The Topological Model of Genome and Evolution PDF Download
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Author: Pradeep Chhaya
Publisher: Springer Nature
ISBN: 9819943183
Category :
Languages : en
Pages : 562
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Book Description
Author: Pradeep Chhaya
Publisher: Springer Nature
ISBN: 9819943183
Category :
Languages : en
Pages : 562
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Book Description
Author: Raul Rabadan
Publisher: Cambridge University Press
ISBN: 1107159547
Category : Science
Languages : en
Pages : 521
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Book Description
An introduction to geometric and topological methods to analyze large scale biological data; includes statistics and genomic applications.
Author: Cedric Chauve
Publisher: Springer Science & Business Media
ISBN: 1447152980
Category : Computers
Languages : en
Pages : 329
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Book Description
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.
Author: Gustavo Caetano-Anoll¿s
Publisher: John Wiley & Sons
ISBN: 1118210719
Category : Science
Languages : en
Pages : 529
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Book Description
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.
Author: Nataša Jonoska
Publisher: Springer Science & Business Media
ISBN: 3642401937
Category : Computers
Languages : en
Pages : 522
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Book Description
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.
Author: Christoph Bleidorn
Publisher: Springer
ISBN: 3319540645
Category : Science
Languages : en
Pages : 227
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Book Description
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.
Author: Laurence Marechal-Drouard
Publisher: Academic Press
ISBN: 0123942799
Category : Science
Languages : en
Pages : 486
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Book Description
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
Author: Axel Meyer
Publisher: Springer Science & Business Media
ISBN: 9401002630
Category : Science
Languages : en
Pages : 242
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Book Description
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.
Author: Giorgio Bernardi
Publisher: Elsevier
ISBN: 0080461875
Category : Science
Languages : en
Pages : 459
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Book Description
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-contained book · Discusses important open problem, without refraining from criticism whenever appropriate
Author: Zhaoming Yin
Publisher:
ISBN:
Category : Algorithms
Languages : en
Pages :
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Book Description
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.
