Bioinformatics Analysis Of Omics Data For Biomarker Identification In Clinical Research Volume Ii

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Bioinformatics Analysis of Omics Data for Biomarker Identification in Clinical Research, Volume II

Author : Lixin Cheng
Publisher : Frontiers Media SA
ISBN 13 : 283253175X
Total Pages : 757 pages
Book Rating : 4.8/5 (325 download)

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Book Synopsis Bioinformatics Analysis of Omics Data for Biomarker Identification in Clinical Research, Volume II by : Lixin Cheng

Download or read book Bioinformatics Analysis of Omics Data for Biomarker Identification in Clinical Research, Volume II written by Lixin Cheng and published by Frontiers Media SA. This book was released on 2023-09-05 with total page 757 pages. Available in PDF, EPUB and Kindle. Book excerpt: This Research Topic is part of a series with, "Bioinformatics Analysis of Omics Data for Biomarker Identification in Clinical Research - Volume I" (https://www.frontiersin.org/research-topics/13816/bioinformatics-analysis-of-omics-data-for-biomarker-identification-in-clinical-research) The advances and the decreasing cost of omics data enable profiling of disease molecular features at different levels, including bulk tissues, animal models, and single cells. Large volumes of omics data enhance the ability to search for information for preclinical study and provide the opportunity to leverage them to understand disease mechanisms, identify molecular targets for therapy, and detect biomarkers of treatment response. Identification of stable, predictive, and interpretable biomarkers is a significant step towards personalized medicine and therapy. Omics data from genomics, transcriptomics, proteomics, epigenomics, metagenomics, and metabolomics help to determine biomarkers for prognostic and diagnostic applications. Preprocessing of omics data is of vital importance as it aims to eliminate systematic experimental bias and technical variation while preserving biological variation. Dozens of normalization methods for correcting experimental variation and bias in omics data have been developed during the last two decades, while only a few consider the skewness between different sample states, such as the extensive over-repression of genes in cancers. The choice of normalization methods determines the fate of identified biomarkers or molecular signatures. From these considerations, the development of appropriate normalization methods or preprocessing strategies may promote biomarker identification and facilitate clinical decision-making.

Bioinformatics Analysis of Omics Data for Biomarker Identification in Clinical Research

Author : Lixin Cheng
Publisher : Frontiers Media SA
ISBN 13 : 2889716635
Total Pages : 574 pages
Book Rating : 4.8/5 (897 download)

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Book Synopsis Bioinformatics Analysis of Omics Data for Biomarker Identification in Clinical Research by : Lixin Cheng

Download or read book Bioinformatics Analysis of Omics Data for Biomarker Identification in Clinical Research written by Lixin Cheng and published by Frontiers Media SA. This book was released on 2022-01-10 with total page 574 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Omics Data Integration towards Mining of Phenotype Specific Biomarkers in Cancer - Volume II

Author : Liang Cheng
Publisher : Frontiers Media SA
ISBN 13 : 2832507387
Total Pages : 793 pages
Book Rating : 4.8/5 (325 download)

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Book Synopsis Omics Data Integration towards Mining of Phenotype Specific Biomarkers in Cancer - Volume II by : Liang Cheng

Download or read book Omics Data Integration towards Mining of Phenotype Specific Biomarkers in Cancer - Volume II written by Liang Cheng and published by Frontiers Media SA. This book was released on 2022-11-29 with total page 793 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Bioinformatics for Omics Data

Author : Bernd Mayer
Publisher : Humana Press
ISBN 13 : 9781493957804
Total Pages : 584 pages
Book Rating : 4.9/5 (578 download)

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Book Synopsis Bioinformatics for Omics Data by : Bernd Mayer

Download or read book Bioinformatics for Omics Data written by Bernd Mayer and published by Humana Press. This book was released on 2016-08-23 with total page 584 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presenting an area of research that intersects with and integrates diverse disciplines, including molecular biology, applied informatics, and statistics, among others, Bioinformatics for Omics Data: Methods and Protocols collects contributions from expert researchers in order to provide practical guidelines to this complex study. Divided into three convenient sections, this detailed volume covers central analysis strategies, standardization and data-management guidelines, and fundamental statistics for analyzing Omics profiles, followed by a section on bioinformatics approaches for specific Omics tracks, spanning genome, transcriptome, proteome, and metabolome levels, as well as an assortment of examples of integrated Omics bioinformatics applications, complemented by case studies on biomarker and target identification in the context of human disease. Written in the highly successful Methods in Molecular BiologyTM series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Bioinformatics for Omics Data: Methods and Protocols serves as an ideal guide to scientists of all backgrounds and aims to convey the appropriate sense of fascination associated with this research field.

Evolution of Translational Omics

Author : Institute of Medicine
Publisher : National Academies Press
ISBN 13 : 0309224187
Total Pages : 354 pages
Book Rating : 4.3/5 (92 download)

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Book Synopsis Evolution of Translational Omics by : Institute of Medicine

Download or read book Evolution of Translational Omics written by Institute of Medicine and published by National Academies Press. This book was released on 2012-09-13 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: Technologies collectively called omics enable simultaneous measurement of an enormous number of biomolecules; for example, genomics investigates thousands of DNA sequences, and proteomics examines large numbers of proteins. Scientists are using these technologies to develop innovative tests to detect disease and to predict a patient's likelihood of responding to specific drugs. Following a recent case involving premature use of omics-based tests in cancer clinical trials at Duke University, the NCI requested that the IOM establish a committee to recommend ways to strengthen omics-based test development and evaluation. This report identifies best practices to enhance development, evaluation, and translation of omics-based tests while simultaneously reinforcing steps to ensure that these tests are appropriately assessed for scientific validity before they are used to guide patient treatment in clinical trials.

Bioinformatics and Biomarker Discovery

Author : Francisco Azuaje
Publisher : John Wiley & Sons
ISBN 13 : 111996430X
Total Pages : 206 pages
Book Rating : 4.1/5 (199 download)

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Book Synopsis Bioinformatics and Biomarker Discovery by : Francisco Azuaje

Download or read book Bioinformatics and Biomarker Discovery written by Francisco Azuaje and published by John Wiley & Sons. This book was released on 2011-08-24 with total page 206 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is designed to introduce biologists, clinicians and computational researchers to fundamental data analysis principles, techniques and tools for supporting the discovery of biomarkers and the implementation of diagnostic/prognostic systems. The focus of the book is on how fundamental statistical and data mining approaches can support biomarker discovery and evaluation, emphasising applications based on different types of "omic" data. The book also discusses design factors, requirements and techniques for disease screening, diagnostic and prognostic applications. Readers are provided with the knowledge needed to assess the requirements, computational approaches and outputs in disease biomarker research. Commentaries from guest experts are also included, containing detailed discussions of methodologies and applications based on specific types of "omic" data, as well as their integration. Covers the main range of data sources currently used for biomarker discovery Covers the main range of data sources currently used for biomarker discovery Puts emphasis on concepts, design principles and methodologies that can be extended or tailored to more specific applications Offers principles and methods for assessing the bioinformatic/biostatistic limitations, strengths and challenges in biomarker discovery studies Discusses systems biology approaches and applications Includes expert chapter commentaries to further discuss relevance of techniques, summarize biological/clinical implications and provide alternative interpretations

Essentials of Bioinformatics, Volume II

Author : Noor Ahmad Shaik
Publisher : Springer Nature
ISBN 13 : 3030183750
Total Pages : 309 pages
Book Rating : 4.0/5 (31 download)

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Book Synopsis Essentials of Bioinformatics, Volume II by : Noor Ahmad Shaik

Download or read book Essentials of Bioinformatics, Volume II written by Noor Ahmad Shaik and published by Springer Nature. This book was released on 2019-10-18 with total page 309 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioinformatics is an integrative field of computer science, genetics, genomics, proteomics, and statistics, which has undoubtedly revolutionized the study of biology and medicine in past decades. It mainly assists in modeling, predicting and interpreting large multidimensional biological data by utilizing advanced computational methods. Despite its enormous potential, bioinformatics is not widely integrated into the academic curriculum as most life science students and researchers are still not equipped with the necessary knowledge to take advantage of this powerful tool. Hence, the primary purpose of our book is to supplement this unmet need by providing an easily accessible platform for students and researchers starting their career in life sciences. This book aims to avoid sophisticated computational algorithms and programming. Instead, it focuses on simple DIY analysis and interpretation of biological data with personal computers. Our belief is that once the beginners acquire these basic skillsets, they will be able to handle most of the bioinformatics tools for their research work and to better understand their experimental outcomes. Our second title of this volume set In Silico Life Sciences: Medicine provides hands-on experience in analyzing high throughput molecular data for the diagnosis, prognosis, and treatment of monogenic or polygenic human diseases. The key concepts in this volume include risk factor assessment, genetic tests and result interpretation, personalized medicine, and drug discovery. This volume is expected to train readers in both single and multi-dimensional biological analysis using open data sets, and provides a unique learning experience through clinical scenarios and case studies.

Bioinformatics for Diagnosis, Prognosis and Treatment of Complex Diseases

Author : Bairong Shen
Publisher : Springer Science & Business Media
ISBN 13 : 9400779755
Total Pages : 219 pages
Book Rating : 4.4/5 (7 download)

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Book Synopsis Bioinformatics for Diagnosis, Prognosis and Treatment of Complex Diseases by : Bairong Shen

Download or read book Bioinformatics for Diagnosis, Prognosis and Treatment of Complex Diseases written by Bairong Shen and published by Springer Science & Business Media. This book was released on 2013-11-25 with total page 219 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book introduces the bioinformatics tools, databases and strategies for the translational research, focuses on the biomarker discovery based on integrative data analysis and systems biological network reconstruction. With the coming of personal genomics era, the biomedical data will be accumulated fast and then it will become reality for the personalized and accurate diagnosis, prognosis and treatment of complex diseases. The book covers both state of the art of bioinformatics methodologies and the examples for the identification of simple or network biomarkers. In addition, bioinformatics software tools and scripts are provided to the practical application in the study of complex diseases. The present state, the future challenges and perspectives were discussed. The book is written for biologists, biomedical informatics scientists and clinicians, etc. Dr. Bairong Shen is Professor and Director of Center for Systems Biology, Soochow University; he is also Director of Taicang Center for Translational Bioinformatics.

Bioinformatics Methods in Clinical Research

Author : Rune Matthiesen
Publisher : Humana
ISBN 13 :
Total Pages : 408 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis Bioinformatics Methods in Clinical Research by : Rune Matthiesen

Download or read book Bioinformatics Methods in Clinical Research written by Rune Matthiesen and published by Humana. This book was released on 2010 with total page 408 pages. Available in PDF, EPUB and Kindle. Book excerpt: Covering the latest developments in clinical omics, this volume details the algorithms currently used in publicly available software tools. It looks at statistics, algorithms, automated data retrieval, and experimental consideration in the various omics areas.

Bioinformatics Tools (and Web Server) for Cancer Biomarker Development, Volume II

Author : Xiangqian Guo
Publisher : Frontiers Media SA
ISBN 13 : 2889763838
Total Pages : 297 pages
Book Rating : 4.8/5 (897 download)

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Book Synopsis Bioinformatics Tools (and Web Server) for Cancer Biomarker Development, Volume II by : Xiangqian Guo

Download or read book Bioinformatics Tools (and Web Server) for Cancer Biomarker Development, Volume II written by Xiangqian Guo and published by Frontiers Media SA. This book was released on 2022-06-16 with total page 297 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Methodologies of Multi-Omics Data Integration and Data Mining

Author : Kang Ning
Publisher : Springer Nature
ISBN 13 : 9811982104
Total Pages : 173 pages
Book Rating : 4.8/5 (119 download)

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Book Synopsis Methodologies of Multi-Omics Data Integration and Data Mining by : Kang Ning

Download or read book Methodologies of Multi-Omics Data Integration and Data Mining written by Kang Ning and published by Springer Nature. This book was released on 2023-01-15 with total page 173 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book features multi-omics big-data integration and data-mining techniques. In the omics age, paramount of multi-omics data from various sources is the new challenge we are facing, but it also provides clues for several biomedical or clinical applications. This book focuses on data integration and data mining methods for multi-omics research, which explains in detail and with supportive examples the “What”, “Why” and “How” of the topic. The contents are organized into eight chapters, out of which one is for the introduction, followed by four chapters dedicated for omics integration techniques focusing on several omics data resources and data-mining methods, and three chapters dedicated for applications of multi-omics analyses with application being demonstrated by several data mining methods. This book is an attempt to bridge the gap between the biomedical multi-omics big data and the data-mining techniques for the best practice of contemporary bioinformatics and the in-depth insights for the biomedical questions. It would be of interests for the researchers and practitioners who want to conduct the multi-omics studies in cancer, inflammation disease, and microbiome researches.

Cancer Genomics

Author : Janet E. Dancey
Publisher : Elsevier Inc. Chapters
ISBN 13 : 0128061049
Total Pages : 37 pages
Book Rating : 4.1/5 (28 download)

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Book Synopsis Cancer Genomics by : Janet E. Dancey

Download or read book Cancer Genomics written by Janet E. Dancey and published by Elsevier Inc. Chapters. This book was released on 2013-11-21 with total page 37 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many hope that the promise that “omics” science holds for medicine will be realized through the development of better biomarkers for patient management. However, the development of omic technologies magnifies the issues and challenges of performing high quality biomarker studies. The complexity of these technologies and of the resulting high-dimensional data require rigorous technical, statistical, bioinformatics, laboratory, and clinical procedures to develop, evaluate and validate these tests. A number of considerations are key to the design and successful execution of genomic biomarker studies. These include the assessment of (1) the complexity and heterogeneity of cancer samples, (2) the quality and quantity of tumor specimens, (3) the potential bias inherent in the assays, (4) the availability of appropriatecontrols or standards, (5) technical validation of assays and bioinformatics analysis, and (6) the validity of the final interpretation of results. In this chapter, we review these key considerations required to design and conduct biomarker studies that will yield results that can confidently inform future clinical research and clinical practice.

Leveraging Biomedical and Healthcare Data

Author : Firas Kobeissy
Publisher : Academic Press
ISBN 13 : 012809561X
Total Pages : 228 pages
Book Rating : 4.1/5 (28 download)

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Book Synopsis Leveraging Biomedical and Healthcare Data by : Firas Kobeissy

Download or read book Leveraging Biomedical and Healthcare Data written by Firas Kobeissy and published by Academic Press. This book was released on 2018-11-23 with total page 228 pages. Available in PDF, EPUB and Kindle. Book excerpt: Leveraging Biomedical and Healthcare Data: Semantics, Analytics and Knowledge provides an overview of the approaches used in semantic systems biology, introduces novel areas of its application, and describes step-wise protocols for transforming heterogeneous data into useful knowledge that can influence healthcare and biomedical research. Given the astronomical increase in the number of published reports, papers, and datasets over the last few decades, the ability to curate this data has become a new field of biomedical and healthcare research. This book discusses big data text-based mining to better understand the molecular architecture of diseases and to guide health care decision. It will be a valuable resource for bioinformaticians and members of several areas of the biomedical field who are interested in understanding more about how to process and apply great amounts of data to improve their research. Includes at each section resource pages containing a list of available curated raw and processed data that can be used by researchers in the field Provides demonstrative and relevant examples that serve as a general tutorial Presents a list of algorithm names and computational tools available for basic and clinical researchers

Next Generation Biomarkers

Author : Wim Van Criekinge
Publisher : Academic Press
ISBN 13 : 9780128143155
Total Pages : 0 pages
Book Rating : 4.1/5 (431 download)

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Book Synopsis Next Generation Biomarkers by : Wim Van Criekinge

Download or read book Next Generation Biomarkers written by Wim Van Criekinge and published by Academic Press. This book was released on 2019-09-15 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Next Generation Biomarkers: From Omics to Precision Medicine offers a clear methodology for successfully discovering and validating biomarkers using next generation sequencing, along with a comprehensive overview of next generation biomarkers currently used in the clinic. With recent advances in genomics and -omics approaches, elaborative molecular profiling is increasingly employed to gain fundamental insights into disease etiology and progression. Through a case-study based approach, the book examines a variety of NGS genomic and omics approaches to biomarker discovery and validation, along with lessons learned from recent studies and clinical trials. Chapters explore common challenges, regulations and strategies for more accurate and efficient development of next generation biomarkers, and NGS approaches, ranging from whole exome sequencing, to whole genome sequencing, epigenomic profiling, transcriptomics, peptidomics, proteomics, liquid biopsy, ethical considerations, and patient empowerment in biomarker development. Establishes a clear methodology for successfully discovering and validating biomarkers using next generation sequencing Provides a comprehensive overview of next generation biomarkers currently used Examines a variety of NGS approaches to biomarker identification, lessons learned from recent studies, common challenges, regulations, and strategies for more accurate and efficient identification of next generation biomarkers for use in precision medicine Covers NGS approaches, ranging from whole exome sequencing, to whole genome sequencing, epigenomic profiling, transcriptomics, peptidomics, proteomics, and liquid biopsy, as well as ethical considerations and patient empowerment in biomarker development Features contributions from leading international researchers working at the forefront of NGS biomarker discovery and validation

Proteomic and Metabolomic Approaches to Biomarker Discovery

Author : Haleem J. Issaq
Publisher : Academic Press
ISBN 13 : 0123947952
Total Pages : 489 pages
Book Rating : 4.1/5 (239 download)

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Book Synopsis Proteomic and Metabolomic Approaches to Biomarker Discovery by : Haleem J. Issaq

Download or read book Proteomic and Metabolomic Approaches to Biomarker Discovery written by Haleem J. Issaq and published by Academic Press. This book was released on 2013-05-20 with total page 489 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteomic and Metabolomic Approaches to Biomarker Discovery demonstrates how to leverage biomarkers to improve accuracy and reduce errors in research. Disease biomarker discovery is one of the most vibrant and important areas of research today, as the identification of reliable biomarkers has an enormous impact on disease diagnosis, selection of treatment regimens, and therapeutic monitoring. Various techniques are used in the biomarker discovery process, including techniques used in proteomics, the study of the proteins that make up an organism, and metabolomics, the study of chemical fingerprints created from cellular processes. Proteomic and Metabolomic Approaches to Biomarker Discovery is the only publication that covers techniques from both proteomics and metabolomics and includes all steps involved in biomarker discovery, from study design to study execution. The book describes methods, and presents a standard operating procedure for sample selection, preparation, and storage, as well as data analysis and modeling. This new standard effectively eliminates the differing methodologies used in studies and creates a unified approach. Readers will learn the advantages and disadvantages of the various techniques discussed, as well as potential difficulties inherent to all steps in the biomarker discovery process. A vital resource for biochemists, biologists, analytical chemists, bioanalytical chemists, clinical and medical technicians, researchers in pharmaceuticals, and graduate students, Proteomic and Metabolomic Approaches to Biomarker Discovery provides the information needed to reduce clinical error in the execution of research. - Describes the use of biomarkers to reduce clinical errors in research - Includes techniques from a range of biomarker discoveries - Covers all steps involved in biomarker discovery, from study design to study execution

Biomedical Informatics for Cancer Research

Author : Michael F. Ochs
Publisher : Springer
ISBN 13 : 9781489984517
Total Pages : 0 pages
Book Rating : 4.9/5 (845 download)

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Book Synopsis Biomedical Informatics for Cancer Research by : Michael F. Ochs

Download or read book Biomedical Informatics for Cancer Research written by Michael F. Ochs and published by Springer. This book was released on 2014-11-26 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: view, showing that multiple molecular pathways must be affected for cancer to develop, but with different specific proteins in each pathway mutated or differentially expressed in a given tumor (The Cancer Genome Atlas Research Network 2008; Parsons et al. 2008). Different studies demonstrated that while widespread mutations exist in cancer, not all mutations drive cancer development (Lin et al. 2007). This suggests a need to target only a deleterious subset of aberrant proteins, since any tre- ment must aim to improve health to justify its potential side effects. Treatment for cancer must become highly individualized, focusing on the specific aberrant driver proteins in an individual. This drives a need for informatics in cancer far beyond the need in other diseases. For instance, routine treatment with statins has become widespread for minimizing heart disease, with most patients responding to standard doses (Wilt et al. 2004). In contrast, standard treatment for cancer must become tailored to the molecular phenotype of an individual tumor, with each patient receiving a different combination of therapeutics aimed at the specific aberrant proteins driving the cancer. Tracking the aberrations that drive cancers, identifying biomarkers unique to each individual for molecular-level di- nosis and treatment response, monitoring adverse events and complex dosing schedules, and providing annotated molecular data for ongoing research to improve treatments comprise a major biomedical informatics need.

The Hidden World of Protein Aggregation

Author :
Publisher : Elsevier
ISBN 13 : 0443293414
Total Pages : 530 pages
Book Rating : 4.4/5 (432 download)

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Book Synopsis The Hidden World of Protein Aggregation by :

Download or read book The Hidden World of Protein Aggregation written by and published by Elsevier. This book was released on 2024-05-30 with total page 530 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Hidden World of Protein Aggregation, Volume 206 provides a comprehensive exploration of protein aggregation, uncovering the factors behind the formation of amorphous aggregates and ordered structures called amyloid fibrils. It delves into the advantages and disadvantages of protein aggregates, addressing topics such as cytotoxicity and disorders linked to misfolding. Specific chapters in this release include Protein Aggregation: An Overview, Pathways of Amyloid Fibril Formation and Aggregation, Factors Influencing Amyloid Fibril Formation, Morphological Features and Types of Aggregated Structures, Each big journey starts with a first step: Importance of Oligomerization, Liquid-Liquid Phase Separation as Triggering Factor of Fibril Formation, and more. Additional sections cover Experimental Techniques for Detecting and Evaluating the Amyloid Fibrils, Prediction of Protein Aggregation, Amyloid Fibril Cytotoxicity and Associated Disorders, Inhibitors of Amyloid Fibril Formation, Therapeutic Approaches in Proteinopathies, Functional Amyloids, Biotechnological Applications of Amyloid Fibrils, and The Hidden World of Protein Aggregation. Provides an introduction to the folding of protein and associated conditions leading to aggregation and linked pathology Discusses structural biology and computational methodologies for analysis of protein (mis)folding and aggregation Describes functional amyloids and their biotechnological applications