Publications

Artificial Intelligence and Quantitative Pathology

  • Kun-Hsing Yu, Vincent Hu, Feiran Wang, Ursula Matulonis, George L. Mutter, Jeffrey A. Golden, Isaac S. Kohane. Deciphering Serous Ovarian Carcinoma Histopathology and Platinum Response by Convolutional Neural Networks. BMC Medicine. 2020 Aug 18;18(1):236. [Pubmed] [Codes]
  • Kun-Hsing Yu, Tsung-Lu Michael Lee, Ming-Hsuan Yen, S. C. Kou, Bruce Rosen, Jung-Hsien Chiang, Isaac S. Kohane. Reproducible Machine Learning Methods for Lung Cancer Detection Using Computed Tomography Images. Journal of Medical Internet Research (JMIR). 2020 Aug 5;22(8):e16709. [Pubmed] [Codes]
  • Kun-Hsing Yu, Feiran Wang, Gerald J. Berry, Christopher Ré, Russ B. Altman, Michael Snyder, Isaac S. Kohane. Classifying Non-Small Cell Lung Cancer Types and Transcriptomic Subtypes using Convolutional Neural Networks. JAMIA. 2020 May 2;27(5):757–769. [PubMed] [Codes]
  • Wei Han, Lei Qin, Camden Bay, Xin Chen, Kun-Hsing Yu, Xiaoyin Xu, Geoffrey Young. Deep Transfer Learning and Radiomics Feature Prediction of Survival of Patients with High-Grade Gliomas. American Journal of Neuroradiology. 2020 Jan;41(1):40-48. [PubMed]
  • Kun-Hsing Yu and Isaac S. Kohane. Framing the challenges of artificial intelligence in medicine. BMJ Quality & Safety. 2019 Mar;28(3):238-241. [PubMed]
  • Kun-Hsing Yu, Tsung-Lu Michael Lee, 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 Dec 7;17(12):4345-4357. [PubMed] [Codes] [Running Server]
  • 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]
  • Kun-Hsing Yu, Andrew L. Beam, Isaac S. Kohane. Artificial Intelligence in Healthcare. Nature Biomedical Engineering. 2018 Oct;2(10):719-731. [PubMed]
  • 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]
  • 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] [Source Codes] [Dataset of Image Features]
  • Kun-Hsing Yu. Quantitative pathology analysis and diagnosis using neural networks. U.S. Patent 16/179,101 Patent assigned to Harvard University.

Integrative Multi-Omics Analyses

  • 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]
  • 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]
  • Kun-Hsing Yu, Michael Snyder. Omics profiling in precision oncology. Molecular & Cellular Proteomics. 2016 Aug;15(8):2525-36. [PubMed]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • Kun-Hsing Yu. Evaluation of Taroni et al.: Understanding Rare Diseases by MultiPLIER. Cell Systems. 2019 May 22;8(5):359-360. [PubMed]

Big Data in Medicine

  • Kun-Hsing Yu, Nathan Palmer, Kathe Fox, Lisa Prock, Kenneth D. Mandl, Isaac S. Kohane, Daria Prilutsky. The Phenotypical Implications of Immune Dysregulation in Fragile X Syndrome. European Journal of Neurology 2020 Mar;27(3):590-593. [PubMed]
  • Brett K. Beaulieu-Jones, Samuel G. Finlayson, William Yuan, Russ B. Altman, Isaac S. Kohane, Vinay Prasad, Kun-Hsing Yu. Examining the Use of Real-World Evidence in the Regulatory Process. Clinical Pharmacology & Therapeutics. 2020 Apr;107(4):843-852. [PubMed]
  • Shihao Yang*, Kun-Hsing Yu*, Nathan Palmer, Kathe Fox, S. C. Kou, Isaac S. Kohane. Autoimmune Effects of Lung Cancer Immunotherapy Revealed by Data-Driven Analysis on a Nationwide Cohort. Clinical Pharmacology & Therapeutics. 2020 Feb;107(2):388-396. [PubMed]
  • William Yuan, Kun-Hsing Yu, Nathan Palmer, Fatima Cody Stanford, Isaac Kohane. Evaluation of the association of bariatric surgery with subsequent depression. International Journal of Obesity. 2019 Dec;43(12):2528-2535. [PubMed]
  • Oren Miron, Kun-Hsing Yu, Rachel Wilf-Miron, Isaac S. Kohane. Suicide Rates Among Adolescents and Young Adults in the United States, 2000-2017. JAMA. 2019 Jun 18;321(23):2362-2364. [PubMed]
  • Iván Sánchez Fernández, Edward Yang, Paola Calvachi, Marta Amengual-Gual, Joyce Y. Wu, Darcy Krueger, Hope Northrup, Martina E. Bebin, Mustafa Sahin, Kun-Hsing Yu, Jurriaan M. Peters, on behalf of the TACERN Study Group. Deep learning in rare disease. Detection of tubers in tuberous sclerosis complex. PLoS One. 2020 Apr 29;15(4):e0232376. [PubMed]
  • Peter T. Campbell, Christine B. Ambrosone, Reiko Nishihara, Hugo J. W. L. Aerts, Melissa Bondy, Nilanjan Chatterjee, Montserrat Garcia-Closas, Marios Giannakis, Jeffrey A. Golden, Yujing J. Heng, N. Sertac Kip, Jill Koshiol, X. Shirley Liu, Camila M. Lopes-Ramos, Lorelei A. Mucci, Jonathan A. Nowak, Amanda I. Phipps, John Quackenbush, Robert E. Schoen, Lynette M. Sholl, Rulla M. Tamimi, Molin Wang, Matty P. Weijenberg, Catherine J. Wu, Kana Wu, Song Yao, Kun-Hsing Yu, Xuehong Zhang, Timothy R. Rebbeck, Shuji Ogino. Proceedings of the fourth international molecular pathological epidemiology (MPE) meeting. Proceedings of the fourth international molecular pathological epidemiology (MPE) meeting. Cancer Causes & Control. 2019 Aug;30(8):799-811. [PubMed]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]