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Automation Genomic And Functional Analyses
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Book Synopsis Automation: Genomic and Functional Analyses by : Alister G. Craig
Download or read book Automation: Genomic and Functional Analyses written by Alister G. Craig and published by Elsevier. This book was released on 1999-02 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Primer to Analysis of Genomic Data Using R by : Cedric Gondro
Download or read book Primer to Analysis of Genomic Data Using R written by Cedric Gondro and published by Springer. This book was released on 2015-05-18 with total page 283 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Automation: Genomic and Functional Analyses by :
Download or read book Automation: Genomic and Functional Analyses written by and published by Academic Press. This book was released on 1999-02-15 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Book Synopsis Automation in Proteomics and Genomics by : Gil Alterovitz
Download or read book Automation in Proteomics and Genomics written by Gil Alterovitz and published by John Wiley & Sons. This book was released on 2009-03-16 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Yeast Gene Analysis written by and published by Elsevier. This book was released on 2011-09-21 with total page 731 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Book Synopsis Measuring Biological Responses with Automated Microscopy by :
Download or read book Measuring Biological Responses with Automated Microscopy written by and published by Elsevier. This book was released on 2006-11-02 with total page 736 pages. Available in PDF, EPUB and Kindle. Book excerpt: The critically acclaimed laboratory standard for more than forty years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with more than 300 volumes (all of them still in print), the series contains much material still relevant today-truly an essential publication for researchers in all fields of life sciences.
Book Synopsis Forensic DNA Typing by : John M. Butler
Download or read book Forensic DNA Typing written by John M. Butler and published by Elsevier. This book was released on 2005-02-08 with total page 679 pages. Available in PDF, EPUB and Kindle. Book excerpt: Forensic DNA Typing, Second Edition, is the only book available that specifically covers detailed information on mitochondrial DNA and the Y chromosome. It examines the science of current forensic DNA typing methods by focusing on the biology, technology, and genetic interpretation of short tandem repeat (STR) markers, which encompass the most common forensic DNA analysis methods used today. The book covers topics from introductory level right up to cutting edge research. High-profile cases are addressed throughout the text, near the sections dealing with the science or issues behind these cases. Ten new chapters have been added to accommodate the explosion of new information since the turn of the century. These additional chapters cover statistical genetic analysis of DNA data, an emerging field of interest to DNA research. Several chapters on statistical analysis of short tandem repeat (STR) typing data have been contributed by Dr. George Carmody, a well-respected professor in forensic genetics. Specific examples make the concepts of population genetics more understandable. This book will be of interest to researchers and practitioners in forensic DNA analysis, forensic scientists, population geneticists, military and private and public forensic laboratories (for identifying individuals through remains), and students of forensic science. *The only book available that specifically covers detailed information on mitochondrial DNA and the Y chromosome*Chapters cover the topic from introductory level right up to "cutting edge" research*High-profile cases are addressed throughout the book, near the sections dealing with the science or issues behind these cases*NEW TO THIS EDITION: D.N.A. Boxes--boxed "Data, Notes & Applications" sections throughout the book offer higher levels of detail on specific questions
Book Synopsis Automation: Genomic and Functional Analyses by :
Download or read book Automation: Genomic and Functional Analyses written by and published by Academic Press. This book was released on 1999-02-15 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Book Synopsis Encyclopedia of Genetics, Genomics, Proteomics, and Informatics by : George P. Rédei
Download or read book Encyclopedia of Genetics, Genomics, Proteomics, and Informatics written by George P. Rédei and published by Springer Science & Business Media. This book was released on 2008-04-25 with total page 2139 pages. Available in PDF, EPUB and Kindle. Book excerpt: This new third edition updates a best-selling encyclopedia. It includes about 56% more words than the 1,392-page second edition of 2003. The number of illustrations increased to almost 2,000 and their quality has improved by design and four colors. It includes approximately 1,800 current databases and web servers. This encyclopedia covers the basics and the latest in genomics, proteomics, genetic engineering, small RNAs, transcription factories, chromosome territories, stem cells, genetic networks, epigenetics, prions, hereditary diseases, and patents. Similar integrated information is not available in textbooks or on the Internet.
Book Synopsis Automated DNA Sequencing and Analysis by : Mark D. Adams
Download or read book Automated DNA Sequencing and Analysis written by Mark D. Adams and published by Elsevier. This book was released on 2012-12-02 with total page 389 pages. Available in PDF, EPUB and Kindle. Book excerpt: A timely book for DNA researchers, Automated DNA Sequencing and Analysis reviews and assesses the state of the art of automated DNA sequence analysis-from the construction of clone libraries to the developmentof laboratory and community databases. It presents the methodologies and strategies of automated DNA sequence analysis in a way that allows them to be compared and contrasted. By taking a broad view of the process of automated sequence analysis, the present volume bridges the gap between the protocols supplied with instrument and reaction kits and the finalized data presented in the research literature. It will be an invaluable aid to both small laboratories that are interested in taking maximum advantageof automated sequence resources and to groups pursuing large-scale cDNA and genomic sequencing projects. The field of automation in DAN sequencing and analysis is rapidly moving, this book fulfils those needs, reviews the history of the art and provides pointers to future development.
Book Synopsis Comparative Genomics and Functional Genomics Analyses in Plants by : Xiaoming Song
Download or read book Comparative Genomics and Functional Genomics Analyses in Plants written by Xiaoming Song and published by Frontiers Media SA. This book was released on 2021-07-05 with total page 479 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Focus on Genome Research by : Clyde R. Williams
Download or read book Focus on Genome Research written by Clyde R. Williams and published by Nova Publishers. This book was released on 2004 with total page 442 pages. Available in PDF, EPUB and Kindle. Book excerpt: The genomic approach of technology development and large-scale generation of community resource data sets has introduced an important new dimension in biological and biomedical research. Interwoven advances in genetics, comparative genomics, high throughput biochemistry and bioinformatics are combining to attack basic understanding of human life and disease and to develop strategies to combat disease. Genomic Research began with The Human Genome Project (HGP), the international research effort that determined the DNA sequence of the entire human genome, completed in April 2003. The HGP also included efforts to characterize and sequence the entire genomes of several other organisms, many of which are used extensively in biological research. Identification of the sequence or function of genes in a model organism is an important approach to finding and elucidating the function of human genes. Integral to the HGP are similar efforts to understand the genomes of various organisms commonly used in biomedical research, such as mice, fruit flies and roundworms. Such organisms are called "model organisms," because they can often serve as research models for how the human organism behaves. This new book brings together leading research from throughout the world in this cutting-edge field.
Book Synopsis Advances in Bioinformatics by : Vijai Singh
Download or read book Advances in Bioinformatics written by Vijai Singh and published by Springer Nature. This book was released on with total page 365 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Automated Genome Wide Variant Analysis and Reporting Pipeline by : Nhat Duong
Download or read book Automated Genome Wide Variant Analysis and Reporting Pipeline written by Nhat Duong and published by . This book was released on 2020 with total page 32 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Book Synopsis Functional analysis of species-specific noncoding RNAs in plants by : Yuepeng Song
Download or read book Functional analysis of species-specific noncoding RNAs in plants written by Yuepeng Song and published by Frontiers Media SA. This book was released on 2023-02-01 with total page 201 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Genome Data Analysis by : Ju Han Kim
Download or read book Genome Data Analysis written by Ju Han Kim and published by Springer. This book was released on 2019-04-30 with total page 367 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook describes recent advances in genomics and bioinformatics and provides numerous examples of genome data analysis that illustrate its relevance to real world problems and will improve the reader’s bioinformatics skills. Basic data preprocessing with normalization and filtering, primary pattern analysis, and machine learning algorithms using R and Python are demonstrated for gene-expression microarrays, genotyping microarrays, next-generation sequencing data, epigenomic data, and biological network and semantic analyses. In addition, detailed attention is devoted to integrative genomic data analysis, including multivariate data projection, gene-metabolic pathway mapping, automated biomolecular annotation, text mining of factual and literature databases, and integrated management of biomolecular databases. The textbook is primarily intended for life scientists, medical scientists, statisticians, data processing researchers, engineers, and other beginners in bioinformatics who are experiencing difficulty in approaching the field. However, it will also serve as a simple guideline for experts unfamiliar with the new, developing subfield of genomic analysis within bioinformatics.
Book Synopsis Glossary of Biotechnology Terms, Fourth Edition by : Kimball Nill
Download or read book Glossary of Biotechnology Terms, Fourth Edition written by Kimball Nill and published by CRC Press. This book was released on 2005-11-16 with total page 413 pages. Available in PDF, EPUB and Kindle. Book excerpt: Even if you studied biotechnology in school, if you haven't stayed current, it's not likely you'll be able to speak the same language as today's biotech scientists. The same is even truer for nanotechnology where everything gets smaller and smaller, except the terminology required to navigate it. In the Glossary of Biotechnology and Nanobiotechnology Terms, Fourth Edition, Kimball Nill continues to improve upon the reference that for over a decade has helped thousands of professionals, including scientists, attorneys, government workers, lobbyists, venture capitalists, and university tech transfer staff, to communicate successfully with those working on the cutting edge of modern science. Now in its fourth edition, Nill has taken the much appreciated step of adding nanotechnology to his glossary. Just by casually perusing the Glossary of Biotechnology and Nanobiotechnology Terms, Fourth Edition you will learn a number of enlightening facts. Even those in related sciences will be surprised to discover what the language unveils. The Glossary of Biotechnology and Nanobiotechnology Terms, Fourth Edition is a handy reference designed for people with little or no training in the biological and chemical sciences, as well as scientists communicating from other disciplines. Unlike other glossaries, this one is both informative and completely accessible. Instead of looking up one term to end up mired in equally difficult terminology, this intelligently designed volume follows what the author refers to as a Reference Chain that steadily leads you to simpler more common terminology, down to a level that anyone with a high school education will be able to understand. The definitions are written utilizing words that enable you to conceptualize the idea embodied in the term, with explanations based on analogy whenever possible. Consider this example: Suppose you just received a funding request, a faculty memo, or patent concern that refers to A-DNA, which happens to be the first definition in the Glossary. A-DNA A particular right-handed helical form of DNA (possessing 11 base pairs per turn), which is the form that DNA molecules exist in when they are partially dehydrated. A-form DNA is found in fibers at 75% relative humidity and requires the presence of sodium, potassium, or cesium as the counterion. Instead of lying flat, the bases are tilted with respect to the helical axis, and there are more base pairs per turn. The A-form is biologically interesting because it is probably very close to the conformation adopted by DNA-RNA hybrids or by RNA-RNA double-stranded regions. The reason is that the presence of the 2'2 hydroxyl group prevents RNA from lying in the B-form. See also B-DNA, DNA-RNA HYBRID, DEOXYRIBONUCLEIC ACID (DNA), BASE PAIR (bp) But then after looking at the above definition, you wonder what exactly is a DNA-RNA Hybrid? DNA-RNA Hybrid A double helix that consists of one chain of DNA hydrogen-bonded to a chain of RNA by means of complementary base pairs. See also HYBRIDIZATION (MOLECULAR GENETICS), HYBRIDIZATION (PLANT GENETICS), DOUBLE HELIX ...however while you've often heard mention of a double helix, you were never quite sure what that meant.... Double Helix The natural coiled conformation of two complementary, antiparallel DNA chains. This structure was first put forward by Watson and Crick in 1953. See also DEOXYRIBONUCLEIC ACID (DNA) And that might brings you to ask, Do you really actually know what DNA is? Deoxyribonucleic Acid (DNA) Discovered by Frederick Miescher in 1869, it is the chemical basis for genes. The chemical building blocks (molecules) of which genes (i.e., paired nucleotide units that code for a protein to be produced by a cell's machinery, such as its ribosomes) are constructed. Every inherited characteristic has its origin somewhere in the code of the organism's complement of DNA. The code is made up of subunits called nucleic acids. The sequence of the four nucleic acids is interpreted by certain molecular systems in order to produce the proteins required by an organism. The structure of the DNA molecule was elucidated in 1953.... The Glossary of Biotechnology and Nanobiotechnology Terms, Fourth Edition is packed with over 400 pages of exceptionally well-organized and cross-referenced terminology, making it an essential reference for anyone working directly or indirectly with those pioneering the frontiers of modern biology.
