microarray books

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DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling

by: Pierre Baldi
publisher: Cambridge University Press, published: 2011-04-28
ASIN: 0521176352
EAN: 9780521176354
sales rank: 1206961
Massive data acquisition technologies--such as genome sequencing, high-throughput drug screening, and DNA arrays--are in the process of revolutionizing biology and medicine. This concise, user-friendly and interdisciplinary guide to DNA microarray technology is an introduction and a reference for both biologists and computational scientists. The authors describe the underlying technologies and offer an awareness of the "noise" and pitfalls present in the data generated. They also provide an idea of the different data mining techniques and algorithms that are available to interpret data, and the advantages and disadvantages of each in differing situations.

Statistics and Data Analysis for Microarrays Using R and Bioconductor, Second Edition (Chapman & Hall/CRC Mathematical & Computational Biology)

by: Sorin Drghici
publisher: Chapman and Hall/CRC, published: 2011-12-06
ASIN: 1439809755
EAN: 9781439809754
sales rank: 245064

Richly illustrated in color, Statistics and Data Analysis for Microarrays Using R and Bioconductor, Second Edition provides a clear and rigorous description of powerful analysis techniques and algorithms for mining and interpreting biological information. Omitting tedious details, heavy formalisms, and cryptic notations, the text takes a hands-on, example-based approach that teaches students the basics of R and microarray technology as well as how to choose and apply the proper data analysis tool to specific problems.

New to the Second Edition
Completely updated and double the size of its predecessor, this timely second edition replaces the commercial software with the open source R and Bioconductor environments. Fourteen new chapters cover such topics as the basic mechanisms of the cell, reliability and reproducibility issues in DNA microarrays, basic statistics and linear models in R, experiment design, multiple comparisons, quality control, data pre-processing and normalization, Gene Ontology analysis, pathway analysis, and machine learning techniques. Methods are illustrated with toy examples and real data and the R code for all routines is available on an accompanying CD-ROM.

With all the necessary prerequisites included, this best-selling book guides students from very basic notions to advanced analysis techniques in R and Bioconductor. The first half of the text presents an overview of microarrays and the statistical elements that form the building blocks of any data analysis. The second half introduces the techniques most commonly used in the analysis of microarray data.

Guide to Analysis of DNA Microarray Data, Second Edition

by: Steen Knudsen
publisher: Wiley-Liss, published: 2004-03-02
ASIN: 0471656046
EAN: 9780471656043
sales rank: 2381686
Written for biologists and medical researchers who don't have any special training in data analysis and statistics, Guide to Analysis of DNA Microarray Data, Second Edition begins where DNA array equipment leaves off: the image produced by the microarray. The text deals with the questions that arise starting at this point, providing an introduction to microarray technology, then moving on to image analysis, data analysis, cluster analysis, and beyond.
With all chapters rewritten, updated, and expanded to include the latest generation of technology and methods, Guide to Analysis of DNA Microarray Data, Second Edition offers practitioners reliable information using concrete examples and a clear, comprehensible style. This Second Edition features entirely new chapters on:
* Image analysis
* Experiment design
* Automated analysis, integrated analysis, and systems biology
* Interpretation of results
Intended for readers seeking practical applications, this text covers a broad spectrum of proven approaches in this rapidly growing technology. Additional features include further reading suggestions for each chapter, as well as a thorough review of available analysis software.

Statistical Methods for Microarray Data Analysis (Methods in Molecular Biology)

publisher: Humana Press, published: 2012-07-31
ASIN: 1603273360
EAN: 9781603273367
sales rank: 2594487
The modern state of the art in methodology of microarray data analysis based on significance testing is far from satisfactory. However "hot" this methodological research trend has been, it is still in its infancy and a real revolution in the field definitely lies ahead. In particular, the basic statistical problems will remain the same even after new digital technologies produced by Solexa and some other companies have become widely available. This volume "Statistical Methods for Microarray Data Analysis" will include selected papers on this subject that meet a high standard of mathematical rigor.

A Practical Approach to Microarray Data Analysis

publisher: Springer, published: 2009-08-17
ASIN: 1441912266
EAN: 9781441912268
sales rank: 1354529
The book addresses the requirement of scientists and researchers to gain a basic understanding of microarray analysis methodologies and tools. It is intended for students, teachers, researchers, and research managers who want to understand the state of the art and of the presented methodologies and the areas in which gaps in our knowledge demand further research and development. The book is designed to be used by the practicing professional tasked with the design and analysis of microarray experiments or as a text for a senior undergraduate- or graduate level course in analytical genetics, biology, bioinformatics, computational biology, statistics and data mining, or applied computer science.

Duplexed sandwich immunoassays on a fiber-optic microarray [An article from: Analytica Chimica Acta]

by: D.M. Rissin
publisher: Elsevier, published: 2006-03-30
ASIN: B000PBZYVY
This digital document is a journal article from Analytica Chimica Acta, published by Elsevier in 2006. The article is delivered in HTML format and is available in your Amazon.com Media Library immediately after purchase. You can view it with any web browser.

Description:
In this paper, we describe a duplexed imaging optical fiber array-based immunoassay for immunoglobulin A (IgA) and lactoferrin. To fabricate the individually addressable array, microspheres were functionalized with highly specific monoclonal antibodies. The microspheres were loaded in microwells etched into the distal face of an imaging optical fiber bundle. Two microsphere-based sandwich immunoassays were developed to simultaneously detect IgA and lactoferrin, two innate immune system proteins found in human saliva. Individual microspheres could be interrogated for the simultaneous measurement of both proteins. The working concentration range for IgA detection was between 700pM and 100nM, while the working concentration range for lactoferrin was between 385pM and 10nM. The cross-reactivity between detection antibodies and their non-specific targets was relatively low in comparison to the signal generated by the specific binding with their targets. These results suggest that the degree of multiplexing on this fiber-optic array platform can be increased beyond a duplex.

Active bead-linked immunoassay on protein microarrays [An article from: Analytica Chimica Acta]

by: V.N. Morozov
publisher: Elsevier, published: 2006-03-30
ASIN: B000PBZYW8
This digital document is a journal article from Analytica Chimica Acta, published by Elsevier in 2006. The article is delivered in HTML format and is available in your Amazon.com Media Library immediately after purchase. You can view it with any web browser.

Description:
Protein microarrays are becoming a powerful tool in proteome, biochemical, and clinical studies. In addition to the quality of arrayed immobilized probe molecules, sensitivity of the microarray-based assay is highly dependent on the detection technique. Here we suggest four simple techniques for rapid detection of analytes bound to protein microarrays. The techniques employ functionalized magnetic and non-magnetic beads moved to, from, or along the array surface by external forces. In contrast to other labeling techniques actively controlled physical labels: (i) make detection extremely fast to allow microarray reading in seconds; (ii) provide a low background due to active removal of weakly bound beads; and (iii) provide a highly sensitive detection, since one antigen-antibody bond is capable of holding bead immobilized on the array surface. In combination with the electrophoretically assisted active immunoassay we described recently such active reading allows to reduce total indirect immunoassay time to 7-10min while having sensitivity in the femtomolar concentration range. High speed, sensitivity, and specificity make active bead-linked detection an ideal choice in rapid high-throughput screening and in emergency diagnostics.

Microarray techniques for more rapid protein quantification: Use of single spot multiplex analysis and a vibration reaction unit [An article from: Analytica Chimica Acta]

by: Y. Sasakura
publisher: Elsevier, published: 2006-03-30
ASIN: B000PBZYWI
This digital document is a journal article from Analytica Chimica Acta, published by Elsevier in 2006. The article is delivered in HTML format and is available in your Amazon.com Media Library immediately after purchase. You can view it with any web browser.

Description:
Protein microarray technology is a powerful, popular tool for the high-throughput analysis of protein interactions. One important use for protein microarray technology is protein quantification by immunoassay, which was originally based on enzyme linked immunosorbent assay (ELISA) methods. Recently, new research and diagnostic applications have created a need for a rapid and easily applied high-throughput protein quantification method. Here, we introduce several novel techniques that address these needs. Our improved protein microarray-based sandwich immunoassay techniques allow researchers to: (1) control the size and shape of protein spots on the microarray using a perforated seal; (2) analyze two proteins within a single spot, thus increasing the number of tests run on a single microarray without increasing the number of protein spots; (3) improve the efficiency and speed of the Ag-Ab interaction through vibratory reagent convection, which increased the signal intensity by more than two-fold and decreased the reaction time from 30 to 10min. These new techniques will facilitate rapid immunoassays for diagnostic purposes and other research areas utilizing protein microarray analysis, such as investigations of ligand-receptor or protein-small molecule interactions.

Increasing robustness and sensitivity of protein microarrays through microagitation and automation [An article from: Analytica Chimica Acta]

by: M. Hartmann
publisher: Elsevier, published: 2006-03-30
ASIN: B000PBZYX2
This digital document is a journal article from Analytica Chimica Acta, published by Elsevier in 2006. The article is delivered in HTML format and is available in your Amazon.com Media Library immediately after purchase. You can view it with any web browser.

Description:
Assay systems that employ protein microarrays for the analysis of complex samples are powerful tools to generate a high amount of data from a limiting amount of sample. Due to miniaturization, these systems are susceptible to fluctuations during signal generation and the use of uniform conditions for sample incubation and during the assay procedure is required to get reproducible results. Diffusion limits may prevent constant conditions on all parts of the array and can lead to the decease of the sensitivity of the array. Therefore, we set-up an automated assay system integrating a novel microagitation device using surface acoustic wave (SAW) technology. Multiplexed assays for the detection of autoantibodies from human serum and sandwich immunoassay for the detection of matrix metalloproteases (MMPs) were used to evaluate the system. Diffusion-rate limited solid phase reactions were enhanced by microagitation using the SAW technology resulting in up to three-fold higher signals.

Advances in cancer tissue microarray technology: Towards improved understanding and diagnostics [An article from: Analytica Chimica Acta]

by: W. Chen
publisher: Elsevier, published: 2006-03-30
ASIN: B000PBZYXC
This digital document is a journal article from Analytica Chimica Acta, published by Elsevier in 2006. The article is delivered in HTML format and is available in your Amazon.com Media Library immediately after purchase. You can view it with any web browser.

Description:
Over the past few years, tissue microarray (TMA) technology has been established as a standard method for assessing the expression of proteins or genes across large sets of tissue specimens. It is being adopted increasingly among leading research institutions around the world and utilized in cancer research in parallel with the cDNA microarray technology. This article summarizes various aspects of cancer understanding and diagnostics in which TMA has had great impact. Although tremendous advances continue to be made to facilitate imaging and archiving of TMA specimens, automatic evaluation and quantitative analysis of TMA still remains an important challenge for modern investigators.

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	DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling by: Pierre Baldi publisher: Cambridge University Press, published: 2011-04-28 ASIN: 0521176352 EAN: 9780521176354 sales rank: 1206961 Massive data acquisition technologies--such as genome sequencing, high-throughput drug screening, and DNA arrays--are in the process of revolutionizing biology and medicine. This concise, user-friendly and interdisciplinary guide to DNA microarray technology is an introduction and a reference for both biologists and computational scientists. The authors describe the underlying technologies and offer an awareness of the "noise" and pitfalls present in the data generated. They also provide an idea of the different data mining techniques and algorithms that are available to interpret data, and the advantages and disadvantages of each in differing situations.
	Statistics and Data Analysis for Microarrays Using R and Bioconductor, Second Edition (Chapman & Hall/CRC Mathematical & Computational Biology) by: Sorin Drghici publisher: Chapman and Hall/CRC, published: 2011-12-06 ASIN: 1439809755 EAN: 9781439809754 sales rank: 245064 Richly illustrated in color, Statistics and Data Analysis for Microarrays Using R and Bioconductor, Second Edition provides a clear and rigorous description of powerful analysis techniques and algorithms for mining and interpreting biological information. Omitting tedious details, heavy formalisms, and cryptic notations, the text takes a hands-on, example-based approach that teaches students the basics of R and microarray technology as well as how to choose and apply the proper data analysis tool to specific problems. *New to the Second Edition* Completely updated and double the size of its predecessor, this timely second edition replaces the commercial software with the open source R and Bioconductor environments. Fourteen new chapters cover such topics as the basic mechanisms of the cell, reliability and reproducibility issues in DNA microarrays, basic statistics and linear models in R, experiment design, multiple comparisons, quality control, data pre-processing and normalization, Gene Ontology analysis, pathway analysis, and machine learning techniques. Methods are illustrated with toy examples and real data and the R code for all routines is available on an accompanying CD-ROM. With all the necessary prerequisites included, this best-selling book guides students from very basic notions to advanced analysis techniques in R and Bioconductor. The first half of the text presents an overview of microarrays and the statistical elements that form the building blocks of any data analysis. The second half introduces the techniques most commonly used in the analysis of microarray data.
	Guide to Analysis of DNA Microarray Data, Second Edition by: Steen Knudsen publisher: Wiley-Liss, published: 2004-03-02 ASIN: 0471656046 EAN: 9780471656043 sales rank: 2381686 Written for biologists and medical researchers who don't have any special training in data analysis and statistics, Guide to Analysis of DNA Microarray Data, Second Edition begins where DNA array equipment leaves off: the image produced by the microarray. The text deals with the questions that arise starting at this point, providing an introduction to microarray technology, then moving on to image analysis, data analysis, cluster analysis, and beyond. With all chapters rewritten, updated, and expanded to include the latest generation of technology and methods, Guide to Analysis of DNA Microarray Data, Second Edition offers practitioners reliable information using concrete examples and a clear, comprehensible style. This Second Edition features entirely new chapters on: * Image analysis * Experiment design * Automated analysis, integrated analysis, and systems biology * Interpretation of results Intended for readers seeking practical applications, this text covers a broad spectrum of proven approaches in this rapidly growing technology. Additional features include further reading suggestions for each chapter, as well as a thorough review of available analysis software.
	Statistical Methods for Microarray Data Analysis (Methods in Molecular Biology) publisher: Humana Press, published: 2012-07-31 ASIN: 1603273360 EAN: 9781603273367 sales rank: 2594487 The modern state of the art in methodology of microarray data analysis based on significance testing is far from satisfactory. However "hot" this methodological research trend has been, it is still in its infancy and a real revolution in the field definitely lies ahead. In particular, the basic statistical problems will remain the same even after new digital technologies produced by Solexa and some other companies have become widely available. This volume "Statistical Methods for Microarray Data Analysis" will include selected papers on this subject that meet a high standard of mathematical rigor.
	A Practical Approach to Microarray Data Analysis publisher: Springer, published: 2009-08-17 ASIN: 1441912266 EAN: 9781441912268 sales rank: 1354529 The book addresses the requirement of scientists and researchers to gain a basic understanding of microarray analysis methodologies and tools. It is intended for students, teachers, researchers, and research managers who want to understand the state of the art and of the presented methodologies and the areas in which gaps in our knowledge demand further research and development. The book is designed to be used by the practicing professional tasked with the design and analysis of microarray experiments or as a text for a senior undergraduate- or graduate level course in analytical genetics, biology, bioinformatics, computational biology, statistics and data mining, or applied computer science.
	Duplexed sandwich immunoassays on a fiber-optic microarray [An article from: Analytica Chimica Acta] by: D.M. Rissin publisher: Elsevier, published: 2006-03-30 ASIN: B000PBZYVY This digital document is a journal article from Analytica Chimica Acta, published by Elsevier in 2006. The article is delivered in HTML format and is available in your Amazon.com Media Library immediately after purchase. You can view it with any web browser. Description: In this paper, we describe a duplexed imaging optical fiber array-based immunoassay for immunoglobulin A (IgA) and lactoferrin. To fabricate the individually addressable array, microspheres were functionalized with highly specific monoclonal antibodies. The microspheres were loaded in microwells etched into the distal face of an imaging optical fiber bundle. Two microsphere-based sandwich immunoassays were developed to simultaneously detect IgA and lactoferrin, two innate immune system proteins found in human saliva. Individual microspheres could be interrogated for the simultaneous measurement of both proteins. The working concentration range for IgA detection was between 700pM and 100nM, while the working concentration range for lactoferrin was between 385pM and 10nM. The cross-reactivity between detection antibodies and their non-specific targets was relatively low in comparison to the signal generated by the specific binding with their targets. These results suggest that the degree of multiplexing on this fiber-optic array platform can be increased beyond a duplex.
	Active bead-linked immunoassay on protein microarrays [An article from: Analytica Chimica Acta] by: V.N. Morozov publisher: Elsevier, published: 2006-03-30 ASIN: B000PBZYW8 This digital document is a journal article from Analytica Chimica Acta, published by Elsevier in 2006. The article is delivered in HTML format and is available in your Amazon.com Media Library immediately after purchase. You can view it with any web browser. Description: Protein microarrays are becoming a powerful tool in proteome, biochemical, and clinical studies. In addition to the quality of arrayed immobilized probe molecules, sensitivity of the microarray-based assay is highly dependent on the detection technique. Here we suggest four simple techniques for rapid detection of analytes bound to protein microarrays. The techniques employ functionalized magnetic and non-magnetic beads moved to, from, or along the array surface by external forces. In contrast to other labeling techniques actively controlled physical labels: (i) make detection extremely fast to allow microarray reading in seconds; (ii) provide a low background due to active removal of weakly bound beads; and (iii) provide a highly sensitive detection, since one antigen-antibody bond is capable of holding bead immobilized on the array surface. In combination with the electrophoretically assisted active immunoassay we described recently such active reading allows to reduce total indirect immunoassay time to 7-10min while having sensitivity in the femtomolar concentration range. High speed, sensitivity, and specificity make active bead-linked detection an ideal choice in rapid high-throughput screening and in emergency diagnostics.
	Microarray techniques for more rapid protein quantification: Use of single spot multiplex analysis and a vibration reaction unit [An article from: Analytica Chimica Acta] by: Y. Sasakura publisher: Elsevier, published: 2006-03-30 ASIN: B000PBZYWI This digital document is a journal article from Analytica Chimica Acta, published by Elsevier in 2006. The article is delivered in HTML format and is available in your Amazon.com Media Library immediately after purchase. You can view it with any web browser. Description: Protein microarray technology is a powerful, popular tool for the high-throughput analysis of protein interactions. One important use for protein microarray technology is protein quantification by immunoassay, which was originally based on enzyme linked immunosorbent assay (ELISA) methods. Recently, new research and diagnostic applications have created a need for a rapid and easily applied high-throughput protein quantification method. Here, we introduce several novel techniques that address these needs. Our improved protein microarray-based sandwich immunoassay techniques allow researchers to: (1) control the size and shape of protein spots on the microarray using a perforated seal; (2) analyze two proteins within a single spot, thus increasing the number of tests run on a single microarray without increasing the number of protein spots; (3) improve the efficiency and speed of the Ag-Ab interaction through vibratory reagent convection, which increased the signal intensity by more than two-fold and decreased the reaction time from 30 to 10min. These new techniques will facilitate rapid immunoassays for diagnostic purposes and other research areas utilizing protein microarray analysis, such as investigations of ligand-receptor or protein-small molecule interactions.
	Increasing robustness and sensitivity of protein microarrays through microagitation and automation [An article from: Analytica Chimica Acta] by: M. Hartmann publisher: Elsevier, published: 2006-03-30 ASIN: B000PBZYX2 This digital document is a journal article from Analytica Chimica Acta, published by Elsevier in 2006. The article is delivered in HTML format and is available in your Amazon.com Media Library immediately after purchase. You can view it with any web browser. Description: Assay systems that employ protein microarrays for the analysis of complex samples are powerful tools to generate a high amount of data from a limiting amount of sample. Due to miniaturization, these systems are susceptible to fluctuations during signal generation and the use of uniform conditions for sample incubation and during the assay procedure is required to get reproducible results. Diffusion limits may prevent constant conditions on all parts of the array and can lead to the decease of the sensitivity of the array. Therefore, we set-up an automated assay system integrating a novel microagitation device using surface acoustic wave (SAW) technology. Multiplexed assays for the detection of autoantibodies from human serum and sandwich immunoassay for the detection of matrix metalloproteases (MMPs) were used to evaluate the system. Diffusion-rate limited solid phase reactions were enhanced by microagitation using the SAW technology resulting in up to three-fold higher signals.
	Advances in cancer tissue microarray technology: Towards improved understanding and diagnostics [An article from: Analytica Chimica Acta] by: W. Chen publisher: Elsevier, published: 2006-03-30 ASIN: B000PBZYXC This digital document is a journal article from Analytica Chimica Acta, published by Elsevier in 2006. The article is delivered in HTML format and is available in your Amazon.com Media Library immediately after purchase. You can view it with any web browser. Description: Over the past few years, tissue microarray (TMA) technology has been established as a standard method for assessing the expression of proteins or genes across large sets of tissue specimens. It is being adopted increasingly among leading research institutions around the world and utilized in cancer research in parallel with the cDNA microarray technology. This article summarizes various aspects of cancer understanding and diagnostics in which TMA has had great impact. Although tremendous advances continue to be made to facilitate imaging and archiving of TMA specimens, automatic evaluation and quantitative analysis of TMA still remains an important challenge for modern investigators.