1. Text Mining in a Biomedical Domain

• Hee-Jin Lee and Jong C. Park, Towards Knowledge Discovery through Automatic Inference with Text Mining in Biology and Medicine, 3rd international symposium on semantic mining in biomedicine, Turku, Finland, September 1-3, 2008. (link)
• Hodong Lee, Gwan-Su Yi and Jong C. Park. E3Miner: a text mining tool for ubiquitin-protein ligases, Nucleic Acids Research, 2008, Vol. 36, Web Server issue Published doi:10.1093/nar/gkn286, 15 May 2008. (link)
• Jong C. Park, Creating Biomedical Resources with NLP-based Information Extraction, Tokyo Forum on Advanced NLP and TM (T-FaNT 07), Tokyo, Japan, March 11-13, 2007. (Invited talk)
• Jong C. Park, Gary G. Lee and Limsoon Wong, Text Mining and Management in Biomedicine, Guest Editors' Introduction to the Special Issue, ACM Transactions on Asian Language Information Processing (TALIP), March, 2006. (link)
• Jong C. Park. Biomedical Text Mining for Knowledge Discovery and Automatic Ontology Extension, Workshop on Text Mining, Ontology, and NLP in Biomedical Fields, Manchester, England, March 20-21, 2006. (invited presentation)
• Jong C. Park and Jung-jae Kim, Named Entity Recognition, Chapter six of the book 'Text Mining for Biology', editors: Ben Stapley and Sophia Ananiadou, Artech House Books, January, 2006.
• Sophia Ananiadou and Jong C. Park, Introduction to the Thematic Session on Text Mining in Biomedicine, Lecture Notes in Artificial Intelligence., Vol. 3248 (revised selected papers from IJCNLP 2004), editors: K-Y Su, J. Tsujii, J.-H. Lee, O. Y. Kwong, p. 776, 2005. (link)
• Jung-jae Kim and Jong C. Park, Research Trends in Bio Text Mining, Korea Information Science Society SIGBIT News Letter, Vol. 2, No. 1, pages 14-31, 2004.
• Jong C. Park, Combinatory Categorial Grammar: from Natural Language Understanding to Biomedical Applications, Workshop on Natural Language Processing and Ontology Building for Biology, Tokyo, Japan, February, 2002.
• Jong C. Park, Recent Issues in Biopathway Extraction from Literature, Institute for Mathematical Sciences (IMS), National University of Singapore, Singapore, February, 2002.
• Jong C. Park, Challenges in Biopathway Extraction from Literature and Ontology Building for Biology, Korea Society for Bioinformatics Workshop, February, 2002. (link)
• Lynette Hirschman, Jong C. Park, Jun-ichi Tsujii, Limsoon Wong, and Cathy Wu, Accomplishments and Challenges in Literature Data Mining for Biology, Bioinformatics, 18(12):1553-1561, 2002. (link)
• Lynette Hirschman, Jong C. Park, Jun-ichi Tsujii, Cathy Wu, and Limsoon Wong, Literature Data Mining for Biology, Proceedings of the Pacific Symposium on Biocomputing (PSB) session, pp. 323-325, Hawaii, USA, 2002. (link)
• Jong C. Park, Natural Language Processing for Biomedical Information Extraction and Automatic Ontology Management, Proceedings of the 2nd Bioinformatics Forum, pp. 145-158, Seoul, Korea, 2002.
• Jong C. Park, Using Combinatory Categorial Grammar to Extract Biomedical Information, IEEE Intelligent Systems, Special Issue on Intelligent Systems in Biology, 16(6):62-67, November-December, 2001. (link)
• Jong C. Park, Biomedical Informatics and Natural Language Processing, Annual Meeting of the Korean Society for Medical Informatics, Jeon-ju, Korea, November, 2001.
• Jong C. Park, Bioinformatics and Natural Language Processing, Special Issue in Korean Information Processing, Communications of the Korea Information Science Society (KISS), Vol. 19, No. 10, pages 46-51, October, 2001. (link)
• Jong C. Park, Customizable Natural Language Interfaces to Data Bases, Pacific Symposium on Biocomputing (PSB), Honolulu, Hawaii, USA, January, 2000. (invited presentation)

2. Extraction of Biological Interactions

• Jung-jae Kim. Bidirectional Incremental Approach to Efficient Information Extraction: Applications to Biomedicine, KAIST, 2006. (Outstanding Ph.D Thesis Award, 2006. 8.) (link)
• Jung-jae Kim and Jong C. Park, Deciding When to Stop: Enhancing the Performance of Information Extraction with Deeper Linguistic Analysis, Proceedings of the 3rd Korea-Singapore Joint Workshop on Bioinformatics and Natural Language Processing, pp. 41-45, Muju Resort, Jeonbuk, South Korea, February, 2005.
• Jung-jae Kim and Jong C. Park, BioIE: Retargetable Information Extraction and Ontological Annotation of Biological Pathways from the Literature, Journal of Bioinformatics and Computational Biology (JBCB), 2(3):551-568, 2004. (link)
• Jong C. Park, Hyun Sook Kim, and Jung-jae Kim, Bidirectional Incremental Parsing for Automatic Pathway Identification with Combinatory Categorial Grammar, Pacific Symposium on Biocomputing (PSB), pp. 396-407, Big Island, Hawaii, USA, January, 2001. (link)

3. Automatic Construction of Gene and Protein Ontologies

• Seung-Cheol Baek and Jong C. Park. Automatic Extraction of the Usage Information from the Component Words in Gene Ontology Terms to Enhance Consistency and Predictability, 3rd International Symposium on Languages in Biology and Medicine (LBM), long paper, Seogwipo, Korea, November, 2009.
• Jong C. Park, Tak-eun Kim, Jinah Park, Monitoring the evolutionary aspect of the Gene Ontology to enhance predictability and usability, BMC Bioinformatics 2008, 9(Suppl 3):7 doi:10.1186/1471-2105-9-S3-S7, 11 April 2008. (link)
• Jin-Bok Lee and Jong C. Park, Automatic Extension of Gene Ontology with Induced Prediction and Flexible Validation of Candidate Terms, 5th Singapore-Korea Workshop on Bioinformatics and Natural Language Processing, National University of Singapore, Singapore, February 22, 2006.
• Jin-Bok Lee, Jung-jae Kim, and Jong C. Park, Automatic extension of Gene Ontology with flexible identification of candidate terms, Bioinformatics, 22(6): 665-670, 2006. (link)
• Jin-Bok Lee, Jung-Jae Kim and Jong C. Park, Induced Extension of Gene Ontology from Biomedical Resources with Flexible Identification of Candidate Terms, The First International Symposium on Semantic Mining in Biomedicine (SMBM), page 13, Cambridge, UK, April, 2005. (link)
• Jung-jae Kim, Jin-Bok Lee, Hye-Jin Min, Ji-yong Jung and Jong C. Park, Logical Representation of Ontological Terminologies in Biomedical Domain, Proc. of the 2nd Annual Conference of The Korean Society for Bioinformatics (KSBI 2003), Daejeon, Korea, pp. 79-85, 2003. (link)
• Jin-Bok Lee and Jong C. Park, Automatic Gene Ontology Extension and Terminology Analysis, Proceedings of the KISS Conference, pp. 229-231, Suwon, Korea, October, 2002. (link)
• Jin-Bok Lee, Jung-jae Kim, and Jong C. Park, Semi-Automatic Extension of Gene Ontology, Human Computer Interaction (HCI) Workshop, Phoenix Park, Korea, January, 2002.
• Jin-Bok Lee and Jong C. Park, Text Data Mining for Automatic Gene Ontology Extension, Intelligent Systems for Molecular Biology (ISMB), Proceedings of the second meeting of the special interest group on Text Data Mining, pp. 22-25, Edmonton, Alberta, Canada, 2002.

4. Visualization of Inferred Gene and Protein Networks

• Tak-eun Kim, Hodong Lee, Jinah Park, and Jong C. Park, Visualizing the temporal distribution of terminologies for biological ontology development, International Conference on Visualization and Data Analysis(VDA), San Jose, USA, 26-31 January, 2008. (link)
• Changsu Lee, Jinah Park, Jong C. Park, Visualization for Digesting a High Volume of the Biomedical Literature, Bioinformatics and Biosystems, Vol. 1, No. 1, pp.51-60, Feb. 2006. (link)
• Tak-Eun Kim and Jong C. Park, Effective text visualization for biomedical information, HCI, Phoenix Park, February, 2007.
• Ho-Joon Lee and Jong C. Park, Augmenting Visualization with Audioization for Enhanced Knowledge Discovery, 5th Singapore-Korea Workshop on Bioinformatics and Natural Language Processing, National University of Singapore, Singapore, February 22, 2006.
• Jinah Park, Changsu Lee and Jong C. Park, Information Visualization in Three-Dimensional Space for Text Data Mining, Key Engineering Materials, Vols. 277-279, pages 259-265, 2005. (link)
• Changsu Lee, Jinah Park and Jong C. Park, A Graphic Tool for Curating Molecular Interaction Networks from the Literature, International Journal of Computers in Biology and Medicine, Vol. 35, pages 555-564, 2005. (link)
• Changsu Lee, Jinah Park and Jong C. Park, Case Study: Visualization and Analysis of Mitogen-Activated Protein Kinase Pathways in the Literature, Conference on Visualization and Data Analysis (VDA), pp. 275-285, San Jose, USA, Janurary, 2004. (link)
• Changsu Lee, Jinah Park and Jong C. Park, Data-oriented Customized Visual Navigation, Proc. HCI/CG/VR/UI/DESIGN, Phoenix Park, 2004.
• Changsu Lee, Applications to Molecular Interactions: Customized Visualization for Knowledge Discovery with Information Extraction, KAIST, 2004. (Outstanding MS Thesis Award, 2004. 2.) (link)
• Jinah Park, Changsu Lee and Jong C. Park, Information Visualization in 3-Dimensional Space for Text Data Mining, International Women's Conference on BIEN-Technology, Daejeon, Korea, November, 2003.
• Changsu Lee, Jinah Park and Jong C. Park, Mediatory Visualization for Structured Data and Textual Information, The 3rd IASTED International Conference on Visualization, Imaging, and Image Processing (VIIP 2003), pp. 926-932, Benalmadena, Spain, 2003. (link)
• Changsu Lee, Jinah Park and Jong C. Park, BiopathwayBuilder: Nested 3D visualization system for complex molecular interactions, International Conference on Genome Informatics (GIW), pp. 447-448, Tokyo, Japan, 2002. (link)
• Changsu Lee, Jinah Park and Jong C. Park, 3D Visualization System for Complex Protein-Protein Interactions from Text Data Mining, IEEE Visualization, Workshop on Visualization in Bioinformatics and Cheminformatics, Boston, USA, 2002.

5. Natural Language Query Interpretation for Heterogenous Database Access

• Hodong Lee and Jong C. Park, Explorative search with relational description of biological entities into multiple heterogeneous databases, 5th Singapore-Korea Workshop on Bioinformatics and Natural Language Processing, National University of Singapore, Singapore, February 22, 2006.
• Hodong Lee and Jong C. Park, Dynamic Informative Link Annotation for Biological Text over Heterogenous Databases, In Proc. of the 16th International Conference on Genome Informatics(GIW), Yokohama, Japan, December, 2005. (link)
• Hodong Lee and Jong C. Park, Dynamic and Informative Linking from Biological Text into Heterogeneous Databases, The First International Symposium on Languages in Biology and Medicine (LBM), Daejeon, Korea, November, 2005.
• Hodong Lee and Jong C. Park, Natural Language Query Interpretation System for Biomedical Database Access, Proceedings of the KISS Spring Conference, pp. 487-489, Han Yang University, April 26-27, 2002. (link)

6. Knowledge Discovery with Protein-Protein Contrasts

• Jung-jae Kim, Zhuo Zhang, Jong C. Park and See-Kiong Ng. BioContrasts: Extracting and Exploiting Protein-Protein Contrastive Relations from Biomedical Literature, Bioinformatics, Vol. 22, No. 5, pages 597-605, March, 2006. (link)
• Jung-jae Kim and Jong C. Park, Extracting contrastive information from negation patterns in biomedical literature, ACM Transactions on Asian Language Information Processing (TALIP), Special Issue on Text Mining and Management in Biomedicine, 2006. (link)

7. Automatic Generation of Gene Summaries

• Jin-Bok Lee, Tak-eun Kim, Chan-Goo Kang and Jong C. Park, Extracting Relational Information for Protein Pairs, 6th Singapore-Korea Workshop on Bioinformatics and Natural Language Processing, Institute for Infocomm Research, Singapore, February 12, 2007.
• Chan-Goo Kang, Generation of Coherent Gene Summary, KAIST, 2006. (link)
• Chan-Goo Kang and Jong C. Park, Generation of Coherent Gene Summary with Concept-Linking Sentences, In Proc. The First International Symposium on Languages in Biology and Medicine (LBM), pp. 41-45, Creative Learning Building, KAIST, Daejeon, Korea, Novermber, 2005.

8. Database for Ubiquitin-Protein Ligases

• Hodong Lee and Jong C. Park. Automatic Data Integration of Ubiquitin-protein Ligases, The 6th Singapore-Korea Joint Workshop on Bioinformatics and Natural Language Processing, Singapore, February 12, 2007.

9. Others

• Hee-Jin Lee and Jong C. Park. Extracting Relational Information for Protein Pairs, The 6th Singapore-Korea Joint Workshop on Bioinformatics and Natural Language Processing, Singapore, February 12, 2007.
• Hye-Jin Min and Jong C. Park, Diagnoses of Emotional Disorders for Amygdala-related Pathway with BioIE, 5th Singapore-Korea Workshop on Bioinformatics and Natural Language Processing, National University of Singapore, Singapore, February 22, 2006.
• Hee-Jin Lee and Jong C. Park, Towards an efficient CCG parser for RNA secondary structure prediction, 5th Singapore-Korea Workshop on Bioinformatics and Natural Language Processing, National University of Singapore, Singapore, February 22, 2006.
• Jung-jae Kim and Jong C. Park, Term Characterization for Information Extraction with Syntactic Pattern Matching, 5th Singapore-Korea Workshop on Bioinformatics and Natural Language Processing, National University of Singapore, Singapore, February 22, 2006.
• Hee-Jin Lee and Jong C. Park, CCG-based RNA Secondary Structure Prediction for Structural Homology Analysis, International Conference on Genome Informatics (GIW), Yokohama, Japan, December, 2005. (link)
• Hee-Jin Lee and Jong C. Park, Prediction of RNA Secondary Structures in a Combinatory Categorial Grammar Framework, In Proc. The First International Symposium on Languages in Biology and Medicine, Creative Learning Building, KAIST, Daejeon, Korea, November, 2005.
• Il Park and Jong C. Park, Modeling Causality in Biological Pathways for Logical Identification of Drug Targets, In Proc. of The 2005 International Joint Conference of InCoB, AASBi and KSBI (Bioinfo 2005), Busan, Korea, September, 2005. (link)
• Jung-jae Kim and Jong C. Park, BioAR: Anaphora Resolution for Relating Protein Names to Proteome Database Entries, ACL Workshop on Reference Resolution and its Applications, pp. 79-86, Barcelona, Spain, 2004. (link)
• Jung-jae Kim and Jong C. Park, Annotation of Gene Products in the Literature with Gene Ontology Terms using Syntactic Dependencies, The 1st International Joint Conferrence on Natural Language Processing (IJCNLP), pp. 528-534, Hainan, P.R.China, 2004. (link)
• Jung-jae Kim and Jong C. Park, Annotation of Gene Products in the Literature with Gene Ontology Terms using Syntactic Dependencies, Lecture Notes on Artificial Intelligence, Post-Conference Book of IJCNLP-04, 2004. (link)