Download or read book The Topological Model of Genome and Evolution written by Pradeep Chhaya and published by Springer Nature. This book was released on with total page 562 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Topological Data Analysis for Genomics and Evolution written by Raul Rabadan and published by Cambridge University Press. This book was released on 2019-12-19 with total page 521 pages. Available in PDF, EPUB and Kindle. Book excerpt: An introduction to geometric and topological methods to analyze large scale biological data; includes statistics and genomic applications.
Download or read book Models and Algorithms for Genome Evolution written by Cedric Chauve and published by Springer Science & Business Media. This book was released on 2013-09-17 with total page 329 pages. Available in PDF, EPUB and Kindle. Book excerpt: This authoritative text/reference presents a review of the history, current status, and potential future directions of computational biology in molecular evolution. Gathering together the unique insights of an international selection of prestigious researchers, this must-read volume examines the latest developments in the field, the challenges that remain, and the new avenues emerging from the growing influx of sequence data. These viewpoints build upon the pioneering work of David Sankoff, one of the founding fathers of computational biology, and mark the 50th anniversary of his first scientific article. The broad spectrum of rich contributions in this essential collection will appeal to all computer scientists, mathematicians and biologists involved in comparative genomics, phylogenetics and related areas.
Download or read book Evolutionary Genomics and Systems Biology written by Gustavo Caetano-Anoll¿s and published by John Wiley & Sons. This book was released on 2011-09-26 with total page 529 pages. Available in PDF, EPUB and Kindle. Book excerpt: A comprehensive, authoritative look at an emergent area in post-genomic science, Evolutionary genomics is an up-and-coming, complex field that attempts to explain the biocomplexity of the living world. Evolutionary Genomics and Systems Biology is the first full-length book to blend established and emerging concepts in bioinformatics, evolution, genomics, and structural biology, with the integrative views of network and systems biology. Three key aspects of evolutionary genomics and systems biology are covered in clear detail: the study of genomic history, i.e., understanding organismal evolution at the genomic level; the study of macromolecular complements, which encompasses the evolution of the protein and RNA machinery that propels life; and the evolutionary and dynamic study of wiring diagrams—macromolecular components in interaction—in the context of genomic complements. The book also features: A solid, comprehensive treatment of phylogenomics, the evolution of genomes, and the evolution of biological networks, within the framework of systems biology A special section on RNA biology—translation, evolution of structure, and micro RNA and regulation of gene expression Chapters on the mapping of genotypes to phenotypes, the role of information in biology, protein architecture and biological function, chromosomal rearrangements, and biological networks and disease Contributions by leading authorities on each topic Evolutionary Genomics and Systems Biology is an ideal book for students and professionals in genomics, bioinformatics, evolution, structural biology, complexity, origins of life, systematic biology, and organismal diversity, as well as those individuals interested in aspects of biological sciences as they interface with chemistry, physics, and computer science and engineering.
Download or read book Discrete and Topological Models in Molecular Biology written by Nataša Jonoska and published by Springer Science & Business Media. This book was released on 2013-12-23 with total page 522 pages. Available in PDF, EPUB and Kindle. Book excerpt: Theoretical tools and insights from discrete mathematics, theoretical computer science, and topology now play essential roles in our understanding of vital biomolecular processes. The related methods are now employed in various fields of mathematical biology as instruments to "zoom in" on processes at a molecular level. This book contains expository chapters on how contemporary models from discrete mathematics – in domains such as algebra, combinatorics, and graph and knot theories – can provide perspective on biomolecular problems ranging from data analysis, molecular and gene arrangements and structures, and knotted DNA embeddings via spatial graph models to the dynamics and kinetics of molecular interactions. The contributing authors are among the leading scientists in this field and the book is a reference for researchers in mathematics and theoretical computer science who are engaged with modeling molecular and biological phenomena using discrete methods. It may also serve as a guide and supplement for graduate courses in mathematical biology or bioinformatics, introducing nontraditional aspects of mathematical biology.
Download or read book Phylogenomics written by Christoph Bleidorn and published by Springer. This book was released on 2017-06-01 with total page 227 pages. Available in PDF, EPUB and Kindle. Book excerpt: This unique textbook provides a clear and concise overview of the key principles of the complex field of phylogenomics, with a particular focus on sequencing technologies that are crucial to studying and understanding interrelations in evolutionary genomics. It includes chapters dedicated to the analysis of nucleotide sequences using assembling and alignment methods and also discusses the main strategies for phylogenetic studies, systematic errors and their correction. This highly readable textbook is intended for graduate students and young researchers with an interest in phylogenetics and evolutionary developmental biology.
Download or read book Genome Evolution written by Axel Meyer and published by Springer Science & Business Media. This book was released on 2011-06-28 with total page 242 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the years since the publication of Susumu Ohno's 1970 landmark book Evolution by gene duplication tremendous advances have been made in molecular biology and especially in genomics. Studies of genome structure and function prerequisite to testing hypotheses of genome evolution were all but impossible until recent methodological advances. This book evaluates newly generated empirical evidence as it pertains to theories of genomic evolutionary patterns and processes. Tests of hypotheses using analyses of complete genomes, interpreted in a phylogenetic context, provide evidence regarding the relative importance of gene duplication. The alternative explanation is that the evolution of regulatory elements that control the expression of and interactions among genes has been a more important force in shaping evolutionary innovation. This collection of papers will be of interest to all academic and industry researchers working in the fields of molecular biology, biotechnology, genomics and genome centers.
Download or read book Structural and Evolutionary Genomics written by Giorgio Bernardi and published by Elsevier. This book was released on 2005-12-19 with total page 459 pages. Available in PDF, EPUB and Kindle. Book excerpt: Structural genomics is the study of the DNA of living organisms. Evolutionary genomics is the study of the history of the genome. These subjects are closely interlinked. They are approached in this book using as a guideline the investigations carried out in the author's laboratory, relevant literature is critically reviewed and some general conclusions are presented. The author and his collaborators have studied a vast number of genomes, ranging from prokaryotes to human, using different approaches, including physical chemistry of DNA, viral integration and molecular cytogenetics. As the subtitle indicates the book discusses the fundamental importance of natural selection in shaping genomes. In terms of numbers, neutral and nearly neutral mutations represent most mutations, but a "regional" control is exerted by natural selection (essentially negative or purifying selection). A "neo-selectionist" model is proposed for genome evolution.· Summarizes the existing knowledge on genome organization and evolution in a self-containedbook· Discusses important open problem, without refraining from criticism wheneverappropriate
Download or read book Mitochondrial Genome Evolution written by Laurence Marechal-Drouard and published by Academic Press. This book was released on 2012-10-03 with total page 486 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Botanical Research publishes in-depth and up-to-date reviews on a wide range of topics in plant sciences. Features a wide range of reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology and ecology. This thematic volume features reviews on Mitochondrial genome evolution. Publishes in-depth and up-to-date reviews on a wide range of topics in plant sciences Features a wide range of reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology and ecology This thematic volume features reviews on mitochondrial genome evolution
Download or read book Enhance the Understanding of Whole genome Evolution by Designing Accelerating and Parallelizing Phylogenetic Algorithms written by Zhaoming Yin and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The advent of new technology enhance the speed and reduce the cost for sequencing biological data. Making biological sense of this genomic data is a big challenge to the algorithm design as well as the high performance computing society. There are many problems in Bioinformatics, such as how new functional genes arise, why genes are organized into chromosomes, how species are connected through the evolutionary tree of life, or why arrangements are subject to change. Phylogenetic analyses have become essential to research on the evolutionary tree of life. It can help us to track the history of species and the relationship between different genes or genomes through millions of years. One of the fundamentals for phylogenetic construction is the computation of distances between genomes. Since there are much more complicated combinatoric patterns in rearrangement events, the distance computation is still a hot topic as much belongs to mathematics as to biology. For the distance computation with input of two genomes containing unequal gene contents (with insertions/deletions and duplications) the problem is especially hard. In this thesis, we will discuss about our contributions to the distance estimation for unequal gene order data. The problem of finding the median of three genomes is the key process in building the most parsimonious phylogenetic trees from genome rearrangement data. For genomes with unequal contents, to the best of our knowledge, there is no algorithm that can help to find the median. In this thesis, we make our contributions to the median computation in two aspects. 1) Algorithm engineering aspect, we harness the power of streaming graph analytics methods to implement an exact DCJ median algorithm which run as fast as the heuristic algorithm and can help construct a better phylogenetic tree. 2) Algorithmic aspect, we theoretically formulate the problem of finding median with input of genomes having unequal gene content, which leads to the design and implementation of an efficient Lin-Kernighan heuristic based median algorithm. Inferring phylogenies (evolutionary history) of a set of given species is the ultimate goal when the distance and median model are chosen. For more than a decade, biologists and computer scientists have studied how to infer phylogenies by the measurement of genome rearrangement events using gene order data. While evolution is not an inherently parsimonious process, maximum parsimony (MP) phylogenetic analysis has been supported by widely applied to the phylogeny inference to study the evolutionary patterns of genome rearrangements. There are generally two problems with the MP phylogenetic arose by genome rearrangement: One is, given a set of modern genomes, how to compute the topologies of the according phylogenetic tree; Another is, given the topology of a model tree, how to infer the gene orders of the ancestor species. To assemble a MP phylogenetic tree constructor, there are multiple NP hard problems involved, unfortunately, they organized as one problem on top of other problems. Which means, to solve a NP hard problem, we need to solve multiple NP hard sub-problems. For phylogenetic tree construction with the input of unequal content genomes, there are three layers of NP hard problems. In this thesis, we will mainly discuss about our contributions to the design and implementation of the software package DCJUC (Phylogeny Inference using DCJ model to cope with Unequal Content Genomes), that can help to achieve both of these two goals. Aside from the biological problems, another issue we need to concern is about the use of the power of parallel computing to assist accelerating algorithms to handle huge data sets, such as the high resolution gene order data. For one thing, all of the method to tackle with phylogenetic problems are based on branch and bound algorithms, which are quite irregular and unfriendly to parallel computing. To parallelize these algorithms, we need to properly enhance the efficiency for localized memory access and load balance methods to make sure that each thread can put their potentials into full play. For the other, there is a revolution taking place in computing with the availability of commodity graphical processors such as Nvidia GPU and with many-core CPUs such as Cray-XMT, or Intel Xeon Phi Coprocessor with 60 cores. These architectures provide a new way for us to achieve high performance at much lower cost. However, code running on these machines are not so easily programmed, and scientific computing is hard to tune well on them. We try to explore the potentials of these architectures to help us accelerate branch and bound based phylogenetic algorithms.
Download or read book Gene Genealogies Variation and Evolution A primer in coalescent theory written by Jotun Hein and published by Oxford University Press, USA. This book was released on 2004-12-09 with total page 298 pages. Available in PDF, EPUB and Kindle. Book excerpt: Authored by leading experts, this seminal text presents a straightforward and elementary account of coalescent theory, which is a central concept in the study of genetic sequence variation observed in a population. Rich in examples and illustrations it is ideal for a graduate course in statistics, population, molecular and medical genetics, bioscience and medicine, and for students studying the evolution of human population and disease. It is also an invaluable reference for bioscientists and statisticians in the pharmaceutical industry and academia - ;Coalescent theory is a central concept in the study of genetic sequence variation that probabilistically describes the genealogy relating the sampled sequences. In this text, besides fulfilling the glaring need for such a book, the authors present this theory in a straightforward and elementary manner and describe the statistical and computational methods used in modelling and analyzing genetic sequence variation. Rich in examples and illustrations the book covers basic concepts, complications arising from geographical structure and recombination before considering aspects of statistical inference based on these models. The book ends with chapters on Gene Mapping, which combines sequence variation data with phenotypic data (such as disease) to define areas of the genome where genes are responsible for the trait, and Human Evolution, a research area that is experiencing a renaissance due to the enormous amounts of data produced in molecular studies. Authored by leading experts, this seminal text presents a straightforward and elementary account of coalescent theory, which is a central concept in the study of genetic sequence variation observed in a population. It is highly suitable for a graduate course in statistics, population, molecular and medical genetics, bioscience and medicine and students studying the evolution of human population and disease, and will be an invaluable reference for bioscientists and statisticians in the pharmaceutical industry and academia - ;an excellent and timely book that should appeal to a variety of people in genetics and applied mathematics. - Professor Montgomery Slatkin (Berkeley);the authors are outstanding experts in the field, and the book is topical and timely. - Professor David Balding (Imperial College);Hein, Schierup and Wiuf have written the first general book on the coalescent. It is an engaging combination of clear mathematical derivation and real data examples. - Professor Joe Felsenstein (University of Washington)
Download or read book Mobile Elements and Plant Genome Evolution Comparative Analyses and Computational Tools Volume II written by Ruslan Kalendar and published by Frontiers Media SA. This book was released on 2023-11-28 with total page 161 pages. Available in PDF, EPUB and Kindle. Book excerpt: This Research Topic is part of the Mobile Elements and Plant Genome Evolution, Comparative Analyses and Computational Tools series: Mobile Elements and Plant Genome Evolution, Comparative Analyses and Computational Tools Transposable elements are very common mobile genetic elements that are composed of several classes and make up the majority of eukaryotic genomes. The movement and accumulation of mobile genetic elements have been a major force in the formation of the genes and genomes of nearly all organisms. As dispersed and ubiquitous mobile elements, their life cycle of replicative transposition leads to genome rearrangements affecting cellular function. Transposable elements are important drivers of species diversity, and they exhibit great variety in structure, size, and mechanisms of transposition, making them important putative actors in genome evolution.
Download or read book The Evolution of the Genome written by T. Ryan Gregory and published by Elsevier. This book was released on 2011-05-04 with total page 768 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Evolution of the Genome provides a much needed overview of genomic study through clear, detailed, expert-authored discussions of the key areas in genome biology. This includes the evolution of genome size, genomic parasites, gene and ancient genome duplications, polypoidy, comparative genomics, and the implications of these genome-level phenomena for evolutionary theory. In addition to reviewing the current state of knowledge of these fields in an accessible way, the various chapters also provide historical and conceptual background information, highlight the ways in which the critical questions are actually being studied, indicate some important areas for future research, and build bridges across traditional professional and taxonomic boundaries. The Evolution of the Genome will serve as a critical resource for graduate students, postdoctoral fellows, and established scientists alike who are interested in the issue of genome evolution in the broadest sense. - Provides detailed, clearly written chapters authored by leading researchers in their respective fields - Presents a much-needed overview of the historical and theoretical context of the various areas of genomic study - Creates important links between topics in order to promote integration across subdisciplines, including descriptions of how each subject is actually studied - Provides information specifically designed to be accessible to established researchers, postdoctoral fellows, and graduate students alike
Download or read book Genomic Control Process written by Isabelle S. Peter and published by Academic Press. This book was released on 2015-01-21 with total page 461 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomic Control Process explores the biological phenomena around genomic regulatory systems that control and shape animal development processes, and which determine the nature of evolutionary processes that affect body plan. Unifying and simplifying the descriptions of development and evolution by focusing on the causality in these processes, it provides a comprehensive method of considering genomic control across diverse biological processes. This book is essential for graduate researchers in genomics, systems biology and molecular biology seeking to understand deep biological processes which regulate the structure of animals during development. - Covers a vast area of current biological research to produce a genome oriented regulatory bioscience of animal life - Places gene regulation, embryonic and postembryonic development, and evolution of the body plan in a unified conceptual framework - Provides the conceptual keys to interpret a broad developmental and evolutionary landscape with precise experimental illustrations drawn from contemporary literature - Includes a range of material, from developmental phenomenology to quantitative and logic models, from phylogenetics to the molecular biology of gene regulation, from animal models of all kinds to evidence of every relevant type - Demonstrates the causal power of system-level understanding of genomic control process - Conceptually organizes a constellation of complex and diverse biological phenomena - Investigates fundamental developmental control system logic in diverse circumstances and expresses these in conceptual models - Explores mechanistic evolutionary processes, illuminating the evolutionary consequences of developmental control systems as they are encoded in the genome
Download or read book Genome Chaos written by Henry H. Heng and published by Academic Press. This book was released on 2019-05-25 with total page 564 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genome Chaos: Rethinking Genetics, Evolution, and Molecular Medicine transports readers from Mendelian Genetics to 4D-genomics, building a case for genes and genomes as distinct biological entities, and positing that the genome, rather than individual genes, defines system inheritance and represents a clear unit of selection for macro-evolution. In authoring this thought-provoking text, Dr. Heng invigorates fresh discussions in genome theory and helps readers reevaluate their current understanding of human genetics, evolution, and new pathways for advancing molecular and precision medicine. - Bridges basic research and clinical application and provides a foundation for re-examining the results of large-scale omics studies and advancing molecular medicine - Gathers the most pressing questions in genomic and cytogenomic research - Offers alternative explanations to timely puzzles in the field - Contains eight evidence-based chapters that discuss 4d-genomics, genes and genomes as distinct biological entities, genome chaos and macro-cellular evolution, evolutionary cytogenetics and cancer, chromosomal coding and fuzzy inheritance, and more
Download or read book Insights in Evolutionary Genomic Microbiology 2022 written by Ernesto Perez-Rueda and published by Frontiers Media SA. This book was released on 2023-10-31 with total page 136 pages. Available in PDF, EPUB and Kindle. Book excerpt: This Research Topic is part of the Insights in Frontiers in Microbiology series. We are now entering the third decade of the 21st Century, and, especially in the last years, the achievements made by scientists in the field of Microbiology have been exceptional, leading to major advancements. Frontiers has organized a series of Research Topics to highlight the latest advancements in science in order to be at the forefront of science in different fields of research. This specific editorial initiative, led by Dr. Ernesto Perez-Rueda and Dr. Feng Gao, is focused on new insights, novel developments, current challenges, latest discoveries, recent advances and future perspectives in the field.
Download or read book Genomes Evolution and Culture written by Rene J. Herrera and published by John Wiley & Sons. This book was released on 2016-03-01 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book combines recent information and discoveries in the field of human molecular biology and human molecular evolution. It provides an interdisciplinary approach drawing together data from various diverse disciplines to address both the more classical anthropological content and the current more contemporary molecular focus of courses. Chapters include a history of human evolutionary genetics; the human genome structure and function; population structure and variability; gene and genomic dynamics; culture; health and disease; bioethics; future.
