Artificial Intelligence and Quantitative Pathology

• Pei-Chen Tsai, Tsung-Hua Lee, Kun-Chi Kuo, Fang-Yi Su, Tsung-Lu Michael Lee, Eliana Marostica, Tomotaka Ugai, Melissa Zhao, Mai Chan Lau, Juha P. Väyrynen, Marios Giannakis, Yasutoshi Takashima, Seyed Mousavi Kahaki, Kana Wu, Mingyang Song, Jeffrey A. Meyerhardt, Andrew T. Chan, Jung-Hsien Chiang, Jonathan Nowak, Shuji Ogino, Kun-Hsing Yu. Histopathology Images Predicted Multi-Omics Aberrations and Prognoses in Colorectal Cancer Patients. Nature Communications. 2023 Apr 13;14(1):2102. [Pubmed] [Codes]
• Guihong Wan*, Nga Nguyen*, Feng Liu*, Mia S. DeSimone, Bonnie W. Leung, Ahmad Rajeh, Michael R. Collier, Min Seok Choi, Munachimso Amadife, Kimberly Tang, Shijia Zhang, Jordan S. Phillipps, Ruple Jairath, Nora A. Alexander, Yining Hua, Meng Jiao, Wenxin Chen, Diane Ho, Stacey Duey, István Balázs Németh, Gyorgy Marko-Varga, Jeovanis Gil Valdés, David Liu, Genevieve M. Boland, Alexander Gusev, Peter K. Sorger, Kun-Hsing Yu^, Yevgeniy R. Semenov^. Prediction of early-stage melanoma recurrence using clinical and histopathologic features. npj Precision Oncology. 2022 Oct 31;6(1):79. [Pubmed]
• Eliana Marostica, Rebecca Barber, Thomas Denize, Isaac S. Kohane, Sabina Signoretti, Jeffrey A Golden, Kun-Hsing Yu. Development of a Histopathology Informatics Pipeline for Classification and Prediction of Clinical Outcome in Subtypes of Renal Cell Carcinoma. Clinical Cancer Research. 2021 May 15;27(10):2868-2878. [Pubmed] [Codes]
• Yasha Ektefaie, William Yuan, Deborah A. Dillon, Nancy U. Lin, Jeffrey A. Golden, Isaac S. Kohane, Kun-Hsing Yu. Integrative Multiomics-histopathology Analysis for Breast Cancer Classification. npj Breast Cancer. 2021 Nov 29;7(1):147. [Pubmed] [Codes]
• 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]
• 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 10,832,406. 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]
• 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]

Big Data in Medicine

• Evan Brociner, Kun-Hsing Yu, Isaac S. Kohane, McGreggor Crowley. Association of Race and Socioeconomic Disadvantage With Missed Telemedicine Visits for Pediatric Patients During the COVID-19 Pandemic. JAMA Pediatrics. 2022 May 23:e221510. doi: 10.1001/jamapediatrics.2022.1510.[PubMed]
• Feicheng Wang, Shihao Yang, Nathan Palmer, Kathe Fox, Isaac S. Kohane, Katherine P. Liao, Kun-Hsing Yu*, S. C. Kou*. Real-World Data Analyses Unveiled the Immune-Related Adverse Effects of Immune Checkpoint Inhibitors Across Cancer Types. npj Precision Oncology. 2021 Sep 10;5(1):82. doi: 10.1038/s41698-021-00223-x. [PubMed]
• 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]
• 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]
• 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]
• 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]

A complete publication list could be found here.