Download or read book Topology of Reticulate Evolution written by Kevin Joseph Emmett and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Network approaches are used to represent the population of S. aureus and analyze the spread of antibiotic resistance genes. The presence of antibiotic resistance genes in the human microbiome is investigated.
Download or read book Reticulate Evolution written by Nathalie Gontier and published by Springer. This book was released on 2015-07-09 with total page 345 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written for non-experts, this volume introduces the mechanisms that underlie reticulate evolution. Chapters are either accompanied with glossaries that explain new terminology or timelines that position pioneering scholars and their major discoveries in their historical contexts. The contributing authors outline the history and original context of discovery of symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow and infectious heredity. By applying key insights from the areas of molecular (phylo)genetics, microbiology, virology, ecology, systematics, immunology, epidemiology and computational science, they demonstrate how reticulate evolution impacts successful survival, fitness and speciation. Reticulate evolution brings forth a challenge to the standard Neo-Darwinian framework, which defines life as the outcome of bifurcation and ramification patterns brought forth by the vertical mechanism of natural selection. Reticulate evolution puts forward a pattern in the tree of life that is characterized by horizontal mergings and lineage crossings induced by symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow and infective heredity, making the “tree of life” look more like a “web of life.” On an epistemological level, the various means by which hereditary material can be transferred horizontally challenges our classic notions of units and levels of evolution, fitness, modes of transmission, linearity, communities and biological individuality. The case studies presented examine topics including the origin of the eukaryotic cell and its organelles through symbiogenesis; the origin of algae through primary and secondary symbiosis and dinoflagellates through tertiary symbiosis; the superorganism and holobiont as units of evolution; how endosymbiosis induces speciation in multicellular life forms; transferrable and non-transferrable plasmids and how they symbiotically interact with their host; the means by which pro- and eukaryotic organisms transfer genes laterally (bacterial transformation, transduction and conjugation as well as transposons and other mobile genetic elements); hybridization and divergence with gene flow in sexually-reproducing individuals; current (human) microbiome and viriome studies that impact our knowledge concerning the evolution of organismal health and acquired immunity; and how symbiosis and symbiogenesis can be modelled in computational evolution.
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 522 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biology has entered the age of Big Data. A technical revolution has transformed the field, and extracting meaningful information from large biological data sets is now a central methodological challenge. Algebraic topology is a well-established branch of pure mathematics that studies qualitative descriptors of the shape of geometric objects. It aims to reduce comparisons of shape to a comparison of algebraic invariants, such as numbers, which are typically easier to work with. Topological data analysis is a rapidly developing subfield that leverages the tools of algebraic topology to provide robust multiscale analysis of data sets. This book introduces the central ideas and techniques of topological data analysis and its specific applications to biology, including the evolution of viruses, bacteria and humans, genomics of cancer, and single cell characterization of developmental processes. Bridging two disciplines, the book is for researchers and graduate students in genomics and evolutionary biology as well as mathematicians interested in applied topology.
Download or read book A Framework for Representing Reticulate Evolution written by Mihaela Baroni and published by . This book was released on 2003 with total page 19 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Studies in the Opuntioideae Cactaceae written by David R. Hunt and published by . This book was released on 2002 with total page 260 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Reticulate Evolution and Humans written by Michael L. Arnold and published by Oxford University Press. This book was released on 2009 with total page 246 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the important role that the transfer of genes between organisms has played during the origin and evolution of humans, and the evolution of organisms on which the human species depends for shelter, sustenance and companionship.
Download or read book Reticulate Evolution written by Kenneth B. Cumming and published by . This book was released on 1997 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Phylogenetic Networks written by Daniel H. Huson and published by Cambridge University Press. This book was released on 2010-12-02 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt: The evolutionary history of species is traditionally represented using a rooted phylogenetic tree. However, when reticulate events such as hybridization, horizontal gene transfer or recombination are believed to be involved, phylogenetic networks that can accommodate non-treelike evolution have an important role to play. This book provides the first interdisciplinary overview of phylogenetic networks. Beginning with a concise introduction to both phylogenetic trees and phylogenetic networks, the fundamental concepts and results are then presented for both rooted and unrooted phylogenetic networks. Current approaches and algorithms available for computing phylogenetic networks from different types of datasets are then discussed, accompanied by examples of their application to real biological datasets. The book also summarises the algorithms used for drawing phylogenetic networks, along with the existing software for their computation and evaluation. All datasets, examples and other additional information and links are available from the book's companion website at www.phylogenetic-networks.org.
Download or read book Conifers of the World written by James E. Eckenwalder and published by Timber Press. This book was released on 2009-11-14 with total page 745 pages. Available in PDF, EPUB and Kindle. Book excerpt: Researched for more than three decades, this definitive work provides up-to-date descriptions of all the true conifers of the world, including 545 species of trees and shrubs. Written for accessibility to both horticultural and botanical audiences, it is the first comprehensive update of conifer taxonomy in nearly a century. Noted conifer taxonomist James E. Eckenwalder also discusses the relationships among the groups, practical usages, champion trees, fossil occurrences, and biology. New identification guides for the families and genera are based whenever possible on foliage features and thus should be easier to use than traditional conifer keys, which focus on seasonal, and often microscopic, cone characters. Eckenwalder shares the reasoning behind his taxonomic decisions, many of which are unique to this book, reflecting a comprehensive reevaluation of conifer classification. He also outlines the features sought in cultivars of each genus, particular cultivation concerns, and conifers recommended for cultivation under various conditions and to achieve different effects. Some 3,000 cultivars have been available in recent times, more than five times the total number of conifer species. Several hundred original illustrations include drawings of the seed cones for all genera as well as for representative species. Maps of the natural distribution of each genus allow for easy comparison of ranges. Handsome black-and-white photographs of species in their natural habitats and attractive color photos further enrich the volume. More than 100 images reproduce foliage of many genera as an aid in identification. With its unprecedented attention to detail and extensive bibliography, this major work is an essential reference for botanists, naturalists, and horticulturists.
Download or read book Bioinformatics and Phylogenetics written by Tandy Warnow and published by Springer. This book was released on 2019-04-08 with total page 410 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents a compelling collection of state-of-the-art work in algorithmic computational biology, honoring the legacy of Professor Bernard M.E. Moret in this field. Reflecting the wide-ranging influences of Prof. Moret’s research, the coverage encompasses such areas as phylogenetic tree and network estimation, genome rearrangements, cancer phylogeny, species trees, divide-and-conquer strategies, and integer linear programming. Each self-contained chapter provides an introduction to a cutting-edge problem of particular computational and mathematical interest. Topics and features: addresses the challenges in developing accurate and efficient software for the NP-hard maximum likelihood phylogeny estimation problem; describes the inference of species trees, covering strategies to scale phylogeny estimation methods to large datasets, and the construction of taxonomic supertrees; discusses the inference of ultrametric distances from additive distance matrices, and the inference of ancestral genomes under genome rearrangement events; reviews different techniques for inferring evolutionary histories in cancer, from the use of chromosomal rearrangements to tumor phylogenetics approaches; examines problems in phylogenetic networks, including questions relating to discrete mathematics, and issues of statistical estimation; highlights how evolution can provide a framework within which to understand comparative and functional genomics; provides an introduction to Integer Linear Programming and its use in computational biology, including its use for solving the Traveling Salesman Problem. Offering an invaluable source of insights for computer scientists, applied mathematicians, and statisticians, this illuminating volume will also prove useful for graduate courses on computational biology and bioinformatics.
Download or read book Topological in Hegel written by Borislav G. Dimitrov and published by Borislav Dimitrov. This book was released on 2018-01-23 with total page 520 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim of this book is to critically examine whether it is methodologically possible to combine mathematical rigor – topology with a systematic dialectical methodology in Hegel, and if so, to provide as result of my interpretation the outline of Hegel’s Analysis Situs, also with the proposed models (build on the topological manifold, cobordism, topological data analysis, persistent homology, simplicial complexes and graph theory, to provide an indication of how the merger of Hegel’s dialectical logic and topology may be instrumental to a systematic logician and of how a systematic dialectical logic perspective may help mathematical model builders.
Download or read book Persistence Theory From Quiver Representations to Data Analysis written by Steve Y. Oudot and published by American Mathematical Soc.. This book was released on 2017-05-17 with total page 229 pages. Available in PDF, EPUB and Kindle. Book excerpt: Persistence theory emerged in the early 2000s as a new theory in the area of applied and computational topology. This book provides a broad and modern view of the subject, including its algebraic, topological, and algorithmic aspects. It also elaborates on applications in data analysis. The level of detail of the exposition has been set so as to keep a survey style, while providing sufficient insights into the proofs so the reader can understand the mechanisms at work. The book is organized into three parts. The first part is dedicated to the foundations of persistence and emphasizes its connection to quiver representation theory. The second part focuses on its connection to applications through a few selected topics. The third part provides perspectives for both the theory and its applications. The book can be used as a text for a course on applied topology or data analysis.
Download or read book The Structure and Stability of Persistence Modules written by Frédéric Chazal and published by Springer. This book was released on 2016-10-08 with total page 123 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a comprehensive treatment of the theory of persistence modules over the real line. It presents a set of mathematical tools to analyse the structure and to establish the stability of such modules, providing a sound mathematical framework for the study of persistence diagrams. Completely self-contained, this brief introduces the notion of persistence measure and makes extensive use of a new calculus of quiver representations to facilitate explicit computations. Appealing to both beginners and experts in the subject, The Structure and Stability of Persistence Modules provides a purely algebraic presentation of persistence, and thus complements the existing literature, which focuses mainly on topological and algorithmic aspects.
Download or read book Combinatorial Algebraic Topology written by Dimitry Kozlov and published by Springer Science & Business Media. This book was released on 2008-01-08 with total page 416 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is the first comprehensive treatment of combinatorial algebraic topology in book form. The first part of the book constitutes a swift walk through the main tools of algebraic topology. Readers - graduate students and working mathematicians alike - will probably find particularly useful the second part, which contains an in-depth discussion of the major research techniques of combinatorial algebraic topology. Although applications are sprinkled throughout the second part, they are principal focus of the third part, which is entirely devoted to developing the topological structure theory for graph homomorphisms.
Download or read book Principles and Techniques of Contemporary Taxonomy written by Donald L.J. Quicke and published by Springer Science & Business Media. This book was released on 2013-03-13 with total page 323 pages. Available in PDF, EPUB and Kindle. Book excerpt: Taxonomy is an ever-changing, controversial and exCitmg field of biology. It has not remained motionless since the days of its founding fathers in the last century, but, just as with other fields of endeavour, it continues to advance in leaps and bounds, both in procedure and in philosophy. These changes are not only of interest to other taxonomists, but have far reaching implications for much of the rest of biology, and they have the potential to reshape a great deal of current biological thought, because taxonomy underpins much of biological methodology. It is not only important that an ethologist. physiologist. biochemist or ecologist can obtain information about the identities of the species which they are investigating; biology is also uniquely dependent on the comparative method and on the need to generalize. Both of these necessitate knowledge of the evolutionary relationships between organisms. and it is the science of taxonomy that can develop testable phylogenetic hypotheses and ultimately provide the best estimates of evolutionary history and relationships.
Download or read book Network Bioscience 2nd Edition written by Marco Pellegrini and published by Frontiers Media SA. This book was released on 2020-03-27 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt: Network science has accelerated a deep and successful trend in research that influences a range of disciplines like mathematics, graph theory, physics, statistics, data science and computer science (just to name a few) and adapts the relevant techniques and insights to address relevant but disparate social, biological, technological questions. We are now in an era of 'big biological data' supported by cost-effective high-throughput genomic, transcriptomic, proteomic, metabolomic data collection techniques that allow one to take snapshots of the cells' molecular profiles in a systematic fashion. Moreover recently, also phenotypic data, data on diseases, symptoms, patients, etc. are being collected at nation-wide level thus giving us another source of highly related (causal) 'big data'. This wealth of data is usually modeled as networks (aka binary relations, graphs or webs) of interactions, (including protein-protein, metabolic, signaling and transcription-regulatory interactions). The network model is a key view point leading to the uncovering of mesoscale phenomena, thus providing an essential bridge between the observable phenotypes and 'omics' underlying mechanisms. Moreover, network analysis is a powerful 'hypothesis generation' tool guiding the scientific cycle of 'data gathering', 'data interpretation, 'hypothesis generation' and 'hypothesis testing'. A major challenge in contemporary research is the synthesis of deep insights coming from network science with the wealth of data (often noisy, contradictory, incomplete and difficult to replicate) so to answer meaningful biological questions, in a quantifiable way using static and dynamic properties of biological networks.
Download or read book Research in Computational Molecular Biology written by Satoru Miyano and published by Springer Science & Business Media. This book was released on 2005-04-28 with total page 646 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains the papers presented at the 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2005), which was held in Cambridge, Massachusetts, on May 14–18, 2005. The RECOMB conference series was started in 1997 by Sorin Istrail, Pavel Pevzner and Michael Waterman. The list of previous meetings is shown below in the s- tion “Previous RECOMB Meetings. ” RECOMB 2005 was hosted by the Broad Institute of MIT and Harvard, and Boston University’s Center for Advanced - nomic Technology, and was excellently organized by the Organizing Committee Co-chairs Jill Mesirov and Simon Kasif. This year, 217 papers were submitted, of which the Program Committee - lected 39 for presentation at the meeting and inclusion in this proceedings. Each submission was refereed by at least three members of the Program Committee. After the completion of the referees’ reports, an extensive Web-based discussion took place for making decisions. From RECOMB 2005, the Steering Committee decided to publish the proceedings as a volume of Lecture Notes in Bioinf- matics (LNBI) for which the founders of RECOMB are also the editors. The prominent volume number LNBI 3500 was assigned to this proceedings. The RECOMB conference series is closely associated with the Journal of Compu- tional Biology which traditionally publishes special issues devoted to presenting full versions of selected conference papers. The RECOMB Program Committee consistedof42members,aslistedonaseparatepage. Iwouldliketothank the RECOMB 2005 Program Committee members for their dedication and hard work.
