Bioinformatics and Biomarker Discovery. Omic Data Analysis for Personalized Medicine

This book is the first to be dedicated to the bioinformatics of carbohydrates and glycoproteins. It provides an introduction to this emerging field of science both for the experimentalist working in glycobiology and glycomics, and also for the computer scientist looking for background information for the development of highly sophisticated algorithmic approaches. The book provides an overview of the state-of-the-art in the field, with reviews on databases, and the tools in use for analysis, interpretation, and prediction of the structures of complex carbohydrates, and demonstrates the value of bioinformatics for glycobiology. The availability of comprehensive databases and corresponding bioinformatics tools, to access and analyse the large amounts of experimental data relating to the structure of carbohydrates, will be a prerequisite for the success of the large-scale glycomics projects that aim to decipher new, so far unknown, biological functions of glycans. Efficient bioinformatics descriptions and tools can considerably enhance the efficiency of glycomics research, in terms of data quality, analysis and experimental costs. For a complete understanding of the molecular processes in which carbohydrates are involved, such as protein–carbohydrate interactions and the impact of glycosylation on protein function, knowledge of the 3D structure of the carbohydrate, the protein–carbohydrate complex, or the glycoprotein is often indispensable. This book provides a thorough introduction into methods used for conformational analysis of carbohydrates. Key features: Describes bioinformatic approaches to handle carbohydrate-active enzymes and glycosylation. Provides an overview on bioinformatics tools that facilitate analysis of carbohydrate structures. Gives introduction into molecular modelling of carbohydrate 3D structure and carbohydrates contained in the Protein Databank. Assumes only a basic knowledge of biology and bioinformatics.

Enables readers to start doing actual data analysis fast for a truly hands-on learning experience This concise and very easy-to-use primer introduces readers to a host of computational tools useful for making sense out of data, whether that data come from the social, behavioral, or natural sciences. The book places great emphasis on both data analysis and drawing conclusions from empirical observations. It also provides formulas where needed in many places, while always remaining focused on concepts rather than mathematical abstraction. SPSS Data Analysis for Univariate, Bivariate, and Multivariate Statistics offers a variety of popular statistical analyses and data management tasks using SPSS that readers can immediately apply as needed for their own research, and emphasizes many helpful computational tools used in the discovery of empirical patterns. The book begins with a review of essential statistical principles before introducing readers to SPSS. The book then goes on to offer chapters on: Exploratory Data Analysis, Basic Statistics, and Visual Displays; Data Management in SPSS; Inferential Tests on Correlations, Counts, and Means; Power Analysis and Estimating Sample Size; Analysis of Variance – Fixed and Random Effects; Repeated Measures ANOVA; Simple and Multiple Linear Regression; Logistic Regression; Multivariate Analysis of Variance (MANOVA) and Discriminant Analysis; Principal Components Analysis; Exploratory Factor Analysis; and Non-Parametric Tests. This helpful resource allows readers to: Understand data analysis in practice rather than delving too deeply into abstract mathematical concepts Make use of computational tools used by data analysis professionals. Focus on real-world application to apply concepts from the book to actual research Assuming only minimal, prior knowledge of statistics, SPSS Data Analysis for Univariate, Bivariate, and Multivariate Statistics is an excellent “how-to” book for undergraduate and graduate students alike. This book is also a welcome resource for researchers and professionals who require a quick, go-to source for performing essential statistical analyses and data management tasks.

Machine learning techniques are increasingly being used to address problems in computational biology and bioinformatics. Novel machine learning computational techniques to analyze high throughput data in the form of sequences, gene and protein expressions, pathways, and images are becoming vital for understanding diseases and future drug discovery. Machine learning techniques such as Markov models, support vector machines, neural networks, and graphical models have been successful in analyzing life science data because of their capabilities in handling randomness and uncertainty of data noise and in generalization. Machine Learning in Bioinformatics compiles recent approaches in machine learning methods and their applications in addressing contemporary problems in bioinformatics approximating classification and prediction of disease, feature selection, dimensionality reduction, gene selection and classification of microarray data and many more.

Clustering techniques are increasingly being put to use in the analysis of high-throughput biological datasets. Novel computational techniques to analyse high throughput data in the form of sequences, gene and protein expressions, pathways, and images are becoming vital for understanding diseases and future drug discovery. This book details the complete pathway of cluster analysis, from the basics of molecular biology to the generation of biological knowledge. The book also presents the latest clustering methods and clustering validation, thereby offering the reader a comprehensive review of clustering analysis in bioinformatics from the fundamentals through to state-of-the-art techniques and applications. Key Features: Offers a contemporary review of clustering methods and applications in the field of bioinformatics, with particular emphasis on gene expression analysis Provides an excellent introduction to molecular biology with computer scientists and information engineering researchers in mind, laying out the basic biological knowledge behind the application of clustering analysis techniques in bioinformatics Explains the structure and properties of many types of high-throughput datasets commonly found in biological studies Discusses how clustering methods and their possible successors would be used to enhance the pace of biological discoveries in the future Includes a companion website hosting a selected collection of codes and links to publicly available datasets

Data Mining for Genomics and Proteomics uses pragmatic examples and a complete case study to demonstrate step-by-step how biomedical studies can be used to maximize the chance of extracting new and useful biomedical knowledge from data. It is an excellent resource for students and professionals involved with gene or protein expression data in a variety of settings.

This book introduces drug researchers to the novel computational approaches of pathway analysis and explains the existing applications that can save time and money in the drug discovery process. It covers traditional computational methods and software for pathway analysis microarray, proteomics, and metabolomics. It explains pathway reconstruction of diseases and toxic states, pathway analysis in various phases, dynamic modeling of drug responses, and more. This is a core resource for drug discovery and pharmaceutical industry researchers, chemists, and biologists and for professionals in related fields.

Data Analysis and Presentation Skills: An Introduction for the Life and Medical Sciences is an invaluable text allowing students to develop appropriate key skills when designing experiments, generating results, analysing data and ultimately presenting findings to academics and referees. Taking a hands-on approach, each of these key areas is introduced clearly and carefully, showing how to access and evaluate information using a variety of resources. Basic analytical theory is gradually introduced alongside practical applications to enhance student understanding. The reader is shown how to present data in charts using Microsoft Excel and statistical analysis is carefully explained showing clearly how to manipulate data in spreadsheets and analyse the results using commonly used tests. A section is also included on the use of PowerPoint as well as giving advice on how to prepare a short talk or seminar. Includes numerous relevant examples and case studies drawn from the Life Sciences Guidance on how to complete and present practical and project work through to postgraduate dissertation. Clear step-by-step introduction to Microsoft Excel, presentation skills and statistical analysis. Invaluable for all students within the Life and Medical Sciences

Praise for the Third Edition “. . . an easy-to read introduction to survival analysis which covers the major concepts and techniques of the subject.” —Statistics in Medical Research Updated and expanded to reflect the latest developments, Statistical Methods for Survival Data Analysis, Fourth Edition continues to deliver a comprehensive introduction to the most commonly-used methods for analyzing survival data. Authored by a uniquely well-qualified author team, the Fourth Edition is a critically acclaimed guide to statistical methods with applications in clinical trials, epidemiology, areas of business, and the social sciences. The book features many real-world examples to illustrate applications within these various fields, although special consideration is given to the study of survival data in biomedical sciences. Emphasizing the latest research and providing the most up-to-date information regarding software applications in the field, Statistical Methods for Survival Data Analysis, Fourth Edition also includes: Marginal and random effect models for analyzing correlated censored or uncensored data Multiple types of two-sample and K-sample comparison analysis Updated treatment of parametric methods for regression model fitting with a new focus on accelerated failure time models Expanded coverage of the Cox proportional hazards model Exercises at the end of each chapter to deepen knowledge of the presented material Statistical Methods for Survival Data Analysis is an ideal text for upper-undergraduate and graduate-level courses on survival data analysis. The book is also an excellent resource for biomedical investigators, statisticians, and epidemiologists, as well as researchers in every field in which the analysis of survival data plays a role.

The only single, up-to-date source for Grid issues in bioinformatics and biology Bioinformatics is fast emerging as an important discipline for academic research and industrial applications, creating a need for the use of Grid computing techniques for large-scale distributed applications. This book successfully presents Grid algorithms and their real-world applications, provides details on modern and ongoing research, and explores software frameworks that integrate bioinformatics and computational biology. Additional coverage includes: * Bio-ontology and data mining * Data visualization * DNA assembly, clustering, and mapping * Molecular evolution and phylogeny * Gene expression and micro-arrays * Molecular modeling and simulation * Sequence search and alignment * Protein structure prediction * Grid infrastructure, middleware, and tools for bio data Grid Computing for Bioinformatics and Computational Biology is an indispensable resource for professionals in several research and development communities including bioinformatics, computational biology, Grid computing, data mining, and more. It also serves as an ideal textbook for undergraduate- and graduate-level courses in bioinformatics and Grid computing.

Leading experts illustrate how sophisticated computational data mining techniques can impact contemporary drug discovery and development In the era of post-genomic drug development, extracting and applying knowledge from chemical, biological, and clinical data is one of the greatest challenges facing the pharmaceutical industry. Pharmaceutical Data Mining brings together contributions from leading academic and industrial scientists, who address both the implementation of new data mining technologies and application issues in the industry. This accessible, comprehensive collection discusses important theoretical and practical aspects of pharmaceutical data mining, focusing on diverse approaches for drug discovery—including chemogenomics, toxicogenomics, and individual drug response prediction. The five main sections of this volume cover: A general overview of the discipline, from its foundations to contemporary industrial applications Chemoinformatics-based applications Bioinformatics-based applications Data mining methods in clinical development Data mining algorithms, technologies, and software tools, with emphasis on advanced algorithms and software that are currently used in the industry or represent promising approaches In one concentrated reference, Pharmaceutical Data Mining reveals the role and possibilities of these sophisticated techniques in contemporary drug discovery and development. It is ideal for graduate-level courses covering pharmaceutical science, computational chemistry, and bioinformatics. In addition, it provides insight to pharmaceutical scientists, principal investigators, principal scientists, research directors, and all scientists working in the field of drug discovery and development and associated industries.