Bioinformatics, computational biology, is a relatively new field that applies computer science and information technology to biology. In recent years, the discipline of bioinformatics has allowed biologists to make full use of the advances in Computer sciences and Computational statistics for advancing the biological data. Researchers in life sciences generate, collect and need to analyze an increasing number of different types of scientific data, DNA, RNA and protein sequences, in-situ and microarray gene expression including 3D protein structures and biological pathways. This book is aiming to provide information on bioinformatics at various levels. The chapters included in this book cover introductory to advanced aspects, including applications of various documented research work and specific case studies related to bioinformatics. This book will be of immense value to readers of different backgrounds such as engineers, scientists, consultants and policy makers for industry, government, academics and social and private organisations.
This textbook presents mathematical models in bioinformatics and describes biological problems that inspire the computer science tools used to manage the enormous data sets involved. The first part of the book covers mathematical and computational methods, with practical applications presented in the second part. The mathematical presentation avoids unnecessary formalism, while remaining clear and precise. The book closes with a thorough bibliography, reaching from classic research results to very recent findings. This volume is suited for a senior undergraduate or graduate course on bioinformatics, with a strong focus on mathematical and computer science background.
Bioinformatics is an evolving field that is gaining popularity due to genomics, proteomics and other high-throughput biological methods. The function of bioinformatic scientists includes biological data storage, retrieval and in silico analysis of the results from large-scale experiments. This requires a grasp of knowledge mining algorithms, a thorough understanding of biological knowledge base, and the logical relationship of entities that describe a process or the system. Bioinformatics researchers are required to be trained in multidisciplinary fields of biology, mathematics and computer science. Currently the requirements are satisfied by ad hoc researchers who have specific skills in biology or mathematics/computer science. But the learning curve is steep and the time required to communicate using domain specific terms is becoming a major bottle neck in scientific productivity. This workbook provides hands-on experience which has been lacking for qualified bioinformatics researchers.
As more species' genomes are sequenced, computational analysis of these data has become increasingly important. The second, entirely updated edition of this widely praised textbook provides a comprehensive and critical examination of the computational methods needed for analyzing DNA, RNA, and protein data, as well as genomes. The book has been rewritten to make it more accessible to a wider audience, including advanced undergraduate and graduate students. New features include chapter guides and explanatory information panels and glossary terms. New chapters in this second edition cover statistical analysis of sequence alignments, computer programming for bioinformatics, and data management and mining. Practically oriented problems at the ends of chapters enhance the value of the book as a teaching resource. The book also serves as an essential reference for professionals in molecular biology, pharmaceutical, and genome laboratories.
In Bioinformatics: Methods and Protocols, hands-on users and experts survey the key biological software packages, offering useful tips and an overview of current developments. Among the sequence analysis systems reviewed are GCG, Omiga, MacVector, DNASTAR, PepTool, GeneTool, and Staden. Molecular biology software includes Genotator and sequence-similarity searching using FASTA, CLUSTAL multiple sequence alignment, and phylogenic analysis. Web-based resources are examined for primary sequence databases, primary sequence analysis methods, and clinical databases useful in molecular medicine. The book also includes a set of guidelines for designing and teaching an introductory bioinformatics course and numerous illustrative examples to teach the reader how to solve problems. Bioinformatics: Methods and Protocols offers to experienced and novice biologists a broad overview of the computational tools that have reshaped modern biology. It constitutes a gold-standard reference for today's scientists who wish to develop and hone their bioinformatics skills towards the discovery of new biological relationships.
The field of bioinformatics continues to develop energetically. This second edition covers new findings using the formula of the original text. It is self-contained, bringing together the multiple disciplines necessary for a profound grasp of the field.
Bioinformatics is a relatively new field of research. It evolved from the requirement to process, characterize, and apply the information being produced by DNA sequencing technology. The production of DNA sequence data continues to grow exponentially. At the same time, improved bioinformatics such as faster DNA sequence search methods have been combined with increasingly powerful computer systems to process this information. Methods are being developed for the ever more detailed quantification of gene expression, providing an insight into the function of the newly discovered genes, while molecular genetic tools provide a link between these genes and heritable traits. Genetic tests are now available to determine the likelihood of suffering specific ailments and can predict how plant cultivars may respond to the environment. The steps in the translation of the genetic blueprint to the observed phenotype is being increasingly understood through proteome, metabolome and phenome analysis, all underpinned by advances in bioinformatics. Bioinformatics is becoming increasingly central to the study of biology, and a day at a computer can often save a year or more in the laboratory. The volume is intended for graduate-level biology students as well as researchers who wish to gain a better understanding of applied bioinformatics and who wish to use bioinformatics technologies to assist in their research. The volume would also be of value to bioinformatics developers, particularly those from a computing background, who would like to understand the application of computational tools for biological research. Each chapter would include a comprehensive introduction giving an overview of the fundamentals, aimed at introducing graduate students and researchers from diverse backgrounds to the field and bring them up-to-date on the current state of knowledge. To accommodate the broad range of topics in applied bioinformatics, chapters have been grouped into themes: gene and genome analysis, molecular genetic analysis, gene expression analysis, protein and proteome analysis, metabolome analysis, phenome data analysis, literature mining and bioinformatics tool development. Each chapter and theme provides an introduction to the biology behind the data describes the requirements for data processing and details some of the methods applied to the data to enhance biological understanding.
This text is a resource for academics and students who want to develop collaborative learning environments. Dr. Hassan cites recent progress in bioinformatics databases that gives a hands-on, in-depth understanding that goes beyond rote memorization. Students interested in acquiring a working knowledge of the fundamentals of bioinformatics can easily become overwhelmed by the vast abundance of information on the subject. Bioinformatics: Principles and Basic Internet Applications has been specially designed to provide a concise yet comprehensive introduction to the field of bioinformatics. This brief, practical, tightly organized text shows you how to perform the biological applications. It is the only guide you need for bioinformatics every time.
Structural Bioinformatics was the first major effort to showthe application of the principles and basic knowledge of the largerfield of bioinformatics to questions focusing on macromolecularstructure, such as the prediction of protein structure and howproteins carry out cellular functions, and how the application ofbioinformatics to these life science issues can improve healthcareby accelerating drug discovery and development. Designed primarilyas a reference, the first edition nevertheless saw widespread useas a textbook in graduate and undergraduate university coursesdealing with the theories and associated algorithms, resources, andtools used in the analysis, prediction, and theoreticalunderpinnings of DNA, RNA, and proteins. This new edition contains not only thorough updates of theadvances in structural bioinformatics since publication of thefirst edition, but also features eleven new chapters dealing withfrontier areas of high scientific impact, including: sampling andsearch techniques; use of mass spectrometry; genome functionalannotation; and much more. Offering detailed coverage for practitioners while remainingaccessible to the novice, Structural Bioinformatics, SecondEdition is a valuable resource and an excellent textbook for arange of readers in the bioinformatics and advanced biologyfields. Praise for the previous edition: "This book is a gold mine of fundamental and practicalinformation in an area not previously well represented in bookform." —Biochemistry and Molecular Education "... destined to become a classic reference work for workers atall levels in structural bioinformatics...recommended with greatenthusiasm for educators, researchers, and graduatestudents." —BAMBED "...a useful and timely summary of a rapidly expandingfield." —Nature Structural Biology "...a terrific job in this timely creation of a compilation ofarticles that appropriately addresses this issue." —Briefings in Bioinformatics
Bioinformatics is an upcoming discipline of Life Sciences. It is an integration of computer science, and mathematical and statistical methods to manage and analyze the biological data. The fundamental issues that directly impact an understanding of life at structural, functional and molecular level, and regulation of gene expression can be studied by using bioinformatics tools. The Fundamentals of Bioinformatics is a comprehensive book for undergraduates, postgraduates and research scholars, who urge to learn about theoretical as well as practical aspects of this upcoming field. This pioneering book provides up-to-date information on bioinformatics and emphasizes recent topics like drug design technology, pharmacogenomics, proteomics and genomics. The present textbook will be an asset to Life sciences and technology institutions, since it has been designed based on the prescribed syllabus of various Indian Universities and aboard, and cover all the important topics on Bioinformatics.
1. Introduction to Bioinformatics 2. Introduction to Computers 3. Introduction to Internet 4. Search Engines: Tools for Web Search 5. Programming Languages 6. Genomics and Proteomics 7. Biological Databases 8. Sequence Analysis 9. Phylogenetic Analysis 10. Microarray Technology: A Boon to Biological Sciences 11. Bioinformatic..s in Drug Discovery: A Brief Overview 12. Genome Sequencing Projects 13. BTIS Network In India Index
Examines how technology has transformed the study of genetics and how researchers are using computers to analyze genes and genomes in human health, disease, and development. Discusses how this research is being used to develop cures for some diseases and to learn how to prevent them.
Being an interdisciplinary subject, Bioinformatics is today covering a range of interest both among the students and teaching communities. Taking this increasing interest into account, this book gives a comprehensive introduction to the subject. The text not only deals with the basic concepts but it also emphasizes the technical and practical aspects of the subject. The book covers the computational tools in bioinformatics, algorithmic aspects as well as technological aspects. Besides it gives a clear exposition of Viterbi algorithm, Hidden Markov models, UPGMA, FM algorithm, heuristic, developing and using substitution matrices, HMMs and derivation of a number of standard formulae in information theory and statistics. Finally the text focusses on the technological aspects of bioinformatics such as sequencing through shot gun methods, microarrays, with a variety of unsupervised methods in data analysis with examples, as well as interdisciplinary research in systems biology. The book is primarily intended as a text for the students of Computer Science, Information Technology, undergraduate students of Bioinformatics, PGDCA and biological sciences and biotechnology. The book should also be of considerable interest for research scientist in Chemistry and Pharmacy.
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.
The heart of the book lies in the collaboration efforts of eight distinct bioinformatics teams that describe their own unique approaches to data integration and interoperability. Each system receives its own chapter where the lead contributors provide precious insight into the specific problems being addressed by the system, why the particular architecture was chosen, and details on the system's strengths and weaknesses. In closing, the editors provide important criteria for evaluating these systems that bioinformatics professionals will find valuable. * Provides a clear overview of the state-of-the-art in data integration and interoperability in genomics, highlighting a variety of systems and giving insight into the strengths and weaknesses of their different approaches.-
This book is an excellent introductory text describing the use of bioinformatics to analyze genomic and post-genomic data. It has been translated from the original popular French edition, which was based on a course taught at the well-respected École Polytechnique in Palaiseau. This edition has been fully revised and updated by the authors. After a brief introduction to gene structure and sequence determination, it describes the techniques used to identify genes, their protein-coding sequences and regulatory regions. The book discusses the methodology of comparative genomics, using information from different organisms to deduce information about unknown sequences. There is a comprehensive chapter on structure prediction, covering both RNA and protein. Finally, the book describes the complex networks of RNA and protein that exist within the cell and their interactions, ending with a discussion of the simulation approaches that can be used to model these networks. Praise from the reviews: “In context of the new developments the genomic era has brought, Bioinformatics: Genomics and Post-Genomics becomes a fundamental and indispensable resource for undergraduate and early graduate students...insightfully authored...will immensely help students...in establishing important foundations while shaping their careers.” NEWSLETTER, BRITISH SOCIETY OF CELL BIOLOGY
The genomic revolution that has spawned microarrays and high throughput technologies has produced vast amounts of complex biological data that require integration and multidimensional analysis. Bioinformatics incorporates sub-disciplines ranging from databases and ontologies to the modelling of complex biological systems by way of molecular evolution and protein structure prediction. This new book provides state-of-the-art research from around the world.
Bioinformatics provides in depth coverage of the principles and applications of bioinformatic analyses of nucleic acid and protein sequences, databases and data mining. Dynamic programming algorithms of Needleman-Wunsch and Smith-Waterman, amino acid exchange matrices such as Dayhoff PAM series matrices and BLOSSUM series matrices and DOT matrix are discussed in detail along with pair-wise sequence alignment tools such as BLAST, FASTA and their variants, multiple sequence alignment tools such as CLUSTAL-W, CLUSTAL-X, SAGA, and progressive alignment and profile alignment. The book describes methods of detection and prediction of genes, ORFs, promoters, motifs, mRNA, tRNA, miRNA, their structure and function and protein structure and function using ab initio HMM and Neural Networks. Software programs like GeneID, Genescan, Genie, GeneModeler, GRAIL and GeneMARK for gene detection and visual mining tools available are discussed while Gene Ontology (GO) and use of sequence information for phylogenetic inferences are illustrated.
Author: Charlie Hodgman,Andrew French,David Westhead
Publisher: Garland Science
The second edition of Instant Notes in Bioinformatics introduced the readers to the themes and terminology of bioinformatics. It is divided into three parts: the first being an introduction to bioinformatics in biology; the second covering the physical, mathematical, statistical and computational basis of bioinformatics, using biological examples wherever possible; the third describing applications, giving specific detail and including data standards. The applications covered are sequence analysis and annotation, transcriptomics, proteomics, metabolite study, supramolecular organization, systems biology and the integration of-omic data, physiology, image analysis, and text analysis.
A Practical Guide to the Analysis of Genes and Proteins
Author: Andreas D. Baxevanis,B. F. Francis Ouellette
Publisher: John Wiley & Sons
"In this book, Andy Baxevanis and Francis Ouellette . . . haveundertaken the difficult task of organizing the knowledge in thisfield in a logical progression and presenting it in a digestibleform. And they have done an excellent job. This fine text will makea major impact on biological research and, in turn, on progress inbiomedicine. We are all in their debt." —Eric Lander from the Foreword Reviews from the First Edition "...provides a broad overview of the basic tools for sequenceanalysis ... For biologists approaching this subject for the firsttime, it will be a very useful handbook to keep on the shelf afterthe first reading, close to the computer." —Nature Structural Biology "...should be in the personal library of any biologist who usesthe Internet for the analysis of DNA and protein sequencedata." —Science "...a wonderful primer designed to navigate the novice throughthe intricacies of in scripto analysis ... The accomplished genesearcher will also find this book a useful addition to theirlibrary ... an excellent reference to the principles ofbioinformatics." —Trends in Biochemical Sciences This new edition of the highly successful Bioinformatics:A Practical Guide to the Analysis of Genes and Proteinsprovides a sound foundation of basic concepts, with practicaldiscussions and comparisons of both computational tools anddatabases relevant to biological research. Equipping biologists with the modern tools necessary to solvepractical problems in sequence data analysis, the Second Editioncovers the broad spectrum of topics in bioinformatics, ranging fromInternet concepts to predictive algorithms used on sequence,structure, and expression data. With chapters written by experts inthe field, this up-to-date reference thoroughly covers vitalconcepts and is appropriate for both the novice and the experiencedpractitioner. Written in clear, simple language, the book isaccessible to users without an advanced mathematical or computerscience background. This new edition includes: All new end-of-chapter Web resources, bibliographies, andproblem sets Accompanying Web site containing the answers to the problems,as well as links to relevant Web resources New coverage of comparative genomics, large-scale genomeanalysis, sequence assembly, and expressed sequence tags A glossary of commonly used terms in bioinformatics andgenomics Bioinformatics: A Practical Guide to the Analysis of Genesand Proteins, Second Edition is essential reading forresearchers, instructors, and students of all levels in molecularbiology and bioinformatics, as well as for investigators involvedin genomics, positional cloning, clinical research, andcomputational biology.