Publications by Year

Manuscripts Under Review

  1. Zhe He, Laura A. Barrett, Rubina F. Rizvi, Seyedeh Neelufar Payrovnaziri, and Rui Zhang. Assessing the Use and Perception of Dietary Supplements Among Obese Patients with National Health and Nutrition Examination Survey. AMIA 2019 Annual Symposium. Under review.
  2. Nur Hafieza Ismail, Ninghao Liu, Mengnan Du, Zhe He, Xia Ben Hu. Using Deep Neural Network to Identify Cancer Survivors Living with Post-Traumatic Stress Disorder on Social Media. AMIA 2019 Annual Symposium. Under review.
  3. Qian Li, Zhe He, Yi Guo, Hansi Zhang, Thomas J George Jr, William Hogan, Neil Charness, Jiang Bian, Assessing the Validity of a a prior Patient-Trial Generalizability Score using Real-world Data from a Large Clinical Data Research Network: A Colorectal Cancer Clinical Trial Case Study. AMIA 2019 Annual Symposium. Under review.
  4. Lynette Hammond Gerido , Xiang Tang , Brittany Ernst , Aisha Langford, and Zhe He. Addressing Health Disparities among Older Adults: Intersecting Patient Engagement in Medical Research with Health Informatics. Under preparation.
  5. Vipina K. Keloth, Zhe He, Gai Elhanan, and James Geller. Alternative Classification of Identical Concepts in Different Ontologies: Different Ways to View the Medical World. Journal of Biomedical Informatics. Acceptable pending minor revision.
  6. Biyang Yu, Zhe He, and Mia Liza Lustria. Developing a Text Complexity Measurement Framework to Assess the Language Use of Health Consumers: Implications for e-Health Literacy Divide. Under review.
  7. Zhe He, Wallace M Douglas, Michael Perlis, Andrea Barnes, Girardin Jean-Louis, and Natasha Williams. Reporting results in U.S. clinical trials for obstructive sleep apnea and insomnia: how transparent are they? Sleep Health. Under review.
  8. Jinghui Hou, Joshua Hendrickse, Zhe He, Jingbo Meng, Hansi Zhang, Sanghee Oh, and Jiang Bian. Health Information Seeking Over Time: A Qualitative Analysis of Information Needs of Patients with Chronic Diseases on a Social Q&A Site. Translational Behavioral Medicine, Under review.

2019 (1 edited book, 1 book chapter, 3 journal papers, 6 conference papers)

  1. Jiang Bian, Yi Guo, Zhe He, and Xia Hu. Social Web and Health Research - Benefits, Limitations and Best Practice. Springer International Publishing AG. To be published in June 2019
  2. Zhe He. Understanding and Bridging the Language and Terminology Gap between Health Professionals and Consumers Using Social Media. Social Web and Health Research: Benefits, Limitations, and Best Practices. To be published in June 2019 (Book Chapter)
  3. Xing He, Rui Zhang, Rubina Rizvi, Jake Vasilakes, Xi Yang, Yi Guo, Zhe He, Mattia Prosperi, Jinhai Huo, Jordan Alpert, Jiang Bian. ALOHA: Developing an Interactive Graph-based Visualization for Dietary Supplement Knowledge Graph through User-centered Design. BMC Medical Informatics and Decision Making. In press.
  4. Canlin Zhang*, Daniel Biś*, Xiuwen Liu, and Zhe He, Biomedical Word Sense Disambiguation with Bidirectional Long Short-Term Memory and Attention-based Neural Networks. BMC System Biology. In press.
  5. Seyedeh Neelufar Payrovnaziri, Laura A. Barrett, Daniel Bis, Jiang Bian, and Zhe He. Enhancing Prediction Models for One-Year Mortality in Patients with Acute Myocardial Infarction and Post Myocardial Infarction Syndrome. MEDINFO 2019. August 26-30, 2019. Lyon, France. Studies in Health Technology and Informatics. In press.
  6. Zhan Zhang, Yu Lu, Yubo Kou, Danny Wu, Jina Huh-Yoo, and Zhe He. Understanding Patient Information Needs about their Clinical Laboratory Results: A Study of Social Q&A Site. MEDINFO 2019. August 26-30, 2019. Lyon, France. Studies in Health Technology and Informatics. In press.
  7. Rubina F. Rizvi, Yefeng Wang, Thao Nguyen, Jake Vasilakes, Zhe He, and Rui Zhang. Analyzing Social Media Data to Understand Consumers’ Information Needs on Dietary Supplements. MEDINFO 2019. August 26-30, 2019. Lyon, France. Studies in Health Technology and Informatics. In press.
  8. Francisco Modave, Yunpeng Zhao, Janice Krieger, Zhe He, Yi Guo, Jiang Bian. Understanding Perceptions and Attitudes in Breast Cancer Discussions on Twitter. MEDINFO 2019. August 26-30, 2019. Lyon, France. Studies in Health Technology and Informatics. In press.
  9. Pei-Yau Lung, Zhe He, Tingting Zhao, Disa Yu, and Jinfeng Zhang. Extracting chemical-protein interactions from literature using sentence structure analysis and feature engineering. Database: The Journal of Biological Databases and Curation. 2019. 2019:1-8. PMID: 30624652 (SCIE, Impact Factor: 3.98) [Link]
  10. Zhe He, Rubina F. Rizvi, Fan Yang, Terrence J. Adam, and Rui Zhang. Comparing the Study Populations in Dietary Supplement and Drug Clinical Trials for Metabolic Syndrome Related Disorders. AMIA 2019 Informatics Summit. March 25-28, 2019. San Francisco, CA. In press.
  11. Laura A. Barrett, Seyedeh Neelufar Payrovnaziri, Jiang Bian, and Zhe He. Building Computational Models to Predict One-Year Mortality in ICU Patients with Acute Myocardial Infarction and Post Myocardial Infarction Syndrome. AMIA 2019 Informatics Summit. March 25-28, 2019. San Francisco, CA. In press. (Finalist of the Student Paper Award) (Media Report)

2018 (7 journal papers, 5 conference papers)

  1. Zhe He, Vipina Kuttichi Keloth, Yan Chen, and James Geller. Extended Analysis of Topological-Pattern-Based Ontology Enrichment. Proceedings of 2018 IEEE International Conference on Bioinformatics and Biomedicine. December 3-6, 2018, Madrid, Spain. pp.1641-1648. PMID: 30854243. PMCID: PMC6402505 [Link] [PMC]
  2. Xing He, Rui Zhang, Rubina Rizvi, Jake Vasilakes, Xi Yang, Yi Guo, Zhe He, and Jiang Bian. Prototyping an Interactive Visualization of Dietary Supplement Knowledge Graph. Proceedings of 2018 IEEE International Conference on Bioinformatics and Biomedicine. December 3-6, 2018, Madrid, Spain. pp. 1649-1652 [Link]
  3. Tianyong Hao, Raymond Wong, Zhe He, Haoran Xie, Tak-Lam Wong, and Fu Lee Wang. Natural Language Processing Empowered Mobile Computing. Wireless Communication and Mobile Computing. 2018. 2018: 1-2.. DOI: 10.1155/2018/9130545. (Editorial of the special issue) [Link]
  4. *Daniel Biś, *Canlin Zhang, Xiuwen Liu, and Zhe He. Layered Multistep Bidirectional Long Short-Term Memory Networks for Biomedical Word Sense Disambiguation. Proceedings of 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2018). [Link] December 3-6, 2018, Madrid, Spain. pp. 313-320. (Acceptance Rate of Regular Paper: 19.6%) [Link]
  5. Hansi Zhang, Zhe He, Xing He, Yi Guo, David R. Nelson, François Modave, Yonghui Wu, William Hogan, and Jiang Bian. Computable Eligibility Criteria through Ontology-Driven Data Access: A Case Study of Hepatitis C Virus Trials. Proceedings of AMIA 2018 Annual Symposium. November 3-8, 2018. San Francisco, CA. pp. 1601-1610. (Finalist of the Student Paper Award, 8 out of 47 student papers were selected)
  6. Vipina Kuttichi Keloth, Zhe He, Yan Chen, and James Geller. Leveraging Horizontal Density Differences Between Ontologies to Identify Missing Child Concepts: A Proof of Concept. Proceedings of AMIA 2018 Annual Symposium. November 3-8, 2018. San Francisco, CA. pp. 644-653. [PDF]
  7. Zhe He, Cui Tao, Jiang Bian, Rui Zhang, Jingshan, Huang. Introduction: selected extended articles from the 2nd International Workshop on Semantics-Powered Data Analytics (SEPDA 2017). BMC Medical Informatics and Decision Making. 2018. 18 (Suppl 2) :56. DOI: 10.1186/s12911-018-0624-8. PMID: 30066636. (SCIE, Impact Factor: 2.13) [Link] [PubMed] (Editorial of the journal supplement)
  8. *Zhiwei Chen, Zhe He, Xiuwen Liu, and Jiang Bian. Evaluating semantic relations in neural word embeddings using biomedical and general domain knowledge bases. BMC Medical Informatics and Decision Making. 2018. 18 (Suppl 2) :65. DOI: 10.1186/s12911-018-0630-x. PMID: 30066651 (SCIE, Impact Factor: 2.13) [Link] [PubMed] [Correction Article]
  9. Juan Antonio Lossio-Ventura, William Hogan, François Modave, Yi Guo, Zhe He, Xi Yang, Hansi Zhang, and Jiang Bian. OC-2-KB: Integration crowdsourcing into an obesity and cancer knowledge base curation system. BMC Medical Informatics and Decision Making. 2018. 2018. 18 (Suppl 2) :55. DOI: 10.1186/s12911-018-0635-5. PMID: 30066655 (SCIE, Impact Factor: 2.13) [Link] [PubMed]
  10. Huanying Gu, Zhe He, Duo Wei, Gai Elhanan and Yan Chen. Validating UMLS Semantic Type Assignments Using SNOMED CT Semantic Tags. Methods of Information in Medicine. 2018; 57(1): 43-53. PMID: 29621830. (SCI, Impact Factor: 1.53) [Link] [PubMed]
  11. Zhe He, Jiang Bian, Henry Carretta, Jiwon Lee, William Hogan, Elizabeth Shenkman, and Neil Charness. Prevalence of Multiple Chronic Conditions Among Older Adults in Florida and the United States: Comparative Analysis of the OneFlorida Data Trust and National Inpatient Sample. Journal of Medical Internet Research. 2018; 20(4): e137. PMID: 29650502. PMCID: PMC5920146. (SCIE, †: equal-contribution first authors, Impact Factor: 4.67) [Link] [PubMed] [PMC]
  12. Muhammad F. Amith, Zhe He, Jiang Bian, Juan Antonio Lossio-Ventura, and Cui Tao*. Assessing the practice of biomedical ontology evaluation: Gaps and opportunities. Journal of Biomedical Informatics. 2018;80:1-13. DOI: 10.1016/j.jbi.2018.02.010. PMID: 29462669. (†: equal-contribution first authors, SCI, Impact Factor: 2.88, 5-Year Impact Factor: 3.12) [FSU CCI News] [ScienceDirect] [PubMed]

2017 (3 journal papers & 8 conference papers)

  1. Jiang Bian, Yunpeng Zhao, Ramzi G Salloum, Yi Guo, Mo Wang, Mattia Prosperi, Hansi Zhang, Xinsong Du, Laura J Ramirez-Diaz, Zhe He, Yuan Sun. Using Social Media Data to Understand the Impact of Promotional Information on Laypeople's Discussions: A Case Study of Lynch syndrome. Journal of Medical Internet Research. 2017;19(12):e414. DOI: 10.2196/jmir.9266. PMID: 29237586. PMCID: PMC5745354. (SCIE, Impact Factor: 4.67) [Link] [PMC]
  2. Jinchan Qu, Albert Steppi, Jie Hao, Jian Wang, Pei-Yau Lung, Tinting Zhao, Zhe He and Jinfeng Zhang. Mining protein interactions affected by mutations using a NLP based machine learning approach. Proceedings of BioCreative VI Challenge and Workshop. October 18-20, 2017. Bethesda, MD. pp. 132-135. (Invited to give an oral presentation at BioCreative VI Track 4: Mining protein interactions and mutations for precision medicine) [Link]
  3. Pei-Yau Lung, Tingting Zhao, Zhe He and Jinfeng Zhang. Extracting chemical-protein compound interactions from literature. Proceedings of BioCreative VI Challenge and Workshop. October 18-20, 2017. Bethesda, MD. pp. 160-163. (Invited to give an oral presentation at BioCreative VI Track 5: Text mining chemical protein interactions) [Link]
  4. Juan Antonio Lossio-Ventura, William Hogan, Francois Modave, Yi Guo, Zhe He, Amanda Hicks, and Jiang Bian. OC-2-KB: A software pipeline to build an evidence-based obesity and cancer knowledge base. Proceedings of 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2017). November 13 - 16, 2017. Kansas City, MO. pp. 1284-1287. DOI: 10.1109/BIBM.2017.8217845. PMID: 29629236. PMCID: PMC5889048 [IEEE] [PMC]
  5. Biyang Yu and Zhe He. Exploratory Textual Analysis of Consumer Health Languages for People Who are Deaf/Hard of Hearing. Proceedings of 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2017). November 13 - 16, 2017. Kansas City, MO. pp. 1288-1291. DOI: 10.1109/BIBM.2017.8217846 [IEEE]
  6. Zhiwei Chen, Zhe He, Xiuwen Liu, and Jiang Bian. An Exploration of Semantic Relations in Neural Word Embeddings Using Extrinsic Knowledge. Proceedings of 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2017). November 13 - 16, 2017. Kansas City, MO. pp.1246-1251. DOI: 10.1109/BIBM.2017.8217836 [IEEE]
  7. Zhe He, Yehoshua Perl, Gai Elhanan, Yan Chen, James Geller, and Jiang Bian. Auditing the Assignments of Top-Level Semantic Types in the UMLS Semantic Network to UMLS Concepts. Proceedings of 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2017). November 13 - 16, 2017. Kansas City, MO. pp. 1262-1269. DOI: 10.1109/BIBM.2017.8217840. PMID: 29375930. PMCID: PMC5786167 [IEEE] [PMC] [PDF]
  8. Zhe He*, Cui Tao, Jiang Bian, Michel Dumontier, and William Hogan. Semantics-Powered Healthcare Engineering and Data Analytics. Journal of Healthcare Engineering. 2017. DOI: https://doi.org/10.1155/2017/7983473. PMID: 29214005. PMCID: PMC5682067. (SCIE, Impact Factor: 1.26) [Link] [PubMed] [PMC] (Editorial of the Special Issue)
  9. Zhe He, Arturo Gonzalez-Izquierdo, Spiros Denaxas, Andrei Sura, Yi Guo, William R. Hogan, Elizabeth Shenkman, Jiang Bian. Comparing and Contrasting A Priori and A Posteriori Generalizability Assessment of Clinical Trials on Type 2 Diabetes Mellitus. Proceedings of American Medical Informatics Association 2017 Annual Symposium (AMIA 2017). November 4-8, 2017. Washington DC. pp. 849-858. PMID: 29854151. PMCID: PMC5977671 (Distinguished Paper Award of AMIA 2017 Annual Symposium; three awards were selected from 105 accepted paper and 266 paper submissions) [Award Certificate] [CCI News] [PMC]
  10. Zhe He, Zhiwei Chen, Sanghee Oh, Jinghui Hou, and Jiang Bian. Enriching consumer health vocabulary through mining a social Q&A site: a similarity-based approach. Journal of Biomedical Informatics. 2017;69:75-85. PMID: 28359728 (SCI, Impact Factor: 2.88, 5-Year Impact Factor: 3.12) [PubMed] [ScienceDirect]
  11. Zhe He, Yan Chen, and James Geller. Perceiving the Usefulness of National Cancer Institute Metathesaurus for Enriching NCIt with Topological Patterns. Proceedings of the 16th World Congress on Medical and Health Informatics (MEDINFO 2017). August 21-25, 2017. Hangzhou, China. Studies in Health Technology and Informatics. 2017;245: 863-867. PMID: 29295222. DOI:10.3233/978-1-61499-830-3-863 [IOS] [PubMed][PMC]

2016 (6 journal papers & 8 conference papers)

  1. Juan Antonio Lossio-Ventura, William Hogan, François Modave, Amanda Hicks, Yi Guo, Zhe He, and Jiang Bian. Towards an Obesity-Cancer Knowledge Base: Biomedical Entity Identification and Relation Detection. Proceedings of the 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2016). December 15-18, 2016. Shenzhen, China. pp. 1081-1088. DOI: 10.1109/BIBM.2016.7822672. PMID: 28503356. PMCID: PMC5426361. [IEEE] [PMC]
  2. Min Sook Park, Zhe He*, Zhiwei Chen, Sanghee Oh, and Jiang Bian. Consumer's Use of UMLS Concepts on Social Media: Diabetes-Related Textual Data Analysis in Blog and Social Q&A Sites. JMIR Medical Informatics. 2016; 4(4):e41. PMID: 27884812. PMCID: PMC5146325 (ESCI, Park MS and He Z are equal-contribution first authors) [JMIR] [PDF] [PMC]
  3. Zhe He, Zhiwei Chen, and Jiang Bian. Analysis of Temporal Constraints in Qualitative Eligibility Criteria of Cancer Clinical Studies. Proceedings of the 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2016). pp. 717-722. PMID: 29263940. PMCID: PMC5733789. DOI: 10.1109/BIBM.2016.7822607. (Acceptance rate: 19%) [IEEE] [PMC]
  4. Jiang Bian, Kenji Yoshigoe, Amanda Hicks, Jiawei Yuan, Zhe He, Mengjun Xie, Yi Guo, Mattia Prosperi, François Modave. Mining Twitter to assess the public perception of the "Internet of things". PLoS ONE. 2016;11(7): e0158450. PMID: 27391760. PMCID: PMC4938510 (2015 Impact Factor: 2.77) [Link] [PubMed] [PMC]
  5. Zhe He, Yan Chen, Sherri de Coronado, Katrina Piskorski, and James Geller. Topological-Pattern-based Recommendation of UMLS Concepts for National Cancer Institute Thesaurus. Proceedings of American Medical Informatics Association 2016 Annual Symposium (AMIA 2016). 618-627. PMID: 28269858. PMCID: PMC5333219 [Talk Slides] [PMC]
  6. Zhe He, Zhiwei Chen, Thomas J George, Gloria Lipori, and Jiang Bian. Assessing the Population Representativeness of Colorectal Cancer Treatment Clinical Trials. Proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2016). August 16-20, 2016. Orlando, FL. 4 pages. pp.2970-2973. PMID: 28268936 PMCID: PMC5727892. (Acceptance rate for oral presentations: 20%) [IEEE] [PubMed] [PMC]
  7. Zhe He and James Geller. Preliminary Analysis of Difficulty of Importing Pattern-Based Concepts into the National Cancer Institute Thesaurus. Studies in Health Technology and Informatics. 2016. Volume 288: Exploring the Complexity in Health: An Interdisciplinary Systems Approach: 389-393. Medical Informatics Europe 2016 (MIE 2016). PMID: 27577410. [IOS Press] [PubMed] [PMC]
  8. Christopher Ochs, Zhe He, Ling Zheng, James Geller, Yehoshua Perl, George Hripcsak, and Mark Musen. Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies. Journal of Biomedical Informatics. 2016;61:63-76. PMID: 26988001. PMCID: PMC4893909 (SCI, Impact Factor: 2.88, 5-Year Impact Factor: 3.12) [ScienceDirect] [PubMed] [PMC]
  9. 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. PMCID: PMC4837055 (SCI, Impact Factor: 2.88, 5-Year Impact Factor: 3.12) [ScienceDirect] [PubMed] [PMC]
  10. Huanying Gu*, Yan Chen, Zhe He, Michael Halper, and Ling Chen. Quality Assurance of UMLS Semantic Type Assignments Using SNOMED CT Hierarchies. Methods of Information in Medicine. 2016; 55(2):158-165. PMID: 25925776. (2014 Impact Factor: 1.53) [Schattauer] [PubMed]
  11. Zhe He, Neil Charness, Jiang Bian, and William R. Hogan. Assessing the Comorbidity Gap between Clinical Studies and Prevalence in Elderly Patient Populations. Proceedings of 2016 IEEE International Conference on Biomedical and Health Informatics. February 24-27, 2016. Las Vegas, NV. pp.136-139. PMID: 27738664. [IEEE Xplore] [PMC]
  12. Cilia Zayas, Zhe He, Jiawei Yuan, Mildred Maldonado-Molina, William R. Hogan, François Modave, and Jiang Bian. Examining Healthcare Utilization Patterns of Elderly and Mid-Aged Adults in the United States. Proceedings of the 29th International FLAIRS Conference (FLAIRS-29). May 16-18, 2016. Key Largo, FL. pp.361-366. PMID: 27430035. [AAAI] [PMC]
  13. Zhe He*, Min Sook Park*, and Zhiwei Chen. UMLS-Based Analysis of Medical Terminology Coverage for Tags in Diabetes-Related Blogs (*: equal contribution). Proceedings of iConference 2016. March 20-23, 2016. Philadelphia, PA. (Preliminary results paper. Acceptance rate: 30%) (Runner up of the Most Interesting Preliminary Results Paper Award) [Link]
  14. Julia Hoxha, Praveen Chandar, Zhe He, David Hanauer, James J Cimino, Chunhua Weng*. DREAM: Classification Scheme for Dialog Acts in Clinical Research Data Query Mediation. Journal of Biomedical Informatics. 2016;59:89-101. PMID: 26657707. (SCI, Impact Factor: 2.88, 5-Year Impact Factor: 3.12) [ScienceDirect] [PubMed]

2015 (2 journal papers & 4 conference papers)

  1. Zhe He, Praveen Chandar, Patrick Ryan, and Chunhua Weng. Simulation-based Evaluation of the Generalizability Index for Study Traits. Proceedings of American Medical Informatics Association 2015 Annual Symposium (AMIA 2015). November 14-18, 2015. San Francisco, CA. pp.594-603. PMID: 26958194 (Distinguished Paper Award of AMIA 2015 Annual Symposium [Official Announcement] [Award Certificate] [News Article]) [PubMed] [PMC] (Clinical Research Informatics 2016 Year in Review)
  2. Praveen Chandar, Anil Yaman, Julia Hoxha, Zhe He, and Chunhua Weng. Similarity-based Recommendation of New Concepts to a Terminology. Proceedings of American Medical Informatics Association 2015 Annual Symposium (AMIA 2015). November 14-18, 2015. San Francisco, CA. pp.386-395. PMID: 26958170 [PubMed] [PMC]
  3. Zhe He, Shuang Wang, Elhaam Borhanian, and Chunhua Weng. Assessing the Collective Population Representativeness of Type 2 Diabetes Trials by Combining Public Data from ClinicalTrials.gov and NHANES. Proceedings of MEDINFO 2015, August 19-23, 2015, Sao Paulo, Brazil. Studies in Health Technology and Informatics. IOS Press. 2015. 216:569-73. (Student Paper Award Nominee) [PubMed] [PMC] [IOS Press]
  4. Zhe He, and Chunhua Weng. Predicting New Target Conditions for Drug Retesting Using Temporal Patterns in Clinical Trials: A Proof of Concept. Proceedings of American Medical Informatics Association 2015 Joint Summits on Translational Science, March 23 - 27, 2015, San Francisco, CA. pp.445-449. PubMed] [PMC] [Talk Slides] (Student Paper Competition Finalist)
  5. Zhe He*, James Geller, and Yan Chen. A comparative analysis of the density of the SNOMED CT conceptual content for semantic harmonization. Artificial Intelligence in Medicine. 2015;64(1):29-40. PMID: 25890688. (SCI, Impact Factor: 2.88, 5-Year Impact Factor: 2.86) [ScienceDirect] [PubMed] [PMC] (Invited Talk at IHTSDO Implementation SIG Webinar)
  6. Zhe He, Simona Carini, Ida Sim, and Chunhua Weng*. Visual aggregate analysis of eligibility features of clinical trials. Journal of Biomedical Informatics. 2015;54:241-255. PMID: 25615940. (SCI, Impact Factor: 2.88, 5-Year Impact Factor: 3.12) [ScienceDirect] [PubMed] [PMC] [Link to VITTA System] (Clinical Research Informatics 2016 Year in Review)

2014 (1 journal paper & 3 conference papers)

  1. Zhe He*, C. Paul Morrey, Yehoshua Perl, Gai Elhanan, Ling Chen, Yan Chen, and James Geller. Sculpting the UMLS Refined Semantic Network. Online Journal of Public Health Informatics. 2014;(6)2:e181. PMID: 25422719. [PubMed] [PMC]
  2. Zhe He, Simona Carini, Tianyong Hao, Ida Sim, and Chunhua Weng. A Method for Analyzing Commonalities in Clinical Trial Target Populations. Proceedings of American Medical Informatics Association 2014 Annual Symposium (AMIA 2014), November 15 - 19, 2014, Washington D.C. pp.1777-1786. PMID: 25954450. [PubMed] [PMC] [Talk Slides]
  3. Chunhua Weng, Anil Yaman, Kuo Lin, and Zhe He. Trend and Network Analysis of Common Eligibility Features for Cancer Trials in ClinicalTrials.gov. Proceedings of 2014 International Conference for Smart Health, July 10 - 11, 2014, Beijing, China. Smart Health, Lecture Notes in Computer Science, Volume 8549:130-141. PMID: 26998530. [Springer] [PubMed]
  4. Zhe He, James Geller, and Gai Elhanan. Categorizing the Relationships between Structurally Congruent Concepts from Pairs of Terminologies for Semantic Harmonization. Proceedings of 2014 American Medical Informatics Association Joint Summits on Translational Science, April 4 - 11, 2014, San Francisco, CA. pp. 48-53. PMID: 25717400 [PubMed] [Talk Slides]

2013 (2 journal papers & 3 conference papers)

  1. Ankur Agrawal*, Zhe He, Duo Wei, Michael Halper, Yehoshua Perl, and Gai Elhanan. The readiness of SNOMED problem list concepts for meaningful use of electronic health records. Artificial Intelligence in Medicine. 2013;(58)2:73-80. PMID:23602702. (SCI, Impact Factor: 2.88, 5-Year Impact Factor: 2.86) [ScienceDirect] [PubMed](Highly Accessed)
  2. James Geller, Zhe He*, Yehoshua Perl, C. Paul Morrey, and Julia Xu. Rule-based support system for multiple UMLS semantic type assignments. Journal of Biomedical Informatics, 2013;(46)1:97-110. PMID: 23041716. (SCI, Impact Factor: 2.88, 5-Year Impact Factor: 3.12)[ScienceDirect] [PubMed] (Highly Accessed)
  3. Zhe He, Christopher Ochs, Ankur Agrawal, Yehoshua Perl, Dimitrios Zeginis, Konstantinos Tarabanis, Gai Elhanan, Michael Halper, Natasha Noy, and James Geller. A Family-Based Framework for Supporting Quality Assurance of Biomedical Ontologies in BioPortal. Proceedings of American Medical Informatics Association 2013 Annual Symposium (AMIA 2013), November 16 - 20, 2013, Washington D.C. pp. 581-90. PMID: 24551360. [PubMed] [Talk Slides] (Featured in "AMIA 2014 Year in Review")
  4. Zhe He, Christopher Ochs, Larisa Soldatova, Yehoshua Perl, Sivaram Arabandi, and James Geller. Auditing Redundant Import in Reuse of a Top Level Ontology for the Drug Discovery Investigations Ontology. Proceedings of 2013 International Workshop on Vaccine and Drug Ontology Studies (co-located with ICBO 2013), July 7, 2013. Montreal, Qc, Canada.CEUR Proceedings Volume 1061 [Talk Slides]
  5. Christopher Ochs, Zhe He, Yehoshua Perl, Sivaram Arabandi, James Geller, and Michael Halper. Choosing the Granularity of Abstraction Networks for Orientation and Quality Assurance of the Sleep Domain Ontology. Proceedings of the 4th International Conference on Biomedical Ontology (ICBO 2013), July 8 and 9, 2013. Montreal, Qc, Canada. CEUR Proceedings Volume 1060:84-9.

2012 (2 conference/workshop papers)

  1. Zhe He, Michael Halper, Yehoshua Perl, and Gai Elhanan. Clinical Clarity versus Terminological Order - the Readiness of SNOMED CT Concept Descriptors for Primary Care. Proceedings of the 2nd International Workshop on Managing Interoperability and Complexity in Health Systems (MIXHS 2012) (co-located with CIKM 2012), Maui, HI, USA, October 29, 2012. pp.1-6. [ACM Digital Library] [Talk Slides]
  2. Huanying Gu, Gai Elhanan, Michael Halper, and Zhe He. Questionable Relationship Triples in the UMLS. Proceedings of 2012 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI 2012), Hong Kong, January 2-7 2012. pp.713-6. [IEEE Xplore] [Talk Slides]

Poster/Panel/Podium Presentation Abstracts

  1. Zhe He, Rui Zhang, Olivier Bodenreider, and Xinxin Zhu. Developing Careers in Biomedical and Health Informatics. MEDINFO 2019. August 26-30, 2019, Lyon, France. (Panel)
  2. Zhe He, Laura A. Barrett, Rubina F. Rizvi, Seyedeh Neelufar Payrovnaziri, and Rui Zhang. Exploring the Discrepancies in Actual and Perceived Benefits of Dietary Supplements Among Obese Patients. MEDINFO 2019. August 26-30, 2019. Lyon, France. Studies in Health Technology and Informatics. In press. (Poster).
  3. Lynette Hammond Gerido and Zhe He. Improving Patient Participation in Cancer Clinical Trials: A qualitative analysis of HSRProj & RePORTER. MEDINFO 2019. August 26-30, 2019. Lyon, France. Studies in Health Technology and Informatics. In press. (Poster).
  4. Nur Hafieza Ismail, Ninghao Liu, Mengnan Du, Zhe He, Xia Ben Hu. Identification of Cancer Survivors Living with PTSD on Social Media. MEDINFO 2019. August 26-30, 2019. Lyon, France. Studies in Health Technology and Informatics. In press. (Poster).
  5. Zhan Zhang, Yu Lu, Caleb Wilson, and Zhe He. Making Sense of Clinical Laboratory Results: An Analysis of Questions and Replies in a Social Q&A Community. MEDINFO 2019. August 26-30, 2019. Lyon, France. Studies in Health Technology and Informatics. In press. (Poster).
  6. Zhe He and Jiang Bian. Early Findings of a Survey on the Perception of Clinical Trial Generalizability Assessment and Eligibility Criteria Design. AMIA 2019 Informatics Summit. March 25-28, 2019. San Francisco, CA. (Poster)
  7. *Lynette Gerido and Zhe He. Opportunities to Improve Methods for Increasing Participation in Cancer Clinical Trials. AMIA 2018 Annual Symposium. November 3-8, 2018. San Francisco, CA (Poster)
  8. *Lynette Gerido and Zhe He. Patient-Centered Strategies to Increase Participation in Cancer Clinical Trials. The Sixth IEEE International Conference on Healthcare Informatics (ICHI 2018), June 4-7, 2018. New York, NY. pp. 361-362. DOI: 10.1109/ICHI.2018.00056. (Poster) [IEEE]
  9. Biyang Yu, Lynette Gerido, Zhe He. Exploring Text Classification of Social Support in Online Health Communities for People Who are D/deaf and Hard of Hearing. Proceedings of the Association for Information Science and Technology (ASIS&T 2017), 54(1): 840-841.Washington DC. October 27 - November 1, 2017 (Poster)
  10. Lynette Gerido, Michelle Kazmer, Zhe He, Marcia Mardis. Emergent Trends in Research to Increase Participation in Cancer Clinical Trials by Underrepresented Population: A Qualitative Analysis of the HSRProj Database. Proceedings of the Association for Information Science and Technology (ASIS&T 2017), 54(1): 677-678. Washington DC. October 27 - November 1, 2017 (Poster)
  11. Zhe He, Zhiwei Chen, Sarah Mixon, Jiang Bian. A Visual Analysis Tool for Qualitative Eligibility Criteria of Clinical Studies. Proceedings of American Medical Informatics Association 2017 Annual Symposium (AMIA 2017). November 4-8, 2017. Washington DC. pp.2029. (Poster)
  12. Jiang Bian, Andrei Sura, Yi Guo, François Modave, Zhe He, Elizabeth Shenkman, William Hogan. Implementing a Hash-based Privacy-Preserving Entity Resolution Tool in the OneFlorida Clinical Data Research Network. Proceedings of American Medical Informatics Association 2017 Annual Symposium (AMIA 2017). November 4-8, 2017. Washington DC. pp.1953. (Poster)
  13. Juan Antonio Lossio-Ventura, William Hogan, François Modave, Amanda Hicks, Yi Guo, Zhe He, Mirela Vasconcelos, Jiang Bian. Building an Obesity and Cancer Semantic Web Knowledge Base. Proceedings of American Medical Informatics Association 2017 Annual Symposium (AMIA 2017). November 4-8, 2017. Washington DC. pp.2088 (Poster)
  14. Zhe He and Aisha Langford. Comparative Analysis of Geriatric and Adult Drug Clinical Trials on ClinicalTrials.gov. Proceedings of the 16th World Congress on Medical and Health Informatics (MEDINFO 2017). August 21-25, 2017. Hangzhou, China.Studies in Health Technology and Informatics. 2017;245: 1265. PMID: 23295350 (Poster) [PubMed]
  15. Tianyao Huo, Thomas J. George, Yi Guo, Zhe He, Mattia Prosperi, François Modave, and Jiang Bian. Explore Care Pathways of Colorectal Cancer Patients with Social Network Analysis. Proceedings of the 16th World Congress on Medical and Health Informatics (MEDINFO 2017). August 21-25, 2017. Hangzhou, China. Studies in Health Technology and Informatics. 2017;245: 1270. PMID: 29295255 (Poster) [PubMed]
  16. Zhe He, Duo Wei, Jiang Bian, Jianlin Liu, and Yang Gong. Advancing Health Informatics Education and Health IT Workforce Development through Interdisciplinary Collaboration. Proceedings of the 16th World Congress on Medical and Health Informatics (MEDINFO 2017). August 21-25, 2017. Hangzhou, China. (Panel Presentation)
  17. Aisha Langford and Zhe He, Eligibility Criteria for Hypertension-Related Interventions: Are Blacks Included? The 38th Annual Meeting and Scientific Sessions of the Society of Behavioral Medicine (SBM 2017). March 29 - April 1, 2017. San Diego, CA. (Poster)
  18. Natasha Williams, Zhe He, Andrea Barnes, Aisha Langford, and Girardin Jean-Louis. Minority participation in clinical trials for obstructive sleep apnea and insomnia. SLEEP 2017, June 3-7, 2017.Boston, MA. (Poster).
  19. Amanda Hicks, William R. Hogan, Zhe He, Josh Hanna, Besty Shenkman, Jiawei Yuan, Jiang Bian. Using Semantic Queries for Cohort Discovery Across Research Networks. OHDSI Symposium 2015. October 20, 2015, Washington DC. (Poster)
  20. Zhe He, Patrick Ryan, Shuang Wang, and Chunhua Weng. A Method for Assessing the Collective Population Representativeness of Multiple Related Clinical Trials Using Public Data. Proceedings of American Medical Informatics Association 2015 Joint Summits on Translational Science, March 23 - 27, 2015, San Francisco, CA. pp.255-256. (Podium Presentation) [Talk Slides]
  21. James Geller, Christopher Ochs, Zhe He, and Yehoshua Perl. A Structural Meta-ontology for the BioPortal ontologies. Proceedings of Bio-ontologies 2013 (co-located with ISMB/ECCB 2013), July 20, Berlin, Germany. (Poster)