Computational and Systems Biology (2012-2013)

Computational Bioinformatics and Systems 2012 Biology 2012/13

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Bioinformatics Textbook

UNIX and Perl to the Rescue!

A Field Guide for the Life Sciences (and Other Data-rich Pursuits) Keith Bradnam and Ian Korf University of California, Davis

Written in a fun, accessible style, this step-by-step guide teaches nonprogrammers the key aspects of Unix and Perl. No prior experience is required and new concepts are introduced using code examples for readers to try themselves. Essential reading for those who want to work more effectively with large data sets.

Contents: Part I. Introduction and Background; Part II. Installing Unix and Perl; Part III. Essential Unix; Part IV. Essential Perl; Part V. Advanced Unix; Part VI. Advanced Perl; Part VII. Programming Topics.

2012 247 x 174 mm 428pp 5 b/w illus.

978-1-107-00068-1 Hardback £75.00 978-0-521-16982-0 Paperback £29.99 eBook available

www.cambridge.org/9781107000681

Textbook

Genomics and Bioinformatics An Introduction to Programming Tools for Life Scientists Tore Samuelsson Göteborgs Universitet, Sweden

Designed for biologists without programming experience, this textbook provides a hands-on introduction to Unix and Perl tools for bioinformatics.

Relevant biological examples are combined with practical computational

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procedures, teaching students how to proceed from biological problem to bioinformatics solution. An accompanying website provides files, scripts and solutions to end-of-chapter exercises.

Contents: Preface; Acknowledgements; Design and conventions of this book; 1. Introduction – working with the molecules of life in the computer; 2. Gene technology – cutting DNA; 3. Gene technology – knocking genes down; 4. Gene technology – amplifying DNA; 5. Human disease – when DNA sequences are toxic; 6. Human disease – iron imbalance and the iron responsive element; 7. Human disease – cancer as a result of aberrant proteins; 8. Evolution – what makes us human?; 9. Evolution – resolving a criminal case; 10. Evolution – the sad case of the Tasmanian tiger; 11. A function to every gene – termites, metagenomics and learning about the function of a sequence; 12. A function to every gene – royal blood and order in the sequence universe; 13. A function to every gene – a slimy molecule; 14. Information resources – learning about flu viruses; 15. Finding genes – going ashore at CpG islands; 16. Finding genes – in the world of snurps; 17. Finding genes – hunting for the distant RNA relatives; 18. Personal genomes – the differences between you and me; 19. Personal genomes – what’s in my genome?; 20. Personal genomes – details of family genetics; Appendix I. Brief Unix reference; Appendix II. A selection of biological sequence analysis software; Appendix III. Short Perl reference; Appendix IV. Brief introduction to R; Index.

2012 246 x 189 mm 356pp 20 b/w illus. 70 colour illus. 23 tables 60 exercises 978-1-107-00856-4 Hardback £75.00 978-1-107-40124-2 Paperback £29.99 www.cambridge.org/9781107008564

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Bioinformatics Textbook

Bioinformatics for Biologists Edited by Pavel Pevzner University of California, San Diego

and Ron Shamir Tel-Aviv University

Contents: Preface; Acknowledgements; Introduction; Part I. Genomes: 1. Identifying the genetic basis of disease; 2. Pattern identification in a haplotype block; 3. Genome reconstruction: a puzzle with a billion pieces; 4. Dynamic programming: one algorithmic key for many biological locks; 5. Measuring evidence: who’s your daddy?; Part II. Gene Transcription and Regulation: 6. How do replication and transcription change genomes?; 7. Modeling regulatory motifs; 8. How does influenza virus jump from animals to humans?; Part III. Evolution: 9. Genome rearrangements; 10. The crisis of the tree of life concept and the search for order in the phylogenetic forest; 11. Reconstructing the history of large-scale genomic changes: biological questions and computational challenges; Part IV. Phylogeny: 12. Figs, wasps, gophers, and lice: a computational exploration of coevolution; 13. Big cat phylogenies, consensus trees, and computational thinking; 14. Algorithm design for large-scale phylogeny; Part V. Regulatory Networks: 15. Biological networks uncover evolution, disease, and gene functions; 16. Regulatory network inference; Index.

2011 246 x 189 mm 392pp 37 b/w illus. 105 colour illus. 4 tables 978-1-107-01146-5 Hardback £91.00 978-1-107-64887-6 Paperback £40.00 eBook available

www.cambridge.org/9781107011465

‘This volume contains a remarkable collection of individually-authored chapters cutting a wide swathe across the field as it is currently constituted.

What is noteworthy, aside from the wide angle of the snapshot of today’s bioinformatics, something the editors promise to update in future editions, is the innovative and effective pedagogical emphasis apparent throughout … The editors set out to provide a resource for teaching bioinformatics to life science undergraduates, and this is reflected in the language, organization and mathematical restraint of the different chapters … It is highly suitable as a text or reference for bioinformatics courses at the graduate level, for biologists, medical students and computer scientists. Biological naïveté in thinking and writing plagues bioinformatics, and Pevzner and Shamir’s Bioinformatics for Biologists offers a wonderful therapy for that condition as well as an effective palliative for life science students’ math phobias.’

Professor David Sankoff, University of Ottawa

‘A serious and valuable effort to bring essential and much-needed training in the computational sciences to students of modern biology.’

Michael Waterman, University of Southern California

Bioinformatics

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Textbook

Principles of Computational Modelling in Neuroscience

‘Here at last is a book that is aware of my problem, as an experimental neuroscientist, in understanding the maths … I expect it to be as mind expanding as my involvement with its authors was over the years. I only wish I had had the whole book sooner – then my students and post-docs would have been able to understand what I was trying to say and been able to derive the critical tests of the ideas that only the rigor of the mathematical formulation of them could have generated.’

David Sterratt University of Edinburgh

Bruce Graham University of Stirling

Andrew Gillies Psymetrix Limited, Edinburgh

and David Willshaw University of Edinburgh

For neuroscientists at all levels and for people from the informational and physical sciences who want to develop computational models of the neuron and neural circuits. It presents the principles of computational neuroscience in a clear and coherent manner, and addresses practical issues that arise in modelling projects.

Gordon W. Arbuthnott, Okinawa Institute of Science and Technology

Contents: Preface; 1. Introduction; 2. The basis of electrical activity in the neuron; 3. The Hodgkin Huxley model of the action potential; 4. Compartmental models; 5. Models of active ion channels; 6. Intracellular mechanisms; 7. The synapse; 8. Simplified models of neurons; 9. Networks; 10. The development of the nervous system; Appendix A. Resources; Appendix B. Mathematical methods; References.

2011 246 x 189 mm 402pp 178 b/w illus. 7 tables 978-0-521-87795-4 Hardback

£43.00

eBook available

www.cambridge.org/9780521877954

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6

Bioinformatics Systems Biology: Simulation of Dynamic Network States Bernhard Ø. Palsson University of California, San Diego

Large omics data sets are difficult to interpret and use, but this practical book teaches how to build complex dynamical models of biochemical networks and simulate their responses. All examples in the text are available in MATLAB and MATHEMATICA® workbooks, allowing easy hands-on practice.

• Shows how dynamic models are built and simulated in the modern omics era • Provides a unified framework that allows the treatment of metabolites, enzymes and binding protein simultaneously • Material for instructors and students is available from http://systemsbiology. ucsd.edu 2011 247 x 174 mm 332pp 126 b/w illus.

978-1-107-00159-6 Hardback £48.00 eBook available

www.cambridge.org/9781107001596

Textbook

Systems Biology Properties of Reconstructed Networks Bernhard O. Palsson University of California, San Diego

This textbook devoted to systems biology describes how to model networks, how to determine their properties, and how to relate these to phenotypic functions. The links between the mathematical ideas and biological processes are made clear, and the book reflects the irreversible trend of increasing mathematical content in biology education. To assist both teacher and student, an associated web site provides problem sets. ‘… [deserves] serious attention from any quantitative scientist or physicist who hopes to learn about modern biology. … a welcome departure from the typical biology textbook. … a very readable introduction to the subject … this is an exciting time for biology.

The author exposes readers to enough material that the research literature in quantitative systems biology should become accessible.’

Physics Today 2006 253 x 177 mm 336pp 978-0-521-85903-5 Hardback

£51.00

eBook available

www.cambridge.org/9780521859035

Bioinformatics Mining of Massive Datasets Anand Rajaraman WalmartLabs

and Jeffrey David Ullman

New in Paperback

Bayesian Inference for Gene Expression and Proteomics Edited by Kim-Anh Do

Stanford University, California

Written by two authorities in database and Web technologies, this book is essential reading for students and practitioners alike. It teaches algorithms that have been used in practice to solve key problems in data mining and includes exercises suitable for students from the advanced undergraduate level and beyond.

Contents: 1. Data mining; 2. Large-scale file systems and map-reduce; 3. Finding similar items; 4. Mining data streams; 5. Link analysis; 6. Frequent itemsets; 7. Clustering; 8. Advertising on the Web; 9. Recommendation systems; Index.

• Teaching material has been ‘roadtested’ for several years at Stanford University • Includes a range of exercises to challenge even the most able student • Resources for instructors are available online, including slides, homework assignments, project requirements and exams 2011 246 x 189 mm 326pp 90 b/w illus. 160 exercises 978-1-107-01535-7 Hardback

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MD Anderson Cancer Center

and Peter Müller Swiss Federal Institute of Technology, Zürich

Marina Vannucci Rice University, Houston

A basic overview of the biological and technical principles behind multi-platform high-throughput experimentation followed by expert reviews of Bayesian methodology, tools and software for single group inference, group comparisons, classification and clustering, motif discovery and regulatory networks, and Bayesian networks and gene interactions.

‘This book should be required reading for all graduate students of statistics, statistical researchers in this field, and students and researchers in other fields that use these technologies.’

Tapabrata Maita, Journal of the American Statistician 2012 228 x 152 mm 456pp 22 tables 978-1-107-63698-9 Paperback £30.00 Also available 978-0-521-86092-5 Hardback £60.00 eBook available

£40.00

www.cambridge.org/9781107636989

eBook available

www.cambridge.org/9781107015357

Order online at www.cambridge.org/bio

8

Bioinformatics Optimal HighThroughput Screening Practical Experimental Design and Data Analysis for GenomeScale RNAi Research Xiaohua Douglas Zhang Merck Research Laboratories, Pennsylvania

This concise, cohesive book focuses on commonly used and recently developed methods for designing and analyzing high-throughput screening (HTS) experiments from a statistically sound basis. Combining biology, computing and statistics, the author explains experimental designs and analytic methods that are amenable to rigorous analysis and interpretation of RNAi HTS experiments.

2011 253 x 215 mm 232pp 47 b/w illus. 23 tables 978-0-521-51771-3 Hardback 978-0-521-73444-8 Paperback

£64.00 £26.99

eBook available

www.cambridge.org/9780521517713

Genomic Clinical Trials and Predictive Medicine Richard M. Simon National Cancer Institute

This book focuses on novel approaches that provide a reliable basis for identifying which patients are likely to benefit from each treatment. Aimed at both clinical investigators and statisticians, it covers the development and validation of prognostic and predictive biomarkers and their integration into clinical trials.

Contents: 1. Clinical trial basics; 2. Actionable prognostic biomarkers; 3. Phase II designs; 4. Enrichment designs; 5. Including both test positive and test negative patients; 6. Adaptive threshold design; 7. Multiple predictive biomarkers predictive analysis of clinical trials; 8. Prospective – retrospective design; Appendix A. Statistics background; Appendix B. Prognostic classifiers based on high dimensional data.

• Book presents new clinical trials designs and statistical analysis for personalized medicine • Discusses novel methods for analyzing clinical trials for personalizing treatment decisions • Covers state-of-the-art adaptive designs and the development and validation of probabilistic classifiers Practical Guides to Biostatistics and Epidemiology

2013 247 x 174 mm 164pp 11 b/w illus. 3 tables 978-1-107-00880-9 Hardback c. £70.00 978-1-107-40135-8 Paperback c. £27.99 Publication February 2013 www.cambridge.org/9781107008809

Bioinformatics Epigenomics

Chemical Genomics

From Chromatin Biology to Therapeutics Edited by Krishnarao Appasani

Edited by Haian Fu

GeneExpression Systems, Inc.

Leading experts from academia, the biotechnology and pharmaceutical industries introduce the emerging field of epigenomics, covering a wide range of topics and methods such as basic chromatin biology, imprinting at genome-wide level, and the role of epigenomics in disease biology and epidemiology.

• Contributions from leading experts from academia and the biotechnology and pharmaceutical industries, covering the role of epigenomics in a range of contexts • Covers basic chromatin biology, imprinting at a genome-wide level, and epigenomics in disease biology and epidemiology, making it a valuable guide for newcomers as well as experienced scientists

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Emory University, Atlanta

This edited text, with contributions from experts in the field, discusses the new techniques and applications that help further the study of chemical genomics.

It will be valuable to researchers, professionals and graduate students in many fields, including biology, biomedicine and chemistry.

Contents: Part I. Overviews; Part II. Molecules for Chemical Genomics; Part III. Basics of High Throughput Screening; Part IV. Chemical Genomics Assays and Screens; Part V. Chemical Genomics and Medicine.

2012 300 X 216 mm 344pp 27 b/w illus. 142 colour illus. 21 tables 978-0-521-88948-3 Hardback £90.00 eBook available

www.cambridge.org/9780521889483

• Explores historical aspects along with information on assays and sequencing technology 2012 247 x 174 mm 548pp 100 b/w illus. 24 colour illus. 24 tables 978-1-107-00382-8 Hardback £125.00 eBook available

www.cambridge.org/9781107003828

eBooks available at www.cambridge.org/ebookstore

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Bioinformatics Textbook

Bayesian Reasoning and Machine Learning David Barber University College London

This practical introduction for final-year undergraduate and graduate students is ideally suited to computer scientists without a background in calculus and linear algebra. Numerous examples and exercises are provided. Additional resources available online and in the comprehensive software package include computer code, demos and teaching materials for instructors.

Contents: Preface; Part I. Inference in Probabilistic Models: 1. Probabilistic reasoning; 2. Basic graph concepts; 3. Belief networks; 4. Graphical models; 5. Efficient inference in trees; 6. The junction tree algorithm; 7. Making decisions; Part II. Learning in Probabilistic Models: 8. Statistics for machine learning; 9. Learning as inference; 10. Naive Bayes; 11. Learning with hidden variables; 12. Bayesian model selection; Part III. Machine Learning: 13. Machine learning concepts; 14. Nearest neighbour classification; 15. Unsupervised linear dimension reduction; 16. Supervised linear dimension reduction; 17. Linear models; 18. Bayesian linear models; 19. Gaussian processes; 20. Mixture models; 21. Latent linear models; 22. Latent ability models; Part IV. Dynamical Models: 23. Discretestate Markov models; 24. Continuousstate Markov models; 25. Switching linear dynamical systems; 26. Distributed computation; Part V. Approximate Inference: 27. Sampling; 28. Deterministic approximate inference; Appendix.

Background mathematics; Bibliography; Index.

‘With approachable text, examples, exercises, guidelines for teachers, a MATLAB toolbox and an accompanying website, Bayesian Reasoning and Machine Learning by David Barber provides everything needed for your machine learning course. Only students not included.’

Jaakko Hollmén, Aalto University

‘The chapters on graphical models form one of the clearest and most concise presentations I have seen … The exposition throughout uses numerous diagrams and examples, and the book comes with an extensive software toolbox – these will be immensely helpful for students and educators. It’s also a great resource for self-study.’

Arindam Banerjee, University of Minnesota

‘My students praise this book because it is both coherent and practical, and because it makes fewer assumptions regarding the reader’s statistical knowledge and confidence than many books in the field.’

Amos Storkey, University of Edinburgh 2012 246 x 189 mm 728pp 287 b/w illus. 1 table 260 exercises 978-0-521-51814-7 Hardback £45.00 eBook available

www.cambridge.org/9780521518147

Bioinformatics Methodologies for Metabolomics

Networks in Cell Biology

Experimental Strategies and Techniques Edited by Norbert Lutz

Edited by Mark Buchanan Guido Caldarelli

University Aix-Marseille, France

Paolo De Los Rios

Jonathan Sweedler

École Polytechnique Fédérale, Lausanne

University of Illinois, Urbana-Champaign

Francesco Rao

and Ron Wevers

University of Freiburg

University Medical Center Nijmegen, The Netherlands

and Michele Vendruscolo

Provides comprehensive descriptions of the newest strategies in metabolomic research. While a broad range of methodologies are presented, so too are applications including in vivo metabolomics in humans and animals as well as in vitro analysis of tissue samples, cultured cells and biofluids.

Key introductory text for graduate students and researchers in physics, biology and biochemistry. Experts in network theory and modern cell biology introduce readers to ideas outside their field.

• Provides examples of using metabolomics methods in other relevant biological applications • Clear focus on methods, especially spectroscopic methods • Presents state-of-the-art techniques 2013 253 x 177 mm 500pp 152 b/w illus. 20 colour illus. 31 tables 978-0-521-76590-9 Hardback c. £80.00 Publication January 2013 www.cambridge.org/9780521765909

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Consiglio Nazionale delle Ricerche (CNR), Rome

University of Cambridge

‘With contributions from the best in the field, it is a valuable addition to the shelf of anyone interested in this exciting area.’

Albert-László Barabási, Northeastern University and Harvard Medical School

‘This book describes the state of the art in understanding cellular networks through contributions by leaders in modern cell biology and network theory. It is clearly organized and exhibits an excellent balance between empirical studies and theory. The biological underpinnings are explained clearly and comprehensively, and the appendices give a great primer to the key mathematical concepts necessary for network analysis and modeling.

This book will be of great use as a course textbook or for self-study.’

Reka Albert, Pennsylvania State University 2010 247 x 174 mm 280pp 73 b/w illus.

978-0-521-88273-6 Hardback £54.00 eBook available

www.cambridge.org/9780521882736

Order online at www.cambridge.org/bio

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Bioinformatics Phylogenetic Networks Concepts, Algorithms and Applications Daniel H. Huson Regula Rupp Eberhard-Karls-Universität Tübingen, Germany

and Celine Scornavacca Centre National de la Recherche Scientifique (CNRS), Paris

Phylogenetic networks are used to model and represent evolutionary history in the presence of reticulate events such as hybridization, horizontal gene transfer or recombination. This book addresses the biological background, the underlying mathematics, the computational algorithms and the software available.

‘This book will further transform the way biologists use genomic data to study evolution. The Tübingen group has led the development of phylogenetic network algorithms, and this book delivers a clear exposition for biologists bewildered by a plethora of recent methods, as well as for bioinformaticians aiming to develop the field further. It is essential reading for any scientist or student seeking to understand how genomic data can be used to represent and study the intricate ‘web of life’.’

Mike Steel, University of Canterbury

‘This textbook, by one of the leaders of the field (Daniel Huson) and his co-authors, provides a mathematically rigorous introduction to one of the most exciting and beautiful research areas in computational biology: phylogenetic networks. The text is clear and provides all the necessary biology background; it should be accessible to graduate students (or

upper-division undergraduates) in mathematics, computer science, or statistics.’

Tandy Warnow, University of Texas

‘This wonderfully accessible book is by far the most thorough and upto-date treatment of phylogenetic networks about. Many evolutionary processes in nature do not conform to the simple model of phylogenetic trees; examples are hybridizations, symbioses, and lateral gene transfer.

The more we probe nature with genomics, the more significant and numerous these examples become, so there is a real need for using networks in phylogenetics. This volume is a must for researchers working with phylogenetic networks. It is for an advanced college audience. Beautifully organized and clearly written, it really fills a void.’

Bill Martin, University of Düsseldorf

‘… a brave and ambitious attempt to describe the field of phylogenetic networks anno 2012 from a motivated algorithmic perspective … a formidable achievement … It will deservedly become essential reading for both mathematically inclined researchers already working in the field and those looking for an easy way to enter the field. … an important milestone in the development of the field.’

Systematic Biology 2010 247 x 174 mm 374pp 189 b/w illus. 80 exercises 978-0-521-75596-2 Hardback

£36.99

eBook available

www.cambridge.org/9780521755962

Bioinformatics Basic Phylogenetic Combinatorics

The Phylogenetic Handbook

Andreas Dress

A Practical Approach to Phylogenetic Analysis and Hypothesis Testing 2nd Edition Philippe Lemey,

Universität Bielefeld, Germany

Katharina T. Huber University of East Anglia

Jacobus Koolen Pohang University of Science and Technology, Republic of Korea

Vincent Moulton University of East Anglia

and Andreas Spillner Ernst-Moritz-Arndt-Universität Greifswald, Germany

The biosciences are generating new research directions in mathematical sciences. This book presents a new combinatorial theory that forms the basis for understanding structures such as phylogenetic trees and networks.

Results are presented in full detail, so the reader can quickly reach the forefront of this fascinating new area.

• The first systematic introduction to this exciting new field • Contains full proofs of all the fundamental results for easy reference • Suitable for readers with only a basic knowledge of combinatorics • Introduces a new generation of mathematicians to the fascinating problems that can arise in evolutionary and molecular biology

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University of Oxford

Marco Salemi, University of California, Irvine

Anne-Mieke Vandamme, Katholieke Universiteit Leuven, Belgium

A broad, hands on guide to the theory and practice of nucleotide and protein phylogenetic analysis.

This second edition includes six new chapters, covering topics such as Bayesian inference, tree topology testing and the impact of recombination on phylogenies, as well as a detailed section on molecular adaptation.

There is a stronger focus on hypothesis testing than in the previous edition, with more extensive discussions on recombination analysis, detecting molecular adaptation and genealogybased population genetics 2009 247 x 174 mm 750pp 57 b/w illus.

978-0-521-73071-6 Paperback £33.00 eBook available

www.cambridge.org/9780521730716

2011 228 x 152 mm 276pp 55 b/w illus.

978-0-521-76832-0 Hardback £40.00 eBook available

www.cambridge.org/9780521768320

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EMBOSS Guides The European Molecular Biology Open Software Suite (EMBOSS) is a high quality package of open source software tools for molecular biology.

EMBOSS Administrator’s Guide

EMBOSS Developer’s Guide

Bioinformatics Software Management Alan J. Bleasby Jon C. Ison and Peter M. Rice

Bioinformatics Programming Jon C. Ison Peter M. Rice and Alan J. Bleasby

European Bioinformatics Institute, Hinxton

European Bioinformatics Institute, Hinxton

This is the official EMBOSS Administrator’s Guide is the official, definitive and comprehensive guide to EMBOSS installation and maintenance:

The official and definitive guide to developing software under EMBOSS. It includes extensive and extensible C programming libraries, providing a powerful and robust toolkit for developing new bioinformatics tools from scratch. With comprehensive reference information and guidelines, including step-by-step instructions and real-world code examples:

• Find all the information needed to configure, install and maintain EMBOSS, including recent additions for version 6.2 • Step-by-step instructions with real-world examples – saves readers time and helps them avoid the pitfalls on all the common platforms • In-depth reference to database configuration – learn how to set up and use databases under EMBOSS • Includes EMBOSS Frequently Asked Questions (FAQ) with answers Over 200 applications are integrated with a range of popular third party software packages. Tools are available from a wide range of graphical interfaces, including easy to use web interfaces and powerful workflow software.

Contents: Acknowledgements; Preface; 1. Conventions; 2. Welcome to the EMBOSS administrator’s manual; 3. Building EMBOSS; 4. Building EMBASSY; 5. Building Jemboss; 6. Databases; 7. Resources; 8. Frequently asked questions (FAQ).

2011 247 x 174 mm 174pp 5 tables 978-0-521-18815-9 Paperback £40.00 eBook available

www.cambridge.org/9780521188159

• Learn how to write fully-featured tools guided by the people who developed EMBOSS • Step-by-step guide to writing EMBOSS applications, illustrated with functional, deployed code • ACD file development – learn how to customise existing tools without coding, or design and write entirely new application interfaces • EMBOSS API programming guidelines • Wrapping and porting applications under EMBOSS – learn how to incorporate third-party tools Contents: Acknowledgements; Preface; 1. Conventions; 2. Welcome to the EMBOSS developer’s manual; 3. Getting started; 4. Your first EMBOSS application; 5. Software development under EMBOSS; 6. A complete application; 7. ACD file development; 8. C programming; 9. Programming with AJAX; 10. Programming with NUCLEUS; 11. Incorporating third-party applications; 12. ACD syntax reference; 13. AJAX library reference; 14. NUCLEUS library reference; 15. Resources.

2011 247 x 174 mm 652pp 978-0-521-60724-7 Paperback

£55.00

eBook available

www.cambridge.org/9780521607247

Bioinformatics

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EMBOSS User’s Guide Practical Bioinformatics Peter M. Rice Alan J. Bleasby and Jon C. Ison

• Data types and file formats – see the biological data that can be manipulated and analysed

European Bioinformatics Institute, Hinxton

• Practical guides to popular EMBOSS GUIs (wEMBOSS and Jemboss)

• In-depth explanation of the EMBOSS command line – learn advanced ‘power user’ features

With contributions by Lisa Mullan and Guy Bottu

The official and definitive guide to using the package.

It includes over 200 applications for molecular sequence analysis and general bioinformatics including sequence alignment, rapid database searching and sequence retrieval, motif identification and pattern analysis and much more.

• No prior experience with EMBOSS necessary • Quick set up and maintenance • Hands-on tutorial – learn EMBOSS by working through practical examples

Contents: Acknowledgements; 1. Preface; 2. Conventions used in the manual; 3. Welcome to the EMBOSS user’s manual; 4. Background to EMBOSS; 5. Basic set-up and maintenance; 6. Getting started; 7. Tutorial; 8. File formats; 9. The EMBOSS command line; 10. Applications and packages; 11. EMBOSS application reference; 12. EMBASSY application reference; 13. Interfaces; 14. Using EMBOSS under wEMBOSS; 15. Using EMBOSS under Jemboss.

2011 247 x 174 mm 394pp 9 b/w illus. 50 tables 978-0-521-60725-4 Paperback £29.95 www.cambridge.org/9780521607254

Visit the EMBOSS website: http://emboss.open-bio.org

eBooks available at www.cambridge.org/ebookstore

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Of related interest Textbook

New in Paperback

Introduction to Cancer Biology

What Makes Biology Unique?

Robin Hesketh

Considerations on the Autonomy of a Scientific Discipline Ernst Mayr

University of Cambridge

A concise overview of the fundamental concepts of cancer biology, ideal for those with little or no background in the field. From cancer epidemiology and the underlying mechanisms, through to tumour detection and treatment, the comprehensive picture revealed will enable students to move into the cancer field with confidence.

Contents: Introduction; 1. Lessons from epidemiology; 2. Causes of cancer; 3. Signalling in normal cells; 4. ‘Cancer genes’: mutations and cancer development; 5. What is a tumour?; 6. Cancer signalling networks; 7. The future of cancer prevention, diagnosis and treatment; 8. The future of cancer in the post-genomic era; Ten major cancers at a glance; Appendix. Targets of specific anti-cancer drugs; Glossary; Further reading; Index.

2012 246 x 189 mm 348pp 130 b/w illus. 38 colour illus.

978-1-107-01398-8 Hardback c. £75.00 978-1-107-60148-2 Paperback c. £29.99 Publication November 2012 www.cambridge.org/9781107013988

Harvard University, Massachusetts

This book is a collection of essays from the most eminent evolutionary biologist of the twentieth century.

‘In this first book of the second century of his long career, the biologist Ernst Mayr at age 100 has given us his reflections on the most interesting and important questions about life: why living things can’t be understood just as very complex machines, how humans evolved, why we haven’t yet communicated with any extraterrestrials, and others.

Written with a clarity and vigor that shine from every page, this book is best summarized in one word: exciting!’

Jared Diamond, UCLA, author of Guns, Germs and Steel (Pulitzer Prize, 1998) 2007 228 x 152 mm 246pp 1 table 978-0-521-70034-4 Paperback £20.99 Also available 978-0-521-84114-6 Hardback £43.00 eBook available

www.cambridge.org/9780521700344

Of related interest Alan M. Turing

What is Life?

Centenary Edition Sara Turing Afterword by John F. Turing Foreword by Lyn Irvine and Martin Davis

With Mind and Matter and Autobiographical Sketches Erwin Schrodinger Foreword by Roger Penrose

To commemorate the centenary of Turing’s birth, this republication of his mother’s biography contains a new foreword by Martin Davis and a never-before-published memoir by Alan’s brother. The contrast between this memoir and the original biography sheds new light on Turing’s relationship with his family, and on the man himself.

‘The book is full of brilliant treasures, anecdotal accounts of Turing’s eccentricity and genius, and insights into his science ... This little book, with its kaleidoscopic picture of Alan Turing’s short life, goes some way towards de-coding his mind, and his family.’

The Guardian 2012 228 x 152 mm 194pp 7 b/w illus.

978-1-107-02058-0 Hardback £17.99 eBook available

www.cambridge.org/9781107020580

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Nobel laureate Erwin Schrödinger’s What is Life? is one of the great science classics of the twentieth century. The philosopher Karl Popper hailed it as a ‘beautiful and important book’ by ‘a great man to whom I owe a personal debt for many exciting discussions’.

Canto Classics

2012 216 x 138 mm 194pp 978-1-107-60466-7 Paperback £10.99 www.cambridge.org/9781107604667

Human Identity and Identification Rebecca Gowland University of Durham

and Tim Thompson Teesside University

Reflecting upon recent developments in research on the relationship between the body, environment and society, this book examines the role of the body in human identification and in the forging of identities. It integrates biological perspectives with current discourse in the social sciences, focusing particularly on bioarchaeology and forensic science.

2013 247 x 174 mm 248pp 9 b/w illus. 4 tables 978-0-521-88591-1 Hardback c. £75.00 978-0-521-71366-5 Paperback c. £29.99 Publication January 2013 www.cambridge.org/9780521885911

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Of related interest Privacy, Confidentiality, and Health Research William W. Lowrance

New technologies and increased data sharing have a great potential to advance health research, but our current safeguards for privacy, confidentiality and consent may no longer be sufficient.

In this book, William Lowrance draws on examples from a variety of jurisdictions to suggest ways forward.

Cambridge Bioethics and Law, 20

2012 228 x 152 mm 202pp 1 b/w illus.

978-1-107-02087-0 Hardback £55.00 eBook available

www.cambridge.org/9781107020870

Textbook

Bioethics An Introduction Marianne Talbot University of Oxford

This accessible introduction explains bioethical issues and their philosophical foundations to science students, giving them confidence to debate important issues in the ethics of biotechnology.

It includes over 200 activities, detailed case studies and explanatory podcasts.

‘This book is an excellent, unique and comprehensive resource for either an undergraduate or a graduate course.

With its wonderful introduction into ethical theory and a multifaceted approach, it is an incomparable resource for the successful teaching of bioethics. The author’s eloquent writing … carefully examines practically every aspect of [this] exciting interdisciplinary [field] … a valuable reading of interest for both students and scholar[s], alike.’

Mirjana Brockett, Georgia Institute of Technology, Atlanta

Contents: Preface; Using this book; Notes for instructors; Part I. Bioethics and Ethics: 1. Biotechnology and bioethics: what it’s all about; 2. Ethics in general: ethics, action and freedom; 3. Ethics in the context of society: ethics, society and the law; 4. Ethical theories: virtue, duty and happiness; 5. Identifying and evaluating arguments: logic and morality; 6. General arguments: unnatural, disgusting, risky, only opinion; Part II. The Beginning and End of Life; Section 1. Cloning: 7. Therapeutic cloning: the moral status of embryos; 8. Reproductive cloning: science and science fiction; Section 2. Reproduction: 9. Reproductive freedom: rights, responsibilities and choice; 10. The resources of reproduction: eggs, sperm and wombs for sale; 11. Screening and embryo selection: eliminating disorders or people?; Section 3. Ageing and Death: 12. Ageing and immortality: the search for longevity; 13. Death and killing: the quality and value of life; Part III. In The Midst of Life; Section 1. Our Duties to Ourselves: 14. Human enhancement: the more the better?; 15. Bio-information: databases, privacy and the fight against crime; 16. Security and defence: security sensitivity, publication and warfare; Section 2. Our Duties to Each Other: 17. Food and energy security: GM food, biofuel and the media; 18. Bioownership: who owns the stuff of life?; 19. Human justice: the developed and developing worlds; Section 3. Our Duties to Nature: 20. Non-human animals: consciousness, rationality and animal rights; 21. The living and non-living environment: spaceship Earth; Index.

2012 246 x 189 mm 478pp 54 b/w illus. 1 table 233 exercises 978-0-521-88833-2 Hardback £60.00 978-0-521-71459-4 Paperback £27.99 eBook available

www.cambridge.org/9780521888332

Of related interest Multiscale Modeling of the Skeletal System Marco Viceconti

Biosimulation Simulation of Living Systems Daniel A. Beard

Istituti Ortopedici Rizzoli, Bologna, Italy

Medical College of Wisconsin

This book presents an integrative, multiscale computational approach to skeletal research. Addressing biomechanical and mechanobiological processes, it shows how computational modeling can determine the relationship between bone mechanics and disease.

A hands-on guide to devising, designing and analyzing simulations of biophysical processes for applications in biological and biomedical sciences. Practical examples are given throughout, representing real-world case studies of key application areas, and all data and complete codes for simulation and data analysis are provided online.

‘Professor Viceconti is one of the pioneers of the integrative approach to biological systems and his book is a beautiful illustration of this approach. Beautiful in all senses: sound intellectual argument, clear informative illustrations, fascinating practical applications, and it forms a sustained development of a field of research that is fundamental to the success of any attempt to create the Virtual Physiological Human.’

Denis Noble, University of Oxford

‘[Marco Viceconti’s] speciality is musculo-skeletal modelling and in this book he brings a unique combination of technical expertise (including modelling strategies and numerical methods), clinical experience and modelling philosophy, always guided by the pragmatic problem solving approach of an engineer. The book is a delightful combination of philosophical musings, personal anecdotes, scientific insights and technical advice. It will be of great value to the musculo-skeletal research community, particularly those interested in the clinical application of multi-scale modelling.‘

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Contents: 1. Introduction to simulation of biological systems; 2. Transport and reaction of solutes in biological systems; 3. Physiologically-based pharmacokinetic modeling; 4. Cardiovascular systems simulation; 5. Chemical reaction systems: thermodynamics; 6. Chemical reaction systems: kinetics; 7. Chemical reaction systems: large-scale systems simulation; 8. Cellular electrophysiology; 9. Appendices: mathematical and computational techniques.

Cambridge Texts in Biomedical Engineering

2012 247 x 174 mm 320pp 115 b/w illus. 19 tables 50 exercises 978-0-521-76823-8 Hardback £55.00 eBook available

www.cambridge.org/9780521768238

Peter Hunter, University of Auckland 2011 247 x 174 mm 222pp 40 b/w illus.

978-0-521-76950-1 Hardback £65.00 eBook available

www.cambridge.org/9780521769501

Order online at www.cambridge.org/bio

20

Of related interest Partial Differential Equation Analysis in Biomedical Engineering Case Studies with Matlab William E. Schiesser Lehigh University, Pennsylvania

Mechanics of the Cell Second edition David Boal Simon Fraser University, British Columbia

This textbook is ideal for advanced undergraduate and graduate students in physics and biomedical engineering.

Aimed at graduates and researchers, this introduction to computer-based partial differential equation (PDE) modeling provides readers with the practical tools necessary to develop and use mathematical models in biomedical engineering. With step-bystep guidelines and detailed examples, the reader will learn how PDE analysis is formulated, implemented and tested.

Reviews of the first edition: ‘In Mechanics of the Cell David Boal explains the mechanical properties of the biopolymers found within cells … for graduate students in the general field and for biotechnologists required to consider added dimensions to their work it represents a comprehensive text that ought to make it a standard reference for many years.’

Ian Jones, Chemistry in Britain

Contents: 1. Introduction to partial differential equation integration in space and time; 2. Antibody binding kinetics; 3. Acid-mediated tumour growth; 4. Retinal oxygen transport; 5. Hemodialyzer dynamics; 6. Epidermal wound healing; 7. Drug distribution from a polymer matrix.

• Now in full color with new chapters on complex filaments, the cell division cycle, the mechanisms of control and organization in the cell, and fluctuation phenomena

2012 247 x 174 mm 448pp 20 b/w illus. 15 tables 978-1-107-02280-5 Hardback c. £65.00 Publication October 2012 www.cambridge.org/9781107022805

• Features around 280 end-of-chapter exercises exploring further applications and online resources include extra support material, diagrams and lecture notes • Covers a range of topics around the mechanical properties of the cell, mixing theory and experiment and emphasizing physics concepts 2012 246 x 189 mm 622pp 282 colour illus. 283 exercises 978-0-521-11376-2 Hardback £90.00 978-0-521-13069-1 Paperback £50.00 eBook available

www.cambridge.org/9780521113762

Professional Development How to Write and Illustrate a Scientific Paper

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Developing a Talent for Science Ritsert Jansen Rijksuniversiteit Groningen, The Netherlands

Second edition Bjorn Gustavii University Hospital, Lund, Sweden

This second edition has been broadened to include comprehensive advice on writing compilation theses for doctoral degrees, preparing case reports, advice on when to get a professional artist to redraw figures, what to include in figure legends and how to present them, and how to present statistical results.

‘This book ranks with the best in the field. It is brief, to the point and easy to follow … useful to the author and editor … and so recommended.’

Research Communications in Molecular Pathology and Pharmacology ‘… short and straightforward … complete and user-friendly … for those to make their first public steps in science, Gustavii´s book is certainly very useful.’

Annals of Human Biology

How can you make the most of your talent for science? This practical guide offers valuable recommendations, real-life stories and practical exercises to enable students, postdoctorates and professors to develop their skills and succeed in academia, industry or elsewhere.

‘This insightful book offers guidance toward an enhanced productive academic or professional scientific career … a must-read for any professional in the geophysical community and for those pursuing studies in this field.’

The Leading Edge 2011 228 x 152 mm 182pp 20 b/w illus.

978-0-521-19312-2 Hardback £48.00 978-0-521-14961-7 Paperback £16.99 eBook available

www.cambridge.org/9780521193122

‘… an ideal reference book to have at hand when writing and organizing many types of scientific literature.’

The British Society for Cell Biology 2008 228 x 152 mm 180pp 978-0-521-87890-6 Hardback 978-0-521-70393-2 Paperback

£45.00 £16.99

eBook available

www.cambridge.org/9780521878906

eBooks available at www.cambridge.org/ebookstore

22

Professional Development Successful Scientific Writing A Step-by-Step Guide for the Biological and Medical Sciences Third edition Janice R. Matthews Scientific Editing Services, Athens, Georgia

and Robert W. Matthews University of Georgia

Provides user-friendly, detailed and practical advice for students and researchers, enabling them to communicate their work effectively through published literature. The abundant examples and self-help exercises can be applied to many scientific writing contexts. Wellstructured, comprehensive and entertaining, it is useful for courses, seminars or improving individual skills.

‘This book is beyond reproach and should be regarded as compulsory reading for all biomedical and science undergraduate and postgraduate students and all others likely to have to write or edit scientific reports.’

Times Higher Education Supplement ‘… will soon become one of the more well-thumbed volumes on our laboratory bookshelf.’

Trends in Neuroscience ‘… pragmatic, well-written and comprehensive … each stage – from marshalling ideas through bashing out a first draft, revising it, honing it for publication and correcting it in proof – is demystified with exercises and examples.’

New Scientist

2007 228 x 152 mm 256pp 37 b/w illus. 31 tables 27 exercises 978-0-521-69927-3 Paperback £25.99 eBook available

www.cambridge.org/9780521699273

The Art of Being a Scientist A Guide for Graduate Students and their Mentors Roel Snieder and Ken Larner Colorado School of Mines

This is a hands-on guide for graduate students, junior researchers and mentors in all fields of science, engineering and humanities to perfect the practical skills needed for a successful research career.

Sections include choosing a research topic, making a work plan, publishing papers, and planning a scientific career. ‘… this book will be an important resource for students considering entering careers in science, and I would definitely encourage students to read it.’

Kurt Haas, Cold Spring Harbor L research as a passion and as a practical reality.

It contains a wealth of positive and useful advice that should be of great benefit to young researchers.’

Frits van Oostrom, Utrecht University, Emeritus President of the Royal Netherlands Academy of Arts and Sciences 2009 228 x 152 mm 296pp 6 b/w illus.

978-0-521-74352-5 Paperback £22.99 www.cambridge.org/9780521743525

Professional Development Successful Science Communication

Scientific Method in Brief

Telling It Like It Is Edited by David J. Bennett

Hugh G. Gauch, Jr

Technische Universiteit Delft, The Netherlands

and Richard C. Jennings University of Cambridge

Foreword by Walter Bodmer

Bringing together more than 30 experienced and successful science communicators from across the academic, commercial and media worlds ‘telling it like it is’, this practical, one-stop resource is essential reading for practising scientists and other professionals wanting to share their knowledge. ‘… a book that should be recommended reading for all those who are involved in any way with science. There is no better current comprehensive and succinct source that gives such an excellent background to the issues around science communication and explains how to engage with the public, with much valuable practical advice.’

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Specifically designed to enhance perspective and encourage productivity, this is a guide to the key principles of scientific method including deductive and inductive logic, probability, parsimony and hypothesis testing.

The examples and case studies span the physical, biological and social sciences and also highlight science’s interrelationship with the humanities.

It is an ideal resource for anyone undertaking a systematic study of scientific method for the first time, from undergraduates to professionals.

2012 228 x 152 mm 303pp 37 b/w illus.

3 tables 978-1-107-66672-6 Paperback £24.99 eBook available

www.cambridge.org/9781107666726

Sir Walter Bodmer, FRS 2011 228 x 152 mm 492pp 62 b/w illus.

978-1-107-00332-3 Hardback £65.00 978-0-521-17678-1 Paperback £27.99 eBook available

www.cambridge.org/9781107003323

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