Kyubum Lee (Ph.D.)

Postdoctoral Fellow at BioNLP Lab,
National Center for Biotechnology Information (NCBI),
National Library of Medicine (NLM),
National Institutes of Health (NIH),
Bethesda, Maryland, USA

E-mail: KYUBUM [dot] LEE [at] nih [dot] gov
            KYUBUMLEE [at] gmail [dot] com

Research Interests
  • Machine Learning (Including Deep Learning), Data Mining
  • Text Mining, BioNLP, Data Integration
  • Biomedical Informatics
Experience



Recent Projects

Literature Triage using Machine Learning (First Author) [GitHub] [Publication in PLOS Computational Biology]

VarDrugPub: Variant-Gene-Drug relations Database (First Author) [Link] [Publication in BMC Bioinformatics] 

LitVar: Search Engine for Genomic Variants in PubMed and PMC [Link]

HiPub: An application that translates biomedical texts to networks (First Author) [Link] [Publication in Bioinformatics] [AltMetric]

BRONCO: Biomedical entity Relation ONcology COrpus for extracting gene-variant-disease-drug relations (First Author) [Link] [Publication in Database]

ChimerDB (Co-first author, Built a fusion gene DB using Text-mining - ChimerPub) [Link] [Publication in Nucleic Acids Research] [PDF]

BEST:  Biomedical Entity Search Tool (Actively Involved) [Link] [Publication in PLOS ONE]

BEReX:  Biomedical Entity-Relationship eXplorer (Actively Involved) [Link] [Publication in Bioinformatics]

DSigDB: 
 Drug SIGnatures DataBase (Involved in building text-mined drug-gene sets) [Link] [Publication in Bioinformatics]


Links:

Google ScholarResearchGatePubMedLinkedIn


Awards:
  • Recognition for Honorary Award (Recognition and Appreciation of Special Achievement): National Library of Medicine, National Institutes of Health, U.S. Department of Health and Human Services; Dec. 2018
  • Best Paper Award: Korea University; Feb. 2017

Publications:

Journals:

  • Kyubum Lee Maria Livia Famiglietti, Aoife McMahon, Chih-Hsuan Wei, Jacqueline Ann Langdon MacArthur, Sylvain Poux, Lionel Breuza, Alan Bridge, Fiona Cunningham, Ioannis Xenarios and Zhiyong Lu*Scaling up data curation using deep learning: An application to literature triage in genomic variation resources. PLOS Computational Biology, 2018. [Full Text] [Hot paper of the week at NIH Intramural Research News Letter]
  • Alexis Allot†, Yifan Peng†, Chih-Hsuan Wei, Kyubum Lee, Lon Phan, and Zhiyong Lu*LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC. Nucleic Acids Research 2018. [Full Text] [Database Link]
  • Kyubum Lee, Byounggun Kim, Yonghwa Choi, Sunkyu Kim, Wonho Shin, Sunwon Lee, Sungjoon Park, Seongsoon Kim, Aik Choon Tan* and Jaewoo Kang*Deep learning of mutation-gene-drug relations from the literature. BMC Bioinformatics, 2018. DOI: 10.1186/s12859-018-2029-1 [Full Text] [Database Link]
  • Sangrak Lim, Kyubum Lee, Jaewoo Kang: Drug-drug interaction extraction from the literature using a recursive neural network. PLoS ONE, 2018. DOI: 10.1371/journal.pone.0190926 [Full Text]
  • Seongsoon Kim, Donghyeon Park, Yonghwa Choi, Kyubum Lee, Byounggun Kim, Minji Jeon, Jihye Kim, Aik Choon Tan, Jaewoo Kang*A Pilot Study of Biomedical Text Comprehension using an Attention-Based Deep Neural Reader: Design and Experimental Analysis JMIR Medical Informatics 2017. DOI: 10.2196/medinform.8751 [Full Text]
  • Myunggyo Lee†, Kyubum Lee†, Namhee Yu†, Insu Jang†, Ikjung Choi, Pora Kim, Ye Eun Jang, Byounggun Kim, Sunkyu Kim, Byungwook Lee, Jaewoo Kang*, and Sanghyuk Lee*: ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data miningNucleic Acids Research 2017. DOI:10.1093/nar/gkw1083 ( These authors contributed equally) [Full Text] [Database Link]
  • Kyubum Lee, Wonho Shin, Byunggun Kim, Sunwon Lee, Yonghwa Choi, Sunkyu Kim, Minji Jeon, Aik Choon Tan* and Jaewoo Kang*: HiPub: Translating PubMed and PMC Texts to Networks for Knowledge Discovery. Bioinformatics 08/2016; 32(18). DOI:10.1093/bioinformatics/btw511 [Full Text] [Link]
  • Kyubum Lee, Sunwon Lee, Sungjoon Park, Sunkyu Kim, Suhkyung Kim, Kwanghun Choi, Aik Choon Tan* and Jaewoo Kang*: BRONCO: Biomedical entity Relation ONcology COrpus for extracting gene-variant-disease-drug relations. Database The Journal of Biological Databases and Curation 04/2016; 2016. DOI:10.1093/database/baw043 [Full Text]
  • Jocelyn Barbosa, Kyubum Lee, Sunwon Lee, Bilal Lodhi, Jae-Gu Cho, Woo-Keun Seo, Jaewoo Kang*: Efficient quantitative assessment of facial paralysis using iris segmentation and active contour-based key points detection with hybrid classifier. BMC Medical Imaging 12/2016; 16(1). DOI:10.1186/s12880-016-0117-0 [Full Text]
  • Sunwon Lee†, Donghyeon Kim†, Kyubum Lee, Jaehoon Choi, Seongsoon Kim, Minji Jeon, Sangrak Lim, Donghee Choi, Sunkyu Kim, Aik-Choon Tan, Jaewoo Kang*: BEST: Next-Generation Biomedical Entity Search Tool for Knowledge Discovery from Biomedical Literature. PLoS ONE 10/2016; 11(10). DOI:10.1371/journal.pone.0164680 († These authors contributed equally to the work.) [Full Text] [Link]
  • Minjae Yoo, Jimin Shin, Jihye Kim, Karen A Ryall, Kyubum Lee, Sunwon Lee, Minji Jeon, Jaewoo Kang, Aik Choon Tan*: DSigDB: Drug Signatures Database for Gene Set Analysis. Bioinformatics 05/2015; 31(18). DOI:10.1093/bioinformatics/btv313 [Link] [Full Text]
  • Woo Keun Seo, Jaewoo Kang, Minji Jeon, Kyubum Lee, Sunwon Lee, Ji Hyun Kim, Kyungmi Oh, Seong Beom Koh: Feasibility of Using a Mobile Application for the Monitoring and Management of Stroke-Associated Risk Factors. Journal of Clinical Neurology 04/2015; 11(2). DOI:10.3988/jcn.2015.11.2.142 [Link]
  • Minji Jeon, Sunwon Lee, Kyubum Lee, Aik-Choon Tan, Jaewoo Kang*: BEReX: Biomedical Entity-Relationship eXplorer. Bioinformatics 01/2014; 30(1). DOI:10.1093/bioinformatics/btt598 [Link] [Full Text]
  • Junkyu Lee, Seongsoon Kim, Sunwon Lee, Kyubum Lee, Jaewoo Kang*: On the efficacy of per-relation basis performance evaluation for PPI extraction and a high-precision rule-based approach. BMC Medical Informatics and Decision Making 04/2013; 13(1). DOI:10.1186/1472-6947-13-S1-S7 [Link]
  • Jaehoon Choi, Donghyeon Kim, Seongsoon Kim, Sunwon Lee, Kyubum Lee, Jaewoo Kang*: BOSS: Context-enhanced search for biomedical objects. BMC Medical Informatics and Decision Making 04/2012; 12 Suppl 1(Suppl 1). DOI:10.1186/1472-6947-12-S1-S7 [Link]
  • Hanjun Shin, Ki Hoon Kim, Chihwan Song, Injoon Lee, Kyubum Lee, Jaewoo Kang, Yoon Kyoo Kang*: Electrodiagnosis support system for localizing neural injury in an upper limb. Journal of the American Medical Informatics Association 05/2010; 17(3). DOI:10.1136/jamia.2009.001594 [Link]
  • Sunwon Lee, Kyubum Lee, Jaewoo Kang*, Jaehoon Choi, Junho Oh:   Trends in Personalized Medicine Research. Communications of the Korean Institute of Information Scientists and Engineers, Vol.29, Issue 4, Pages:19-25, Apr 2011 [Written in Korean]

        Conferences / Meetings:

             Proceedings:

  • Chih-Hsuan Wei, Kyubum Lee, Robert Leaman, Zhiyong Lu: Biomedical Mention Disambiguation Using a Deep Learning Approach. The 10th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB 2019), Niagara Falls, NY; Sept 2019 [Accepted]
  • Donghyeon Kim†, Sunwon Lee†, Kyubum Lee, Jaehoon Choi, Seongsoon Kim, Minji Jeon, Sangrak Lim, Donghee Choi, Aik-Choon Tan, Jaewoo Kang*: BEST: Next-Generation Biomedical Entity Search Tool for Knowledge Discovery from Biomedical LiteratureThe 5th Annual Translational Bioinformatics Conference (TBC 2015), Tokyo, Japan; Sept. 2015  († These authors contributed equally to the work.)
  • Kyubum Lee, Sunwon Lee, Minji Jeon, Jaehoon Choi, Jaewoo Kang*: Drug-drug interaction analysis using heterogeneous biological information network. IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012), Philadelphia, USA; Oct. 2012 [Link]
  • Junkyu Lee, Seongsoon Kim, Sunwon Lee, Kyubum Lee, Jaewoo Kang*: High Precision Rule Based PPI Extraction and Per-Pair Basis Performance Evaluation. ACM sixth international workshop on Data and text mining in biomedical informatics (DTMBIO 2012), Maui, Hawaii, USA; Oct. 2012
  • Kyubum Lee, Sunwon Lee, Jaewoo Kang*: SNP Grouping Method Based on PPI Network Information. The 37th Conference of the Korea Information Processing Society, Apr 2012 [Written in Korean]
  • Taewon Joh, Kyubum Lee, Jaewoo Kang*: Comparative analysis of Biomedical Databases and Text mining Technologies. The 34th Conference of the Korea Information Processing Society, Nov 2010 [Written in Korean]
  • Hojun Kim, Seongyeon Won, Seungwoo Gang, Kyubum Lee, Byounggun Kim, Sunkyu Kim, Jaewoo Kang*Research on Identifying Mutation-Drug Relationship in Biomedical Literature Using Biomedical Context based pre-trained word embedding (KIPS 2017 Spring), Jeju, Korea; April 2017 [Written in Korean]
    Posters:
  • Kyubum Lee, Chih-Hsuan Wei, Livia Famiglietti, Sylvain Poux, Lionel Breuza, Alan Bridge, Ioannis Xenarios and Zhiyong Lu*: Scaling up data curation using deep learning: An application to literature triage in genomic variation resources. ISMB 2018, Chicago, USA; July 2018 
  • Kyubum Lee, Byounggun Kim, Yonghwa Choi, Sunkyu Kim, Wonho Shin, Sunwon Lee, Sungjoon Park, Seongsoon Kim, Aik Choon Tan and Jaewoo Kang*Deep learning of mutation-gene-drug relations from the literature for precision medicine. ISMB/ECCB 2017, Prague, Czech Republic; July 2017 (doi: 10.7490/f1000research.1114641.1) [Poster] [Link]
    Talks:
  • Scaling up data curation using machine learning: An application to literature triage in genomic variation resources. CBB Seminar, NCBI, NLM, NIH; Feb. 2019
  • Biomedical Literature Search, Mining and Applications: College of Medicine, Seoul National University; Nov. 2018 [Online talk]
  • Machine-assisted Variant CurationBiomedical Linked Annotation Hackathon 4 (BLAH4), Kashiwa, Japan; Jan. 2018 [Link]

Education:

Data Mining & Information Systems Lab
            9/12 – 2/17
Korea University, Seoul, Korea
Ph.D. in Computer Science and Engineering (Data Mining and Machine Learning)
Advisor : Prof. Jaewoo Kang

Data Mining & Information Systems Lab            9/10 – 8/12
Korea University, Seoul, Korea
M.S. in Computer Science & Bioinformatics
(Interdisciplinary Graduate Program in Bioinformatics)
Advisor : Prof. Jaewoo Kang

Korea University, Seoul, Korea                              9/08 – 8/10
B.S. in Computer Science

Korea University, Seoul, Korea                              3/02 – 8/08
B.S. in Life Science (On leave: 9/03 – 8/05, Military Service)