Special Issue "High-Throughput Microarray for Protein Biomarker Discovery"

A special issue of Microarrays (ISSN 2076-3905).

Deadline for manuscript submissions: closed (30 June 2015).

Special Issue Editor

Prof. Quan-Zhen Li
E-Mail Website
Guest Editor
Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Interests: developing and using high through-put microarray; 2nd-generation sequencing and other genomic analysis tools to identify and characterize disease-related genes and pathways

Special Issue Information

Dear Colleagues,

Proteomic microarrays have been widely used for profiling biomarkers related with disease development and progression. The advantage of microarrays is that they allow for high throughput screening of large amounts of biomarkers using small amounts of samples. High throughput proteomic microarray analysis provides powerful tools for the discovery of novel biomarkers, which could possibly be used in the diagnosis and/or prognosis of diseases. In this Special Issue, we will collect papers on the following topics:

  1. The development of high-throughput proteomic microarrays for biomarker screening and discovery.
  2. The identification of disease-related biomarkers using high throughput microarray platforms.
  3. The application of proteomic microarrays on biological research concerning molecular interaction, therapeutic targets, diseases diagnosis, and prognosis.
  4. Data analysis algorithms and software development for high throughput proteomic microarrays.

Professor Quan-Zhen Li
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microarrays is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 350 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • proteomic microarray
  • high-throughput screening
  • biomarkers
  • diseases

Published Papers (3 papers)

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Research

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Article
Serology in the Digital Age: Using Long Synthetic Peptides Created from Nucleic Acid Sequences as Antigens in Microarrays
Microarrays 2016, 5(3), 22; https://doi.org/10.3390/microarrays5030022 - 10 Aug 2016
Cited by 3 | Viewed by 2345
Abstract
Background: Antibodies to microbes, or to autoantigens, are important markers of disease. Antibody detection (serology) can reveal both past and recent infections. There is a great need for development of rational ways of detecting and quantifying antibodies, both for humans and animals. Traditionally, [...] Read more.
Background: Antibodies to microbes, or to autoantigens, are important markers of disease. Antibody detection (serology) can reveal both past and recent infections. There is a great need for development of rational ways of detecting and quantifying antibodies, both for humans and animals. Traditionally, serology using synthetic antigens covers linear epitopes using up to 30 amino acid peptides. Methods: We here report that peptides of 100 amino acids or longer (“megapeptides”), designed and synthesized for optimal serological performance, can successfully be used as detection antigens in a suspension multiplex immunoassay (SMIA). Megapeptides can quickly be created just from pathogen sequences. A combination of rational sequencing and bioinformatic routines for definition of diagnostically-relevant antigens can, thus, rapidly yield efficient serological diagnostic tools for an emerging infectious pathogen. Results: We designed megapeptides using bioinformatics and viral genome sequences. These long peptides were tested as antigens for the presence of antibodies in human serum to the filo-, herpes-, and polyoma virus families in a multiplex microarray system. All of these virus families contain recently discovered or emerging infectious viruses. Conclusion: Long synthetic peptides can be useful as serological diagnostic antigens, serving as biomarkers, in suspension microarrays. Full article
(This article belongs to the Special Issue High-Throughput Microarray for Protein Biomarker Discovery)
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Review

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Review
Aptamer-Based Screens of Human Body Fluids for Biomarkers
Microarrays 2015, 4(3), 424-431; https://doi.org/10.3390/microarrays4030424 - 22 Sep 2015
Cited by 5 | Viewed by 2574
Abstract
In recent years, aptamers have come to replace antibodies in high throughput multiplexed experiments. The aptamer-based biomarker screening technology, which kicked off in 2010, is capable of interrogating thousands of proteins in a very small sample volume. With this new technology, researchers hope [...] Read more.
In recent years, aptamers have come to replace antibodies in high throughput multiplexed experiments. The aptamer-based biomarker screening technology, which kicked off in 2010, is capable of interrogating thousands of proteins in a very small sample volume. With this new technology, researchers hope to find clinically appropriate biomarkers for a myriad of illnesses by screening human body fluids. In this work, we have reviewed a total of eight studies utilizing aptamer-based biomarker screens of human body fluids, and have highlighted novel protein biomarkers discovered. Full article
(This article belongs to the Special Issue High-Throughput Microarray for Protein Biomarker Discovery)
Review
Microarray Meta-Analysis and Cross-Platform Normalization: Integrative Genomics for Robust Biomarker Discovery
Microarrays 2015, 4(3), 389-406; https://doi.org/10.3390/microarrays4030389 - 21 Aug 2015
Cited by 50 | Viewed by 5392
Abstract
The diagnostic and prognostic potential of the vast quantity of publicly-available microarray data has driven the development of methods for integrating the data from different microarray platforms. Cross-platform integration, when appropriately implemented, has been shown to improve reproducibility and robustness of gene signature [...] Read more.
The diagnostic and prognostic potential of the vast quantity of publicly-available microarray data has driven the development of methods for integrating the data from different microarray platforms. Cross-platform integration, when appropriately implemented, has been shown to improve reproducibility and robustness of gene signature biomarkers. Microarray platform integration can be conceptually divided into approaches that perform early stage integration (cross-platform normalization) versus late stage data integration (meta-analysis). A growing number of statistical methods and associated software for platform integration are available to the user, however an understanding of their comparative performance and potential pitfalls is critical for best implementation. In this review we provide evidence-based, practical guidance to researchers performing cross-platform integration, particularly with an objective to discover biomarkers. Full article
(This article belongs to the Special Issue High-Throughput Microarray for Protein Biomarker Discovery)
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