Euna Jeong. Curriculum Vitae

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1 Euna Jeong Curriculum Vitae Institute of Medical Science University of Tokyo Shirokanedai, Minato-ku, Tokyo JAPAN Phone: Fax: Research Interests Ontology design and validation for biological pathways Biological pathway modeling and simulation Protein-RNA interaction Education Ph.D. in Computer Science Dissertation: Ontology Integration in XML M.Sc. in Computer Science Thesis: A Gateway for Mediating Databases and the WWW B.Sc. in Science Department of Biology Education, Seoul National University, Korea Research Experience Postdoctoral Researcher (April 2003 present) DNA Information Analysis Lab, Institute of Medical Science, University of Tokyo, Japan Research Intern of Korean Science and Engineering Foundation (March 2002 March 2003) Biocomputing Lab, School of Computer Science and Engineering, Inha University, Korea Research Assistant (September 1999 January 2002) Adaptive Intelligent Internet Agents Lab, Institute of Information Science, Academia Sinica, Taiwan Publications Refereed Journal Papers [1] Euna Jeong, Masao Nagasaki, and Satoru Miyano, Rule-based reasoning for systems dynamics in cell systems, Genome Informatics (in press), 2008 [2] Masao Nagasaki, Ayumu Saito, Chen Li, Euna Jeong and Satoru Miyano, Systematic reconstruction of TRANSPATH data into Cell System Markup Language, BMC Systems Biology, 2:53, 2008 [3] Euna Jeong, Masao Nagasaki, Ayumu Saito, and Satoru Miyano, Cell System Ontology: representation for modeling, visualizing, and simulating biological pathways, In Silico Biology, 7(6): ,

2 [4] Euna Jeong, Masao Nagasaki, and Satoru Miyano, Conversion from BioPAX to CSO for system dynamics and visualization of biological pathway, Genome Informatics 18: , 2007 [5] Kaname Kojima, Masao Nagasaki, Euna Jeong, Mitsuru Kato, and Satoru Miyano, An efficient grid layout algorithm for biological networks utilizing various biological attributes, BMC Bioinformatics, 8:76, 2007 [6] Euna Jeong and Satoru Miyano, A weighted profile based method for protein-rna interacting residue prediction, Transactions on Computational Systems Biology IV, LNCS 3939: , 2006 [7] Seiya Imoto, Tomoyuki Higuchi, SunYong Kim, Euna Jeong and Satoru Miyano, Residual bootstrapping and median filtering for robust estimation of gene networks from microarray data, Lecture Notes in Computer Science, 3082: , 2005 [8] Euna Jeong, I-Fang Chung, and Satoru Miyano, A neural network method for identification of RNAinteracting residues in protein, Genome Informatics, 15(1): , 2004 [9] Euna Jeong, Hyunwoo Kim, Seongwook Lee and Kyungsook Han, Discovering interaction propensities of amino acids and nucleotides from the Protein-RNA Complexes, Molecules and Cells, 16(2): , 2003 [10] Hyunwoo Kim, Euna Jeong, Seongwook Lee and Kyungsook Han, Computational analysis of hydrogen bonds in protein-rna complexes for Interaction Patterns, FEBS Letters, 552(2-3): , 2003 [11] Euna Jeong and Chun-Nan Hsu, View inference for heterogeneous XML information integration, Journal of Intelligent Information Systems, 20(1):81-99, 2003 [12] Yanga Byun, Euna Jeong, and Kyungsook Han, A partitioned approach to protein interaction mapping, Lecture Notes in Computer Science, 2528: , 2002 Refereed Conference Paper [13] Hyunwoo Kim, Euna Jeong, and Kyungsook Han, Structural analysis of protein-rna complexes, Annual Meeting of Korean Society for Bioinformatics, Pusan, Korea, 2002 [14] Euna Jeong and Chun-Nan Hsu, Induction of integrated schema for XML data with heterogeneous DTDs, 10th Int l Conf. on Information and Knowledge Management (ACM CIKM01), Atlanta, GA, 2001 [15] Euna Jeong and Chun-Nan Hsu, Integration and reuse of heterogeneous XML DTDs for information agents, 2nd Int l Conf. on Intelligent Agent Technology (IAT01), Maebashi, Japan, 2001 [16] Euna Jeong and Chun-Nan Hsu, Ontology integration in XML, 7th Int l Conf. on Artificial Intelligence, Austin, Texas, 2000 [17] Euna Jeong and Yung-Jen Hsu, A form-based gateway for Web databases, World Conference of WWW, Internet & Intranet (WebNet97), Toronto, Canada, 1997 Refereed Demonstration Papers [18] Euna Jeong, Masao Nagasaki, Ayumu Saito, and Satoru Miyano, Ontology-based representation for Cell System Markup Language, 17th Int l Conf. on Genome Informatics, 2006 [19] Masao Nagasaki, Atsushi Doi, Ayumu Saito, Emi Ikeda, Kazuko Ueno, Euna Jeong, ChristopherJ. Savoie, and Satoru Miyano, Cell Illustrator3.0: a platform for biopathway modeling and simulation, 17th Int l Conf. on Genome Informatics, 2006 [20] Kaname Kojima, Masao Nagasaki, Euna Jeong, Mitsuru Kato, and Satoru Miyano, A new grid layout algorithm with swap operation that extends the search space while keeping the time complexity, 17th Int l Conf. on Genome Informatics, 2006 [21] Euna Jeong and Satoru Miyano A weighting profile method for protein-rna interaction prediction, 16th Int l Conf. on Genome Informatics,

3 [22] Euna Jeong, I-Fang Chung, and Satoru Miyano, Prediction of residues in protein-rna interaction sites by neural networks, 14th Int l Conf. on Genome Informatics, 2003 [23] Hyunwoo Kim, Euna Jeong, and Kyungsook Han, Analysis of protein-rna interactions at atomic level, 13th Int l Conf. on Genome Informatics, 2002 Unrefereed Technical Report [24] Euna Jeong and Yung-Jen Hsu et al., The Health Care Passport System, Technical Report: NTUCSIE 96-05, National Taiwan University, 1996 Research Projects DNA Information Analysis Lab, Institute of Medical Science, University of Tokyo Cell System Ontology (CSO): Ontological representation for cell system (April 2005 present) As a complementary project of the Cell System Markup Language (CSML) project, we have developed a formal ontology for representing biological pathways in OWL. CSO is based on a mathematical model called hybrid functional Petri net with extension. The aim of CSO is to represent pathway modeling and related information including kinetics for simulation, graphics for visualization, and animation of simulation, which are rarely implemented in other approaches. In addition, CSO can be used to create diverse biological pathways such as metabolic interactions, signal transduction pathways, gene regulatory networks, and cell-cell interaction. In this project I am responsible for the design of CSO, implementation of on-line ontology viewer in Perl, implementation of conversion tool between CSO and other formats including CSML and BioPAX. The prototype is available on A detailed presentation is in preparation in [3] and [5]. Biological pathway data conversion and integration (April 2007 ) We have developed mapping rules for conversion from biological resources to CSO/CSML (XML version of CSO). Biological resources which do not contain mathematical models are converted into CSO. Transforming data from those biological resources to CSO not only allows an analysis of the dynamic behaviors in molecular interactions but also allows the results to be stored in CSO for further biological investigations, which are not possible in other resources. Related works are BioPAX2CSO [4] and Transpath2CSML [2]. Ontology validation (January 2008 ) The goal of this work is to generate valid biological models in terms of both Petri nets and biological meaning. For this goal, we propose a rule-based approach to extend the expressiveness of OWL and to complement an OWL ontology by reasoning, which aims at providing a qualified pathway knowledge base. This approach helps researchers to explore dynamic modeling and simulation tasks without prior knowledge. The preliminary results are reported in [1]. Prediction of residues binding with RNA based on neural network (April 2003 March 2005) The objective of this project was to investigate a predicting problem of the protein-rna interaction. A prediction system based on artificial neural networks was developed to identify accurate residues involved in protein-rna interaction sites from combining the residue sequence and the protein secondary structure information. Results of this work were presented in [8]. Furthermore, to improve the prediction performance, we proposed a weighting profile method which represents the importance of the presence of specific residues at specific positions. The experimental results showed that the proposed method could capture the correlation between consecutive residues and improve the prediction performance. This work were presented in [6]. Biocomputing Lab, School of Computer Science and Engineering, Inha University Computer modeling for predicting RNA structures binding to proteins (March 2002 March 2003) This project aims to provide a systematic method for automatically identifying protein-rna interaction patterns. We designed an propensity function to analyze protein-rna interactions at atomic level. The interaction patterns discovered from the analysis provided us with useful information in predicting the 3

4 structure of the RNA binding protein and the structure of the protein binding RNA. The outcome of this work were published in [9], [10], and [13]. Basic research for in silico physiome modeling of protein-protein interactions (March 2002 March 2003) We developed a new program for drawing protein interactions in three-dimensional space. The algorithm was based on force-directed layouts. The experimental results showed that the program generated a clear and aesthetically pleasing drawing of large-scale protein interaction networks and that it is an order of magnitude faster than other force-directed layouts. My task was to refine the layout algorithm. Results of this work were presented in [12]. Adaptive Intelligent Internet Agents Lab, Institute of Information Science, Academia Sinica Information integration for heterogeneous XML document type (August 2000 January 2002) In this research project, we proposed a system to automatically integrate heterogeneous XML DTDs. The aim of this approach is that an information agent can be easily extended to integrate heterogeneous XML-based contents and perform federated searches. Based on a tree grammar inference technique, the approach derives an integrated view and source descriptions of XML DTDs in an information integration framework. The algorithms and results were presented in [11], [14-16]. Intelligent Agents Lab, Department of Computer Science and Information Engineering, National Taiwan University Information sever for virtual semi-conductor manufacturing (August 1998 July 2001) The aim of this project was to develop an intelligent information server for a virtual factory of semiconductor manufacturing, which provides an integrated information service for both clients and managers and supports an easy-of-use interface for communication. I was responsible for comparative study of data and operation mapping, implementation of web-enabled user interface, and wrapper development. National Health Care Passport System (July 1996 December 1996) The project was designed to promote standard computerized personal health records and insurance claims in order to optimize the quality and costs of medical services. My contribution was to design the database schema. This work was presented in [24]. Scholarships National Taiwan University Scholarship for Foreign Graduate Students (2001) YEN TJING LING Industrial Research Institute Scholarship, Taiwan (July 2001) AAAI/IAAI 2000 Doctoral Consortium Scholarship (July 2000) Educational Department Scholarship for Foreign Graduate Students, Taiwan (September 1998 August 1999) Miscellaneous Citizenship: Korean (by birth) Language: English (Fluent), Chinese (Fluent), Japanese (Intermediate), Korean (native Speaker), Operating Systems: UNIX (Solaris, Linux), Windows, MacOS Computer Skills: programming languages (Perl, C, Java, Lisp), web languages (XML, OWL), ontology tools. 4

5 Professional Activities Reviewer Journal of Theoretical Biology (2007 present) 3rd Int l Conf. on Intelligent Computing (ICIC 2007) BMC Bioinformatics (2005) 3rd Int l Conf. on Autonomous Agents & Multi Agent Systems (AAMAS 2004) Journal of Intelligent Information Systems (2002) Member of Japan Society for Bioinformatics (2007) Member of Korean Society for Bioinformatics (2002) Member of Special Interest Group for Artificial Intelligence ( ) Teaching Activities (February 1998 January 1999): Teaching Assistant (September 1998 January 1999): Responsible for the preparation and presentation of teaching assignments of the Artificial Intelligence course (February 1998 July 1998): Responsible for the preparation and presentation of teaching assignments of the Introduction to Computer Software course Updated: November 17,