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| bioinformatics a practical approach: Bioinformatics Shui Qing Ye, 2007-08-20 An emerging, ever-evolving branch of science, bioinformatics has paved the way for the explosive growth in the distribution of biological information to a variety of biological databases, including the National Center for Biotechnology Information. For growth to continue in this field, biologists must obtain basic computer skills while computer spe |
| bioinformatics a practical approach: Bioinformatics Andreas D. Baxevanis, B. F. Francis Ouellette, 2004-03-24 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. |
| bioinformatics a practical approach: Introduction to Bioinformatics Stephen A. Krawetz, David D. Womble, 2003-01-31 to Bioinformatics A Theoretical and Practical Approach Edited by Stephen A. Krawetz, PhD Wayne State University School of Medicine, Detroit MI and David D. Womble, PhD Wayne State University School of Medicine, Detroit, MI ~ Springer Science+ ~ Business Media, LLC © 2003 Springer Science+Business Media New York Originally published by Humana Press !ne. in 2003 Softcover reprint of the hardcover 1 st edition 2003 humanapress.com Ali rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise without written permission from the Publisher. Ali papers, comments, opinions, conclusions, or recommendations are those of the author(s), and do not necessarily reflect the views of the publisher. This publication is printed on acid-free paper. G) ANSI Z39.48-1984 (American Standards Institute) Permanence of Paper for Printed Library Materials. Production Editor: Mark J. Breaugh. Cover design by Patricia F. Cleary and Paul A. Thiessen. Cover illustration by Paul A. Thiessen, chemicalgraphics.com. |
| bioinformatics a practical approach: Bioinformatics Hamid D. Ismail, 2022-03-22 Bioinformatics: A Practical Guide to NCBI Databases and Sequence Alignments provides the basics of bioinformatics and in-depth coverage of NCBI databases, sequence alignment, and NCBI Sequence Local Alignment Search Tool (BLAST). As bioinformatics has become essential for life sciences, the book has been written specifically to address the need of a large audience including undergraduates, graduates, researchers, healthcare professionals, and bioinformatics professors who need to use the NCBI databases, retrieve data from them, and use BLAST to find evolutionarily related sequences, sequence annotation, construction of phylogenetic tree, and the conservative domain of a protein, to name just a few. Technical details of alignment algorithms are explained with a minimum use of mathematical formulas and with graphical illustrations. Key Features Provides readers with the most-used bioinformatics knowledge of bioinformatics databases and alignments including both theory and application via illustrations and worked examples. Discusses the use of Windows Command Prompt, Linux shell, R, and Python for both Entrez databases and BLAST. The companion website (http://www.hamiddi.com/instructors/) contains tutorials, R and Python codes, instructor materials including slides, exercises, and problems for students. This is the ideal textbook for bioinformatics courses taken by students of life sciences and for researchers wishing to develop their knowledge of bioinformatics to facilitate their own research. |
| bioinformatics a practical approach: Practical Bioinformatics Janusz M. Bujnicki, 2007-09-12 This book presents applications of bioinformatics tools that experimental research scientists use in daily practice. Its interdisciplinary approach combines computational and experimental methods to solve scientific problems. The book begins with reviews of computational methods for protein sequence-structure-function analysis, followed by methods that use experimental data obtained in the laboratory to improve functional predictions. |
| bioinformatics a practical approach: Genome Analysis And Bioinformatics: A Practical Approach T. R. Sharma, 2009-01-01 With the decoding of whole genome sequences of many organisms, new vistas of research have emerged in computational biology. The scientific community has free access to the genome sequence data from the public databases. Many times, it is really hard to make sense of these huge data of DNA and protein sequences. Therefore, bioinformatics tools are used to handle, store and analyze genome sequence data for the benefit of mankind. The book has been written in a simplest possible manner so that every one should understand the basic concepts of genome sequence analysis and bioinformatics. The book is structured in such a way so that readers should first know about how whole genome sequences are generated by using high throughput DNA sequencing technologies and then storing of sequences in biological databases. Second part deals with the basic principals involved in sequence analysis and applications of softwares along with practical exercises. Thirdly, data mining approaches for the discovery of genes and DNA markers have also been discussed. Besides, glossary of important terms and introduction to basic bioinformatics softwares has been included for the benefits of readers. The book will serve as a text book to the B. Tech (Bioinformatics & Biotechnology) students and would also be useful reference book to the postgraduate students and research scientists working in the areas of life sciences, genomics, biotechnology and molecular biology as well as Masters in Computer Applications (MCA) who are interested in bioinformatics. |
| bioinformatics a practical approach: Exploring Bioinformatics Caroline St. Clair, Jonathan E. Visick, 2013-12-12 Thoroughly revised and updated, Exploring Bioinformatics: A Project-Based Approach, Second Edition is intended for an introductory course in bioinformatics at the undergraduate level. Through hands-on projects, students are introduced to current biological problems and then explore and develop bioinformatic solutions to these issues. Each chapter presents a key problem, provides basic biological concepts, introduces computational techniques to address the problem, and guides students through the use of existing web-based tools and software solutions. This progression prepares students to tackle the On-Your-Own Project, where they develop their own software solutions. Topics such as antibiotic resistance, genetic disease, and genome sequencing provide context and relevance to capture student interest. |
| bioinformatics a practical approach: Bioinformatics Data Skills Vince Buffalo, 2015-07 Learn the data skills necessary for turning large sequencing datasets into reproducible and robust biological findings. With this practical guide, youâ??ll learn how to use freely available open source tools to extract meaning from large complex biological data sets. At no other point in human history has our ability to understand lifeâ??s complexities been so dependent on our skills to work with and analyze data. This intermediate-level book teaches the general computational and data skills you need to analyze biological data. If you have experience with a scripting language like Python, youâ??re ready to get started. Go from handling small problems with messy scripts to tackling large problems with clever methods and tools Process bioinformatics data with powerful Unix pipelines and data tools Learn how to use exploratory data analysis techniques in the R language Use efficient methods to work with genomic range data and range operations Work with common genomics data file formats like FASTA, FASTQ, SAM, and BAM Manage your bioinformatics project with the Git version control system Tackle tedious data processing tasks with with Bash scripts and Makefiles |
| bioinformatics a practical approach: Introduction to Bioinformatics Stephen A. Krawetz, 2003 |
| bioinformatics a practical approach: An Introduction to Bioinformatics Algorithms Neil C. Jones, Pavel A. Pevzner, 2004-08-06 An introductory text that emphasizes the underlying algorithmic ideas that are driving advances in bioinformatics. This introductory text offers a clear exposition of the algorithmic principles driving advances in bioinformatics. Accessible to students in both biology and computer science, it strikes a unique balance between rigorous mathematics and practical techniques, emphasizing the ideas underlying algorithms rather than offering a collection of apparently unrelated problems. The book introduces biological and algorithmic ideas together, linking issues in computer science to biology and thus capturing the interest of students in both subjects. It demonstrates that relatively few design techniques can be used to solve a large number of practical problems in biology, and presents this material intuitively. An Introduction to Bioinformatics Algorithms is one of the first books on bioinformatics that can be used by students at an undergraduate level. It includes a dual table of contents, organized by algorithmic idea and biological idea; discussions of biologically relevant problems, including a detailed problem formulation and one or more solutions for each; and brief biographical sketches of leading figures in the field. These interesting vignettes offer students a glimpse of the inspirations and motivations for real work in bioinformatics, making the concepts presented in the text more concrete and the techniques more approachable.PowerPoint presentations, practical bioinformatics problems, sample code, diagrams, demonstrations, and other materials can be found at the Author's website. |
| bioinformatics a practical approach: Bioinformatics Programming in Python Ruediger-Marcus Flaig, 2008-03-31 This first introductory book designed to train novice programmers is based on a student course taught by the author, and has been optimized for biology students without previous experience in programming. By interspersing theory chapters with numerous small and large programming exercises, the author quickly shows readers how to do their own programming, and throughout uses anecdotes and real-life examples from the biosciences to 'spice up' the text. This practical book thus teaches essential programming skills for life scientists who want -- or need -- to write their own bioinformatics software tools. |
| bioinformatics a practical approach: Bioinformatics Computing Bryan P. Bergeron, 2003 Comprehensive and concise, this handbook has chapters on computing visualization, large database designs, advanced pattern matching and other key bioinformatics techniques. It is a practical guide to computing in the growing field of Bioinformatics--the study of how information is represented and transmitted in biological systems, starting at the molecular level. |
| bioinformatics a practical approach: RNA-seq Data Analysis Eija Korpelainen, Jarno Tuimala, Panu Somervuo, Mikael Huss, Garry Wong, 2015 RNA-seq offers unprecedented information about transcriptome, but harnessing this information with bioinformatics tools is typically a bottleneck. This self-contained guide enables researchers to examine differential expression at gene, exon, and transcript level and to discover novel genes, transcripts, and whole transcriptomes. Each chapter starts with theoretical background, followed by descriptions of relevant analysis tools. The book also provides examples using command line tools and the R statistical environment. For non-programming scientists, the same examples are covered using open source software with a graphical user interface. |
| bioinformatics a practical approach: Introduction to Computational Biology Michael S. Waterman, 2018-05-02 Biology is in the midst of a era yielding many significant discoveries and promising many more. Unique to this era is the exponential growth in the size of information-packed databases. Inspired by a pressing need to analyze that data, Introduction to Computational Biology explores a new area of expertise that emerged from this fertile field- the combination of biological and information sciences. This introduction describes the mathematical structure of biological data, especially from sequences and chromosomes. After a brief survey of molecular biology, it studies restriction maps of DNA, rough landmark maps of the underlying sequences, and clones and clone maps. It examines problems associated with reading DNA sequences and comparing sequences to finding common patterns. The author then considers that statistics of pattern counts in sequences, RNA secondary structure, and the inference of evolutionary history of related sequences. Introduction to Computational Biology exposes the reader to the fascinating structure of biological data and explains how to treat related combinatorial and statistical problems. Written to describe mathematical formulation and development, this book helps set the stage for even more, truly interdisciplinary work in biology. |
| bioinformatics a practical approach: Computational Biology Röbbe Wünschiers, 2012-12-06 -Teaches the reader how to use Unix, which is the key to basic computing and allows the most flexibility for bioinformatics applications -Written specifically with the needs of molecular biologists in mind -Easy to follow, written for beginners with no computational knowledge -Includes examples from biological data analysis -Can be use either for self-teaching or in courses |
| bioinformatics a practical approach: Introduction to Bioinformatics Anna Tramontano, 2018-10-03 Guiding readers from the elucidation and analysis of a genomic sequence to the prediction of a protein structure and the identification of the molecular function, Introduction to Bioinformatics describes the rationale and limitations of the bioinformatics methods and tools that can help solve biological problems. Requiring only a limited mathematical and statistical background, the book shows how to efficiently apply these approaches to biological data and evaluate the resulting information. The author, an expert bioinformatics researcher, first addresses the ways of storing and retrieving the enormous amount of biological data produced every day and the methods of decrypting the information encoded by a genome. She then covers the tools that can detect and exploit the evolutionary and functional relationships among biological elements. Subsequent chapters illustrate how to predict the three-dimensional structure of a protein. The book concludes with a discussion of the future of bioinformatics. Even though the future will undoubtedly offer new tools for tackling problems, most of the fundamental aspects of bioinformatics will not change. This resource provides the essential information to understand bioinformatics methods, ultimately facilitating in the solution of biological problems. |
| bioinformatics a practical approach: Basic Applied Bioinformatics Chandra Sekhar Mukhopadhyay, Ratan Kumar Choudhary, Mir Asif Iquebal, 2017-09-15 An accessible guide that introduces students in all areas of life sciences to bioinformatics Basic Applied Bioinformatics provides a practical guidance in bioinformatics and helps students to optimize parameters for data analysis and then to draw accurate conclusions from the results. In addition to parameter optimization, the text will also familiarize students with relevant terminology. Basic Applied Bioinformatics is written as an accessible guide for graduate students studying bioinformatics, biotechnology, and other related sub-disciplines of the life sciences. This accessible text outlines the basics of bioinformatics, including pertinent information such as downloading molecular sequences (nucleotide and protein) from databases; BLAST analyses; primer designing and its quality checking, multiple sequence alignment (global and local using freely available software); phylogenetic tree construction (using UPGMA, NJ, MP, ME, FM algorithm and MEGA7 suite), prediction of protein structures and genome annotation, RNASeq data analyses and identification of differentially expressed genes and similar advanced bioinformatics analyses. The authors Chandra Sekhar Mukhopadhyay, Ratan Kumar Choudhary, and Mir Asif Iquebal are noted experts in the field and have come together to provide an updated information on bioinformatics. Salient features of this book includes: Accessible and updated information on bioinformatics tools A practical step-by-step approach to molecular-data analyses Information pertinent to study a variety of disciplines including biotechnology, zoology, bioinformatics and other related fields Worked examples, glossary terms, problems and solutions Basic Applied Bioinformatics gives students studying bioinformatics, agricultural biotechnology, animal biotechnology, medical biotechnology, microbial biotechnology, and zoology an updated introduction to the growing field of bioinformatics. |
| bioinformatics a practical approach: EMBOSS User's Guide Peter M. Rice, Alan J. Bleasby, Jon C. Ison, 2011-06-16 The European Molecular Biology Open Source Software Suite (EMBOSS) is the premier Open Source package of tools for molecular biology analysis and bioinformatics. Practical Bioinformatics with EMBOSS is the official and definitive guide to the package. It includes comprehensive information and practical instructions, including an in-depth tutorial and guidelines on common ways to use the package. It is written specifically for biologists, bioinformaticians and other end-users, and no prior experience with EMBOSS is assumed. |
| bioinformatics a practical approach: Algorithms in Bioinformatics Wing-Kin Sung, 2009-11-24 Thoroughly Describes Biological Applications, Computational Problems, and Various Algorithmic Solutions Developed from the author's own teaching material, Algorithms in Bioinformatics: A Practical Introduction provides an in-depth introduction to the algorithmic techniques applied in bioinformatics. For each topic, the author clearly details the bi |
| bioinformatics a practical approach: Mastering Python for Bioinformatics Ken Youens-Clark, 2021-05-05 Life scientists today urgently need training in bioinformatics skills. Too many bioinformatics programs are poorly written and barely maintained, usually by students and researchers who've never learned basic programming skills. This practical guide shows postdoc bioinformatics professionals and students how to exploit the best parts of Python to solve problems in biology while creating documented, tested, reproducible software. Ken Youens-Clark, author of Tiny Python Projects (Manning), demonstrates not only how to write effective Python code but also how to use tests to write and refactor scientific programs. You'll learn the latest Python features and tools including linters, formatters, type checkers, and tests to create documented and tested programs. You'll also tackle 14 challenges in Rosalind, a problem-solving platform for learning bioinformatics and programming. Create command-line Python programs to document and validate parameters Write tests to verify refactor programs and confirm they're correct Address bioinformatics ideas using Python data structures and modules such as Biopython Create reproducible shortcuts and workflows using makefiles Parse essential bioinformatics file formats such as FASTA and FASTQ Find patterns of text using regular expressions Use higher-order functions in Python like filter(), map(), and reduce() |
| bioinformatics a practical approach: Neuroscience Databases Rolf Kötter, 2012-12-06 Neuroscience Databases: A Practical Guide is the first book providing a comprehensive overview of these increasingly important databases. This volume makes the results of the Human Genome Project and other recent large-scale initiatives in the neurosciences available to a wider community. It extends the scope of bioinformatics from the molecular to the cellular, microcircuitry and systems levels, dealing for the first time with complex neuroscientific issues and leading the way to a new culture of data sharing and data mining necessary to successfully tackle neuroscience questions. Aimed at the novice user who wants to access the data, it provides clear and concise instructions on how to download the available data sets and how to use the software with a minimum of technical detail with most chapters written by the database creators themselves. |
| bioinformatics a practical approach: The Practical Bioinformatician Limsoon Wong, 2004 Computer scientists have increasingly been enlisted as bioinformaticians to assist molecular biologists in their research. This book is a practical introduction to bioinformatics for these computer scientists. The chapters are in-depth discussions by expert bioinformaticians on both general techniques and specific approaches to a range of selected bioinformatics problems. The book is organized into clusters of chapters on the following topics: - Overview of modern molecular biology and a broad spectrum of techniques from computer science -- data mining, machine learning, mathematical modeling, sequence alignment, data integration, workflow development, etc. - In-depth discussion of computational recognition of functional and regulatory sites in DNA sequences. - Incisive discussion of computational prediction of secondary structure of RNA sequences. - Overview of computational prediction of protein cellular localization, and selected discussions of inference of protein function. - Overview of methods for discovering protein-protein interactions. - Detailed discussion of approaches to gene expression analysis for the diagnosis of diseases, the treatment of diseases, and the understanding of gene functions. - Case studies on analysis of phylogenies, functional annotation of proteins, construction of purposebuilt integrated biological databases, and development of workflows underlying the large-scale-effort gene discovery. - Written in a practical, in-depth tutorial style - Covers a broad range of bioinformatics topics and of techniques used in bioinformatics - Comprehensive overviews of the development of various approaches in a number of selectedtopics - In-depth exposition of a number of important topics - Contributions by prominent researchers: Vladimir Bajic, Ming Li, Kenta Nakai, Limsoon Wong, Cathy Wu, etc. - Extensive, integrated references to background liter |
| bioinformatics a practical approach: Bioinformatics Algorithms Phillip Compeau, Pavel Pevzner, 1986-06 Bioinformatics Algorithms: an Active Learning Approach is one of the first textbooks to emerge from the recent Massive Online Open Course (MOOC) revolution. A light-hearted and analogy-filled companion to the authors' acclaimed online course (http://coursera.org/course/bioinformatics), this book presents students with a dynamic approach to learning bioinformatics. It strikes a unique balance between practical challenges in modern biology and fundamental algorithmic ideas, thus capturing the interest of students of biology and computer science students alike.Each chapter begins with a central biological question, such as Are There Fragile Regions in the Human Genome? or Which DNA Patterns Play the Role of Molecular Clocks? and then steadily develops the algorithmic sophistication required to answer this question. Hundreds of exercises are incorporated directly into the text as soon as they are needed; readers can test their knowledge through automated coding challenges on Rosalind (http://rosalind.info), an online platform for learning bioinformatics.The textbook website (http://bioinformaticsalgorithms.org) directs readers toward additional educational materials, including video lectures and PowerPoint slides. |
| bioinformatics a practical approach: Developing Bioinformatics Computer Skills Cynthia Gibas, Per Jambeck, 2001 This practical, hands-on guide shows how to develop a structured approach to biological data and the tools needed to analyze it. It's aimed at scientists and students learning computational approaches to biological data, as well as experienced biology researchers starting to use computers to handle data. |
| bioinformatics a practical approach: Metabolomics Ron Wehrens, International Agency for Research on Can, 2019-08-19 Metabolomics is the scientific study of the chemical processes in a living system, environment and nutrition. It is a relatively new omics science, but the potential applications are wide, including medicine, personalized medicine and intervention studies, food and nutrition, plants, agriculture and environmental science. The topics presented and discussed in this book are based on the European Molecular Biology Organization (EMBO) practical courses in metabolomics bioinformatics taught to those working in the field, from masters to postgraduate students, PhDs, postdoctoral and early PIs. The book covers the basics and fundamentals of data acquisition and analytical technologies, but the primary focus is data handling and data analysis. The mentioning and usage of a particular data analysis tool has been avoided; rather, the focus is on the concepts and principles of data processing and analysis. The material has been class-tested and includes lots of examples, computing and exercises. Key Features: Provides an overview of qualitative /quantitative methods in metabolomics Offers an introduction to the key concepts of metabolomics, including experimental design and technology Covers data handling, processing, analysis, data standards and sharing Contains lots of examples to illustrate the topics Includes contributions from some of the leading researchers in the field of metabolomics with extensive teaching experiences |
| bioinformatics a practical approach: Beginning Perl for Bioinformatics James Tisdall, 2001 This book shows biologists with little or no programming experience how to use Perl, the ideal language for biological data analysis. Each chapter focuses on solving a particular problem or class of problems, so you'll finish the book with the skills to tackle more advanced bioinformatics programming. |
| bioinformatics a practical approach: Bioinformatics for Diagnosis, Prognosis and Treatment of Complex Diseases Bairong Shen, 2013-11-25 The book introduces the bioinformatics tools, databases and strategies for the translational research, focuses on the biomarker discovery based on integrative data analysis and systems biological network reconstruction. With the coming of personal genomics era, the biomedical data will be accumulated fast and then it will become reality for the personalized and accurate diagnosis, prognosis and treatment of complex diseases. The book covers both state of the art of bioinformatics methodologies and the examples for the identification of simple or network biomarkers. In addition, bioinformatics software tools and scripts are provided to the practical application in the study of complex diseases. The present state, the future challenges and perspectives were discussed. The book is written for biologists, biomedical informatics scientists and clinicians, etc. Dr. Bairong Shen is Professor and Director of Center for Systems Biology, Soochow University; he is also Director of Taicang Center for Translational Bioinformatics. |
| bioinformatics a practical approach: Advances in Biological Science Research Surya Nandan Meena, Milind Naik, 2019-05-17 Advances in Biological Science Research: A Practical Approach provides discussions on diverse research topics and methods in the biological sciences in a single platform. This book provides the latest technologies, advanced methods, and untapped research areas involved in diverse fields of biological science research such as bioinformatics, proteomics, microbiology, medicinal chemistry, and marine science. Each chapter is written by renowned researchers in their respective fields of biosciences and includes future advancements in life science research. - Discusses various research topics and methods in the biological sciences in a single platform - Comprises the latest updates in advanced research techniques, protocols, and methods in biological sciences - Incorporates the fundamentals, advanced instruments, and applications of life science experiments - Offers troubleshooting for many common problems faced while performing research experiments |
| bioinformatics a practical approach: R Programming for Bioinformatics Robert Gentleman, 2008-07-14 Due to its data handling and modeling capabilities as well as its flexibility, R is becoming the most widely used software in bioinformatics. R Programming for Bioinformatics explores the programming skills needed to use this software tool for the solution of bioinformatics and computational biology problems. Drawing on the author’s first-hand experiences as an expert in R, the book begins with coverage on the general properties of the R language, several unique programming aspects of R, and object-oriented programming in R. It presents methods for data input and output as well as database interactions. The author also examines different facets of string handling and manipulations, discusses the interfacing of R with other languages, and describes how to write software packages. He concludes with a discussion on the debugging and profiling of R code. With numerous examples and exercises, this practical guide focuses on developing R programming skills in order to tackle problems encountered in bioinformatics and computational biology. |
| bioinformatics a practical approach: Python for Bioinformatics Sebastian Bassi, 2017-08-07 In today's data driven biology, programming knowledge is essential in turning ideas into testable hypothesis. Based on the author’s extensive experience, Python for Bioinformatics, Second Edition helps biologists get to grips with the basics of software development. Requiring no prior knowledge of programming-related concepts, the book focuses on the easy-to-use, yet powerful, Python computer language. This new edition is updated throughout to Python 3 and is designed not just to help scientists master the basics, but to do more in less time and in a reproducible way. New developments added in this edition include NoSQL databases, the Anaconda Python distribution, graphical libraries like Bokeh, and the use of Github for collaborative development. |
| bioinformatics a practical approach: The Ten Most Wanted Solutions in Protein Bioinformatics Anna Tramontano, 2005-05-24 Utilizing high speed computational methods to extrapolate to the rest of the protein universe, the knowledge accumulated on a subset of examples, protein bioinformatics seeks to accomplish what was impossible before its invention, namely the assignment of functions or functional hypotheses for all known proteins.The Ten Most Wanted Solutions in Pro |
| bioinformatics a practical approach: Bioinformatics Stanley I. Letovsky, 2013-04-10 Bioinformatics brings computational methods to the analysis and processing of genomic data. Bioinformatics: Databases and Systems focuses on the issues of system building and data curation that dominate the day-to-day concerns of bioinformatics practitioners. Included are chapters by many of today's leading bioinformatics practitioners, describing most of the current paradigms of system building and curation, including both their strengths and weaknesses. Biological topics covered include sequence databases, metabolic pathways, phenotypes, variety collections, gene expression atlases and neuroinformatics. Species range from bacteria to mammals to plants. Software systems and technologies covered include OPM, CORBA, SRS, KLEISLI, ACEDB, Web-based integration and laboratory workflow. Bioinformatics: Databases and Systems provides a valuable introduction for newcomers to the field, and a useful reference for veterans. |
| bioinformatics a practical approach: Structural Bioinformatics Zoltán Gáspári, 2020-02-01 This volume looks at the latest techniques used to perform comparative structure analyses, and predict and evaluate protein-ligand interactions. The chapters in this book cover tools and servers such as LiteMol; Bio3D-Web; DALI; CATH; HoTMuSiC, a contact-base protein structure analysis tool known as CAD-Score; PyDockSaxs and HADDOCK; CombDock and DockStar; the BioMagResBank database; as well as BME and CoNSEnsX+. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Structural Bioinformatics: Methods and Protocols is a practical guide for researchers to learn more about the aforementioned tools to further enhance their studies in the growing field of structural bioinformatics. Chapter 13 is available open access under a CC-BY 4.0 license via link.springer.com. |
| bioinformatics a practical approach: Medical Bioinformatics and Biochemistry (diabormatics) Rajneesh Prajapat, Ijen Bhattacharya, 2019 The first edition of Medical Bioinformatics and Biochemistry (Diabormatics) explains how medical biochemistry and bioinformatics could be used as a tool for analyzing the research data related to disease diagnosis and treatment. Bioinformatics is an interdisciplinary approach that includes concepts of biotechnology, microbiology, molecular biology, medicine and forensic science. This book is based on the recent development in the research dynamics of medical bioinformatics, biochemistry and progress in these fields. The book provides reference material for students of medical and life sciences. The development in genomic sequencing and in silico biology has provided the data needed to accomplish comparisons of derived nucleotide and protein sequences. The results of analysis may be used to formulate and test hypotheses about biochemical function. This first edition provides readers with a practical guide covering the full scope of concepts in medical bioinformatics and biochemistry related to diabetes. The basic purpose of this book is for students of medical and life sciences to understand the research methods of biochemistry and bioinformatics. This includes storing, receiving, and analyzing data from databases using various in silico tools. This book is a useful source of knowledge for MBBS, B.Sc, M.Sc / M.D. / M.S. and Ph.D level students looking for an accessible introduction to the subject. |
| bioinformatics a practical approach: Bioinformatics for Beginners Supratim Choudhuri, 2018-10-30 Bioinformatics for Beginners: Genes, Genomes, Molecular Evolution, Databases and Analytical Tools provides a coherent and friendly treatment of bioinformatics for any student or scientist within biology who has not routinely performed bioinformatic analysis. The book discusses the relevant principles needed to understand the theoretical underpinnings of bioinformatic analysis and demonstrates, with examples, targeted analysis using freely available web-based software and publicly available databases. Eschewing non-essential information, the work focuses on principles and hands-on analysis, also pointing to further study options. |
| bioinformatics a practical approach: Introduction to Bioinformatics Attwood, 1999 |
| bioinformatics a practical approach: R Bioinformatics Cookbook Dan MacLean, 2019-10-11 Over 60 recipes to model and handle real-life biological data using modern libraries from the R ecosystem Key Features Apply modern R packages to handle biological data using real-world examples Represent biological data with advanced visualizations suitable for research and publications Handle real-world problems in bioinformatics such as next-generation sequencing, metagenomics, and automating analyses Book Description Handling biological data effectively requires an in-depth knowledge of machine learning techniques and computational skills, along with an understanding of how to use tools such as edgeR and DESeq. With the R Bioinformatics Cookbook, you'll explore all this and more, tackling common and not-so-common challenges in the bioinformatics domain using real-world examples. This book will use a recipe-based approach to show you how to perform practical research and analysis in computational biology with R. You will learn how to effectively analyze your data with the latest tools in Bioconductor, ggplot, and tidyverse. The book will guide you through the essential tools in Bioconductor to help you understand and carry out protocols in RNAseq, phylogenetics, genomics, and sequence analysis. As you progress, you will get up to speed with how machine learning techniques can be used in the bioinformatics domain. You will gradually develop key computational skills such as creating reusable workflows in R Markdown and packages for code reuse. By the end of this book, you'll have gained a solid understanding of the most important and widely used techniques in bioinformatic analysis and the tools you need to work with real biological data. What you will learn Employ Bioconductor to determine differential expressions in RNAseq data Run SAMtools and develop pipelines to find single nucleotide polymorphisms (SNPs) and Indels Use ggplot to create and annotate a range of visualizations Query external databases with Ensembl to find functional genomics information Execute large-scale multiple sequence alignment with DECIPHER to perform comparative genomics Use d3.js and Plotly to create dynamic and interactive web graphics Use k-nearest neighbors, support vector machines and random forests to find groups and classify data Who this book is for This book is for bioinformaticians, data analysts, researchers, and R developers who want to address intermediate-to-advanced biological and bioinformatics problems by learning through a recipe-based approach. Working knowledge of R programming language and basic knowledge of bioinformatics are prerequisites. |
生物信息学领域有哪些牛刊？ - 知乎
BMC genomics，BMC bioinformatics，BMC medical genomics. 练气期：这是修仙的基础阶段，研究生修行者开始吸收天地灵气，将其转化为体内的元力。 Briefings in …
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请问生物信息学有什么书可以推荐一下么？ - 知乎
Nov 16, 2021 · Bioinformatics: Genes, Proteins And Computers（无中文版） 生物信息学：基因、蛋白质和计算机 是解决复杂生物学问题的生物学概念和计算方法的结合。 本书首先讨论了细 …
如何评价2021中科院分区将Bioinformatic分为三区，BiB为二区综 …
Dec 21, 2021 · bioinformatics三区，审稿周期3-4个月. pgb一区，审稿周期一年. 按照三篇三区等于一篇一区，那发三篇bioinformatics的时间和收益等于发一篇pgb。 以后大家都发pgb，nar bib …
如何看待生信期刊Briefings in bioinformatics 最新影响因子11.622
Jul 7, 2021 · 总的来说，文章的平均质量远远不如Bioinformatics杂志，而且主要以发表综述为主。 文章的质量和文章的被引用次数没有任何相关性。 现在确实到来不能以影响因子论英雄的阶 …
生物信息学 (Bioinformatics) 和医学/健康信息学哪个就业前景好？
本人复旦生物系本科，但在生物信息（bioinformatics）实验室做了三年研究，之后去哥伦比亚大学生物医学信息学（biomedical informatics）系读硕士，选择医学track研读。现在在上海做医学 …
为什么edge浏览器访问网站显示已拒绝连接？其他浏览器正常？
知乎，中文互联网高质量的问答社区和创作者聚集的原创内容平台，于 2011 年 1 月正式上线，以「让人们更好的分享知识、经验和见解，找到自己的解答」为品牌使命。知乎凭借认真、专业 …
爱思唯尔with editor一般多长时间？已经快一个月了。？ - 知乎
知乎，中文互联网高质量的问答社区和创作者聚集的原创内容平台，于 2011 年 1 月正式上线，以「让人们更好的分享知识、经验和见解，找到自己的解答」为品牌使命。知乎凭借认真、专业 …
本科生信发了一篇一作BIB（Briefings in Bioinformatics）是什么水 …
本科生信发了一篇一作BIB（Briefings in Bioinformatics）是什么水平？ 如题，BIB的IF最新是快14，有可能靠这篇文章申请到好学校的phd吗，文章非综述（大概是搭建了一个生信管道） 显 …
briefing in bioinformatics这个期刊有latex的模板吗？ - 知乎
Jan 3, 2023 · 这个去官网就有，但是就是OUP的通用模板，我也用的这个，但是不知道BIB有没有自己的专用模板，我在overleaf上没找到反正应该是没有，但是又感觉和BIB已经发表的论文格 …
生物信息学领域有哪些牛刊？ - 知乎
BMC genomics，BMC bioinformatics，BMC medical genomics. 练气期：这是修仙的基础阶段，研究生修行者开始吸收天地灵气，将其转化为体内的元力。 Briefings in …
Biostatistics（生物统计学）和 bioinformatics （生物信息学）有什 …
而Bioinformatics领域，统计学家的成果还是发表在很多顶尖杂志。 Nature Genetics高达38分，Nature Method高达28分，往下还有很多十几分的杂志，大量统计学家的team在这些杂志上 …
请问生物信息学有什么书可以推荐一下么？ - 知乎
Nov 16, 2021 · Bioinformatics: Genes, Proteins And Computers（无中文版） 生物信息学：基因、蛋白质和计算机 是解决复杂生物学问题的生物学概念和计算方法的结合。 本书首先讨论了细 …
如何评价2021中科院分区将Bioinformatic分为三区，BiB为二区综 …
Dec 21, 2021 · bioinformatics三区，审稿周期3-4个月. pgb一区，审稿周期一年. 按照三篇三区等于一篇一区，那发三篇bioinformatics的时间和收益等于发一篇pgb。 以后大家都发pgb，nar bib …
如何看待生信期刊Briefings in bioinformatics 最新影响因子11.622
Jul 7, 2021 · 总的来说，文章的平均质量远远不如Bioinformatics杂志，而且主要以发表综述为主。 文章的质量和文章的被引用次数没有任何相关性。 现在确实到来不能以影响因子论英雄的阶 …
生物信息学 (Bioinformatics) 和医学/健康信息学哪个就业前景好？
本人复旦生物系本科，但在生物信息（bioinformatics）实验室做了三年研究，之后去哥伦比亚大学生物医学信息学（biomedical informatics）系读硕士，选择医学track研读。现在在上海做医学 …
为什么edge浏览器访问网站显示已拒绝连接？其他浏览器正常？
知乎，中文互联网高质量的问答社区和创作者聚集的原创内容平台，于 2011 年 1 月正式上线，以「让人们更好的分享知识、经验和见解，找到自己的解答」为品牌使命。知乎凭借认真、专业 …
爱思唯尔with editor一般多长时间？已经快一个月了。？ - 知乎
知乎，中文互联网高质量的问答社区和创作者聚集的原创内容平台，于 2011 年 1 月正式上线，以「让人们更好的分享知识、经验和见解，找到自己的解答」为品牌使命。知乎凭借认真、专业 …
本科生信发了一篇一作BIB（Briefings in Bioinformatics）是什么水 …
本科生信发了一篇一作BIB（Briefings in Bioinformatics）是什么水平？ 如题，BIB的IF最新是快14，有可能靠这篇文章申请到好学校的phd吗，文章非综述（大概是搭建了一个生信管道） 显 …
briefing in bioinformatics这个期刊有latex的模板吗？ - 知乎
Jan 3, 2023 · 这个去官网就有，但是就是OUP的通用模板，我也用的这个，但是不知道BIB有没有自己的专用模板，我在overleaf上没找到反正应该是没有，但是又感觉和BIB已经发表的论文格 …
