Bioinformatics Algorithms

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Bioinformatics Algorithms

Bioinformatics Algorithms
  • Author : Phillip Compeau,Pavel Pevzner
  • Publisher : Unknown
  • Release Date : 1986-06
  • Total pages : 229
  • ISBN : 0990374637
  • File Size : 13,6 Mb
  • Total Download : 170
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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 Algorithms

Bioinformatics Algorithms
  • Author : Phillip Compeau,Pavel Pevzner
  • Publisher : Unknown
  • Release Date : 2014-05-20
  • Total pages : 392
  • ISBN : 0990374602
  • File Size : 27,7 Mb
  • Total Download : 644
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Bioinformatics Algorithms: an Active Learning Approach is one of the first textbooks to emerge from the recent Massive Open Online Course (MOOC) revolution. A light-hearted and analogy-filled companion to the authors' acclaimed MOOC on Coursera, 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 both biology and computer science. 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 the Rosalind Bioinformatics Textbook Track. A website augments the textbook by providing additional educational materials, including video lectures and PowerPoint slides.--Book website.

Bioinformatics Algorithms

Bioinformatics Algorithms
  • Author : Phillip Compeau
  • Publisher : Unknown
  • Release Date : 2015
  • Total pages : 229
  • ISBN : OCLC:947030152
  • File Size : 17,7 Mb
  • Total Download : 324
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PDF book entitled Bioinformatics Algorithms written by Phillip Compeau and published by Unknown which was released on 2015 with total hardcover pages 229, the book become popular and critical acclaim.

Bioinformatics Algorithms

Bioinformatics Algorithms
  • Author : Miguel Rocha,Pedro G. Ferreira
  • Publisher : Academic Press
  • Release Date : 2018-06-08
  • Total pages : 400
  • ISBN : 9780128125212
  • File Size : 31,7 Mb
  • Total Download : 385
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Bioinformatics Algorithms: Design and Implementation in Python provides a comprehensive book on many of the most important bioinformatics problems, putting forward the best algorithms and showing how to implement them. The book focuses on the use of the Python programming language and its algorithms, which is quickly becoming the most popular language in the bioinformatics field. Readers will find the tools they need to improve their knowledge and skills with regard to algorithm development and implementation, and will also uncover prototypes of bioinformatics applications that demonstrate the main principles underlying real world applications. Presents an ideal text for bioinformatics students with little to no knowledge of computer programming Based on over 12 years of pedagogical materials used by the authors in their own classrooms Features a companion website with downloadable codes and runnable examples (such as using Jupyter Notebooks) and exercises relating to the book

An Introduction to Bioinformatics Algorithms

An Introduction to Bioinformatics Algorithms
  • Author : Neil C. Jones,Pavel A. Pevzner
  • Publisher : MIT Press
  • Release Date : 2004-08-06
  • Total pages : 460
  • ISBN : 0262101068
  • File Size : 31,5 Mb
  • Total Download : 722
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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 Algorithms

Bioinformatics Algorithms
  • Author : Ion Mandoiu,Alexander Zelikovsky
  • Publisher : John Wiley & Sons
  • Release Date : 2008-02-25
  • Total pages : 528
  • ISBN : 9780470097731
  • File Size : 22,9 Mb
  • Total Download : 390
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Presents algorithmic techniques for solving problems in bioinformatics, including applications that shed new light on molecular biology This book introduces algorithmic techniques in bioinformatics, emphasizing their application to solving novel problems in post-genomic molecular biology. Beginning with a thought-provoking discussion on the role of algorithms in twenty-first-century bioinformatics education, Bioinformatics Algorithms covers: General algorithmic techniques, including dynamic programming, graph-theoretical methods, hidden Markov models, the fast Fourier transform, seeding, and approximation algorithms Algorithms and tools for genome and sequence analysis, including formal and approximate models for gene clusters, advanced algorithms for non-overlapping local alignments and genome tilings, multiplex PCR primer set selection, and sequence/network motif finding Microarray design and analysis, including algorithms for microarray physical design, missing value imputation, and meta-analysis of gene expression data Algorithmic issues arising in the analysis of genetic variation across human population, including computational inference of haplotypes from genotype data and disease association search in case/control epidemiologic studies Algorithmic approaches in structural and systems biology, including topological and structural classification in biochemistry, and prediction of protein-protein and domain-domain interactions Each chapter begins with a self-contained introduction to a computational problem; continues with a brief review of the existing literature on the subject and an in-depth description of recent algorithmic and methodological developments; and concludes with a brief experimental study and a discussion of open research challenges. This clear and approachable presentation makes the book appropriate for researchers, practitioners, and graduate students alike.

Bioinformatics Algorithms

Bioinformatics Algorithms
  • Author : Ion Mandoiu,Alexander Zelikovsky
  • Publisher : John Wiley & Sons
  • Release Date : 2008-02-15
  • Total pages : 520
  • ISBN : 0470253428
  • File Size : 26,5 Mb
  • Total Download : 858
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Download Bioinformatics Algorithms in PDF, Epub, and Kindle

Presents algorithmic techniques for solving problems in bioinformatics, including applications that shed new light on molecular biology This book introduces algorithmic techniques in bioinformatics, emphasizing their application to solving novel problems in post-genomic molecular biology. Beginning with a thought-provoking discussion on the role of algorithms in twenty-first-century bioinformatics education, Bioinformatics Algorithms covers: General algorithmic techniques, including dynamic programming, graph-theoretical methods, hidden Markov models, the fast Fourier transform, seeding, and approximation algorithms Algorithms and tools for genome and sequence analysis, including formal and approximate models for gene clusters, advanced algorithms for non-overlapping local alignments and genome tilings, multiplex PCR primer set selection, and sequence/network motif finding Microarray design and analysis, including algorithms for microarray physical design, missing value imputation, and meta-analysis of gene expression data Algorithmic issues arising in the analysis of genetic variation across human population, including computational inference of haplotypes from genotype data and disease association search in case/control epidemiologic studies Algorithmic approaches in structural and systems biology, including topological and structural classification in biochemistry, and prediction of protein-protein and domain-domain interactions Each chapter begins with a self-contained introduction to a computational problem; continues with a brief review of the existing literature on the subject and an in-depth description of recent algorithmic and methodological developments; and concludes with a brief experimental study and a discussion of open research challenges. This clear and approachable presentation makes the book appropriate for researchers, practitioners, and graduate students alike.

Algorithms in Bioinformatics

Algorithms in Bioinformatics
  • Author : Paul A. Gagniuc
  • Publisher : John Wiley & Sons
  • Release Date : 2021-08-10
  • Total pages : 532
  • ISBN : 9781119697961
  • File Size : 33,8 Mb
  • Total Download : 616
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ALGORITHMS IN BIOINFORMATICS Explore a comprehensive and insightful treatment of the practical application of bioinformatic algorithms in a variety of fields Algorithms in Bioinformatics: Theory and Implementation delivers a fulsome treatment of some of the main algorithms used to explain biological functions and relationships. It introduces readers to the art of algorithms in a practical manner which is linked with biological theory and interpretation. The book covers many key areas of bioinformatics, including global and local sequence alignment, forced alignment, detection of motifs, Sequence logos, Markov chains or information entropy. Other novel approaches are also described, such as Self-Sequence alignment, Objective Digital Stains (ODSs) or Spectral Forecast and the Discrete Probability Detector (DPD) algorithm. The text incorporates graphical illustrations to highlight and emphasize the technical details of computational algorithms found within, to further the reader’s understanding and retention of the material. Throughout, the book is written in an accessible and practical manner, showing how algorithms can be implemented and used in JavaScript on Internet Browsers. The author has included more than 120 open-source implementations of the material, as well as 33 ready-to-use presentations. The book contains original material that has been class-tested by the author and numerous cases are examined in a biological and medical context. Readers will also benefit from the inclusion of: A thorough introduction to biological evolution, including the emergence of life, classifications and some known theories and molecular mechanisms A detailed presentation of new methods, such as Self-sequence alignment, Objective Digital Stains and Spectral Forecast A treatment of sequence alignment, including local sequence alignment, global sequence alignment and forced sequence alignment with full implementations Discussions of position-specific weight matrices, including the count, weight, relative frequencies, and log-likelihoods matrices A detailed presentation of the methods related to Markov Chains as well as a description of their implementation in Bioinformatics and adjacent fields An examination of information and entropy, including sequence logos and explanations related to their meaning An exploration of the current state of bioinformatics, including what is known and what issues are usually avoided in the field A chapter on philosophical transactions that allows the reader a broader view of the prediction process Native computer implementations in the context of the field of Bioinformatics Extensive worked examples with detailed case studies that point out the meaning of different results Perfect for professionals and researchers in biology, medicine, engineering, and information technology, as well as upper level undergraduate students in these fields, Algorithms in Bioinformatics: Theory and Implementation will also earn a place in the libraries of software engineers who wish to understand how to implement bioinformatic algorithms in their products.

Algorithms in Bioinformatics

Algorithms in Bioinformatics
  • Author : Wing-Kin Sung
  • Publisher : CRC Press
  • Release Date : 2009-11-24
  • Total pages : 407
  • ISBN : 9781420070347
  • File Size : 37,5 Mb
  • Total Download : 507
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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

Pattern Discovery in Bioinformatics

Pattern Discovery in Bioinformatics
  • Author : Laxmi Parida
  • Publisher : CRC Press
  • Release Date : 2007-07-04
  • Total pages : 512
  • ISBN : 9781420010732
  • File Size : 44,9 Mb
  • Total Download : 482
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The computational methods of bioinformatics are being used more and more to process the large volume of current biological data. Promoting an understanding of the underlying biology that produces this data, Pattern Discovery in Bioinformatics: Theory and Algorithms provides the tools to study regularities in biological data. Taking a systema

Algorithmic Aspects of Bioinformatics

Algorithmic Aspects of Bioinformatics
  • Author : Hans-Joachim Böckenhauer,Dirk Bongartz
  • Publisher : Springer Science & Business Media
  • Release Date : 2007-06-06
  • Total pages : 396
  • ISBN : 9783540719137
  • File Size : 28,6 Mb
  • Total Download : 880
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This book introduces some key problems in bioinformatics, discusses the models used to formally describe these problems, and analyzes the algorithmic approaches used to solve them. After introducing the basics of molecular biology and algorithmics, Part I explains string algorithms and alignments; Part II details the field of physical mapping and DNA sequencing; and Part III examines the application of algorithmics to the analysis of biological data. Exciting application examples include predicting the spatial structure of proteins, and computing haplotypes from genotype data. Figures, chapter summaries, detailed derivations, and examples, are provided.

Multiobjective Genetic Algorithms for Clustering

Multiobjective Genetic Algorithms for Clustering
  • Author : Ujjwal Maulik,Sanghamitra Bandyopadhyay,Anirban Mukhopadhyay
  • Publisher : Springer Science & Business Media
  • Release Date : 2011-09-01
  • Total pages : 281
  • ISBN : 9783642166150
  • File Size : 21,5 Mb
  • Total Download : 350
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Download Multiobjective Genetic Algorithms for Clustering in PDF, Epub, and Kindle

This is the first book primarily dedicated to clustering using multiobjective genetic algorithms with extensive real-life applications in data mining and bioinformatics. The authors first offer detailed introductions to the relevant techniques – genetic algorithms, multiobjective optimization, soft computing, data mining and bioinformatics. They then demonstrate systematic applications of these techniques to real-world problems in the areas of data mining, bioinformatics and geoscience. The authors offer detailed theoretical and statistical notes, guides to future research, and chapter summaries. The book can be used as a textbook and as a reference book by graduate students and academic and industrial researchers in the areas of soft computing, data mining, bioinformatics and geoscience.

Structural Bioinformatics

Structural Bioinformatics
  • Author : Forbes J. Burkowski
  • Publisher : CRC Press
  • Release Date : 2008-10-30
  • Total pages : 429
  • ISBN : 9781420011791
  • File Size : 38,8 Mb
  • Total Download : 441
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The Beauty of Protein Structures and the Mathematics behind Structural Bioinformatics Providing the framework for a one-semester undergraduate course, Structural Bioinformatics: An Algorithmic Approach shows how to apply key algorithms to solve problems related to macromolecular structure. Helps Students Go Further in Their Study of Structural Biology Following some introductory material in the first few chapters, the text solves the longest common subsequence problem using dynamic programming and explains the science models for the Nussinov and MFOLD algorithms. It then reviews sequence alignment, along with the basic mathematical calculations needed for measuring the geometric properties of macromolecules. After looking at how coordinate transformations facilitate the translation and rotation of molecules in a 3D space, the author introduces structural comparison techniques, superposition algorithms, and algorithms that compare relationships within a protein. The final chapter explores how regression and classification are becoming more useful in protein analysis and drug design. At the Crossroads of Biology, Mathematics, and Computer Science Connecting biology, mathematics, and computer science, this practical text presents various bioinformatics topics and problems within a scientific methodology that emphasizes nature (the source of empirical observations), science (the mathematical modeling of the natural process), and computation (the science of calculating predictions and mathematical objects based on mathematical models).

Molecular Bioinformatics

Molecular Bioinformatics
  • Author : Steffen Schulze-Kremer
  • Publisher : Walter de Gruyter
  • Release Date : 1996
  • Total pages : 324
  • ISBN : 3110141132
  • File Size : 14,9 Mb
  • Total Download : 813
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PDF book entitled Molecular Bioinformatics written by Steffen Schulze-Kremer and published by Walter de Gruyter which was released on 1996 with total hardcover pages 324, the book become popular and critical acclaim.

Algorithms on Strings, Trees and Sequences

Algorithms on Strings, Trees and Sequences
  • Author : Dan Gusfield
  • Publisher : Cambridge University Press
  • Release Date : 1997-05-28
  • Total pages : 229
  • ISBN : 9781139811002
  • File Size : 43,6 Mb
  • Total Download : 931
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String algorithms are a traditional area of study in computer science. In recent years their importance has grown dramatically with the huge increase of electronically stored text and of molecular sequence data (DNA or protein sequences) produced by various genome projects. This 1997 book is a general text on computer algorithms for string processing. In addition to pure computer science, the book contains extensive discussions on biological problems that are cast as string problems, and on methods developed to solve them. It emphasises the fundamental ideas and techniques central to today's applications. New approaches to this complex material simplify methods that up to now have been for the specialist alone. With over 400 exercises to reinforce the material and develop additional topics, the book is suitable as a text for graduate or advanced undergraduate students in computer science, computational biology, or bio-informatics. Its discussion of current algorithms and techniques also makes it a reference for professionals.

Introduction to Protein Structure Prediction

Introduction to Protein Structure Prediction
  • Author : Huzefa Rangwala,George Karypis
  • Publisher : John Wiley & Sons
  • Release Date : 2011-03-16
  • Total pages : 520
  • ISBN : 111809946X
  • File Size : 11,6 Mb
  • Total Download : 770
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A look at the methods and algorithms used to predict proteinstructure A thorough knowledge of the function and structure of proteinsis critical for the advancement of biology and the life sciences aswell as the development of better drugs, higher-yield crops, andeven synthetic bio-fuels. To that end, this reference sheds lighton the methods used for protein structure prediction and revealsthe key applications of modeled structures. This indispensable bookcovers the applications of modeled protein structures and unravelsthe relationship between pure sequence information andthree-dimensional structure, which continues to be one of thegreatest challenges in molecular biology. With this resource, readers will find an all-encompassingexamination of the problems, methods, tools, servers, databases,and applications of protein structure prediction and they willacquire unique insight into the future applications of the modeledprotein structures. The book begins with a thorough introduction tothe protein structure prediction problem and is divided into fourthemes: a background on structure prediction, the prediction ofstructural elements, tertiary structure prediction, and functionalinsights. Within those four sections, the following topics arecovered: Databases and resources that are commonly used for proteinstructure prediction The structure prediction flagship assessment (CASP) and theprotein structure initiative (PSI) Definitions of recurring substructures and the computationalapproaches used for solving sequence problems Difficulties with contact map prediction and how sophisticatedmachine learning methods can solve those problems Structure prediction methods that rely on homology modeling,threading, and fragment assembly Hybrid methods that achieve high-resolution proteinstructures Parts of the protein structure that may be conserved and usedto interact with other biomolecules How the loop prediction problem can be used for refinement ofthe modeled structures The computational model that detects the differences betweenprotein structure and its modeled mutant Whether working in the field of bioinformatics or molecularbiology research or taking courses in protein modeling, readerswill find the content in this book invaluable.

Bioinformatics and RNA

Bioinformatics and RNA
  • Author : Dolly Sharma,Shailendra Singh,Mamta Mittal
  • Publisher : CRC Press
  • Release Date : 2021-08-18
  • Total pages : 148
  • ISBN : 9781000428339
  • File Size : 47,8 Mb
  • Total Download : 530
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This book offers a unique balance between a basic introductory knowledge of bioinformatics and a detailed study of algorithmic techniques. Bioinformatics and RNA: A Practice-Based Approach is a complete guide on the fundamental concepts, applications, algorithms, protocols, new trends, challenges, and research results in the area of bioinformatics and RNA. The book offers a broad introduction to the explosively growing new discipline of bioinformatics. It covers theoretical topics along with computational algorithms. It explores RNA bioinformatics, which contribute to therapeutics and drug discovery. Implementation of algorithms in a DotNet Framework with code and complete insight on the state-of-the-art and recent advancements are presented in detail. The book targets both novice readers as well as practitioners in the field. FEATURES Offers a broad introduction to the explosively growing new discipline of bioinformatics Covers theoretical topics and computational algorithms Explores RNA bioinformatics to unleash the potential from therapeutics to drug discovery Discusses implementation of algorithms in DotNet Frameworks with code Presents insights into the state of the art and recent advancements in bioinformatics The book is useful to undergraduate students with engineering, science, mathematics, or biology backgrounds. Researchers will be equally interested.

Bioinformatics

Bioinformatics
  • Author : N. Gautham
  • Publisher : Alpha Science Int'l Ltd.
  • Release Date : 2006
  • Total pages : 268
  • ISBN : 1842653008
  • File Size : 28,8 Mb
  • Total Download : 937
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This text features detailed descriptions of methods of bio molecular sequence and structure analyses of interest to students and practitioners of bioinformatics both in the corporate and academic sectors.

Algorithms for Computational Biology

Algorithms for Computational Biology
  • Author : Carlos Martín-Vide,Miguel A. Vega-Rodríguez,Travis Wheeler
  • Publisher : Springer Nature
  • Release Date : 2021-05-31
  • Total pages : 173
  • ISBN : 9783030744328
  • File Size : 11,7 Mb
  • Total Download : 140
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This book constitutes the proceedings of the 8th International Conference on Algorithms for Computational Biology, AlCoB 2020, was planned to be held in Missoula, MT, USA in June 2021. Due to the Covid-19 pandemic, AlCoB 2020 and AlCoB 2021 were merged and held on these dates together. AlCoB 2020 proceedings were published as LNBI 12099. The 12 full papers included in this volume were carefully reviewed and selected from 22 submissions. They were organized in topical sections on genomics, phylogenetics, and RNA-Seq and other biological processes. The scope of AlCoB includes topics of either theoretical or applied interest, namely: sequence analysis; sequence alignment; sequence assembly; genome rearrangement; regulatory motif finding; phylogeny reconstruction; phylogeny comparison; structure prediction; compressive genomics; proteomics: molecular pathways, interaction networks, mass spectrometry analysis; transcriptomics: splicing variants, isoform inference and quantification, differential analysis; next-generation sequencing: population genomics, metagenomics, metatranscriptomics, epigenomics; genome CD architecture; microbiome analysis; cancer computational biology; and systems biology.

Genome-Scale Algorithm Design

Genome-Scale Algorithm Design
  • Author : Veli Mäkinen,Djamal Belazzougui,Fabio Cunial,Alexandru I. Tomescu
  • Publisher : Cambridge University Press
  • Release Date : 2015-05-07
  • Total pages : 415
  • ISBN : 9781107078536
  • File Size : 11,9 Mb
  • Total Download : 370
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Provides an integrated picture of the latest developments in algorithmic techniques, with numerous worked examples, algorithm visualisations and exercises.

Bioinformatics for Biologists

Bioinformatics for Biologists
  • Author : Pavel Pevzner,Ron Shamir
  • Publisher : Cambridge University Press
  • Release Date : 2011-09-15
  • Total pages : 229
  • ISBN : 9781139501613
  • File Size : 26,6 Mb
  • Total Download : 591
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The computational education of biologists is changing to prepare students for facing the complex datasets of today's life science research. In this concise textbook, the authors' fresh pedagogical approaches lead biology students from first principles towards computational thinking. A team of renowned bioinformaticians take innovative routes to introduce computational ideas in the context of real biological problems. Intuitive explanations promote deep understanding, using little mathematical formalism. Self-contained chapters show how computational procedures are developed and applied to central topics in bioinformatics and genomics, such as the genetic basis of disease, genome evolution or the tree of life concept. Using bioinformatic resources requires a basic understanding of what bioinformatics is and what it can do. Rather than just presenting tools, the authors - each a leading scientist - engage the students' problem-solving skills, preparing them to meet the computational challenges of their life science careers.