Publications

Kun-Hsing Yu, Oren Miron, Nathan Palmer, Dario Lemos, Kathe Fox, S. C. Kou, Mustafa Sahin, Isaac S. Kohane. Data-Driven Analyses Revealed the Comorbidity Landscape of Tuberous Sclerosis Complex. Neurology. 2018 Nov 20;91(21):974-976. [PubMed]
Devised a data-driven algorithm to systematically identify the comorbidities of tuberous sclerosis complex
Kun-Hsing Yu, Andrew L. Beam, Isaac S. Kohane. Artificial Intelligence in Healthcare. Nature Biomedical Engineering. 2018 Oct. 10;2:719–731. [Paper]
Summarized the current progress of artificial intelligence research and applications in healthcare
Kun-Hsing Yu, Tsung-Lu Michael Lee, Chi-Shiang Wang, Yu-Ju Chen, Christopher Ré, Samuel C. Kou, Jung-Hsien Chiang, Michael Snyder, Isaac S. Kohane. A Cloud-Based Metabolite and Chemical Prioritization System for the Biology/Disease-Driven Human Proteome Project. Journal of Proteome Research. 2018 Aug 21;17(12):4345-4357. [PubMed] [Codes] [Running Server]
Deployed a cloud-based metabolite and chemical prioritization system for the human proteome project
Kun-Hsing Yu and Isaac S. Kohane. Framing the challenges of artificial intelligence in medicine. BMJ Quality & Safety. 2019 Mar;28(3):238-241. [Epub ahead of print] [PubMed]
Investigated the limitations of the current machine learning paradigm and their implications in medicine
Kun-Hsing Yu, Tsung-Lu Michael Lee, Chi-Shiang Wang, Yu-Ju Chen, Christopher Ré, Samuel C. Kou, Jung-Hsien Chiang, Isaac S. Kohane, Michael Snyder. Systematic Protein Prioritization for Targeted Proteomics Studies through Literature Mining. Journal of Proteome Research. 2018 Apr 6;17(4):1383-1396. [PubMed] [Codes] [Running Server]
Developed an automated literature mining system for protein prioritization
Kun-Hsing Yu, Gerald J. Berry, Daniel L. Rubin, Christopher Ré, Russ B. Altman, Michael Snyder Association of Omics Features with Histopathology Patterns in Lung Adenocarcinoma. Cell Systems. 2017 Dec 27;5(6):620-627.e3. [PubMed]
Integrated functional omics and histopathology patterns for clinical predictions
Kun-Hsing Yu, Michael R. Fitzpatrick, Luke Pappas, Warren Chan, Jessica Kung, Michael Snyder. Omics AnalySIs System for PRecision Oncology (OASISPRO): A Web-based Omics Analysis Tool for Clinical Phenotype Prediction. Bioinformatics,. 2018 Jan 15;34(2):319-320. [PubMed] [Codes] [Running Server]
Designed an interactive cloud-based system for functional omics data mining 
Kirk Roberts, Mary Regina Boland, Lisiane Pruinelli, Jina Dcruz, Andrew Berry, Mattias Georgsson, Rebecca Hazen, Raymond F. Sarmiento, Uba Backonja, Kun-Hsing Yu, Yun Jiang, Patricia Flatley Brennan. Biomedical informatics advancing the national health agenda: The AMIA 2015 Year-in-Review in clinical & consumer informatics. Journal of American Medical Informatics Association. 2017 Apr 1;24(e1):e185-e190. [PubMed]
Reviewed recent progresses in clinical decision support systems
Kun-Hsing Yu, Steven Hart, Rachel Goldfeder, Qiangfeng Cliff Zhang, Stephen Parker, Michael Snyder. Harnessing Big Data for Precision Medicine: Infrastructures and Applications. Pacific Symposium on Biocomputing. 2017;22:635-639. [PubMed]
Recapitulate computational advancements and ongoing challenges in large-scale precision medicine studies
Kun-Hsing Yu, Ce Zhang, Gerald J. Berry, Russ B. Altman, Christopher Ré, Daniel L. Rubin, Michael Snyder. Predicting Non-Small Cell Lung Cancer Prognosis by Fully Automated Microscopic Pathology Image Features. Nature Communications. 2016 Aug 16;7:12474. [PubMed]
Characterized objective histopathology image features associated with non-small cell lung cancer prognosis [Source Codes] [Dataset of Image Features]
Kun-Hsing Yu, Douglas A. Levine, Hui Zhang, Daniel W. Chan, Zhen Zhang, Michael Snyder. Predicting Ovarian Cancer Patients' Clinical Response to Platinum-based Chemotherapy by their Tumor Proteomic Signatures. Journal of Proteome Research. 2016 Aug 5;15(8):2455-65. [PubMed]
Identified proteomic profiles predicting chemotherapy response through bioinformatic analysis
Kun-Hsing Yu, Michael Snyder. Omics profiling in precision oncology. Molecular & Cellular Proteomics. 2016 Aug;15(8):2525-36. [PubMed]
Reviewed recent advancements in precision cancer medicine
Hui Zhang, Tao Liu, Zhen Zhang, Samuel H Payne, Jason E McDermott, Jian-Ying Zhou, Vladislav A Petyuk, Lily Chen, Debjit Ray, Shisheng Sun, Feng Yang, Bai Zhang, Jing Wang, Seong Won Cha, Lijun Chen, Sunghee Woo, Punit Shah, Paul Aiyetan, Yuan Tian, Caitlin Choi, Marina A Gritsenko, Ronald J Moore, Matthew E Monroe, Kun-Hsing Yu, David Tabb, David Fenyo, Vineet Bafna, Joseph Wang, Ie-Ming Shih, Akhilesh Pandey, Bing Zhang, Michael Snyder, Doug Levine, Richard D Smith, Daniel W Chan, Karin D Rodland and the TCGA investigators. Deep proteogenomic characterization of human ovarian cancer. Cell. 2016 Jul 28;166(3):755-65. [PubMed]
Predicted clinical responses to platinum-based chemotherapeutics in ovarian cancer patients using tumor proteomic profiles
Kun-Hsing Yu, Jingjing Li, Michael Snyder, Gary M. Shaw, Hugh M. O'Brodovich. The Genetic Predisposition to Bronchopulmonary Dysplasia. Current Opinion in Pediatrics. 2016 Jun;28(3): 318-23. [PubMed]
Reviewed recent papers on genetics contributions to bronchopulmonary dysplasia
Elena Matsa, Paul W. Burridge, Kun-Hsing Yu, John H. Ahrens, Haodi Wu, Praveen Shukla, Jared M. Churko, Joseph D. Gold, Michael P. Snyder, Joseph C. Wu. Transcriptomic analysis of inter and intra patient variation in hiPSC-cardiomyocytes is predictive of patient-specific cardiotoxicity. Cell Stem Cell. 2016 Sep 1;19(3):311-25. [PubMed]
Determined the inter-individual transcriptomic variation in hiPSC-cardiomyocytes
Jingjing Li*, Kun-Hsing Yu*, John Oehlert, Laura L Jeliffe-Pawlowski, Jeffrey B Gould, David K Stevenson, Michael Snyder, Gary M Shaw, Hugh M O’Brodovich. Exome Sequencing of Neonatal Blood Spots Identifies Genes Implicated in Bronchopulmonary Dysplasia. American Journal of Respiratory and Critical Care Medicine. 2015 Sep 1;192(5):589-96. [PubMed]
Co-first authored the genomic variations analysis of patients with bronchopulmonary dysplasia
Su-Chien Chiang, Chia-Li Han, Kun-Hsing Yu, Yu-Ju Chen, Kun-Pin Wu. Prioritization of cancer marker candidates based on the immunohistochemistry staining images deposited in the Human Protein Atlas. PLOS One. 2013 8(11): e81079. [PubMed]
Developed an informatics pipeline for cancer marker identification
Chia-Li Han, Jinn-Shiun Chen, Err-Cheng Chan, Chien-Peng Wu, Kun-Hsing Yu, Chia-Feng Tsai, Guei-Tian Chen, Chih-Wei Chien, Yung-Bin Kuo, Pei-Yi Lin, Chung-Chuan Chan, Jao-Song Yu, Yu-Ju Chen. An Informatics-assisted Label-free Approach for Personalized Tissue Membrane Proteomics: Case Study on Colorectal Cancer. Molecular & Cellular Proteomics. 2011 Apr;10(4):M110.003087. [PubMed]
Discovered STOML2 as an early stage colorectal cancer marker through bioinformatics methods
Ming-Jung Ho, Kun-Hsing Yu, Hui Pan, Jessie L. Norris, You-Sin Liang, Jia-Ning Li, David Hirsh. A Tale of Two Cities: Understanding Constructs of Medical Professionalism in Two Chinese Cultural Contexts. Academic Medicine. 2014 Jun;89(6):944-50. [PubMed]
Integrated quantitative and qualitative studies on medical education
Ming-Jung Ho, Kun-Hsing Yu, David Hirsh, Tien-Shiang Huang, Pan-Chyr Yang. Does One Size Fit All? – Building a Framework for Medical Professionalism. Academic Medicine. 2011 Nov;86(11):1407-1414. [PubMed]
Initiated the data mining process and conceptualized the professionalism framework
Kun-Hsing Yu, Tien-Shang Huang, Pan-Chyr Yang, Ming-Jung Ho. Medical Professionalism Revisited: Application of the Nominal Group Technique. Journal of Medical Education. 2010; 14: 15-22. [Paper]
Investigated factors of medical professionalism through statistical analysis