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: i) the secondly analysis of EHR data for patient care, ii) pharmacovigilance knowledge discovery through mining biomedical literature and iii) creation of knowledge base through database integration, terminology and ontology.

Current projects include: i) developing NLP methods and applications to extract information from clinical reports; ii) mining biomedical literature to discover novel drug-supplement interactions through genetic pathways; iii) Repurposing existing drugs for COVID-19 treatment through link predictions and literature-based discovery; iv) developing computational methods to predict personalized cancer treatment caused cardiotoxicity in EHRs; v) developing conversational agent for consumers with developed knowledge base.

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. (in press). 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: https://doi.org/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: https://doi.org/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.

Hultman, G., McEwan, R., Knoll, B., Zhang, R., Pakhomov, S., NLP-PIER 2.0: A Redesigned Clinical Document Search Interface for Researchers. AMIA Clinical Informatics.

Zhang, R. "(Invited) Biomedical natural language processing for information extraction and knowledge discovery", Indiana University/Regenstrief Institute, 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 03, 2018.

He, X., Zhang, R. "Prototyping an Interactive Visualization of Dietary Supplement Knowledge Graph", IEEE International Conference on Bioinformatics and Biomedicine. December 03, 2018.

Zhang, R. "Data science in healthcare: natural language processing to unlock healthcare information", Wayne State University, Detriot, 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, New York. October 22, 2018.

Zhang, R. "Analyzing clinical texts for computational health sciences", Anthem Inc, , Chicago. October 11, 2018.

Zhang, R. "Mining adverse events of supplements using product labeling data", NIH, Office of Dietary Supplements. September 18, 2018.

Zhang, R. "Data Science for Discovering and Monitoring Drug Safety on Biomedical Big Data", COP 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, 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 07, 2018.

Rizvi, R., (Author & Presenter), Zhang, R., (Author) "Comparing Existing Resources to Represent Dietary Supplements ", American Medical Informatics Association Annual Symposium, AMIA, San Francisco, California, United States. March 01, 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, United States. November 13, 2017.

Sun, D. "Causal Phenotyping for Susceptibility to Cardiotoxicity from Antineoplastic Breast Cancer Medications", Proceedings of the American Medical Informatics Association Symposium, Philips, Washington DC. November 08, 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, University of Minnesota. October 03, 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 01, 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 01, 2017.

Sun, D., (Author & Presenter) "Phenotyping and Visualizing Infustion-related Reactions for Breast Cancer Patients.", The 16th World Congress on Medical and Health Informatics, Philips, Hangzhou, China. August 01, 2017.

Zhang, R. "Health Informatics to facilitate clinical and translational research", College of Pharmacy Clinical Retreat, University of Minnesota, University of Minnesota, Minneapolis, Minnesota. June 08, 2017.

Zhang, R. "Unlocking patient information and pharmacovigilance knowledge from clinical narratives and biomedical literature", Department of Medicine, University of Minnesota, Minneapolis, Minnesota. March 06, 2017.

Zhang, R. "Natural language processing in healthcare domain", Biomedical informatics, Department of health outcomes and policy, College of Medicine, University of Florida, University of Minnesota. February 22, 2017.

Zhang, R. "Big data science for drug safety", College of Pharmacy, University of Minnesota, Minneapolis, Minnesota. February 07, 2017.

Zhang, R., (Author & Presenter) "Detecting Clinically Relevant New Information in Clinical Notes Across Specialties and Settings", ICIBM, Houston, Texas. December 08, 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 01, 2016.

Marc, D. "Assessing Metadata Quality of a Federally Sponsored Health Data Repository", AMIA Annual Symposium, AMIA Annual Symposium, Chicago, Illinois. November 01, 2016.

Wang, Y., (Author & Presenter) "Term Coverage of Herb and Dietary Supplements in Product Labels", AMIA Annual Symposium, Chicago, Illinois. November 01, 2016.

Zhang, R. "Applying Active Learning to Semantic Predications in SemMedDB", Department of Surgery Graduation Day Poster Session. University of Minnesota, 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, University of Minnesota, 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 01, 2016.

Chen, X. "Applying Active Learning to Semantic Predications in SemMedDB", IEEE International Conference on Biomedical and Health Informatics, Las Vegas, Nevada. February 01, 2016.

Zhang, R. "Applying Active Learning to Semantic Predications in SemMedDB", IEEE International Conference on Biomedical and Health Informatics., Las vegas, Nevada. February 01, 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 01, 2015.

Manohar, N. "Evaluation of herbal and nutritional supplement resource term coverage", MEDINFO '15, West Side Community Health Services, São Paulo, Brazil. August 01, 2015.

Marc, D. "Indexing Publicly Available Health Data with Medical Subject Headings (MeSH): An Evaluation of Term Coverage", MEDINFO '15, São Paulo, Brazil. August 01, 2015.

Zhang, R. "Mining Biomedical Literature to Explore Interactions between Cancer Drugs and Dietary Supplements", American Medical Informatics Association Translational Bioinformatics Summit, University of Minnesota, 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 DC. November 01, 2014.

Zhang, R. "Mining textual information in clinical notes and biomedical literature", Academic Health Center informatics grand round, University of Minnesota, Minneapolis, Minnesota. October 09, 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, University of Minnesota. October 02, 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, University of Minnesota. August 26, 2014.

Zhang, R. "Introduction to Clinical Informatics", Department of Social and Public Health, Ohio University, University of Minnesota, Athen, 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 09, 2013.

Zhang, R. "Natural Language Processing in Health Sciences", University of Minnesota, Briarcliff Mano, New York. April 08, 2013.

Zhang, R. "Natural Language Processing in Health Sciences", School of Information Studies, University of Wisconsin, University of Minnesota, Milwaukee, Wisconsin. March 08, 2013.

Zhang, R., (Author & Presenter) "Automated Assessment of Medical Training Evaluation Text.", American Medical Informatics Association Symposium, University of Minnesota, Chicago, Illinois. November 01, 2012.

Zhang, R. "Discovery of potential drug interactions from biomedical literatures", Seminar, Department of Experimental and Clinical Pharmacy, University of Minnesota, Minneaplois, Minnesota. September 01, 2012.

Zhang, R. "Evaluating measures of redundancy in clinical texts", Seminar, Institute for Health Informatics, University of Minnesota,, Minneapolis, Minnesota. September 01, 2012.

Zhang, R. "Using semantic predications to uncover drug-drug interactions in clinical notes", Seminar, National Library of Medicine, National Institutes of Health,, University of Minnesota, 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 01, 2012.

Zhang, R., (Author & Presenter) " Evaluating measures of redundancy in clinical text", American Medical Informatics Association Symposium, University of Minnesota, Washington DC. October 01, 2011.

American Medical Informatics Association

AMIA Education Committee

AMIA Membership/Outreach Committee

AMIA Student Working Group

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

• 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