Automation Genomic And Functional Analyses

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Automation Genomic And Functional Analyses

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Author : Alister G. Craig
language : en
Publisher: Elsevier
Release Date : 1999-02

Automation Genomic And Functional Analyses written by Alister G. Craig and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 1999-02 with Science categories.

Evaluation and functional analysis, to provide insight into this "new age" of research based on genomic and chemical screening. Key Features * Describes automated procedures used in microbiology and molecular biology * Includes developments in robotics and vision systems * Features automation in library picking, presentation and analysis * Discusses paralogous duplications in microbial genomes * Covers deciphering genomes through automated large-scale sequencing * Describes and stresses the need for functional analyses * Internationally acclaimed contributors, including Professor Leroy Hood.

Primer To Analysis Of Genomic Data Using R

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Author : Cedric Gondro
language : en
Publisher: Springer
Release Date : 2015-05-18

Primer To Analysis Of Genomic Data Using R written by Cedric Gondro and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-05-18 with Medical categories.

Through this book, researchers and students will learn to use R for analysis of large-scale genomic data and how to create routines to automate analytical steps. The philosophy behind the book is to start with real world raw datasets and perform all the analytical steps needed to reach final results. Though theory plays an important role, this is a practical book for graduate and undergraduate courses in bioinformatics and genomic analysis or for use in lab sessions. How to handle and manage high-throughput genomic data, create automated workflows and speed up analyses in R is also taught. A wide range of R packages useful for working with genomic data are illustrated with practical examples. The key topics covered are association studies, genomic prediction, estimation of population genetic parameters and diversity, gene expression analysis, functional annotation of results using publically available databases and how to work efficiently in R with large genomic datasets. Important principles are demonstrated and illustrated through engaging examples which invite the reader to work with the provided datasets. Some methods that are discussed in this volume include: signatures of selection, population parameters (LD, FST, FIS, etc); use of a genomic relationship matrix for population diversity studies; use of SNP data for parentage testing; snpBLUP and gBLUP for genomic prediction. Step-by-step, all the R code required for a genome-wide association study is shown: starting from raw SNP data, how to build databases to handle and manage the data, quality control and filtering measures, association testing and evaluation of results, through to identification and functional annotation of candidate genes. Similarly, gene expression analyses are shown using microarray and RNAseq data. At a time when genomic data is decidedly big, the skills from this book are critical. In recent years R has become the de facto tool for analysis of gene expression data, in addition to its prominent role in analysis of genomic data. Benefits to using R include the integrated development environment for analysis, flexibility and control of the analytic workflow. Included topics are core components of advanced undergraduate and graduate classes in bioinformatics, genomics and statistical genetics. This book is also designed to be used by students in computer science and statistics who want to learn the practical aspects of genomic analysis without delving into algorithmic details. The datasets used throughout the book may be downloaded from the publisher’s website.

Automation Genomic And Functional Analyses

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Author :
language : en
Publisher: Academic Press
Release Date : 1999-02-15

Automation Genomic And Functional Analyses 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 1999-02-15 with Science categories.

Automation is the major future trend for many areas in microbiology, molecular biology, and biochemistry, among other disciplines. It is an enormously exciting area, where techniques and assays that were once repetitive, tedious, and time consuming can be performed robotically, liberating the time of researchers and hospital laboratory workers for more interesting work. Many techniques have now been automated and often miniaturized, including PCR analysis, DNA/RNA preparation, diagnostic test (e.g., Pap tests), compound screening, and of course, sequencing. Some major advances, notably in Professor Leroy Hood's group, have resulted in the ability to perform thousands of assays simultaneously on a normal microscope slide. Automation, edited by two of the leading experts in the field, presents the very latest experimental techniques explained in detail. This book has succeeded in bringing together researchers at the forefront of clone library construction, genome analysis, sequencing, computational data evaluation and functional analysis, to provide insight into this "new age" of research based on genomic and chemical screening. Describes automated procedures used in microbiology and molecular biology Includes developments in robotics and vision systems Features automation in library picking, presentation and analysis Discusses paralogous duplications in microbial genomes Covers deciphering genomes through automated large-scale sequencing Describes and stresses the need for functional analyses Internationally acclaimed contributors, including Professor Leroy Hood

Automation In Proteomics And Genomics

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Author : Gil Alterovitz
language : en
Publisher: John Wiley & Sons
Release Date : 2009-03-16

Automation In Proteomics And Genomics written by Gil Alterovitz and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-03-16 with Science categories.

In the last decade DNA sequencing costs have decreased over a magnitude, largely because of increasing throughput by incremental advances in tools, technologies and process improvements. Further cost reductions in this and in related proteomics technologies are expected as a result of the development of new high-throughput techniques and the computational machinery needed to analyze data generated. Automation in Proteomics & Genomics: An Engineering Case-Based Approach describes the automation technology currently in the areas of analysis, design, and integration, as well as providing basic biology concepts behind proteomics and genomics. The book also discusses the current technological limitations that can be viewed as an emerging market rather than a research bottleneck. Topics covered include: molecular biology fundamentals: from ‘blueprint’ (DNA) to ‘task list’ (RNA) to ‘molecular machine’ (protein); proteomics methods and technologies; modelling protein networks and interactions analysis via automation: DNA sequencing; microarrays and other parallelization technologies; protein characterization and identification; protein interaction and gene regulatory networks design via automation: DNA synthesis; RNA by design; building protein libraries; synthetic networks integration: multiple modalities; computational and experimental methods; trends in automation for genomics and proteomics new enabling technologies and future applications Automation in Proteomics & Genomics: An Engineering Case-Based Approach is an essential guide to the current capabilities and challenges of high-throughput analysis of genes and proteins for bioinformaticians, engineers, chemists, and biologists interested in developing a cross-discipline problem-solving based approach to systems biology.

Automation Genomic And Functional Analyses

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Author :
language : en
Publisher: Academic Press
Release Date : 1999-02-15

Automation Genomic And Functional Analyses 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 1999-02-15 with Science categories.

Automation is the major future trend for many areas in microbiology, molecular biology, and biochemistry, among other disciplines. It is an enormously exciting area, where techniques and assays that were once repetitive, tedious, and time consuming can be performed robotically, liberating the time of researchers and hospital laboratory workers for more interesting work. Many techniques have now been automated and often miniaturized, including PCR analysis, DNA/RNA preparation, diagnostic test (e.g., Pap tests), compound screening, and of course, sequencing. Some major advances, notably in Professor Leroy Hood's group, have resulted in the ability to perform thousands of assays simultaneously on a normal microscope slide. Automation, edited by two of the leading experts in the field, presents the very latest experimental techniques explained in detail. This book has succeeded in bringing together researchers at the forefront of clone library construction, genome analysis, sequencing, computational data evaluation and functional analysis, to provide insight into this "new age" of research based on genomic and chemical screening. Describes automated procedures used in microbiology and molecular biology Includes developments in robotics and vision systems Features automation in library picking, presentation and analysis Discusses paralogous duplications in microbial genomes Covers deciphering genomes through automated large-scale sequencing Describes and stresses the need for functional analyses Internationally acclaimed contributors, including Professor Leroy Hood

Comparative Genomics And Functional Genomics Analyses In Plants

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Author : Xiaoming Song
language : en
Publisher: Frontiers Media SA
Release Date : 2021-07-05

Comparative Genomics And Functional Genomics Analyses In Plants written by Xiaoming Song and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-07-05 with Science categories.

Automated Genome Wide Variant Analysis And Reporting Pipeline

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Author : Nhat Duong
language : en
Publisher:
Release Date : 2020

Automated Genome Wide Variant Analysis And Reporting Pipeline written by Nhat Duong and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020 with Bioinformatics categories.

The field of bioinformatics contains many pipelines for different purposes. These pipelines are often for data processing which are used to process raw files into ready to be analyzed files. Despite availability of many different pipelines, the process of going from processed files to analysis the data and making a report from the results are still largely done manually. Among different data analyses, a commonly used analysis applicable across a variety of data is the genetic/mutation load analysis on cohort data (cases vs controls groups). It is thus desirable to produce a fully automated and flexible pipeline capable of going from the variant discovery VCF file and BED file all the way to a final interactive report file which can be presented to clinicians or principle investigators. The pipeline was made using Snakemake as the workflow management tool. The pipeline starts with a VCF file that is derived from the user's preferred variant discovery method. This file then gets filtered, reformatted, statistically analyzed and the results are stored and displayed in an interactive webpage. This pipeline also takes in copy number variation information in the form of a BED file and performs analyses independent of the short variants data. The MetaP Fisher method was added to the pipeline to combine the p-values from the two independent analyses (short variant and copy number variation) which can buttress any positive results. Results from these analyses would get stored in a database and displayed in an interactive webpage. An application of the pipeline was done to study congenital heart defects (CHD) in a cohort of 22q11.2 deletion syndrome patients. 22q11.2 deletion syndrome (22q11.2DS) is the absence of a DNA segment - roughly 3 million base pairs in size - on one copy of chromosome 22. The pipeline mentioned above was used with whole exome sequencing samples of 380 22q11.2DS patients as the VCF input. After QC, there remains 147 cases (22q11.2DS patients with CHD) vs 132 controls (22q11.2DS patients without CHD) samples. The pipeline compared the genetic loads between the case and control cohorts by performing gene-gene and functional term analyses. The goal was to identify mutations that are significantly over-represented in cases as compared to controls. Successful run of the pipeline's gene-gene analysis was able to identify a gene cluster on chromosome 9 - mostly 9q - that is significantly over-represented in 22q11.2DS patients with CHD. Most genes in this cluster are closely associated with early cell and embryonic development. The functional-based analysis - using GO terms and mammalian phenotypes - resulted in numerous cardiac related functions significantly over-represented in 22q11.2DS patients with CHD as well. Some of the most significant functions include heart trabecula and cardiac ventricle morphogenesis. All of these results were reported using an HTML file. This result suggests that further interrogation of the loci on human chromosome 9 and the cardiac functions identified from the functional analysis are warranted. Most importantly, however, it shows that the pipeline was successful in performing a cohort study and generating an interactive report file. Keywords: 22q11.2 Deletion Syndrome, CNVs, Short Variants

Advances In Bioinformatics

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Author : Vijai Singh
language : en
Publisher: Springer Nature
Release Date :

Advances In Bioinformatics written by Vijai 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 with categories.

Yeast Gene Analysis

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Author :
language : en
Publisher: Elsevier
Release Date : 2011-09-21

Yeast Gene Analysis written by and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-09-21 with Science categories.

Focusing on Saccharomyces cerevisiae, the second edition of Yeast Gene Analysis represents a major reworking of the original edition, with many completely new chapters and major revisions to all previous chapters. Originally published shortly after completion of the yeast genome sequence, the new edition covers many of the major genome-wide strategies that have been developed since then such as microarray analysis of transcription, synthetic gene array studies, protein microarrays and chemical genetic approaches. It represents a valuable resource for any research laboratory using budding yeast as their experimental system in which to identify new yeast gene functions. The chapters are written in a readable style with useful background information, technical tips and specific experimental protocols included as appropriate, enabling both the novice and the experienced yeast researcher to adopt new procedures with confidence. New chapters on: Strain construction; genome-wide two-hybrid approaches; use of microarrays for transcript analysis; real-time analysis of chromosome behaviour and FRET; synthetic gene array technology and protein arrays; chemical genomics and yeast prions; RNA gene analysis and mitochondrial gene function analysis; phylogenetic footprinting; discovering human gene function and predicting yeast gene function

Genome Annotation

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Author : Jung Soh
language : en
Publisher: CRC Press
Release Date : 2016-04-19

Genome Annotation written by Jung Soh and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-04-19 with Computers categories.

The success of individualized medicine, advanced crops, and new and sustainable energy sources requires thoroughly annotated genomic information and the integration of this information into a coherent model. A thorough overview of this field, Genome Annotation explores automated genome analysis and annotation from its origins to the challenges of next-generation sequencing data analysis. The book initially takes you through the last 16 years since the sequencing of the first complete microbial genome. It explains how current analysis strategies were developed, including sequencing strategies, statistical models, and early annotation systems. The authors then present visualization techniques for displaying integrated results as well as state-of-the-art annotation tools, including MAGPIE, Ensembl, Bluejay, and Galaxy. They also discuss the pipelines for the analysis and annotation of complex, next-generation DNA sequencing data. Each chapter includes references and pointers to relevant tools. As very few existing genome annotation pipelines are capable of dealing with the staggering amount of DNA sequence information, new strategies must be developed to accommodate the needs of today’s genome researchers. Covering this topic in detail, Genome Annotation provides you with the foundation and tools to tackle this challenging and evolving area. Suitable for both students new to the field and professionals who deal with genomic information in their work, the book offers two genome annotation systems on an accompanying downloadable resources.