BMME 8053 - Introduction to Bioinformatics
Course guide for Introduction to Bioinformatics (BMME 8053)
Featured Resources
Bioinformatics and Functional Genomics by
The bestselling introduction to bioinformatics and genomics - now in its third edition Widely received in its previous editions, Bioinformatics and Functional Genomics offers the most broad-based introduction to this explosive new discipline. Now in a thoroughly updated and expanded third edition, it continues to be the go-to source for students and professionals involved in biomedical research. This book provides up-to-the-minute coverage of the fields of bioinformatics and genomics. Features new to this edition include: Extensive revisions and a slight reorder of chapters for a more effective organization A brand new chapter on next-generation sequencing An expanded companion website, also updated as and when new information becomes available Greater emphasis on a computational approach, with clear guidance of how software tools work and introductions to the use of command-line tools such as software for next-generation sequence analysis, the R programming language, and NCBI search utilities The book is complemented by lavish illustrations and more than 500 figures and tables - many newly-created for the third edition to enhance clarity and understanding. Each chapter includes learning objectives, a problem set, pitfalls section, boxes explaining key techniques and mathematics/statistics principles, a summary, recommended reading, and a list of freely available software. Readers may visit a related Web page for supplemental information such as PowerPoints and audiovisual files of lectures, and videocasts of how to perform many basic operations: www.wiley.com/go/pevsnerbioinformatics. Bioinformatics and Functional Genomics, Third Edition serves as an excellent single-source textbook for advanced undergraduate and beginning graduate-level courses in the biological sciences and computer sciences. It is also an indispensable resource for biologists in a broad variety of disciplines who use the tools of bioinformatics and genomics to study particular research problems; bioinformaticists and computer scientists who develop computer algorithms and databases; and medical researchers and clinicians who want to understand the genomic basis of viral, bacterial, parasitic, or other diseases.
Call Number: QH441.2 .P48 2015ISBN: 9781118581780Publication Date: 2015-10-26
R Programming for Bioinformatics by
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."
Call Number: QH324.2 .G46 2009ISBN: 1420063677Publication Date: 2008-07-14
Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics by
Available in print and online, this unique reference brings together all four fields of genetics, genomics, proteomics, and bioinformatics to meet your dynamic research requirements. It brings together the latest concepts in these vibrant areas and ensures a truly multidisciplinary approach. Topics include genetic variation and evolution, epigenetics, the human genome, expression profiling, proteome families, structural proteomics, gene finding/gene structure, protein function and annotation, and more. The work incorporates a vast amount of topical information, profiles cutting-edge techniques, and presents the very latest findings from an international team of over five hundred contributors. With articles for both students and more experienced scientists, this is a key reference source for everyone. Contains more than 450 articles covering all aspects of genomics, proteomics, bioinformatics and related technologies Includes a glossary containing over 550 clear and concise definitions "I am pleased to recommend it heartily as a essential reference tool...should remain the definitive work...for many years to come." THE CHEMICAL EDUCATOR "Jorde...and co-editors have done a remarkable job in coordinating this information, distilling it into a package that is both easy to navigate and over-flowing in discovery." ELECTRIC REVIEW
Call Number: E-BOOKISBN: 9780470849743Publication Date: 2005-11-11
Bioinformatics Books & E-Books
Python for Scientists by
The third edition of this practical introduction to Python has been thoroughly updated, with all code migrated to Jupyter notebooks. The notebooks are available online with executable versions of all of the book's content (and more). The text starts with a detailed introduction to the basics of the Python language, without assuming any prior knowledge. Building upon each other, the most important Python packages for numerical math (NumPy), symbolic math (SymPy), and plotting (Matplotlib) are introduced, with brand new chapters covering numerical methods (SciPy) and data handling (Pandas). Further new material includes guidelines for writing efficient Python code and publishing code for other users. Simple and concise code examples, revised for compatibility with Python 3, guide the reader and support the learning process throughout the book. Readers from all of the quantitative sciences, whatever their background, will be able to quickly acquire the skills needed for using Python effectively.
Call Number: Q183.9 .S865 2023ISBN: 9781009014809Publication Date: 2023-08-31
RNA Worlds by
RNA (ribonucleic acid) molecules drive much of cellular action. Messenger RNA (mRNA) relays genetic information from DNA to ribosomes to direct the formation of proteins. At the same time, noncoding RNAs act as enzymes, scaffolds, and regulatory molecules, contributing greatly to theregulation of gene activity, RNA splicing, protein synthesis, and even DNA replication.This new edition of the highly successful RNA Worlds series focuses on emerging tools for analysis of RNA biology and how these tools are driving our understanding of RNA structure and function. The contributors review new approaches for imaging RNA molecules in cells, techniques for analyzing thebehavior of single RNA molecules in vitro and in vivo, transcriptome-wide analyses, and novel methods for determining the structure of RNA and RNP (ribonucleoprotein) complexes. They discuss the insights these provide into the transcription and splicing machinery, ribosomes, reverse transcriptases,and subcellular structures such as stress granules.Also included are chapters exploring CRISPR editing, RNA switches for use in synthetic biology, and development of novel drugs targeting pathogenic RNA structures. In addition, the book covers recent insights into the primordial RNA World, including protocells and homochirality. It will therefore beof interest not only to biochemists and molecular biologists but to evolutionary biologists pondering the emergence of life on Earth.
Call Number: QH450.R635 2019ISBN: 9781621822240Publication Date: 2018-12-31
Computational Biology by
An introduction to the world of bioinformatics Massive increases in computing power and the ability to routinely sequence whole genomes of living organisms have begun to fundamentally alter our understanding of biology, medicine, and agriculture. At the intersection of the growing information and genomics revolutions sits bioinformatics, which uses modern computational power to reveal patterns in biological data sets, especially DNA, RNA, and protein sequences.Computational Biology: A Hypertextbook, by Scott Kelley and Dennis Didulo, provides a wonderful introduction for anyone who wants to learn the basics of bioinformatics. This book is more than a textbook because of the wealth of online ancillary materials and how the print and electronic components are integrated to form a complete educational resource. Aspects that make Computational Biology: A Hypertextbook a unique and valuable tool for teaching and learning bioinformatics include: Clear explanations of the basic biology of DNA, RNA, and proteins and how the related bioinformatics algorithms work; Extensive exercises that enable students to practice with the same bioinformatics applications that are used by scientists worldwide; Tutorials, sample data sets, and interactive learning tools developed with teachers in mind and field-tested by hundreds of students; Online tutorials and curated web links that are accurate (instead of frustrating!) and won't lead to dead ends; Online resources that work on multiple platforms and electronic devices. Computational Biology: A Hypertextbook is written in an accessible voice, punctuated with humor, and designed to significantly increase computational competencies. Biology and computer science undergraduate and graduate students will thoroughly enjoy learning from this unique hypertextbook, as will anyone with an interest in exploring this burgeoning topic. Scott T. Kelley is a professor of biology at San Diego State University. He received his doctoral degree from the University of Colorado and his bachelor's degree from Cornell University. His lab uses phylogenetic methods and culture-independent molecular tools to study environmental microbiology, and Kelley has published extensively on the human microbiome, built environment, and numerous natural environments.Dennis Didulo is a data analytics and software engineer working at Becton, Dickinson and Company. He received his master's degree in information technology at De La Salle University andhis second master's degree in bioinformatics at San Diego State University. He has development expertise in more than a dozen computer languages, as well as in database management, algorithm design, and systems engineering.
Call Number: QH324.2 .K45 2018ISBN: 9781683670025Publication Date: 2018-01-01
Practical Protein Bioinformatics by
This book describes more than 60 web-accessible computational tools for protein analysis and is totally practical, with detailed explanations on how to use these tools and interpret their results and minimal mentions to their theoretical basis (only when that is required for making a better use of them).
Call Number: QH324.2 .P396 2015ISBN: 9783319127262Publication Date: 2015
Introduction to Bioinformatics by
This text describes how bioinformatics can be used as a powerful set of tools for retrieving and analysing this biological data, and how bioinformatics can be applied to a wide range of disciplines such as molecularbiology, medicine, biotechnology, forensic science and anthropology.
Call Number: QH507 .L47 2014ISBN: 9780199651566Publication Date: 2014-01-01
Genome Annotation by
Genome Annotation explores automated genome analysis and annotation from its origins to the challenges of next-generation sequencing data analysis. The book initially takes you through the last 16 years since the sequencing of the first complete microbial genome. It explains how current analysis strategies were developed, including sequencing strategies, statistical models, and early annotation systems. The authors then present visualization techniques for displaying integrated results as well as state-of-the-art annotation tools, including MAGPIE, Ensembl, Bluejay, and Galaxy. They also discuss the pipelines for the analysis and annotation of complex, next-generation DNA sequencing data.
Call Number: QH447 .S634 2013ISBN: 9781439841174Publication Date: 2012-08-30
Bioinformatics by
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.
Call Number: QH324.2 .M38 2009ISBN: 9780387848693Publication Date: 2008-10-20
Bioinformatics and Systems Biology by
Collaborative research in bioinformatics and systems biology is a key element of modern biology and health research. This book highlights and provides access to many of the methods, environments, results and resources involved, including integral laboratory data generation and experimentation and clinical activities. Collaborative projects embody a research paradigm that connects many of the top scientists, institutions, their resources and research worldwide, resulting in first-class contributions to bioinformatics and systems biology. Central themes include describing processes and results in collaborative research projects using computational biology and providing a guide for researchers to access them. The book is also a practical guide on how science is managed. It shows how collaborative researchers are putting results together in a way accessible to the entire biomedical community.
Call Number: QH324.2 .M365 2008ISBN: 9783540783527Publication Date: 2008-07-31
Bioinformatics by
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 specialists must possess a fundamental understanding of biological problems. Bridging the gap between biology and computer science, Bioinformatics: A Practical Approach assimilates current bioinformatics knowledge and tools relevant to the omics age into one cohesive, concise, and self-contained volume. Written by expert contributors from around the world, this practical book presents the most state-of-the-art bioinformatics applications. The first part focuses on genome analysis, common DNA analysis tools, phylogenetics analysis, and SNP and haplotype analysis. After chapters on microarray, SAGE, regulation of gene expression, miRNA, and siRNA, the book presents widely applied programs and tools in proteome analysis, protein sequences, protein functions, and functional annotation of proteins in murine models. The last part introduces the programming languages used in biology, website and database design, and the interchange of data between Microsoft Excel and Access. Keeping complex mathematical deductions and jargon to a minimum, this accessible book offers both the theoretical underpinnings and practical applications of bioinformatics.
Call Number: QH324.2 .Y42 2008ISBN: 1584888113Publication Date: 2007-08-20
Practical Bioinformatics by
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.
Call Number: QP260 .N795 2004ISBN: 3540206132Publication Date: 2004-03-03
Bioinformatics by
Life science data integration and interoperability is one of the most challenging problems facing bioinformatics today. In the current age of the life sciences, investigators have to interpret many types of information from a variety of sources: lab instruments, public databases, gene expression profiles, raw sequence traces, single nucleotide polymorphisms, chemical screening data, proteomic data, putative metabolic pathway models, and many others. Unfortunately, scientists are not currently able to easily identify and access this information because of the variety of semantics, interfaces, and data formats used by the underlying data sources. Bioinformatics: Managing Scientific Data tackles this challenge head-on by discussing the current approaches and variety of systems available to help bioinformaticians with this increasingly complex issue. 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. * Discusses shared vocabulary, design issues, complexity of use cases, and the difficulties of transferring existing data management approaches to bioinformatics systems, which serves to connect computer and life scientists. * Written by the primary contributors of eight reputable bioinformatics systems in academia and industry including: BioKris, TAMBIS, K2, GeneExpress, P/FDM, MBM, SDSC, SRS, and DiscoveryLink.
Call Number: QH324.2 .B55 2003ISBN: 155860829XPublication Date: 2003-07-18
Introduction to Bioinformatics by
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 #65533; 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.
Call Number: QH507 .I575 2003ISBN: 1588290646Publication Date: 2003-01-31
Research Anthology on Bioinformatics, Genomics, and Computational Biology by Call Number: E-BOOKISBN: 9798369330272Publication Date: 2024-03-19
R Bioinformatics Cookbook by
Discover over 80 recipes for modeling and handling real-life biological data using modern libraries from the R ecosystem Key Features Apply modern R packages to process biological data using real-world examples Represent biological data with advanced visualizations and workflows suitable for research and publications Solve real-world bioinformatics problems such as transcriptomics, genomics, and phylogenetics Purchase of the print or Kindle book includes a free PDF eBook Book Description The updated second edition of R Bioinformatics Cookbook takes a recipe-based approach to show you how to conduct practical research and analysis in computational biology with R. You'll learn how to create a useful and modular R working environment, along with loading, cleaning, and analyzing data using the most up-to-date Bioconductor, ggplot2, and tidyverse tools.This book will walk you through the Bioconductor tools necessary for you to understand and carry out protocols in RNA-seq and ChIP-seq, phylogenetics, genomics, gene search, gene annotation, statistical analysis, and sequence analysis. As you advance, you'll find out how to use Quarto to create data-rich reports, presentations, and websites, as well as get a clear understanding of how machine learning techniques can be applied in the bioinformatics domain. The concluding chapters will help you develop proficiency in key skills, such as gene annotation analysis and functional programming in purrr and base R. Finally, you'll discover how to use the latest AI tools, including ChatGPT, to generate, edit, and understand R code and draft workflows for complex analyses.By the end of this book, you'll have gained a solid understanding of the skills and techniques needed to become a bioinformatics specialist and efficiently work with large and complex bioinformatics datasets. What you will learn Set up a working environment for bioinformatics analysis with R Import, clean, and organize bioinformatics data using tidyr Create publication-quality plots, reports, and presentations using ggplot2 and Quarto Analyze RNA-seq, ChIP-seq, genomics, and next-generation genetics with Bioconductor Search for genes and proteins by performing phylogenetics and gene annotation Apply ML techniques to bioinformatics data using mlr3 Streamline programmatic work using iterators and functional tools in the base R and purrr packages Use ChatGPT to create, annotate, and debug code and workflows 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 via a recipe-based approach. Working knowledge of the R programming language and basic knowledge of bioinformatics are prerequisites. ]]>
Call Number: E-BOOKISBN: 9781837634279Publication Date: 2023-10-31
Bioinformatics by
The book discusses the recent techniques in NGS data analysis which is the most needed material by biologists (students and researchers) in the wake of numerous genomic projects and the trend toward genomic research. The book includes both theory and practice for the NGS data analysis. So, readers will understand the concept and learn how to do the analysis using the most recent programs. The steps of application workflows are written in a manner that can be followed for related projects. Each chapter includes worked examples with real data available on the NCBI databases. Programming codes and outputs are accompanied with explanation. The book content is suitable as teaching material for biology and bioinformatics students. Meets the requirements of a complete semester course on Sequencing Data Analysis Covers the latest applications for Next Generation Sequencing. Covers data reprocessing, genome assembly, variant discovery, gene profiling, epigenetics, and metagenomics
Call Number: E-BOOKISBN: 9781032408910Publication Date: 2023-06-29
All about Bioinformatics by
All About Bioinformatics: From Beginner to Expert provides readers with an overview of the fundamentals and advances in the _x001F_field of bioinformatics, as well as some future directions. Each chapter is didactically organized and includes introduction, applications, tools, and future directions to cover the topics thoroughly. The book covers both traditional topics such as biological databases, algorithms, genetic variations, static methods, and structural bioinformatics, as well as contemporary advanced topics such as high-throughput technologies, drug informatics, system and network biology, and machine learning. It is a valuable resource for researchers and graduate students who are interested to learn more about bioinformatics to apply in their research work. Presents a holistic learning experience, beginning with an introduction to bioinformatics to recent advancements in the field Discusses bioinformatics as a practice rather than in theory focusing on more application-oriented topics as high-throughput technologies, system and network biology, and workflow management systems Encompasses chapters on statistics and machine learning to assist readers in deciphering trends and patterns in biological data
Call Number: E-BOOKISBN: 9780443152511Publication Date: 2023-04-05
Bioinformatics with Python Cookbook by
Discover modern, next-generation sequencing libraries from the powerful Python ecosystem to perform cutting-edge research and analyze large amounts of biological data Key Features: Perform complex bioinformatics analysis using the most essential Python libraries and applicationsImplement next-generation sequencing, metagenomics, automating analysis, population genetics, and much moreExplore various statistical and machine learning techniques for bioinformatics data analysis Book Description: Bioinformatics is an active research field that uses a range of simple-to-advanced computations to extract valuable information from biological data, and this book will show you how to manage these tasks using Python. This updated third edition of the Bioinformatics with Python Cookbook begins with a quick overview of the various tools and libraries in the Python ecosystem that will help you convert, analyze, and visualize biological datasets. Next, you'll cover key techniques for next-generation sequencing, single-cell analysis, genomics, metagenomics, population genetics, phylogenetics, and proteomics with the help of real-world examples. You'll learn how to work with important pipeline systems, such as Galaxy servers and Snakemake, and understand the various modules in Python for functional and asynchronous programming. This book will also help you explore topics such as SNP discovery using statistical approaches under high-performance computing frameworks, including Dask and Spark. In addition to this, you'll explore the application of machine learning algorithms in bioinformatics. By the end of this bioinformatics Python book, you'll be equipped with the knowledge you need to implement the latest programming techniques and frameworks, empowering you to deal with bioinformatics data on every scale. What You Will Learn: Become well-versed with data processing libraries such as NumPy, pandas, arrow, and zarr in the context of bioinformatic analysisInteract with genomic databasesSolve real-world problems in the fields of population genetics, phylogenetics, and proteomicsBuild bioinformatics pipelines using a Galaxy server and SnakemakeWork with functools and itertools for functional programmingPerform parallel processing with Dask on biological dataExplore principal component analysis (PCA) techniques with scikit-learn Who this book is for: This book is for bioinformatics analysts, data scientists, computational biologists, researchers, and Python developers who want to address intermediate-to-advanced biological and bioinformatics problems. Working knowledge of the Python programming language is expected. Basic knowledge of biology will also be helpful.
Call Number: E-BOOKISBN: 9781803236421Publication Date: 2022-09-27
Basic Applied Bioinformatics by
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.
Call Number: E-BOOKISBN: 9781119244332Publication Date: 2017-11-13- Bioinformatics and Functional Genomics by
The bestselling introduction to bioinformatics and genomics - now in its third edition Widely received in its previous editions, Bioinformatics and Functional Genomics offers the most broad-based introduction to this explosive new discipline. Now in a thoroughly updated and expanded third edition, it continues to be the go-to source for students and professionals involved in biomedical research. This book provides up-to-the-minute coverage of the fields of bioinformatics and genomics. Features new to this edition include: Extensive revisions and a slight reorder of chapters for a more effective organization A brand new chapter on next-generation sequencing An expanded companion website, also updated as and when new information becomes available Greater emphasis on a computational approach, with clear guidance of how software tools work and introductions to the use of command-line tools such as software for next-generation sequence analysis, the R programming language, and NCBI search utilities The book is complemented by lavish illustrations and more than 500 figures and tables - many newly-created for the third edition to enhance clarity and understanding. Each chapter includes learning objectives, a problem set, pitfalls section, boxes explaining key techniques and mathematics/statistics principles, a summary, recommended reading, and a list of freely available software. Readers may visit a related Web page for supplemental information such as PowerPoints and audiovisual files of lectures, and videocasts of how to perform many basic operations: www.wiley.com/go/pevsnerbioinformatics. Bioinformatics and Functional Genomics, Third Edition serves as an excellent single-source textbook for advanced undergraduate and beginning graduate-level courses in the biological sciences and computer sciences. It is also an indispensable resource for biologists in a broad variety of disciplines who use the tools of bioinformatics and genomics to study particular research problems; bioinformaticists and computer scientists who develop computer algorithms and databases; and medical researchers and clinicians who want to understand the genomic basis of viral, bacterial, parasitic, or other diseases.
Call Number: E-BOOKISBN: 9781118581780Publication Date: 2015-10-26
Bioinformatics Data Skills by
Learn the data skills necessary for turning large sequencing datasets into reproducible and robust biological findings. With this practical guide, you’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 life’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, you’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
Call Number: E-BOOKISBN: 9781449367374Publication Date: 2015-07-23
Bioinformatics by
Features: explains the fundamentals of information science relevant to biology; covers both organismal (ontogeny and phylogeny, as well as genome structure) and molecular aspects; examines the most important practical applications of bioinformatics, providing detailed descriptions of both the experimental process and the data analysis; provides a varied selection of problems throughout the book, to stimulate further thinking.
Call Number: E-BOOKISBN: 9781447167020Publication Date: 2015-06-14
Statistical Bioinformatics by
This book provides an essential understanding of statistical concepts necessary for the analysis of genomic and proteomic data using computational techniques. The author presents both basic and advanced topics, focusing on those that are relevant to the computational analysis of large data sets in biology. Chapters begin with a description of a statistical concept and a current example from biomedical research, followed by more detailed presentation, discussion of limitations, and problems. The book starts with an introduction to probability and statistics for genome-wide data, and moves into topics such as clustering, classification, multi-dimensional visualization, experimental design, statistical resampling, and statistical network analysis. Clearly explains the use of bioinformatics tools in life sciences research without requiring an advanced background in math/statistics Enables biomedical and life sciences researchers to successfully evaluate the validity of their results and make inferences Enables statistical and quantitative researchers to rapidly learn novel statistical concepts and techniques appropriate for large biological data analysis Carefully revisits frequently used statistical approaches and highlights their limitations in large biological data analysis Offers programming examples and datasets Includes chapter problem sets, a glossary, a list of statistical notations, and appendices with references to background mathematical and technical material Features supplementary materials, including datasets, links, and a statistical package available online Statistical Bioinformatics is an ideal textbook for students in medicine, life sciences, and bioengineering, aimed at researchers who utilize computational tools for the analysis of genomic, proteomic, and many other emerging high-throughput molecular data. It may also serve as a rapid introduction to the bioinformatics science for statistical and computational students and audiences who have not experienced such analysis tasks before.
Call Number: E-BOOKISBN: 9780471692720Publication Date: 2014-06-23
Building Bioinformatics Solutions by
Bioinformatics encompasses a broad and ever-changing range of activities involved with the management and analysis of data from molecular biology experiments. Despite the diversity of activities and applications, the basic methodology and core tools needed to tackle bioinformatics problems is common to many projects. This unique book provides an invaluable introduction to three of the main tools used in the development of bioinformatics software - Perl, R and MySQL - and explains how these can be used together to tackle the complex data-driven challenges that typify modern biology. These industry standard open source tools form the core of many bioinformatics projects, both in academia and industry. The methodologies introduced are platform independent, and all the examples that feature have been tested on Windows, Linux and Mac OS. Building Bioinformatics Solutions is suitable for graduate students and researchers in the life sciences who wish to automate analyses or create their own databases and web-based tools. No prior knowledge of software development is assumed. Having worked through the book, the reader should have the necessary core skills to develop computational solutions for their specific research programmes. The book will also help the reader overcome the inertia associated with penetrating this field, and provide them with the confidence and understanding required to go on to develop more advanced bioinformatics skills.
Call Number: E-BOOKISBN: 9781306474054Publication Date: 2014-04-01
Specific Gene Expression and Epigenetics by
This new volume on gene expression and epigenetics discusses environmental effects related to specific gene expression. The book also shows methods for bioinformatic analysis of the epigenome. The book is broken into two sections: the first looks at eukaryotic DNA methylation and the second addresses how to integrate genomic medicine into clinical practice. The book includes chapters on these topics: * Gene expression in colon cancer tissue * Epigenetics in human acute kidney injury * Embryologically relevant candidate genes in MRKH patients * DNA methylation in common skeletal disorders * Causal relationships in genomics * Predicting severe asthma exacerbations in children * Epigenetic understanding of gene-environment interactions in psychiatric disorders
Call Number: E-BOOKISBN: 1771880368Publication Date: 2014-03-18
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