Theoretical And Computational Methods In Genome Research

Author : Sándor Suhai
Publisher : Springer Science & Business Media
Page : 332 pages
File Size : 51,5 Mb
Release : 2012-12-06
Category : Science
ISBN : 9781461559030

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Theoretical and Computational Methods in Genome Research by Sándor Suhai Pdf

The application ofcomputational methods to solve scientific and practical problems in genome research created a new interdisciplinary area that transcends boundaries tradi tionally separating genetics, biology, mathematics, physics, and computer science. Com puters have, of course, been intensively used in the field of life sciences for many years, even before genome research started, to store and analyze DNA or protein sequences; to explore and model the three-dimensional structure, the dynamics, and the function of biopolymers; to compute genetic linkage or evolutionary processes; and more. The rapid development of new molecular and genetic technologies, combined with ambitious goals to explore the structure and function ofgenomes ofhigher organisms, has generated, how ever, not only a huge and exponentially increasing body of data but also a new class of scientific questions. The nature and complexity of these questions will also require, be yond establishing a new kind ofalliance between experimental and theoretical disciplines, the development of new generations both in computer software and hardware technolo gies. New theoretical procedures, combined with powerful computational facilities, will substantially extend the horizon of problems that genome research can attack with suc cess. Many of us still feel that computational models rationalizing experimental findings in genome research fulfill their promises more slowly than desired. There is also an uncer tainty concerning the real position of a "theoretical genome research" in the network of established disciplines integrating their efforts in this field.

Author : Sandor Suhai
Publisher : Unknown
Page : 346 pages
File Size : 52,6 Mb
Release : 1997-06-30
Category : Electronic
ISBN : 1461559049

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Theoretical and Computational Methods in Genome Research by Sandor Suhai Pdf

Author : Sándor Suhai
Publisher : Springer Science & Business Media
Page : 230 pages
File Size : 45,9 Mb
Release : 2012-12-06
Category : Science
ISBN : 9781461524519

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Computational Methods in Genome Research by Sándor Suhai Pdf

The application of computational methods to solve scientific and pratical problems in genome research created a new interdisciplinary area that transcends boundaries traditionally separating genetics, biology, mathematics, physics, and computer science. Computers have been, of course, intensively used for many year~ in the field of life sciences, even before genome research started, to store and analyze DNA or proteins sequences, to explore and model the three-dimensional structure, the dynamics and the function of biopolymers, to compute genetic linkage or evolutionary processes etc. The rapid development of new molecular and genetic technologies, combined with ambitious goals to explore the structure and function of genomes of higher organisms, has generated, however, not only a huge and burgeoning body of data but also a new class of scientific questions. The nature and complexity of these questions will require, beyond establishing a new kind of alliance between experimental and theoretical disciplines, also the development of new generations both in computer software and hardware technologies, respectively. New theoretical procedures, combined with powerful computational facilities, will substantially extend the horizon of problems that genome research can ·attack with success. Many of us still feel that computational models rationalizing experimental findings in genome research fulfil their promises more slowly than desired. There also is an uncertainity concerning the real position of a 'theoretical genome research' in the network of established disciplines integrating their efforts in this field.

Author : Ying Xu,J Peter Gogarten
Publisher : World Scientific
Page : 496 pages
File Size : 46,7 Mb
Release : 2008-08-06
Category : Science
ISBN : 9781908979018

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Computational Methods for Understanding Bacterial and Archaeal Genomes by Ying Xu,J Peter Gogarten Pdf

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. Contents: General Characteristics of Prokaryotic Genomes (J Mrázek & A O Summers)Genes in Prokaryotic Genomes and Their Computational Prediction (R K Azad)Evolution of the Genetic Code: Computational Methods and Inferences (G Fournier)Dynamics of Prokaryotic Genome Evolution (P Lapierre)Mobile Genetic Elements and Their Prediction (M G I Langille et al.)Horizontal Gene Transfer: Its Detection and Role in Microbial Evolution (J P Gogarten & O Zhaxybayeva)Genome Reduction During Prokaryotic Evolution (F J Silva & A Latorre)Comparative Mechanisms for Transcription and Regulatory Signals in Archaea and Bacteria (A Martínez-Antonio & J Collado-Vides)Computational Techniques for Orthologous Gene Prediction in Prokaryotes (M Poptsova)Computational Elucidation of Operons and Uber-Operons (P Dam et al.)Prediction of Regulons Through Comparative Genome Analyses (Z-C Su et al.)Prediction of Biological Pathways Through Data Mining and Information Fusion (F-L Mao et al.)Microbial Pathway Models (S R Veflingstad et al.)Metagenomics (K Arima & J Wooley) Readership: Graduate students and microbiologists in microbial genomics and bioinformatics. Keywords:Bacteria;Archaea;Genomes;Genome Evolution;Orthologs;Genomic Structure;Operons;Regulons;Comparative Genomics;Microbial Pathways;Gene Duplication;Gene TransferKey Features:Tightly integrates theoretical discussions and computational approaches pertaining to prokaryotic genomesProvides, where appropriate, comparative studies of bacterial versus archaeal genomesIncludes contributions from leading researchers in the field, including Peter Gogarten, Anne Summers, Julio Collado Vides, Eberhard Volt, Ying Xu, and John Wooley

Author : Shili Lin,Hongyu Zhao
Publisher : Springer Science & Business Media
Page : 340 pages
File Size : 51,7 Mb
Release : 2009-10-13
Category : Medical
ISBN : 9783540692645

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Handbook on Analyzing Human Genetic Data by Shili Lin,Hongyu Zhao Pdf

This handbook offers guidance on selections of appropriate computational methods and software packages for specific genetic problems. Coverage strikes a balance between methodological expositions and practical guidelines for software selections. Wherever possible, comparisons among competing methods and software are made to highlight the relative advantages and disadvantage of the approaches.

Author : Maria Anisimova
Publisher : Humana Press
Page : 484 pages
File Size : 54,9 Mb
Release : 2016-05-01
Category : Medical
ISBN : 1493959085

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Evolutionary Genomics by Maria Anisimova Pdf

This book examines developments in statistical methodology and the challenges that followed rapidly improving sequencing technologies.Includes articles encompassing theoretical works and hands-on tutorials, as well as many reviews with key biological insight."

Author : Maria Anisimova
Publisher : Humana Press
Page : 556 pages
File Size : 51,7 Mb
Release : 2012-03-08
Category : Medical
ISBN : 1617795844

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Evolutionary Genomics by Maria Anisimova Pdf

Together with early theoretical work in population genetics, the debate on sources of genetic makeup initiated by proponents of the neutral theory made a solid contribution to the spectacular growth in statistical methodologies for molecular evolution. Evolutionary Genomics: Statistical and Computational Methods is intended to bring together the more recent developments in the statistical methodology and the challenges that followed as a result of rapidly improving sequencing technologies. Presented by top scientists from a variety of disciplines, the collection includes a wide spectrum of articles encompassing theoretical works and hands-on tutorials, as well as many reviews with key biological insight. Volume 2 begins with phylogenomics and continues with in-depth coverage of natural selection, recombination, and genomic innovation. The remaining chapters treat topics of more recent interest, including population genomics, -omics studies, and computational issues related to the handling of large-scale genomic data. Written in the highly successful Methods in Molecular BiologyTM series format, this work provides the kind of advice on methodology and implementation that is crucial for getting ahead in genomic data analyses. Comprehensive and cutting-edge, Evolutionary Genomics: Statistical and Computational Methods is a treasure chest of state-of the-art methods to study genomic and omics data, certain to inspire both young and experienced readers to join the interdisciplinary field of evolutionary genomics.

Author : Xun Gu
Publisher : OUP Oxford
Page : 272 pages
File Size : 43,8 Mb
Release : 2010-11-04
Category : Science
ISBN : 9780199213269

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Statistical Theory and Methods for Evolutionary Genomics by Xun Gu Pdf

Summarises the statistical framework of evolutionary genomics, and illustrates how statistical modelling and testing can enhance our understanding of functional genomic evolution.

Author : Altuna Akalin
Publisher : CRC Press
Page : 0 pages
File Size : 51,6 Mb
Release : 2023-01-09
Category : Electronic
ISBN : 0367634600

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Computational Genomics with R by Altuna Akalin Pdf

This book has fundamental theoretical and practical aspects of data analysis, useful for beginners and experienced researchers that are looking for a recipe or an analysis approach. Since R has many packages, even experienced researchers look for how particular functions are used in an analysis workflow.

Author : Jamie A. Goode,Derek J. Chadwick
Publisher : John Wiley & Sons
Page : 272 pages
File Size : 48,5 Mb
Release : 2008-04-30
Category : Science
ISBN : 9780470515785

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Rice Biotechnology by Jamie A. Goode,Derek J. Chadwick Pdf

Rice is the most important food crop for half the world's population. Over the last three decades, the imporvement in human nutrition and health in Asia has largely been attributable to a relatively stable and affordable rice supply. The challenge to produce enough rice for the future, however, remains daunting, as the current rate of population growth outpaces that of increases in rice production. Science has a central role to play in raising rice productivity and this book highlights areas of plant science that are particularly relevant to solving the major constraints on rice production. Examining molecular, genetic and cellular techniques, it considers recent advances in four research approaches for increasing yields and improving the nutritional quality of rice. Plant genomics: knowing the identity and location of each gene in the rice genome is of immense value in all aspects of rice science and cultivar improvement. Molecular biological approaches to increase yield: to produce more biomass by increasing photosynthetic rate and duration, and by improving grain filling. Enhancing tolerance to biotic and abiotic stresses: with new DNA array technologies, it is now possible to assess global genomic response to stresses. Understanding the relationships among stress pathways may create new opportunities for gene manipulation to enhance tolerance to multiple biotic and abiotic stresses. Improving nutritional quality in the grain: knowledge of the biosynthesis of micronutrients in plants permits genetic engineering of metabolic pathways to enhance the availability of micronutrients.

Author : Ashish Ghosh,Shigeyoshi Tsutsui
Publisher : Springer Science & Business Media
Page : 1001 pages
File Size : 40,5 Mb
Release : 2012-12-06
Category : Computers
ISBN : 9783642189654

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Advances in Evolutionary Computing by Ashish Ghosh,Shigeyoshi Tsutsui Pdf

This book provides a collection of fourty articles containing new material on both theoretical aspects of Evolutionary Computing (EC), and demonstrating the usefulness/success of it for various kinds of large-scale real world problems. Around 23 articles deal with various theoretical aspects of EC and 17 articles demonstrate the success of EC methodologies. These articles are written by leading experts of the field from different countries all over the world.

Author : Ion Mandoiu,Alexander Zelikovsky
Publisher : John Wiley & Sons
Page : 460 pages
File Size : 53,6 Mb
Release : 2016-10-03
Category : Computers
ISBN : 9781118169483

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Computational Methods for Next Generation Sequencing Data Analysis by Ion Mandoiu,Alexander Zelikovsky Pdf

Introduces readers to core algorithmic techniques for next-generation sequencing (NGS) data analysis and discusses a wide range of computational techniques and applications This book provides an in-depth survey of some of the recent developments in NGS and discusses mathematical and computational challenges in various application areas of NGS technologies. The 18 chapters featured in this book have been authored by bioinformatics experts and represent the latest work in leading labs actively contributing to the fast-growing field of NGS. The book is divided into four parts: Part I focuses on computing and experimental infrastructure for NGS analysis, including chapters on cloud computing, modular pipelines for metabolic pathway reconstruction, pooling strategies for massive viral sequencing, and high-fidelity sequencing protocols. Part II concentrates on analysis of DNA sequencing data, covering the classic scaffolding problem, detection of genomic variants, including insertions and deletions, and analysis of DNA methylation sequencing data. Part III is devoted to analysis of RNA-seq data. This part discusses algorithms and compares software tools for transcriptome assembly along with methods for detection of alternative splicing and tools for transcriptome quantification and differential expression analysis. Part IV explores computational tools for NGS applications in microbiomics, including a discussion on error correction of NGS reads from viral populations, methods for viral quasispecies reconstruction, and a survey of state-of-the-art methods and future trends in microbiome analysis. Computational Methods for Next Generation Sequencing Data Analysis: Reviews computational techniques such as new combinatorial optimization methods, data structures, high performance computing, machine learning, and inference algorithms Discusses the mathematical and computational challenges in NGS technologies Covers NGS error correction, de novo genome transcriptome assembly, variant detection from NGS reads, and more This text is a reference for biomedical professionals interested in expanding their knowledge of computational techniques for NGS data analysis. The book is also useful for graduate and post-graduate students in bioinformatics.

Author : Tieng K. Yap,Ophir Frieder,Robert L. Martino
Publisher : Springer Science & Business Media
Page : 219 pages
File Size : 53,5 Mb
Release : 2012-12-06
Category : Computers
ISBN : 9781461313915

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High Performance Computational Methods for Biological Sequence Analysis by Tieng K. Yap,Ophir Frieder,Robert L. Martino Pdf

High Performance Computational Methods for Biological Sequence Analysis presents biological sequence analysis using an interdisciplinary approach that integrates biological, mathematical and computational concepts. These concepts are presented so that computer scientists and biomedical scientists can obtain the necessary background for developing better algorithms and applying parallel computational methods. This book will enable both groups to develop the depth of knowledge needed to work in this interdisciplinary field. This work focuses on high performance computational approaches that are used to perform computationally intensive biological sequence analysis tasks: pairwise sequence comparison, multiple sequence alignment, and sequence similarity searching in large databases. These computational methods are becoming increasingly important to the molecular biology community allowing researchers to explore the increasingly large amounts of sequence data generated by the Human Genome Project and other related biological projects. The approaches presented by the authors are state-of-the-art and show how to reduce analysis times significantly, sometimes from days to minutes. High Performance Computational Methods for Biological Sequence Analysis is tremendously important to biomedical science students and researchers who are interested in applying sequence analyses to their studies, and to computational science students and researchers who are interested in applying new computational approaches to biological sequence analyses.

Author : Leon Gradon,J.C. Marijnissen
Publisher : Springer Science & Business Media
Page : 330 pages
File Size : 45,9 Mb
Release : 2003-11-30
Category : Medical
ISBN : 1402016514

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Optimization of Aerosol Drug Delivery by Leon Gradon,J.C. Marijnissen Pdf

Aerosol therapy has significantly improved the treatment of a variety of respiratory diseases. Besides the treatment of respiratory diseases there is currently also a great interest to use the lungs as a portal to introduce drugs for systemic therapy. The success of therapy with the application of aerosolized medicaments depends on the possibility to deliver the proper amount of drug to the appropriate sites in the respiratory system, thus limiting the side effects to a minimum. Aerosolized delivery of drugs to the lung is optimized if, for a given chemical composition of a medicine, the target of deposition and the required mass of drug to be deposited are precisely defined. The next step is the specification of the number of respirable particles or droplets, to be generated by appropriate devices. Another very important factor for successful aerosol therapy is the condition of the patient coupled with his or her inhalation technique.

Author : Ying Xu,J. Peter Gogarten
Publisher : World Scientific
Page : 494 pages
File Size : 46,6 Mb
Release : 2008
Category : Medical
ISBN : 9781860949821

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Computational Methods for Understanding Bacterial and Archaeal Genomes by Ying Xu,J. Peter Gogarten Pdf

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.