Bayesian Phylogenetics

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Bayesian Phylogenetics

Author : Ming-Hui Chen
Publisher : CRC Press
ISBN 13 : 1466500794
Total Pages : 398 pages
Book Rating : 4.4/5 (665 download)

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Book Synopsis Bayesian Phylogenetics by : Ming-Hui Chen

Download or read book Bayesian Phylogenetics written by Ming-Hui Chen and published by CRC Press. This book was released on 2014-05-27 with total page 398 pages. Available in PDF, EPUB and Kindle. Book excerpt: Offering a rich diversity of models, Bayesian phylogenetics allows evolutionary biologists, systematists, ecologists, and epidemiologists to obtain answers to very detailed phylogenetic questions. Suitable for graduate-level researchers in statistics and biology, Bayesian Phylogenetics: Methods, Algorithms, and Applications presents a snapshot of current trends in Bayesian phylogenetic research. Encouraging interdisciplinary research, this book introduces state-of-the-art phylogenetics to the Bayesian statistical community and, likewise, presents state-of-the-art Bayesian statistics to the phylogenetics community. The book emphasizes model selection, reflecting recent interest in accurately estimating marginal likelihoods. It also discusses new approaches to improve mixing in Bayesian phylogenetic analyses in which the tree topology varies. In addition, the book covers divergence time estimation, biologically realistic models, and the burgeoning interface between phylogenetics and population genetics.

Bayesian Phylogenetics

Author : Ming-Hui Chen
Publisher : CRC Press
ISBN 13 : 1466500824
Total Pages : 391 pages
Book Rating : 4.4/5 (665 download)

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Book Synopsis Bayesian Phylogenetics by : Ming-Hui Chen

Download or read book Bayesian Phylogenetics written by Ming-Hui Chen and published by CRC Press. This book was released on 2014-05-27 with total page 391 pages. Available in PDF, EPUB and Kindle. Book excerpt: Offering a rich diversity of models, Bayesian phylogenetics allows evolutionary biologists, systematists, ecologists, and epidemiologists to obtain answers to very detailed phylogenetic questions. Suitable for graduate-level researchers in statistics and biology, Bayesian Phylogenetics: Methods, Algorithms, and Applications presents a snapshot of c

Bayesian Evolutionary Analysis with BEAST

Author : Alexei J. Drummond
Publisher : Cambridge University Press
ISBN 13 : 1316298345
Total Pages : 263 pages
Book Rating : 4.3/5 (162 download)

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Book Synopsis Bayesian Evolutionary Analysis with BEAST by : Alexei J. Drummond

Download or read book Bayesian Evolutionary Analysis with BEAST written by Alexei J. Drummond and published by Cambridge University Press. This book was released on 2015-08-06 with total page 263 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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. This practical guide: • Addresses the theoretical aspects of the field • Advises on how to prepare and perform phylogenetic analysis • Helps with interpreting analyses and visualisation of phylogenies • Describes the software architecture • Helps developing BEAST 2.2 extensions to allow these models to be extended further. With an accompanying website providing example files and tutorials (http://beast2.org/), 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.

Analysis of Phylogenetics and Evolution with R

Author : Emmanuel Paradis
Publisher : Springer Science & Business Media
ISBN 13 : 0387351000
Total Pages : 221 pages
Book Rating : 4.3/5 (873 download)

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Book Synopsis Analysis of Phylogenetics and Evolution with R by : Emmanuel Paradis

Download or read book Analysis of Phylogenetics and Evolution with R written by Emmanuel Paradis and published by Springer Science & Business Media. This book was released on 2006-11-25 with total page 221 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book integrates a wide variety of data analysis methods into a single and flexible interface: the R language. The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters.

The Phylogenetic Handbook

Author : Marco Salemi
Publisher : Cambridge University Press
ISBN 13 : 0521877105
Total Pages : 750 pages
Book Rating : 4.5/5 (218 download)

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Book Synopsis The Phylogenetic Handbook by : Marco Salemi

Download or read book The Phylogenetic Handbook written by Marco Salemi and published by Cambridge University Press. This book was released on 2009-03-26 with total page 750 pages. Available in PDF, EPUB and Kindle. Book excerpt: A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.

Phylogenetics

Author : E. O. Wiley
Publisher : John Wiley & Sons
ISBN 13 : 1118017870
Total Pages : 444 pages
Book Rating : 4.1/5 (18 download)

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Book Synopsis Phylogenetics by : E. O. Wiley

Download or read book Phylogenetics written by E. O. Wiley and published by John Wiley & Sons. This book was released on 2011-10-11 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: The long-awaited revision of the industry standard on phylogenetics Since the publication of the first edition of this landmark volume more than twenty-five years ago, phylogenetic systematics has taken its place as the dominant paradigm of systematic biology. It has profoundly influenced the way scientists study evolution, and has seen many theoretical and technical advances as the field has continued to grow. It goes almost without saying that the next twenty-five years of phylogenetic research will prove as fascinating as the first, with many exciting developments yet to come. This new edition of Phylogenetics captures the very essence of this rapidly evolving discipline. Written for the practicing systematist and phylogeneticist, it addresses both the philosophical and technical issues of the field, as well as surveys general practices in taxonomy. Major sections of the book deal with the nature of species and higher taxa, homology and characters, trees and tree graphs, and biogeography—the purpose being to develop biologically relevant species, character, tree, and biogeographic concepts that can be applied fruitfully to phylogenetics. The book then turns its focus to phylogenetic trees, including an in-depth guide to tree-building algorithms. Additional coverage includes: Parsimony and parsimony analysis Parametric phylogenetics including maximum likelihood and Bayesian approaches Phylogenetic classification Critiques of evolutionary taxonomy, phenetics, and transformed cladistics Specimen selection, field collecting, and curating Systematic publication and the rules of nomenclature Providing a thorough synthesis of the field, this important update to Phylogenetics is essential for students and researchers in the areas of evolutionary biology, molecular evolution, genetics and evolutionary genetics, paleontology, physical anthropology, and zoology.

The Handbook of Historical Linguistics, Volume II

Author : Richard D. Janda
Publisher : John Wiley & Sons
ISBN 13 : 111873226X
Total Pages : 705 pages
Book Rating : 4.1/5 (187 download)

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Book Synopsis The Handbook of Historical Linguistics, Volume II by : Richard D. Janda

Download or read book The Handbook of Historical Linguistics, Volume II written by Richard D. Janda and published by John Wiley & Sons. This book was released on 2020-09-15 with total page 705 pages. Available in PDF, EPUB and Kindle. Book excerpt: An entirely new follow-up volume providing a detailed account of numerous additional issues, methods, and results that characterize current work in historical linguistics. This brand-new, second volume of The Handbook of Historical Linguistics is a complement to the well-established first volume first published in 2003. It includes extended content allowing uniquely comprehensive coverage of the study of language(s) over time. Though it adds fresh perspectives on several topics previously treated in the first volume, this Handbook focuses on extensions of diachronic linguistics beyond those key issues. This Handbook provides readers with studies of language change whose perspectives range from comparisons of large open vs. small closed corpora, via creolistics and linguistic contact in general, to obsolescence and endangerment of languages. Written by leading scholars in their respective fields, new chapters are offered on matters such as the origin of language, evidence from language for reconstructing human prehistory, invocations of language present in studies of language past, benefits of linguistic fieldwork for historical investigation, ways in which not only biological evolution but also field biology can serve as heuristics for research into the rise and spread of linguistic innovations, and more. Moreover, it: offers novel and broadened content complementing the earlier volume so as to provide the fullest available overview of a wholly engrossing field includes 23 all-new contributed chapters, treating some familiar themes from fresh perspectives but mostly covering entirely new topics features expanded discussion of material from language families other than Indo-European provides a multiplicity of views from numerous specialists in linguistic diachrony. The Handbook of Historical Linguistics, Volume II is an ideal book for undergraduate and graduate students in linguistics, researchers and professional linguists, as well as all those interested in the history of particular languages and the history of language more generally.

Molecular Evolution

Author : Ziheng Yang
Publisher : Oxford University Press
ISBN 13 : 0199602603
Total Pages : 509 pages
Book Rating : 4.1/5 (996 download)

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Book Synopsis Molecular Evolution by : Ziheng Yang

Download or read book Molecular Evolution written by Ziheng Yang and published by Oxford University Press. This book was released on 2014 with total page 509 pages. Available in PDF, EPUB and Kindle. Book excerpt: Studies of evolution at the molecular level have experienced phenomenal growth in the last few decades, due to rapid accumulation of genetic sequence data, improved computer hardware and software, and the development of sophisticated analytical methods. The flood of genomic data has generated an acute need for powerful statistical methods and efficient computational algorithms to enable their effective analysis and interpretation. Molecular Evolution: a statistical approach presents and explains modern statistical methods and computational algorithms for the comparative analysis of genetic sequence data in the fields of molecular evolution, molecular phylogenetics, statistical phylogeography, and comparative genomics. Written by an expert in the field, the book emphasizes conceptual understanding rather than mathematical proofs. The text is enlivened with numerous examples of real data analysis and numerical calculations to illustrate the theory, in addition to the working problems at the end of each chapter. The coverage of maximum likelihood and Bayesian methods are in particular up-to-date, comprehensive, and authoritative. This advanced textbook is aimed at graduate level students and professional researchers (both empiricists and theoreticians) in the fields of bioinformatics and computational biology, statistical genomics, evolutionary biology, molecular systematics, and population genetics. It will also be of relevance and use to a wider audience of applied statisticians, mathematicians, and computer scientists working in computational biology.

Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology

Author : László Zsolt Garamszegi
Publisher : Springer
ISBN 13 : 3662435500
Total Pages : 553 pages
Book Rating : 4.6/5 (624 download)

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Book Synopsis Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology by : László Zsolt Garamszegi

Download or read book Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology written by László Zsolt Garamszegi and published by Springer. This book was released on 2014-07-29 with total page 553 pages. Available in PDF, EPUB and Kindle. Book excerpt: Phylogenetic comparative approaches are powerful analytical tools for making evolutionary inferences from interspecific data and phylogenies. The phylogenetic toolkit available to evolutionary biologists is currently growing at an incredible speed, but most methodological papers are published in the specialized statistical literature and many are incomprehensible for the user community. This textbook provides an overview of several newly developed phylogenetic comparative methods that allow to investigate a broad array of questions on how phenotypic characters evolve along the branches of phylogeny and how such mechanisms shape complex animal communities and interspecific interactions. The individual chapters were written by the leading experts in the field and using a language that is accessible for practicing evolutionary biologists. The authors carefully explain the philosophy behind different methodologies and provide pointers – mostly using a dynamically developing online interface – on how these methods can be implemented in practice. These “conceptual” and “practical” materials are essential for expanding the qualification of both students and scientists, but also offer a valuable resource for educators. Another value of the book are the accompanying online resources (available at: http://www.mpcm-evolution.com), where the authors post and permanently update practical materials to help embed methods into practice.

Inferring Phylogenies

Author : Joseph Felsenstein
Publisher : Sinauer Associates Incorporated
ISBN 13 : 9780878931774
Total Pages : 664 pages
Book Rating : 4.9/5 (317 download)

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Book Synopsis Inferring Phylogenies by : Joseph Felsenstein

Download or read book Inferring Phylogenies written by Joseph Felsenstein and published by Sinauer Associates Incorporated. This book was released on 2004-01 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt: Phylogenies, or evolutionary trees, are the basic structures necessary to think about and analyze differences between species. Statistical, computational, and algorithmic work in this field has been ongoing for four decades now, and there have been great advances in understanding. Yet no book has summarized this work. Inferring Phylogenies does just that in a single, compact volume. Phylogenies are inferred with various kinds of data. This book concentrates on some of the central ones: discretely coded characters, molecular sequences, gene frequencies, and quantitative traits. Also covered are restriction sites, RAPDs, and microsatellites.

Handbook of Statistical Genomics

Author : David J. Balding
Publisher : John Wiley & Sons
ISBN 13 : 1119429250
Total Pages : 1740 pages
Book Rating : 4.1/5 (194 download)

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Book Synopsis Handbook of Statistical Genomics by : David J. Balding

Download or read book Handbook of Statistical Genomics written by David J. Balding and published by John Wiley & Sons. This book was released on 2019-07-09 with total page 1740 pages. Available in PDF, EPUB and Kindle. Book excerpt: A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.

Handbook of Evolutionary Research in Archaeology

Author : Anna Marie Prentiss
Publisher : Springer
ISBN 13 : 3030111172
Total Pages : 437 pages
Book Rating : 4.0/5 (31 download)

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Book Synopsis Handbook of Evolutionary Research in Archaeology by : Anna Marie Prentiss

Download or read book Handbook of Evolutionary Research in Archaeology written by Anna Marie Prentiss and published by Springer. This book was released on 2019-06-03 with total page 437 pages. Available in PDF, EPUB and Kindle. Book excerpt: Evolutionary Research in Archaeology seeks to provide a comprehensive overview of contemporary evolutionary research in archaeology. The book will provide a single source for introduction and overview of basic and advanced evolutionary concepts and research programs in archaeology. Content will be organized around four areas of critical research including microevolutionary and macroevolutionary process, human ecology studies (evolutionary ecology, demography, and niche construction), and evolutionary cognitive archaeology. Authors of individual chapters will address theoretical foundations, history of research, contemporary contributions and debates, and implications for the future for their respective topics. As appropriate, authors present or discuss short empirical case studies to illustrate key arguments.

Frontiers of Statistical Decision Making and Bayesian Analysis

Author : Ming-Hui Chen
Publisher : Springer Science & Business Media
ISBN 13 : 1441969446
Total Pages : 631 pages
Book Rating : 4.4/5 (419 download)

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Book Synopsis Frontiers of Statistical Decision Making and Bayesian Analysis by : Ming-Hui Chen

Download or read book Frontiers of Statistical Decision Making and Bayesian Analysis written by Ming-Hui Chen and published by Springer Science & Business Media. This book was released on 2010-07-24 with total page 631 pages. Available in PDF, EPUB and Kindle. Book excerpt: Research in Bayesian analysis and statistical decision theory is rapidly expanding and diversifying, making it increasingly more difficult for any single researcher to stay up to date on all current research frontiers. This book provides a review of current research challenges and opportunities. While the book can not exhaustively cover all current research areas, it does include some exemplary discussion of most research frontiers. Topics include objective Bayesian inference, shrinkage estimation and other decision based estimation, model selection and testing, nonparametric Bayes, the interface of Bayesian and frequentist inference, data mining and machine learning, methods for categorical and spatio-temporal data analysis and posterior simulation methods. Several major application areas are covered: computer models, Bayesian clinical trial design, epidemiology, phylogenetics, bioinformatics, climate modeling and applications in political science, finance and marketing. As a review of current research in Bayesian analysis the book presents a balance between theory and applications. The lack of a clear demarcation between theoretical and applied research is a reflection of the highly interdisciplinary and often applied nature of research in Bayesian statistics. The book is intended as an update for researchers in Bayesian statistics, including non-statisticians who make use of Bayesian inference to address substantive research questions in other fields. It would also be useful for graduate students and research scholars in statistics or biostatistics who wish to acquaint themselves with current research frontiers.

Mathematics of Evolution and Phylogeny

Author : Olivier Gascuel
Publisher : OUP Oxford
ISBN 13 : 9780191513732
Total Pages : 444 pages
Book Rating : 4.5/5 (137 download)

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Book Synopsis Mathematics of Evolution and Phylogeny by : Olivier Gascuel

Download or read book Mathematics of Evolution and Phylogeny written by Olivier Gascuel and published by OUP Oxford. This book was released on 2005-02-24 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book considers evolution at different scales: sequences, genes, gene families, organelles, genomes and species. The focus is on the mathematical and computational tools and concepts, which form an essential basis of evolutionary studies, indicate their limitations, and give them orientation. Recent years have witnessed rapid progress in the mathematics of evolution and phylogeny, with models and methods becoming more realistic, powerful, and complex. Aimed at graduates and researchers in phylogenetics, mathematicians, computer scientists and biologists, and including chapters by leading scientists: A. Bergeron, D. Bertrand, D. Bryant, R. Desper, O. Elemento, N. El-Mabrouk, N. Galtier, O. Gascuel, M. Hendy, S. Holmes, K. Huber, A. Meade, J. Mixtacki, B. Moret, E. Mossel, V. Moulton, M. Pagel, M.-A. Poursat, D. Sankoff, M. Steel, J. Stoye, J. Tang, L.-S. Wang, T. Warnow, Z. Yang, this book of contributed chapters explains the basis and covers the recent results in this highly topical area.

Phylogenetic Supertrees

Author : Olaf R.P. Bininda-Emonds
Publisher : Springer Science & Business Media
ISBN 13 : 1402023308
Total Pages : 547 pages
Book Rating : 4.4/5 (2 download)

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Book Synopsis Phylogenetic Supertrees by : Olaf R.P. Bininda-Emonds

Download or read book Phylogenetic Supertrees written by Olaf R.P. Bininda-Emonds and published by Springer Science & Business Media. This book was released on 2004-05-31 with total page 547 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the first book on "phylogenetic supertrees", a recent, but controversial development for inferring evolutionary trees. Rather than analyze the combined primary character data directly, supertree construction proceeds by combining the tree topologies derived from those data. This difference in strategy has allowed for the exciting possibility of larger, more complete phylogenies than are otherwise currently possible, with the potential to revolutionize evolutionarily-based research. This book provides a comprehensive look at supertrees, ranging from the methods used to build supertrees to the significance of supertrees to bioinformatic and biological research. Reviews of many the major supertree methods are provided and four new techniques, including a Bayesian implementation of supertrees, are described for the first time. The far-reaching impact of supertrees on biological research is highlighted both in general terms and through specific examples from diverse clades such as flowering plants, even-toed ungulates, and primates. The book also critically examines the many outstanding challenges and problem areas for this relatively new field, showing the way for supertree construction in the age of genomics. Interdisciplinary contributions from the majority of the leading authorities on supertree construction in all areas of the bioinformatic community (biology, computer sciences, and mathematics) will ensure that this book is a valuable reference with wide appeal to anyone interested in phylogenetic inference.

Parasite Diversity and Diversification

Author : Serge Morand
Publisher : Cambridge University Press
ISBN 13 : 1107037654
Total Pages : 503 pages
Book Rating : 4.1/5 (7 download)

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Book Synopsis Parasite Diversity and Diversification by : Serge Morand

Download or read book Parasite Diversity and Diversification written by Serge Morand and published by Cambridge University Press. This book was released on 2015-02-26 with total page 503 pages. Available in PDF, EPUB and Kindle. Book excerpt: By joining phylogenetics and evolutionary ecology, this book explores the patterns of parasite diversity while revealing diversification processes.

Handbook of Statistical Genetics

Author : David J. Balding
Publisher : John Wiley & Sons
ISBN 13 : 9780470997628
Total Pages : 1616 pages
Book Rating : 4.9/5 (976 download)

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Book Synopsis Handbook of Statistical Genetics by : David J. Balding

Download or read book Handbook of Statistical Genetics written by David J. Balding and published by John Wiley & Sons. This book was released on 2008-06-10 with total page 1616 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Handbook for Statistical Genetics is widely regarded as the reference work in the field. However, the field has developed considerably over the past three years. In particular the modeling of genetic networks has advanced considerably via the evolution of microarray analysis. As a consequence the 3rd edition of the handbook contains a much expanded section on Network Modeling, including 5 new chapters covering metabolic networks, graphical modeling and inference and simulation of pedigrees and genealogies. Other chapters new to the 3rd edition include Human Population Genetics, Genome-wide Association Studies, Family-based Association Studies, Pharmacogenetics, Epigenetics, Ethic and Insurance. As with the second Edition, the Handbook includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between the chapters, tying the different areas together. With heavy use of up-to-date examples, real-life case studies and references to web-based resources, this continues to be must-have reference in a vital area of research. Edited by the leading international authorities in the field. David Balding - Department of Epidemiology & Public Health, Imperial College An advisor for our Probability & Statistics series, Professor Balding is also a previous Wiley author, having written Weight-of-Evidence for Forensic DNA Profiles, as well as having edited the two previous editions of HSG. With over 20 years teaching experience, he’s also had dozens of articles published in numerous international journals. Martin Bishop – Head of the Bioinformatics Division at the HGMP Resource Centre As well as the first two editions of HSG, Dr Bishop has edited a number of introductory books on the application of informatics to molecular biology and genetics. He is the Associate Editor of the journal Bioinformatics and Managing Editor of Briefings in Bioinformatics. Chris Cannings – Division of Genomic Medicine, University of Sheffield With over 40 years teaching in the area, Professor Cannings has published over 100 papers and is on the editorial board of many related journals. Co-editor of the two previous editions of HSG, he also authored a book on this topic.