Computational Genomic Signatures
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Computational Genomic Signatures
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Author : Ozkan Ufuk Nalbantoglu
language : en
Publisher: Springer Nature
Release Date : 2022-06-01
Computational Genomic Signatures written by Ozkan Ufuk Nalbantoglu and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-06-01 with Technology & Engineering categories.
Recent advances in development of sequencing technology has resulted in a deluge of genomic data. In order to make sense of this data, there is an urgent need for algorithms for data processing and quantitative reasoning. An emerging in silico approach, called computational genomic signatures, addresses this need by representing global species-specific features of genomes using simple mathematical models. This text introduces the general concept of computational genomic signatures, and it reviews some of the DNA sequence models which can be used as computational genomic signatures. The text takes the position that a practical computational genomic signature consists of both a model and a measure for computing the distance or similarity between models. Therefore, a discussion of sequence similarity/distance measurement in the context of computational genomic signatures is presented. The remainder of the text covers various applications of computational genomic signatures in the areas of metagenomics, phylogenetics and the detection of horizontal gene transfer. Table of Contents: Genome Signatures, Definition and Background / Other Computational Characterizations as Genome Signatures / Measuring Distance of Biological Sequences Using Genome Signatures / Applications: Phylogeny Construction / Applications: Metagenomics / Applications: Horizontal DNA Transfer Detection
Computational Genomic Signatures
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Author : Ozkan Ufuk Nalbantoglu
language : en
Publisher: Morgan & Claypool Publishers
Release Date : 2011-05-05
Computational Genomic Signatures written by Ozkan Ufuk Nalbantoglu and has been published by Morgan & Claypool Publishers this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-05-05 with Technology & Engineering categories.
Recent advances in development of sequencing technology has resulted in a deluge of genomic data. In order to make sense of this data, there is an urgent need for algorithms for data processing and quantitative reasoning. An emerging in silico approach, called computational genomic signatures, addresses this need by representing global species-specific features of genomes using simple mathematical models. This text introduces the general concept of computational genomic signatures, and it reviews some of the DNA sequence models which can be used as computational genomic signatures. The text takes the position that a practical computational genomic signature consists of both a model and a measure for computing the distance or similarity between models. Therefore, a discussion of sequence similarity/distance measurement in the context of computational genomic signatures is presented. The remainder of the text covers various applications of computational genomic signatures in the areas of metagenomics, phylogenetics and the detection of horizontal gene transfer. Table of Contents: Genome Signatures, Definition and Background / Other Computational Characterizations as Genome Signatures / Measuring Distance of Biological Sequences Using Genome Signatures / Applications: Phylogeny Construction / Applications: Metagenomics / Applications: Horizontal DNA Transfer Detection
Computational Genomic Signatures And Metagenomics
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Author : Ozkan Ufuk Nalbantoglu
language : en
Publisher:
Release Date : 2011
Computational Genomic Signatures And Metagenomics written by Ozkan Ufuk Nalbantoglu and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011 with Computational biology categories.
Computational Methods For 3d Genome Analysis
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Author : Ryuichiro Nakato
language : en
Publisher: Springer Nature
Release Date : 2024-09-16
Computational Methods For 3d Genome Analysis written by Ryuichiro Nakato and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-09-16 with Science categories.
This volume covers the latest methods and analytical approaches used to study the computational analysis of three-dimensional (3D) genome structure. The chapters in this book are organized into six parts. Part One discusses different NGS assays and the regulatory mechanism of 3D genome folding by SMC complexes. Part Two presents analysis workflows for Hi-C and Micro-C in different species, including human, mouse, medaka, yeast, and prokaryotes. Part Three covers methods for chromatin loop detection, sub-compartment detection, and 3D feature visualization. Part Four explores single-cell Hi-C and the cell-to-cell variability of the dynamic 3D structure. Parts Five talks about the analysis of polymer modelling to simulate the dynamic behavior of the 3D genome structure, and Part Six looks at 3D structure analysis using other omics data, including prediction of 3D genome structure from the epigenome, double-strand break-associated structure, and imaging-based 3D analysis using seqFISH. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and tools, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Computational Methods for 3D Genome Analysis: Methods and Protocols is a valuable resource for researchers interested in using computational methods to further their studies in the nature of 3D genome organization.
Computational Genome Analysis
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Author : Richard C. Deonier
language : en
Publisher: Springer Science & Business Media
Release Date : 2005-12-27
Computational Genome Analysis written by Richard C. Deonier and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005-12-27 with Computers categories.
This book presents the foundations of key problems in computational molecular biology and bioinformatics. It focuses on computational and statistical principles applied to genomes, and introduces the mathematics and statistics that are crucial for understanding these applications. The book features a free download of the R software statistics package and the text provides great crossover material that is interesting and accessible to students in biology, mathematics, statistics and computer science. More than 100 illustrations and diagrams reinforce concepts and present key results from the primary literature. Exercises are given at the end of chapters.
Computational Methods For Understanding Bacterial And Archaeal Genomes
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Author : Ying Xu
language : en
Publisher: World Scientific
Release Date : 2008-08-06
Computational Methods For Understanding Bacterial And Archaeal Genomes written by Ying Xu and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-08-06 with Science categories.
Over 500 prokaryotic genomes have been sequenced to date, and thousands more have been planned for the next few years. While these genomic sequence data provide unprecedented opportunities for biologists to study the world of prokaryotes, they also raise extremely challenging issues such as how to decode the rich information encoded in these genomes. This comprehensive volume includes a collection of cohesively written chapters on prokaryotic genomes, their organization and evolution, the information they encode, and the computational approaches needed to derive such information. A comparative view of bacterial and archaeal genomes, and how information is encoded differently in them, is also presented. Combining theoretical discussions and computational techniques, the book serves as a valuable introductory textbook for graduate-level microbial genomics and informatics courses./a
Computational Systems Bioinformatics
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Author : Peter Markstein
language : en
Publisher: Imperial College Press
Release Date : 2006
Computational Systems Bioinformatics written by Peter Markstein and has been published by Imperial College Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006 with Science categories.
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. There are also abstracts from the keynote addresses and invited talks.The papers cover not only 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.
Fundamentals Of Bioinformatics And Computational Biology
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Author : Gautam B. Singh
language : en
Publisher: Springer Nature
Release Date : 2025-03-24
Fundamentals Of Bioinformatics And Computational Biology written by Gautam B. Singh and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2025-03-24 with Computers categories.
This book comprehensively covers all the core bioinformatics topics and includes practical examples completed using the MATLAB bioinformatics and machine learning toolboxesTM. It is primarily intended as a textbook for engineering and computer science students attending advanced undergraduate and graduate courses in bioinformatics and computational biology. The book develops bioinformatics concepts from the ground up, starting with an introductory chapter on molecular biology and genetics to enable physical science students to appreciate the challenges in biological data management, sequence analysis, and systems biology. The book is divided into five parts. The first one includes a survey of existing biological databases and tools that have become essential in today’s biotechnology research. The second part covers methodologies for retrieving biological information, including fundamental algorithms for sequence comparison, scoring, and determining evolutionary distance. The third part of the book focuses on modeling biological sequences and patterns as Markov chains, covering core principles for analyzing and searching for sequences of significant motifs and biomarkers and developing stochastic ergodic hidden Markov models for biological sequence families. The fourth one is dedicated to systems biology and covers phylogenetic analysis and evolutionary tree computations, as well as gene expression analysis with microarrays. In turn, the last part of the book includes an introduction to machine-learning algorithms for bioinformatics and outlines strategies for developing intelligent diagnostic machine-learning applications, RNA sequence data, and deep learning systems for mass spectrometry data. All in all, this book offers a unique hands-on reference guide to bioinformatics and computational biology. This second edition has been updated to cover additional and most recent databases, and machine learning and deep learning applications in RNA sequence and mass-spectrometry data analysis. Moreover, it presents significant enhancements to the chapter dedicated to microarray analysis, and more practical examples, with additional end-of-chapter problems.
Computational Epigenetics And Diseases
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Author :
language : en
Publisher: Academic Press
Release Date : 2019-02-06
Computational Epigenetics And Diseases written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-02-06 with Medical categories.
Computational Epigenetics and Diseases, written by leading scientists in this evolving field, provides a comprehensive and cutting-edge knowledge of computational epigenetics in human diseases. In particular, the major computational tools, databases, and strategies for computational epigenetics analysis, for example, DNA methylation, histone modifications, microRNA, noncoding RNA, and ceRNA, are summarized, in the context of human diseases. This book discusses bioinformatics methods for epigenetic analysis specifically applied to human conditions such as aging, atherosclerosis, diabetes mellitus, schizophrenia, bipolar disorder, Alzheimer disease, Parkinson disease, liver and autoimmune disorders, and reproductive and respiratory diseases. Additionally, different organ cancers, such as breast, lung, and colon, are discussed. This book is a valuable source for graduate students and researchers in genetics and bioinformatics, and several biomedical field members interested in applying computational epigenetics in their research. - Provides a comprehensive and cutting-edge knowledge of computational epigenetics in human diseases - Summarizes the major computational tools, databases, and strategies for computational epigenetics analysis, such as DNA methylation, histone modifications, microRNA, noncoding RNA, and ceRNA - Covers the major milestones and future directions of computational epigenetics in various kinds of human diseases such as aging, atherosclerosis, diabetes, heart disease, neurological disorders, cancers, blood disorders, liver diseases, reproductive diseases, respiratory diseases, autoimmune diseases, human imprinting disorders, and infectious diseases
Computational Systems Bioinformatics Proceedings Of The Conference Csb 2006
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Author : Peter Markstein
language : en
Publisher: World Scientific
Release Date : 2006-07-28
Computational Systems Bioinformatics Proceedings Of The Conference Csb 2006 written by Peter Markstein and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006-07-28 with Science categories.
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. There are also abstracts from the keynote addresses and invited talks.The papers cover not only 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