Data Management Of Protein Interaction Networks

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Data Management of Protein Interaction Networks

Mario Cannataro,Pietro H. Guzzi
Data Management of Protein Interaction Networks Book PDF

Author : Mario Cannataro,Pietro H. Guzzi
Publisher : John Wiley & Sons
Page : 145 pages
File Size : 40,6 Mb
Release : 2012-02-03
Category : Computers
ISBN : 9781118103739

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Data Management of Protein Interaction Networks by Mario Cannataro,Pietro H. Guzzi Pdf

Current PPI databases do not offer sophisticated querying interfaces and especially do not integrate existing information about proteins. Current algorithms for PIN analysis use only topological information, while emerging approaches attempt to exploit the biological knowledge related to proteins and kinds of interaction, e.g. protein function, localization, structure, described in Gene Ontology or PDB. The book discusses technologies, standards and databases for, respectively, generating, representing and storing PPI data. It also describes main algorithms and tools for the analysis, comparison and knowledge extraction from PINs. Moreover, some case studies and applications of PINs are also discussed.

Biological Data Mining in Protein Interaction Networks

Li, Xiao-Li,Ng, See-Kiong
Biological Data Mining in Protein Interaction Networks Book PDF

Author : Li, Xiao-Li,Ng, See-Kiong
Publisher : IGI Global
Page : 450 pages
File Size : 50,7 Mb
Release : 2009-05-31
Category : Technology & Engineering
ISBN : 9781605663999

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Biological Data Mining in Protein Interaction Networks by Li, Xiao-Li,Ng, See-Kiong Pdf

"The goal of this book is to disseminate research results and best practices from cross-disciplinary researchers and practitioners interested in, and working on bioinformatics, data mining, and proteomics"--Provided by publisher.

Protein Interaction Networks

Aidong Zhang
Protein Interaction Networks Book PDF

Author : Aidong Zhang
Publisher : Cambridge University Press
Page : 283 pages
File Size : 46,7 Mb
Release : 2009-04-06
Category : Computers
ISBN : 9781139479035

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Protein Interaction Networks by Aidong Zhang Pdf

The analysis of protein-protein interactions is fundamental to the understanding of cellular organization, processes, and functions. Proteins seldom act as single isolated species; rather, proteins involved in the same cellular processes often interact with each other. Functions of uncharacterized proteins can be predicted through comparison with the interactions of similar known proteins. Recent large-scale investigations of protein-protein interactions using such techniques as two-hybrid systems, mass spectrometry, and protein microarrays have enriched the available protein interaction data and facilitated the construction of integrated protein-protein interaction networks. The resulting large volume of protein-protein interaction data has posed a challenge to experimental investigation. This book provides a comprehensive understanding of the computational methods available for the analysis of protein-protein interaction networks. It offers an in-depth survey of a range of approaches, including statistical, topological, data-mining, and ontology-based methods. The author discusses the fundamental principles underlying each of these approaches and their respective benefits and drawbacks, and she offers suggestions for future research.

Protein-Protein Interaction Networks

Stefan Canzar,Francisca Rojas Ringeling
Protein Protein Interaction Networks Book PDF

Author : Stefan Canzar,Francisca Rojas Ringeling
Publisher : Humana
Page : 0 pages
File Size : 43,8 Mb
Release : 2019-10-04
Category : Science
ISBN : 1493998722

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Protein-Protein Interaction Networks by Stefan Canzar,Francisca Rojas Ringeling Pdf

This volume explores techniques that study interactions between proteins in different species, and combines them with context-specific data, analysis of omics datasets, and assembles individual interactions into higher-order semantic units, i.e., protein complexes and functional modules. The chapters in this book cover computational methods that solve diverse tasks such as the prediction of functional protein-protein interactions; the alignment-based comparison of interaction networks by SANA; using the RaptorX-ComplexContact webserver to predict inter-protein residue-residue contacts; the docking of alternative confirmations of proteins participating in binary interactions and the visually-guided selection of a docking model using COZOID; the detection of novel functional units by KeyPathwayMiner and how PathClass can use such de novo pathways to classify breast cancer subtypes. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary hardware- and software, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Protein-Protein Interaction Networks: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in learning more about this evolving field.

Protein-protein Interactions and Networks

Anna Panchenko,Teresa M. Przytycka
Protein protein Interactions and Networks Book PDF

Author : Anna Panchenko,Teresa M. Przytycka
Publisher : Springer Science & Business Media
Page : 198 pages
File Size : 40,7 Mb
Release : 2010-04-06
Category : Science
ISBN : 9781848001251

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Protein-protein Interactions and Networks by Anna Panchenko,Teresa M. Przytycka Pdf

The biological interactions of living organisms, and protein-protein interactions in particular, are astonishingly diverse. This comprehensive book provides a broad, thorough and multidisciplinary coverage of its field. It integrates different approaches from bioinformatics, biochemistry, computational analysis and systems biology to offer the reader a comprehensive global view of the diverse data on protein-protein interactions and protein interaction networks.

Scientific Data Management

Arie Shoshani,Doron Rotem
Scientific Data Management Book PDF

Author : Arie Shoshani,Doron Rotem
Publisher : CRC Press
Page : 592 pages
File Size : 43,9 Mb
Release : 2009-12-16
Category : Computers
ISBN : 9781420069815

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Scientific Data Management by Arie Shoshani,Doron Rotem Pdf

Dealing with the volume, complexity, and diversity of data currently being generated by scientific experiments and simulations often causes scientists to waste productive time. Scientific Data Management: Challenges, Technology, and Deployment describes cutting-edge technologies and solutions for managing and analyzing vast amounts of data, helping

Heterogeneous Data Management, Polystores, and Analytics for Healthcare

Vijay Gadepally,Timothy Mattson,Michael Stonebraker,Tim Kraska,Fusheng Wang,Gang Luo,Jun Kong,Alevtina Dubovitskaya
Heterogeneous Data Management Polystores and Analytics for Healthcare Book PDF

Author : Vijay Gadepally,Timothy Mattson,Michael Stonebraker,Tim Kraska,Fusheng Wang,Gang Luo,Jun Kong,Alevtina Dubovitskaya
Publisher : Springer Nature
Page : 235 pages
File Size : 42,8 Mb
Release : 2021-03-03
Category : Computers
ISBN : 9783030710552

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Heterogeneous Data Management, Polystores, and Analytics for Healthcare by Vijay Gadepally,Timothy Mattson,Michael Stonebraker,Tim Kraska,Fusheng Wang,Gang Luo,Jun Kong,Alevtina Dubovitskaya Pdf

This book constitutes revised selected papers from two VLDB workshops: The International Workshop on Polystore Systems for Heterogeneous Data in Multiple Databases with Privacy and Security Assurances, Poly 2020, and the 6th International Workshop on Data Management and Analytics for Medicine and Healthcare, DMAH 2020, which were held virtually on August 31 and September 4, 2020. For Poly 2020, 4 full and 3 short papers were accepted from 10 submissions; and for DMAH 2020, 7 full and 2 short papers were accepted from a total of 15 submissions. The papers were organized in topical sections as follows: Privacy, Security and/or Policy Issues for Heterogenous Data; COVID-19 Data Analytics and Visualization; Deep Learning based Biomedical Data Analytics; NLP based Learning from Unstructured Data; Biomedical Data Modelling and Prediction.

Scientific and Statistical Database Management

Michael Gertz,Bertram Ludäscher
Scientific and Statistical Database Management Book PDF

Author : Michael Gertz,Bertram Ludäscher
Publisher : Springer
Page : 660 pages
File Size : 45,6 Mb
Release : 2010-06-27
Category : Computers
ISBN : 9783642138188

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Scientific and Statistical Database Management by Michael Gertz,Bertram Ludäscher Pdf

This book constitutes the proceedings of the 22nd International Conference on Scientific and Statistical Database Management, SSDBM 2010, held in Heidelberg, Germany in June/July 2010. The 30 long and 11 short papers presented were carefully reviewed and selected from 94 submissions. The topics covered are query processing; scientific data management and analysis; data mining; indexes and data representation; scientific workflow and provenance; and data stream processing.

Protein Interaction Networks in Health and Disease

Spyros Petrakis,Miguel A. Andrade-Navarro
Protein Interaction Networks in Health and Disease Book PDF

Author : Spyros Petrakis,Miguel A. Andrade-Navarro
Publisher : Frontiers Media SA
Page : 91 pages
File Size : 41,6 Mb
Release : 2016-10-19
Category : Genetics
ISBN : 9782889199822

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Protein Interaction Networks in Health and Disease by Spyros Petrakis,Miguel A. Andrade-Navarro Pdf

The identification and mapping of protein-protein interactions (PPIs) is a major goal in systems biology. Experimental data are currently produced in large scale using a variety of high-throughput assays in yeast or mammalian systems. Analysis of these data using computational tools leads to the construction of large protein interaction networks, which help researchers identify novel protein functions. However, our current view of protein interaction networks is still limited and there is an active field of research trying to further develop this concept to include important processes: the topology of interactions and their changes in real time, the effects of competition for binding to the same protein region, PPI variation due to alternative splicing or post-translational modifications, etc. In particular, a clinically relevant topic for development of the concept of protein interactions networks is the consideration of mutant isoforms, which may be responsible for a pathological condition. Mutations in proteins may result in loss of normal interactions and appearance of novel abnormal interactions that may affect a protein’s function and biological cycle. This Research Topic presents novel findings and recent achievements in the field of protein interaction networks with a focus on disease. Authors describe methods for the identification and quantification of PPIs, the annotation and analysis of networks, considering PPIs and protein complexes formed by mutant proteins associated with pathological conditions or genetic diseases.

Scientific and Statistical Database Management

Bertram Ludäscher,Nikos Mamoulis
Scientific and Statistical Database Management Book PDF

Author : Bertram Ludäscher,Nikos Mamoulis
Publisher : Springer
Page : 620 pages
File Size : 45,7 Mb
Release : 2008-07-11
Category : Computers
ISBN : 9783540694977

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Scientific and Statistical Database Management by Bertram Ludäscher,Nikos Mamoulis Pdf

This book constitutes the refereed proceedings of the 20th International Conference on Scientific and Statistical Database Management, SSDBM 2008, held in Hong Kong, China, in July 2008. The 28 revised full papers, 7 revised short papers and 8 poster and demo papers presented together with 3 invited talks were carefully reviewed and selected from 84 submissions. The papers are organized in topical sections on query optimization in scientific databases, privacy, searching and mining graphs, data streams, scientific database applications, advanced indexing methods, data mining, as well as advanced queries and uncertain data.

Computational Prediction of Protein Complexes from Protein Interaction Networks

Sriganesh Srihari,Chern Han Yong,Limsoon Wong
Computational Prediction of Protein Complexes from Protein Interaction Networks Book PDF

Author : Sriganesh Srihari,Chern Han Yong,Limsoon Wong
Publisher : Morgan & Claypool
Page : 295 pages
File Size : 43,5 Mb
Release : 2017-05-30
Category : Science
ISBN : 9781970001549

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Computational Prediction of Protein Complexes from Protein Interaction Networks by Sriganesh Srihari,Chern Han Yong,Limsoon Wong Pdf

Complexes of physically interacting proteins constitute fundamental functional units that drive almost all biological processes within cells. A faithful reconstruction of the entire set of protein complexes (the "complexosome") is therefore important not only to understand the composition of complexes but also the higher level functional organization within cells. Advances over the last several years, particularly through the use of high-throughput proteomics techniques, have made it possible to map substantial fractions of protein interactions (the "interactomes") from model organisms including Arabidopsis thaliana (a flowering plant), Caenorhabditis elegans (a nematode), Drosophila melanogaster (fruit fly), and Saccharomyces cerevisiae (budding yeast). These interaction datasets have enabled systematic inquiry into the identification and study of protein complexes from organisms. Computational methods have played a significant role in this context, by contributing accurate, efficient, and exhaustive ways to analyze the enormous amounts of data. These methods have helped to compensate for some of the limitations in experimental datasets including the presence of biological and technical noise and the relative paucity of credible interactions. In this book, we systematically walk through computational methods devised to date (approximately between 2000 and 2016) for identifying protein complexes from the network of protein interactions (the protein-protein interaction (PPI) network). We present a detailed taxonomy of these methods, and comprehensively evaluate them for protein complex identification across a variety of scenarios including the absence of many true interactions and the presence of false-positive interactions (noise) in PPI networks. Based on this evaluation, we highlight challenges faced by the methods, for instance in identifying sparse, sub-, or small complexes and in discerning overlapping complexes, and reveal how a combination of strategies is necessary to accurately reconstruct the entire complexosome.

Protein-Protein and Domain-Domain Interactions

Pandjassarame Kangueane,Christina Nilofer
Protein Protein and Domain Domain Interactions Book PDF

Author : Pandjassarame Kangueane,Christina Nilofer
Publisher : Springer
Page : 207 pages
File Size : 54,9 Mb
Release : 2018-02-16
Category : Medical
ISBN : 9789811073472

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Protein-Protein and Domain-Domain Interactions by Pandjassarame Kangueane,Christina Nilofer Pdf

This book illustrates the importance and significance of the molecular (physical and chemical) and evolutionary (gene fusion) principles of protein-protein and domain-domain interactions towards the understanding of cell division, disease mechanism and target definition in drug discovery. It describes the complex issues associated with this phenomenon using cutting edge advancement in Bioinformatics and Bioinformation Discovery. The chapters provide current information pertaining to the types of protein-protein complexes (homodimers, heterodimers, multimer complexes) in context with various specific and sensitive biological functions. The significance of such complex formation in human biology in the light of molecular evolution is also highlighted using several examples. The chapters also describe recent advancements on the molecular principles of protein-protein interaction with reference to evolution towards target identification in drug discovery. Finally, the book also elucidates a comprehensive yet a representative description of a large number of challenges associated with the molecular interaction of proteins.

Protein Interaction Networks

Aidong Zhang
Protein Interaction Networks Book PDF

Author : Aidong Zhang
Publisher : Unknown
Page : 278 pages
File Size : 51,9 Mb
Release : 2009
Category : Protein-protein interactions
ISBN : 1107201136

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Protein Interaction Networks by Aidong Zhang Pdf

The first comprehensive survey of statistical, topological, data-mining, and ontology-based methods for analysing protein-protein interaction networks.

New Approaches of Protein Function Prediction from Protein Interaction Networks

Jingyu Hou
New Approaches of Protein Function Prediction from Protein Interaction Networks Book PDF

Author : Jingyu Hou
Publisher : Academic Press
Page : 124 pages
File Size : 51,7 Mb
Release : 2017-01-13
Category : Mathematics
ISBN : 9780128099445

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New Approaches of Protein Function Prediction from Protein Interaction Networks by Jingyu Hou Pdf

New Approaches of Protein Function Prediction from Protein Interaction Networks contains the critical aspects of PPI network based protein function prediction, including semantically assessing the reliability of PPI data, measuring the functional similarity between proteins, dynamically selecting prediction domains, predicting functions, and establishing corresponding prediction frameworks. Functional annotation of proteins is vital to biological and clinical research and other applications due to the important roles proteins play in various biological processes. Although the functions of some proteins have been annotated via biological experiments, there are still many proteins whose functions are yet to be annotated due to the limitations of existing methods and the high cost of experiments. To overcome experimental limitations, this book helps users understand the computational approaches that have been rapidly developed for protein function prediction. Provides innovative approaches and new developments targeting key issues in protein function prediction Presents heuristic ideas for further research in this challenging area

Biological Network Analysis

Pietro Hiram Guzzi,Swarup Roy
Biological Network Analysis Book PDF

Author : Pietro Hiram Guzzi,Swarup Roy
Publisher : Elsevier
Page : 212 pages
File Size : 54,7 Mb
Release : 2020-05-11
Category : Science
ISBN : 9780128193518

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Biological Network Analysis by Pietro Hiram Guzzi,Swarup Roy Pdf

Biological Network Analysis: Trends, Approaches, Graph Theory, and Algorithms considers three major biological networks, including Gene Regulatory Networks (GRN), Protein-Protein Interaction Networks (PPIN), and Human Brain Connectomes. The book's authors discuss various graph theoretic and data analytics approaches used to analyze these networks with respect to available tools, technologies, standards, algorithms and databases for generating, representing and analyzing graphical data. As a wide variety of algorithms have been developed to analyze and compare networks, this book is a timely resource. Presents recent advances in biological network analysis, combining Graph Theory, Graph Analysis, and various network models Discusses three major biological networks, including Gene Regulatory Networks (GRN), Protein-Protein Interaction Networks (PPIN) and Human Brain Connectomes Includes a discussion of various graph theoretic and data analytics approaches