About the Contributors

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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 editorial 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 bioinformatics 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.

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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

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 applications 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

402 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 of Health and the National Science Founda- tion of the USA.

David La is a PhD candidate in the Department of Biological Sciences at Purdue University. Prior to start- ing his graduate studies at Purdue University, he received his MS degree from the California State Polytechnic University at Pomona where his thesis work involved the computational prediction of protein functional sites and their application at a proteome-scale. Currently, his research is focused on gaining greater insight to the evolution and prediction of protein-protein binding regions.

Takashi Makino is the research fellow in the Genetics Department at Trinity College Dublin. His research focuses on evolution of protein interaction networks and comparative genomics of vertebrates. He studied molecular evolution under his supervisor who is prof. Takashi Gojobori in National institute of genetics, Mishima, Japan. His work has been published in international journals including PLoS Biology, Molecular Biology and Evolution, Nucleic Acids Research and GENE.

Hiroshi Mamitsuka received the BS in biochemistry and biophysics, the ME in information engineering and the PhD in information sciences from the University of Tokyo in Japan, in 1988, 1991 and 1999, respectively. He worked with NEC Corporation in Japan on developing machine learning and data mining techniques and their applications to problems in industry and the sciences for eleven years since 1991. He joined the Institute for Chemical Research (ICR) of Kyoto University in 2002, focusing on research matters in molecular biology. Currently he is a professor of ICR, being jointly appointed as a faculty of the School of Pharmaceutical Sciences of the same university. His present research interests include bioinformatics, data mining, machine learning and information retrieval.

403 About the Contributors

After graduating in 2003 at the “Sapienza” University of Rome in Control Engineering, Paolo Marcatili directed his interest to the study of system level description and modeling of biological data, with a specific focus on protein-protein interaction in immunology and pathology. Currently he is working for his PhD at the “Sapienza” University under the supervision of Anna Tramontano.

Alex Marshall is a systems biologist with a biology background, specialising in bioinformatics and network biology in plants. Alex recently gained an MSc in bioinformatics at Cranfield University (UK) and that has sparked her interest in systems-based research. Currently, Alex is studying a PhD in plant cross-species transcriptomics and systems biology at the Multidisciplinary Centre for Integrative Biology at the University of Nottingham (UK).

Aoife McLysaght is the principal investigator of the Molecular Evolution research group in the Genetics Department at Trinity College Dublin. Her research focuses on comparative genomics of vertebrates and virus genome evolution. Dr. McLysaght is an associate editor for the Journal of Molecular Biology and Evolution, the leading specialist journal in her field. Her work has been published in major international journals including Nature, Nature Genetics, and the Proceedings of the National Academy of Sciences, USA and Trends in Genetics. In 2005 she was awarded a prestigious President of Ireland Young Researcher Award by Science Foundation Ireland.

Pablo Minguez is a PhD student at the Bioinformatics Department of the Centro de Investigación Principe Felipe, Valencia, Spain. He has been working in functional genomics since 2004 developing methodologies for the functional profiling of genome-scale experiments augmenting the discovery possibilities of the field by in- troducing new sources of annotation such as bioentities associated to genes by co-occurrences in the scientific literature, phenotype specific expression levels and protein-protein interactions. He is the developer of several modules in the Babelomics suite for functional profiling of genome-scale experiments including SNOW, a program to infer functional modules from transcriptomic and protein-protein interaction data and a method to evaluate its significance in cellular processes.

Smita Mohanty is currently pursuing her PhD in the field of computational biology from Molecular Biophysics Unit of the Indian Institute of Science, Bangalore. Her research focuses on understanding protein-protein interactions at the level of domain families and applying this knowledge into effective prediction of protein-protein interactions. The major thrust of her work is in understanding the biology of the malarial parasite P.falciparum, especially focusing on the role of protein-protein interactions in the parasite’s life-cycle.

Luigi Palopoli is a professor of computer science at DEIS of Università della Calabria, where he chairs the School of Computer Engineering, and research associate with ICAR-CNR. He was a visiting scholar at UCLA (Los Angeles, USA), AT&T Laboratories (Murray Hills, USA), Oxford University (Oxford, UK) and Technical University of Wien (Wien, Austria). His research interests are in the areas of information systems and databases, artificial intelligence, game theory and bioinformatics. He authored about 150 papers appearing in refereed journals and conference proceedings. He serves in the editorial board of AI Communications – The European J. on AI , and in several conference program committees.

Shashi Bhushan Pandit completed his PhD at the Indian Institute of Science Bangalore. During his Ph.D, he worked on sequence analysis of proteins with emphasis on the function prediction at the genomic scale. After his Ph.D he joined the research group of Dr. Skolnick at Center of Excellence in Bioinformatics, Buffalo, USA to pursue his research in the field of protein tertiary structure prediction. Presently, he is working at Georgia Institute of Technology, Atlanta, USA. His current research focuses on the development of tools for the protein tertiary and quaternary structure modeling and its application at the genomic scale.

404 About the Contributors

Martin S.R. Paradesi graduated with a master’s degree in computer science from Kansas State University in 2008. Prior to that, he obtained a bachelor’s degree in computer science and engineering from Jawaharlal Nehru Technological University in 2005. His research interests include bioinformatics, machine learning, artificial intelligence and data mining. This book chapter is a partial result of his Master’s thesis that investigated the effect of accuracy and other statistical metrics caused by the use of graph features in predicting protein interactions.

Clara Pizzuti received the Laurea degree in Mathematics from the University of Calabria, Italy. She is a senior researcher at the Institute of High Performance Computing and Networking (ICAR) of the Italian National Research Council (CNR). Since 1995 she is also a contract professor in the department of Computer Science at the University of Calabria. In the past, she worked in the research division of a software company on deductive databases, advanced logic based systems, and abduction. She has published more than seventy papers in conference proceedings and journals. Her research interests include knowledge discovery in databases, data mining, bioinformatics, evolutionary computation, genetic algorithms, and genetic programming. She is serving as program committee member of international conferences, and as reviewer for several international journals.

Simona Ester Rombo received the Laurea degree in electronic engeneering and the PhD in computer science from the University “Mediterranea”of Reggio Calabria, Italy. She is a post-doc fellow at DEIS, Università della Calabria. Since 2006 she is also a contract professor at the University of Calabria. Her research interests data mining, bioinformatics, combinatorial algorithms. She is serving as program committee member of international conferences, and as reviewer for international journals.

Christian Schönbach’s research expertise lies in computational and functional genomics. Currently, he is an associate professor at Division of Genomics and Genetics, School of Biological of Biological Sciences, Nanyang Technological University (Singapore). Previous positions included team leader at RIKEN Genomic Sciences Center (Japan), principal investigator at Kent Ridge Digital Labs (Singapore), and research scientist at Chugai Research Institute for Molecular Medicine, Inc. (Japan). He obtained his doctor degree from Eberhard Karls University Tübingen (Germany) through immunogenetics research at Max-Planck Institute for Biology, and did his post-doctoral training in experimental and computational immunology at The University of Tokyo.

Narayanaswamy Srinivasan obtained his PhD at the Indian Institute of Science and had three postdoctoral stints in the UK: Birkbeck College, London, Ludwig Institute for Cancer Research, London and Department of Biochemistry, University of Cambridge. He is currently leading a research team working on protein structure, function and interactions at the Molecular Biophysics Unit, Indian Institute of Science. He is in the editorial boards of a few journals including Bioinformatics. He is a visiting professor at the Reunion university, France, senior fellow of the Manchester University, UK and a fellow of two of the Academies of Sciences in India.

Kar Leong Tew graduated from University of Exeter with a bachelor in computer science (Hons) in 2005. He is current working as a research officer in the Data Mining Department at Institute for Infocomm Research (I2R) which is one of the research institute under Agency for Science, Technology and Research (A*Star). His current research works involves networking mining, data mining, bioinformatics, and social networks.

Anna Tramontano graduated in physics at the University of Naples, Italy. She was a post-doc at UCSF and a staff scientist in the Biocomputing programme of the EMBL in Heidelberg. In 1990, she went back to Italy to work at the Merck Research Laboratories near Rome. In 2001, she returned to academia as Chair Professor of Biochemistry at the “Sapienza” University where she works on protein structure prediction and analysis. She is a member of the European Molecular Biology Organization, the Scientific Council of Institute Pasteur-Fondazione Cenci Bolognetti, and of the organizing committee of the Critical Assessment of Techniques for Protein Structure

405 About the Contributors

Prediction (CASP) initiative. She is also the director of the Bioinformatics Center of CRS4 in Pula, Sardinia and of a Master program in bioinformatics.

Koji Tsuda is project leader at Max Planck Institute for Biological Cybernetics, Tuebingen, Germany. In 2001-2002 and 2005, he worked as a research scientist in AIST Computational Biology Research Center, Tokyo, Japan. In 2000-2001, he was a visiting scholar at GMD FIRST, Berlin, Germany. He received doctor of engineering degree from Kyoto University in 1998. His scientific interests are in the fields of machine learning, data mining and bioinformatics.

Raymond Wan received the BSc degree in computer science from the University of British Columbia, Canada, in 1997 and the PhD degree from the University of Melbourne, Australia, in 2004. His doctoral dissertation, “Browsing and Searching Compressed Documents”, describes a method for browsing the phrases of a compressed document collection through minimal decompression. Since graduation, he has been a post-doctoral fellow in bioinformatics at Kyoto University, Japan, working on microarray analysis and text retrieval from biomedical texts. His current research interests include bioinformatics, graph theory, machine learning, information retrieval, and text compression.

Hugo Willy received his bachelor of computing degree from the National University of Singapore (NUS), in 2003. He is currently pursuing his study as a PhD candidate under the joint research programme between the School of Computing, National University of Singapore and the Institute of Infocomm Research, Singapore. His early research was on the structure-templated RNA secondary structure inference by arc-annotated sequence model. Currently, he is working on mining sequence and structural motifs implicated in Protein-Protein Interaction.

Limsoon Wong is a professor in the School of Computing and the School of Medicine at the National Uni- versity of Singapore. He is currently working mostly on knowledge discovery technologies and is especially interested in their application to biomedicine. He serves on the editorial boards of Journal of Bioinformatics and Computational Biology (ICP), Bioinformatics (OUP), and Drug Discovery Today (Elsevier).

After completing a BSc in applied biology at the University of Bath and an MSc in bioinformatics at Shef- field Hallam University,Daniel Zadik is working towards completing a PhD at the Multidisciplinary Centre for Integrative Biology (MyCIB) at the University of Nottingham. His PhD involves the construction of a network model of dog metabolism and its control mechanisms, with the aim of better understanding the relationships between genetics, nutrition and health, and elucidating the specific dietary requirements of dog breeds. In the past, he has worked as a laboratory scientist at University College London, and a bioinformatician at the Uni- versity of Nottingham.

Michael Q. Zhang is professor and the director of the Bioinformatics Core of Cancer Center at CSHL. He is also an adjunct professor at Stony Brook University and a Chang Jiang Chair (Guest) Professor at Tsinghua University. He holds degrees in mechanical engineering (BS), and physics (PhD). Michael has co-edited, Cur- rent Topics in Computational Molecular Biology. Michael has published his research in a number of high-impact journals including Cell, Nat. Genet.s, Nat. Cell Biol., Gene & Dev., Mol. Sys.. Biol., PNAS, Genome Res., TIG, PLoS Comp. Biol., Nucl. Acid. Res. and Bioinformatics. associate editor of the BMC journals, and editor for Bio- informatics, J Bioinfo. Comp. Biol., Systems and Synthetic Biol., Comparative and Func. Genomics. His research interests include computational biology and bioinformatics.

406 About the Contributors

Xiaoyue Zhao is research scientist at Bionovo Inc., located in Emeryville, CA, USA. She received PhD degree in statistics from the University of California, Berkeley and did postdoc training at Cold Spring Harbor Laboratory. Her research interests include developing and applying statistical methods for understanding biology and human diseases, specifically related to women’s health and neurological disorders. She focuses on addressing statistical challenges from high-throughput genomic data, such as protein-protein interaction, microarray and sequencing data. Dr. Zhao’s research was published in a number of high-impact journals including Proceedings of National Academy of Sciences, Genome Biology, Journal of Computational Biology, Annals of the Institute of Statistical Mathematics, Molecular Endocrinology, and Endocrinology. She also contributed in the book Bioinformatics for Geneticists: A Bioinformatics Primer for the Analysis of Genetic Data

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