Mathematics Of Bioinformatics

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Mathematics of Bioinformatics

Matthew He,Sergey Petoukhov
Mathematics of Bioinformatics Book PDF

Author : Matthew He,Sergey Petoukhov
Publisher : John Wiley & Sons
Page : 231 pages
File Size : 53,7 Mb
Release : 2011-03-16
Category : Computers
ISBN : 9781118099520

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Mathematics of Bioinformatics by Matthew He,Sergey Petoukhov Pdf

Mathematics of Bioinformatics: Theory, Methods, and Applications provides a comprehensive format for connecting and integrating information derived from mathematical methods and applying it to the understanding of biological sequences, structures, and networks. Each chapter is divided into a number of sections based on the bioinformatics topics and related mathematical theory and methods. Each topic of the section is comprised of the following three parts: an introduction to the biological problems in bioinformatics; a presentation of relevant topics of mathematical theory and methods to the bioinformatics problems introduced in the first part; an integrative overview that draws the connections and interfaces between bioinformatics problems/issues and mathematical theory/methods/applications.

Introduction to Mathematical Methods in Bioinformatics

Alexander Isaev
Introduction to Mathematical Methods in Bioinformatics Book PDF

Author : Alexander Isaev
Publisher : Springer Science & Business Media
Page : 316 pages
File Size : 50,7 Mb
Release : 2006-09-19
Category : Science
ISBN : 3540219730

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Introduction to Mathematical Methods in Bioinformatics by Alexander Isaev Pdf

This book looks at the mathematical foundations of the models currently in use. All existing books on bioinformatics are software-orientated and they concentrate on computer implementations of mathematical models of biology. This book is unique in the sense that it looks at the mathematical foundations of the models, which are crucial for correct interpretation of the outputs of the models.

Theory and Mathematical Methods in Bioinformatics

Shiyi Shen
Theory and Mathematical Methods in Bioinformatics Book PDF

Author : Shiyi Shen
Publisher : Springer Science & Business Media
Page : 450 pages
File Size : 52,7 Mb
Release : 2008-01-26
Category : Science
ISBN : 9783540748915

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Theory and Mathematical Methods in Bioinformatics by Shiyi Shen Pdf

This monograph addresses, in a systematic and pedagogical manner, the mathematical methods and the algorithms required to deal with the molecularly based problems of bioinformatics. Prominent attention is given to pair-wise and multiple sequence alignment algorithms, stochastic models of mutations, modulus structure theory and protein configuration analysis. Strong links to the molecular structures of proteins, DNA and other biomolecules and their analyses are developed.

Statistical Methods in Bioinformatics

Warren J. Ewens,Gregory R. Grant
Statistical Methods in Bioinformatics Book PDF

Author : Warren J. Ewens,Gregory R. Grant
Publisher : Springer Science & Business Media
Page : 616 pages
File Size : 44,5 Mb
Release : 2005-09-30
Category : Science
ISBN : 9780387400822

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Statistical Methods in Bioinformatics by Warren J. Ewens,Gregory R. Grant Pdf

Advances in computers and biotechnology have had a profound impact on biomedical research, and as a result complex data sets can now be generated to address extremely complex biological questions. Correspondingly, advances in the statistical methods necessary to analyze such data are following closely behind the advances in data generation methods. The statistical methods required by bioinformatics present many new and difficult problems for the research community. This book provides an introduction to some of these new methods. The main biological topics treated include sequence analysis, BLAST, microarray analysis, gene finding, and the analysis of evolutionary processes. The main statistical techniques covered include hypothesis testing and estimation, Poisson processes, Markov models and Hidden Markov models, and multiple testing methods. The second edition features new chapters on microarray analysis and on statistical inference, including a discussion of ANOVA, and discussions of the statistical theory of motifs and methods based on the hypergeometric distribution. Much material has been clarified and reorganized. The book is written so as to appeal to biologists and computer scientists who wish to know more about the statistical methods of the field, as well as to trained statisticians who wish to become involved with bioinformatics. The earlier chapters introduce the concepts of probability and statistics at an elementary level, but with an emphasis on material relevant to later chapters and often not covered in standard introductory texts. Later chapters should be immediately accessible to the trained statistician. Sufficient mathematical background consists of introductory courses in calculus and linear algebra. The basic biological concepts that are used are explained, or can be understood from the context, and standard mathematical concepts are summarized in an Appendix. Problems are provided at the end of each chapter allowing the reader to develop aspects of the theory outlined in the main text. Warren J. Ewens holds the Christopher H. Brown Distinguished Professorship at the University of Pennsylvania. He is the author of two books, Population Genetics and Mathematical Population Genetics. He is a senior editor of Annals of Human Genetics and has served on the editorial boards of Theoretical Population Biology, GENETICS, Proceedings of the Royal Society B and SIAM Journal in Mathematical Biology. He is a fellow of the Royal Society and the Australian Academy of Science. Gregory R. Grant is a senior bioinformatics researcher in the University of Pennsylvania Computational Biology and Informatics Laboratory. He obtained his Ph.D. in number theory from the University of Maryland in 1995 and his Masters in Computer Science from the University of Pennsylvania in 1999. Comments on the first edition: "This book would be an ideal text for a postgraduate course...[and] is equally well suited to individual study.... I would recommend the book highly." (Biometrics) "Ewens and Grant have given us a very welcome introduction to what is behind those pretty [graphical user] interfaces." (Naturwissenschaften) "The authors do an excellent job of presenting the essence of the material without getting bogged down in mathematical details." (Journal American Statistical Association) "The authors have restructured classical material to a great extent and the new organization of the different topics is one of the outstanding services of the book." (Metrika)

Mathematical Principles in Bioinformatics

Stephen S.-T. Yau,Xin Zhao,Kun Tian,Hongyu Yu
Mathematical Principles in Bioinformatics Book PDF

Author : Stephen S.-T. Yau,Xin Zhao,Kun Tian,Hongyu Yu
Publisher : Springer Nature
Page : 177 pages
File Size : 54,7 Mb
Release : 2024-01-11
Category : Science
ISBN : 9783031482953

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Mathematical Principles in Bioinformatics by Stephen S.-T. Yau,Xin Zhao,Kun Tian,Hongyu Yu Pdf

This textbook introduces bioinformatics to students in mathematics with no biology background assumed and it provides solid mathematical tools for biology students along with an understanding of how to implement them in bioinformatics problems. In addition to the basics, the text offers new approaches to understanding biological sequences. The concise presentation distinguishes itself from others on the subject, discussing and providing principles that relate to current open problems in bioinformatics as well as considering a variety of models. The convex hull principle is highlighted, opening a new interdisciplinary research area at the intersection of biology, mathematics, and computer science. Prerequisites include first courses in linear algebra, probability and statistics, and mathematical analysis. Researchers in mathematics, biology, and math-biology, will also find aspects of this text useful. This textbook is written based on the authors' research works that have been published in various journals along with the lecture notes used when teaching bioinformatics courses at the University of Illinois at Chicago and at Tsinghua University. The content may be divided into two parts. The first part includes three chapters, introducing some basic concepts. Chapter 1 provides biological background in molecular biology for mathematicians. Chapter 2 describes biological databases that are commonly used. Chapter 3 is concerned with alignment methods including global/local alignment, heuristic alignment, and multiple alignment. The second part consisting of five chapters, describes several bioinformatics principles using a rigorous mathematical formulation. Chapter 4 introduces the time-frequency spectral principle and its applications in bioinformatics. In Chapters 5 and 6, two strategies are used, the graphical representation and the natural vector method, to represent biological sequences, and conduct sequence comparison and phylogenetic analysis without alignment. Chapter 7 presents the convex hull principle and shows how it can be used to mathematically determine whether a certain amino acid sequence can be a protein. The last chapter summarizes additional mathematical ideas relating to sequence comparisons, such as new feature vectors and metrics. This part focuses on the governing principle in biology and provides plenty of alignment-free methods, which cannot be found in any other book.

Introduction to Mathematical Methods in Bioinformatics

Alexander Isaev
Introduction to Mathematical Methods in Bioinformatics Book PDF

Author : Alexander Isaev
Publisher : Springer
Page : 294 pages
File Size : 48,5 Mb
Release : 2006-10-04
Category : Science
ISBN : 9783540484264

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Introduction to Mathematical Methods in Bioinformatics by Alexander Isaev Pdf

This book looks at the mathematical foundations of the models currently in use. All existing books on bioinformatics are software-orientated and they concentrate on computer implementations of mathematical models of biology. This book is unique in the sense that it looks at the mathematical foundations of the models, which are crucial for correct interpretation of the outputs of the models.

Bioinformatics

Andrzej Polanski,Marek Kimmel
Bioinformatics Book PDF

Author : Andrzej Polanski,Marek Kimmel
Publisher : Springer Science & Business Media
Page : 386 pages
File Size : 41,8 Mb
Release : 2007-04-19
Category : Computers
ISBN : 9783540241669

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Bioinformatics by Andrzej Polanski,Marek Kimmel Pdf

This textbook presents mathematical models in bioinformatics and describes biological problems that inspire the computer science tools used to manage the enormous data sets involved. The first part of the book covers mathematical and computational methods, with practical applications presented in the second part. The mathematical presentation avoids unnecessary formalism, while remaining clear and precise. The book closes with a thorough bibliography, reaching from classic research results to very recent findings. This volume is suited for a senior undergraduate or graduate course on bioinformatics, with a strong focus on mathematical and computer science background.

Theory And Mathematical Methods For Bioinformatics, 1/e

Shen,Jack A Tuszynski,Shiyi
Theory And Mathematical Methods For Bioinformatics 1 e Book PDF

Author : Shen,Jack A Tuszynski,Shiyi
Publisher : Unknown
Page : 128 pages
File Size : 43,6 Mb
Release : 2010-12-01
Category : Electronic
ISBN : 8184896255

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Theory And Mathematical Methods For Bioinformatics, 1/e by Shen,Jack A Tuszynski,Shiyi Pdf

This monograph addresses, in a systematic and pedagogical manner, the mathematical methods and the algorithms required to deal with the molecularly based problems of bioinformatics. The book will be useful to students, research scientists and practitioners of bioinformatics and related fields, especially those who are interested in the underlying mathematical methods and theory. Among the methods presented in the book, prominent attention is given to pair-wise and multiple sequence alignment algorithms, stochastic models of mutations, modulus structure theory and protein configuration analysis. Strong links to the molecular structures of proteins, DNA and other biomolecules and their analyses are developed. In particular, for proteins an in-depth exposition of secondary structure prediction methods should be a valuable tool in both molecular biology and in applications to rational drug design. The book can also be used as a textbook and for this reason most of the chapters include exercises and problems at the level of a graduate program in bioinformatics.

Encyclopedia of Bioinformatics and Computational Biology

Anonim
Encyclopedia of Bioinformatics and Computational Biology Book PDF

Author : Anonim
Publisher : Elsevier
Page : 3421 pages
File Size : 41,9 Mb
Release : 2018-08-21
Category : Medical
ISBN : 9780128114322

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Encyclopedia of Bioinformatics and Computational Biology by Anonim Pdf

Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases

Symmetrical Analysis Techniques for Genetic Systems and Bioinformatics: Advanced Patterns and Applications

Petoukhov, Sergey,He, Matthew
Symmetrical Analysis Techniques for Genetic Systems and Bioinformatics Advanced Patterns and Applications Book PDF

Author : Petoukhov, Sergey,He, Matthew
Publisher : IGI Global
Page : 290 pages
File Size : 40,5 Mb
Release : 2009-10-31
Category : Computers
ISBN : 9781605661254

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Symmetrical Analysis Techniques for Genetic Systems and Bioinformatics: Advanced Patterns and Applications by Petoukhov, Sergey,He, Matthew Pdf

"This book compiles studies that demonstrate effective approaches to the structural analysis of genetic systems and bioinformatics"--Provided by publisher.

Algebraic and Discrete Mathematical Methods for Modern Biology

Raina Robeva
Algebraic and Discrete Mathematical Methods for Modern Biology Book PDF

Author : Raina Robeva
Publisher : Academic Press
Page : 382 pages
File Size : 41,8 Mb
Release : 2015-05-09
Category : Mathematics
ISBN : 9780128012710

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Algebraic and Discrete Mathematical Methods for Modern Biology by Raina Robeva Pdf

Written by experts in both mathematics and biology, Algebraic and Discrete Mathematical Methods for Modern Biology offers a bridge between math and biology, providing a framework for simulating, analyzing, predicting, and modulating the behavior of complex biological systems. Each chapter begins with a question from modern biology, followed by the description of certain mathematical methods and theory appropriate in the search of answers. Every topic provides a fast-track pathway through the problem by presenting the biological foundation, covering the relevant mathematical theory, and highlighting connections between them. Many of the projects and exercises embedded in each chapter utilize specialized software, providing students with much-needed familiarity and experience with computing applications, critical components of the "modern biology" skill set. This book is appropriate for mathematics courses such as finite mathematics, discrete structures, linear algebra, abstract/modern algebra, graph theory, probability, bioinformatics, statistics, biostatistics, and modeling, as well as for biology courses such as genetics, cell and molecular biology, biochemistry, ecology, and evolution. Examines significant questions in modern biology and their mathematical treatments Presents important mathematical concepts and tools in the context of essential biology Features material of interest to students in both mathematics and biology Presents chapters in modular format so coverage need not follow the Table of Contents Introduces projects appropriate for undergraduate research Utilizes freely accessible software for visualization, simulation, and analysis in modern biology Requires no calculus as a prerequisite Provides a complete Solutions Manual Features a companion website with supplementary resources

Emergent Computation

Matthew Simon
Emergent Computation Book PDF

Author : Matthew Simon
Publisher : Springer Science & Business Media
Page : 431 pages
File Size : 42,7 Mb
Release : 2005-11-10
Category : Science
ISBN : 9780387272702

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Emergent Computation by Matthew Simon Pdf

Emergent Computation emphasizes the interrelationship of the different classes of languages studied in mathematical linguistics (regular, context-free, context-sensitive, and type 0) with aspects to the biochemistry of DNA, RNA, and proteins. In addition, aspects of sequential machines such as parity checking and semi-groups are extended to the study of the Biochemistry of DNA, RNA, and proteins. Mention is also made of the relationship of algebraic topology, knot theory, complex fields, quaternions, and universal turing machines and the biochemistry of DNA, RNA, and proteins. Emergent Computation tries to avoid an emphasis upon mathematical abstraction ("elegance") at the expense of ignoring scientific facts known to Biochemists. Emergent Computation is based entirely upon papers published by scientists in well-known and respected professional journals. These papers are based upon current research. A few examples of what is not ignored to gain "elegance": - DNA exists as triple and quadruple strands - Watson-Crick complementary bases have mismatches - There can be more than four bases in DNA - There are more than sixty-four codons - There may be more that twenty amino acids in proteins While Emergent Computation emphasizes bioinformatics applications, the last chapter studies mathematical linguistics applied to areas such as languages found in birds, insects, medical applications, anthropology, etc. Emergent Computation tries to avoid unnecessary mathematical abstraction while still being rigorous. The demands made upon the knowledge of chemistry or mathematics is minimized as well. The collected technical references are valuable in itself for additional reading.

Modeling in Computational Biology and Biomedicine

Frédéric Cazals,Pierre Kornprobst
Modeling in Computational Biology and Biomedicine Book PDF

Author : Frédéric Cazals,Pierre Kornprobst
Publisher : Springer Science & Business Media
Page : 333 pages
File Size : 43,9 Mb
Release : 2012-11-06
Category : Mathematics
ISBN : 9783642312083

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Modeling in Computational Biology and Biomedicine by Frédéric Cazals,Pierre Kornprobst Pdf

Computational biology, mathematical biology, biology and biomedicine are currently undergoing spectacular progresses due to a synergy between technological advances and inputs from physics, chemistry, mathematics, statistics and computer science. The goal of this book is to evidence this synergy by describing selected developments in the following fields: bioinformatics, biomedicine and neuroscience. This work is unique in two respects - first, by the variety and scales of systems studied and second, by its presentation: Each chapter provides the biological or medical context, follows up with mathematical or algorithmic developments triggered by a specific problem and concludes with one or two success stories, namely new insights gained thanks to these methodological developments. It also highlights some unsolved and outstanding theoretical questions, with a potentially high impact on these disciplines. Two communities will be particularly interested in this book. The first one is the vast community of applied mathematicians and computer scientists, whose interests should be captured by the added value generated by the application of advanced concepts and algorithms to challenging biological or medical problems. The second is the equally vast community of biologists. Whether scientists or engineers, they will find in this book a clear and self-contained account of concepts and techniques from mathematics and computer science, together with success stories on their favorite systems. The variety of systems described represents a panoply of complementary conceptual tools. On a practical level, the resources listed at the end of each chapter (databases, software) offer invaluable support for getting started on a specific topic in the fields of biomedicine, bioinformatics and neuroscience.

Bioinformatics Algorithms

Phillip Compeau,Pavel Pevzner
Bioinformatics Algorithms Book PDF

Author : Phillip Compeau,Pavel Pevzner
Publisher : Unknown
Page : 128 pages
File Size : 54,5 Mb
Release : 1986-06
Category : Electronic
ISBN : 0990374637

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Bioinformatics Algorithms by Phillip Compeau,Pavel Pevzner Pdf

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 and the Cell

Xuhua Xia
Bioinformatics and the Cell Book PDF

Author : Xuhua Xia
Publisher : Springer Science & Business Media
Page : 376 pages
File Size : 42,5 Mb
Release : 2007-05-08
Category : Science
ISBN : UVA:X030261416

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Bioinformatics and the Cell by Xuhua Xia Pdf

Biological and biomedical sciences are becoming more interdisciplinary, and scientists of the future need inte rdisciplinary training instead of the conventional disciplinary training. Just as Sean Eddy (2005) wiselypointed out that sending monolingual diplomats to the United Nations maynot enhance international collaborations, combining strictly disciplinary scientists trained in either mathematics, computational science or molecular biology will not create a productive inte rdisciplinary team ready to solve interdisciplinary problems. Molecular biology is an interdiscip linary science back in its heyday, and founders of molecular biology were ofte n interdisciplinary scientists. Indeed, Francis Crick considered himself as “a mixture of crystallographer, biophysicist, biochemist, and geneticist” (Crick, 1965). Because it was too cumbersome to explain to people that he was such a mixture, the term “molecular biologist” came handy. To get the crystallographer, biophysicist, biochemist, and geneticist within hi mself to collaborate with each other probably worked better than a team with a crystallographer, a biophysicist, a biochemist and a geneticist who maynot even be interested in each other’s problems.