Rui Zhang, PhD, FAMIA

Dr. Zhang's research lab focuses on the development of novel natural language processing (NLP) methods to analyze biomedical big data, including published biomedical literature, electronic health records (EHRs), patient-generated data from millions of patients. This research includes: 

1. Secondly analysis of EHR data for patient care
2. Pharmacovigilance knowledge discovery through mining biomedical literature
3. Creation of knowledge base through database integration, terminology and ontology

Current projects include:

1. Developing NLP methods and applications to extract information from clinical reports
2. Mining biomedical literature to discover novel drug-supplement interactions through genetic pathways
3. Repurposing existing drugs for COVID-19 treatment through link predictions and literature-based discovery
4. Developing computational methods to predict personalized cancer treatment caused cardiotoxicity in EHRs
5. Developing conversational agent for consumers with developed knowledge base.

• Outstanding Teaching and Dedication, Center for Educational Innovation, UMN, 2019
• Student paper competition finalist, Post-doctorate associate’s manuscript (senior author) , AMIA Translational Bioinformatics , 2018
• Undergraduate Research Opportunity Program (UROP) Award, Advisor for undergraduate students, University of Minnesota, 2018
• Doctoral Dissertation Fellowship, PhD student awarded the (as her primary advisor), University of Minnesota, 2018
• Student paper competition, PhD student’s manuscript (senior author), AMIA Translational Bioinformatics , 2017
• McKnight Land-Grant Professorship Award , University of Minnesota, 2017
• Research project highlighted, How Your Supplements Interact With Prescription Drugs, The Wall Street Journal Health Headline, 2016
• Best Poster Award, IEEE International Conference on Biomedical and Health Informatics , 2016
• Distinguished Paper Award , AMIA Annual Symposium , 2016
• Marco Ramoni Distinguished Paper Award , Manuscript (first author) , Translational Bioinformatics, 2015
• University of Minnesota Informatics Institute (UMII) On the Horizon Award , University of Minnesota, 2014
• Student paper competition finalist, Manuscript (first author) , AMIA Joint Summits on Translational Science , 2014
• Editors’ Choice, Journal of Biomedical Informatics , 2014
• Scholarship, Health Information and Management Systems Society (HIMSS) Minnesota Chapter, 2013
• Student paper competition finalist, Manuscript (first author) , MEDINFO - The14th World Congress on Medical and Health Informatics of the International Medical Informatics Association, 2013
• Travel Award, Association for Computing Machinery , 2012
• Travel Award, University of Minnesota, 2012
• Health Informatics Graduate Fellowship, University of Minnesota, 2012
• Doctoral Dissertation Fellowship (All-University Competition), University of Minnesota, 2012
• Fellowship of the International Partnership in Health Informatics Education (IPHIE) Master Class, , University of Heidelberg-University of Heilbronn, Germany, 2011
• Student paper competition finalist, Manuscript (first author) , AMIA Annual Symposium , 2011
• Travel Award, American Medical Informatics Association, 2011

• AMIA Education Committee
• AMIA Membership/Outreach Committee
• AMIA Student Working Group
• American Medical Informatics Association

• Research Spotlight: Dr. Zhang Received an R01 Renewal Developing Novel AI Approach to Mine Effective & Safe Use of Dietary Supplements
• Dr. Zhang Received a New R01 to Research Drug Repurposing for Alzheimer's Disease
• U of M researchers receive $1.2M to study role of AI in breast cancer treatment
• Center for Learning Health System Sciences: All of Us Risk Modeling
• Detecting synergistic effects of pharmacological and non-pharmacological interventions for Alzheimer's disease and related dementia

• Bompelli, A., Silverman, G., Finzel, R., Vasilakes, J., Knoll, B., Pakhomov, S., Zhang, R., 2020. Comparing NLP Systems to Extract Entities of Eligibility Criteria in Dietary Supplements Clinical Trials Using NLP-ADAPT. International Conference on Artificial Intelligence in Medicine 67-77.
• Yi, Y., Shen, Z., Bompelli, A., Yu, F., Wang, Y., Zhang, R., 2020. Natural Language Processing Methods to Extract Lifestyle Exposures for Alzheimer’s Disease from Clinical Notes. IEEE ICHI. HealthNLP Workshop 2020
• He, Z., Barrett, L. A., Rizvi, R., Tang, X., Payrovnaziri, S. N., Zhang, R., 2020. Assessing the Use and Perception of Dietary Supplements Among Obese Patients with National Health and Nutrition Examination Survey. AMIA Summits on Translational Science Proceedings, 2020: 231.
• Vasilakes, J., Rizvi, R., Terrence, A., R, Z., 2019. Detecting Signals of Dietary Supplement Adverse Events from the CFSAN Adverse Event Reporting System (CAERS). AMIA Informatics Summit
• He, Z., Rizvi, R., Terrence, A., Zhang, R., 2019. Comparing the Study Populations in Dietary Supplement and Drug Clinical Trials for Metabolic Syndrome and Related Disorders. AMIA Informatics Summit
• Ma, S., Zhang, R., Shanahan, L., Munroe, J., Horn, S., Speedie, S., 2018. Estimating New York Heart Association Classification for Heart Failure Patients from Information in the Electronic Health Record. IEEE International conference on Bioinformatics and Biomedicine
• He, X., Zhang, R., Rizvi, R., Vasilakes, J., Yang, X., Guo, Y., He, Z., Bian, J., 2018. Prototyping an Interactive Visualization of Dietary Supplement Knowledge Graph. IEEE International Conference on Bioinformatics and Biomedicine
• Rizvi, R. F., Adam, T. J., Lindemann, E. A., Vasilakes, J., Pakhomov, S. V., Bishop, J. R., Melton, G. B., Zhang, R., 2018. Comparing Existing Resources to Represent Dietary Supplements. AMIA Summits on Translational Science Proceedings, 2017: 207-216.
• Fan, Y., Zhang, R., 2018. Using natural language processing methods to classify use status of dietary supplements in clinical notes. BMC medical informatics and decision making, 18 (Suppl 2): 51.
• Zhang, R., Meng, J., Lian, Q., Chen, X., Bauman, B., Chu, H., Segura, B., Roy, S., 2018. Prescription opioids are associated with higher mortality in patients diagnosed with sepsis: A retrospective cohort study using electronic health records. PLoS ONE, 13 (1): e0190362. doi: 10.1371/journal.pone.0190362
• Vasilakes, J., Rizvi, R., Melton, G. B., Pakhomov, S., Zhang, R., 2018. Evaluating active learning methods for annotating semantic predications. JAMIA Open, 1 (2): 275-282.
• Breitenstein, M. K., Liu, H., Maxwell, K. N., Pathak, J., Zhang, R., 2018. Electronic Health Record Phenotypes for Precision Medicine: Perspectives and Caveats from Treatment of Breast Cancer at a Single Institution. Clinical and Translational Science, 11 (1): 85-92. doi: 10.1111/cts.12514
• Pope, Z., Zeng, N., Zhang, R., Lee, H., Gao, Z., 2018. Effectiveness of Combined Smartwatch and Social Media Intervention on Breast Cancer Survivor Health Outcomes: A 10-Week Pilot Randomized Trial. Journal of clinical medicine, 7 (6): 140.
• Zhang, R., Ma, S., Shanahan, L., Munroe, J., Horn, S., Speedie, S., 2018. Discovering and identifying New York heart association classification from electronic health records. BMC medical informatics and decision making, 18 (2): 48.
• He, Z., Tao, C., Bian, J., Zhang, R., Huang, J., 2018. Introduction: selected extended articles from the 2nd International Workshop on Semantics-Powered Data Analytics (SEPDA 2017). BioMed Central
• Wang, Y., Zhao, Y., Bian, J., Zhang, R., 2018. Detecting Signals of Associations Between Dietary Supplement Use and Mental Disorders from Twitter. 2018 IEEE International Conference on Healthcare Informatics Workshop (ICHI-W) 53-54.

• Zhang, R. (Invited), "Biomedical natural language processing for information extraction and knowledge discovery," Indiana University/Regenstrief Institute, Indianapolis, Indiana, January 22, 2019
• Ma, S. (Author & Presenter), Zhang, R. (Author), "Estimating New York Heart Association Classification for Heart Failure Patients from Information in the Electronic Health Record," IEEE International Conference on Bioinformatics and Biomedicine, December 3, 2018
• He, X., Zhang, R., "Prototyping an Interactive Visualization of Dietary Supplement Knowledge Graph," IEEE International Conference on Bioinformatics and Biomedicine, December 3, 2018
• Zhang, R., "Data science in healthcare: natural language processing to unlock healthcare information," Wayne State University, Detroit, Michigan, November 18, 2018
• Zhang, R., "Biomedical text analytics for computational health sciences," Weill Cornell Medical College, Cornell University, Weill Cornell Medical College, Cornell University, New York City, New York, October 22, 2018
• Zhang, R., "Analyzing clinical texts for computational health sciences," Anthem Inc., Chicago, Illinois, October 11, 2018
• Zhang, R., "Mining adverse events of supplements using product labeling data," National Institutes of Health (NIH), Office of Dietary Supplements, September 18, 2018
• Zhang, R., "Data Science for Discovering and Monitoring Drug Safety on Biomedical Big Data," College of Pharmacy presentation for Shenyang Pharmaceutical University, University of Minnesota, August 17, 2018
• Zhang, R., "Unlocking clinical records for computational health sciences," University of California, San Francisco, California, July 25, 2018
• Wang, Y. (Author & Presenter), Zhang, R. (Author), "Detecting Signals of Associations Between Dietary Supplement Use and Mental Disorders from Twitter," 2018 IEEE International Conference on Healthcare Informatics Workshop (ICHI-W), June 7, 2018
• Rizvi, R. (Author & Presenter), Zhang, R. (Author), "Comparing Existing Resources to Represent Dietary Supplements," American Medical Informatics Association Annual Symposium, San Francisco, California, March 1, 2018
• Fan, Y. (Author & Presenter), "Evaluating Automatic Methods to Extract Patients’ Supplement Use from Clinical Reports," IEEE International Conference on Bioinformatics and Biomedicine, Kansas City, Kansas, November 13, 2017
• Zhang, R. (Author & Presenter), "Automatic Methods to Extract New York Heart Association Classification from Clinical Notes," IEEE International Conference on Bioinformatics and Biomedicine, Kansas City, Kansas, November 13, 2017
• Sun, D., "Causal Phenotyping for Susceptibility to Cardiotoxicity from Antineoplastic Breast Cancer Medications," Proceedings of the American Medical Informatics Association Symposium, Washington D.C., November 8, 2017
• Zhang, R., "Data Science for Discovering and Monitoring Adverse Drug Events," Department of Surgery Resident Research Enrichment Program, University of Minnesota, Minneapolis, Minnesota, October 26, 2017
• Zhang, R., "Health Informatics to support Precision Medicine," The Minnesota Precision Medicine Collaborative Seminar, University of Minnesota, Minneapolis, Minnesota, October 06, 2017
• Zhang, R., "Natural language processing to support dietary supplement research," American Medical Informatics Association NLP working group webinar, October 3, 2017
• Fan, Y., "Detecting Signals of Interactions between Warfarin and Supplements in Electronic Health Records," The 16th World Congress on Medical and Health Informatics, Hangzhou, China, August 1, 2017
• Wang, Y. (Author & Presenter), "Mining Adverse Events of Dietary Supplements from Product Labels by Topic Modeling," The 16th World Congress on Medical and Health Informatics, Hangzhou, China, August 1, 2017
• Sun, D. (Author & Presenter), "Phenotyping and Visualizing Infusion-related Reactions for Breast Cancer Patients," The 16th World Congress on Medical and Health Informatics, Hangzhou, China, August 1, 2017
• Zhang, R., "Health Informatics to facilitate clinical and translational research," College of Pharmacy Clinical Retreat, University of Minnesota, Minneapolis, Minnesota, June 8, 2017
• Zhang, R., "Unlocking patient information and pharmacovigilance knowledge from clinical narratives and biomedical literature," Department of Medicine, University of Minnesota, Minneapolis, Minnesota, March 6, 2017
• Zhang, R., "Natural language processing in healthcare domain," Biomedical Informatics, Department of Health Outcomes and Policy, College of Medicine, University of Florida, Gainesville, Florida, February 22, 2017
• Zhang, R., "Big data science for drug safety," College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, February 7, 2017
• Zhang, R. (Author & Presenter), "Detecting Clinically Relevant New Information in Clinical Notes Across Specialties and Settings," ICIBM, Houston, Texas, December 8, 2016
• Fan, Y. (Author & Presenter), "Classification of Status for Supplement Use in Clinical Notes," Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, Shenzhen, China, December 1, 2016
• Marc, D., "Assessing Metadata Quality of a Federally Sponsored Health Data Repository," AMIA Annual Symposium, Chicago, Illinois, November 1, 2016
• Wang, Y. (Author & Presenter), "Term Coverage of Herb and Dietary Supplements in Product Labels," AMIA Annual Symposium, Chicago, Illinois, November 1, 2016
• Zhang, R., "Applying Active Learning to Semantic Predications in SemMedDB," Department of Surgery Graduation Day Poster Session, University of Minnesota, Minneapolis, Minnesota, June 14, 2016
• Zhang, R., "Health Informatics: when informatics and health big data meet," Computer Engineering and Systems, Texas A&M University, College Station, Texas, April 14, 2016
• Zhang, R., "Big Data to Knowledge (BD2K): mining literature to discover drug-supplement interactions," Surgical Ground Rounds, University of Minnesota, Minneapolis, Minnesota, March 1, 2016
• Chen, X., "Applying Active Learning to Semantic Predications in SemMedDB," IEEE International Conference on Biomedical and Health Informatics, Las Vegas, Nevada, February 1, 2016
• Zhang, R., "Applying Active Learning to Semantic Predications in SemMedDB," IEEE International Conference on Biomedical and Health Informatics, Las Vegas, Nevada, February 1, 2016
• Zhang, R. (Author & Presenter), "Evaluating Term Coverage of Herbal and Dietary Supplements in Electronic Health Records," Proceedings of the American Medical Informatics Association Symposium, San Francisco, California, November 1, 2015
• Manohar, N., "Evaluation of herbal and nutritional supplement resource term coverage," MEDINFO '15, West Side Community Health Services, São Paulo, Brazil, August 1, 2015
• Marc, D., "Indexing Publicly Available Health Data with Medical Subject Headings (MeSH): An Evaluation of Term Coverage," MEDINFO '15, São Paulo, Brazil, August 1, 2015
• Zhang, R., "Mining Biomedical Literature to Explore Interactions between Cancer Drugs and Dietary Supplements," American Medical Informatics Association Translational Bioinformatics Summit, University of California, San Francisco, California, March 24, 2015
• Zhang, R. (Author & Presenter), "Using Language Models to Identify Relevant New Information in Inpatient Clinical Notes," American Medical Informatics Association Annual Symposium, Washington D.C., November 1, 2014
• Zhang, R., "Mining textual information in clinical notes and biomedical literature," Academic Health Center Informatics Grand Rounds, University of Minnesota, Minneapolis, Minnesota, October 9, 2014
• Zhang, R., "Getting the Most out of the AMIA 2014 Annual Symposium: Participating in AMIA as a Student Attendee," American Medical Informatics Association Symposium webinar, October 2, 2014
• Zhang, R., "Leveraging natural language processing in health sciences," Department of Surgery Monthly Research Seminar, University of Minnesota, Minneapolis, Minnesota, September 18, 2014
• Zhang, R., "Preparing for scholarly presentations for AMIA Annual Symposium," American Medical Informatics Association Symposium webinar, August 26, 2014
• Zhang, R., "Introduction to Clinical Informatics," Department of Social and Public Health, Ohio University, Athens, Ohio, April 12, 2013
• Zhang, R., "Automatic methods to identify new information of patients from clinical texts," Doctoral Research Showcase, University of Minnesota, Minneapolis, Minnesota, April 9, 2013
• Zhang, R., "Natural Language Processing in Health Sciences," Briarcliff Manor, New York, April 8, 2013
• Zhang, R., "Natural Language Processing in Health Sciences," School of Information Studies, University of Wisconsin, Milwaukee, Wisconsin, March 8, 2013
• Zhang, R. (Author & Presenter), "Automated Assessment of Medical Training Evaluation Text," American Medical Informatics Association Symposium, University of Illinois, Chicago, Illinois, November 1, 2012
• Zhang, R., "Discovery of potential drug interactions from biomedical literatures," Department of Experimental and Clinical Pharmacology Seminar, University of Minnesota, Minneapolis, Minnesota, September 1, 2012
• Zhang, R., "Evaluating measures of redundancy in clinical texts," Institute for Health Informatics Seminar, University of Minnesota, Minneapolis, Minnesota, September 1, 2012
• Zhang, R., "Using semantic predications to uncover drug-drug interactions in clinical notes," National Library of Medicine Seminar, National Institutes of Health, University of Maryland, Bethesda, Maryland, August 22, 2012
• Zhang, R., "Automated identification of new useful information in clinical narrative," 2nd ACM SIGHIT (SIG on Health Informatics) International Health Informatics Symposium, Miami Beach, Florida, January 1, 2012
• Zhang, R. (Author & Presenter), "Evaluating measures of redundancy in clinical text," American Medical Informatics Association Symposium, Washington D.C., October 1, 2011