Verfügbarkeit: Encyclopedia of bioinformatics and computational biology

Encyclopedia of bioinformatics and computational biology: Volume 1 Methods

Gespeichert in:

Bibliographische Detailangaben
Weitere beteiligte Personen:	Cannataro, Mario (HerausgeberIn), Ranganathan, Shoba (HerausgeberIn), Gribskov, Michael (HerausgeberIn), Nakai, Kenta (HerausgeberIn)
Format:	Buch
Sprache:	Englisch
Veröffentlicht:	Amsterdam ; Boston ; Heidelberg Elsevier [2019]
Schlagwörter:	Aufsatzsammlung
Links:	http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030621680&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA
Umfang:	xxi, 1108 Seiten Illustrationen, Diagramme
ISBN:	9780128153642

Internformat

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Datensatz im Suchindex

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adam_text	CONTENTS OF VOLUME 1 Editors in Chief v Volume Editors vii List of Contributors for Volume 1 xvii Preface xxi VOLUME 1 Algorithms Foundations Nadia Pisanti 1 Techniques for Designing Bioinformatics Algorithms Massimo Cafaro, Italo Epicoco, and Marco Pulimeno 5 Algorithms for Strings and Sequences: Searching Motifs Francesco Cauteruccio, Giorgio Terracina, and Domenico Ursino 15 Algorithms for Strings and Sequences: Pairwise Alignment Stefano Beretta 22 Algorithms for Strings and Sequences: Multiple Alignment Pietro H Guzzi 30 Algorithms for Structure Comparison and Analysis: Prediction of Tertiary Structures of Proteins Giuseppe Tradigo, Francesca Rondinelli, and Gianluca Pollastri 32 Algorithms for Structure Comparison and Analysis: Homology Modelling of Proteins Marco Wiltgen 38 Ab initio Protein Structure Prediction Rahul Kaushik, Ankita Singh, and B Jayaram 62 Algorithms for Structure Comparison and Analysis: Docking Giuseppe Tradigo, Francesca Rondinelli, and Gianluca Pollastri 77 Algorithms for Graph and Network Analysis: Graph Indexes/Descriptors Lo Giudice Paolo and Domenico Ursino 81 Algorithms for Graph and Network Analysis: Traversing/Searching/Sampling Graphs Paolo Lo Giudice and Domenico Ursino 89 Algorithms for Graph and Network Analysis: Clustering and Search of Motifs in Graphs Clara Pizzuti and Simona E Rombo 95 Algorithms for Graph and Network Analysis: Graph Alignment Luigi Palopoli and Simona E Rombo 102 Bioinformatics Data Models, Representation and Storage Mariaconcetta Bilotta, Giuseppe Tradigo, and Pierangelo Veltri 110 Data Storage and Representation Antonella Guzzo 117 Experimental Platforms for Extracting Biological Data: Mass Spectrometry, Microarray, Next Generation Sequencing Barbara Calabrese 126 ix x Contents of Volume 1 Standards and Models for Biological Data: Common Formats Barbara Calabrese 130 Standards and Models for Biological Data: FGED and HUPO Barbara Calabrese 137 Standards and Models for Biological Data: SBML Giuseppe Agapito 142 Standards and Models for Biological Data: BioPAX Giuseppe Agapito 147 Models for Computable Phenotyping Alfredo Tirado-Ramos and Laura Manuel 154 Computing for Bioinformatics Mario Cannataro and Giuseppe Agapito 160 Computing Languages for Bioinformatics: Perl Giuseppe Agapito 176 Computing Languages for Bioinformatics: BioPerl Giuseppe Agapitoa 187 Computing Languages for Bioinformatics: Python Pietro H Guzzi 195 Computing Languages for Bioinformatics: R Marianna Milano 199 Computing Languages for Bioinformatics: Java Pietro H Guzzi 206 Parallel Architectures for Bioinformatics Ivan Merelli 209 Models and Languages for High-Performance Computing Domenico Talia 215 MapReduce in Computational Biology Via Hadoop and Spark Giuseppe Cattaneo, Raffaele Giancarlo, Umberto Ferraro Petrillo, and Gianluca Roscigno 221 Infrastructure for High-Performance Computing: Grids and Grid Computing Ivan Merelli 230 Infrastructures for High-Performance Computing: Cloud Computing Paolo Trunfio 236 Infrastructures for High-Performance Computing: Cloud Infrastructures Fabrizio Marozzo 240 Infrastructures for High-Performance Computing: Cloud Computing Development Environments Fabrizio Marozzo and Paolo Trunfio 247 Cloud-Based Bioinformatics Tools Barbara Calabrese 252 Cloud-Based Bioinformatics Platforms Barbara Calabrese 257 Cloud-Based Molecular Modeling Systems Barbara Calabrese 261 The Challenge of Privacy in the Cloud Francesco Buccafurri, Vincenzo De Angelis, Gianluca Lax, Serena Nicolazzo, and Antonino Nocera 265 Contents ot Volume 1 xi Artificial Intelligence and Machine Learning in Bioinformatics Kaitao Lai, Natalie Twine, Aidan O Brien, Yi Guo, and Denis Bauer 272 Artificial Intelligence Francesco Scarcello 287 Knowledge and Reasoning Francesco Ricca and Giorgio Terracina 294 Machine Learning in Bioinformatics Jyotsna T Wassan, Haiying Wang, and Huiru Zheng 300 Intelligent Agents and Environment Alfredo Garro, Max Miihlhauser, Andrea Tundis, Stefano Mariani, Andrea Omicini, and Giuseppe Vizzari 309 Intelligent Agents: Multi-Agent Systems Alfredo Garro, Max Miihlhauser, Andrea Tundis, Matteo Baldoni, Cristina Baroglio, Federico Bergenti, and Paolo Torroni 315 Stochastic Methods for Global Optimization and Problem Solving Giovanni Stracquadanio and Panos M Pardalos 321 Data Mining in Bioinformatics Chiara Zucco 328 Knowledge Discovery in Databases Massimo Guarascio, Giuseppe Manco, and Ettore Ritacco 336 Supervised Learning: Classification Mauro Castelli, Leonardo Vanneschi, and Alvaro Rubio Largo 342 Unsupervised Learning: Clustering Angela Sena and Roberto Tagliaferri 350 Data Mining: Mining Frequent Patterns, Associations Rules, and Correlations Massimo Cafaro, halo Epicoco, and Marco Pulimeno 358 Association Rules and Frequent Patterns Giuseppe Di Fatta 367 Decision Trees and Random Forests Michele Fratello and Roberto Tagliaferri 374 Data Mining: Classification and Prediction Alfonso Urso, Antonino Fiannaca, Massimo La Rosa, Valentina Ravi, and Riccardo Rizzo 384 Bayes Theorem and Naive Bayes Classifier Daniel Benar 403 Data Mining: Prediction Methods Alfonso Urso, Antonino Fiannaca, Massimo La Rosa, Valentina Ravi, and Riccardo Rizzo 413 Data Mining: Accuracy and Error Measures for Classification and Prediction Paola Galdi and Roberto Tagliafeni 431 Data Mining: Clustering Alessia Amelio and Andrea Tagarelli 437 Computation Cluster Validation in the Big Data Era Raffaele Giancarlo and Filippo Utro 449 Data Mining: Outlier Detection Fabrizio Angiulli 456 xii Contents of Volume 1 Pre-Processing: A Data Preparation Step Swamp Roy, Pooja Sharma, Keshab Nath, Dhruba K Bhattacharyya, and Jugal K Kalita 463 Data Cleaning 472 Barbara Calabrese Data Integration and Transformation 477 Barbara Calabrese Data Reduction Barbara Calabrese 480 Dimensionality Reduction Italia De Feis 486 Kernel Machines: Introduction Italo Zoppis, Giancarlo Mauri, and Riccardo Dondi 495 Kernel Methods: Support Vector Machines Italo Zoppis, Giancarlo Mauri, and Riccardo Dondi 503 Kernel Machines: Applications Italo Zoppis, Giancarlo Mauri, and Riccardo Dondi 511 Multiple Learners Combination: Introduction Chiara Zucco 519 Multiple Learners Combination: Bagging Chiara Zucco 525 Multiple Learners Combination: Boosting Chiara Zucco 531 Multiple Learners Combination: Stacking Chiara Zucco 536 Multiple Learners Combination: Cascading Chiara Zucco 539 Cross-Validation Daniel Berrar 542 Performance Measures for Binary Classification Daniel Berrar 546 Natural Language Processing Approaches in Bioinformatics Xu Han and Chee K Kwoh 561 Text Mining Basics in Bioinformatics Carmen De Maio, Giuseppe Fenza, Vincenzo Loia, and Mimmo Parente 575 Data-Information-Concept Continuum From a Text Mining Perspective Danilo Cavaliere, Sabrina Senatore, and Vincenzo Loia 586 Text Mining for Bioinformatics Using Biomedical Literature Andre Lamurias and Francisco M Couto 602 Multilayer Perceptrons Leonardo Vanneschi and Mauro Castelli 612 Delta Rule and Backpropagation Leonardo Vanneschi and Mauro Castelli 621 Deep Learning Massimo Guarascio, Giuseppe Manco, and Ettore Ritacco 634 Contents of Volume 1 xiii Introduction to Biostatistics Antonella luliano and Monica Franzese 648 Descriptive Statistics Monica Franzese and Antonella luliano 672 Measurements of Accuracy in Biostatistics Haiying Wang, Jyotsna T Wassan, and Huiru Zheng 685 Hypothesis Testing Claudia Angelini 691 Statistical Inference Techniques Daniela De Candidis 698 Correlation Analysis Monica Franzese and Antonella luliano 706 Regression Analysis Claudia Angelini 722 Nonlinear Regression Models Audrone Jakaitiene 731 Parametric and Multivariate Methods Luisa Cutillo 738 Stochastic Processes Maria Francesca Carfora 747 Hidden Markov Models Monica Franzese and Antonella luliano 753 Linkage Disequilibrium Barbara Calabrese 763 Introduction to the Non-Parametric Bootstrap Daniel Berrar 766 Population-Based Sampling and Fragment-Based De Novo Protein Structure Prediction David Simoncini and Kam YJ Zhang 774 Ontology: Introduction Gianluigi Greco, Marco Manna, and Francesco Ricca 785 Ontology: Definition Languages Valeria Fionda and Giuseppe Pirrd 790 Ontology: Querying Languages and Development Valeria Fionda and Giuseppe Pirrd 800 Ontology in Bioinformatics Pietro Hiram Guzzi 809 Biological and Medical Ontologies: Introduction Marco Masseroli 813 Biological and Medical Ontologies: GO and GOA Marco Masseroli 823 Biological and Medical Ontologies: Protein Ontology (PRO) Davide Chicco and Marco Masseroli 832 Biological and Medical Ontologies: Disease Ontology (DO) Anna Bemasconi and Marco Masseroli 838 xiv Contents of Volume 1 Biological and Medical Ontologies: Human Phenotype Ontology (HPO) Anna Bernasconi and Marco Masseroli 848 Biological and Medical Ontologies: Systems Biology Ontology (SBO) Anna Bernasconi and Marco Masseroli 858 Ontology-Based Annotation Methods 867 Pietro H Guzzi Semantic Similarity Definition Francisco M Couto and Andre Lamurias 870 Semantic Similarity Functions and Measures Giuseppe Pirn 877 Tools for Semantic Analysis Based on Semantic Similarity Marianna Milano 889 Functional Enrichment Analysis Methods Pietro H Guzzi 896 Gene Prioritization Using Semantic Similarity Erinija Pranckeviciene 898 Gene Prioritization Tools Marianna Milano 907 Networks in Biology Valeria Fionda 915 Graph Theory and Definitions Stefano Beretta, Luca Denti, and Marco Previtali 922 Network Properties Stefano Beretta, Luca Denti, and Marco Previtali 928 Graph Isomorphism Riccardo Dondi, Giancarlo Mauri, and Italo Zoppis 933 Graph Algorithms Riccardo Dondi, Giancarlo Mauri, and Italo Zoppis 940 Network Centralities and Node Ranking Raffaele Giancarlo, Daniele Greco, Francesco Landolina, and Simona E Rombo 950 Network Topology Giuseppe Manco, Ettore Ritacco, and Massimo Guarascio 958 Network Models Massimo Guarascio, Giuseppe Manco, and Ettore Ritacco 968 Community Detection in Biological Networks Marco Pellegrini 978 Protein-Protein Interaction Databases Max Kotlyar, Chiara Pastrello, Andrea EM Rossos, and Igor Jurisica 988 Alignment of Protein-Protein Interaction Networks Swamp Roy, Hazel N Manners, Ahed Elmsallati, and Jugal K Kalita 997 Visualization of Biomedical Networks Anne-Christin Hauschild, Chiara Pastrello, Andrea EM Rossos, and Igor Jurisica 1016 Cluster Analysis of Biological Networks Asuda Sharma, Hesham Ali, and Dario Ghersi 1036 Contents of Volume 1 xv Biological Pathways Giuseppe Agapito 1047 Biological Pathway Data Formats and Standards Ramakanth C Venkata and Dario Ghersi 1063 Biological Pathway Analysis Ramakanth Chirravuri Venkata and Dario Ghersi 1067 Two Decades of Biological Pathway Databases: Results and Challenges Sara Rahmati, Chiara Pastrello, Andrea EM Rossos, and Igor Jurisica 1071 Visualization of Biological Pathways Giuseppe Agapito 1085 Integrative Bioinformatics Marco Masseroli 1092 Integrative Bioinformatics of Transcriptome: Databases, Tools and Pipelines Maria T Di Martino and Pietro H Guzzi 1099 Information Retrieval in Life Sciences Pietro Cinaglia, Domenico Mirarchi, and Pierangelo Veltri 1104
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title	Encyclopedia of bioinformatics and computational biology
title_auth	Encyclopedia of bioinformatics and computational biology
title_exact_search	Encyclopedia of bioinformatics and computational biology
title_full	Encyclopedia of bioinformatics and computational biology Volume 1 Methods editors in chief: Shoba Ranganathan, Macquarie University, Sydney, NSW, Australia, Michael Gribskov, Purdue University, West Lafayette, IN, United States, Kenta Nakai, The University of Tokyo, Tokyo, Japan, Christian Schönbach, Nazarbayev University, School of Science and Technology, Department of Biology, Astana, Kazakhstan
title_fullStr	Encyclopedia of bioinformatics and computational biology Volume 1 Methods editors in chief: Shoba Ranganathan, Macquarie University, Sydney, NSW, Australia, Michael Gribskov, Purdue University, West Lafayette, IN, United States, Kenta Nakai, The University of Tokyo, Tokyo, Japan, Christian Schönbach, Nazarbayev University, School of Science and Technology, Department of Biology, Astana, Kazakhstan
title_full_unstemmed	Encyclopedia of bioinformatics and computational biology Volume 1 Methods editors in chief: Shoba Ranganathan, Macquarie University, Sydney, NSW, Australia, Michael Gribskov, Purdue University, West Lafayette, IN, United States, Kenta Nakai, The University of Tokyo, Tokyo, Japan, Christian Schönbach, Nazarbayev University, School of Science and Technology, Department of Biology, Astana, Kazakhstan
title_short	Encyclopedia of bioinformatics and computational biology
title_sort	encyclopedia of bioinformatics and computational biology methods
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