* 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.
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.
In the second edition, the book continues to integrate a wide variety of data analysis methods into a single and flexible interface: the R language. This open source language is available for a wide range of computer systems and has been adopted as a computational environment by many authors of statistical software. Adopting R as a main tool for phylogenetic analyses will ease the workflow in biologists' data analyses, ensure greater scientific repeatability, and enhance the exchange of ideas and methodological developments. The second edition is completed updated, covering the full gamut of R packages for this area that have been introduced to the market since its previous publication five years ago. There is also a new chapter on the simulation of evolutionary data.
Graduate students and researchers in evolutionary biology can use this book as a reference for data analyses, whereas researchers in bioinformatics interested in evolutionary analyses will learn how to implement these methods in R. 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: manipulation of phylogenetic data, phylogeny estimation, tree drawing, phylogenetic comparative methods, and estimation of ancestral characters. 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.
Written by a chemometrician and a statistician, the book reflects the practical approach of chemometrics and the more formally oriented one of statistics. To enable a better understanding of the statistical methods, the authors apply them to real data examples from chemistry. They also examine results of the different methods, comparing traditional approaches with their robust counterparts. In addition, the authors use the freely available R package to implement methods, encouraging readers to go through the examples and adapt the procedures to their own problems.
Focusing on the practicality of the methods and the validity of the results, this book offers concise mathematical descriptions of many multivariate methods and employs graphical schemes to visualize key concepts. It effectively imparts a basic understanding of how to apply statistical methods to multivariate scientific data.
What is neuroplasticity? Is it possible to change your brain? Norman Doidge’s inspiring guide to the new brain science explains all of this and more
An astonishing new science called neuroplasticity is overthrowing the centuries-old notion that the human brain is immutable, and proving that it is, in fact, possible to change your brain. Psychoanalyst, Norman Doidge, M.D., traveled the country to meet both the brilliant scientists championing neuroplasticity, its healing powers, and the people whose lives they’ve transformed—people whose mental limitations, brain damage or brain trauma were seen as unalterable. We see a woman born with half a brain that rewired itself to work as a whole, blind people who learn to see, learning disorders cured, IQs raised, aging brains rejuvenated, stroke patients learning to speak, children with cerebral palsy learning to move with more grace, depression and anxiety disorders successfully treated, and lifelong character traits changed. Using these marvelous stories to probe mysteries of the body, emotion, love, sex, culture, and education, Dr. Doidge has written an immensely moving, inspiring book that will permanently alter the way we look at our brains, human nature, and human potential.
Grunt tackles the science behind some of a soldier's most challenging adversaries—panic, exhaustion, heat, noise—and introduces us to the scientists who seek to conquer them. Mary Roach dodges hostile fire with the U.S. Marine Corps Paintball Team as part of a study on hearing loss and survivability in combat. She visits the fashion design studio of U.S. Army Natick Labs and learns why a zipper is a problem for a sniper. She visits a repurposed movie studio where amputee actors help prepare Marine Corps medics for the shock and gore of combat wounds. At Camp Lemmonier, Djibouti, in east Africa, we learn how diarrhea can be a threat to national security. Roach samples caffeinated meat, sniffs an archival sample of a World War II stink bomb, and stays up all night with the crew tending the missiles on the nuclear submarine USS Tennessee. She answers questions not found in any other book on the military: Why is DARPA interested in ducks? How is a wedding gown like a bomb suit? Why are shrimp more dangerous to sailors than sharks? Take a tour of duty with Roach, and you’ll never see our nation’s defenders in the same way again.
In this Pulitzer Prize finalist and national bestseller, one of the world's leading cognitive scientists tackles the workings of the human mind. What makes us rational—and why are we so often irrational? How do we see in three dimensions? What makes us happy, afraid, angry, disgusted, or sexually aroused? Why do we fall in love? And how do we grapple with the imponderables of morality, religion, and consciousness? How the Mind Works synthesizes the most satisfying explanations of our mental life from cognitive science, evolutionary biology, and other fields to explain what the mind is, how it evolved, and how it allows us to see, think, feel, laugh, interact, enjoy the arts, and contemplate the mysteries of life.
This edition of Pinker's bold and buoyant classic is updated with a new foreword by the author.