The book also contains an introductory chapter, as well as one on general statistical modeling and computational techniques in molecular biology. Each chapter presents a self-contained review of a specific subject.

March 2002

 7 x 9, 540 pp., 100 illus.                           $55.00/£37.95 (CLOTH)

 

·         MIT Press

ISBN 0-262-10092-4

 

24

Pavel A. Pevzner

Computational Molecular Biology: An Algorithmic Approach

omputer science and mathematics are transforming molecular biology from an informational to a computational science. Drawing on computational, statistical, experimental, and technological methods, the new discipline of computational molecular biology is dramatically increasing the discovery of new technologies and tools for molecular biology.

August 2000

332 pp., 100 illus.                           $50.00/£34.95 (CLOTH)

 

·         MIT Press

ISBN 0-262-16197-4

25

Julio Collado-Vides and Ralf Hofestädt

Gene Regulation and Metabolism: Post-Genomic Computational Approaches

This book focuses on current computational approaches to understanding the complex networks of metabolic and gene regulatory capabilities of the cell. The contributors look well beyond the state of the art in computational biology to anticipate what biological research will be like in a post-genomic world.

July 2002

7 x 9, 295 pp., 68 illus.

                           $45.00/£30.95 (CLOTH)

·         MIT Press

ISBN 0-262-03297-X

 

26

Stephen Misener (Editor), Stephen A. Krawetz (Editor)

Bioinformatics: Methods and Protocols

 

Hardcover - 500 pages 1st edition (January 15, 2000)

·         Humana Press

Dimensions (in inches): 1.38 x 9.27 x 6.21

ISBN: 0896037320

27

Peter Clote, Rolf Backofen

Computational Molecular Biology: An Introduction

·         Preface

·         Molecular Biology

·         Math Primer

·         Sequence Alignment

·         All About Eve

·         Hidden Markov Models

·         Structure Prediction

·         Appendix A Mathematical Background

·         Appendix B Resources

·         References

·         Index

Paper

300 Pages                                         September 2000

$55.00

·         John Wiley & Sons

ISBN: 0-471-87252-0

28

Dan Gusfield

Algorithms on Strings, Trees

and Sequences

Part I. Exact String Matching: The Fundamental String Problem: 1. Exact matching: fundamental preprocessing and first algorithms;

2. Exact matching: classical comparison-based methods;

3. Exact matching: a deeper look at classical methods;

4. Semi-numerical string matching;

Part II. Suffix Trees And Their Uses:

5. Introduction to suffix trees;

6. Linear time construction of suffix trees;

7. First applications of suffix trees;

8. Constant time lowest common ancestor retrieval;

9. More applications of suffix trees;

Part III. Inexact Matching, Sequence Alignment, And Dynamic Programming:

10. The importance of (sub)sequence comparison in molecular biology;

11. Core string edits, alignments, and dynamic programming;

12. Refining core string edits and alignments;

13. Extending the core problems;

14. Multiple string comparison: the Holy Grail;

15. Sequence database and their uses: the motherlode;

Part IV. Currents, Cousins And Cameos:

16. Maps, mapping, sequencing and superstrings;

17. Strings and evolutionary trees;

18. Three short topics;

19. Models of genome-level mutations

P rice: GBP 47.50

Binding: Hardback                                                   Size: 262 x 185 mm

Pages: 554                                                    Weight: 1.185kg

Figures: 145 line diagrams

·         Cambridge

ISBN: 0521585198

29

Stanley Letovsky (Editor)

Bioinformatics: Databases and Systems

Introduction; S. Letovsky. Databases.

1. NCBI: Integrated Data for Molecular Biology Research; K.

Sirotkin.

2. Hovergen: Comparative Analysis of Homologous Vertebrate Genes; L. Duret, et al.

3. WIT/WIT2: Metabolic Reconstruction Systems; R. Overbeek, et al.

4. EcoCyc: The Resource and the

Lessons Learned; P.D. Karp, M. Riley.

5. KEGG: From Genes to Biochemical Pathways; M. Kanehisa.

6.OMIM: Online Mendelian Inheritance in Man; A.F. Scott, et al. 7. GDB: Integrating Genomic Maps; S.

Letovsky.

8. HGMD: The Human Gene Mutation Database; M. Krawczak, et al.

9. Senselab: Modeling Heterogenous Data on the Nervous System; P. Nadkarni, et al.

10. The Mouse Genome Database and The Gene Expression Database: Genotype to Phenotype; J.T. Eppig, et al.

11. The Edinburgh Mouse Atlas: Basic Structure and Informatics; R.A. Baldock, et al.

12. FlyBase: Genomic and Post-Genomic Viewpoints; The FlyBase Consortium.

13. MaizeDB: The Maize Genome Database; M. Polacco, E. Coe.

14. AGIS: Using the Agricultural Genome Information System; S.M. Beckstrom-Sternberg, D.C. Jamison.

15. CGSC: The E. coli Genetic Stock Center Database; M.K.B. Berlyn. Systems.

16. OPM: Object-Protocol Model Data Management Tools '97; V.M. Markowitz, et al.

17. BioKleisli: Integrating Biomedical Data and Analysis Packages; S.B. Davidson, et al.

18. SRS: Analyzing and Using Data from Heterogenous Textual Databanks; P. Carter, et al.

19. Biology Workbench: A Computing and Analysis

Environment for the Biological Sciences; R. Unwin, et al.

20. EBI: CORBA and the EBI Databases; K.

Jungfer, et al.

21. Biowidgets: Reusable Visualization Components for Bioinformatics; J. Crabtree, et al.

22. ACEDB: The ACE Database Manager; J. Thierry-Mieg, et al. 23. LABBASE: Data and Workflow Management for Large Scale Biological Research; N. Goodman, et al.

Index.

Hardcover - 304 pages 1st edition (September 15, 1999)

·         Kluwer Academic Publisher

 

EUR 154.50 /  USD 146.50 /  GBP 112.50

ISBN: 079238573X

30

Timo Koski

Hidden Markov Models for Bioinformatics

Foreword.

1.Prerequisites in probability calculus.

2. Information and the Kullback Distance.

3. Probabilistic Models and Learning.

4. EM Algorithm.

5. Alignment and Scoring.

6. Mixture Models and Profiles.

7. Markov Chains.

8. Learning of Markov Chains.

9. Markovian Models for DNA sequences.

10.Hidden Markov Models: an Overview.

11. HMM for DNA Sequences.

12. Left to Right HMM for Sequences.

13. Derin's Algorithm.

14. Forward - Backward Algorithm.

15. Baum - Welch Learning Algorithm.

16. Limit Points of Baum - Welch.

17. Asymptotics of Learning.

18. Full Probabilistic HMM.

Index.

·         Kluwer Academic Publishers, Dordrecht

                                                                            Hardbound, ISBN 1-4020-0135-5                                                                            November 2001 , 416 pp.                                                                         EUR 150.00 /  USD 138.00 /  GBP 94.00

                                                                            Paperback, ISBN 1-4020-0136-3                                                                               November 2001 , 416 pp.                                                                          EUR 34.00 /  USD 31.00 /  GBP 21.00

31

Stuart M. Brown

Bioinformatics : A Biologist's Guide to Biocomputing and the Internet

 

Hardcover - 188 pages (January 15, 2000)

·         Eaton Pub Co;

ISBN: 188129918X

32

David Sankoff

Joseph H. Nadeau

Comparative Genomics:                                              Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families

Preface.

Foreword; W.F. Doolittle.

Introduction. Comparative Genomics; D. Sankoff, J.H. Nadeau.

1.Mechanisms. Cytogenetics, Molecular Genetics, Population Genetics.

2. Organelles: Mitochondria and Chloroplast. Rearrangements in Small Genomes.

3. Combinatorial Algorithms. A New Set of Problems for a New Kind of Data. 4. Prokaryotes. Genome Scrambling versus Functional Clustering.

5. Statistics. The Quantification of Comparative Mapping.

6. Nuclear Genomes. Evolutionary Inference from Comparative Mapping.

7. Gene and Genome Duplication and Multi-gene Families. How Can Duplication by Analyzed

·         Kluwer Academic Publishers, Dordrecht                                                                            

Hardbound, ISBN 0-7923-6583-6                                                                               September 2000 , 568 pp.                                                                         EUR 206.50 /  USD 240.00 /  GBP 150.00

                                                                            Paperback, ISBN 0-7923-6584-4                                                                               September 2000 , 568 pp.                                                                          EUR 68.00 /  USD 79.00 /  GBP 49.00

 

33

H.A. Lim, J.W. Fickett, C.R. Cantor (Editor)

Bioinformatics, Supercomputing and Complex Genome

·         Linguistic Approaches

·         Mapping and Sequencing I

·         Genome Map

·         Mapping & Sequencing II

·         Databases

·         Applications of Neural-Net

·         Genome Sequence Analysis

Hardcover (September 1993)

·         World Scientific Pub Co;

ISBN: 9810211570

34

Steffen Schulze-Kremer

Molecular Bioinformatics : Algorithms and Applications

 

Library Binding - 300 pages (October 1995)

·         Walter De Gruyter;

US$ 68.00

 

ISBN: 3110141132

35

Bruno Gaeta, Kirsten Balding

ANGIS Bioinformatics Handbooks: Four Volume Set

 

Paperback (1997)

·         CSIRO Publishing;

ISBN: 0643062785

36

M. J. Bishop

Genetics Databases

·         M. Bishop, Introduction.

·         G. Williams, Nucleic Acid and Protein Sequence Databases.

·         R. Cotton, Phenotype, Mutation, and Genetic Linkage Databases and Their Links to Sequence Databases.

·         R. Guigo,DNA Composition, Codon Usage, and Exon Prediction. W. Taylor, Properties of Amino Acids in Sequences.

·         M. Gribskov, Sequence Comparison.

·         J. Epplen, Simple Repetitive Sequences in DNA Databanks.

·         P. Bucher, Gene Feature Identification.

·         D. Higgins, Multiple Sequence Alignment.

·         K. Triman, RNAs.

·         C. Ponting and D.J. Blake, Predicting the Evolution, Structure, and Function of Proteins from Sequence Information.

·         D. Jones, Structure Databases and Structure Alignments.

·         M. Gribskov, Bourne, Smith, Integrated Data Resource for Protein Kinases.

·         R. Baldock, Gene Expression Databases.

·         P.D. Karp, Pathways and Development.

Paperback - 320 pages Casebound edition (September 1999)

·         Academic Pr

US49.95

ISBN: 0121016250

37

Richard Durbin, Sean R. Eddy, Anders Krogh,

Graeme Mitchison

Biological Sequence Analysis

1. Introduction;

2. Pairwise sequence alignment;

3. Multiple alignments;

4. Hidden Markov models;

5. Hidden Markov models applied to biological sequences;

6. The Chomsky hierarchy of formal grammars;

7. RNA and stochastic context-free grammars;

8. Phylogenetic trees;

9. Phylogeny and alignment;

Index.

Binding: Paperback (Hardback)

Size: 248 x 175 mm                                                   Pages: 368

Weight: 0.627kg

·         Cambridge

GBP 22.95

ISBN: 0521629713

38

Michael J. E. Sternberg

Protein Structure Prediction - A Practical                                                        Approach

·         Protein structure prediction - principles and approaches

·         Protein sequence alignment and database scanning

·         Identification of protein sequence motifs

·         Prediction of secondary structure

·         Prediction of transmembrane protein topology

·         Comparative modelling of proteins

·         Antibody combining sites: structure and prediction

·         Protein folds and their recognition from sequence

·         The combinatorial approach

·         Modelling protein conformation by molecular mechanics and dynamics Docking ligands to proteins

·         The prediction challenge

Price: £30.00 (Paperback)

                                                          0-19-963496-3

                                                          Publication date: 28 November 1996

·         OUP

                                                          IRL Press 318 pages

 

39

Joao Carlos Setubal, Joao Meidanis, Jooao Carlos Setubal

Introduction to Computational Molecular Biology

 

Hardcover - 320 pages 1st edition (January 16, 1997)

·         Brooks/Cole Pub Co;

ISBN: 0534952623

40

Arthur M. Lesk

Introduction to Bioinformatics

·         1 Introduction to bioinformatics

·         2 Genome organization and evolution

·         3 Archives and information retrieval

·         4 Alignments and phylogenetic trees

·         5 Protein structure and drug design

Price: £19.99 (Paperback )

                                                                                                                                                  Publication date: 14 February  2002                                                                                                                                        320 pages, numerous figures,

                                                                         246mm x 189mm

 

·         OUP

ISBN:0-19-925196-7

41

Jean-Michel Claverie and Cedric Notredame

Bioinformatics for Dummies

Introduction.

Part I: Getting Started in Bioinformatics.

·         Chapter 1: Finding Out What Bioinformatics Can Do for You.

·         Chapter 2: How Most People Use Bioinformatics.

Part II: A Survival Guide to Bioinformatics.

·         Chapter 3: Using Nucleotide Sequence Databases.

·         Chapter 4: Using Protein and Specialized Sequence Databases.

·         Chapter 5: Working with a Single DNA Sequence.

·         Chapter 6: Working with a Single Protein Sequence.

Part III: Becoming a Pro in Sequence Analysis.

·         Chapter 7: Similarity Searches on Sequence Databases.

·         Chapter 8: Comparing Two Sequences.

·         Chapter 9: Building a Multiple Sequence Alignment.

·         Chapter 10: Editing and Publishing Alignments.

Part IV: Becoming a Specialist: Advanced Bioinformatics Techniques.

·         Chapter 11: Working with Protein 3-D Structures.

·         Chapter 12: Working with RNA.

·         Chapter 13: Building Phylogenetic Trees.

Part V: The Part of Tens.

·         Chapter 14: The Ten Commandments When Using Servers.

·         Chapter 15: Some Useful Bioinformatics Resources.

Glossary

Index.

ISBN: 0-7645-1696-5
Paperback
480 Pages
January 2003
US $29.99

John-Wiley

42

Bryan P. Bergeron

Bioinformatics Computing

·         Preface.

·         1. The Central Dogma.

·         2. Databases.

·         3. Networks.

·         4. Search Engines.

·         5. Visualization.

·         6. Statistics.

·         7. Data Mining.

·         8. Pattern Matching.

·         9. Modeling and Simulation.

·         10. Communications.

·         Bibliography.

·         Index.

Paper, 439 pp.

ISBN: 0131008250

Published: NOV 19, 2002

Prentice Hall

43

Philip E. Bourne,

Helge Weissig

Structural Bioinformatics

Preface (J. Wooley).

Introductory Comments (The Editors).

SECTION I: INTRODUCTION.

·         What is Bioinformatics and Structural Bioinformatics (R. Altman & J. Dugan).

·         Fundamentals of Protein Structure (E. Scheeff & L. Fink).

·         Fundamentals of DNA and RNA Structure (S. Neidle, et al.).

·         Computational Aspects of High-Throughput Crystallographic Macromolecular Structure Determination (P. Adams, et al.).

·         Macromolecular Structure Determination by NMR Spectroscopy (J. Markley, et al.).

·         Electron Microscopy (N. Volkmann & D. Hanein).

·         Molecular Visualization (J. Tate).

SECTION II: DATA REPRESENTATION AND DATABASES.

·         The PDB Format, mmCIF Formats and Other Data Formats (J. Westbrook & P. Fitzgerald).

·         The Protein Data Bank (The PDB Team).

·         The Nucleic Acid Database (H. Berman, et al.).

·         Other Structure Based Databases (H. Weissig & P. Bourne).

SECTION III: COMPARATIVE FEATURES.

·         Protein Structure Evolution and the SCOP Database (B. Reddy & P. Bourne).

·         The CATH Domain Structure Database (C. Orengo, et al.).

·         Structural Quality Assurance (R. Laskowski).

·         All-Atom Contacts: A New Approach to Structure Validation (J. Richardson).

·         Structure-Structure Comparison and Alignment (I. Shinadyalov & P. Bourne).

SECTION IV: STRUCTURE AND FUNCTIONAL ASSIGNMENT.

·         Secondary Structure Assignment (C. Andersen & B. Rost).

·         Identifying Structural Domains in Proteins (L. Wernisch & S. Wodak).

·         Inferring Protein Function from Structure (G. Bartlett, et al.).

SECTION V: PROTEIN INTERACTIONS.

·         Prediction of Protein-Protein Interactions from Evolutionary Information (A. Valencia & F. Pazos).

·         Electrostatic Interactions (N. Baker & J. McCammon).

SECTION VI: PROTEINS AS DRUG TARGETS.

·         Principles and Methods of Docking and Ligand Design (J. Krumrine, et al.).

·         Structural Bioinformatics in Drug Discovery (E. Fauman, et al.).

SECTION VII: STRUCTURE PREDICTION.

·         The CASP Experiment and Its Findings (TBN).

·         Homology Modeling (E. Krieger, et al.).

·         Fold Recognition Methods (A. Godzik).

·         Ab Initio Methods (D. Chivian, et al.).

·         Prediction in 1D: Secondary Structure, Membrane Helices, and Accessibility (B. Rost).

SECTION VIII: THE FUTURE.

·         Structural Genomics (S. Burley & J. Bonanno).

Epilogue.

 

ISBN: 0-471-20200-2
Hardcover
649 Pages
February 2003
US $150.00

John Wiley

 

44

Michael Barnes, Ian C Gray

Bioinformatics for Geneticists

·         SECTION I: AN INTRODUCTION TO BIOINFORMATICS FOR THE GENETICIST.

·         Introduction: The Role of Genetic Bioinformatics (Michael R. Barnes and Ian C. Gray).

·         Internet Resources for the Geneticist (Michael R. Barnes and Christopher Southan).

·         Human Genetic Variation  Databases and Concepts (Michael R. Barnes).

·         Finding, Delineating and Analysing Genes (Christopher Southan).

SECTION II: THE IMPACT OF COMPLETE GENOME SEQUENCES ON GENETICS.

·         Assembling a View of the Human Genome (Colin A. Semple).

·         Mouse and Rat Genome Informatics (Judith A. Blake, Janan Eppig and Carol J. Bult).

·         Genetic and Physical Map Resources - An Integrated View (Michael R. Barnes).

SECTION III: BIOINFORMATICS FOR GENETIC STUDY DESIGN.

·         From Linkage Peak to Culprit Gene: Following Up Linkage Analysis of Complex Phenotypes with Population-based Association Studies (Ian C. Gray).

·         Genetic Studies from Genomic Sequence (Michael R. Barnes).

·         SNP Discovery and PCR-based Assay Design: From In Silico Data to the Laboratory Experiment (Ellen Vieux, Gabor Marth and Pui Kwok).

·         Tools for Statistical Analysis of Genetic Data (Aruna Bansal, Peter R. Boyd and Ralph McGinnis).

SECTION IV: BIOLOGICAL SEQUENCE ANALYSIS AND CHARACTERIZATION.

·         Predictive Functional Analysis of Polymorphisms - An Overview (Michael R. Barnes).

·         Functional In Silico Analysis of Non-Coding SNPs (Thomas Werner).

·         Amino Acid Properties and Consequences of Substitutions (Matthew J. Betts and Robert B. Russell).

SECTION V: GENETICS/GENOMICS INTERFACES.

·         Gene Expression Informatics and Analysis (A. H. C. van Kampen, J. M. Ruijter, B. D. C. van Schaik, H. N. Caron and R. Versteeg).

·         Proteomic Informatics (Jirtme Wojcik and Alexandre Hamburger).

·         Concluding Remarks: Final Thoughts and Future Trends (Michael R. Barnes and Ian C. Gray).

ISBN: 0-470-84394-2
Paperback
350 Pages
April 2003
US $65.00

John WIley

45

A. Malcolm Campbell,

Laurie J. Heyer

Discovering Genomics, Proteomics, and Bioinformatics

GENOMIC SEQUENCES

·         Genome Sequence Acquisition and Analysis

·         Genome Sequences to Answer Interesting Questions

·         Genomic Variations

GENOMIC EXPRESSION

·         Basic Research with DNA Microarrays

·         Applied Research with Microarrays

·         Proteomics

WHOLE GENOME PERSPECTIVE

·         Genomic Circuitry in Single Genes

·         Integrated Genomic Circuits

·         Modeling Whole-Genome Circuits

TRANSITION FROM GENETICS TO GENOMICS: MEDICAL CASE STUDIES

·         Whats Wrong with My Child?

·         Why Can't I Just Take a Pill to Lose Weight?

·         Why Can't We Cure More Diseases?

·         Appendix A: Introduction to Genomics on the Web

2003

352 pp. + appendix
Paperback w/CD–ROM USD $70.60

ISBN 0-8053-4722-4

CSHL Press

46

Isaac S. Kohane, 

Alvin Kho,

Atul J. Butte

Microarrays for an Integrative Genomics

·         Introduction

·         Experimental Design

·         Microarray measurements to analyses

·         Genomic Data Mining Techniques

·         Bio-Ontologies, Data Models, Nomenclature

·         From Functional Genomics to Clinical Relevance

·         The Near Future

 

 

August 2002

ISBN 0-262-11271-X

8 x 9, 326 pp., 82 illus.

$40.00/£26.95 (CLOTH)

MIT Press

 

47

Rex A. Dwyer

Genomic Perl: From Bioinformatics Basics to Working Code

·         The central dogma;

·         RNA secondary structure;

·         Comparing DNA sequences;

·         Statistical models;

·         Substitution matrices for amino acids;

·         Sequence databases;

·         Local alignment and the BLAST heuristic;

·         Statistics of BLAST database searches;

·         Multiple sequence alignment I;

·         Multiple sequence alignment II;

·         Phylogeny reconstruction;

·         Protein motifs and PROSITE;

·         Fragment assembly;

·         Coding sequence prediction with dicodon frequencies;

·         Satellite identification;

·         Restriction mapping;

·         Hybridization mapping;

·         Genome rearrangement: gates and hurdles;

·         Now what?; A. Drawing RNA cloverleaves; B. Space-saving strategies for alignment; C. A data structure for disjoint sets; D. A data structure for set operations.

£45.00

February 2003

Hardback

352 pages 100 exercises  ISBN: 052180177X

Cambridge University Press

 

48

Gary B. Fogel,

David W. Corne

Evolutionary Computation in Bioinformatics

PART I - Introduction to the Concepts of Bioinformatics and Evolutionary Computation  
 
Chapter 1. An Introduction to Bioinformatics for Computer Scientists  
By David W. Corne and Gary B. Fogel  
Chapter 2. An Introduction to Evolutionary Computation for Biologists  
By Gary B. Fogel and David W. Corne  
 
PART II - Sequence and Structure Alignment  
Chapter 3. Determining Genome Sequences from Experimental Data Using Evolutionary Computation  
By Jacek Blazewic and Marta Kasprzak  
Chapter 4. Protein Structure Alignment Using Evolutionary Computation  
By Joseph D. Szustakowski and Zhipeng Weng  
 
Chapter 5. Using Genetic Algorithms for Pairwise and Multiple Sequence Alignments  
By Cédric Notredame  
 
PART III - Protein Folding  
Chapter 6. On the Evolutionary Search for Solutions to the Protein Folding Problem  
By Garrison W. Greenwood and Jae-Min Shin  
Chapter 7. Toward Effective Polypeptide Structure Prediction with Parallel Fast Messy Genetic Algorithms  
By Gary B. Lamont and Laurence D. Merkle  
 
Chapter 8. Application of Evolutionary Computation to Protein Folding with Specialized Operators  
By Steffen Schulze-Kremer  
 
PART IV - Machine Learning and Inference  
Chapter 9. Identification of Coding Regions in DNA Sequences Using Evolved Neural Networks  
By Gary B. Fogel, Kumar Chellapilla, and David B. Fogel  
Chapter 10. Clustering Microarray Data with Evolutionary Algorithms  
By Emanuel Falkenauer and Arnaud Marchand  
 
Chapter 11. Evolutionary Computation and Fractal Visualization of Sequence Data  
By Dan Ashlock and Jim Golden  
 
Chapter 12. Identifying Metabolic Pathways and Gene Regulation Networks with Evolutionary Algorithms  
By Junji Kitagawa and Hitoshi Iba  
 
Chapter 13. Evolutionary Computational Support for the Characterization of Biological Systems  
By Bogdan Filipic and Janez Strancar  
 
PART V - Feature Selection  
Chapter 14. Discovery of Genetic and Environmental Interactions in Disease Data Using Evolutionary Computation  
By Laetitia Jourdan, Clarisse Dhaenens[AQ2], and El-Ghazali Talbi  
Chapter 15. Feature Selection Methods Based on Genetic Algorithms for in Silico Drug Design  
By Mark J. Embrechts, Muhsin Ozdemir, Larry Lockwood, Curt Breneman, Kristin Bennet, Dirk Devogelaere, and Marcel Rijkaert  
 
Chapter 16. Interpreting Analytical Spectra with Evolutionary Computation  
By Jem J. Rowland  
 
Appendix: Internet Resources for Bioinformatics Data and Tools

ISBN 1558607978 · Hardback · 450 Pages

Morgan Kaufmann · Published September 2002

Price: £ 43.95

 

49

Dan E. Krane,

Michael L. Raymer

Fundamental Concepts of Bioinformatics

I. MOLECULAR BIOLOGY AND BIOLOGICAL CHEMISTRY

II. DATA SEARCHES AND PAIRWISE ALIGNMENTS

III. SUBSTITUTION PATTERNS.

IV. DISTANCE-BASED METHODS OF PHYLOGENETICS

V. CHARACTER-BASED APPROACHES TO PHYLOGENETICS

VI. GENOMICS AND GENE RECOGNITION

VII. PROTEIN FOLDING

VIII. PROTEOMICS

Appendix 1: A gentle introduction to programming and data structures

Appendix 2: Enzyme kinetics

Appendix 3: Sample programs in PERL and worksets

ISBN: 0-8053-4633-3
Publisher: Benjamin Cummings
Copyright: 2003
Format: Paper; 320 pp
Published: 09/12/2002
Status: Instock

US: $70.60

 

50

Westhead, D.R., Parish, J.H., Twyman R.M.

Instant Notes Bioinformatics

·         SECTION A - OVERVIEW OF BIOINFORMATICS

·         SECTION B - DATA ACQUISITION

·         SECTION C - DATABASES – CONTENTS STRUCTURE AND ANNOTATION

·         SECTION D - RETRIEVAL OF BIOLOGICAL DATA

·         SECTION E - SEARCHING SEQUENCE DATABASES BY SEQUENCE SIMILARITY CRITERIA

·         SECTION F - MULTIPLE SEQUENCE ALIGNMENT: GENE AND PROTEIN FAMILIES

·         SECTION G - PHYLOGENETICS

·         SECTION H - SEQUENCE ANNOTATION

·         SECTION I - STRUCTURAL BIOINFORMATICS

·         SECTION J - MICROARRAY DATA ANALYSIS

·         SECTION K - PROTEOMIC DATA ANALYSIS

·         SECTION M - CHEMINFORMATICS IN BIOLOGY

·         SECTION N - BIOINFORMATICS IN THE PHARMACEUTICAL INDUSTRY

·         SECTION O - BASIC PRINCIPLES OF COMPUTING IN BIOINFORMATICS

 

ISBN: 1859962726

Published: Sep 2002

Series: Instant Notes

Paperback; 272 pages
150 b/w line drawings

£17.99

 

BIOS Scientific Publishers

 

 

51

Scott Markel, 

Darryl León

Sequence Analysis in a Nutshell
A Guide to Common Tools and Databases

I. Data Formats

·         1. FASTA Format

·         2. GenBank/EMBL/DDBJ

·         3. SWISS-PROT

·         4. Pfam

·         5. PROSITE

II. Tools

·         6. Readseq

·         7. BLAST

·         8. BLAT

·         9. ClustalW

·         10. HMMER

·         11. MEME/MAST

·         12. EMBOSS

III. Appendixes

·         A. Nucleotide and Amino Acid Tables

·         B. Genetic Codes

·         C. Resources

·         D. Future Plans

·         Index

January 2003 

0-596-00494-X,

Order Number: 494X

302 pages,

$29.95 US,

$46.95 CA,

£20.95 UK

Sequence Analysis in a Nutshell

 

52

Pierre Baldi, G. Wesley Hatfield

DNA Microarrays and Gene Expression

From Experiments to Data Analysis and Modeling

·         Preface;

·         1. A brief history of genomics;

·         2. DNA array formats;

·         3. DNA array readout methods;

·         4. Gene expression profiling experiments: problems, pitfalls and solutions;

·         5. Statistical analysis of array data: inferring changes;

·         6. Statistical analysis of array data: dimensionality reduction, clustering, and regulatory regions;

·         7. Survey of current DNA array applications;

·         8. Systems biology: overview of regulatory, metabolic and signaling networks.

£35.00

September 2002

Hardback

230 pages 16 line diagrams 1 half-tone 16 figures

ISBN: 0521800226

Cambridge University Press

 

 

53

Julio Collado-Vides and Ralf Hofestädt

Gene Regulation and Metabolism
Post-Genomic Computational Approaches

·          

July 2002
ISBN 0-262-03297-X
7 x 9, 320 pp., 68 illus.
$45.00/£29.95 (CLOTH)

MIT Press

54

Hiroaki Kitano

Foundations of Systems Biology

·          

October 2001
ISBN 0-262-11266-3
7 x 9, 320 pp., 100 illus.
$47.95/£31.95 (CLOTH)

MIT Press

55

Tamar Schlick

Molecular Modeling and Simulation
An Interdisciplinary Guide

·         Biomolecular Structure and Modeling: Historical Perspective

·         Biomolecular Structure and Modeling: Problem and Application Perspective

·         Protein Structure Introduction

·         Protein Structure Hierarchy

·         Nucleic Acids Structure Minitutorial

·         Topics in Nucleic Acids Structure

·         Theoretical and Computational Approaches to Biomolecular Structure

·         Force Fields

·         Nonbonded Computations

·         Multivariate Minimization in Computational Chemistry

·         Monte Carlo Techniques

·         Molecular Dynamics: Basics

·         Molecular Dynamics: Further Topics

·         Similarity and Diversity in Chemical Design

·         Epilogue

·         Appendices

·         Index

Price: $79.95
656 pages , 6 1/8 x 9 , 147 illus., hardcover
ISBN: 0-387-95404-X, published 2002
Textbook

Springer-Verlag

56

C.A. Orengo, D.T. Jones and J.M. Thornton

Bioinformatics
Genes, proteins and computers

CH 1. MOLECULAR EVOLUTION (S. Nagl)
CH 2. GENE FINDING (J. G. Sgorous and R. M. Twyman)
CH 3. SEQUENCE COMPARISON METHODS (C. Orengo)
CH 4. AMINO ACID RESIDUE CONSERVATION (W. S. J. Valdar and D. T. Jones)
CH 5. FUNCTION PREDICTION FROM PROTEIN SEQUENCE (S. B. Nagl)
CH 6. PROTEIN STRUCTURE COMPARISON (I. Sillitoe and C. Orengo)
CH 7. PROTEIN STRUCTURE CLASSIFICATIONS (F. Pearl and C. Orengo)
CH 8. COMPARATIVE MODELING (A. C. R. Martin)
CH 9. PROTEIN STRUCTURE PREDICTION (D. T. Jones)
CH 10. FROM PROTEIN STRUCTURE TO FUNCTION (A. E. Todd)
CH 11. FROM STRUCTURE-BASED GENOME ANNOTATION TO UNDERSTANDING GENES AND PROTEINS (S. A. Teichmann)
CH 12. GLOBAL APPROACHES FOR STUDYING PROTEIN-PROTEIN INTERACTIONS (S.A. Teichmann)
CH 13. PREDICTING THE STRUCTURE OF PROTEIN-BIOMOLECULAR INTERACTIONS (R.M. Jackson)
CH 14. EXPERIMENTAL USE OF DNA ARRAYS (P. Kellam and X. Liu)
CH 15. MINING GENE EXPRESSION DATA (X. Liu and P. Kellam)
CH 16. PROTEOMICS (M. P. Weir, P. Blackstock and R. M. Twyman)
CH 17. DATA MANAGEMENT OF BIOLOGICAL INFORMATION (N. J. Martin )
CH 18. INTERNET TECHNOLOGIES FOR BIOINFORMATICS (A. C. R. Martin)

ISBN: 1859960545

Published: Dec 2002

Series: Advanced Texts

Paperback; 320 pages
114 b/w & colour line drawings

£29.99

BIOS Scientific Publishers

57

Daniel Sorensen,
Daniel Gianola

Likelihood, Bayesian and MCMC Methods in Quantitative Genetics

I. Review of Probability and Distribution Theory

·         Probability and Random Variables

·         Functions of Random Variables

II. Inference Methods

·         An Introduction to Likelihood Inference

·         Further Topics in Likelihood Inference

·         An Introduction to Bayesian Inference

·         Bayesian Analysis of Linear Models

·         The Prior Distribution and Bayesian Analysis

·         Bayesian Assessment of Hypotheses and Models

·         Approximate Methods of Inference Via the EM Algorithm

III. Markov Chain Monte Carlo Methods

·         An Overview of Discrete Markov Chains

·         Markov Chain Monte Carlo

·         Implementation and Analysis of MCMC Samples

IV. Applications in Quantitative Genetics

·         Gaussian and Thick-tailed Linear Models

·         Threshold Models for Categorical Respomses

·         Bayesian Analysis of Longitudinal Data

·         Segregation and QTL Analysis

References.

Price: $89.95
760 pages , 6 1/8 x 9 , hardcover
ISBN: 0-387-95440-6, published 2002

Springer-Verlag

58

Eric Marland,

 John Wagner
John Tyson

Computational Cell Biology

·         Preface

·         Dynamic Phenomena in Cells

·         Voltage Gated Ionic Currents

·         Transporters and Pumps

·         Fast and Slow Time Scales

·         Whole Cell Models

·         Intercellular Communication

·         Spatial Modeling

·         Modeling Intracellular Calcium Waves and Sparks

·         Biochemical Oscillations

·         Cell Cycle Controls

·         Modeling the Stochastic Gating of Ion Channels

·         Molecular Motors: Theory

·         Molecular Motors: Examples

·         Appendices

Price: $59.95
488 pages , 7 X 9 1/4, 210 illus., hardcover
ISBN: 0-387-95369-8, published 2002

Springer-Verlag

59

Terry Speed

Statistical Analysis of Gene Expression Microarray Data

·         MODEL-BASED ANALYSIS OF OLIGONUCLEOTIDE ARRAYS AND ISSUES IN cDNA MICROARRAY ANALYSIS, Cheng Li, George C. Tseng, and Wing Hung Wong

·         DESIGN AND ANALYSIS OF COMPARATIVE MICROARRAY EXPERIMENTS, Yee Hwa Yang and Terry Speed

·         CLASSIFICATION IN MICROARRAY EXPERIMENTS, \ Sandrine Dudoit and Jane Fridlyand

·         CLUSTERING MICROARRAY DATA, Hugh Chipman, Trevor J. Hastie, and Robert Tibshirani

·         REFERENCES

·         INDEX

Price: $69.95

ISBN: 1584883278

Publication Date: 3/26/2003

Number of Pages: 240

Chapman & Hall/CRC Press

60

Sorin Draghici

Data Analysis Tools for DNA Microarrays

·         PREFACE

·         INTRODUCTION

·         MICROARRAYS

·         IMAGE PROCESSING

·         ELEMENTS OF STATISTICS

·         STATISTICAL HYPOTHESIS TESTING

·         CLASSICAL APPROACHES TO DATA ANALYSIS

·         ANALYSIS OF VARIANCE - ANOVA

·         EXPERIMENT DESIGN

·         MULTIPLE COMPARISONS

·         ANALYSIS AND VISUALIZATION TOOLS

·         CLUSTER ANALYSIS

·         DATA PRE-PROCESSING AND NORMALIZATION

·         METHODS FOR SELECTING DIFFERENTIALLY REGULATED GENES

·         ANOVA

·         FUNCTIONAL ANALYSIS AND BIOLOGICAL INTERPRETATION OF MICROARRAY DATA

·         FOCUSED MICROARRAYS - COMPARISON AND SELECTION

·         COMMERCIAL APPLICATIONS

·         THE ROAD AHEAD

·         REFERENCES

List Price: $79.95

ISBN: 1584883154

Publication Date: 6/4/2003

Number of Pages: 512

Chapman & Hall/CRC Press

61

Jonathan Pevsner

Bioinformatics and Functional Genomics

·         PART I: ANALYZING DNA, RNA, AND PROTEIN SEQUENCES IN DATABASES.

·         1. Introduction.

·         2. Access to Sequence Data and Literature Information.

·         3. Pairwise Sequence Alignment.

·         4. Basic Local Alignmnet Search Tool (BLAST).

·         5. Advanced BLAST Searching.

·         PART II: GENOMEWIDE ANALYSIS OF RNA AND PROTEIN.

·         6. Bioinformatic Approaches to Gene Expression.

·         7. Gene Expression: Microarrays Data Analysis.

·         8. Protein Analysis and Proteomics.

·         9. Protein Structure.

·         10. Multiple Sequence Alignment.

·         11. Molecular Phylogeny and Evolution.

·         PART III: GENOME ANALYSIS.

·         12. Completed Genomes and the Tree of Life.

·         13. Completed Genomes: Viruses.

·         14. Completed Genomes: Bacteria and Archaea.

·         15. Eukaryotic Genomes: Fungi

·         16. Eukaryotic Genomes: From Parasites to Primates.

·         17. The Human Genome.

·         18. Human Disease.

ISBN: 0-471-21004-8

Paperback

753 pages

November 2003

£56.50 / €78.30

http://www.bioinfbook.org/

62

Gary Fogel  and

David Corne  (Editors)

Evolutionary Computation in Bioinformatics

·         PART I - Introduction to the Concepts of Bioinformatics and Evolutionary Computation

·         Chapter 1. An Introduction to Bioinformatics for Computer Scientists By David W. Corne and Gary B. Fogel

·         Chapter 2. An Introduction to Evolutionary Computation for Biologists By Gary B. Fogel and David W. Corne

 

·         PART II - Sequence and Structure Alignment

·         Chapter 3. Determining Genome Sequences from Experimental Data Using Evolutionary Computation  By Jacek Blazewic and Marta Kasprzak

·         Chapter 4. Protein Structure Alignment Using Evolutionary Computation  By Joseph D. Szustakowski and Zhipeng Weng

·         Chapter 5. Using Genetic Algorithms for Pairwise and Multiple Sequence Alignments By Cédric Notredame

 

·         PART III - Protein Folding

·         Chapter 6. On the Evolutionary Search for Solutions to the Protein Folding Problem By Garrison W. Greenwood and Jae-Min Shin

·         Chapter 7. Toward Effective Polypeptide Structure Prediction with Parallel Fast Messy Genetic Algorithms By Gary B. Lamont and Laurence D. Merkle

·          

·         Chapter 8. Application of Evolutionary Computation to Protein Folding with Specialized Operators By Steffen Schulze-Kremer

 

·         PART IV - Machine Learning and Inference

·         Chapter 9. Identification of Coding Regions in DNA Sequences Using Evolved Neural Networks By Gary B. Fogel, Kumar Chellapilla, and David B. Fogel

·         Chapter 10. Clustering Microarray Data with Evolutionary Algorithms By Emanuel Falkenauer and Arnaud Marchand

·         Chapter 11. Evolutionary Computation and Fractal Visualization of Sequence Data By Dan Ashlock and Jim Golden

·         Chapter 12. Identifying Metabolic Pathways and Gene Regulation Networks with Evolutionary Algorithms By Junji Kitagawa and Hitoshi Iba

·         Chapter 13. Evolutionary Computational Support for the Characterization of Biological Systems By Bogdan Filipic and Janez Strancar

 

·         PART V - Feature Selection

·         Chapter 14. Discovery of Genetic and Environmental Interactions in Disease Data Using Evolutionary Computation By Laetitia Jourdan, Clarisse Dhaenens[AQ2], and El-Ghazali Talbi

·         Chapter 15. Feature Selection Methods Based on Genetic Algorithms for in Silico Drug Design By Mark J. Embrechts, Muhsin Ozdemir, Larry Lockwood, Curt Breneman, Kristin Bennet, Dirk Devogelaere, and Marcel Rijkaert

·         Chapter 16. Interpreting Analytical Spectra with Evolutionary Computation By Jem J. Rowland

 

·         Appendix: Internet Resources for Bioinformatics Data and Tools

ISBN: 1-55860-797-8     Book/Hardback

Measurements: 187 X 235 mm

Pages: 393

Imprint: Morgan Kaufmann

Publication Date: 27 September 2002

Price: £44.99

63

Zoé Lacroix  and

Terence Critchlow (Editors)

Bioinformatics

Managing Scientific Data

·         1 Introduction  By Zoe Lacroix and Terence Critchlow

·         2 Challenges Faced in the Integration of Biological Information By Su Yun Chung and John C. Wooley

·         3 A Practitioner's Guide to Data Management and Data Integration in Bioinformatics By Barbara A. Eckman

·         4 Issues to Address While Designing a Biological Information System By Zoe Lacroix

·         5 SRS: An Integration Platform for Databanksand Analysis Tools in Bioinformatics By Thure Etzold, Howard Harris, and Simon Beaulah

·         6 The Kleisli Query System as a Backbone for Bioinformatics Data Integration and Analysis By Jing Chen, Su Yun Chung, and Limsoon Wong

·         7 Complex Query Formulation Over Diverse Information Sources in TAMBIS By Robert Stevens, Carole Goble, Norman W. Paton, Sean Bechhofer, Gary Ng, Patricia Baker, and Andy Brass

·         8 The Information Integration System K2 By Val Tannen, Susan B. Davidson, and Scott Harker

·         9 P/FDM Mediator for a Bioinformatics Database Federation By Graham J. L. Kemp and Peter M. D. Gray

·         10 Integration Challenges in Gene Expression Data Management By Victor M. Markowitz, John Campbell, I-Min A. Chen, Anthony Kosky, Krishna Palaniappan, and Thodoros Topaloglou

·         11 DiscoveryLink By Laura M. Haas, Barbara A. Eckman, Prasad Kodali, Eileen T. Lin, Julia E. Rice, and Peter M. Schwarz

·         12 A Model-Based Mediator System for Scientific Data Management By Bertram Ludascher, Amarnath Gupta, and Maryann E. Martone

·         13 Compared Evaluation of Scientific Data Management Systems By Zoe Lacroix and Terence Critchlow

ISBN: 1-55860-829-X     Book/Hardback

Measurements: 187 X 235 mm

Pages: 441

Imprint: Morgan Kaufmann

Publication Date: 8 September 2003

Price: £35.99

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