Zhe He profile picture CCI FSU Tallahassee FL

Zhe He

Assistant Professor

LSB 271

Dr. Zhe He is an Assistant Professor in the School of Information at the Florida State University (Florida's iSchool) and a Core Affiliate of the Institute for Successful Longevity.

Before joining FSU, Dr. He was a Postdoctoral Research Scientist (2014-2015) in the Department of Biomedical informatics at Columbia University, working with Dr. Chunhua Weng. In his postdoctoral research, he has developed methods for assessing the collective population representativeness of clinical studies with the goal of improving the transparency of study generalizability to the real-world population.

During his PhD studies in Computer Science at New Jersey Institute of Technology (2009-2014). He worked with Dr. James Geller and Dr. Yehoshua Perl in the Structural Analysis of Biomedical Ontologies Center (SABOC). His doctoral dissertation "Using Structural and Semantic Methodologies to Enhance Biomedical Terminologies" introduced a variety of quality assurance methodologies for controlled terminologies and ontologies e.g., Unified Medical Language System (UMLS), SNOMED CT, and domain ontologies in BioPortal.

As the first author, he has published in leading biomedical informatics journals such as Journal of Biomedical Informatics, Artificial Intelligence in Medicine, and mainstream informatics conferences such as American Medical Informatics Association (AMIA) Annual Symposium, and World Congress on Health and Biomedical Informatics (MEDINFO). His papers were nominated as Student Paper Award of AMIA 2015 Summit on Clinical Research Informatics and MEDINFO 2015. His AMIA 2013 paper was selected as the representative paper on "biomedical ontologies" in the "Informatics Year In Review". He is a recipient of the Distinguished Paper Award of AMIA 2015 Annual Symposium.

During his PhD studies, he was inducted into Alpha Epsilon Lambda National Graduate and Professional Honor Society. He received his MS from Columbia University and his BS from Beijing University of Posts and Telecommunications, both in Computer Science.

In his spare time, Zhe loves photography and traveling. This is his Photography Studio Website .

Find more information about Zhe and reach out to him at his website.


  • Postdoctoral Training. 2015: Columbia University, Biomedical Informatics
  • Ph.D. 2014; New Jersey Institute of Technology (NJIT), Computer Science
  • M.S. 2009; Columbia University, Computer Science
  • B.E. 2007; Beijing University of Posts and Telecommunications, Computer Science

Research Interests

Dr. He has broad interests in biomedical and health informatics, clinical research informatics, knowledge discovery, and ontology-based data analytics. On the foundational track, he is developing semantic and structural methods to enhance controlled terminologies/ontologies and improve their utility in natural language processing, clinical decision support, data analytics, and electronic health records. On the application track, his research aims to improve the representation of underserved population subgroups in clinical studies such as older adults with multiple chronic conditions. Another line of his research is to bridge the terminology gap between health information consumers and health professionals. He has published in the following topics:

    Quality assurance of biomedical ontologies (e.g, domain ontologies in BioPortal)
    Quality assurance of controlled vocabularies (e.g., SNOMED CT, UMLS)
    Data-driven conceptual content enrichment for ontologies/terminologies (e.g., SNOMED CT, NCIt)
    Clinical trial generalizability assessment and improvement
    Consumer Health Vocabulary

Teaching Interests

This semester he is teaching an undergraduate special topic course "Data Analytics" (LIS 4930). In the 2016 Fall semester, he is going to teach graduate courses "Database Management Systems" (LIS 5782) and "Management of Health Information Technology" (LIS 5788).

Publications & Research

Selected Publications (All Publications)
Clinical Research Informatics
  • Zhe He, Patrick Ryan, Julia Hoxha, Shuang Wang, Simona Carini, Ida Sim, and Chunhua Weng. Multivariate analysis of the population representativeness of related clinical studies. Journal of Biomedical Informatics. 2016;60:66-76. PMID: 26820188. (IF: 2.19, 5-Year IF: 3.44) [ScienceDirect] [PubMed] [PDF]
  • Zhe He, Praveen Chandar, Patrick Ryan, and Chunhua Weng. Simulation-based Evaluation of the Generalizability Index for Study TraitsProceedings of AMIA 2015 Annual Symposium. November 14-18, 2015. San Francisco, CA. pp.594-602. PMID: 26958194 [PDF] (Distinguished Paper Award)
  • Zhe He, Shuang Wang, Elhaam Borhanian, and Chunhua Weng. Assessing the Population Representativeness of Type 2 Diabetes Trials by Combining Public Data from ClinicalTrials.gov and NHANESProceedings of MEDINFO 2015, August 19-23, 2015, Sao Paulo, Brazil. Studies in Health Technology and Informatics. 2015;216:569-73. PMID: 26262115 [PDF]  (Student Paper Competition Finalist)
  • Zhe He, Simona Carini, Ida Sim, and Chunhua Weng. Visual aggregate analysis of eligibility features of clinical trialsJournal of Biomedical Informatics. 2015;(54):241-255. PMID: 25615940. [ScienceDirect] [PubMed] [PDF]
  • Zhe He, and Chunhua Weng. Predicting New Target Conditions for Drug Retesting Using Temporal Patterns in Clinical Trials: A Proof of ConceptProceedings of AMIA 2015 Joint Summits on Translational Science, March 23 - 27, 2015, San Francisco, CA. pp.445-9. PMID: 26306283. [PDF] [Talk Slides] (Student Paper Competition Finalist)
  • Zhe He, Simona Carini, Tianyong Hao, Ida Sim, and Chunhua Weng. A Method for Analyzing Commonalities in Clinical Trial Target PopulationsProceedings of AMIA 2014 Annual Symposium (AMIA 2014), November 15 - 19, 2014, Washington D.C. pp.1777-1786. PMID: 25954450. [PubMed] [PDF] [Talk Slides]
Biomedical Terminologies / Ontologies

Grants & Awards

  • First Year Assistant Professor Grant. Council on Research and Creativity, Florida State University,05/2016-08/2016
  • Runner-up, the Most Interesting Preliminary Results Paper Award, iConference 2016,03/2016
  • Amazon Web Services Education Research Grant Award, Amazon Inc. 12/2015-12/2016
  • Distinguished Paper Award, AMIA 2015 Annual Symposium, 11/2015
  • Finalist of Student Paper Award, the 15th World Congress on Health and Biomedical Informatics, 08/2015
  • Finalist of Student Paper Award, American Medical Informatics Association 2015 Clinical Research Informatics, 04/2015
  • Paper Selection in the 2014 Informatics Year in Review, 11/2014
  • Third Place Poster Award, the 1st Columbia University Postdoctoral Research and Career Symposium, 03/2014
  • Outstanding Student Leader Award of 2013-2014, New Jersey Institute of Technology, 05/2014
  • Student Achievement Award, New Jersey Institute of Technology Graduate Student Association, 10/2012
  • Distinguished Graduates of Beijing, Beijing Municipality Education Committee, 07/2007