Tomas Gonzalez Zarzar, Brian Lee, Rory Coughlin, Dokyoon Kim, Li Shen, and Molly A. Hall*. Sex differences in the metabolize of Alzheimer's disease progression. Frontiers in Radiology (Submitted)

Brenda Xiao, Digna Velez Edwards, Anastasia Lucas, Theodore Drivas, Kathryn Gray, Brendan Keating, Chunhua Weng, Gail Jarvik, Hakon Hakonarson, Leah Kottyan, Noemie Elhadad, Wei-Qi Wei, Yuan Luo, Dokyoon Kim, Marylyn Ritchie, and Shefali Verma*. Evaluation of cardiometabolic polygenic risk scores and mendelian randomization study demonstrates putative causal relationships across women's health conditions. Circulation (Submitted)

Jae-Seung Yun§, Sang-Hyuk Jung§, Manu Shivakumar, Brenda Xiao, Amit V. Khera, Hong-Hee Won*, Dokyoon Kim*. Polygenic risk for type 2 diabetes, lifestyle, metabolic health, and cardiovascular disease: a prospective UK Biobank study. BMJ  (Submitted)

Mansu Kim§, Jaesik Kim§, Jeffrey Qu, Hong Huang, Kyung-Ah Sohn, Qi Long, Dokyoon Kim, Li Shen*. Identifying highly heritable brain amyloid phenotypes through mining Alzheimer's imaging and sequencing biobank data. IEEE BIBM 2021 (Submitted)

Seung Mi Lee§, Manu Shivakumar§, Brenda Xiao, Sang-Hyuk Jung, Yonghyun Nam, Jae-Seung Yun, Eun Kyung Choe, Soo Heon Kwak, Kwangsoo Kim, Young Mi Jung, Sohee Oh, Chan-Wook Park, Joong Shin Park, Jong Kwan Jun, Dokyoon Kim*. Genome-wide polygenic risk scores for hypertensive disease during pregnancy identify women at risk for long-term cardiovascular disease. Circulation (Submitted)

Sang-Hyuk Jung§, Jie Hao§, Manu Shivakumar, Yonghyun Nam, Jaesik Kim, Min Jung Kim, Seung-Bum Ryoo, Eun Kyung Cho, Seung-Yong Jeong, Kyu Joo Park, Sung Chan Park, Dae Kyung Sohn, Jae Hwan Oh, Hong-Hee Won, Dokyoon Kim*, Ji Won Park*. Development and validation of a novel strong prognostic index for colon cancer through a robust combination of laboratory features for systemic inflammation: A prognostic immune nutritional index. British Journal of Cancer (Submitted)

Seung Mi Lee, Manu Shivakumar, Ji Won Park, Young Mi Jung, Eun Kyung Choe, Soo Heon Kwak, Sohee Oh, Chan-Wook Park, Joong Shin Park, Jong Kwan Jun, Dokyoon Kim*, Jae-Seung Yun*. Long-term cardiovascular outcomes of gestational diabetes mellitus: A prospective population-based UK biobank study. Circulation (Submitted)

Yonghyun Nam§, Sang-Hyuk Jung§, Jae-Seung Yun, Anurag Verma, Vivek Sriram, Hyunjung Shin, Hong-Hee Won*, Dokyoon Kim*. Discovering comorbid diseases based on the inter-disease directional network using biobank-scale PheWAS data. Nature Communications (Submitted)

Jaesik Kim, Kyung-Ah Sohn, Sang-Hyuk Jung, Jung-Hak Kwak, Min Jung Kim, Seung-Bum Ryoo, Seung-Yong Jeong, Kyu Joo Park, Hyun-Cheol Kang, Eui Kyu Chie, Dokyoon Kim*, Ji Won Park*. A novel scoring system for response of preoperative chemoradiotherapy in locally advanced rectal cancer using early-treatment blood features derived from machine learning. Cancers (Submitted)

Eun Kyung Choe§, Manu Shivakumar§, Seung Mi Lee, Anurag Verma*, Dokyoon Kim*. Dissecting the clinical relevance of polygenic risk score for obesity in the Korean population - cross sectional, longitudinal analysis. International Journal of Obesity (Submitted)

Jae-Seung Yun§, Jaesik Kim§, Sang-Hyuk Jung, Sean-Ah Cha, Seung-Hyun Ko, You-Bae Ahn, Hong-Hee Won, Kyung-Ah Sohn*, Dokyoon Kim*. A Deep Learning Model for Screening Type 2 Diabetes from Retinal Photographs. Nutrition, Metabolism and Cardiovascular Diseases  (Submitted) [Preprint]

Seung Mi Lee§, Yonghyun Nam§, Eun Saem Choi, Young Mi Jung, Vivek Sriram, Jacob Leiby, Ja Nam Koo, Ig Hwan Oh, Byoung Jae Kim, Sun Min Kim, Sang Youn Kim, Gyoung Min Kim, Sae Kyung Joo, Sue Shin, Errol R. Norwitz, Chan-Wook Park, Jong Kwan Jun, Won Kim, Dokyoon Kim*, Joong Shin Park*. Early prediction of pregnancy-associated hypertension: Development of novel strategies with semi-supervised learning. Scientific Reports (Submitted)

Jae-Seung Yun§, Sang-Hyuk Jung§, Manu Shivakumar, Brenda Xiao, Amit V. Khera, Hong-Hee Won*, Dokyoon Kim*. Polygenic risk, lifestyle, and cardiovascular mortality: a prospective population-based UK biobank study. Diabetes Care  (Submitted) [Preprint]

Eun Kyung Choe§, Manu Shivakumar§, Anurag Verma, Shefali Verma, Seung Ho Choi, Joo Sung Kim, Dokyoon Kim*. Genetic associations across 136 clinical phenotypes from a comprehensive health check-up database in Korean population. Scientific Reports (Submitted) [Preprint]

Vivek Sriram§, Manu Shivakumar§, Sang-Hyuk Jung, Yonghyun Nam, Lisa Bang, Anurag Verma, Seunggeun Lee, Eun Kyung Choe, Dokyoon Kim*. NETMAGE: a human-disease phenotype map for the visualization of PheWAS. GigaScience (Submitted) [Preprint]

Yonghyun Nam, Seung Mi Lee, Ji Won Park, Jae-Seung Yun, Anurag Verma, Xia Ning, Li Shen,  Dokyoon Kim*. Drug repurposing on SARS-Cov-2 and COVID-19 with network reinforcement. (In preparation) [Preprint]


Yonghyun Nam§, Sang-Hyuk Jung§, Anurag Verma, Vivek Sriram, Hong-Hee Won, Jae-Seung Yun, Dokyoon Kim*. netCRS: Network-based comorbidity risk score for prediction of myocardial infarction using biobank-scaled PheWAS data. Pacific Symposium on Biocomputing (PSB) (Accepted)

Jingxuan Bao, Zixuan Wen, Mansu Kim, Xiwen Zhao, Brian N. Lee, Sang-Hyuk Jung, Christos Davatzikos, Andrew J. Saykin, Paul M. Thompson, Dokyoon Kim, Yize Zhao, Li Shen, and for the Alzheimer's disease Neuroimaging Initiative. Identifying highly heritable brain amyloid phenotypes through mining Alzheimer's imaging and sequencing biobank data. Pacific Symposium on Biocomputing (PSB) (Accepted)

Hung Mai, Jingxuan Bao, Paul M. Thompson, Dokyoon Kim, Li Shen. Identifying genes associated with brain volumetric changes through tissue specific transcriptomic inference from GWAS summary data. BMC Bioinformatics (Accepted)

John Holmes, James Beinlich, Mary Boland, Kathryn Bowles, Yong Chen, Tessa Cook, George Demiris, Michael Draugelis, Laura Fluharty, Peter Gabriel, Robert Grundmeier, C. Hanson, Daniel Herman, Blanca Himes, Rebecca Hubbard, Charles Kahn, Jr., Dokyoon Kim, Ross Koppel, Qi Long, Bebojsa Mirkovic, Jeffery Morris, Danielle Mowery, Marylyn Ritchie, Ryan Urbanowicz, Jason Moore. Why is the electronic health record so challenging for research and clinical care? Methods of Information in Medicine (Accepted)

Manu Shivakumar, Jason E. Miller, Venkata Ramesh Dasari, Yanfei Zhang, Ming Ta Michael Lee, David Carey, Radhika Gogoi*, Dokyoon Kim*. Genetic analysis of functional rare germline variants across 9 cancer types from an electronic health record linked biobank. Cancer Epidemiology, Biomarkers & Prevention (Accepted) [Preprint]

Lisa Bang, Manu Shivakumar, Tullika Garg*, Dokyoon Kim*. Genetic analysis reveals rare variants in T-cell response gene MR1 associated with poor overall survival after urothelial cancer diagnosis. Cancers (Accepted)

Jaesik Kim, Dokyoon Kim*, Kyung-Ah Sohn*. HiG2Vec: Hierarchical representations of gene ontology and genes in the Poincare ball. 

Bioinformatics (Accepted) [Preprint]

Manu Shivakumar§, Seonggyun Han§, Younghee Lee*, Dokyoon Kim*. Epigenetic interplay between methylation and miRNA in bladder cancer: Focus on isoform expression. BMC Genomics (Accepted)

So Yeon Kim, Eun Kyung Choe, Manu Shivakumar, Dokyoon Kim*, Kyung-Ah Sohn*. Multi-layered network-based pathway activity inference using directed random walks: application to predicting clinical outcomes in urologic cancer. Bioinformatics , doi: 10.1093/bioinformatics/btab086 [PubMed]

Eun Kyung Choe§, Sangwoo Lee§, So Yeon Kim, Manu Shivakumar, Kyu Joo Park, Young Jun Chai, Dokyoon Kim*. Prognostic effect of inflammatory genes on stage I-III colorectal cancer - integrative analysis of TCGA data. Cancers, 13(4):751, 2021 [PubMed]


Dokyoon Kim, Ju Han Kim, Jason H. Moore. Translational bioinformatics: Integrating electronic health record and omics data. Pacific Symposium on Biocomputing (PSB), 26:356-359, 2021 [PubMed]

Brett Beaulieu-Jones, Christian Darabos, Dokyoon Kim, Anurag Verma, Shilpa Nadimpalli Kobren. Innovative methodological approaches for data integration to derive patterns across diverse, large-scale biomedical datasets. Pacific Symposium on Biocomputing (PSB), 26:256-260, 2021 [PubMed]

Yoon-Seong Jeon, Chang-Sung Kim, Manu Shivakumar, Dokyoon Kim, Jung-Seok Lee. Reliability of microarray analysis for studying periodontitis: low consistency in two periodontitis cohort data sets from different platforms and an integrative meta-analysis. Journal of Periodontal & Implant Science, 50(6):e40, 2020 [PubMed]

Sangwoo Lee§, Eun Kyung Choe§, So Yeon Kim, Hua Sun Kim, Kyu Joo Park*, Dokyoon Kim*. Liver imaging features by convolutional neural network to predict the metachronous liver metastasis in stage I-III colorectal cancer patients based on preoperative abdominal CT scan. BMC Bioinformatics, 21(Suppler 13):382, 2020 [PubMed]

Jason H. Moore, Ian Barnett, Mary Regina Boland, Yong Chen, George Demiris, Graciela Gonzalez-Hernandez, Daniel S. Herman, Blanca E. Times, Rebecca A. Hubbard, Dokyoon Kim, Jeffrey S. Morris, Danielle L. Mowery, Marylyn D. Ritchie, Li Shen, Ryan Urbanowicz and John H. Holmes. Ideas for how informaticians can get involved with COVID-19 research. BioData Mining , 13:3, 2020 [PubMed]

Joseph Glessner, Jin Li, Akash Kini, Melody Rynerson, Dokyoon Kim, Anastasia Lucas, Benjamin Chang, John Connolly, Marne Castillo, John Harley, Gail Jarvik, Marylyn D Ritchie, Patrick Sleiman, David Crosslin, Hakon Hakonarson. CNV association of diverse clinical phenotypes from eMERGE reveals novel disease biology underlying cardiovascular disease. International Journal of Cardiology, doi: 10.1016/j.ijcard.2019.07.058, 2020 [PubMed

Shilpa Nadimpalli Kobren, Brett Beaulieu-Jones, Christian Darabos, Dokyoon Kim, Anurag Verma. Ongoing challenges and innovative approaches for recognizing patterns across large-scale, integrative biomedical datasets. Pacific Symposium on Biocomputing (PSB), 25:286-294, 2020 [PubMed]


Jong Jin Oh§, Manu Shivakumar§, Jason E Miller, Shefali Verma, Hakmin Lee, Sung Kyu Hong, Sang Eun Lee, Soo Ji Lee, Joohon Sung, 

Dokyoon Kim*, Seok-Soo Byun*. An exome-wide rare variant analysis of Korean men identifies three novel genes predisposing to prostate cancer. Scientific Reports, 9(1):17173, 2019 [PubMed

Manu Shivakumar, Jason E. Miller, Venkata Ramesh Dasari, Radhika Gogoi*, Dokyoon Kim*, on behalf of the DiscovEHR collaboration. Exome-wide rare variant analysis from the DiscovEHR study identifies novel candidate predisposition genes for endometrial cancer. Frontiers in Oncology, doi: 10.3389/fonc.2019.00574, 2019 [PubMed

Garam Lee, Byungkon Kang, Kwangsik Nho, Kyung-Ah Sohn*, Dokyoon Kim*. MildInt: Deep learning-based multimodal longitudinal data integration framework. Frontiers in Genetics, doi: 10.3389/fgene.2019.00617, 2019 [PubMed]

Jason E Miller, Raghu P Metpally, Thomas N Pearson, Sarathbabu Krishnamurthy, Venkata Ramesh Dasari, Daniel R Lavage, Adam M Cook, John Nash, David J Carey, Marylyn D Ritchie, Dokyoon Kim, Radhika Gogoi, on behalf of the DiscovEHR collaboration. Systematic characterization of germline variants from the DiscovEHR study endometrial carcinoma population. BMC Medical Genomics, 12(1):59, 2019 [PubMed]

Gahyun Bang§, Venkata Ramesh Dasari§, Dokyoon Kim, Radhika Gogoi. Differential gene expression induced by Verteporfin in endometrial cancer cells. Scientific Reports, 9(1):3839, 2019 [PubMed]

Jason H. Moore, Mary Regina Boland, Pablo G. Camara, Hannah Chervitz, Graciela Gonzalez, Blanca E. Himes, Dokyoon Kim, Danielle L. Mowery, Marylyn D. Ritchie, Li Shen, Ryan J. Urbanowicz, John H. Holmes. Preparing next generation scientists for biomedical big data: Artificial intelligence approaches. Personalized Medicine, doi: 10.2217/pme-2018-0145,  2019  [PubMed]

Garam Lee§, Kwangsik Nho§, Byungkon Kang, Kyung-Ah Sohn*, Dokyoon Kim*. Predicting Alzheimer's disease progression using multi-modal deep learning approach. Scientific Reports, 9(1):1952,  2019  [PubMed]

Seonggyun Han, Seyoun Byun, Jason E. Miller, Dokyoon Kim, Shannon Risacher, Andrew Saykin, Younghee Lee, Kwangsik Nho. Identification of exon skipping events associated with Alzheimer’s disease in the human hippocampus. BMC Medical Genomics, 12(Suppl 1):13,  2019  [PubMed]

Anurag Verma, Lisa Bang, Jason E. Miller, Yanfei Zhang, Ming Ta Michael Lee, Yu Zhang, Marta Bryska-Bishop, David J. Carey, Marylyn D. Ritchie, Sarah A. Pendergrass, Dokyoon Kim*, on behalf of the DiscovEHR collaboration. Human-disease phenotype map derived from PheWAS across 38,682 individuals. American Journal of Human Genetics, 104(1):55-64,  2019  [PubMed]


Shefali S. Verma, Anurag Verma, Dokyoon Kim, Christian Darabos. Session Introduction - Pattern recognition in biomedical data: Challenges in putting big data to work. Pacific Symposium on Biocomputing 2019 (PSB),,  2018  [PubMed]

Jason E Miller, Manu Shivakumar, Younghee Lee, Seonggyun Han, Emrin Horgousluoglu, Shannon L. Risacher, Andrew J. Saykin, Kwangsik Nho*, 

Dokyoon Kim*. Rare variants in the splicing regulatory elements of EXOC3L4 are associated with brain glucose metabolism in Alzheimer’s disease. 

BMC Medical Genomics, 11(Suppl 3):76,  2018  [PubMed

Yasser EL-Manzalawy, Tsung-Yu Hsieh, Manu Shivakumar, Dokyoon Kim*, Vasant Honavar*. Min-redundancy and max-relevance multi-view feature selection for predicting ovarian cancer survival using multi-omics data. BMC Medical Genomics, 11(Suppl 3):71,  2018  [PubMed]

Shefali Verma, Anastasia M Lucas, Xinyuan Zhang, Yogasudha Veturi, Scott Dudek, Binglan Li, Ruowang Li, Ryan Urbanowicz, Jason H Moore, Dokyoon Kim, Marylyn D Ritchie. Collective feature selection to identify crucial epistatic variants. BioData Mining, doi: 10.1186/s13040-018-0168-6,  2018  [PubMed

Ruowang Li, Dokyoon Kim, Scott Dudek, Heather Wheeler, Eileen Dolan, Marylyn D Ritchie. Integration of genetic and functional genomics data to uncover chemotherapeutic induced cytotoxicity. Pharmacogenomics, doi: 10.1038/s41397-018-0024-6,  2018  [PubMed

Seonggyun Han, Dongwook Kim, Youngjun Kim, Kanghoon Choi, Jason Miller, Dokyoon Kim, Younghee Lee*. CAS-viewer: Web-based tool for splicing-guided integrative analysis of multi-omics cancer data. BMC Medical Genomics, 11(Suppl 2):25,  2018  [PubMed]

Younghee Lee, Seonggyun Han, Dongwook Kim, Dokyoon Kim, Emrin Horgousluoglu, Shannon L. Risacher, Andrew J. Saykin, Kwangsik Nho. Genetic variation affecting exon skipping contributes to brain structural atrophy in Alzheimer’s disease. AMIA 2018 Informatics Summit, 2017:124-131,  2018 [PubMed]

Dongwook Kim, Manu Shivakumar, Michael Sinclair, Youngji Lee, Dokyoon Kim*, Younghee Lee*. Population-dependent Intron Retention and DNA Methylation in Breast Cancer. Molecular Cancer Research, 16(3):461-469,  2018  [PubMed]

Han Seonggyun, Dongwook Kim, Manu Shivakumar, Jason E Miller, Youngji Lee, Tullika Garg, Ju Han Kim*, Dokyoon Kim*, Younghee Lee*. The effects of alternative splicing on miRNA binding sites in bladder cancer. PLoS ONE, 13(1):e0190708,  2018  [PubMed

Jason E Miller, Manu K. Shivakumar, Shannon L. Risacher, Andrew J. Saykin, Seunggeun Lee, Kwangsik Nho*, Dokyoon Kim*. Codon bias among synonymous rare variants is associated with Alzheimer’s disease imaging biomarker. Pacific Symposium on Biocomputing 2018 (PSB), 23:365-376,  2018  [PubMed


Molly A Hall, John Wallace, Anastasia Lucas, Dokyoon Kim, Anna Basile, Shefali S Verma, Cathy A McCarty, Murray Brilliant, Peggy L. Peissig, Terrie Kitchner, Anurag Verma, Sarah Pendergrass, Scott Dudek, Jason H. Moore, Marylyn D. Ritchie. PLATO software provides analytic framework for investigating complexity beyond genome-wide association studies. Nature Communications, 8(1):1167,  2017  [PubMed]

Manu Shivakumar§, Younghee Lee§, Lisa Bang, Tullika Garg, Kyung-ah Sohn*, Dokyoon Kim*. Identification of epigenetic interactions between miRNA and  DNA methylation associated with gene expression as potential prognostic markers in bladder cancer. BMC Medical Genomics, 10(Suppl 1):30,  2017 [PubMed]

Jong Jin OH, Soo Ji Lee, Joo-Yeon Hwang, Dokyoon Kim, Sang Eun Lee, Sung Kyu Hong, Jin-Nyoung Ho, Sungroh Yoon, Joohon Sung, Wun-Jae Kim, Seok-Soo Byun. Exome-based genome-wide association study and risk assessment using genetic risk score to prostate cancer in the Korean population, Oncotarget, 8(27):43934-43943,  2017  [PubMed]

Dokyoon Kim, Anna O. Basile, Lisa Bang, Emrin Horgusluoglu, Seunggeun Lee, Marylyn D. Ritchie, Andrew J. Saykin, Kwangsik Nho. Knowledge-driven binning approach for rare variant association analysis: Application to neuroimaging biomarkers in Alzheimer’s disease. BMC Medical Informatics and Decision Making, 17(Suppl 1):61,  2017  [PubMed]

Garam Lee, Lisa Bang, So Yeon Kim, Dokyoon Kim*, Kyung-Ah Sohn*. Identifying subtype-specific associations between gene expression and DNA methylation profiles in breast cancer. BMC Medical Genomics, 10(Suppl 1):28,  2017  [PubMed]

Ruowang Li, Dokyoon Kim, Marylyn D. Ritchie. Methods to analyze big data in pharmacogenomics research. Pharmacogenomics, 18(8):807-820,  2017  [PubMed]

Kwangsik Nho, Sungeun Kim, Emrin Horgusluoglu, Shannon L. Risacher, Li Shen, Dokyoon Kim, Seunggeun Lee, Tatiana Foroud, Leslie M. Shaw, John Q. Trojanowski, Paul S. Aisen, Ronald C. Petersen, Clifford R. Jack, Michael W. Weiner, Robert C. Green, Arthur W. Toga, Andrew J. Saykin. Association analysis of rare variants near the APOE region with CSF and neuroimaging biomarkers of Alzheimer’s disease. BMC Medical Genomics, 10(Suppl 1):29,  2017  [PubMed]

Dokyoon Kim, Heather Volk, Santhosh Girirajan, Sarah Pendergrass, Molly Hall, Shefali Setia, Rebecca J. Schmidt, Robin L. Hansen, Debashis Ghosh, Kyoungmi Kim, Marylyn D. Ritchie, Irva Hertz-Picciotto, Scott Selleck. Interactions between air pollution exposure and copy number variation confer significant risk for autism. Autism Research, 10(9):1470-1480,  2017  [PubMed]

Sehee Wang, Hyung-hwan Jeong, Dokyoon Kim, Kyubum Wee, Hae-Sim Park, Seung-Hyun Kim, Kyung-Ah Sohn. Integrative information theoretic network analysis for genome-wide association study of aspirin exacerbated respiratory disease in Korea. BMC Medical Genomics, 10(Suppl 1):31, 2017  [PubMed]


Dokyoon Kim, Ruowang Li, Anastasia Lucas, Shefali Verma, Scott Dudek, Marylyn Ritchie. Using knowledge-driven genomic interactions for multi-omics data analysis: metadimensional models for predicting clinical outcomes in ovarian carcinoma. J Am Med Inform Assoc, 24(3):577-587,  2016 (Selected in Russ Altman’s Year in Review 2017)  [PubMed]

Ruowang Li, Scott Dudek, Dokyoon Kim, Molly A. Hall, Yuki Bradford, Peggy Peissig, Murray Brilliant, James Linneman, Catherine A. McCarty, Le Bao, Marylyn D. Ritchie. Identification of genetic interaction networks via an evolutionary algorithm evolved Bayesian network. BioData Mining, 9:18,  2016  [PubMed]

Kwangsik Nho, Emrin Horgusluoglu, Sungeun Kim, Shannon Risacher, Dokyoon Kim, Tatiana Foroud, Paul Aisen, Ronald Petersen, Clifford Jack, Leslie Shaw, John Trojanowski, Michael Weiner, Robert Green, Arthur Toga and Andrew J. Saykin Andrew J. Saykin. Integration of bioinformatics and imaging informatics for identifying rare PSEN1 variants in Alzheimer’s disease. BMC Med Genomics, 9 Suppl 1:30,  2016  [PubMed]

Dokyoon Kim, Anastasia Lucas, Joseph Glessner, Shefali S. Verma, Yuki Bradford, Ruowang Li, Alex T. Frase, Hakon Hakonarson, Catherine A. McCarty, Peggy Peissig, Murray Brilliant, Marylyn D. Ritchie. Biofilter as a functional annotation pipeline for common and rare copy number burden. Pacific Symposium on Biocomputing 2017 (PSB), 21:357-68,  2016  [PubMed]


Marylyn D. Ritchie, Emily R. Holzinger, Ruowang Li, Sarah A. Pendergrass, Dokyoon Kim. Methods of integrating data to uncover genotype-phenotype interactions. Nature Reviews Genetics, 16(2), 85-97,  2015  [PubMed]

Dokyoon Kim, Ruowang Li, Scott M. Dudek, Marylyn D. Ritchie. Predicting censored survival data based on the interactions between meta-dimensional omics data in breast cancer. J Biomed Inform, 56, 220-228,  2015  [PubMed]

Dokyoon Kim, Ruowang Li, Scott M. Dudek, John R. Wallace, Marylyn D. Ritchie. Binning somatic mutations based on biological knowledge for predicting survival: an application in renal cell carcinoma. Pacific Symposium on Biocomputing 2016 (PSB), 96-107,  2015  [PubMed]


Dokyoon Kim, Ruowang Li, Scott M. Dudek, Alex T. Frase, Sarah A. Pendergrass, Marylyn D. Ritchie. Knowledge-driven genomic interactions: an application in ovarian cancer. BioData Mining, 7, 20,  2014  [PubMed]

Dokyoon Kim, Je-Gun Joung, Kyung-Ah Sohn, Hyunjung Shin, Marylyn D. Ritchie, Ju Han Kim. Knowledge Boosting: A graph-based integration approach with multi-omics data and genomic knowledge for cancer clinical outcome prediction. J Am Med Inform Assoc, doi:10.1136/amiajnl-2013-002481,  2014  [PubMed]

Ruowang Li, Dokyoon Kim, Scott M. Dudek, Marylyn D. Ritchie. An integrated analysis of genome-wide DNA methylation and genetic variants underlying etoposide-induced cytotoxicity in European and African populations. Lect Notes Comput Sci, 8602:928-938,  2014  [PubMed]

Je-Gun Joung, Dokyoon Kim, Su-Yeon Lee, Hwa Jung Kang, Ju Han Kim. Integrated analysis of microRNA-target interactions with clinical outcomes for cancers. BMC Med Genomics, 7(Suppl 1):S10,  2014  [PubMed]

Dokyoon Kim, Marylyn D. Ritchie. Data integration for cancer clinical outcome prediction. J Health Med Informat, doi:10.4172/2157-7420.1000e122,  2014  [PubMed]

Dokyoon Kim, Hyunjung Shin, Kyung-Ah Sohn, Anurag Verma, Marylyn D. Ritchie, Ju Han Kim. Incorporating inter-relationships between different levels of genomic data into cancer clinical outcome prediction. Methods, 67(3):344-53,  2014  [PubMed]

Jong Jin Oh, Seok Soo Byun, Sang Eun Lee, Sung Kyu Hong, Chang Wook Jeong, Won Suk Choi, Dokyoon Kim, Hae Jong Kim, Soon Chul Myung. Genetic variants in the CYP24A1 gene associated with prostate cancer risk and aggressiveness in a Korean study population. Prostate Cancer P D, 17(2):149-56,  2014  [PubMed]

Jong Jin Oh, Seok Soo Byun, Sang Eun Lee, Sung Kyu Hong, Chang Wook Jeong, Dokyoon Kim, Hae Jong Kim, Soon Chul Myung. Genetic variations in VDR associated with prostate cancer risk and progression in a Korean population. Gene, 533(1):86-93,  2014  [PubMed]


Dokyoon Kim, Ruowang Li, Scott M. Dudek, Marylyn D. Ritchie. ATHENA: Identifying interactions between different levels of genomic data associated with cancer clinical outcomes using grammatical evolution neural network. BioData Mining, 6(1):23,  2013  [PubMed]

Kyung-Ah Sohn§, Dokyoon Kim§, Jaehyun Lim, Ju Han Kim. Relative impact of multi-layered genomic data on gene expression phenotypes in serous ovarian tumors. BMC Systems Biology, 7(Suppl 6):S9,  2013  [PubMed]

Dokyoon Kim, Sungeun Kim, Shannon L. Risacher, Li Shen, Marylyn D. Ritchie, Michael W. Weiner, Andrew J. Saykin, Kwangsik Nho. A graph-based integration of multimodal brain imaging data for the detection of early mild cognitive impairment (E-MCI). Lect Notes Comput Sci, 8159:159-169,  2013  [PubMed]

Dokyoon Kim,§ Hyunjung Shin§, Su-Yeon Lee, Je-Gun Jeong, Ju Han Kim. Intra-relation reconstruction from inter-relation: miRNA to gene expression. BMC Systems Biology, 7(Suppl 3):S8,  2013  [PubMed]

Kanghee Park, Amna Ali, Dokyoon Kim, Yeolwoo An, Minkoo Kim, Hyunjung Shin. Robust predictive model for evaluating breast cancer survivability. Eng Appl Artif Intel, 26(9):2194-2205,  2013  [PubMed]

Je-Gun Jeong, Dokyoon Kim, Kyung Hwa Kim, Ju Han Kim. Extracting coordinated patterns of DNA methylation and gene expression in ovarian cancer. J Am Med Inform Assoc, 20(4):637-642,  2013  [PubMed]


Dokyoon Kim§, Hyunjung Shin§, Young Soo Song, Ju Han Kim. Synergistic effect of different levels of genomic data for cancer clinical outcome prediction. J Biomed Inform, 45(6):1191-1198,  2012  [PubMed]

Heewon Seo, Dokyoon Kim, Jong-Hee Chae, Hee Gyung Kang, Byung Chan Lim, Hae Il Cheong, Ju Han Kim. Development of Korean rare disease knowledge base. Health Inform Res, 18(4):272-278,  2012  [PubMed]

Young Soo Song, Hye Won Lee, Yu Rang Park, Dokyoon Kim, Jaehyun Sim, Hyunseok Peter Kang, Ju Han Kim. TMA-TAB: A spreadsheet-based document for exchange of tissue microarray data based on the Tissue Microarray-Object Model. J Biomed Inform, 43:435-441,  2010  [PubMed]