The book will be useful for many specialists, e.g., epidemiologists, oncologists, medical researchers, biologists, public health and environmental specialists, and specialists in mathematical modeling. Medical, biology and math undergraduates and postgraduates, as well as basic and applied researchers attempting to extend their studies in collaboration with other specialists in interdisciplinary teams, will find practical information here. Biomedical specialists could be interested in historical aspects of cancer treatment and prevention, mechanisms of carcinogenesis, cancer risk factors, cancer mortality and morbidity trends in the U.S. over a more than 50-year period, as well as specific features of cancer histotypes, and recent approaches to cancer prevention. Readers interested in analytic aspects can find information on existing and innovative approaches used in interdisciplinary studies such as stochastic process models, microsimulation of interventions, and empirical Bayes approaches.
This book was written by authors with different backgrounds who teamed in an interdisciplinary group. Kenneth G. Manton, Ph.D. (Demography) is Research Professor of Demographic Studies at Duke University (Durham, NC). He was Head of the W.H.O. Collaborating Center for Research and Training in the Methods of Assessing Risk and Forecasting Health Status Trends. He has authored more than 450 peer-reviewed publications, including several books.
Igor Akushevich, Ph.D. (Theoretical and Mathematical Physics), Center for Population Health and Aging at Duke University, authored more than 70 peer-reviewed publications.
Julia Kravchenko, MD, Ph.D. (Internal Diseases, Biochemistry), Duke Comprehensive Cancer Center in the School of Medicine. She is author of more than 30 peer-reviewed publications.
* import and preprocessing of data from various sources
* statistical modeling of differential gene expression
* biological metadata
* application of graphs and graph rendering
* machine learning for clustering and classification problems
* gene set enrichment analysis
Each chapter of this book describes an analysis of real data using hands-on example driven approaches. Short exercises help in the learning process and invite more advanced considerations of key topics. The book is a dynamic document. All the code shown can be executed on a local computer, and readers are able to reproduce every computation, figure, and table.
This book provides an introduction to some of these new methods. The main biological topics treated include sequence analysis, BLAST, microarray analysis, gene finding, and the analysis of evolutionary processes. The main statistical techniques covered include hypothesis testing and estimation, Poisson processes, Markov models and Hidden Markov models, and multiple testing methods.
The second edition features new chapters on microarray analysis and on statistical inference, including a discussion of ANOVA, and discussions of the statistical theory of motifs and methods based on the hypergeometric distribution. Much material has been clarified and reorganized.
The book is written so as to appeal to biologists and computer scientists who wish to know more about the statistical methods of the field, as well as to trained statisticians who wish to become involved with bioinformatics. The earlier chapters introduce the concepts of probability and statistics at an elementary level, but with an emphasis on material relevant to later chapters and often not covered in standard introductory texts. Later chapters should be immediately accessible to the trained statistician. Sufficient mathematical background consists of introductory courses in calculus and linear algebra. The basic biological concepts that are used are explained, or can be understood from the context, and standard mathematical concepts are summarized in an Appendix. Problems are provided at the end of each chapter allowing the reader to develop aspects of the theory outlined in the main text.
Warren J. Ewens holds the Christopher H. Brown Distinguished Professorship at the University of Pennsylvania. He is the author of two books, Population Genetics and Mathematical Population Genetics. He is a senior editor of Annals of Human Genetics and has served on the editorial boards of Theoretical Population Biology, GENETICS, Proceedings of the Royal Society B and SIAM Journal in Mathematical Biology. He is a fellow of the Royal Society and the Australian Academy of Science.
Gregory R. Grant is a senior bioinformatics researcher in the University of Pennsylvania Computational Biology and Informatics Laboratory. He obtained his Ph.D. in number theory from the University of Maryland in 1995 and his Masters in Computer Science from the University of Pennsylvania in 1999.
Comments on the First Edition. "This book would be an ideal text for a postgraduate course...[and] is equally well suited to individual study.... I would recommend the book highly" (Biometrics). "Ewens and Grant have given us a very welcome introduction to what is behind those pretty [graphical user] interfaces" (Naturwissenschaften.). "The authors do an excellent job of presenting the essence of the material without getting bogged down in mathematical details" (Journal. American Staistical. Association). "The authors have restructured classical material to a great extent and the new organization of the different topics is one of the outstanding services of the book" (Metrika).
Rui Jiang and Xuegong Zhang are both professors at the Department of Automation, Tsinghua University, China. Professor Michael Q. Zhang works at the Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.