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Analysis of MALDI-TOF Serum Profiles for Biomarker Selection and Sample Classification

Analysis of MALDI-TOF Serum Profiles for Biomarker Selection and Sample Classification
Author:
Publisher:
Total Pages: 8
Release: 2005
Genre:
ISBN:

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Mass spectrometric profiles of peptides and proteins obtained by current technologies are characterized by complex spectra, high dimensionality, and substantial noise. These characteristics generate challenges in discovery of proteins and protein-profiles that distinguish disease states, e.g. cancer patients from healthy individuals. A challenging aspect of biomarker discovery in serum is the interference of abundant proteins with identification of disease-related proteins and peptides. We present data processing methods and computational intelligence that combines support vector machines (SVM) with particle swarm optimization (PSO) for biomarker selection from MALDI-TOF spectra of enriched serum. SVM classifiers were built for various combinations of m/z windows guided by the PSO algorithm. The method identified mass points that achieved high classification accuracy in distinguishing cancer patients from non-cancer controls. Based on their frequency of occurrence in multiple runs, six m/z windows were selected as candidate biomarkers. These biomarkers yielded 100% sensitivity and 91% specificity in distinguishing liver cancer patients from healthy individuals in an independent dataset.


Kernel Methods in Computational Biology

Kernel Methods in Computational Biology
Author: Bernhard Schölkopf
Publisher: MIT Press
Total Pages: 428
Release: 2004
Genre: Computers
ISBN: 9780262195096

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A detailed overview of current research in kernel methods and their application to computational biology.


Pharmacoproteomics

Pharmacoproteomics
Author: Seth K. Amponsah
Publisher: Springer Nature
Total Pages: 479
Release:
Genre:
ISBN: 3031640217

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Applications of MALDI-TOF Spectroscopy

Applications of MALDI-TOF Spectroscopy
Author: Zongwei Cai
Publisher: Springer
Total Pages: 220
Release: 2014-07-08
Genre: Science
ISBN: 3642356656

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MALDI-ToF Mass Spectrometry for Studying Noncovalent Complexes of Biomolecules, by Stefanie Mädler, Elisabetta Boeri Erba, Renato Zenobi Application of MALDI-TOF-Mass Spectrometry to Proteome Analysis Using Stain-Free Gel Electrophoresis, by Iuliana Susnea, Bogdan Bernevic, Michael Wicke, Li Ma, Shuying Liu, Karl Schellander, Michael Przybylski MALDI Mass Spectrometry for Nucleic Acid Analysis, by Xiang Gao, Boon-Huan Tan, Richard J. Sugrue, Kai Tang Determination of Peptide and Protein Disulfide Linkages by MALDI Mass Spectrometry, by Hongmei Yang, Ning Liu, Shuying Liu MALDI In-Source Decay, from Sequencing to Imaging, by Delphine Debois, Nicolas Smargiasso, Kevin Demeure, Daiki Asakawa, Tyler A. Zimmerman, Loïc Quinton, Edwin De Pauw Advances of MALDI-TOF MS in the Analysis of Traditional Chinese Medicines, by Minghua Lu, Zongwei Cai Chemical and Biochemical Applications of MALDI TOF-MS Based on Analyzing the Small Organic Compounds, by Haoyang Wang, Zhixiong Zhao, Yinlong Guo Bioinformatic Analysis of Data Generated from MALDI Mass Spectrometry for Biomarker Discovery, by Zengyou He, Robert Z. Qi, Weichuan Yu


Multivariate Data Reduction and Discrimination with SAS Software

Multivariate Data Reduction and Discrimination with SAS Software
Author: Ravindra Khattree
Publisher: Wiley-SAS
Total Pages: 0
Release: 2000-08-14
Genre: Mathematics
ISBN: 9780471323006

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Easy to read and comprehensive, this book presents descriptive multivariate (DMV) statistical methods using real-world problems and data sets. It offers a unique approach to integrating statistical methods, various kinds of advanced data analyses, and applications of the popular SAS software aids. Emphasis is placed on the correct interpretation of output to draw meaningful conclusions in a variety of disciplines and industries.


Medical Applications of Mass Spectrometry

Medical Applications of Mass Spectrometry
Author: Karoly Vekey
Publisher: Elsevier
Total Pages: 607
Release: 2011-08-11
Genre: Science
ISBN: 0080554652

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Mass spectrometry is fast becoming an indispensable field for medical professionals. The mass spectrometric analysis of metabolites and proteins promises to revolutionize medical research and clinical diagnostics. As this technology rapidly enters the medical field, practicing professionals and students need to prepare to take full advantage of its capabilities. Medical Applications of Mass Spectrometry addresses the key issues in the medical applications of mass spectrometry at the level appropriate for the intended readership. It will go a long way to help the utilization of mass spectrometry in medicine.The book comprises five parts. A general overview is followed by a description of the basic sampling and separation methods in analytical chemistry. In the second part a solid foundation in mass spectrometry and modern techniques of data analysis is presented. The third part explains how mass spectrometry is used in exploring various classes of biomolecules, including proteins and lipids. In the fourth section mass spectrometry is introduced as a diagnostic tool in clinical treatment, infectious pathogen research, neonatal diagnostics, cancer, brain and allergy research, as well as in various fields of medicine: cardiology, pulmonology, neurology, psychiatric diseases, hemato-oncology, urologic diseases, gastrointestinal diseases, gynecology and pediatrics. The fifth part covers emerging applications in biomarker discovery and in mass spectrometric imaging. * Provides a broad look at how the medical field is benefiting from advances in mass spectrometry.* Guides the reader from basic principles and methods to cutting edge applications.* There is NO comparable book on the market to fill this fast growing field.


Handbook of Glycosyltransferases and Related Genes

Handbook of Glycosyltransferases and Related Genes
Author: Naoyuki Taniguchi
Publisher: Springer Science & Business Media
Total Pages: 668
Release: 2011-06-28
Genre: Science
ISBN: 4431678778

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The so-called postgenomic research era has now been launched, and the field of gly cobiology and glycotechnology has become one of the most important areas in life science because glycosylation is the most common post-translational modification reaction of proteins in vivo. On the basis of Swiss-Prot data, over 50% proteins are known to undergo glycosylation, but in fact the actual functions of most of the sugar chains in the glycoconjugates remain unknown. The complex carbohydrate chains of glycoproteins, glycolipids, and proteoglycans represent the secondary gene products formed through the reactions of glycosyl transferases. The regulation of the biosynthesis of sugar chains is under the control of the expression of glycosyltransferases, their substrate specificity, and their local ization in specific tissue sites. There is a growing body of evidence to suggest that these enzymes play pivotal roles in a variety of important cellular differentiation and developmental events, as well as in disease processes. Over 300 glycosyltransferases appear to exist in mammalian tissues. If the genes that have been purified and cloned from various species such as humans, cattle, pigs, rats and mice are counted as one, approximately 110 glycogenes that encode glycosyltransferases and related genes have been cloned at present, and this number continues to grow each day. However, most of the functions of the glycosyltransferase genes and related genes are unknown. This fact has stimulated numerous new and interesting approaches in molecular biologi cal investigations.


Cancer Theranostics

Cancer Theranostics
Author: Xiaoyuan Chen
Publisher: Academic Press
Total Pages: 543
Release: 2014-03-20
Genre: Medical
ISBN: 0124078842

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Aiding researchers seeking to eliminate multi-step procedures, reduce delays in treatment and ease patient care, Cancer Theranostics reviews, assesses, and makes pertinent clinical recommendations on the integration of comprehensive in vitro diagnostics, in vivo molecular imaging, and individualized treatments towards the personalization of cancer treatment. Cancer Theranostics describes the identification of novel biomarkers to advance molecular diagnostics of cancer. The book encompasses new molecular imaging probes and techniques for early detection of cancer, and describes molecular imaging-guided cancer therapy. Discussion also includes nanoplatforms incorporating both cancer imaging and therapeutic components, as well as clinical translation and future perspectives. Supports elimination of multi-step approaches and reduces delays in treatments through combinatorial diagnosis and therapy Fully assesses cancer theranostics across the emergent field, with discussion of biomarkers, molecular imaging, imaging guided therapy, nanotechnology, and personalized medicine Content bridges laboratory, clinic, and biotechnology industries to advance biomedical science and improve patient management


Data Mining for Genomics and Proteomics

Data Mining for Genomics and Proteomics
Author: Darius M. Dziuda
Publisher: John Wiley & Sons
Total Pages: 348
Release: 2010-07-16
Genre: Computers
ISBN: 0470593407

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Data Mining for Genomics and Proteomics uses pragmatic examples and a complete case study to demonstrate step-by-step how biomedical studies can be used to maximize the chance of extracting new and useful biomedical knowledge from data. It is an excellent resource for students and professionals involved with gene or protein expression data in a variety of settings.


Measuring Immunity

Measuring Immunity
Author: Michael T. Lotze
Publisher: Elsevier
Total Pages: 759
Release: 2011-05-04
Genre: Medical
ISBN: 0080479332

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Most of the diseases of modern mankind involve either acute or chronic inflammation. Measuring Immunity integrates the current information available on biomarkers and surrogate assays into a single handbook. It highlights the principles behind various applications, gives a brief summary on how they are conducted and provides detailed and critical analyses of murine models of immunity, clinical trials, and tests to predict utility and benefit. Measuring Immunity is indispensable for scientists and clinicians interested in the clinical applications of modern immunobiology. * Defines which assays of immune function are helpful in the assessment of clinical disorders involving inflammation and immunity* Assesses the dynamics of cellular and soluble factors in the peripheral blood using modern techniques * Includes basic science foundations as well as the approaches currently applied