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About the Contributors 0 About the Contributors Xiao-Li Li is currently a principal investigator at the Data Mining Department, Institute for Infocomm Re- search, A*Star. He also holds an appointment of adjunct assistant professor at the School of Computer Engineering, Nanyang Technological University. Xiao-Li received his PhD degree in computer science from Chinese Academy of Sciences in 2001. He was with National University of Singapore (School of Computing/Singapore-MIT Alli- ance) as a research fellow from 2001 to 2004 before he joined the Institute for Infocomm Research. His research interests include bioinformatics, data mining and machine learning. He has been serving as the members of edi- torial boards or technical program committees in numerous bioinformatics, data mining and machine learning related conferences and journals. In 2005, he received best paper award in the 16th International Conference on Genome Informatics (GIW 2005). In 2008, he received the best poster award in the 12th Annual International Conference Research in Computational Molecular Biology (RECOMB 2008). Dr. Li is also co-editor-in-chief of the International Journal of Knowledge Discovery in Bioinformatics. See-Kiong Ng is currently the department head of the Data Mining Department at Institute for Infocomm Research. He is also an adjunct associate professor at the School of Computer Engineering, Nanyang Techno- logical University. See-Kiong obtained his PhD in computer science from Carnegie Mellon University. When he was a graduate student at CMU, See-Kiong wrote the TrueAllele software which was used by biotech and pharmaceutical companies to fully automate the analysis of data from large-scale genotyping studies. Since then, See-Kiong has continued his journey into the exciting field of genomics as a computer scientist, publishing award-winning papers and serving on the editorial boards or technical program committees in major bioinfor- matics conferences and journals. See-Kiong’s current research focuses on unraveling the underlying functional mechanisms of protein interaction networks as well as other real-world networks. His continuing and emerging diverse and cross-disciplinary research interests include bioinformatics, text mining, social network mining, and privacy-preserving data mining. Dr. Ng is also co-editor-in-chief of the International Journal of Knowledge Discovery in Bioinformatics. * * * Tero Aittokallio received his PhD in applied mathematics from the University of Turku in 2001. He is Research Fellow of the Academy of Finland at the Department of Mathematics, University of Turku, Finland. He has authored more than 50 articles in international peer-reviewed journals. His main research field is model- based analysis of biological systems, with special focus on developing mathematical and statistical data mining approaches to address concrete biomedical problems. Tatsuya Akutsu received BEng and MEng in aeronautics and DEng in information engineering from Uni- versity of Tokyo, 1984, 1986 and 1989, respectively. From 1989 to 1994, he was with Mechanical Engineering Laboratory, Japan. From 1994 to 1996, he was an associate professor in the Department of Computer Science Copyright © 2009, IGI Global, distributing in print or electronic forms without written permission of IGI Global is prohibited. About the Contributors at Gunma University. From 1996 to 2001, he was an associate professor in Human Genome Center, Institute of Medical Science, University of Tokyo. Since 2001, he has been a professor in Bioinformatics Center, Institute for Chemical Research, Kyoto University. His research interests include bioinformatics and the design and analysis of algorithms. Doina Caragea is an assistant professor at Kansas State University. Her research interests include artificial intelligence, machine learning, data mining, information integration and information visualization, with applica- tions to bioinformatics. Doina received her PhD in computer science from Iowa State University in August 2004 and was honored with the Iowa State University Research Excellence Award for her work. She has published more than 20 refereed conference and journal articles and contributed to the design and implementation of INDUS (an open source system for Intelligent Data Understanding). Doina is teaching machine learning, data mining and bioinformatics courses. Hon Nian Chua is a research engineer at the Data Mining Department of the Institute for Infocomm Research, A*STAR. He obtained his PhD degree in bioinformatics from the National University of Singapore in 2008, under the support of the A*STAR Graduate Scholarship. His current research interest is in the application of machine learning and graph-based techniques in biological and medical research. Joaquin Dopazo is the head of the Department of Bioinformatics and Genomics at the CIPF (Valencia). In previous appointments he was responsible of Bioinformatics units at the CNIO (Madrid) and at GlaxoWellcome SA (Madrid). He has supervised several large scale projects of software development, as the GEPAS (http://www. gepas.org) or the Babelomics (http://www.Babelomics.org) where more than 1000 microarray experiments are daily analysed. J. Dopazo has a master degree in chemistry (Universidad de Valencia) and a PhD in biology (Uni- versidad de Valencia). He has more than one hundred papers published in international peer reviewed journals and has edited a book on genomic data analysis. His main interests include functional and comparative genomics. Valeria Fionda is currently attending the second year of the “Dottorato in Matematica e Informatica” (Doc- torate in Mathematics and Computer Science) at the Department of Mathematics, Università della Calabria. Her research interests include issues related to bioinformatics, computational biology and graph matching. Sirisha Gollapudi is a PhD student at the University of Nottingham, within the Multidisciplinary Centre for Integrative Biology (MyCIB). She obtained a BSc in computer science from the University of Nottingham, and a postgraduate certificate in bioinformatics from the University of Manchester. Her PhD research focuses on the use of web service technology to expose software for the analysis of biological networks, including holistic models of metabolism and protein-protein interactions. Her main research interest is the combination of such web services into scientific workflows to automate analyses and query heterogeneous data resources. Morihiro Hayashida received BSci and MSci in information science from University of Tokyo, 2000 and 2002, and DInf in informatics from Kyoto University, 2005. Since 2005, he has been an assistant professor in Bioinformatics Center, Institute for Chemical Research, Kyoto University. His research interests include issues related to protein function prediction and bioinformatics. Charlie Hodgman dates his first bioinformatics project to 1980. During the 1980s and 90s, he acquired an international reputation for elucidating biomolecular function using informatics approaches. Since the mid-90s, his attention has turned to interaction networks and dynamic modelling of multi-scale systems. His research career began in ICI Ltd (UK) in the 1970s. Following fifteen years in Cambridge and nine in GlaxoSmithKline, he is now Professor of Bioinformatics and Systems Biology and director of the Multidisciplinary Centre for 0 About the Contributors Integrative Biology in the University of Nottingham (UK). He was also an associate editor of Bioinformatics from 2000 to 2006. William H. Hsu is an associate professor in the Department of Computing and Information Sciences at Kansas State University. He received a BS in mathematical sciences and computer science and an MSEng in computer science from Johns Hopkins University in 1993, and a PhD in computer science from the University of Illinois at Urbana-Champaign in 1998. His research interests include machine learning and probabilistic reasoning, with applications to information extraction, time series prediction, link mining, and bioinformatics (especially computational genomics and proteomics). Lilia M. Iakoucheva is a research assistant professor at the Rockefeller University in New York, NY, USA. She holds a PhD degree in molecular biology and immunology, which she received in Moscow, Russia. Her research interests are focused on understanding how alterations in protein structure, function and interactions contribute to human disease. Dr. Iakoucheva is interested in investigating this question from two different levels, molecular and systems biology. She uses both computational and experimental approaches to investigate these questions. Another aspect of her scientific interests includes investigation of functional properties of intrinsically disordered proteins. Dr. Iakoucheva’s research was published in a number of high-impact journals including Bioinformatics, PLoS Computational Biology, Nucleic Acids Research, Journal of Molecular Biology, Protein Science, Journal of Proteome Research, and Biochemistry. Her research was supported by the National Science Foundation (NSF) and the National Institutes of Health (NIH). Daisuke Kihara PhD is an assistant professor in the Departments of Biological Sciences and Computer Science at Purdue University. He received his PhD degree from Kyoto University in 1999. His research projects include protein function and structure prediction and protein surface shape searching for function prediction and docking. His research projects are funded by the National Institutes
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