Kyubum Lee (Ph.D.)
Data Mining and Information Systems Lab [Link]
Research Professor - Postdoctoral Researcher
Korea University.
Seoul, Korea
Email : kyubumlee [at] korea [dot] ac [dot] kr
            kyubumlee [at] gmail [dot] com


Research Interests
Data Mining, Text Mining, Deep Learning,
Biomedical Informatics, BioNLP,
Data Integration


Educations
Data Mining & Information Systems Lab            9/12 – 2/17
Korea University, Seoul, Korea
Ph.D. in Computer Science.
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)


Experience
Data Mining & Information Systems Lab            2/17 – Present
Korea University, Seoul, Korea
Research Professor - Postdoctoral Researcher (PI: Prof. Jaewoo Kang)

Translational Bioinformatics and Cancer Systems Biology Laboratory [Link]      8/14 – 2/15
 University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
Exchange Researcher (PI: Prof. Aik-Choon Tan)
 - Research on cancer mutation knowledge-base
 - Research on DSigDB and Biomedical Entity Relation Corpus (BRONCO)


Recent Projects
VarDrugPub: Variant-Gene-Drug relations Database (First Author)
[Link] (Under Review)

HiPub: An application that translates biomedical texts to networks (First Author)

BRONCO: Biomedical entity Relation ONcology COrpus for extracting gene-variant-disease-drug relations (First Author)

ChimerDB (Co-first author, Built a fusion gene DB using Text-mining - ChimerPub)

BEST:  Biomedical Entity Search Tool (Actively Involved)

BEReX:  Biomedical Entity-Relationship eXplorer (Actively Involved)

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


Links
ResearchGate
Google Scholar
PubMed

Publications

Journals:

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 mining. Nucleic Acids Research 2017. DOI:10.1093/nar/gkw1083 († These authors contributed equally) [Full Text] [Link]

Kyubum Lee, Wonho Shin, Byunggun Kim, Sunwon Lee, Yonghwa Choi, Sunkyu Kim, Minji Jeon, Aik Choon Tan, 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, 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:

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]

Kyubum Lee, Sunwon Lee, Jaewoo Kang: Extracting Knowledge from Biomedical Literature. The 1st International Conferences on Interdisciplinary research on Computer science, Psychology, and Education (ICICPE 2017), Da Nang, Vietnam; Feb. 2017 [Poster]

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 Literature. The 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]