Computational & systems biology cluster 2015 by Cambridge University Press

Computational & Systems Biology 2015

www.cambridge.org/csb

Featured textbooks

Systems biology and networks

Genetics and genomics

Computational neuroscience

Knowledge management and data mining

Pattern recognition and machine learning

Statistics and Mathematical Modeling

Also of interest

Bioethics 34 Professional development

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Featured textbooks Textbook Highlight

Genome-Scale Algorithm Design Biological Sequence Analysis in the Era of High-Throughput Sequencing Veli Mäkinen Djamal Belazzougui Fabio Cunial and Alexandru I. Tomescu University of Helsinki

Outlining the fundamental algorithms and data structures that power modern sequence analysis workflows, this book provides a powerful toolkit for students and researchers in bioinformatics and computer science. Its numerous examples and exercises are designed to help readers understand applications of the latest algorithm techniques, providing tools for further research. Contents: Notation; Preface; Part I. Preliminaries: 1. Molecular biology and high-throughput sequencing; 2. Algorithm design; 3. Data structures; 4. Graphs; 5. Network flows; Part II. Fundamentals of Biological Sequence Analysis: 6. Alignments; 7. Hidden Markov models (HMMs); Part III. Genome-Scale Index Structures: 8. Classical indexes; 9. Burrows–Wheeler indexes; Part IV. Genome-Scale Algorithms: 10. Read alignment; 11. Genome analysis and comparison; 12. Genome compression; 13. Fragment assembly; Part V. Applications: 14. Genomics; 15. Transcriptomics; 16. Metagenomics; References; Index.

“…a timely, rigorous and comprehensive systematization of the concepts and tools at the core of postgenome bioinformatics … The authors have created a rare, self-contained reference that will smoothly introduce the neophyte and assist the seasoned researcher… This is an ideal textbook for courses directed at a mixed audience coming from diverse, even distant backgrounds.” Alberto Apostolico, Georgia Tech, USA.

“The … scope, clarity, and mathematically precise, compelling explanations make advanced topics in genome-wide bioinformatics accessible to a wide audience.” Christina Boucher, Colorado State University, USA.

“…a new reference for string data structures and algorithms, and for their applications in genome analysis. The technically precise style, illustrated with a great collection of well-designed examples and many exercises, makes it an ideal resource for researchers, students and teachers.” Jens Stoye, Universität Bielefeld, Germany.

“… a well-thought-out, integrated book that fills a gap in the recent literature of textbooks in algorithmic bioinformatics.” Nadia Pisanti, University of Pisa, Italy.

2015 247 x 174 mm 400pp 90 b/w illus. 4 tables 269 exercises 978-1-107-07853-6 Hardback £39.99 / US$64.99 Publication May 2015 For all formats available, see

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Featured textbooks Textbook Highlight

Systems Biology Constraint-based Reconstruction and Analysis Bernhard Ø. Palsson University of California, San Diego

Reflecting the latest developments, this textbook explains how quantitative and computable genotype-phenotype relationships can be built using a genome-wide basis of information about the gene portfolio of an organism. It has been developed through extensive classroom use, providing a conceptual framework in addition to invaluable modelling tools and computational approaches. ‘One of the defining challenges of systems biology is to determine the structures and mechanisms by which complex networks of genes, proteins and metabolites control cell processes and molecular dynamics. Bernhard Palsson is a leading pioneer in constructing and analyzing genomescale models of such networks. Here Palsson offers students an insider’s guided tour of the concepts, principles and techniques underlying this emerging field. The book is brilliantly laid out and offers professors wellstructured, much-needed material for a graduate-level course in systems biology and network science.’ James J. Collins, Massachusetts Institute of Technology

‘This is a real tour de force. With enormous clarity, Bernhard Palsson sets out the what, why and how of network and systems biology, and of the important role of genome-wide reconstructions – especially, to date,

of metabolism – in realising it … this is a masterful survey of the field by one of its leading practitioners. The development is nicely logical … If you are interested in network biology at all, then this book is for you.’ Douglas Kell, University of Manchester

Contents: Preface; 1. Introduction; Part I. Network Reconstruction: 2. Network reconstruction: the concept; 3. Network reconstruction: the process; 4. Metabolism in Escherichia coli; 5. Prokaryotes; 6. Eukaryotes; 7. Biochemical reaction networks; 8. Metastructures of genomes; Part II. Mathematical Properties of Reconstructed Networks: 9. The stoichiometric matrix; 10. Simple topological network properties; 11. Fundamental network properties; 12. Pathways; 13. Use of pathway vectors; 14. Randomized sampling; Part III. Determining the Phenotypic Potential of Reconstructed Networks: 15. Dual causality; 16. Functional states; 17. Constraints; 18. Optimization; 19. Determining capabilities; 20. Equivalent states; 21. Distal causation; Part IV. Basic and Applied Uses: 22. Environmental parameters; 23. Genetic parameters; 24. Analysis of omic data; 25. Model driven discovery; 26. Adaptive laboratory evolution; 27. Model driven design; Part V. Conceptual Foundations: 28. Teaching systems biology; 29. Epilogue; References; Index. 2015 247 x 174 mm 550pp 27 b/w illus. 244 colour illus. 45 tables 978-1-107-03885-1 Hardback £44.99 / US$79.99 For all formats available, see

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Featured textbooks Textbook Highlight

Python Programming for Biology Bioinformatics and Beyond Tim J. Stevens MRC Laboratory of Molecular Biology, Cambridge

and Wayne Boucher University of Cambridge

This book presents core concepts in computational biology in an accessible, jargon-free manner and offers a complete foundation course in the Python language, with entry points for novices and experienced programmers alike. Material covers traditional bioinformatics and many topics beyond, with practical examples for Python versions 2 and 3. ‘As a long-time advocate of Python as the language of choice for both the bulk of biological data analysis and for teaching computer programming to molecular life scientists, I am delighted to see this book. [It] provides a well-focused introduction to Python programming but then goes on to use the clarity of the Python language to demystify a wide range of commonly applied data processing and analysis techniques that arise in modern cell and molecular biology. The integration of straightforward introductions to sequence analysis, image processing and statistical analysis (amongst others) into a book on Python is inspired. The clarity of the Python language helps to show that often ‘yes it really is that simple’, in a way that staring at a mathematical

expression often fails to, and the programming element allows the reader to become actively involved.’ Jeremy Craven, University of Sheffield

Contents: Preface; Acknowledgements; 1. Prologue; 2. Beginners’ guide; 3. Python basics; 4. Program control and logic; 5. Functions; 6. Files; 7. Object orientation; 8. Object data modelling; 9. Mathematics; 10. Coding tips; 11. Biological sequences; 12. Pairwise sequence alignments; 13. Multiple sequence alignments; 14. Sequence variation and evolution; 15. Macromolecular structures; 16. Array data; 17. High-throughput sequence analyses; 18. Images; 19. Signal processing; 20. Databases; 21. Probability; 22. Statistics; 23. Clustering and discrimination; 24. Machine learning; 25. Hard problems; 26. Graphical interfaces; 27. Improving speed; Appendix 1: simplified language reference; Appendix 2: selected standard type methods and operations; Appendix 3: standard module highlights; Appendix 4: string formatting; Appendix 5: regular expressions; Appendix 6: further statistics; Glossary; Index. 2015 247 x 174 mm 711pp 91 b/w illus. 11 colour illus. 3 tables 978-0-521-89583-5 Hardback £84.99 / US$139.99 978-0-521-72009-0 Paperback £44.99 / US$69.99 For all formats available, see

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Featured textbooks Textbook Highlight

Computing for Biologists Python Programming and Principles Ran Libeskind-Hadas Harvey Mudd College, California

and Eliot Bush Harvey Mudd College, California

Specifically designed for life science students with no prior computing experience, this textbook teaches computational problem-solving along with Python programming skills. The chapters cover three key tools – gene finding, sequence alignment and phylogenetic methods. An accompanying website features numerous integrated exercises, equipping students with the skills to write programs independently. ‘In my twenty years as a professor, I have never run across a textbook on bioinformatics algorithms that a biologist can read from cover to cover and understand. This is the one.’ Pavel Pevzner, Ronald R. Taylor Distinguished Professor of Computer Science, University of California, San Diego

‘This is an awesome book for anyone to get into computing. It is easy to follow and clearly structured so the reader understands what they are learning and why. The book provides the fundamentals concepts of computational biology and bioinformatics in parallel to gaining actual skills in computing and the ability to write your own Python programs! What I love about the book is how the authors ensured the concepts and skills are applicable to a clear and define biological problem.

The authors help demystify the various topics and bring the reader to understand the algorithms behind and the programming tools by applying these to resolve an actual biological problem. This book is also an excellent resource for those involved in training and education and provides plenty of exercise to use in the actual classroom.’ Maria Victoria Schneider, The Genome Analysis Centre (TGAC), UK

Contents: Preface; Meet python; Part I. Python versus Pathogens: 1. Computing GC content; 2. Pathogenicity islands; 3. Open reading frames and genes; 4. Finding genes (at last!); Part II. Sequence Alignment and Sex Determination: 5. Recursion; 6. The use-it-or-lose-it principle; 7. Dictionaries, memoization, and speed; 8. Sequence alignments and the evolution of sex chromosomes; Part III. Phylogenetic Reconstruction and the Origin of Modern Humans: 9. Representing and working with trees; 10. Drawing trees; 11. The UPGMA algorithm; Part IV. Additional Topics: 12. RNA secondary structure prediction; 13. Gene regulatory networks and the maximum likelihood method; 14. Birds, bees, and genetic algorithms; Where to go from here; Index. 2014 246 x 189 mm 217pp 8 b/w illus. 33 colour illus. 1 table 978-1-107-04282-7 Hardback £60.00 / US$99.00 978-1-107-64218-8 Paperback £29.99 / US$49.99 For all formats available, see

www.cambridge.org/9781107042827

Featured textbooks Textbook

Textbook

Genomics and Bioinformatics

UNIX and Perl to the Rescue!

An Introduction to Programming Tools for Life Scientists Tore Samuelsson

A Field Guide for the Life Sciences (and Other Data-rich Pursuits) Keith Bradnam

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 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. ‘The book provides a lively and accessible introduction to current research in the life sciences, and it does so in a succinct way by grounding the explanations with simple algorithms expressed in Perl code. As such, the book can be very useful to a general science audience, particularly those with a computer science background, whether established researchers or undergraduate students. The writing is inspiring and engaging, and the inclusion of Perl code makes it easy for readers to apply the knowledge and observe the outcomes.’ Sara Kalvala, Computing Reviews

University of California, Davis

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. ‘UNIX and Perl to the Rescue! is a book I highly recommend for all those students, post-docs, and academics who are scared of programming but can benefit immensely from the power of Unix and scripting languages. It’s time to come out of your shell.’ Dr M. D. Sharma, Genetics Society News 2012 247 x 174 mm 428pp 5 b/w illus. 978-1-107-00068-1 Hardback £84.99 / US$134.99 978-0-521-16982-0 Paperback £29.99 / US$49.99 For all formats available, see

www.cambridge.org/9781107000681

2012 246 x 189 mm 358pp 20 b/w illus. 70 colour illus. 23 tables 60 exercises 978-1-107-00856-4 Hardback £84.99 / US$134.99 978-1-107-40124-2 Paperback £34.99 / US$64.99 For all formats available, see

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Featured textbooks Textbook

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

and Ron Shamir Tel-Aviv University

A team of renowned bioinformaticians take fresh approaches to lead biology students from first principles towards computational thinking. Intuitive explanations promote deep understanding, using little mathematical formalism. Covering essential bioinformatic topics in a concise textbook, the authors prepare students to meet the computational challenges of their life science careers. ‘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 2011 246 x 189 mm 394pp 37 b/w illus. 105 colour illus. 4 tables 978-1-107-01146-5 Hardback £99.99 / US$179.99 978-1-107-64887-6 Paperback £49.99 / US$74.99 For all formats available, see

www.cambridge.org/9781107011465

Systems biology and networks Highlight

Systems Genetics Linking Genotypes and Phenotypes Edited by Florian Markowetz Cancer Research UK Cambridge Research Institute German Cancer Research Center, Heidelberg

Systems Biology of Cancer Edited by Sam Thiagalingam Boston University School of Medicine

Cancer is a complex group of diseases with many possible causes. Bringing together the state-of-the-art contributions of international experts, Systems Biology of Cancer proposes an ultimate goal for the whole scientific community: exploiting systems biology to generate in-depth knowledge based on blueprints that are unique to each type of cancer.

C amb r i dg e S e r i e S i n S yS t e mS g e n e t i C S

Whereas genetic studies have traditionally focused on explaining heritance of single traits and their

phenotypes, recent technological advances have made it possible to comprehensively dissect the

genetic architecture of complex traits and to quan-

mathematical models of complex biological systems and analysing large-scale molecular data. His research interests

fields, integrating a range of approaches and ex-

ical data to inference of cellular networks from high-throughput gene perturbation screens and integration of heterogeneous data sources using machines learning techniques and probabilistic graphic models.

Gathering the contributions of leading scientists,

Michael Boutros is a Group Leader at

both computational and experimental, this book

the German Cancer Research Centre

shows how experimental perturbations can help

(DKFZ) in Heidelberg, where he heads

us to understand the link between genotype and

phenotype. A snapshot of current research activity and state-of-the-art approaches to systems genetics is provided, including work from model organisms such as Saccharomices cerevisiae,

Drosophila melanogaster, as well as from human studies.

Researchers and graduate students in genetics,

the Division of Signalling and Functional Genomics. He also holds a Professorship at the University of Heidelberg. His research focuses on the systematic dissection signalling pathways in Drosophila and mammalian cells, which are important during development and cancer. He attempts to define key components of signalling pathways, discovering interac-

Systems Genetics

ploiting our increased ability to obtain quantitative and detailed measurements on a broad spectrum of phenotypes.

Markowetz & Boutros. 9781107013841 PPC. C M Y K

Contents: List of contributors; 1. An introduction to systems genetics; 2. Computational paradigms for analyzing genetic interaction networks; 3. Mapping genetic interactions across many phenotypes in metazoan cells; 4. Genetic interactions and network reliability; 5. Synthetic lethality and chemoresistance in cancer; 6. Joining the dots – network analysis of gene perturbation data; 7. High content screening in infectious diseases: new drugs against bugs; 8. Inferring genetic architecture from systems genetics studies; 9. Bayesian inference for model selection: an application to aberrant signalling pathways in chronic myeloid leukaemia; 10. Dynamic network models of protein complexes; 11. Phenotype state spaces and strategies for exploring them; 12. Automated behavioural fingerprinting of C. elegans mutants; Index.

at Cancer Research UK’s Cambridge Research Institute. His research is con cerned with developing statistical and

range from the analysis of molecular clin-

etics and is born out of a synthesis of multiple

Gathering contributions from leading scientists, both computational and experimental, this book shows how experimental perturbations can help us to understand the link between genotype and phenotype. Researchers and graduate students in genetics, functional genomics, bioinformatics, computational biology, systems biology and biotechnology will find this a valuable and timely tool.

Florian Markowetz is a Group Leader

tify how genes interact to shape phenotypes. This exciting new area has been termed systems gen-

Markowetz and Boutros

and Michael Boutros

Systems Genetics

tion between pathways, and character-

functional genomics, bioinformatics, compu-

isation of signalling networks under

tational biology, systems biology and biotech-

normal and perturbed conditions.

nology will find this a valuable and timely resource.

Contents: Contributors; Preface; Part I. Introduction to Modular Organization of the Networks of Gene Functions and Cancer; Part II. Alterations in the Regulatory Networks of Fundamental Cellular and Molecular Events in Cancer; Part III. Networks of Events Responsible for the Manifestation of Aberrant Genetic and Epigenetic Codes in Cancer; Part IV. Functional Networks of Events that Modulate Phenotypic Manifestation of Cancer; Part V. Current State of the Evolving MMMN Cancer Progression Models of Cancer; Part VI. Applications of Comprehensive Cancer Progression Models in the Fight against Cancer; Index. 2015 246 x 189 mm 548pp 83 b/w illus. 20 tables 978-0-521-49339-0 Hardback £85.00 / US$135.00 For all formats available, see

www.cambridge.org/9780521493390

Cambridge Series in Systems Genetics

2015 247 x 174 mm 300pp 101 b/w illus. 12 tables 978-1-107-01384-1 Hardback £69.99 / US$115.00 Publication July 2015 For all formats available, see

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Linking genotypes and phenotypes

eBooks available at www.cambridge.org/ebookstore

Edited by

Florian Markowetz and

Michael Boutros

Systems biology and networks Highlight

Models of Life Dynamics and Regulation in Biological Systems Kim Sneppen Niels Bohr Institutet, Copenhagen

Focusing on simple models, this book describes methods for studying the quantitative aspects of life through physical modelling, using E. coli and phage lambda as key examples. It encompasses fields such as quantitative molecular biology, systems biology and biophysics, providing a tool for students from both biological and physical science backgrounds. ‘Models of Life is an insight of a physicist into biological regulatory mechanisms. It provides a quantitative basis of how many of the biological systems work. Using simple logic and mathematics, Kim Sneppen, a world renowned scientist and thinker, has created a must-read for investigators in quantitative biology. The book provides a clear explanation of triumphant experiments in a lucid way with crisp figures. The brilliance of the author’s analytical mind is on display when one sees how he explains some of the exciting paradigmatic regulatory systems, beginning with the basics of molecular biology. The book is also replete with intellectually challenging problem questions for readers, making the book an excellent text for students as well.’ Sankar Adhya, National Cancer Institute, Maryland 2014 247 x 174 mm 350pp 25 b/w illus. 193 colour illus. 5 tables 165 exercises 978-1-107-06190-3 Hardback £40.00 / US$65.00 For all formats available, see

www.cambridge.org/9781107061903

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. 2011 247 x 174 mm 332pp 126 b/w illus. 978-1-107-00159-6 Hardback £54.99 / US$99.99 For all formats available, see

www.cambridge.org/9781107001596

Systems biology and networks Textbook

Systems Biology

Networks in Cell Biology

Properties of Reconstructed Networks Bernhard Ø. Palsson

Edited by Mark Buchanan Guido Caldarelli

University of California, San Diego

Paolo De Los Rios

This 2006 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. Therefore to assist both teacher and student, in an associated web site Palsson provides problem sets.

École Polytechnique Fédérale de Lausanne

‘… [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 £54.99 / US$94.99 For all formats available, see

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Consiglio Nazionale delle Ricerche (CNR), Rome

Francesco Rao University of Freiburg

and Michele Vendruscolo University of Cambridge

With contributions from leaders in both network theory and modern cell biology, this comprehensive introduction is the first book on the subject. It is a key introductory text for graduate students and researchers in physics, biology and biochemistry, presenting ideas and techniques outside the reader’s own area of specialization. ‘Network science has experienced a spectacular explosion in the past decade, influencing a wide range of fields, from computer science to sociology. Yet, nowhere is the impact of the new theoretical framework as promising as it is in cell biology – many of the difficult open questions cannot be understood without a network based approach. Networks in Cell Biology offers an excellent introduction to this frontier, at the same time capturing the current state of research. 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 2010 247 x 174 mm 280pp 73 b/w illus. 978-0-521-88273-6 Hardback £59.99 / US$99.99 For all formats available, see

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Genetics and genomics New in Paperback

Epigenomics From Chromatin Biology to Therapeutics Edited by Krishnarao Appasani

Basic Phylogenetic Combinatorics Andreas Dress Universität Bielefeld, Germany

Katharina T. Huber

GeneExpression Systems, Inc.

University of East Anglia

Leading experts from academia and both 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.

Jacobus Koolen

‘This is an excellent work, highly readable and well documented by more than a hundred scientists from academia and industry. The extensive coverage of current theory, new technologies, and disease mechanisms, all associated with epigenomics, make this book invaluable to students and researchers in a wide range of disciplines. Recommended for all academic libraries.’ Atsuo Ogura, RIKEN BioResource Center 2014 244 x 170 mm 574pp 100 b/w illus. 24 colour illus. 24 tables 978-1-107-69783-6 Paperback £45.00 / US$75.00 Also available 978-1-107-00382-8 Hardback £139.99 / US$224.99 For all formats available, see

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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. 2011 228 x 152 mm 276pp 55 b/w illus. 978-0-521-76832-0 Hardback £49.99 / US$82.99 For all formats available, see

www.cambridge.org/9780521768320

Genetics and genomics

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

Regula Rupp Eberhard-Karls-Universität Tübingen, Germany

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

Mike Steel, University of Canterbury 2010 247 x 174 mm 376pp 189 b/w illus. 80 exercises 978-0-521-75596-2 Hardback £38.99 / US$67.00 For all formats available, see

www.cambridge.org/9780521755962

Alexei J. Drummond University of Auckland

and Remco R. Bouckaert University of Auckland

“Want to construct a phylogeny, add in calibrated time points or work out the past history of an epidemic? The open source package BEAST has established itself as the industry standard for all this and more. This definitive book, explaining what is under the hood, how the user can customize extensions and most critically, a simple ‘how to’ users guide, is necessary reading for beginners and specialists alike.” Laurence D. Hurst, University of Bath, UK “…Bayesian inference has revolutionized population genetics, phylogenetics, and divergence time estimation … This book is an accessible and thorough introduction to these Bayesian procedures … includes clear guides on how to use the BEAST 2 software for performing Bayesian analyses and how to visualize the results … timely and is written by two of the leaders of the field. I highly recommend it. Jeff Thorne, North Carolina State University, USA What are the models used in phylogenetic analysis and what exactly is involved in Bayesian evolutionary analysis using Markov chain Monte Carlo (MCMC) methods? How can you choose and apply these models, which parameterisations and priors make sense and how can you diagnose Bayesian MCMC when things go wrong? These are just a few of the questions answered in this comprehensive overview of Bayesian approaches to phylogenetics. From addressing theoretical aspects of the field to providing pragmatic advice on how to prepare and perform phylogenetic analysis, this practical guide also includes coverage of the interpretation of analyses and visualisation of phylogenies. The software architecture is described and a guide to developing BEAST 2.2 extensions is provided to allow these models to be extended further. With an accompanying website (http://beast2.org/) providing example files and tutorials, this one-stop reference to applying the latest phylogenetic models in BEAST 2 will provide essential guidance for all users – from those using phylogenetic tools, to computational biologists and Bayesian statisticians. Alexei J. Drummond is Professor of Computational Biology and Principal Investigator at the Allan Wilson Centre of Molecular Ecology and Evolution. He is the lead author of the BEAST software package and has gained a reputation in the field as one of the most knowledgeable experts for Bayesian evolutionary analyses. Remco R. Bouckaert is a computer scientist with a strong background in Bayesian methods. He is the main architect of version 2 of BEAST and has been working on extensions to the BEAST software and other phylogenetics projects in Alexei Drummond’s group at the University of Auckland.

Bayesian Evolutionary Analysis with BEAST

Bayesian Evolutionary Analysis with BEAST 2

Drummond and Bouckaert

‘Networks – rather than just trees – are fast becoming the essential tool for making sense of the complexities of evolution, and conflicting signal[s] in genomic data. Phylogenetic Networks provides a long-overdue exposition of networkbased methods, their possible uses, and details on practical software. A detailed and unified treatment of the many different types of networks is complemented by a crisp synopsis of the underlying theory. Numerous example[s] and illustrations make the text easy to follow. 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’.’

9781107019652 Drummond & Bouckaert PPC C M Y K

An alternative to describing evolutionary history using phylogenetic trees, 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.

Bayesian Evolutionary Analysis with BEAST

Alexei J. Drummond and Remco R. Bouckaert

Cover illustration: three phylogenetic trees from the posterior sample of a Bayesian evolutionary analysis of Dengue virus samples. © Alexei J. Drummond.

A comprehensive overview of Bayesian approaches to phylogenetics using Markov chain Monte Carlo (MCMC) methods, offering theoretical insight, pragmatic advice and tools to develop further models. This title is a onestop reference to applying the latest phylogenetic models in BEAST 2, interpreting the analyses and extending these models further. 2015 247 x 174 mm 272pp 21 b/w illus. 70 colour illus. 9 tables 978-1-107-01965-2 Hardback £39.99 / US$64.99 Publication May 2015 For all formats available, see

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Genetics and genomics Textbook

The Phylogenetic Handbook A Practical Approach to Phylogenetic Analysis and Hypothesis Testing Second edition Edited by Philippe Lemey University of Oxford

Marco Salemi University of California, Irvine

and Anne-Mieke Vandamme Katholieke Universiteit Leuven, Belgium

With a stronger focus on hypothesis testing, elaborate practical sections and recent versions of sequence analysis and software, this edition includes six new chapters. Topics on Bayesian inference, tree topology testing and the impact of recombination on phylogenies have been added as well as a detailed section on molecular adaptation. 2009 247 x 174 mm 750pp 57 b/w illus. 18 tables 978-0-521-73071-6 Paperback £44.99 / US$69.99 For all formats available, see

www.cambridge.org/9780521730716

Methodologies for Metabolomics Experimental Strategies and Techniques Edited by Norbert W. Lutz University Aix-Marseille, France

Jonathan V. Sweedler University of Illinois, Urbana-Champaign

and Ron A. Wevers University Medical Center Nijmegen, The Netherlands

Methodologies for Metabolomics 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. 2013 253 x 177 mm 640pp 84 b/w illus. 83 colour illus. 37 tables 978-0-521-76590-9 Hardback £104.99 / US$164.99 For all formats available, see

www.cambridge.org/9780521765909

Genetics and genomics

Bacterial Genomics Genome Organization and Gene Expression Tools Aswin Sai Narain Seshasayee Tata Institute of Fundamental Research, Mumbai, India

This book presents a review of the cutting-edge literature – emphasising data analysis and interpretation – in a format that can be accessible to biologists. Simultaneously, the book provides materials to stimulate bioinformaticians and computational biologists working on cancer biology, mammalian development and epigenetics. 2015 244 x 170 mm 230pp 978-1-107-07983-0 Hardback £65.00 / US$99.00 For all formats available, see

www.cambridge.org/9781107079830

Genetic Mapping in Experimental Populations J. W. Van Ooijen Kyazma B.V., Wageningen, The Netherlands

and J. Jansen Biometris, Wageningen University and Research Centre, The Netherlands

This concise introduction to genetic mapping in diploid species teaches the theory behind map construction, explains the computations involved at each stage, and provides exercises and problem-solving tips. It will enable graduate students and researchers in the life sciences to employ methods effectively and to achieve more reliable results. 2013 247 x 174 mm 166pp 20 b/w illus. 978-1-107-01321-6 Hardback £75.00 / US$120.00 978-1-107-60103-1 Paperback £29.99 / US$48.00 For all formats available, see

www.cambridge.org/9781107013216

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Computational neuroscience Neuronal Dynamics From Single Neurons to Networks and Models of Cognition Wulfram Gerstner École Polytechnique Fédérale de Lausanne

Werner M. Kistler Richard Naud University of Ottawa

and Liam Paninski Columbia University, New York

Exploring neuron models, the neural code, decision making and learning, this textbook provides a thorough and up-to-date introduction to computational neuroscience for advanced undergraduate and beginning graduate students. With step-by-step explanations, end-of-chapter summaries and classroom-tested exercises, it is ideal for courses or for self-study. 2014 247 x 174 mm 578pp 280 b/w illus. 6 tables 80 exercises 978-1-107-06083-8 Hardback £65.00 / US$99.00 978-1-107-63519-7 Paperback £32.00 / US$50.00 For all formats available, see

www.cambridge.org/9781107060838

Brain-Computer Interfacing An Introduction Rajesh P. N. Rao University of Washington

This introduction to the field of braincomputer interfacing is designed as a textbook for upper-level undergraduate and first-year graduate courses in neural engineering or brain-computer interfacing for students from a wide range of disciplines. It can also be used as a reference by neuroscientists, computer scientists, engineers, and medical practitioners. ‘Rajesh Rao has written the perfect introduction to the exciting world of brain-computer interfaces. The book is remarkably comprehensive – not only including full descriptions of classic and current experiments but also covering essential background concepts, from the brain to Bayes and back. Brain-Computer Interfacing will be welcomed by a wide range of intelligent readers interested in understanding the first steps toward the symbiotic merger of brains and computers.’ Eberhard E. Fetz, University of Washington 2013 253 x 177 mm 337pp 130 b/w illus. 16 colour illus. 3 tables 179 exercises 978-0-521-76941-9 Hardback £50.00 / US$80.00 For all formats available, see

www.cambridge.org/9780521769419

Computational neuroscience Textbook

Principles of Computational Modelling in Neuroscience

2011 246 x 189 mm 401pp 178 b/w illus. 7 tables 978-0-521-87795-4 Hardback £49.99 / US$79.99 For all formats available, see

www.cambridge.org/9780521877954

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. ‘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.’ Gordon W. Arbuthnott, Okinawa Institute of Science and Technology

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Knowledge management and data mining Data-Intensive Computing

Mining of Massive Datasets

Architectures, Algorithms, and Applications Edited by Ian Gorton

Second edition Jure Leskovec

Pacific Northwest National Laboratory

Anand Rajaraman

and Deborah K. Gracio

Milliways Laboratories

Pacific Northwest National Laboratory

and Jeffrey David Ullman

This reference for computing professionals and researchers describes the general principles of the emerging field of data-intensive computing, along with methods for designing, managing and analyzing the big data sets of today. Applications in bioinformatics and cybersecurity illustrate these principles in practice.

Stanford University, California

2012 228 x 152 mm 297pp 82 b/w illus. 8 tables 978-0-521-19195-1 Hardback £58.00 / US$89.99 For all formats available, see

www.cambridge.org/9780521191951

Stanford University, California

Essential reading for students and practitioners, this book focuses on practical algorithms used to solve key problems in data mining, with exercises suitable for students from the advanced undergraduate level and beyond. This second edition includes new and extended coverage on social networks, machine learning and dimensionality reduction. 2014 247 x 174 mm 476pp 150 b/w illus. 210 exercises 978-1-107-07723-2 Hardback £45.00 / US$70.00 For all formats available, see

www.cambridge.org/9781107077232

Statistics

Social Media Mining An Introduction Reza Zafarani Arizona State University

Mohammad Ali Abbasi Arizona State University

and Huan Liu Arizona State University

Social Media Mining integrates social media, social network analysis, and data mining to provide a coherent platform for students, practitioners, researchers and project managers to understand the basics and potentials of social media mining. It presents fundamental concepts, emerging issues, and effective algorithms for network analysis and data mining. ‘This is an exceptionally wellconstructed book on social media that will be useful to academia and industry alike. The book covers the entire area of social network analysis in a comprehensive and understandable way.’ Charu Aggarwal, IBM T. J. Watson Research Center

Textbook

Data Mining and Analysis Fundamental Concepts and Algorithms Mohammed J. Zaki Rensselaer Polytechnic Institute, New York

and Wagner Meira, Jr Universidade Federal de Minas Gerais, Brazil

The fundamental algorithms in data mining and analysis are the basis for business intelligence and analytics, automated methods to analyze patterns, and models of data. This textbook for senior undergraduate and graduate data mining courses provides a comprehensive overview from an algorithmic perspective, integrating concepts from machine learning and statistics. 2014 253 x 177 mm 562pp 186 b/w illus. 85 tables 130 exercises 978-0-521-76633-3 Hardback £40.00 / US$65.00 For all formats available, see

www.cambridge.org/9780521766333

2014 234 x 156 mm 332pp 109 b/w illus. 20 tables 107 exercises 978-1-107-01885-3 Hardback £40.00 / US$60.00 For all formats available, see

www.cambridge.org/9781107018853

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Pattern recognition and machine learning 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. ‘This book is an exciting addition to the literature on machine learning and graphical models. What makes it unique and interesting is that it provides a unified treatment of machine learning and related fields through graphical models, a framework of growing importance and popularity. Another feature of this book lies in its smooth transition from traditional artificial intelligence to modern machine learning. The book is well-written and truly pleasant to read. I believe that it will appeal to students and researchers with or without a solid mathematical background.’ Zheng-Hua Tan, Aalborg University, Denmark 2012 246 x 189 mm 720pp 287 b/w illus. 1 table 260 exercises 978-0-521-51814-7 Hardback £54.99 / US$89.99 For all formats available, see

www.cambridge.org/9780521518147

Textbook

Machine Learning The Art and Science of Algorithms that Make Sense of Data Peter Flach University of Bristol

Machine Learning brings together all the state-of-the-art methods for making sense of data. With hundreds of worked examples and explanatory figures, the book explains the principles behind these methods in an intuitive yet precise manner and will appeal to novice and experienced readers alike. 2012 246 x 189 mm 410pp 120 colour illus. 15 tables 978-1-107-09639-4 Hardback £84.99 / US$134.99 978-1-107-42222-3 Paperback £36.99 / US$64.00 For all formats available, see

www.cambridge.org/9781107096394

Pattern recognition and machine learning

Kernel Methods and Machine Learning

Understanding Machine Learning

S. Y. Kung

From Theory to Algorithms Shai Shalev-Shwartz

Princeton University, New Jersey

Containing numerous algorithms and major theorems, this step-by-step guide covers the fundamentals of kernel-based learning theory. Including over 200 problems and real-world examples, it is an essential resource for graduate students and professionals in computer science, electrical and biomedical engineering. Solutions to problems are provided online for instructors. 2014 247 x 174 mm 572pp 136 b/w illus. 21 tables 978-1-107-02496-0 Hardback £55.00 / US$90.00 For all formats available, see

www.cambridge.org/9781107024960

Hebrew University of Jerusalem

and Shai Ben-David University of Waterloo, Ontario

Machine learning is one of the fastest growing areas of computer science, with far-reaching applications. This book explains the principles behind the automated learning approach and the considerations underlying its usage. The authors explain the ‘hows’ and ‘whys’ of machine-learning algorithms, making the field accessible to both students and practitioners. ‘This elegant book covers both rigorous theory and practical methods of machine learning. This makes it a rather unique resource, ideal for all those who want to understand how to find structure in data.’ Bernhard Schölkopf, Max Planck Institute for Intelligent Systems, Germany 2014 253 x 177 mm 409pp 47 b/w illus. 123 exercises 978-1-107-05713-5 Hardback £37.50 / US$60.00 For all formats available, see

www.cambridge.org/9781107057135

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Statistics and Mathematical Modeling A Primer on Mathematical Models in Biology Lee A. Segel

series; Appendix B. Complex numbers; Appendix C. A review of basic theory of electricity; Appendix D. Proofs of Boolean algebra rules; Appendix E. XPP files for models in this book; Bibliography; Index.

Weizmann Institute of Science, Israel

and Leah Edelstein-Keshet University of British Columbia, Vancouver

A textbook on mathematical modelling techniques for advanced undergraduate and graduate students in both biology and applied mathematics. Mathematical techniques are presented alongside powerful applications to biology, with emphasis on molecular events, excitable systems, and small protein and genetic circuits. Includes exercises, and appendices containing useful background material. Contents: List of figures; List of tables; Acknowledgments; Preface; 1. Introduction; 2. Introduction to biochemical kinetics; 3. Review of linear differential equations; 4. Introduction to nondimensionalization and scaling; 5. Qualitative behavior of simple differential equation models; 6. Developing a model from the ground up: case study of the spread of an infection; 7. Phase plane analysis; 8. Quasi steady state and enzyme-mediated biochemical kinetics; 9. Multiple sub-unit enzymes and proteins: cooperativity; 10. Dynamic behavior of neuronal membranes; 11. Excitable systems and the FitzHugh–Nagumo equations; 12. Biochemical modules; 13. Discrete networks of genes and cells; 14. For further study; 15. Extended exercises and projects; Appendix A. The Taylor approximation and Taylor

2013 247 x 174 mm 450pp 978-1-61197-249-8 Paperback £48.00 / c. US$75.00 For all formats available, see

www.cambridge.org/9781611972498

Statistics and Mathematical Modeling

Measuring and Reasoning Numerical Inference in the Sciences Fred L. Bookstein University of Washington and Universität Wien, Austria

This exploration of empirical inference in science ranges over topics as diverse as the mass extinction of the dinosaurs, Peirce’s concept of abduction, multiple regression, and the analysis of patterns in astrophysics. At its heart is a formal description of the process by which scientific measurements support convincing explanations of the world around us. 2014 234 x 156 mm 559pp 180 b/w illus. 978-1-107-02415-1 Hardback £50.00 / US$75.00 For all formats available, see

www.cambridge.org/9781107024151

Advances in Statistical Bioinformatics Models and Integrative Inference for High-Throughput Data Edited by Kim-Anh Do University of Texas, MD Anderson Cancer Center

Zhaohui Steve Qin Emory University, Atlanta

and Marina Vannucci Rice University, Houston

Within the context of genomic medicine and with a strong focus on cancer research, this book describes the integration of high-throughput bioinformatics data from multiple platforms to inform our understanding of the functional consequences of genomic alterations. This material is written for statisticians who are interested in modeling and analyzing high-throughput data. 2013 228 x 152 mm 514pp 120 b/w illus. 17 colour illus. 20 tables 978-1-107-02752-7 Hardback £80.00 / US$120.00 For all formats available, see

www.cambridge.org/9781107027527

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Statistics and Mathematical Modeling New in Paperback

Bayesian Inference for Gene Expression and Proteomics Edited by Kim-Anh Do University of Texas, 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. ‘A text that has a systematic account of Bayesian analysis in computational biology has been needed for a long time. This book is a timely publication entirely devoted to cutting-edge Bayesian methods in genomics and proteomics research and many of its contributors are leading authorities in the field. It is thus an indispensable reference for researchers who are interested in applying Bayesian techniques in their own biological research.’ Ping Ma, Department of Statistics and Institute for Genomic Biology, University of Illinois, Urbana-Champaign 2012 228 x 152 mm 456pp 22 tables 978-1-107-63698-9 Paperback £34.99 / US$59.99 Also available 978-0-521-86092-5 Hardback £69.99 / US$124.99 For all formats available, see

www.cambridge.org/9781107636989

New in Paperback

Large-Scale Inference Empirical Bayes Methods for Estimation, Testing, and Prediction Bradley Efron Stanford University, California

Modern scientific technology (e.g. microarrays, fMRI machines) produces data in vast quantities. Bradley Efron explains the empirical Bayes methods that help make sense of a new statistical world. This is essential reading for professional statisticians and graduate students wishing to use and understand important new techniques like false discovery rates. ‘In the last decade, Efron has played a leading role in laying down the foundations of large-scale inference, not only in bringing back and developing old ideas, but also linking them with more recent developments, including the theory of false discovery rates and Bayes methods. We are indebted to him for this timely, readable and highly informative monograph, a book he is uniquely qualified to write. It is a synthesis of many of Efron’s own contributions over the last decade with that of closely related material, together with some connecting theory, valuable comments, and challenges for the future. His avowed aim is ‘not to have the last word’ but to help us deal ‘with the burgeoning statistical problems of the twenty-first century’. He has succeeded admirably.’ Terry Speed, International Statistical Review Institute of Mathematical Statistics Monographs, 1

2012 228 x 152 mm 276pp 65 b/w illus. 10 colour illus. 105 exercises 978-1-107-61967-8 Paperback £26.99 / US$44.99 For all formats available, see

www.cambridge.org/9781107619678

Statistics and Mathematical Modeling

Modeling Count Data Joseph M. Hilbe Arizona State University

Written for researchers with little or no background in advanced statistics, this book provides guidelines and fully worked examples of how to select, construct, interpret and evaluate the full range of count models. Stata, R, and SAS code enable readers in a variety of disciplines to adapt models for their own purposes. ‘This is a first-rate introductory book for modeling count data, a key challenge in applied statistics. Hilbe’s experience and affability shine in the text. His careful emphasis on establishing the defensibility of models, for example, in the face of overdispersion, will greatly benefit the beginning statistician. His clear informal explanations of important and complicated statistical principles are invaluable.’ Andrew Robinson, University of Melbourne

PROSE Award for Mathematics 2015 – Honourable mention 2014 234 x 177 mm 300pp 10 b/w illus. 81 tables 978-1-107-02833-3 Hardback £60.00 / US$99.00 978-1-107-61125-2 Paperback £23.99 / US$37.99 For all formats available, see

www.cambridge.org/9781107028333

Highlight

Causal Inference for Statistics, Social, and Biomedical Sciences An Introduction Guido W. Imbens Stanford University, California

and Donald B. Rubin Harvard University, Massachusetts

In this groundbreaking text, two worldrenowned experts present statistical methods for studying causal effects: how can we learn about the expected effect of an intervention or a change in environment? The authors discuss how we can assess such effects in simple randomized experiments, where the researcher controls the treatments, and in observational studies, where the subjects themselves may affect which treatment they receive. Advance praise: ‘This book offers a definitive treatment of causality using the potential outcomes approach. Both theoreticians and applied researchers will find this an indispensable volume for guidance and reference.’ Hal Varian, Chief Economist, Google and Emeritus Professor, University of California, Berkeley 2015 253 x 177 mm 592pp 18 b/w illus. 97 tables 978-0-521-88588-1 Hardback £40.00 / US$60.00 Publication May 2015 For all formats available, see

www.cambridge.org/9780521885881

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Statistics and Mathematical Modeling

Case-Control Studies Ruth H. Keogh London School of Hygiene and Tropical Medicine

and D. R. Cox University of Oxford

The case-control approach is a powerful method for investigating factors that may explain a particular event and is extensively used in epidemiology. With a particular focus on statistical analysis, this book is ideal for applied and theoretical statisticians wanting an up-to-date introduction to case-control studies. ‘This book will rapidly become the bible for researchers using case control studies. It covers essentially all aspects of such designs and their application.’ David J. Hand, Imperial College London Institute of Mathematical Statistics Monographs, 4

2014 228 x 152 mm 293pp 30 b/w illus. 20 tables 978-1-107-01956-0 Hardback £50.00 / US$80.00 For all formats available, see

www.cambridge.org/9781107019560

Textbook

Analysis of Multivariate and HighDimensional Data Inge Koch University of Adelaide

‘Big data’ poses challenges that require both classical multivariate methods and modern machine-learning techniques. This coherent treatment integrates theory with data analysis, visualisation and interpretation of the analysis. Problems, data sets and Matlab code complete the package. Suitable for master’s/graduate students in statistics and working scientists in data-rich disciplines. Cambridge Series in Statistical and Probabilistic Mathematics, 32

2014 253 x 177 mm 526pp 5 b/w illus. 98 colour illus. 76 tables 138 exercises 978-0-521-88793-9 Hardback £55.00 / US$89.00 For all formats available, see

www.cambridge.org/9780521887939

Statistics and Mathematical Modeling

Handbook of Functional MRI Data Analysis

Genomic Clinical Trials and Predictive Medicine

Russell A. Poldrack

Richard M. Simon

University of Texas, Austin

National Cancer Institute

Jeanette A. Mumford

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.

University of Texas, Austin

and Thomas E. Nichols University of Warwick

This book provides a comprehensive and practical introduction to the methods used for fMRI data analysis. Using minimal jargon, it explains the concepts behind processing fMRI data, focusing on the techniques that are most commonly used in the field. Readers will obtain a deep and effective knowledge of how to employ fMRI analysis to ask scientific questions and become more sophisticated users of fMRI analysis software. ‘Wow! Very often in neuroimaging a title has little relationship to what follows. That is clearly not the case with the Handbook of Functional MRI Data Analysis by Poldrack, Mumford, and Nichols. This relatively slender volume is all that a handbook should be: it is crafted by true experts in the field, it is structured so that a newcomer can understand a method’s strengths and weaknesses, but it also contains meaty information useful to experts. The book touches on all of the major analytical approaches current in the field and, while I don’t agree with every choice the authors make, their advice is always well-conceived. This will be a standard reference on every neuroimager’s shelf.’

Practical Guides to Biostatistics and Epidemiology

2013 247 x 174 mm 153pp 11 b/w illus. 3 tables 978-1-107-00880-9 Hardback £74.99 / US$114.99 978-1-107-40135-8 Paperback £29.99 / US$44.99 For all formats available, see

www.cambridge.org/9781107008809

Steven Petersen, Washington University, St Louis 2011 253 x 215 mm 238pp 96 b/w illus. 5 tables 978-0-521-51766-9 Hardback £54.99 / US$94.99 For all formats available, see

www.cambridge.org/9780521517669

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Statistics and Mathematical Modeling

Integrating Omics Data George C. Tseng University of Pittsburgh

Debashis Ghosh Pennsylvania State University

and Xianghong Jasmine Zhou University of Southern California

This book provides comprehensive coverage of information integration of omics, experimental data, and databases. It introduces state-of-the-art methods developed by leaders in the field to handle information integration problems of omics data. Popular technologies include microarray, nextgeneration sequencing, and proteomic experiments. 2015 228 x 152 mm 488pp 147 b/w illus. 23 colour illus. 31 tables 978-1-107-06911-4 Hardback £80.00 / US$125.00 Publication September 2015 For all formats available, see

www.cambridge.org/9781107069114

Core Statistics Simon Wood University of Bath

Core Statistics is a compact starter course on the fundamentals of inference for parametric statistical models, including both theory and practical numerical computation. It delivers the theory and tools that a beginning graduate student, or any quantitative scientist, needs to make informed use of powerful statistical methods. ‘The author keeps this book concise by focusing entirely on topics that are most relevant for scientific modeling via maximum likelihood and Bayesian inference. This makes it an ideal text and handy reference for any mathliterate scientist who wants to learn how to build sophisticated parametric models and fit them to data using modern computational approaches. I will be recommending this wellwritten book to my collaborators.’ Murali Haran, Pennsylvania State University Institute of Mathematical Statistics Textbooks, 6

2015 228 x 152 mm 258pp 43 b/w illus. 2 tables 51 exercises 978-1-107-07105-6 Hardback £60.00 / US$99.00 978-1-107-41504-1 Paperback £24.99 / US$39.99 For all formats available, see

www.cambridge.org/9781107071056

Also of interest Fred Sanger – Double Nobel Laureate A Biography George G. Brownlee University of Oxford

Foreword by Edwin Southern University of Oxford

Drawing, in part, on a rare interview by the author, this is the first full biography of Fred Sanger to be published. Brownlee highlights the remarkable extent of Sanger’s scientific achievements, providing a real portrait of the man behind them and considering his continuing legacy as ‘the father of genomics’. ‘Fred Sanger’s innovation and achievements enabled us to read the code of life. His breakthroughs transformed science, medicine, industry and society, and continue to open our eyes to a new knowledge and understanding of how life works … This book provides a rare opportunity to see a glimpse of a remarkable man who changed the world.’ David Bentley, Vice-President and chief scientist, Illumina Inc. 2014 228 x 152 mm 223pp 94 b/w illus. 8 colour illus. 978-1-107-08334-9 Hardback £27.99 / US$39.99 For all formats available, see

29 New in Paperback

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

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 2014 216 x 140 mm 194pp 7 b/w illus. 978-1-107-52422-4 Paperback £9.99 / US$15.99 Also available 978-1-107-02058-0 Hardback £19.99 / US$29.99 For all formats available, see

www.cambridge.org/9781107524224

www.cambridge.org/9781107083349

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Also of interest

The Systems View of Life A Unifying Vision Fritjof Capra Lawrence Berkeley National Laboratory, Berkeley, California

and Pier Luigi Luisi Università degli Studi Roma Tre

Taking a broad sweep through history and across scientific disciplines, this volume integrates the ideas, models, and theories underlying the systems view of life into a single coherent framework. Life’s biological, cognitive, social, and ecological dimensions are presented and its philosophical, spiritual, and political implications discussed. ‘A magisterial study of the scientific basis for an integrated worldview grounded in the wholeness that generations of one-eyed reductionists could not see. The authors succeed brilliantly!’ David W. Orr, Oberlin College 2014 247 x 174 mm 510pp 81 b/w illus. 978-1-107-01136-6 Hardback £24.99 / US$40.00 For all formats available, see

www.cambridge.org/9781107011366

Human Evolution Genes, Genealogies and Phylogenies Graeme Finlay University of Auckland

In the past decade the human genome project and genetic sequencing of many other species have provided unambiguous genetic markers that establish our evolutionary relationships with other mammals. Human Evolution: Genes, Genealogies and Phylogenies recognises and explains these identifiable, rare and complex markers. ‘In this book Dr Finlay takes several examples to illustrate our evolutionary tree at the molecular and genomic level. Step by step he provides a wealth of cumulative evidence that demonstrates how our genomes are related to other primates and to our more distant biological relatives. The evidence is compelling and shows the elegant ways in which we are connected to the rest of biology. Nonetheless we are more than just intelligent apes, and Finlay is careful to emphasise that our genomes are only part of the story of what it means to be human and that we have also been shaped by historical, cultural and religious factors that may not affect our physiology and anatomy but define us a human beings.’ Keith R. Fox, University of Southampton 2013 247 x 174 mm 368pp 101 b/w illus. 11 tables 978-1-107-04012-0 Hardback £45.00 / US$75.00 For all formats available, see

www.cambridge.org/9781107040120

Also of interest

Introduction to Cancer Biology

Methods of Molecular Analysis in the Life Sciences

Robin Hesketh

Andreas Hofmann

Textbook

University of Cambridge

Griffith University, Queensland

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.

With contributions by Anne Simon

‘Robin Hesketh has produced a remarkable introduction to cancer biology which covers all of the key areas of current knowledge and brings them up to date to current research concepts and developments remarkably. He writes in an accessible way that will be valuable for students fresh to biology but also produces a book that will be very useful to experienced biologists and physicians who want to have to hand a broad overview of this fast moving and diverse field … The structure of the book is clear and informative and encompasses critically important biological knowledge from the level of the cell to population studies in epidemiology … it is very challenging to introduce a book which is really useful both for new students and established practitioners. Robin Hesketh has succeeded remarkably well in doing so.’ Peter Selby, Director, Leeds Institute of Molecular Medicine 2012 246 x 189 mm 351pp 130 b/w illus. 38 colour illus. 978-1-107-01398-8 Hardback £79.99 / US$124.99 978-1-107-60148-2 Paperback £31.99 / US$54.99 For all formats available, see

www.cambridge.org/9781107013988

Université Lyon I

Tanja Grkovic Griffith University, Queensland

and Malcolm Jones Queensland Institute of Medical Research

This concise text presents the fundamental principles of the most popular and contemporary analytical methods for studying the properties of biological molecules and their interactions. Advanced undergraduates and graduates will find this a valuable source to enhance their understanding of these cutting-edge techniques, used in research across the life sciences. ‘The book by Hofmann et al. is an invaluable tool for students (and even more advanced practitioners) in the field of experimental biochemistry and biophysics. It covers in considerable detail a variety of methods and provides very clear explanation on how they can be applied and what can be learned during the process. The book is very well illustrated and uses relatively simple language, although never oversimplified. Its particular strength is in covering a number of methods in a single volume, making it a great reference.’ Alexander Wlodawer, Macromolecular Crystallography Laboratory, National Cancer Institute, Maryland 2014 247 x 174 mm 250pp 12 b/w illus. 77 colour illus. 22 tables 978-1-107-04470-8 Hardback £75.00 / US$120.00 978-1-107-62276-0 Paperback £29.99 / US$50.00 For all formats available, see

www.cambridge.org/9781107044708

Also of interest

Privacy, Big Data, and the Public Good Frameworks for Engagement Edited by Julia Lane American Institutes for Research, Washington DC

Victoria Stodden

if we continue to rely on the tools that we employ today to protect it. [This book] represents a useful and approachable introduction to these important issues.’ Science

Stefan Bender

2014 228 x 152 mm 344pp 4 b/w illus. 978-1-107-06735-6 Hardback £55.00 / US$85.00

Institute for Employment Research of the German Federal Employment Agency

978-1-107-63768-9 Paperback £19.99 / US$29.99

and Helen Nissenbaum

For all formats available, see

Columbia University, New York

New York University

The book discusses access to big data for city, state, and federal government agencies and legal, social science, statistical, and technical communities interested in enabling research on big data. The authors’ goal is to move the conversation to a vision of what frameworks should and could guide data access. “Big data’ – the collection, aggregation or federation, and analysis of vast amounts of increasingly granular data – present[s] serious challenges not only to personal privacy but also to the tools we use to protect it. Privacy, Big Data, and the Public Good focuses valuable attention on two of these tools: notice and consent, and de-identification – the process of preventing a person’s identity from being linked to specific data. [It] presents a collection of essays from a variety of perspectives, in chapters by some of the heavy hitters in the privacy debate, who make a convincing case that the current framework for dealing with consumer privacy does not adequately address issues posed by big data … As society becomes more ‘datafied’ – a term coined to describe the digital quantification of our existence – our privacy is ever more at risk, especially

www.cambridge.org/9781107067356

Textbook

Membrane Structural Biology With Biochemical and Biophysical Foundations Second edition Mary Luckey San Francisco State University

Provides a strong foundation and comprehensive overview for students and an invaluable synthesis of cuttingedge research for working scientists. This edition is expanded to include and make accessible all the latest developments and topics, with more than twenty new high resolution structures. Links between membrane research and human health are emphasised throughout. 2014 279 x 215 mm 423pp 184 b/w illus. 610 colour illus. 16 tables 978-1-107-03063-3 Hardback £45.00 / US$85.00 For all formats available, see

www.cambridge.org/9781107030633

Also of interest

Molecular Communication

Python for Scientists John M. Stewart University of Cambridge

Tadashi Nakano University of Osaka, Japan

Andrew W. Eckford York University, Toronto

and Tokuko Haraguchi National Institute of Information and Communications Technology (NICT), Hyogo, Japan

This detailed, accessible guide, by pioneers in the field, provides an introduction to the relevant aspects of biology and information theory, and to the practical applications of molecular communication. Ideal for graduate students, researchers and practitioners looking to get up to speed on the current practice in this growing field.

Python is a free and easy-to-use software tool that offers a significant alternative to proprietary packages such as MATLAB and Mathematica. This book explains Python from scratch, covering everything students and researchers need to get up and running. No previous knowledge of the software is required. 2014 247 x 174 mm 230pp 36 b/w illus. 978-1-107-06139-2 Hardback £65.00 / US$100.00 978-1-107-68642-7 Paperback £27.95 / US$40.00 For all formats available, see

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‘… hits the spot … clearly written, relatively easy to read, yet very comprehensive. It gives an overview of potential solutions, supported by success stories, and explains the mechanisms of operations from the very outset. It is definitely a recommended position for those who start with nanoscale communication concepts in biological systems.’ IEEE Communications Magazine 2013 247 x 174 mm 192pp 59 b/w illus. 4 tables 978-1-107-02308-6 Hardback £60.00 / US$99.00 For all formats available, see

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Bioethics 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 233pp 9 b/w illus. 4 tables 978-0-521-88591-1 Hardback £79.99 / US$124.99 978-0-521-71366-5 Paperback £29.99 / US$49.99 For all formats available, see

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Bioethics An Introduction Marianne Talbot University of Oxford

This accessible introduction clearly explains bioethical issues and their philosophical foundations to science students, providing them with the confidence needed to debate important issues in the ethics of biotechnology. Written informally, including over 200 activities, detailed case studies and explanatory podcasts, it encourages students to formulate and evaluate their own arguments. ‘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 2012 246 x 189 mm 478pp 54 b/w illus. 1 table 233 exercises 978-0-521-88833-2 Hardback £69.99 / US$104.99 978-0-521-71459-4 Paperback £34.99 / US$59.99 For all formats available, see

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Professional development Reporting Research A Biologist’s Guide to Articles, Talks, and Posters R. S. Clymo Queen Mary, University of London

Want to learn how to present your research successfully? This concise guide offers step-by-step advice to help you write scientific articles, prepare posters and talks, and develop a critical attitude towards your own work as well as that of your colleagues. A must-read for graduates and postdoctoral scholars in biology. 2014 228 x 152 mm 347pp 28 b/w illus. 28 tables 978-1-107-05389-2 Hardback £60.00 / US$95.00 978-1-107-64046-7 Paperback £24.99 / US$39.99 For all formats available, see

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Scientific Method in Brief Hugh G. Gauch, Jr Cornell University, New York

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. ‘A welcome, and well-informed, introduction for budding scientists to the general principles undergirding the rationality of science. The book draws powerful attention to the fact that future scientific advance itself depends on a proper understanding of scientific method.’ Roger Trigg, Emeritus Professor of Philosophy, University of Warwick, Senior Research Fellow, University of Oxford, and founding chair of the British Philosophical Association 2012 228 x 152 mm 303pp 37 b/w illus. 3 tables 978-1-107-66672-6 Paperback £29.99 / US$44.99 For all formats available, see

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Professional development Textbook

How to Prepare a Scientific Doctoral Dissertation Based on Research Articles Björn Gustavii Lund University Hospital, Sweden

The article-based thesis is becoming increasingly common, especially in the ‘hard’ sciences such as biology, medicine and technology. Detailing examples of good versus bad practice, this concise, easy-to-read guide shows the PhD student how to prepare a thesis in this format. 2012 228 x 152 mm 101pp 40 b/w illus. 2 tables 978-1-107-66904-8 Paperback £14.99 / US$24.99 For all formats available, see

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How to Write and Illustrate a Scientific Paper Second edition Björn Gustavii Lund University Hospital, 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 2008 228 x 152 mm 180pp 978-0-521-87890-6 Hardback £59.99 / US$109.99 978-0-521-70393-2 Paperback £16.99 / US$29.99 For all formats available, see

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Professional development

Funding your Career in Science

Developing a Talent for Science

From Research Idea to Personal Grant Ritsert C. Jansen

Ritsert C. Jansen

Rijksuniversiteit Groningen, The Netherlands

How can you get the funding to establish or consolidate a career in science? This concise guide offers step-by-step advice, real-life stories and practical exercises to help you prepare effective career grant applications and optimise your funding opportunities. A must-read for students, postdocs, professors, and anyone else serious about science. ‘This is a well-written text for the purposes of enlightening the readership on proposal writing. I highly recommend it for use by those in the early stages of seeking funding for their careers in science and engineering.’ IEEE Pulse 2013 228 x 152 mm 216pp 15 b/w illus. 978-1-107-04006-9 Hardback £45.00 / US$75.00

Rijksuniversiteit Groningen, The Netherlands

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 £59.99 / US$104.99 978-0-521-14961-7 Paperback £16.99 / US$29.99 For all formats available, see

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978-1-107-62417-7 Paperback £16.99 / US$27.99 For all formats available, see

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Professional development

Successful Scientific Writing A Step-by-Step Guide for the Biological and Medical Sciences Fourth edition Janice R. Matthews Scientific Editing Services

and Robert W. Matthews University of Georgia

The new edition of this best-selling guide has been thoroughly updated for today’s digital world, covering all aspects of the writing process and now including extensive coverage of ethical issues, including plagiarism. It offers a rich blend of practical advice, abundant examples from actual manuscripts, and hands-on exercises. Review of previous edition: ‘… does not disappoint. It is everything a ‘how to’ book needs to be, stuffed with plain common sense and sprinkled with useful tips.’ The Biologist 2014 228 x 152 mm 304pp 37 b/w illus. 31 tables 30 exercises 978-1-107-69193-3 Paperback £24.99 / US$39.99 For all formats available, see

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Successful Grant Proposals in Science, Technology, and Medicine A Guide to Writing the Narrative Sandra Oster Oster-Edits, Oregon

and Paul Cordo Oregon Health Sciences University

A practical guide to writing effective narrative sections for scientific grant applications, this book is designed to enable you to successfully acquire research funding. The authors draw on real-life examples from more than twenty years of research, covering the content, organisation, phrasing, and scientific argumentation of narratives. 2015 228 x 152 mm 387pp 6 b/w illus. 20 tables 978-1-107-03809-7 Hardback £60.00 / US$90.00 978-1-107-65930-8 Paperback £29.99 / US$45.00 For all formats available, see

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