Rhee, Je-Keun



Rhee, Je-Keun
 
Assistant Professor, Ph. D
School of Systems Biomedical Science, 
Soongsil University 
 
 
    Education
  • 2014. 2. Ph.D. in Bioinformatics, Seoul National University, Seoul, Korea
  • 2004. 2. (double major) BS in Computer Science & Engineering, Korea University, Seoul, Korea
  • 2004. 2. BS in Life Science, Korea University, Seoul, Korea


    Professional Experiences
  • 2019. 9 ~   : Assistant Professor, School of systems Biomedical Science, Soongsil University
  • 2018. 9 ~ 2019. 8. : Assistant Professor, Department of Life Science in Dentistry, School of Dentistry, Pusan National University 
  • 2014. 4. ~ 2018. 8. : Research Professor, Cancer Research Institute / Department of Medical Informatics, The Catholic University of Korea 
  • 2014. 3. ~ 2014. 8. : Lecturer, Soongsil University, College of Information Technology
  • 2012. 5. ~ 2014. 3. : Researcher, University of Ulsan College of Medicine (Asan Medical Center)
  • 2011. 3. ~ 2011. 8. : Visiting Scholar, School of Informatics and Computing (SoIC), Indiana University, USA
  • 2004. 3. ~ 2014. 2. : Researcher, Center for Bioinformation Technology (CBIT), Institute of Computer Technology (ICT), Seoul National University
 

 
    Journal Papers
  • H. Lee, S. Jeong, Y. Yu, J. Kang, H. Sun, J.-K. Rhee, Y. H. Kim, Risk of metastatic pheochromocytoma and paraganglioma in SDHx mutation carriers: A systematic review and updated meta-analysis, Journal of Medical Genetics, 2019 (Accepted)
  • Joong Chae Na, Inbok Lee, Je-Keun Rhee*, and Soo-Yong Shin*, Fast single individual haplotyping method using GPGPU, Computers in Biology and Medicine, 2019 (In Press)
  • Inki Kim, Yeon‐Sook Choi, Jae Hwi Song, Eun A Choi, Sojung Park, Eun Ji Lee, Je‐Keun Rhee, Song Cheol Kim, Suhwan Chang, A drug‐repositioning screen for primary pancreatic ductal adenocarcinoma cells identifies 6‐thioguanine as an effective therapeutic agent for TPMT‐low cancer cells, Molecular Oncology, 12(9):1526-1539, 2018.
  • Je-Keun Rhee, Soo-Jin Kim, Byoung-Tak Zhang, Identifying DNA Methylation Modules Associated with a Cancer by Probabilistic Evolutionary Learning , IEEE Computational Intelligence Magazine, 13(3): 12-19, 2018.
  • Je-Keun Rhee and Tae-Min Kim, Population-based statistical inference for temporal sequence of somatic mutations in cancer genomes, BMC Medical Genomics, 11(Suppl 2):29, 2018.
  • Dinh-Duc Nguyen, Dong Gyu Lee, Sinae Kim, Keunsoo Kang, Je-Keun Rhee, Suhwan Chang, Integrative Bioinformatics and Functional Analyses of GEO, ENCODE, and TCGA Reveal FADD as a Direct Target of the Tumor Suppressor BRCA1. Int. J. Mol. Sci. 2018, 19, 1458.
  • Je-Keun Rhee*, Jinseon Yoo, Kyu Ryung Kim, Jeeyoon Kim, Yong-Jae Lee, Byoung Chul Cho, and Tae-Min Kim, Identification of local clusters of mutation hotspots in cancer-related genes and their biological relevance, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018. doi: 10.1109/TCBB.2018.2813375 (In Press)
  • Joong Chae Na, Jong-Chan Lee, Je-Keun Rhee*, and Soo-Yong Shin*, PEATH: Single Individual Haplotyping by Probabilistic Evolutionary Algorithm with Toggling, Bioinformtics, 34(11): 1801-1807, 2018. (* Co-coresponding author)
  • Je-Keun Rhee*, Yu Chae Jung*, Kyu Ryung Kim, Jinseon Yoo, Jeeyoon Kim, Yong-Jae Lee, Yoon Ho Ko, Han Hong Lee, Byoung Chul Cho, and Tae-Min Kim, Impact of tumor purity on immune gene expression and clustering analyses across multiple cancer types, Cancer Immunology Research, 6(1):87-97, 2018.
  • Jo-Eun Jeong, Je-Keun Rhee, Tae-Min Kim, Su-Min Kwak, Sol-hee Bang, Hyun Cho, Young-Hoon Cheon, Jung Ah Min, Gil Sang Yoo, Kyudong Kim, Jung-Seok Choi, Sam-Wook Choi, Dai-Jin Kim, The association between the nicotinic acetylcholine receptor α4 subunit gene (CHRNA4) rs1044396 and Internet gaming disorder in Korean male adults, PLoS One, 12(12): e0188358, 2017.
  • Myoungshin Kim*, Je-Keun Rhee*, Hayoung Choi, Ahlm Kwon, Jiyeon Kim, Gun Dong Lee, Dong Wook Jekarl, Seungok Lee, Yonggoo Kim, Tae-Min Kim, Passage-dependent accumulation of somatic mutations in mesenchymal stromal cells during in vitro culture revealed by whole genome sequencing, Scientific Reports, 7: 14508, 2017.
  • Je-Keun Rhee, Sejoon Lee, Woong-Yang Park, Young-Ho Kim, Tae-Min Kim., Allelic imbalance of somatic mutations in cancer genomes and transcriptomes, Scientific Reports, 7: 1653, 2017.
  • Je-Keun Rhee, Jin-Hee Lee, Hae Hyung Yang, Tae-Min Kim, Kun-Ho Yoon, DNA methylation profiles of blood cells are distinct between early-onset obese and control individuals, Genomic & Informatics, 15(1):28-37, 2017.
  • Sung Hak Lee*, Seung Hyun Jung*, Tae-Min Kim, Je-Keun Rhee, Hyeon-Chun Park, Min Sung Kim, Sung Soo Kim, Chang Hyeok An, Sug Hyung Lee, Yeun-Jun Chung, Whole-exome sequencing identified mutational profiles of high-grade colon adenomas, OncoTarget, 8:6579-6588, 2017.
  • Youn Jin Choi*, Je-Keun Rhee*, Soo Young Hur, Min Sung Kim, Sung Hak Lee, Yeun-Jun Chung, Tae-Min Kim, Sug Hyung Lee, Intra-individual genomic heterogeneity of high-grade serous carcinoma of ovary and clinical utility of ascitic cancer cells for mutation profiling, Journal of Pathology, 241(1):57-66, 2017.
  • Jeong-Yu Kim, Jo-Eun Jeong, Je-Keun Rhee, Hyun Cho, Ji-Won Chun, Tae-Min Kim, Sam-Wook Choi, Jung-Seok Choi, Dai-Jin Kim, Targeted exome sequencing for the identification of a protective variant against Internet gaming disorder at rs2229910 of neurotrophic tyrosine kinase receptor, type 3 (NTRK3): A pilot study, Journal of Behavioral Addictions, 5(4):631-638, 2016.
  • Jaeyun Jung*, Hyun Cue Lee*, Hyang Sook Seol, Yeon Sook Choi, Eunji Kim, Eun Ji Lee, Je-Keun Rhee, Shree Ram Singh, Eun Sung Jun, Buhm Han, Seung Mo Hong, Song Cheol Kim, Suhwan Chang, Generation and molecular characterization of pancreatic cancer patient-derived xenografts reveals their heterologous natureOncoTarget, 7(38):62533-62546, 2016.
  • Chul-Hyun Lim, Yu Kyung Cho, Sang Woo Kim, Myung-Gyu Choi, Je-Keun Rhee, Yeun-Jun Chung, Sug-Hyung Lee, Tae-Min Kim, The chronological sequence of somatic mutations in early gastric carcinogenesis inferred from multiregion sequencing of gastric adenomas, OncoTarget, 7(26):39758-39767, 2016.
  • Young-Ho Kim, Eun-Kyung Hong, Sun-Young Kong, Sung-Sik Han, Seoung-Hoon Kim, Je-Keun Rhee, Soo-Kyung Hwang, Sang-Jae Park, Tae-Min Kim, Two classes of intrahepatic cholangiocarcinoma defined by relative abundance of mutations and copy number alterations, OncoTarget, 7(17):23825-23836, 2016.
  • Kie Kyon Huang, Kang Won Jang, Sangwoo Kim, Han Sang Kim, Sung-Moo Kim, Hyeong Ju Kwon, Hye Ryun Kim, Hwan Jung Yun, Myung Ju Ahn, Keon Uk Park, Kalpana Ramnayanan, John McPherson, Shenli Zhang, Je-Keun Rhee, André Vettore, Kakoli Das, Takatsugu Ishimoto, Joo-Hang Kim, Yoon Woo Koh, Se Hun Kim, Eun Chang Choi, Bin Tean Teh, Steve Rozen, Tae-Min Kim, Patrick Tan, and Byoung Chul Cho, Exome sequencing reveals recurrent REV3L mutations in cisplatin-resistant squamous cell carcinoma of head and neck, Scientific Reports, 6: 19552, 2016.
  • Hyang Sook Seol, Sang Eun Lee, Joon Seon Song, Je-Keun Rhee, Shree Ram Singh, Suhwan Chang, Se Jin Jang, Complement proteins C7 and CFH control the stemness of liver cancer cells via LSF-1, Cancer Letters, 372 (1): 24–35, 2016.
  • Je-Keun Rhee, Honglan Li, Je-Gun Joung, Kyu-Baek Hwang, Byoung-Tak Zhang, Soo-Yong Shin, Survey of Computational Haplotype Determination Methods for Single Individual, Genes & Genomics, Volume 38, Issue 1, 1-12, 2016.
  • Tae-Min Kim, Chang Hyeok An, Je-Keun Rhee, Seung-Hyun Jung, Sung Hak Lee, In-Pyo Baek, Min Sung Kim, Sug Hyung Lee, Yeun-Jun Chung, Clonal origins and parallel evolution of regionally synchronous colorectal adenoma and carcinoma. Oncotarget, 6(29):27725-27735, 2015
  • Tae-Min Kim,  Seung-Hyun Jung, Chang-Hyeok An, Sung-Hak Lee, In-Pyo Baek, Min Kim, Sung-Won Park, Je-Keun Rhee, Sug H Lee, and Yeun-Jun Chung, Subclonal genomic architectures of primary and metastatic colorectal cancer based on intratumoral genetic heterogeneity, Clinincal Cancer Research, 21:4461-4472, 2015
  • Kim S, Rhee J, Yu HJ, Lee HJ, Lee EJ, Lee JW, Yu JH, Son BH, Gong G, Kim SB, Singh SR, Ahn SH, Chang S, Bioinformatic and metabolomic analysis reveals miR-155 regulates thiamine level in breast cancer, Cancer Lett., 357(2):488-497, 2015
  • J.-K. Rhee and S.-Y. Shin, Computational approaches for reconstruction of single individual haplotypes (in Korean), Communications of the Korea Information Science Society, 32(3): 33-40, 2014.
  • H. Li, J.-K. Rhee, B.-T. Zhang, K.-B. Hwang, S.-Y. Shin, A Survey on Computational Methods for Haplotype Phasing (in Korean), Journal of the Korea Information Science Society: Software and Applications, 40(11): 663-674, 2013.
  • J.-K. Rhee, S.-Y. Shin, B.-T. Zhang, Construction of microRNA functional families by a mixture model of position weight matrices, PeerJ, 1: e199, 2013.
  • J.-K. Rhee, K. Kim, H. Chae, J. Evans, P. Yan, B.-T. Zhang, J. Gray, P. Spellman, T. H-M Huang, K. P. Nephew and S. Kim, Integrated analysis of genome-wide DNA methylation and gene expression profiles in molecular subtypes of breast cancer, Nucleic Acids Research, 41(18): 8464-8474, 2013.
  • X. Rao, J. Evans, H. Chae, J. Pilrose, S. Kim, P. Yan, R.-L. Huang, H.-C. Lai, H. Lin, Y. Liu, D. Miller, J.-K. Rhee, Y.-W. Huang, F. Gu, J.W. Gray, T.M. Huang and K.P. Nephew, CpG island shore methylation regulates caveolin-1 expression in breast cancer, Oncogene, 32: 4519-4528, 2013.
  • Je-Keun Rhee, Je-Gun Joung, Jeong-Ho Chang, Zhangjun Fei and Byoung-Tak Zhang, Identification of cell cycle-related regulatory motifs using a kernel canonical correlation analysis, BMC Genomics, 10(Suppl 3):S29, 2009.
  • Je-Keun Rhee, Jung-Woo Ha, Seol-Hui Bae, Soo-Jin Kim, Min Su Lee, Keun-Joon Park, and Byoung-Tak Zhang, Identifying Compound Risk Factors of Disease by Evolutionary Learning of SNP Combinatorial Features (in Korean), Journal of KIISE : Computing Practices and Letters, 15(12):928-932, 2009.
  • M. Oh, H. Lee, Y.-K. Kim, J.-W. Nam, J.-K. Rhee, B.-T. Zhang, V.N. Kim, I. Lee, Identification and characterization of small RNAs from vernalized Arabidopsis thaliana, Journal of Plant Biology, 50(5):562-572, 2007.
  • K.-B. Hwang, J.-G. Joung, J.-W. Nam, B.-H. Kim, J.-K. Rhee, and B.-T. Zhang, Machine learning methods for the analysis of biological data (in Korean), Communications of the Korea Information Science Society, 25(3):35-45, 2007.
  • S.-K. Kim*, J.-W. Nam*, J.-K. Rhee, W.-J. Lee, B.-T. Zhang. miTarget: microRNA target-gene prediction using a Support Vector Machine. BMC Bioinformatics 7(1): 411, 2006.
  • Jinju Han*, Yoontae Lee*, Kyu-Hyun Yeom*, Jin-Wu Nam, Inha Hur, Je-Keun Rhee, Sunyoung Son, Yunje Cho, Byoung-Tak Zhang and V. Narry Kim. Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex, Cell 125: 887-901, 2006.

                    (* These authors equally contributed to that work.)

 
    Invited Talks & Lectures
  • Machine learning in genome, transcriptome, and epigenome data analysis, Gacheon University, Incheon, Korea, Sept. 6, 2019
  • Genomic and epigenomic data analysis using probabilistic evolutionary learning, The 17th ABC (Asian Bioioformatics Consortium) Symposium, Gui'an, Guizhou Province, China, Aug. 23, 2019
  • Multi-omics data analysis, 14th Asian Institute in Statistical Genetics and Genomics, Korea, July 19-20, 2019
  • Artificial intelligence for biomedical data analysis, AI+X forum, IBS, Daejeon, Korea, June 21, 2019
  • Computational analysis of single-to-multi-omics data in human disease, Interdisciplinary Society of Genetic & Genomic Medicine, Daegu, Korea, Mar. 8, 2019.
  • Computational analysis of biomedical data, Korean Society for Vascular Biology and Medicine, Busan, Korea, Feb. 14, 2019
  • Machine Learning in Biomedical Data Analysis (Tutorial), KSC2018, Korea, Dec. 19, 2018
  • Genome and epigenome data analysis using probabilistic evolutionary algorithm, Department of Computer Science, Sookmyoung Women's University, Seoul, Korea, Nov. 26, 2018
  • Computational analysis of high-thoughput sequencing data in biomedical research, BK21 plus seminar, Pusan National University, Yangsan-si, Korea, Oct. 30, 2018
  • Understanding cancer genome through computational analysis of next-generation sequencing data, Biomedical Research Institute, Pusan National University Hospital, Korea, Sept. 6, 2018
  • Needs for Bio-IT expertise, Becoming a Software Convergence Expert, Career-linking Program, Department of Computer Science, Sookmyoung Women's University, Seoul, Korea, Sept. 11, 2017
  • Cancer Genome Analysis, Bioinformatics & Machine Learning for Life Scientists (BIML 2017) Workshop, Korean Society for Bioinformaitcs (KSBI), Feb. 17, 2017
  • Bigdata Analysis with R, Department of Multimedia Science, Sookmyoung Women's University, Seoul, Korea, Sept. 25, 2015
  • Introduction to R for Bigdata Analysis, Department of Multimedia Science, Sookmyoung Women's University, Seoul, Korea, Sept. 18, 2015
  • Machine Learning for Data-Driven Biolgy, Hanyang Universiy, Seoul, Korea, July 23-24, 2015
  • Clustering and Classification Analysis, Department of Multimidia Science, Sookmyoung Women's University, Seoul, Korea, June 2 - June 4, 2015
  • Bigdata mining with R, CogAnalytics Tutorial #8, National Association of Cognitive Science Industries (NACSI), Seoul National University, Seoul, Korea, Apr. 17, 2015
  • Introduction to Machine Learning, Department of Multimidia Science, Sookmyoung Women's University, Seoul, Korea, May 31 - April 2, 2015
  • Database for Bio-BigData Analysis, Certified Scientist in BioMedical Informatics (CSBMI), Biomedical Informatics Eductaion and Training Center (BITEC), Seoul National University Hospital (SNUH), Seoul, Korea, Nov. 6 - 27, 2014
  • Single individual haplotype phasing, Sejong University, Seoul, Korea, Nov. 25, 2014
  • Machine Learning with R, CogAnalytics Tutorial, National Association of Cognitive Science Industries (NACSI), Seoul National University, Seoul, Korea, Oct. 17, 2014
  • Sequence Analysis, Tutorial for Bioinformatics, Hanyang University, Seoul, Korea, Aug. 29, 2014
  • Computational analysis of DNA methylation status in cancer, Hanyang University, Seoul, Korea, March 4, 2014
  • Data Mining, School of Computing, College of Information Technology, Soongsil University, Seoul, Korea, Spring Semester, 2014
  • Machine Learning Algorithm Practice - Classification and Evolutionary Algorithms, Samsung Advanced Technology Traning Institute, Samsung Electronics Co. Ltd., Nov. 12-15, 2013.
  • Machine Learning - Practices in Classification and Bayesian Networks, Samsung Advanced Technology Traning Institute, Samsung Electronics Co. Ltd., Oct. 28-31, 2013.
  • Integrated analysis of genome-wide DNA methylation and gene expression profiles in molecular subtypes of breast cancer, Bioinformatics Day, Seoul National University, Oct. 7, 2013.
  • Machine Learning - Practices in Clustering and Bayesian Networks, Samsung Advanced Technology Traning Institute, Samsung Electronics Co. Ltd., Sept. 10-13, 2013.
  • Machine Learning Algorithm Practice - Classficiation and Evolutionary Algorithms, Samsung Advanced Technology Traning Institute, Samsung Electronics Co. Ltd., June 11-14, 2013.
  • Machine Learning Algorithm Practice - Classficiation and Evolutionary Algorithms, Samsung Advanced Technology Traning Institute, Samsung Electronics Co. Ltd., April 23-26, 2013.
  • Cognitive Computing - Practices in Bayesian Networks, Samsung Advanced Technology Traning Institute, Samsung Electronics Co. Ltd., March 12, 2013.
  • Machine Learning Algorithm Practice - Classficiation and Evolutionary Algorithms, Samsung Advanced Technology Traning Institute, Samsung Electronics Co. Ltd., Nov. 12-15, 2012.
  • Machine Learning Algorithm Practice - Classficiation and Evolutionary Algorithms, Samsung Advanced Technology Traning Institute, Samsung Electronics Co. Ltd., May. 21-24, 2012.
  • Cognitive Computing - Practices in Bayesian Networks, Samsung Advanced Technology Traning Institute, Samsung Electronics Co. Ltd., April. 10, 2012.
  • Computer Programming, Quality of Life Technology (QoLT) Center, Seoul National University, Jan. 2 - 30, 2012.
  • Machine Learning - Practices in Classification and Bayesian Networks, Samsung Advanced Technology Traning Institute, Samsung Electronics Co. Ltd., Nov. 7-9, 2011.
  • Cognitive Computing - Practices in Classification Methods, Samsung Advanced Technology Traning Institute, Samsung Electronics Co. Ltd., Sep. 27, 2011.
  • Machine Learning Tutorial - Part I: Classification, KSCI Symposium on Real-Life Intelligence, Dec. 23, 2010.
  • Cognitive Computing - Practices in Bayesian Networks, Samsung Advanced Technology Traning Institute, Samsung Electronics Co. Ltd., April 29, 2010.
  • microRNAs: Regulatory Functions in Biological Networks, School of Medicine, Ajou University, April 27, 2010.
  • Cognitive Computing - Practices in Machine Learning, Samsung Advanced Technology Traning Institute, Samsung Electronics Co. Ltd., Sep. 24, 2009.
  • Bio-Convergence Technology (Biodata Analysis using Computational Approches), Institute of Bio Engineering, Seoul National University, June 27 - July 18, 2009.
  • Support Vector Machine & Its Biological Applications, Smallsoft Co., Ltd., July 16, 2008.