Faculty

Dokyoon Kim, PhD

faculty photo
Assistant Professor of Informatics in Biostatistics and Epidemiology
Department: Biostatistics and Epidemiology

Contact information
B304 Richards Building
3700 Hamilton Walk
University of Pennsylvania
Philadelphia, PA 19104-6116
Office: (215)573-5336
Education:
B.S. (Computer Science)
Korea University, South Korea, 2006.
Ph.D. (Biomedical Informatics)
Seoul National University College of Medicine, South Korea, 2013.
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Description of Research Expertise

- Our research entails the development and application of data integration approach to improve the ability to diagnose, treat, and prevent complex diseases

- Our long-term research goal is to develop and evaluate sophisticated data integration methods that simultaneously combine people’s individual variations in genomic (‘omic) data, imaging data, phenotype data derived from EHR, and environment/lifelog data for advancing precision medicine

- Our past and ongoing projects have been both theoretical and applied, mainly in (but, not limited to) cancer and Alzheimer’s disease

- Keywords: Multi-omics data, data integration, translational informatics, precision medicine, machine learning, deep learning, cancer genomics, imaging genomics, EHR, network analysis

Selected Publications

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 37(16): 2405-2413, August 2021.

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, February 2021.

Jaesik Kim, Dokyoon Kim*, Kyung-Ah Sohn*.: HiG2Vec: Hierarchical representations of gene ontology and genes in the Poincare ball. Bioinformatics 37(18): 2971-2980, September 2021.

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 30(9): 1681-1688, September 2021.

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 60(1-02): 32-48, May 2021.

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, January 2021.

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 13(8): 1864, April 2021.

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, January 2021.

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 298(1): 107-113, January 2020 Notes: doi: 10.1016/j.ijcard.2019.07.058.

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

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, October 2017.

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, January 2015.

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, January 2019.

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

Jason H Moore, Mary Reginal 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 16(3), February 2019 Notes: doi:10.2217/pme-2018-0145.

Manu Shivakumar, Jason E. Miller, Venkata Ramesh Dasari, Radhika Gogoi*, Dokyoon Kim*, on behalf of the DiscovEHR collaboration.: Exomewide rare variant analysis from the DiscovEHR study identifies novel candidate predisposition genes for endometrial cancer. Frontiers in Oncology 9(57): 574, July 2019 Notes: doi:10.3389/fonc.2019.00574.

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), November 2019.

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) January 2020.

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), May 2020.

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 Suppl 13(382), September 2020.

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Last updated: 11/05/2021
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