HMM Specialization with Selective Lexicalization. - Jin-Dong Kim; Sang-Zoo Lee; Hae-Chang Rim (EMNLP, 1999)

KCAT: A Korean Corpus Annotating Tool Minimizing Human Intervention. - Won-Ho Ryu; Jin-Dong Kim; Hae-Chang Rim; Heui-Seok Lim (COLING, 2000)

Stretching TEI: Converting the Genia Corpus. - Tomaz Erjavec; Jin-Dong Kim; Tomoko Ohta; Yuka Tateisi; Jun'ichi Tsujii (LINC@EACL, 2003)

Self-Organizing Markov Models and Their Application to Part-of-Speech Tagging. - Jin-Dong Kim; Hae-Chang Rim; Jun'ichi Tsujii (ACL, 2003)

Encoding Biomedical Resources in TEI: The Case of the GENIA Corpus. - Tomaz Erjavec; Jin-Dong Kim; Tomoko Ohta; Yuka Tateisi; Jun'ichi Tsujii (BioNLP@ACL, 2003)

GENIA corpus - a semantically annotated corpus for bio-textmining. - Jin-Dong Kim; Tomoko Ohta; Yuka Tateisi; Jun'ichi Tsujii (ISMB (Supplement of Bioinformatics), 2003)

Introduction to the Bio-entity Recognition Task at JNLPBA. - Nigel Collier; Jin-Dong Kim (NLPBA/BioNLP, 2004)

Word Folding: Taking the Snapshot of Words Instead of the Whole. - Jin-Dong Kim; Jun'ichi Tsujii (IJCNLP, 2004)

Developing a Robust Part-of-Speech Tagger for Biomedical Text. - Yoshimasa Tsuruoka; Yuka Tateishi; Jin-Dong Kim; Tomoko Ohta; John McNaught; Sophia Ananiadou; Jun'ichi Tsujii (Panhellenic Conference on Informatics, 2005)

Topic Document Model Approach for Naive Bayes Text Classification. - Sang-Bum Kim; Hae-Chang Rim; Jin-Dong Kim (IEICE Trans. Inf. Syst., 2005)

An Intelligent Search Engine and GUI-based Efficient MEDLINE Search Tool Based on Deep Syntactic Parsing. - Tomoko Ohta; Yusuke Miyao; Takashi Ninomiya; Yoshimasa Tsuruoka; Akane Yakushiji; Katsuya Masuda; Jumpei Takeuchi; Kazuhiro Yoshida; Tadayoshi Hara; Jin-Dong Kim; Yuka Tateisi; Jun'ichi Tsujii (ACL, 2006)

Linguistic and Biological Annotations of Biological Interaction Events. - Tomoko Ohta; Yuka Tateisi; Jin-Dong Kim; Akane Yakushiji; Jun'ichi Tsujii (LREC, 2006)

Extraction of Gene-Disease Relations from Medline Using Domain Dictionaries and Machine Learning. - Hong-Woo Chun; Yoshimasa Tsuruoka; Jin-Dong Kim; Rie Shiba; Naoki Nagata; Teruyoshi Hishiki; Jun'ichi Tsujii (Pacific Symposium on Biocomputing, 2006)

Automatic Recognition of Topic-Classified Relations between Prostate Cancer and Genes from Medline Abstracts. - Hong-Woo Chun; Yoshimasa Tsuruoka; Jin-Dong Kim; Rie Shiba; Naoki Nagata; Teruyoshi Hishiki; Jun'ichi Tsujii (SMBM, 2006)

Automatic recognition of topic-classified relations between prostate cancer and genes using MEDLINE abstracts. - Hong-Woo Chun; Yoshimasa Tsuruoka; Jin-Dong Kim; Rie Shiba; Naoki Nagata; Teruyoshi Hishiki; Jun'ichi Tsujii (BMC Bioinform., 2006)

From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical Literature. - Jin-Dong Kim; Tomoko Ohta; Kanae Oda; Jun'ichi Tsujii (APBC, 2008)

Prediction of Protein Sub-cellular Localization using Information from Texts and Sequences. - Hong-Woo Chun; Chisato Yamasaki; Naomi Saichi; Masayuki Tanaka 009; Teruyoshi Hishiki; Tadashi Imanishi; Takashi Gojobori; Jin-Dong Kim; Jun'ichi Tsujii; Toshihisa Takagi (BioNLP, 2008)

Raising the Compatibility of Heterogeneous Annotations: A Case Study on. - Yue Wang 040; Kazuhiro Yoshida; Jin-Dong Kim; Rune Saetre; Jun'ichi Tsujii (BioNLP, 2008)

Exploring Domain Differences for the Design of a Pronoun Resolution System for Biomedical Text. - Ngan L. T. Nguyen; Jin-Dong Kim (COLING, 2008)

Challenges in Pronoun Resolution System for Biomedical Text. - Ngan L. T. Nguyen; Jin-Dong Kim; Jun'ichi Tsujii (LREC, 2008)

Corpus annotation for mining biomedical events from literature. - Jin-Dong Kim; Tomoko Ohta; Jun'ichi Tsujii (BMC Bioinform., 2008)

New challenges for text mining: mapping between text and manually curated pathways. - Kanae Oda; Jin-Dong Kim; Tomoko Ohta; Daisuke Okanohara; Takuya Matsuzaki; Yuka Tateisi; Jun'ichi Tsujii (BMC Bioinform., 2008)

Overview of BioNLP'09 Shared Task on Event Extraction. - Jin-Dong Kim; Tomoko Ohta; Sampo Pyysalo; Yoshinobu Kano; Jun'ichi Tsujii (BioNLP@HLT-NAACL (Shared Task), 2009)

Incorporating GENETAG-style annotation to GENIA corpus. - Tomoko Ohta; Jin-Dong Kim; Sampo Pyysalo; Yue Wang 040; Jun'ichi Tsujii (BioNLP@HLT-NAACL, 2009)

Static Relations: a Piece in the Biomedical Information Extraction Puzzle. - Sampo Pyysalo; Tomoko Ohta; Jin-Dong Kim; Jun'ichi Tsujii (BioNLP@HLT-NAACL, 2009)

Bridging the Gap between Domain-Oriented and Linguistically-Oriented Semantics. - Sumire Uematsu; Jin-Dong Kim; Jun'ichi Tsujii (BioNLP@HLT-NAACL, 2009)

Opinion classification with tree kernel SVM using linguistic modality analysis. - Takeshi S. Kobayakawa; Tadashi Kumano; Hideki Tanaka; Naoaki Okazaki; Jin-Dong Kim; Jun'ichi Tsujii (CIKM, 2009)

GuideLink: A Corpus Annotation System that Integrates the Management of Annotation Guidelines. - Kenta Oouchida; Jin-Dong Kim; Toshihisa Takagi; Jun'ichi Tsujii (PACLIC, 2009)

Investigating heterogeneous protein annotations toward cross-corpora utilization. - Yue Wang 040; Jin-Dong Kim; Rune Sætre; Sampo Pyysalo; Jun'ichi Tsujii (BMC Bioinform., 2009)

Extracting Protein Sub-cellular Localizations from Literature. - Hong-Woo Chun; Jin-Dong Kim; Yunsoo Choi; Won-Kyung Sung (AMT, 2010)

Natural Language Query Processing for Life Science Knowledge - Position Paper. - Jin-Dong Kim; Yasunori Yamamoto; Atsuko Yamaguchi; Mitsuteru Nakao; Kenta Oouchida; Hong-Woo Chun; Toshihisa Takagi (AMT, 2010)

Event Extraction for Post-Translational Modifications. - Tomoko Ohta; Sampo Pyysalo; Makoto Miwa; Jin-Dong Kim; Jun'ichi Tsujii (BioNLP@ACL, 2010)

Event Extraction with Complex Event Classification Using Rich Features. - Makoto Miwa; Rune Sætre; Jin-Dong Kim; Jun'ichi Tsujii (J. Bioinform. Comput. Biol., 2010)

A Re-Evaluation of Biomedical Named Entity-Term Relations. - Tomoko Ohta; Sampo Pyysalo; Jin-Dong Kim; Jun'ichi Tsujii (J. Bioinform. Comput. Biol., 2010)

Improving the Inter-Corpora Compatibility for protein Annotations. - Yue Wang 040; Jin-Dong Kim; Rune Sætre; Sampo Pyysalo; Tomoko Ohta; Jun'ichi Tsujii (J. Bioinform. Comput. Biol., 2010)

Discriminative Application of String Similarity Methods to Chemical and Non-chemical Names for Biomedical Abbreviation Clustering. - Atsuko Yamaguchi; Yasunori Yamamoto; Jin-Dong Kim; Toshihisa Takagi; Akinori Yonezawa (BIBM, 2011)

Parsing Natural Language Queries for Life Science Knowledge. - Tadayoshi Hara; Yuka Tateisi; Jin-Dong Kim; Yusuke Miyao (BioNLP@ACL, 2011)

Overview of BioNLP Shared Task 2011. - Jin-Dong Kim; Sampo Pyysalo; Tomoko Ohta; Robert Bossy; Ngan L. T. Nguyen; Jun'ichi Tsujii (BioNLP@ACL (Shared Task), 2011)

Overview of Genia Event Task in BioNLP Shared Task 2011. - Jin-Dong Kim; Yue Wang 040; Toshihisa Takagi; Akinori Yonezawa (BioNLP@ACL (Shared Task), 2011)

Overview of BioNLP 2011 Protein Coreference Shared Task. - Ngan L. T. Nguyen; Jin-Dong Kim; Jun'ichi Tsujii (BioNLP@ACL (Shared Task), 2011)

BioNLP Shared Task 2011: Supporting Resources. - Pontus Stenetorp; Goran Topic; Sampo Pyysalo; Tomoko Ohta; Jin-Dong Kim; Jun'ichi Tsujii (BioNLP@ACL (Shared Task), 2011)

Poster: Analysis of gene ranking algorithms with extraction of relevant biomedical concepts from PubMed publications. - Simon Kocbek; Rune Sætre; Gregor Stiglic; Jin-Dong Kim; Igor Pernek; Yoshimasa Tsuruoka; Peter Kokol; Sophia Ananiadou; Jun'ichi Tsujii (ICCABS, 2011)

Discriminative Optimization of String Similarity and Its Application to Biomedical Abbreviation Clustering. - Atsuko Yamaguchi; Yasunori Yamamoto; Jin-Dong Kim; Toshihisa Takagi; Akinori Yonezawa (ICMLA (2), 2011)

AGRA: analysis of gene ranking algorithms. - Simon Kocbek; Rune Sætre; Gregor Stiglic; Jin-Dong Kim; Igor Pernek; Yoshimasa Tsuruoka; Peter Kokol; Sophia Ananiadou; Jun'ichi Tsujii (Bioinform., 2011)

U-Compare bio-event meta-service: compatible BioNLP event extraction services. - Yoshinobu Kano; Jari Björne; Filip Ginter; Tapio Salakoski; Ekaterina Buyko; Udo Hahn; K. Bretonnel Cohen; Karin Verspoor; Christophe Roeder; Lawrence E. Hunter; Halil Kilicoglu; Sabine Bergler; et al. (BMC Bioinform., 2011)

Extracting Bio-molecular Events from literature - the BioNLP'09 Shared Task. - Jin-Dong Kim; Tomoko Ohta; Sampo Pyysalo; Yoshinobu Kano; Jun'ichi Tsujii (Comput. Intell., 2011)

CSAF - a community-sourcing annotation framework. - Jin-Dong Kim; Yue Wang 040 (LAW@ACL, 2012)

PubAnnotation - a persistent and sharable corpus and annotation repository. - Jin-Dong Kim; Yue Wang 040 (BioNLP@HLT-NAACL, 2012)

New Resources and Perspectives for Biomedical Event Extraction. - Sampo Pyysalo; Pontus Stenetorp; Tomoko Ohta; Jin-Dong Kim; Sophia Ananiadou (BioNLP@HLT-NAACL, 2012)

Boosting the protein name recognition performance by bootstrapping on selected text. - Yue Wang 040; Jin-Dong Kim (BioNLP@HLT-NAACL, 2012)

Visual Presentation of Mappings Between Biomedical Ontologies. - Simon Kocbek; Jean-Luc Perret; Jin-Dong Kim (SWAT4LS, 2012)

The Genia Event and Protein Coreference tasks of the BioNLP Shared Task 2011. - Jin-Dong Kim; Ngan L. T. Nguyen; Yue Wang 040; Jun'ichi Tsujii; Toshihisa Takagi; Akinori Yonezawa (BMC Bioinform., 2012)

Improving protein coreference resolution by simple semantic classification. - Ngan L. T. Nguyen; Jin-Dong Kim; Makoto Miwa; Takuya Matsuzaki; Junichi Tsujii (BMC Bioinform., 2012)

Evaluation of SPARQL query generation from natural language questions. - K. Bretonnel Cohen; Jin-Dong Kim (SWAIE@RANLP, 2013)

The Genia Event Extraction Shared Task, 2013 Edition - Overview. - Jin-Dong Kim; Yue Wang 040; Yasunori Yamamoto (BioNLP@ACL (Shared Task), 2013)

Overview of BioNLP Shared Task 2013. - Claire Nédellec; Robert Bossy; Jin-Dong Kim; Jung-Jae Kim 001; Tomoko Ohta; Sampo Pyysalo; Pierre Zweigenbaum (BioNLP@ACL (Shared Task), 2013)

Visualizing ontology mappings to help ontology engineers identify relevant ontologies for their reuse. - Simon Kocbek; Jin-Dong Kim; Jean-Luc Perret; Patricia L. Whetzel (ICBO, 2013)

A Generalized LCS Algorithm and Its Application to Corpus Alignment. - Jin-Dong Kim (IJCNLP, 2013)

Literature Mining Solutions for Life Science Research. - Jörg Hakenberg; Goran Nenadic; Dietrich Rebholz-Schuhmann; Jin-Dong Kim (Adv. Bioinformatics, 2013)

Introducing glycomics data into the Semantic Web. - Kiyoko F. Aoki-Kinoshita; Jerven T. Bolleman; Matthew P. Campbell; Shin Kawano; Jin-Dong Kim; Thomas Lütteke; Masaaki Matsubara; Shujiro Okuda; René Ranzinger; Hiromichi Sawaki; Toshihide Shikanai; Daisuke Shinmachi; et al. (J. Biomed. Semant., 2013)

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. - Toshiaki Katayama; Mark D. Wilkinson; Kiyoko F. Aoki-Kinoshita; Shuichi Kawashima; Yasunori Yamamoto; Atsuko Yamaguchi; Shinobu Okamoto; Shin Kawano; Jin-Dong Kim; Yue Wang 040; Hongyan Wu; Yoshinobu Kano; et al. (J. Biomed. Semant., 2014)

Dynamic Join Order Optimization for SPARQL Endpoint Federation. - Hongyan Wu; Atsuko Yamaguchi; Jin-Dong Kim (SSWS@ISWC, 2015)

Extending the evaluation of Genia Event task toward knowledge base construction and comparison to Gene Regulation Ontology task. - Jin-Dong Kim; Jung-Jae Kim 001; Xu Han 008; Dietrich Rebholz-Schuhmann (BMC Bioinform., 2015)

Refactoring the Genia Event Extraction Shared Task Toward a General Framework for IE-Driven KB Development. - Jin-Dong Kim; Yue Wang 040; Nicola Colic; Seung-Han Baek; Yong Hwan Kim; Min Song 001 (BioNLP (Shared Task), 2016)

OKBQA: an Open Collaboration Framework for Development of Natural Language Question-Answering over Knowledge Bases. - Jin-Dong Kim; Christina Unger; Axel-Cyrille Ngonga Ngomo; André Freitas; YoungGyun Hahm; Jiseong Kim; Gyu-Hyun Choi; Jeonguk Kim; Ricardo Usbeck; Myoung-Gu Kang; Key-Sun Choi (ISWC (Posters, Demos & Industry Tracks), 2017)

SIGIR 2017 Workshop on Open Knowledge Base and Question Answering (OKBQA2017). - Key-Sun Choi; Teruko Mitamura; Piek Vossen; Jin-Dong Kim; Axel-Cyrille Ngonga Ngomo (SIGIR, 2017)

Biomedical Natural Language Processing. - Jin-Dong Kim (Comput. Linguistics, 2017)

Guideline Design of an Active Gene Annotation Corpus for the Purpose of Drug Repurposing. - Yuxing Wang; Xinzhi Yao; Kaiyin Zhou; Xuan Qin; Jin-Dong Kim; Kevin Bretonnel Cohen; Jingbo Xia (CISP-BMEI, 2018)

Trigger Words Detection by Integrating Attention Mechanism into Bi-LSTM Neural Network - A Case Study in PubMED-Wide Trigger Words Detection for Pancreatic Cancer. - Kaiyin Zhou; Xinzhi Yao; Shuguang Wang; Jin-Dong Kim; Kevin Bretonnel Cohen; Ruiying Chen; Yuxing Wang; Jingbo Xia (CCL, 2018)

A Quantitative Evaluation of Natural Language Question Interpretation for Question Answering Systems. - Takuto Asakura; Jin-Dong Kim; Yasunori Yamamoto; Yuka Tateisi; Toshihisa Takagi (JIST, 2018)

Mining Biomedical Publications With The LAPPS Grid. - Nancy Ide; Keith Suderman; Jin-Dong Kim (LREC, 2018)

Analysis of Distant Supervision for Relation Extraction Dataset. - Kijong Han; Sangha Nam; YoungGyun Hahm; Jiseong Kim; Jiho Kim; Jin-Dong Kim; Key-Sun Choi (ISWC (P&D/Industry/BlueSky), 2018)

A Multi-Platform Annotation Ecosystem for Domain Adaptation. - Richard Eckart de Castilho; Nancy Ide; Jin-Dong Kim; Jan-Christoph Klie; Keith Suderman (LAW@ACL, 2019)

An Active Gene Annotation Corpus and Its Application on Anti-epilepsy Drug Discovery. - Yuxing Wang; Jingbo Xia; Kaiyin Zhou; Jin-Dong Kim; Kevin Cohen 001; Mina Gachloo; Yuxin Ren; Shanghui Nie; Xuan Qin; Panzhong Lu (BIBM, 2019)

Open Agile text mining for bioinformatics: the PubAnnotation ecosystem. - Jin-Dong Kim; Yue Wang 040; Toyofumi Fujiwara; Shujiro Okuda; Tiffany J. Callahan; K. Bretonnel Cohen (Bioinform., 2019)

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. - Toshiaki Katayama; Shuichi Kawashima; Gos Micklem; Shin Kawano; Jin-Dong Kim; Simon Kocbek; Shinobu Okamoto; Yue Wang 040; Hongyan Wu; Atsuko Yamaguchi; Yasunori Yamamoto; Erick Antezana; et al. (F1000Research, 2019)

Towards Standardization of Web Service Protocols for NLPaaS. - Jin-Dong Kim; Nancy Ide; Keith Suderman (IWLTP@LREC, 2020)

Enhancing Quality of Corpus Annotation: Construction of the Multi-Layer Corpus Annotation and Simplified Validation of the Corpus Annotation. - Youngbin Noh; Kuntae Kim; Minho Lee; Cheolhun Heo; Yongbin Jeong; Yoosung Jeong; Younggyun Hahm; Taehwan Oh; Hyonsu Choe; Seokwon Park; Jin-Dong Kim; Key-Sun Choi (PACLIC, 2020)

BioHackathon 2015: Semantics of data for life sciences and reproducible research. - Rutger A. Vos; Toshiaki Katayama; Hiroyuki Mishima; Shin Kawano; Shuichi Kawashima; Jin-Dong Kim; Yuki Moriya; Toshiaki Tokimatsu; Atsuko Yamaguchi; Yasunori Yamamoto; Hongyan Wu; Peter Amstutz; et al. (F1000Research, 2020)

Bridging heterogeneous mutation data to enhance disease gene discovery. - Kaiyin Zhou; Yuxing Wang; Kevin Bretonnel Cohen; Jin-Dong Kim; Xiaohang Ma; Zhixue Shen; Xiangyu Meng; Jingbo Xia (Briefings Bioinform., 2021)

COVID-19 Mythbusters in World Languages. - Mana Ashida; Jin-Dong Kim; Seunghun Lee (LREC, 2022)

Knowledge-Driven Mechanistic Enrichment of the Preeclampsia Ignorome. - Tiffany J. Callahan; Adrianne L. Stefanski; Jin-Dong Kim; William A. Baumgartner Jr.; Jordan M. Wyrwa; Lawrence E. Hunter (CoRR, 2022)

High-quality gene/disease embedding in a multi-relational heterogeneous graph after a joint matrix/tensor decomposition. - Kaiyin Zhou; Sheng Zhang; Yuxing Wang; Kevin Bretonnel Cohen; Jin-Dong Kim; Qi Luo; Xinzhi Yao; Xingyu Zhou 003; Jingbo Xia (J. Biomed. Informatics, 2022)

Repurposing Annotation Guidelines to Instruct LLM Annotators: A Case Study. - Kon Woo Kim; Rezarta Islamaj; Jin-Dong Kim; Florian Boudin; Akiko Aizawa (NLDB (2), 2025)

Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features. - Shuya Ikeda; Kiyoko F. Aoki-Kinoshita; Hirokazu Chiba; Susumu Goto; Masae Hosoda; Shuichi Kawashima; Jin-Dong Kim; Yuki Moriya; Tazro Ohta; Hiromasa Ono; Terue Takatsuki; Yasunori Yamamoto; et al. (J. Biomed. Semant., 2025)