International Journal

† Joint first author, * Corresponding author

• Assessment of the Limits of Predictability of Protein and Phosphorylation Levels in Cancer
  Mi Yang, Francesca Petralia, Zhi Li, Hongyang Li, Xiaoyu Song, Sunkyu Kim, Heewon Lee, Han Yu, Bora Lee, Seohui Bae, Eunji Heo, Jan Kaczmarczyk, Piotr Stępniak, Michał Warchoł, Thomas Yu, Anna Calinawan, Paul Boutros, Samuel Payne, Emily Boja, Henry Rodriguez, Gustavo Stolovitzky, Yuanfang Guan, Jaewoo Kang, Pei Wang, David Fenyö*
  Cell systems, in press

• Bipartite Link Prediction by Intra-class Connection based Triadic Closure
  Jungwoon Shin, Keonwoo Kim, Donghyeon Park, Sunkyu Kim, Jaewoo Kang*
  IEEE Access, July 2020

• Improved survival analysis by learning shared genomic information from pan-cancer data
  Sunkyu Kim, Keonwoo Kim, Junseok Choe, Inggeol Lee, Jaewoo Kang*
  Bioinformatics, July 2020

• Building PubMed Knowledge Graph
  Jian Xu, Sunkyu Kim, Min Song, Minbyul Jeong, Donghyeon Kim, Jaewoo Kang, Justin F. Rousseau, Xin Li, Weijia Xu, Vetle I. Torvik, Yi Bu, Chongyan Chen, Islam Akef Ebeid, Daifeng Li, Ying Ding*
  Scientific data, June 2020

• Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease
  Mike J. Mason, Carolina Schinke, Christine L. P. Eng, Fadi Towfic, Fred Gruber, Andrew Dervan, Brian S. White, Aditya Pratapa, Yuanfang Guan, Hongjie Chen, Yi Cui, Bailiang Li, Thomas Yu, Elias Chaibub Neto, Konstantinos Mavrommatis, Maria Ortiz, Valeriy Lyzogubov, Kamlesh Bisht, Hongyue Y. Dai, Frank Schmitz, Erin Flynt, Dan Rozelle, Samuel A. Danziger, Alexander Ratushny, Multiple Myeloma DREAM Consortium, William S. Dalton, Hartmut Goldschmidt, Herve Avet-Loiseau, Mehmet Samur, Boris Hayete, Pieter Sonneveld, Kenneth H. Shain, Nikhil Munshi, Daniel Auclair, Dirk Hose, Gareth Morgan, Matthew Trotter, Douglas Bassett, Jonathan Goke, Brian A. Walker, Anjan Thakurta & Justin Guinney*
  Leukemia, Feb. 2020

• ChimerDB 4.0: an updated and expanded database of fusion genes
  Ye Eun Jang†, Insu Jang†, Sunkyu Kim†, Subin Cho†, Daehan Kim, Keonwoo Kim, Jaewon Kim, Jimin Hwang, Sangok Kim, Jaesang Kim, Jaewoo Kang, Byungwook Lee*, Sanghyuk Lee*
  Nucleic Acids Research, Nov. 2019

• BioBERT: pre-trained biomedical language representation model for biomedical text mining
  Jinhyuk Lee†, Wonjin Yoon†, Sungdong Kim, Donghyeon Kim, Sunkyu Kim, Chan Ho So, Jaewoo Kang*
  Bioinformatics, Sep. 2019

• ReSimNet: Drug Response Similarity Prediction using Siamese Neural Networks
  Minji Jeon†, Donghyeon Park†, Jinhyuk Lee, Hwisang Jeon, Miyoung Ko, Sunkyu Kim, Yonghwa Choi, Aik-Choon Tan, Jaewoo Kang*
  Bioinformatics, May 2019

• Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
  Michael P. Menden, Dennis Wang, Mike J. Mason, Bence Szalai, Krishna C. Bulusu, Yuanfang Guan, Thomas Yu, Jaewoo Kang, Minji Jeon, Russ Wolfinger, Tin Nguyen, Mikhail Zaslavskiy, AstraZeneca-Sanger Drug Combination DREAM Consortium, In Sock Jang, Zara Ghazoui, Mehmet Eren Ahsen, Robert Vogel, Elias Chaibub Neto, Thea Norman, Eric KY Tang, Mathew J Garnett, Giovanni Di Veroli, Stephen Fawell, Gustavo Stolovitzky, Justin Guinney, Jonathan R Dry, Julio Saez-Rodriguez*
  Nature Communications, June 2019 (Consortium Author)

• Deep learning of mutation-gene-drug relations from the literature
  Kyubum Lee†, Byounggun Kim†, Yonghwa Choi, Sunkyu Kim, Wonho Shin, Sunwon Lee, Sungjoon Park, Seongsoon Kim, Aik Choon Tan, Jaewoo Kang*
  BMC bioinformatics, Dec. 2018

• Mut2Vec: distributed representation of cancerous mutations
  Sunkyu Kim†, Heewon Lee†, Keonwoo Kim, Jaewoo Kang*
  BMC medical genomics, Apr. 2018

• In silico drug combination discovery for personalized cancer therapy
  Minji Jeon, Sunkyu Kim, Sungjoon Park, Heewon Lee, Jaewoo Kang*
  BMC systems biology, Mar. 2018

• ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining
  Myunggyo Lee†, Kyubum Lee†, Namhee Yu†, Insu Jang†, Ikjung Choi, Pora Kim, Ye Eun Jang, Byounggun Kim, Sunkyu Kim, Byungwook Lee, Jaewoo Kang*, Sanghyuk Lee*
  Nucleic Acids Research, Nov. 2016

• BEST: next-generation biomedical entity search tool for knowledge discovery from biomedical literature
  Sunwon Lee†, Donghyeon Kim†, Kyubum Lee, Jaehoon Choi, Seongsoon Kim, Minji Jeon, Sangrak Lim, Donghee Choi, Sunkyu Kim, Aik-Choon Tan, Jaewoo Kang*
  PloS one, Oct. 2016

• HiPub: translating PubMed and PMC texts to networks for knowledge discovery
  Kyubum Lee, Wonho Shin, Byounggun Kim, Sunwon Lee, Yonghwa Choi, Sunkyu Kim, Minji Jeon, Aik Choon Tan*, Jaewoo Kang*
  Bioinformatics, Aug. 2016

• BRONCO: Biomedical entity Relation ONcology COrpus for extracting gene-variant-disease-drug relations
  Kyubum Lee, Sunwon Lee, Sungjoon Park, Sunkyu Kim, Suhkyung Kim, Kwanghun Choi, Aik Choon Tan*, Jaewoo Kang*
  Database, Jan. 2016

International Conference

• Improved survival analysis by learning shared genomic information from pan-cancer data
  Sunkyu Kim, Keonwoo Kim, Junseok Choe, Inggeol Lee, Jaewoo Kang*
  ISMB 2020; Virtual conference; Oral proceeding presentation

Domestic Conference

• Diagnostic Model for Korean Major Depressive Disorder using Multi-Modal Data
  Yonghwa Choi, Minji Jeon, Sunkyu Kim, Kyu-Man Han, Eunsoo Won, Aram Kim, Byung-Joo Ham, and Jaewoo Kang*
  Korean Institute of Information Scientists and Engineers (KIISE), Dec. 2018

• Predicting The Liveliness In Korean Educational Videos Using Various Machine Learning Techniques
  Daehan Kim, Sunkyu Kim, Yonghwa Choi, Hwisang Jeon, Jaewoo Kang*
  Korean Institute of Information Scientists and Engineers (KIISE), Dec. 2018

• Development and utilization of Biomedical Entity Search Tool API
  Sunkyu Kim, Sunwon Lee, Kyubum Lee, Minji Jeon, Kwanghun Choi, Sungjoon Park, Jaewoo Kang*
  Korean Institute of Information Scientists and Engineers (KIISE), Dec. 2015