A Combinatorial Approach to Genome-wide Ortholog Assignment Via Genome Rearrangement PDF Download
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Author: Zheng Fu
Publisher:
ISBN:
Category : Gene mapping
Languages : en
Pages : 282
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Book Description
Author: Zheng Fu
Publisher:
ISBN:
Category : Gene mapping
Languages : en
Pages : 282
Get Book Here
Book Description
Author: Guanqun Shi
Publisher:
ISBN: 9781124940571
Category : Bioinformatics
Languages : en
Pages : 75
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Book Description
The accurate identification of orthologous genes across different species is a critical and challenging problem in comparative genomics and has a wide spectrum of biological applications including gene function inference, evolutionary studies and systems biology. During the past several years, many methods have been proposed for ortholog assignment based on sequence similarity, phylogenetic approaches, synteny information, and genome rearrangement. Although these methods share many commonly assigned orthologs, each method tends to produce an ortholog assignment significantly different from the others.
Author: Josep Diaz
Publisher: Springer
ISBN: 3540380450
Category : Computers
Languages : en
Pages : 532
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Book Description
This is the joint refereed proceedings of the 9th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX 2006 and the 10th International Workshop on Randomization and Computation, RANDOM 2006. The book presents 44 carefully reviewed and revised full papers. Among the topics covered are design and analysis of approximation algorithms, hardness of approximation problems, small spaces and data streaming algorithms, embeddings and metric space methods, and more.
Author: Peter Markstein
Publisher: World Scientific
ISBN: 1908979097
Category : Science
Languages : en
Pages : 472
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Book Description
This volume contains about 40 papers covering many of the latest developments in the fast-growing field of bioinformatics. The contributions span a wide range of topics, including computational genomics and genetics, protein function and computational proteomics, the transcriptome, structural bioinformatics, microarray data analysis, motif identification, biological pathways and systems, and biomedical applications. Abstracts from the keynote addresses and invited talks are also included.The papers not only cover theoretical aspects of bioinformatics but also delve into the application of new methods, with input from computation, engineering and biology disciplines. This multidisciplinary approach to bioinformatics gives these proceedings a unique viewpoint of the field./a
Author: Peter Markstein
Publisher: World Scientific
ISBN: 1860948731
Category : Computers
Languages : en
Pages : 472
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Book Description
This volume contains about 40 papers covering many of the latest developments in the fast-growing field of bioinformatics. The contributions span a wide range of topics, including computational genomics and genetics, protein function and computational proteomics, the transcriptome, structural bioinformatics, microarray data analysis, motif identification, biological pathways and systems, and biomedical applications. Abstracts from the keynote addresses and invited talks are also included. The papers not only cover theoretical aspects of bioinformatics but also delve into the application of new methods, with input from computation, engineering and biology disciplines. This multidisciplinary approach to bioinformatics gives these proceedings a unique viewpoint of the field. Sample Chapter(s). Chapter 1: Whole-Genome Analysis of Dorsal Gradient Thresholds in the Drosophila Embryo (102 KB). Contents: Learning Predictive Models of Gene Regulation (C Leslie); Algorithms for Selecting Breakpoint Locations to Optimize Diversity in Protein Engineering by Site-Directed Protein Recombination (W Zheng et al.); Cancer Molecular Pattern Discovery by Subspace Consensus Kernel Classification (X Han); Transcriptional Profiling of Definitive Endoderm Derived from Human Embryonic Stem Cells (H Liu et al.); A Markov Model Based Analysis of Stochastic Biochemical Systems (P Ghosh et al.); Clustering of Main Orthologs for Multiple Genomes (Z Fu & T Jiang); Extraction, Quantification and Visualization of Protein Pockets (X Zhang & C Bajaj); Consensus Contact Prediction by Linear Programming (X Gao et al.); An Active Visual Search Interface for Medline (W Xuan et al.); Exact and Heuristic Algorithms for Weighted Cluster Editing (S Rahmann et al.); Reconcilation with Non-binary Species Trees (B Vernot et al.); and other papers. Readership: Research and application community in bioinformatics, systems biology, medicine, pharmacology and biotechnology. Graduate researchers in bioinformatics and computational biology.
Author: Guillaume Bourque
Publisher: Springer Science & Business Media
ISBN: 3540445293
Category : Science
Languages : en
Pages : 239
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Book Description
This book constitutes the refereed proceedings of the 4th RECOMB Comparative Genomics Satellite Workshop, RECOMB-CG 2006. The 17 revised full papers presented were carefully reviewed and selected from 34 initial submissions. The papers address a broad variety of aspects and components of the field of comparative genomics, ranging from new quantitative discoveries about genome structure and process to theorems on the complexity of computational problems inspired by genome comparison.
Author: Hervé Tettelin
Publisher: Springer Nature
ISBN: 3030382818
Category : Science
Languages : en
Pages : 311
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Book Description
This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.
Author: Olivier Gascuel
Publisher: OUP Oxford
ISBN: 9780191513732
Category : Mathematics
Languages : en
Pages : 444
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Book Description
This book considers evolution at different scales: sequences, genes, gene families, organelles, genomes and species. The focus is on the mathematical and computational tools and concepts, which form an essential basis of evolutionary studies, indicate their limitations, and give them orientation. Recent years have witnessed rapid progress in the mathematics of evolution and phylogeny, with models and methods becoming more realistic, powerful, and complex. Aimed at graduates and researchers in phylogenetics, mathematicians, computer scientists and biologists, and including chapters by leading scientists: A. Bergeron, D. Bertrand, D. Bryant, R. Desper, O. Elemento, N. El-Mabrouk, N. Galtier, O. Gascuel, M. Hendy, S. Holmes, K. Huber, A. Meade, J. Mixtacki, B. Moret, E. Mossel, V. Moulton, M. Pagel, M.-A. Poursat, D. Sankoff, M. Steel, J. Stoye, J. Tang, L.-S. Wang, T. Warnow, Z. Yang, this book of contributed chapters explains the basis and covers the recent results in this highly topical area.
Author: Guillaume Fertin
Publisher: MIT Press
ISBN: 0262062828
Category : Combinatorial analysis
Languages : en
Pages : 305
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Book Description
A comprehensive survey of a rapidly expanding field of combinatorial optimization, mathematically oriented but offering biological explanations when required. From one cell to another, from one individual to another, and from one species to another, the content of DNA molecules is often similar. The organization of these molecules, however, differs dramatically, and the mutations that affect this organization are known as genome rearrangements. Combinatorial methods are used to reconstruct putative rearrangement scenarios in order to explain the evolutionary history of a set of species, often formalizing the evolutionary events that can explain the multiple combinations of observed genomes as combinatorial optimization problems. This book offers the first comprehensive survey of this rapidly expanding application of combinatorial optimization. It can be used as a reference for experienced researchers or as an introductory text for a broader audience. Genome rearrangement problems have proved so interesting from a combinatorial point of view that the field now belongs as much to mathematics as to biology. This book takes a mathematically oriented approach, but provides biological background when necessary. It presents a series of models, beginning with the simplest (which is progressively extended by dropping restrictions), each constructing a genome rearrangement problem. The book also discusses an important generalization of the basic problem known as the median problem, surveys attempts to reconstruct the relationships between genomes with phylogenetic trees, and offers a collection of summaries and appendixes with useful additional information.
Author: Debmalya Barh
Publisher: Academic Press
ISBN: 0128170778
Category : Science
Languages : en
Pages : 476
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Book Description
Pan-genomics: Applications, Challenges, and Future Prospects covers current approaches, challenges and future prospects of pan-genomics. The book discusses bioinformatics tools and their applications and focuses on bacterial comparative genomics in order to leverage the development of precise drugs and treatments for specific organisms. The book is divided into three sections: the first, an "overview of pan-genomics and common approaches, brings the main concepts and current approaches on pan-genomics research; the second, “case studies in pan-genomics, thoroughly discusses twelve case, and the last, “current approaches and future prospects in pan-multiomics , encompasses the developments on omics studies to be applied on bacteria related studies. This book is a valuable source for bioinformaticians, genomics researchers and several members of biomedical field interested in understanding further bacterial organisms and their relationship to human health. Covers the entire spectrum of pangenomics, highlighting the use of specific approaches, case studies and future perspectives Discusses current bioinformatics tools and strategies for exploiting pangenomics data Presents twelve case studies with different organisms in order to provide the audience with real examples of pangenomics applicability
