Biological Knowledge Discovery Handbook
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"This book is a unique resource for practitioners and researchers in computer science, life science, and mathematics." (Zentralblatt MATH, 1 June 2015)More details
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PREFACE xiii
CONTRIBUTORS xv
SECTION I BIOLOGICAL DATA PREPROCESSING
PART A: BIOLOGICAL DATA MANAGEMENT
1 GENOME AND TRANSCRIPTOME SEQUENCE DATABASES FOR DISCOVERY, STORAGE, AND REPRESENTATION OF ALTERNATIVE SPLICING EVENTS 5
Bahar Taneri and Terry Gaasterland
2 CLEANING, INTEGRATING, AND WAREHOUSING GENOMIC DATA FROM BIOMEDICAL RESOURCES 35
Fouzia Moussouni and Laure Berti-Equille
3 CLEANSING OF MASS SPECTROMETRY DATA FOR PROTEIN IDENTIFICATION AND QUANTIFICATION 59
Penghao Wang and Albert Y. Zomaya
4 FILTERING PROTEIN-PROTEIN INTERACTIONS BY INTEGRATION OF ONTOLOGY DATA 77
Young-Rae Cho
PART B: BIOLOGICAL DATA MODELING
5 COMPLEXITY AND SYMMETRIES IN DNA SEQUENCES 95
Carlo Cattani
6 ONTOLOGY-DRIVEN FORMAL CONCEPTUAL DATA MODELING FOR BIOLOGICAL DATA ANALYSIS 129
Catharina Maria Keet
7 BIOLOGICAL DATA INTEGRATION USING NETWORK MODELS 155
Gaurav Kumar and Shoba Ranganathan
8 NETWORK MODELING OF STATISTICAL EPISTASIS 175
Ting Hu and Jason H. Moore
9 GRAPHICAL MODELS FOR PROTEIN FUNCTION AND STRUCTURE PREDICTION 191
Mingjie Tang, Kean Ming Tan, Xin Lu Tan, Lee Sael, Meghana Chitale, Juan Esquivel-Rodrýguez, and Daisuke Kihara
PART C: BIOLOGICAL FEATURE EXTRACTION
10 ALGORITHMS AND DATA STRUCTURES FOR NEXT-GENERATION SEQUENCES 225
Francesco Vezzi, Giuseppe Lancia, and Alberto Policriti
11 ALGORITHMS FOR NEXT-GENERATION SEQUENCING DATA 251
Costas S. Iliopoulos and Solon P. Pissis
12 GENE REGULATORY NETWORK IDENTIFICATION WITH QUALITATIVE PROBABILISTIC NETWORKS 281
Zina M. Ibrahim, Alioune Ngom, and Ahmed Y. Tawfik
PART D: BIOLOGICAL FEATURE SELECTION
13 COMPARING, RANKING, AND FILTERING MOTIFS WITH
CHARACTER CLASSES: APPLICATION TO BIOLOGICAL SEQUENCES ANALYSIS 309
Matteo Comin and Davide Verzotto
14 STABILITY OF FEATURE SELECTION ALGORITHMS AND ENSEMBLE FEATURE SELECTION METHODS IN
BIOINFORMATICS 333
Pengyi Yang, Bing B. Zhou, Jean Yee-Hwa Yang, and Albert Y. Zomaya
15 STATISTICAL SIGNIFICANCE ASSESSMENT FOR BIOLOGICAL FEATURE SELECTION: METHODS AND ISSUES 353
Juntao Li, Kwok Pui Choi, Yudi Pawitan, and Radha Krishna Murthy Karuturi
16 SURVEY OF NOVEL FEATURE SELECTION METHODS FOR CANCER CLASSIFICATION 379
Oleg Okun
17 INFORMATION-THEORETIC GENE SELECTION IN EXPRESSION DATA 399
Patrick E. Meyer and Gianluca Bontempi
18 FEATURE SELECTION AND CLASSIFICATION FOR GENE EXPRESSION DATA USING EVOLUTIONARY COMPUTATION 421
Haider Banka, Suresh Dara, and Mourad Elloumi
SECTION II BIOLOGICAL DATA MINING
PART E: REGRESSION ANALYSIS OF BIOLOGICAL DATA
19 BUILDING VALID REGRESSION MODELS FOR BIOLOGICAL DATA USING STATA AND R 445
Charles Lindsey and Simon J. Sheather
20 LOGISTIC REGRESSION IN GENOMEWIDE ASSOCIATION ANALYSIS 477
Wentian Li and Yaning Yang
21 SEMIPARAMETRIC REGRESSION METHODS IN LONGITUDINAL DATA: APPLICATIONS TO AIDS CLINICAL TRIAL DATA 501
Yehua Li
PART F: BIOLOGICAL DATA CLUSTERING
22 THE THREE STEPS OF CLUSTERING IN THE POST-GENOMIC ERA 521
Raffaele Giancarlo, Giosüe Lo Bosco, Luca Pinello, and Filippo Utro
23 CLUSTERING ALGORITHMS OF MICROARRAY DATA 557
Haifa Ben Saber, Mourad Elloumi, and Mohamed Nadif
24 SPREAD OF EVALUATION MEASURES FOR MICROARRAY CLUSTERING 569
Giulia Bruno and Alessandro Fiori
25 SURVEY ON BICLUSTERING OF GENE EXPRESSION DATA 591
Adelaide Valente Freitas, Wassim Ayadi, Mourad Elloumi, Jose Luis Oliveira, and Jin-Kao Hao
26 MULTIOBJECTIVE BICLUSTERING OF GENE EXPRESSION DATA WITH BIOINSPIRED ALGORITHMS 609
Khedidja Seridi, Laetitia Jourdan, and El-Ghazali Talbi
27 COCLUSTERING UNDER GENE ONTOLOGY DERIVED CONSTRAINTS FOR PATHWAY IDENTIFICATION 625
Alessia Visconti, Francesca Cordero, Dino Ienco, and Ruggero G. Pensa
PART G: BIOLOGICAL DATA CLASSIFICATION
28 SURVEY ON FINGERPRINT CLASSIFICATION METHODS FOR BIOLOGICAL SEQUENCES 645
Bhaskar DasGupta and Lakshmi Kaligounder
29 MICROARRAY DATA ANALYSIS: FROM PREPARATION TO CLASSIFICATION 657
Luciano Cascione, Alfredo Ferro, Rosalba Giugno, Giuseppe Pigola, and Alfredo Pulvirenti
30 DIVERSIFIED CLASSIFIER FUSION TECHNIQUE FOR GENE EXPRESSION DATA 675
Sashikala Mishra, Kailash Shaw, and Debahuti Mishra
31 RNA CLASSIFICATION AND STRUCTURE PREDICTION: ALGORITHMS AND CASE STUDIES 685
Ling Zhong, Junilda Spirollari, Jason T. L. Wang, and Dongrong Wen
32 AB INITIO PROTEIN STRUCTURE PREDICTION: METHODS AND CHALLENGES 703
Jad Abbass, Jean-Christophe Nebel, and Nashat Mansour
33 OVERVIEW OF CLASSIFICATION METHODS TO
SUPPORT HIV/AIDS CLINICAL DECISION MAKING 725
Khairul A. Kasmiran, Ali Al Mazari, Albert Y. Zomaya, and Roger J. Garsia
PART H: ASSOCIATION RULES LEARNING FROM BIOLOGICAL DATA
34 MINING FREQUENT PATTERNS AND ASSOCIATION RULES FROM BIOLOGICAL DATA 737
Ioannis Kavakiotis, George Tzanis, and Ioannis Vlahavas
35 GALOIS CLOSURE BASED ASSOCIATION RULE MINING FROM BIOLOGICAL DATA 761
Kartick Chandra Mondal and Nicolas Pasquier
36 INFERENCE OF GENE REGULATORY NETWORKS BASED ON ASSOCIATION RULES 803
Cristian Andres Gallo, Jessica Andrea Carballido, and Ignacio Ponzoni
PART I: TEXT MINING AND APPLICATION TO BIOLOGICAL DATA
37 CURRENT METHODOLOGIES FOR BIOMEDICAL NAMED ENTITY RECOGNITION 841
David Campos, Sergio Matos, and José Luýs Oliveira
38 AUTOMATED ANNOTATION OF SCIENTIFIC DOCUMENTS: INCREASING ACCESS TO BIOLOGICAL KNOWLEDGE 869
Evangelos Pafilis, Heiko Horn, and Nigel P. Brown
39 AUGMENTING BIOLOGICAL TEXT MINING WITH SYMBOLIC INFERENCE 901
Jong C. Park and Hee-Jin Lee
40 WEB CONTENT MINING FOR LEARNING GENERIC RELATIONS AND THEIR ASSOCIATIONS FROM TEXTUAL BIOLOGICAL DATA 919
Muhammad Abulaish and Jahiruddin
41 PROTEIN-PROTEIN RELATION EXTRACTION FROM BIOMEDICAL ABSTRACTS 943
Syed Toufeeq Ahmed, Hasan Davulcu, Sukru Tikves, Radhika Nair, and Chintan Patel
PART J: HIGH-PERFORMANCE COMPUTING FOR BIOLOGICAL DATA MINING
42 ACCELERATING PAIRWISE ALIGNMENT ALGORITHMS BY USING GRAPHICS PROCESSOR UNITS 971
Mourad Elloumi, Mohamed Al Sayed Issa, and Ahmed Mokaddem
43 HIGH-PERFORMANCE COMPUTING IN HIGH-THROUGHPUT SEQUENCING 981
Kamer Kaya, Ayat Hatem, Hatice Gulcin Ozer, Kun Huang, and Umit V. Catalyurek
44 LARGE-SCALE CLUSTERING OF SHORT READS FOR METAGENOMICS ON GPUs 1003
Thuy Diem Nguyen, Bertil Schmidt, Zejun Zheng, and Chee Keong Kwoh
SECTION III BIOLOGICAL DATA POSTPROCESSING
PART K: BIOLOGICAL KNOWLEDGE INTEGRATION AND VISUALIZATION
45 INTEGRATION OF METABOLIC KNOWLEDGE FOR GENOME-SCALE METABOLIC RECONSTRUCTION 1027
Ali Masoudi-Nejad, Ali Salehzadeh-Yazdi, Shiva Akbari-Birgani, and Yazdan Asgari
46 INFERRING AND POSTPROCESSING HUGE PHYLOGENIES 1049
Stephen A. Smith and Alexandros Stamatakis
47 BIOLOGICAL KNOWLEDGE VISUALIZATION 1073
Rodrigo Santamarýa
48 VISUALIZATION OF BIOLOGICAL KNOWLEDGE BASED ON MULTIMODAL BIOLOGICAL DATA 1109
Hendrik Rohn and Falk Schreiber
INDEX 1127
Contributors
Jad Abbass, Faculty of Science, Engineering and Computing, Kingston University, London, United Kingdom and Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon
Muhammad Abulaish, Center of Excellence in Information Assurance, King Saud University, Riyadh, Saudi Arabia and Department of Computer Science, Jamia Millia Islamia (A Central University), New Delhi, India
Syed Toufeeq Ahmed, Vanderbilt University Medical Center, Nashville, Tennessee
Shiva Akbari-Birgani, Laboratory of Systems Biology and Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
Ali Al Mazari, School of Information Technologies, The University of Sydney, Sydney, Australia
Mohamed Al Sayed Issa, Computers and Systems Department, Faculty of Engineering, Zagazig University, Egypt
Yazdan Asgari, Laboratory of Systems Biology and Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
Wassim Ayadi, Laboratory of Technologies of Information and Communication and Electrical Engineering (LaTICE) and LERIA, University of Angers, Angers, France
Haider Banka, Department of Computer Science and Engineering, Indian School of Mines, Dhanbad, India
Laure Berti-Équille, Institut de Recherche pour le DÉveloppement, Montpellier, France
Gianluca Bontempi, Machine Learning Group, Computer Science Department, UniversitÉ Libre de Bruxelles, Brussels, Belgium
Nigel P. Brown, BioQuant, University of Heidelberg, Heidelberg, Germany
Giulia Bruno, Dipartimento di Ingegneria Gestionale e della Produzione, Politecnico di Torino, Torino, Italy
David Campos, DETI/IEETA, University of Aveiro, Aveiro, Portugal xv
Jessica Andrea Carballido, Laboratorio de Investigación y Desarrollo en Computación Científica (LIDeCC), Dept. Computer Science and Engineering, Universidad Nacional del Sur, Bahía Blanca, Argentina
Luciano Cascione, Department of Clinical and Molecular Biomedicine, University of Catania, Italy
Ümit V. ÇatalyÜrek, Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
Carlo Cattani, Department of Mathematics, University of Salerno, Fisciano (SA), Italy
Meghana Chitale, Department of Computer Science, Purdue University, West Lafayette, Indiana
Young-Rae Cho, Department of Computer Science, Baylor University, Waco, Texas
Kwok Pui Choi, Department of Statistics and Applied Probability, National University of Singapore, Singapore
Matteo Comin, Department of Information Engineering, University of Padova, Padova, Italy
Francesca Cordero, Department of Computer Science, University of Torino, Turin, Italy
Suresh Dara, Department of Computer Science and Engineering, Indian School of Mines, Dhanbad, India
Bhaskar DasGupta, Department of Computer Science, University of Illinois at Chicago, Chicago, Illinois
Hasan Davulcu, Department of Computer Science and Engineering, Ira A. Fulton Engineering, Arizona State University, Tempe, Arizona
Mourad Elloumi, Laboratory of Technologies of Information and Communication and Electrical Engineering (LaTICE) and University of Tunis-El Manar, Tunisia
Juan Esquivel-Rodríguez, Department of Computer Science, Purdue University, West Lafayette, Indiana
Alfredo Ferro, Department of Clinical and Molecular Biomedicine, University of Catania, Italy
Alessandro Fiori, Dipartimento di Automatica e Informatica, Politecnico di Torino, Torino, Italy
Adelaide Valente Freitas, DMat/CIDMA, University of Aveiro, Portugal
Terry Gaasterland, Scripps Genome Center, University of California San Diego, San Diego, California
Cristian AndrÉs Gallo, Laboratorio de Investigación y Desarrollo en Computación Científica (LIDeCC), Dept. Computer Science and Engineering, Universidad Nacional del Sur, Bahía Blanca, Argentina
Roger J. Garsia, Department of Clinical Immunology, Royal Prince Alfred Hospital, Sydney, Australia
Raffaele Giancarlo, Department of Mathematics and Informatics, University of Palermo, Palermo, Italy
Rosalba Giugno, Department of Clinical and Molecular Biomedicine, University of Catania, Italy
Jin-Kao Hao, LERIA, University of Angers, Angers, France
Ayat Hatem, Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
Heiko Horn, Department of Disease Systems Biology, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
Ting Hu, Computational Genetics Laboratory, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire
Kun Huang, Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
Zina M. Ibrahim, Social Genetic and Developmental Psychiatry Centre, King's College London, London, United Kingdom
Dino Ienco, Institut de Recherche en Sciences et Technologies pour l'Environnement, Montpellier, France
Costas S. Iliopoulos, Department of Informatics, King's College London, Strand, London, United Kingdom and Digital Ecosystems & Business Intelligence Institute, Curtin University, Centre for Stringology & Applications, Perth, Australia
Jahiruddin, Department of Computer Science, Jamia Millia Islamia (A Central University), New Delhi, India
Laetitia Jourdan, INRIA Lille Nord Europe, Villeneuve d'Ascq, France
Lakshmi Kaligounder, Department of Computer Science, University of Illinois at Chicago, Chicago, Illinois
Radha Krishna Murthy Karuturi, Computational and Mathematical Biology, Genome Institute of Singapore, Singapore
Khairul A. Kasmiran, School of Information Technologies, The University of Sydney, Sydney, Australia
Ioannis Kavakiotis, Department of Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece
Kamer Kaya, Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
Catharina Maria Keet, School of Computer Science, University of KwaZulu-Natal, Durban, South Africa
Daisuke Kihara, Department of Computer Science, Purdue University, West Lafayette, Indiana and Department of Biological Sciences, Purdue University, West Lafayette, Indiana
Gaurav Kumar, Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, Australia
Chee Keong Kwoh, School of Computer Engineering, Nanyang Technological University, Singapore
Giuseppe Lancia, Department of Mathematics and Informatics, University of Udine, Udine, Italy
Hee-Jin Lee, Department of Computer Science, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
Juntao Li, Computational and Mathematical Biology, Genome Institute of Singapore, Singapore and Department of Statistics and Applied Probability, National University of Singapore, Singapore
Wentian Li, Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore LIJ Health Systems, Manhasset, New York
Yehua Li, Department of Statistics and Statistical Laboratory, Iowa State University, Ames, Iowa
Charles Lindsey, StataCorp, College Station, Texas
GiosuÉ Lo Bosco, Department of Mathematics and Informatics, University of Palermo, Palermo, Italy and I.E.ME.S.T., Istituto Euro Mediterraneo di Scienza e Tecnologia, Palermo, Italy
Nashat Mansour, Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon
Ali Masoudi-Nejad, Laboratory of Systems Biology and Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
SÉrgio Matos, DETI/IEETA, University of Aveiro, Aveiro, Portugal
Patrick E. Meyer, Machine Learning Group, Computer Science Department, UniversitÉ Libre de Bruxelles, Brussels, Belgium
Debahuti Mishra, Institute of Technical Education and Research, Siksha O Anusandhan University, Bhubaneswar, Odisha, India
Sashikala Mishra, Institute of Technical Education and Research, Siksha O Anusandhan University, Bhubaneswar, Odisha, India
Ahmed Mokaddem, Laboratory of Technologies of Information and Communication and Electrical Engineering (LaTICE) and University of Tunis-El Manar, El Manar, Tunisia
Kartick Chandra Mondal, Laboratory I3S, University of Nice Sophia-Antipolis, Sophia-Antipolis, France
Jason H. Moore, Computational Genetics Laboratory, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire
Fouzia Moussouni, UniversitÉ de Rennes 1, Rennes, France
Mohamed Nadif, LIPADE, University of Paris-Descartes, Paris, France
Radhika Nair, Department of Computer Science and Engineering, Ira A. Fulton Engineering, Arizona State University, Tempe, Arizona
Jean-Christophe Nebel, Faculty of Science, Engineering and Computing, Kingston University, London, United Kingdom
Alioune Ngom, School of Computer Science, University of Windsor, Windsor, Ontario, Canada
Thuy Diem...
