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Pathway Analysis for Drug Discovery by Anton Yuryev Pdf
This book introduces drug researchers to the novel computational approaches of pathway analysis and explains the existing applications that can save time and money in the drug discovery process. It covers traditional computational methods and software for pathway analysis microarray, proteomics, and metabolomics. It explains pathway reconstruction of diseases and toxic states, pathway analysis in various phases, dynamic modeling of drug responses, and more. This is a core resource for drug discovery and pharmaceutical industry researchers, chemists, and biologists and for professionals in related fields.
Computational Methods for Processing and Analysis of Biological Pathways by Anastasios Bezerianos,Andrei Dragomir,Panos Balomenos Pdf
This work offers a guided walkthrough of one of the most promising research areas in modern life sciences, enabling a deeper understanding of involved concepts and methodologies via an interdisciplinary view, focusing on both well-established approaches and cutting-edge research. Highlighting what pathway analysis can offer to both the experimentalist and the modeler, the text opens with an introduction to a general methodology that outlines common workflows shared by several methods. This is followed by a review of pathway and sub-pathway based approaches for systems pharmacology. The work then presents an overview of pathway analysis methods developed to model the temporal aspects of drug- or disease-induced perturbations and extract relevant dynamic themes. The text concludes by discussing several state-of-the-art methods in pathway analysis, which address the important problem of identifying differentially expressed pathways and sub-pathways.
Bioinformatics and Drug Discovery by Richard S. Larson Pdf
Recent advances in drug discovery have been rapid. The second edition of Bioinformatics and Drug Discovery has been completely updated to include topics that range from new technologies in target identification, genomic analysis, cheminformatics, protein analysis, and network or pathway analysis. Each chapter provides an extended introduction that describes the theory and application of the technology. In the second part of each chapter, detailed procedures related to the use of these technologies and software have been incorporated. Written in the highly successful Methods in Molecular BiologyTM series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, Bioinformatics and Drug Discovery, Second Edition seeks to aid scientists in the further study of the rapidly expanding field of drug discovery.
Biological Networks and Pathway Analysis by Tatiana V. Tatarinova,Yuri Nikolsky Pdf
In this volume, expert practitioners present a compilation of methods of functional data analysis (often referred to as “systems biology”) and its applications in drug discovery, medicine, and basic disease research. It covers such important issues as the elucidation of protein, compound and gene interactions, as well as analytical tools, including networks, interactome and ontologies, and clinical applications of functional analysis. As a volume in the highly successful Methods in Molecular Biology series, this work provides detailed description and hands-on implementation advice. Reputable, comprehensive, and cutting-edge, Biological Networks and Pathway Analysis presents both “wet lab” experimental methods and computational tools in order to cover a broad spectrum of issues in this fascinating new field.
Biochips as Pathways to Drug Discovery by Gary Hardiman Pdf
In the fiercely competitive pharmaceutical marketplace, your organization cannot afford to spend excess dollars developing drugs that will fail to get FDA approval or have profoundly poor characteristics. Biochips as Pathways to Drug Discovery takes a comprehensive look at how the industry faces these challenges, using new technologies such as biochips to reduce the cost of drug discovery and improve drug safety. The book explores the tools and skills required at each step of the discovery process when using biochips to determine biological outcomes. The authors provide an in-depth review of the clinical and pharmacogenomic relevance of biochips, ChIP-chip assays, and high-throughput approaches. They discuss how biochips are used to develop biomarkers in the drug discovery process, primarily for gene expression profiling and Single Nucleotide Polymorphism (SNP) analysis. The book includes coverage of experimental theory, quality control, clinical laboratory sampling considerations, database concepts, industrial laboratory design, and the analysis of the resultant large data sets. It discusses the application of biochips to the study of malaria, toxicogenomics, and SNPs, as well as intellectual property and market overviews. The book concludes with a comprehensive overview of how these chips are employed from early target discovery through preclinical toxicology and on through to pharmacogenomic and proof of concept studies in humans. Written in an easily accessible style, the breadth of coverage introduces the subject to those new to the field, while the depth of coverage forms a foundation for future work. The book gives you the knowledge required to leverage the technology into bona fide discoveries. Daniel E. Levy, editor of the Drug Discovery Series, is the founder of DEL BioPharma, a consulting service for drug discovery programs. He also maintains a blog that explores organic chemistry.
Author : Daniel L. Young,Seth Michelson Publisher : John Wiley & Sons Page : 398 pages File Size : 55,7 Mb Release : 2011-10-18 Category : Medical ISBN : 9780470261231
Systems Biology in Drug Discovery and Development by Daniel L. Young,Seth Michelson Pdf
The first book to focus on comprehensive systems biology as applied to drug discovery and development Drawing on real-life examples, Systems Biology in Drug Discovery and Development presents practical applications of systems biology to the multiple phases of drug discovery and development. This book explains how the integration of knowledge from multiple sources, and the models that best represent that integration, inform the drug research processes that are most relevant to the pharmaceutical and biotechnology industries. The first book to focus on comprehensive systems biology and its applications in drug discovery and development, it offers comprehensive and multidisciplinary coverage of all phases of discovery and design, including target identification and validation, lead identification and optimization, and clinical trial design and execution, as well as the complementary systems approaches that make these processes more efficient. It also provides models for applying systems biology to pharmacokinetics, pharmacodynamics, and candidate biomarker identification. Introducing and explaining key methods and technical approaches to the use of comprehensive systems biology on drug development, the book addresses the challenges currently facing the pharmaceutical industry. As a result, it is essential reading for pharmaceutical and biotech scientists, pharmacologists, computational modelers, bioinformaticians, and graduate students in systems biology, pharmaceutical science, and other related fields.
Protein Networks and Pathway Analysis by Yuri Nikolsky,Julie Bryant Pdf
From the beginning of the OMICs biology era, science has been pursuing the reduction of the complex "genome-wide" assays in order to understand the essential biology that lies beneath it. In Protein Networks and Pathway Analysis, expert practitioners present a compilation of methods of functional data analysis, often referred to as "systems biology," and its applications in drug discovery, medicine and basic disease research. The volume is divided into three convenient sections, covering the elucidation of protein, compound and gene interactions, analytical tools, including networks, interactome and ontologies, and applications of functional analysis. As a volume in the highly successful Methods in Molecular BiologyTM series, this work provides detailed descriptions and hands-on implementation advice. Authoritative and cutting-edge, Protein Networks and Pathway Analysis presents both "wet lab" experimental methods and computational tools in order to cover a broad spectrum of issues in this fascinating new field.
Author : Alexander Alex,C. John Harris,Dennis A. Smith Publisher : John Wiley & Sons Page : 370 pages File Size : 45,6 Mb Release : 2015-12-02 Category : Medical ISBN : 9781118679678
Attrition in the Pharmaceutical Industry by Alexander Alex,C. John Harris,Dennis A. Smith Pdf
With a focus on case studies of R&D programs in a variety of disease areas, the book highlights fundamental productivity issues the pharmaceutical industry has been facing and explores potential ways of improving research effectiveness and efficiency. • Takes a comprehensive and holistic approach to the problems and potential solutions to drug compound attrition • Tackles a problem that adds billions of dollars to drug development programs and health care costs • Guides discovery and development scientists through R&D stages, teaching requirements and reasons why drugs can fail • Discusses potential ways forward utilizing new approaches and opportunities to reduce attrition
Microbial Genomics and Drug Discovery by Thomas J. Dougherty,Steven J. Projan Pdf
Exploring innovative routes of drug discovery in the postgenomic era, Microbial Genomics and Drug Discovery examines bioinformatic and genomic approaches for the identification, detection, selection, and validation of new antibacterial targets and vaccine candidates. The book discusses potential pathways for effective infection control, inhibition of antibacterial resistance, and acceleration of the drug discovery process. This comprehensive reference describes procedures to recognize common targets in various bacterial species for the design of broad-spectrum antibiotics and clearly illustrates the use of pathway tools in a genomics-based drug discovery project.
Disease Pathways by Anastasia P. Nesterova,Anton Yuryev,Eugene A. Klimov,Maria Zharkova,Maria Shkrob,Natalia V. Ivanikova,Sergey Sozin,Vladimir Sobolev Pdf
Disease Pathways: An Atlas of Human Disease Signaling Pathways is designed to fill a void of illustrated reviews about the cellular mechanisms of human diseases. It covers 42 of the most common non-oncologic diseases and illustrates the connections between the molecular causes of the disease and its symptoms. This resource provides readers with detailed information about the disease molecular pathways, while keeping the presentation simple. Pathway models that aggregate the knowledge about protein–protein interactions have become indispensable tools in many areas of molecular biology, pharmacology, and medicine. In addition to disease pathways, the book includes a comprehensive overview of molecular signaling biology and application of pathway models in the analysis of big data for drug discovery and personalized medicine. This is a must-have reference for general biologists, biochemists, students, medical workers, and everyone interested in the cellular and molecular mechanisms of human disease. Over 145 full-color illustrations of the molecular and cellular cascades underlying the disease pathology. Disease pathways are based on computational models from Elsevier’s Disease Pathway Collection, published for the first time outside of Pathway Studio® commercial software. Each relationship on the pathway models is supported by references to scientific articles and can be examined at freely available online resources.
Semantic Breakthrough in Drug Discovery by Bin Chen,Huijun Wang,Ying Ding,David Wild Pdf
The current drug development paradigm---sometimes expressed as, ``One disease, one target, one drug''---is under question, as relatively few drugs have reached the market in the last two decades. Meanwhile, the research focus of drug discovery is being placed on the study of drug action on biological systems as a whole, rather than on individual components of such systems. The vast amount of biological information about genes and proteins and their modulation by small molecules is pushing drug discovery to its next critical steps, involving the integration of chemical knowledge with these biological databases. Systematic integration of these heterogeneous datasets and the provision of algorithms to mine the integrated datasets would enable investigation of the complex mechanisms of drug action; however, traditional approaches face challenges in the representation and integration of multi-scale datasets, and in the discovery of underlying knowledge in the integrated datasets. The Semantic Web, envisioned to enable machines to understand and respond to complex human requests and to retrieve relevant, yet distributed, data, has the potential to trigger system-level chemical-biological innovations. Chem2Bio2RDF is presented as an example of utilizing Semantic Web technologies to enable intelligent analyses for drug discovery.Table of Contents: Introduction / Data Representation and Integration Using RDF / Data Representation and Integration Using OWL / Finding Complex Biological Relationships in PubMed Articles using Bio-LDA / Integrated Semantic Approach for Systems Chemical Biology Knowledge Discovery / Semantic Link Association Prediction / Conclusions / References / Authors' Biographies
This book introduces “network pharmacology” as an emerging frontier subject of systematic drug research in the era of artificial intelligence and big data. Network Pharmacology is an original subject of fusion system biology, bioinformatics, network science and other related disciplines. It emphasizes on starting from the overall perspective of the system level and biological networks, the analysis of the laws of molecular association between drugs and their treatment objects, reveals the systematic pharmacological mechanisms of drugs, and guides the research and development of new drugs and clinical diagnosis and treatment. After it was proposed, network pharmacology has been paid attention by researchers, and it has been rapidly developed and widely used. In order to systematically reveal the biological basis of diagnosis and treatment in traditional Chinese medicine and modern medicine, we proposed a new concept of "network target" for the first time, which has become the core theory of "network pharmacology". The core principle of a network target is to construct a biological network that can be used to decipher complex diseases. The network is then used as the therapeutic target, to which multicomponent remedies are applied. This book mainly includes four parts: 1) The concept and theory of network pharmacology; 2) Common analysis methods, databases and software in network pharmacological research; 3) Typical cases of traditional Chinese medicine modernization and modern drug research based on network pharmacology; 4) Network pharmacology practice process based on drugs and diseases.
Target Discovery and Validation by Alleyn T. Plowright Pdf
The modern drug developers? guide for making informed choices among the diverse target identification methods Target Discovery and Validation: Methods and Strategies for Drug Discovery offers a hands-on review of the modern technologies for drug target identification and validation. With contributions from noted industry and academic experts, the book addresses the most recent chemical, biological, and computational methods. Additionally, the book highlights techologies that are applicable to ?difficult? targets and drugs directed at multiple targets, including chemoproteomics, activity-based protein profiling, pathway mapping, genome-wide association studies, and array-based profiling. Throughout, the authors highlight a range of diverse approaches, and target validation studies reveal how these methods can support academic and drug discovery scientists in their target discovery and validation research. This resource: -Offers a guide to identifying and validating targets, a key enabling technology without which no new drug development is possible -Presents the information needed for choosing the appropriate assay method from the ever-growing range of available options -Provides practical examples from recent drug development projects, e. g. in kinase inhibitor profiling Written for medicinal chemists, pharmaceutical professionals, biochemists, biotechnology professionals, and pharmaceutical chemists, Target Discovery and Validation explores the current methods for the identification and validation of drug targets in one comrpehensive volume. It also includes numerous practical examples.
Institute of Medicine,Board on Health Sciences Policy,Forum on Neuroscience and Nervous System Disorders
Author : Institute of Medicine,Board on Health Sciences Policy,Forum on Neuroscience and Nervous System Disorders Publisher : National Academies Press Page : 118 pages File Size : 55,7 Mb Release : 2014-02-06 Category : Medical ISBN : 9780309292498
Improving and Accelerating Therapeutic Development for Nervous System Disorders by Institute of Medicine,Board on Health Sciences Policy,Forum on Neuroscience and Nervous System Disorders Pdf
Improving and Accelerating Therapeutic Development for Nervous System Disorders is the summary of a workshop convened by the IOM Forum on Neuroscience and Nervous System Disorders to examine opportunities to accelerate early phases of drug development for nervous system drug discovery. Workshop participants discussed challenges in neuroscience research for enabling faster entry of potential treatments into first-in-human trials, explored how new and emerging tools and technologies may improve the efficiency of research, and considered mechanisms to facilitate a more effective and efficient development pipeline. There are several challenges to the current drug development pipeline for nervous system disorders. The fundamental etiology and pathophysiology of many nervous system disorders are unknown and the brain is inaccessible to study, making it difficult to develop accurate models. Patient heterogeneity is high, disease pathology can occur years to decades before becoming clinically apparent, and diagnostic and treatment biomarkers are lacking. In addition, the lack of validated targets, limitations related to the predictive validity of animal models - the extent to which the model predicts clinical efficacy - and regulatory barriers can also impede translation and drug development for nervous system disorders. Improving and Accelerating Therapeutic Development for Nervous System Disorders identifies avenues for moving directly from cellular models to human trials, minimizing the need for animal models to test efficacy, and discusses the potential benefits and risks of such an approach. This report is a timely discussion of opportunities to improve early drug development with a focus toward preclinical trials.
Pharmacogenomics in Drug Discovery and Development by Qing Yan Pdf
This new edition offers a state-of-the-art and integrative vision of pharmacogenomics by exploring new concepts and practical methodologies focusing on disease treatments, from cancers to cardiovascular and neurodegenerative disorders and more. The collection of these theoretical and experimental approaches facilitates problem-solving by tackling the complexity of personalized drug discovery and development. Written by leading experts in their fields for the highly successful Methods in Molecular Biology series, the book aims to provide across-the-board resources to support the translation of pharmacogenomics into better individualized health care. Authoritative and up-to-date, Pharmacogenomics in Drug Discovery and Development, Third Edition aims to aid researchers in approaching the challenges in pharmacogenomics and personalized medicine with the introduction of these novel ideas and cutting-edge methodologies.