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Practical Bioinformatics Michael Agostino

Dr. Agostino received his PhD in Molecular Biology from Roswell Park Memorial Institute. He currently is a member of Pfizer’s Analysis and Mining group where he provides bioinformatics analysis support for many sites of the Pfizer Research organization. He is also an Adjunct Professor at Merrimack College.

KEY FEATURES • Using compelling biological examples, sequence analysis problems are shown and solved. • Exercises help solidify the understanding of concepts and help the student learn how to solve biological problems. Many exercises can be adapted to accommodate a reader’s gene of interest. • Screen shots from actual websites (for example, NCBI) are used to illustrate the examples and exercises. • Each chapter begins with an introduction to the topic and skills to be learned.

ONLINE RESOURCES Online resources for qualified instructors can be found at practical-bioinformatics. • Artwork in JPEG & PPT formats. • Solutions to exercises.

Practical Bioinformatics is specifically designed for biology majors, with a heavy emphasis on the steps required to perform bioinformatics analysis to answer biological questions. It is written for courses that have a practical, hands-on element and contains many exercises (for example, database searches, protein analysis, data interpretation) to complement the straightforward and practical topics. The chapters are focused on DNA, RNA, and protein sequence analysis—a frequently performed subset of the field of bioinformatics—taking the reader through the commonly asked question “what can I learn about this sequence?”

CONTENTS 1. 2. 3. 4. 5. 6.

Introduction to Bioinformatics and Sequence Analysis Introduction to Internet Resources Introduction to the BLAST Suite and BLASTN Protein BLAST: BLASTP Cross-Molecular Searches: LASTX and TBLASTN Advanced Topics in BLAST

7. Bioinformatics Tools for the Laboratory 8. Protein Analysis 9. Explorations of Short Nucleotide Sequences 10. MicroRNAs and Pathway Analysis 11. Multiple Sequence Alignments 12. Browsing the Genome

A sample chapter and detailed table of contents are available at

September 2012 394 Pages • 296 illustrations Pb: 978-0-8153-4456-8 • £25.00

Phylogenomics: a Primer

Rob DeSalle and Jeffrey Rosenfeld Dr. DeSalle is a Curator in the Sackler Institute for Comparative Genomics at the American Museum of Natural History. Dr. Rosenfeld is a Scientific Programmer in the Division of High Performance and Research Computing at the University of Medicine and Dentistry of New Jersey and Research Associate, Sackler Institute for Comparative Genomics at the American Museum of Natural History.

Phylogenomics: A Primer is for advanced undergradute and graduate biology students studying molecular biology, comparative biology, evolution, genomics, and biodiversity. It explores the origins of organic life on the planet, examines the use of scientific databases to understand the function of proteins within organisms, and provides insight into the interpretation of linear sequence information in the context of organismal change. This book explains the essential concepts underlying the storage and manipulation of genomics level data, construction of phylogenetic trees, population genetics, natural selection, the tree of life, DNA barcoding, and metagenomics. The inclusion of problemsolving exercises in each chapter provides students with a solid grasp of the important molecular and evolutionary questions facing modern biologists as well as the tools needed to answer them. Online exercises are also available to assist students in working with the programs and databases used to analyze phylogenomic data.

CONTENTS 1. Why Phylogenomics Matters 2. The Biology of Linear Molecules: DNA and Proteins 3. Evolutionary Principles: Populations and Trees 4. Databases 5. Homology and Pairwise Alignment 6. Multiple Alignments and Constructing Phylogenomic Matrices 7. Genome Sequencing and Annotation 8. Tree Building 9. Robustness and Rate Heterogeneity in Phylogenomics 10. A Beginner’s Guide to Bayesian Approaches in Evolution

11. Incongruence 12. Adapting Population Genetics to Genomics 13. Detecting Natural Selection: The Basics 14. Refining the Approach to Natural Selection at the Molecular Level 15. Genome-Level Approaches in Population Genetics 16. Genome Content Analysis 17. A Phylogenomic Perspective of Biological Diversity: Tree of Life, DNA Barcoding and Metagenomics 18. Microarrays in Evolutionary Studies and Functional Phylogenomics

KEY FEATURES • Step-by-step techniques and methods are described in sidebars. • Additional information about databases and techniques is provided in boxes. • Discussion questions and suggestions for further reading are listed at the end of each chapter.

ONLINE RESOURCES Online resources for qualified instructors can be found at phylogenomics. • Artwork in JPEG and PPT formats. • Exercises, algorithms, annotated data sets, and links to biological databases.

December 2012 352 Pages • 160 illustrations Pb: 978-0-8153-4211-3 • £38.00

3 Park Square, Milton Park Abingdon, OXON, OX14 4RN


March 2012 | 496 Pages Pb: 9780815344674 | £46.00

September 2007 | 798 Pages Pb: 9780815340249 | £47.00

Practical Bioinformatics and Phylogenomics: A Primer, both published by Garland Science  

Recently published by Garland Science: Practical Bioinformatics by Michael Agostino and Phylogenomics: A Primer by Rob DeSalle and Jeffrey R...