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Bayesian Methods in Structural Bioinformatics by Thomas Hamelryck,Kanti Mardia,Jesper Ferkinghoff-Borg Pdf
This book is an edited volume, the goal of which is to provide an overview of the current state-of-the-art in statistical methods applied to problems in structural bioinformatics (and in particular protein structure prediction, simulation, experimental structure determination and analysis). It focuses on statistical methods that have a clear interpretation in the framework of statistical physics, rather than ad hoc, black box methods based on neural networks or support vector machines. In addition, the emphasis is on methods that deal with biomolecular structure in atomic detail. The book is highly accessible, and only assumes background knowledge on protein structure, with a minimum of mathematical knowledge. Therefore, the book includes introductory chapters that contain a solid introduction to key topics such as Bayesian statistics and concepts in machine learning and statistical physics.
Bayesian Modeling in Bioinformatics by Dipak K. Dey,Samiran Ghosh,Bani K. Mallick Pdf
Bayesian Modeling in Bioinformatics discusses the development and application of Bayesian statistical methods for the analysis of high-throughput bioinformatics data arising from problems in molecular and structural biology and disease-related medical research, such as cancer. It presents a broad overview of statistical inference, clustering, and c
Advance in Structural Bioinformatics by Dongqing Wei,Qin Xu,Tangzhen Zhao,Hao Dai Pdf
This text examines in detail mathematical and physical modeling, computational methods and systems for obtaining and analyzing biological structures, using pioneering research cases as examples. As such, it emphasizes programming and problem-solving skills. It provides information on structure bioinformatics at various levels, with individual chapters covering introductory to advanced aspects, from fundamental methods and guidelines on acquiring and analyzing genomics and proteomics sequences, the structures of protein, DNA and RNA, to the basics of physical simulations and methods for conformation searches. This book will be of immense value to researchers and students in the fields of bioinformatics, computational biology and chemistry. Dr. Dongqing Wei is a Professor at the Department of Bioinformatics and Biostatistics, College of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, China. His research interest is in the general area of structural bioinformatics.
Structural Bioinformatics by Forbes J. Burkowski Pdf
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).
Structural Bioinformatics by Jenny Gu,Philip E. Bourne Pdf
Structural Bioinformatics was the first major effort to show the application of the principles and basic knowledge of the larger field of bioinformatics to questions focusing on macromolecular structure, such as the prediction of protein structure and how proteins carry out cellular functions, and how the application of bioinformatics to these life science issues can improve healthcare by accelerating drug discovery and development. Designed primarily as a reference, the first edition nevertheless saw widespread use as a textbook in graduate and undergraduate university courses dealing with the theories and associated algorithms, resources, and tools used in the analysis, prediction, and theoretical underpinnings of DNA, RNA, and proteins. This new edition contains not only thorough updates of the advances in structural bioinformatics since publication of the first edition, but also features eleven new chapters dealing with frontier areas of high scientific impact, including: sampling and search techniques; use of mass spectrometry; genome functional annotation; and much more. Offering detailed coverage for practitioners while remaining accessible to the novice, Structural Bioinformatics, Second Edition is a valuable resource and an excellent textbook for a range of readers in the bioinformatics and advanced biology fields. Praise for the previous edition: "This book is a gold mine of fundamental and practical information in an area not previously well represented in book form." —Biochemistry and Molecular Education "... destined to become a classic reference work for workers at all levels in structural bioinformatics...recommended with great enthusiasm for educators, researchers, and graduate students." —BAMBED "...a useful and timely summary of a rapidly expanding field." —Nature Structural Biology "...a terrific job in this timely creation of a compilation of articles that appropriately addresses this issue." —Briefings in Bioinformatics
Author : Ian L. Dryden,John T. Kent Publisher : John Wiley & Sons Page : 432 pages File Size : 55,5 Mb Release : 2015-09-03 Category : Mathematics ISBN : 9781118866603
Geometry Driven Statistics by Ian L. Dryden,John T. Kent Pdf
A timely collection of advanced, original material in the area of statistical methodology motivated by geometric problems, dedicated to the influential work of Kanti V. Mardia This volume celebrates Kanti V. Mardia's long and influential career in statistics. A common theme unifying much of Mardia’s work is the importance of geometry in statistics, and to highlight the areas emphasized in his research this book brings together 16 contributions from high-profile researchers in the field. Geometry Driven Statistics covers a wide range of application areas including directional data, shape analysis, spatial data, climate science, fingerprints, image analysis, computer vision and bioinformatics. The book will appeal to statisticians and others with an interest in data motivated by geometric considerations. Summarizing the state of the art, examining some new developments and presenting a vision for the future, Geometry Driven Statistics will enable the reader to broaden knowledge of important research areas in statistics and gain a new appreciation of the work and influence of Kanti V. Mardia.
Bayesian Analysis of Gene Expression Data by Bani K. Mallick,David Gold,Veera Baladandayuthapani Pdf
The field of high-throughput genetic experimentation is evolving rapidly, with the advent of new technologies and new venues for data mining. Bayesian methods play a role central to the future of data and knowledge integration in the field of Bioinformatics. This book is devoted exclusively to Bayesian methods of analysis for applications to high-throughput gene expression data, exploring the relevant methods that are changing Bioinformatics. Case studies, illustrating Bayesian analyses of public gene expression data, provide the backdrop for students to develop analytical skills, while the more experienced readers will find the review of advanced methods challenging and attainable. This book: Introduces the fundamentals in Bayesian methods of analysis for applications to high-throughput gene expression data. Provides an extensive review of Bayesian analysis and advanced topics for Bioinformatics, including examples that extensively detail the necessary applications. Accompanied by website featuring datasets, exercises and solutions. Bayesian Analysis of Gene Expression Data offers a unique introduction to both Bayesian analysis and gene expression, aimed at graduate students in Statistics, Biomedical Engineers, Computer Scientists, Biostatisticians, Statistical Geneticists, Computational Biologists, applied Mathematicians and Medical consultants working in genomics. Bioinformatics researchers from many fields will find much value in this book.
Bayesian Analysis with Python by Osvaldo Martin Pdf
Learn the fundamentals of Bayesian modeling using state-of-the-art Python libraries, such as PyMC, ArviZ, Bambi, and more, guided by an experienced Bayesian modeler who contributes to these libraries Key Features Conduct Bayesian data analysis with step-by-step guidance Gain insight into a modern, practical, and computational approach to Bayesian statistical modeling Enhance your learning with best practices through sample problems and practice exercises Purchase of the print or Kindle book includes a free PDF eBook. Book DescriptionThe third edition of Bayesian Analysis with Python serves as an introduction to the main concepts of applied Bayesian modeling using PyMC, a state-of-the-art probabilistic programming library, and other libraries that support and facilitate modeling like ArviZ, for exploratory analysis of Bayesian models; Bambi, for flexible and easy hierarchical linear modeling; PreliZ, for prior elicitation; PyMC-BART, for flexible non-parametric regression; and Kulprit, for variable selection. In this updated edition, a brief and conceptual introduction to probability theory enhances your learning journey by introducing new topics like Bayesian additive regression trees (BART), featuring updated examples. Refined explanations, informed by feedback and experience from previous editions, underscore the book's emphasis on Bayesian statistics. You will explore various models, including hierarchical models, generalized linear models for regression and classification, mixture models, Gaussian processes, and BART, using synthetic and real datasets. By the end of this book, you will possess a functional understanding of probabilistic modeling, enabling you to design and implement Bayesian models for your data science challenges. You'll be well-prepared to delve into more advanced material or specialized statistical modeling if the need arises.What you will learn Build probabilistic models using PyMC and Bambi Analyze and interpret probabilistic models with ArviZ Acquire the skills to sanity-check models and modify them if necessary Build better models with prior and posterior predictive checks Learn the advantages and caveats of hierarchical models Compare models and choose between alternative ones Interpret results and apply your knowledge to real-world problems Explore common models from a unified probabilistic perspective Apply the Bayesian framework's flexibility for probabilistic thinking Who this book is for If you are a student, data scientist, researcher, or developer looking to get started with Bayesian data analysis and probabilistic programming, this book is for you. The book is introductory, so no previous statistical knowledge is required, although some experience in using Python and scientific libraries like NumPy is expected.
Applied Directional Statistics by Christophe Ley,Thomas Verdebout Pdf
This book collects important advances in methodology and data analysis for directional statistics. It is the companion book of the more theoretical treatment presented in Modern Directional Statistics (CRC Press, 2017). The field of directional statistics has received a lot of attention due to demands from disciplines such as life sciences or machine learning, the availability of massive data sets requiring adapted statistical techniques, and technological advances. This book covers important progress in bioinformatics, biology, astrophysics, oceanography, environmental sciences, earth sciences, machine learning and social sciences.
Big Data Analytics in Bioinformatics and Healthcare by Wang, Baoying Pdf
As technology evolves and electronic data becomes more complex, digital medical record management and analysis becomes a challenge. In order to discover patterns and make relevant predictions based on large data sets, researchers and medical professionals must find new methods to analyze and extract relevant health information. Big Data Analytics in Bioinformatics and Healthcare merges the fields of biology, technology, and medicine in order to present a comprehensive study on the emerging information processing applications necessary in the field of electronic medical record management. Complete with interdisciplinary research resources, this publication is an essential reference source for researchers, practitioners, and students interested in the fields of biological computation, database management, and health information technology, with a special focus on the methodologies and tools to manage massive and complex electronic information.
This book provides an accessible approach to Bayesian computing and data analysis, with an emphasis on the interpretation of real data sets. Following in the tradition of the successful first edition, this book aims to make a wide range of statistical modeling applications accessible using tested code that can be readily adapted to the reader's own applications. The second edition has been thoroughly reworked and updated to take account of advances in the field. A new set of worked examples is included. The novel aspect of the first edition was the coverage of statistical modeling using WinBUGS and OPENBUGS. This feature continues in the new edition along with examples using R to broaden appeal and for completeness of coverage.
Algorithms and Methods in Structural Bioinformatics by Nurit Haspel,Filip Jagodzinski,Kevin Molloy Pdf
The three-dimensional structure and function of molecules present many challenges and opportunities for developing an understanding of biological systems. With the increasing availability of molecular structures and the advancing accuracy of structure predictions and molecular simulations, the space for algorithmic advancement on many analytical and predictive problems is both broad and deep. To support this field, a rich set of methods and algorithms are available, addressing a variety of important problems such as protein-protein interactions, the effect of mutations on protein structure and function, and protein structure determination. Despite recent advancements in the field, in particular in protein folding with the development of AlphaFold, many problems still remain unsolved. In this book we focus on a number of topics in Structural Bioinformatics: Cryo-EM structural detection, protein conformational exploration, elucidation of molecular binding surface using geometry, the effect of mutations, insertions and deletions on protein structural stability, and protein-ligand binding.
50 years of Statistical Physics in Mexico: Development, State of the Art and Perspectives by Ramon Castañeda-Priego,Enrique Hernandez-Lemus,Susana Figueroa-Gerstenmaier,Atahualpa Kraemer Pdf
Probabilistic Methods for Bioinformatics by Richard E. Neapolitan Pdf
The Bayesian network is one of the most important architectures for representing and reasoning with multivariate probability distributions. When used in conjunction with specialized informatics, possibilities of real-world applications are achieved. Probabilistic Methods for BioInformatics explains the application of probability and statistics, in particular Bayesian networks, to genetics. This book provides background material on probability, statistics, and genetics, and then moves on to discuss Bayesian networks and applications to bioinformatics. Rather than getting bogged down in proofs and algorithms, probabilistic methods used for biological information and Bayesian networks are explained in an accessible way using applications and case studies. The many useful applications of Bayesian networks that have been developed in the past 10 years are discussed. Forming a review of all the significant work in the field that will arguably become the most prevalent method in biological data analysis. Unique coverage of probabilistic reasoning methods applied to bioinformatics data--those methods that are likely to become the standard analysis tools for bioinformatics. Shares insights about when and why probabilistic methods can and cannot be used effectively; Complete review of Bayesian networks and probabilistic methods with a practical approach.