New High Throughput Technologies For Dna Sequencing And Genomics

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New High Throughput Technologies for DNA Sequencing and Genomics

Keith R. Mitchelson
New High Throughput Technologies for DNA Sequencing and Genomics Book PDF

Author : Keith R. Mitchelson
Publisher : Elsevier
Page : 398 pages
File Size : 50,6 Mb
Release : 2011-09-22
Category : Science
ISBN : 0080471285

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New High Throughput Technologies for DNA Sequencing and Genomics by Keith R. Mitchelson Pdf

Since the independent invention of DNA sequencing by Sanger and by Gilbert 30 years ago, it has grown from a small scale technique capable of reading several kilobase-pair of sequence per day into today's multibillion dollar industry. This growth has spurred the development of new sequencing technologies that do not involve either electrophoresis or Sanger sequencing chemistries. Sequencing by Synthesis (SBS) involves multiple parallel micro-sequencing addition events occurring on a surface, where data from each round is detected by imaging. New High Throughput Technologies for DNA Sequencing and Genomics is the second volume in the Perspectives in Bioanalysis series, which looks at the electroanalytical chemistry of nucleic acids and proteins, development of electrochemical sensors and their application in biomedicine and in the new fields of genomics and proteomics. The authors have expertly formatted the information for a wide variety of readers, including new developments that will inspire students and young scientists to create new tools for science and medicine in the 21st century. Reviews of complementary developments in Sanger and SBS sequencing chemistries, capillary electrophoresis and microdevice integration, MS sequencing and applications set the framework for the book. * 'Hot Topic' with DNA sequencing continuing as a major research activity in many areas of life science and medicine. * Bringing together new developments in DNA sequencing technology * Reviewing issues relevant to the new applications used

Next Generation Sequencing

Jerzy Kulski
Next Generation Sequencing Book PDF

Author : Jerzy Kulski
Publisher : BoD – Books on Demand
Page : 466 pages
File Size : 43,7 Mb
Release : 2016-01-14
Category : Medical
ISBN : 9789535122401

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Next Generation Sequencing by Jerzy Kulski Pdf

Next generation sequencing (NGS) has surpassed the traditional Sanger sequencing method to become the main choice for large-scale, genome-wide sequencing studies with ultra-high-throughput production and a huge reduction in costs. The NGS technologies have had enormous impact on the studies of structural and functional genomics in all the life sciences. In this book, Next Generation Sequencing Advances, Applications and Challenges, the sixteen chapters written by experts cover various aspects of NGS including genomics, transcriptomics and methylomics, the sequencing platforms, and the bioinformatics challenges in processing and analysing huge amounts of sequencing data. Following an overview of the evolution of NGS in the brave new world of omics, the book examines the advances and challenges of NGS applications in basic and applied research on microorganisms, agricultural plants and humans. This book is of value to all who are interested in DNA sequencing and bioinformatics across all fields of the life sciences.

Bioinformatics for High Throughput Sequencing

Naiara Rodríguez-Ezpeleta,Michael Hackenberg,Ana M. Aransay
Bioinformatics for High Throughput Sequencing Book PDF

Author : Naiara Rodríguez-Ezpeleta,Michael Hackenberg,Ana M. Aransay
Publisher : Springer Science & Business Media
Page : 255 pages
File Size : 43,9 Mb
Release : 2011-10-26
Category : Science
ISBN : 1461407826

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Bioinformatics for High Throughput Sequencing by Naiara Rodríguez-Ezpeleta,Michael Hackenberg,Ana M. Aransay Pdf

Next generation sequencing is revolutionizing molecular biology. Owing to this new technology it is now possible to carry out a panoply of experiments at an unprecedented low cost and high speed. These go from sequencing whole genomes, transcriptomes and small non-coding RNAs to description of methylated regions, identification protein – DNA interaction sites and detection of structural variation. The generation of gigabases of sequence information for each of this huge bandwidth of applications in just a few days makes the development of bioinformatics applications for next generation sequencing data analysis as urgent as challenging.

Genome Sequencing Technology and Algorithms

Sun Kim
Genome Sequencing Technology and Algorithms Book PDF

Author : Sun Kim
Publisher : Artech House Publishers
Page : 288 pages
File Size : 47,7 Mb
Release : 2008
Category : Computers
ISBN : STANFORD:36105124046231

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Genome Sequencing Technology and Algorithms by Sun Kim Pdf

The 2003 completion of the Human Genome Project was just one step in the evolution of DNA sequencing. This trailblazing work gives researchers unparalleled access to state-of-the-art DNA sequencing technologies, new algorithmic sequence assembly techniques, and emerging methods for both resequencing and genome analysis.

Next Generation Sequencing Technologies and Challenges in Sequence Assembly

Sara El-Metwally,Osama M. Ouda,Mohamed Helmy
Next Generation Sequencing Technologies and Challenges in Sequence Assembly Book PDF

Author : Sara El-Metwally,Osama M. Ouda,Mohamed Helmy
Publisher : Springer Science & Business
Page : 118 pages
File Size : 52,9 Mb
Release : 2014-04-19
Category : Science
ISBN : 9781493907151

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Next Generation Sequencing Technologies and Challenges in Sequence Assembly by Sara El-Metwally,Osama M. Ouda,Mohamed Helmy Pdf

The introduction of Next Generation Sequencing (NGS) technologies resulted in a major transformation in the way scientists extract genetic information from biological systems, revealing limitless insight about the genome, transcriptome and epigenome of any species. However, with NGS, came its own challenges that require continuous development in the sequencing technologies and bioinformatics analysis of the resultant raw data and assembly of the full length genome and transcriptome. Such developments lead to outstanding improvements of the performance and coverage of sequencing and improved quality for the assembled sequences, nevertheless, challenges such as sequencing errors, expensive processing and memory usage for assembly and sequencer specific errors remains major challenges in the field. This book aims to provide brief overviews the NGS field with special focus on the challenges facing the NGS field, including information on different experimental platforms, assembly algorithms and software tools, assembly error correction approaches and the correlated challenges.

Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing

Ana M. Aransay,José Luis Lavín Trueba
Field Guidelines for Genetic Experimental Designs in High Throughput Sequencing Book PDF

Author : Ana M. Aransay,José Luis Lavín Trueba
Publisher : Springer
Page : 399 pages
File Size : 54,9 Mb
Release : 2016-06-02
Category : Medical
ISBN : 9783319313504

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Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing by Ana M. Aransay,José Luis Lavín Trueba Pdf

High throughput sequencing (HTS) technologies have conquered the genomics and epigenomics worlds. The applications of HTS methods are wide, and can be used to sequence everything from whole or partial genomes, transcriptomes, non-coding RNAs, ribosome profiling, to single-cell sequencing. Having such diversity of alternatives, there is a demand for information by research scientists without experience in HTS that need to choose the most suitable methodology or combination of platforms and to define their experimental designs to achieve their specific objectives. Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing aims to collect in a single volume all aspects that should be taken into account when HTS technologies are being incorporated into a research project and the reasons behind them. Moreover, examples of several successful strategies will be analyzed to make the point of the crucial features. This book will be of use to all scientist that are unfamiliar with HTS and want to incorporate such technologies to their research.

Next-Generation Genome Sequencing

Michal Janitz
Next Generation Genome Sequencing Book PDF

Author : Michal Janitz
Publisher : John Wiley & Sons
Page : 281 pages
File Size : 42,5 Mb
Release : 2011-08-24
Category : Science
ISBN : 9783527644735

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Next-Generation Genome Sequencing by Michal Janitz Pdf

Written by leading experts from industry and academia, this first single comprehensive resource addresses recent developments in next generation DNA sequencing technology and their impact on genome research, drug discovery and health care. As such, it presents a detailed comparative analysis of commercially available platforms as well as insights into alternative, emerging sequencing techniques. In addition, the book not only covers the principles of DNA sequencing techniques but also social, ethical and commercial aspects, the concept of personalized medicine and a five-year perspective of DNA sequencing.

High-Throughput Next Generation Sequencing

Young Min Kwon,Steven C. Ricke
High Throughput Next Generation Sequencing Book PDF

Author : Young Min Kwon,Steven C. Ricke
Publisher : Humana Press
Page : 0 pages
File Size : 41,5 Mb
Release : 2011-03-22
Category : Medical
ISBN : 1617790885

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High-Throughput Next Generation Sequencing by Young Min Kwon,Steven C. Ricke Pdf

Due to their novel concepts and extraordinary high-throughput sequencing capacity, the “next generation sequencing” methods allow scientists to grasp system-wide landscapes of the complex molecular events taking place in various biological systems, including microorganisms and microbial communities. These methods are now being recognized as essential tools for a more comprehensive and deeper understanding of the mechanisms underlying many biological processes. In High-Throughput Next Generation Sequencing: Methods and Applications, experts in the field explore the most recent advances in the applications of next generation sequencing technologies with an emphasis on microorganisms and their communities; however, the methods described in this book will also offer general applications relevant to the study of any living organisms. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, High-Throughput Next Generation Sequencing: Methods and Applications is an excellent collection of chapters to aid all scientists who wish to apply these innovative research tools to enhance their own pursuits in microbiology and also biology in general.

Computational Genomics with R

Altuna Akalin
Computational Genomics with R Book PDF

Author : Altuna Akalin
Publisher : CRC Press
Page : 462 pages
File Size : 52,5 Mb
Release : 2020-12-16
Category : Mathematics
ISBN : 9781498781862

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Computational Genomics with R by Altuna Akalin Pdf

Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.

Advancing Development of Synthetic Gene Regulators

Anandhakumar Chandran
Advancing Development of Synthetic Gene Regulators Book PDF

Author : Anandhakumar Chandran
Publisher : Springer
Page : 114 pages
File Size : 51,9 Mb
Release : 2017-09-19
Category : Science
ISBN : 9789811065477

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Advancing Development of Synthetic Gene Regulators by Anandhakumar Chandran Pdf

This book focuses on an “outside the box” notion by utilizing the powerful applications of next-generation sequencing (NGS) technologies in the interface of chemistry and biology. In personalized medicine, developing small molecules targeting a specific genomic sequence is an attractive goal. N-methylpyrrole (P)–N-methylimidazole (I) polyamides (PIPs) are a class of small molecule that can bind to the DNA minor groove. First, a cost-effective NGS (ion torrent platform)-based Bind-n-Seq was developed to identify the binding specificity of PIP conjugates in a randomized DNA library. Their biological influences rely primarily on selective DNA binding affinity, so it is important to analyze their genome-wide binding preferences. However, it is demanding to enrich specifically the small-molecule-bound DNA without chemical cross-linking or covalent binding in chromatinized genomes. Herein is described a method that was developed using high-throughput sequencing to map the differential binding sites and relative enriched regions of non-cross-linked SAHA-PIPs throughout the complex human genome. SAHA-PIPs binding motifs were identified and the genome-level mapping of SAHA-PIPs-enriched regions provided evidence for the differential activation of the gene network. A method using high-throughput sequencing to map the binding sites and relative enriched regions of alkylating PIP throughout the human genome was also developed. The genome-level mapping of alkylating the PIP-enriched region and the binding sites on the human genome identifies significant genomic targets of breast cancer. It is anticipated that this pioneering low-cost, high through-put investigation at the sequence-specific level will be helpful in understanding the binding specificity of various DNA-binding small molecules, which in turn will be beneficial for the development of small-molecule-based drugs targeting a genome-level sequence.

Analytical Techniques In DNA Sequencing

Brian K. Nunnally
Analytical Techniques In DNA Sequencing Book PDF

Author : Brian K. Nunnally
Publisher : CRC Press
Page : 256 pages
File Size : 46,6 Mb
Release : 2005-06-23
Category : Medical
ISBN : 9781420029086

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Analytical Techniques In DNA Sequencing by Brian K. Nunnally Pdf

While one marvels at the DNA generated by the Human Genome Project, perhaps just as significant and fascinating is the development of the amazing analytical technology that has permitted us entry into the genomic era and a whole new level of scientific understanding. Analytical Techniques in DNA Sequencing takes a look at the various DNA sequencing techniques that were developed and put to use during and after the Human Genome Project. Nunnally makes a special effort to trace the development of this branch of research since the early days of radioisotope sequencing. Special attention is paid to the breakthrough Sanger Method (1977), as well as to several other techniques that improved the accuracy, improved the detection limits, and in a variety of ways dramatically reduced the time needed to generate a DNA sequence. This comprehensive volume describes the improvements in DNA separation based on advanced capillary electrophoresis and microchip sequencing. It also looks at the use of mass spectrometry and single molecule detection, and takes an in-depth look at the use of various fluorescence methods for the detection of sequencing fragments. One chapter is dedicated to chip-based microfabricated sequencing systems, which could well be the future of DNA sequencing. The book’s ten chapters, authored by a variety of leading experts in the field, include many of the far-reaching applications of DNA sequencing. Entire chapters are dedicated to DNA typing for forensics, a reevaluation of ancient DNA, and genome analysis.

Evolution of Translational Omics

Institute of Medicine,Board on Health Sciences Policy,Board on Health Care Services,Committee on the Review of Omics-Based Tests for Predicting Patient Outcomes in Clinical Trials
Evolution of Translational Omics Book PDF

Author : Institute of Medicine,Board on Health Sciences Policy,Board on Health Care Services,Committee on the Review of Omics-Based Tests for Predicting Patient Outcomes in Clinical Trials
Publisher : National Academies Press
Page : 354 pages
File Size : 46,9 Mb
Release : 2012-09-13
Category : Science
ISBN : 9780309224185

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Evolution of Translational Omics by Institute of Medicine,Board on Health Sciences Policy,Board on Health Care Services,Committee on the Review of Omics-Based Tests for Predicting Patient Outcomes in Clinical Trials Pdf

Technologies collectively called omics enable simultaneous measurement of an enormous number of biomolecules; for example, genomics investigates thousands of DNA sequences, and proteomics examines large numbers of proteins. Scientists are using these technologies to develop innovative tests to detect disease and to predict a patient's likelihood of responding to specific drugs. Following a recent case involving premature use of omics-based tests in cancer clinical trials at Duke University, the NCI requested that the IOM establish a committee to recommend ways to strengthen omics-based test development and evaluation. This report identifies best practices to enhance development, evaluation, and translation of omics-based tests while simultaneously reinforcing steps to ensure that these tests are appropriately assessed for scientific validity before they are used to guide patient treatment in clinical trials.

Microbial Technology for the Welfare of Society

Pankaj Kumar Arora
Microbial Technology for the Welfare of Society Book PDF

Author : Pankaj Kumar Arora
Publisher : Springer Nature
Page : 341 pages
File Size : 40,6 Mb
Release : 2019-09-12
Category : Science
ISBN : 9789811388446

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Microbial Technology for the Welfare of Society by Pankaj Kumar Arora Pdf

This book describes various aspects of modern microbiology including microbial enzymes, secondary metabolites, next-generation sequencing, microbial-based biopesticides, microbial-based cancer therapies, biodiesel, and microbial products from fermentation, biodegradation, bioremediation and wastewater treatment. Further, it explains how and why microbes play an important role in preserving the welfare of living beings and the environment. Many bacteria play a significant part in cleaning our environment by detoxifying various xenobiotic compounds, while several microbes produce secondary metabolites that are useful to human beings. The book is divided into 15 chapters that cover various aspects of microorganism-based biotechnology, including recent methodologies such as advanced molecular techniques, as well developments in classical microbiological techniques. The authors also explain how the latest and classical techniques are being used in modern-day microbial biotechnology. All chapters were written by experts from prominent universities, research laboratories, and institutes around the globe. Above all, they focus on recent advances in microbial technology that promote the welfare of living beings and the environment.

Clinical Applications for Next-Generation Sequencing

Urszula Demkow,Rafal Ploski
Clinical Applications for Next Generation Sequencing Book PDF

Author : Urszula Demkow,Rafal Ploski
Publisher : Academic Press
Page : 334 pages
File Size : 41,8 Mb
Release : 2015-09-10
Category : Science
ISBN : 9780128018415

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Clinical Applications for Next-Generation Sequencing by Urszula Demkow,Rafal Ploski Pdf

Clinical Applications for Next Generation Sequencing provides readers with an outstanding postgraduate resource to learn about the translational use of NGS in clinical environments. Rooted in both medical genetics and clinical medicine, the book fills the gap between state-of-the-art technology and evidence-based practice, providing an educational opportunity for users to advance patient care by transferring NGS to the needs of real-world patients. The book builds an interface between genetic laboratory staff and clinical health workers to not only improve communication, but also strengthen cooperation. Users will find valuable tactics they can use to build a systematic framework for understanding the role of NGS testing in both common and rare diseases and conditions, from prenatal care, like chromosomal abnormalities, up to advanced age problems like dementia. Fills the gap between state-of-the-art technology and evidence-based practice Provides an educational opportunity which advances patient care through the transfer of NGS to real-world patient assessment Promotes a practical tool that clinicians can apply directly to patient care Includes a systematic framework for understanding the role of NGS testing in many common and rare diseases Presents evidence regarding the important role of NGS in current diagnostic strategies

Gene Mapping, Discovery, and Expression

Minou Bina
Gene Mapping Discovery and Expression Book PDF

Author : Minou Bina
Publisher : Springer Science & Business Media
Page : 335 pages
File Size : 53,6 Mb
Release : 2008-02-04
Category : Science
ISBN : 9781597450973

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Gene Mapping, Discovery, and Expression by Minou Bina Pdf

Completion of the sequence of the human genome represents an unpar- leled achievement in the history of biology. The project has produced nearly complete, highly accurate, and comprehensive sequences of genomes of s- eral organisms including human, mouse, drosophila, and yeast. Furthermore, the development of high-throughput technologies has led to an explosion of projects to sequence the genomes of additional organisms including rat, chimp, dog, bee, chicken, and the list is expanding. The nearly completed draft of genomic sequences from numerous species has opened a new era of research in biology and in biomedical sciences. In keeping with the interdisciplinary nature of the new scientific era, the chapters in Gene Mapping, Discovery, and Expression: Methods and Protocols recapitulate the necessity of integration of experimental and computational tools for solving - portant research problems. The general underlying theme of this volume is DNA sequence-based technologies. At one level, the book highlights the importance of databases, genome-browsers, and web-based tools for data access and ana- sis. More specifically, sequencing projects routinely deposit their data in p- licly available databases including GenBank, at the National Center of Biotechnology (NCBI) in the United States; EMBL, maintained by the European Bioinformatics Institute; and DDBJ, the DNA Data Bank of Japan. Currently, several browsers offer facile access to numerous genomic DNA sequences for gene mapping and data retrieval.