Bian Publications

Selected Articles (Complete list from Google Scholar (–voAAAAJ&view_op=list_works&sortby=pubdate)

Data Science

  • Prosperi M, Min JS, Bian J, Modave F. Big data hurdles in precision medicine and precision public health. BMC Med Inform Decis Mak. 2018 Dec 29;18(1):139. doi: 10.1186/s12911-018-0719-2. PMID: 30594159 DOI: 10.1186/s12911-018-0719-2
  • He Z, Gonzalez-Izquierdo A, Denaxas S, Dura A, Guo Y, Hogan WR, Shenkman E, Bian J. Comparing and Contrasting A Priori and A Posteriori Generalizability Assessment on Clinical Trials on Type 2 Diabetes Mellitus. AMIA Annual Symposium. 2017. Forthcoming. (Distinguished Paper Award)
  • He Z, Bian J (co-first), Carretta H, Lee J, Hogan W, Shenkman E, Charness N. Comparative analysis of prevalence of multiple chronic conditions among older adults in Florida and the United States: Estimates from the OneFlorida Clinical Research Consortium Data Trust and National Inpatient Sample. J Med Internet Res. 2018 Apr 12;20(4):e137. doi: 10.2196/jmir.8961. PMID: 29650502 PMCID: PMC5920146
  • Mansoor H (g), Elgendy IY, Segal R, Bavry AA, Bian J. Risk prediction model for in-hospital mortality in women with ST-elevation myocardial infarction: A machine learning approach. Heart Lung. 2017 Oct 6. pii: S0147-9563(17)30160-7. doi: 10.1016/j.hrtlng.2017.09.003. PMID: 28992993.
  • Barrett LA, Payrovnaziri SN, Bian J, He Z. 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.


  • Bian J, Guo Y (co-first), Xie M, Parish AE, Wardlaw I, Brown R, Modave F, Zheng D, Perry TT. Exploring the Association Between Self-Reported Asthma Impact and Fitbit-Derived Sleep Quality and Physical Activity Measures in Adolescents. JMIR Mhealth Uhealth 2017;5(7):e105 DOI: 10.2196/mhealth.7346. PMID: 28743679 PMCID: PMC5548986.
  • Guo Y, Bian J, Leavitt T, Vincent HK, Vander Zalm L, Teurlings TL, Smith MD, Modave F. Assessing the Quality of Mobile Exercise Apps Based on the American College of Sports Medicine Guidelines: A Reliable and Valid Scoring Instrument. J Med Internet Res. 2017 Mar 7;19(3):e67. doi: 10.2196/jmir.6976. PMID: 28270378 PMCID: PMC5360889.
  • Perry T, Marshall A, Berlinski A, Rettiganti M, Brown R, Randle S, Luo C, Bian J. Smartphone-Based vs. Paper-Based Asthma Action Plans for Adolescents. Ann Allergy Asthma Immunol. 2017 Jan 19. pii: S1081-1206(16)31362-X. doi: 10.1016/j.anai.2016.11.028. PMID: 28111110.
  • He X, Zhang R, Rizvi R, Vasilakes J, Yang X, Guo Y, He Z, Prosperi M, Bian J. Prototyping an Interactive Visualization of Dietary Supplement Knowledge Graph. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2018. (in press)
  • Modave F, Bian J, Rosenberg E, Mendoza T, Liang Z, Bhosale R, Maeztu C, Rodriguez C, Cardel MI. DiaFit: The Development of a Smart App for Patients with Type 2 Diabetes and Obesity. JMIR Diabetes 2016;1(2):e5. DOI: 10.2196/diabetes.6662.
  • Modave F, Bian J, Leavitt T, Bronmwell J, Harris C, Vincent H. Low Quality of Free Coaching Apps with Respect to the American College of Sports Medicine Guidelines: A Review of Current Mobile Apps. JMIR Mhealth Uhealth. 2015 Jul 24;3(3):e77. doi: 10.2196/mhealth.4669. PMID: 26209109.

Ontology/Semantic Web

  • Zhang H (g), He Z, He X (g), Guo Y, Nelson DR, Modave F, Wu Y, Hogan WR, Bian J. Computable Eligibility Criteria through Ontology-driven Data Access: A Case Study of Hepatitis C Virus Trials. AMIA Annual Symposium. 2018. In Press. (Best Student Paper Finalists)
  • Zhang H, Guo Y, Hogan W, Li Q, George TJ, Shenkman EA, Modave, F, Bian J. An Ontology-guided Semantic Data Integration Framework to Support Integrative Data Analysis of Cancer Survival. BMC Med Inform Decis Mak. 2018 Jul 23;18(Suppl 2):41. doi: 10.1186/s12911-018-0636-4. PMID: 30066664 PMCID: PMC6069766
  • Lossio-Ventura JA, Hogan WR, Modave F, Guo Y, He Z, Yang X, Zhang H, Bian J. OC-2-KB: Integrating crowdsourcing into an obesity and cancer knowledge base curation system. BMC Med Inform Decis Mak. 2018 Jul 23;18(Suppl 2):55. doi: 10.1186/s12911-018-0635-5. PMID: 30066655 PMCID: PMC6069686.
  • Amith MF, He Z, Bian J, Lossio-Ventura JA (p), Tao C. Assessing the Practice of Ontology Evaluation for Biomedical Ontologies in BioPortal: Gaps and Opportunities. J Biomed Inform. 2018 Apr;80:1-13. doi: 0.1016/j.jbi.2018.02.010. PMID: 29462669 PMCID: PMC5882531.
  • Hanna J (g), Bian J, Hogan WR. An Accurate and Precise Representation of Drug Ingredients. J Biomed Semant. 2016 Apr 19;7:7. doi: 10.1186/s13326-016-0048-2. PMID: 27096073.

Informatics Systems

  • Bian J, Xie M, Hogan WR, Hutchins L, Topaloglu U, Lane C, Wells T. CLARA: an integrated clinical research administration system. J Am Med Inform Assoc. 2014;21(e2):e369-73. doi: 10.1136/amiajnl-2013-002616. PMID: 24778201. PMCID: PMC4173184
  • Bian J, Topaloglu U, Lane C. EIR: enterprise imaging repository, an alternative imaging archiving and communication system. Proc IEEE Eng Med Biol Soc. 2009;2009:2168-71. doi: 10.1109/IEMBS.2009.5332428. PMID: 19963537.

Social Media

  • Bian J, Topaloglu U, Yu F. Towards Large-scale Twitter Mining for Drug-related Adverse Events. SHB12 (2012). 2012 Oct 29;2012:25-32. doi: 10.1145/2389707.2389713. PMID: 28967001 PMCID: PMC5619871
  • Hicks A, Hogan WR, Rutherford M, Malin B, Xie M, Fellbaum C, Yin Z, Fabbri D, Hanna J, Bian J. Mining Twitter as a First Step toward Assessing the Adequacy of Gender Identification Terms on Intake Forms. AMIA Annu Symp Proc. 2015;2015:611-620. PMID: 26958196. PMCID: PMC4765681
  • Bian J, Zhao Y (g, co-first), Salloum RG, Guo Y, Wang M, Prosperi M, Zhang H, Du X, Ramirez-Diaz LJ, He Z, Sun Y. Using Social Media Data to Understand the Impact of Promotional Information on Laypeople’s Discussions: A Case Study of Lynch Syndrome. J Med Internet Res 2017;19(12):e414. DOI: 10.2196/jmir.9266. PMID: 29237586.
  • Bian J, Yoshigoe K, Hicks A, Yuan J, He Z, Xie M, Guo Y, Prosperi M, Salloum R, Modave F. Mining Twitter to Assess the Public Perception of the “Internet of Things”. PLoS One. 2016 Jul 8;11(7):e0158450. doi: 10.1371/journal.pone.0158450. PMID: 27391760
  • Wei W, Hernandez I, Newman D, He J, Bian J. Twitter Analysis: Studying U.S. Weekly Trends in Work Stress and Emotion. Applied Psychology: An International Review. 2016;65:355-378. doi: 10.1111/apps.12065.

Data Privacy and Security

  • Yuan J, Malin B, Modave F, Guo Y, Hogan WR, Shenkman E, Bian J. Towards a Privacy Preserving Cohort Discovery Framework for Clinical Research Networks. J Biomed Inform. 2017 Feb;66:42-51. doi: 10.1016/j.jbi.2016.12.008. PMID: 28007583 PMCID: PMC5316314. IF: 2.882 (2018 IMIA Yearbook of Medical Informatics Best Articles in “Between Access and Privacy: Challenges in Sharing Health Data”)

Natural Language Processing

  • Yang X, Bian J, Gong Y, Hogan WR, Wu Y. MADEx: A System for Detecting Medications, Adverse Drug Events, and Their Relations from Clinical Notes. Drug Saf. 2019 Jan 2. doi: 10.1007/s40264-018-0761-0. [Epub ahead of print] PMID: 30600484 DOI: 10.1007/s40264-018-0761-0
  • Lossio-Ventura JA, Bian J, Jonquet C, Roche M, Teisseire M. A novel framework for biomedical entity sense induction. J Biomed Inform. 2018 Jun 20. pii: S1532-0464(18)30113-8. doi: 10.1016/j.jbi.2018.06.007. PMID: 29935347.
  • He Z, Chen Z, Oh S, Hou J, Bian J. Enriching consumer health vocabulary through mining a social Q&A site: a similarity-based approach. J Biomed Inform. 2017 Mar 27. pii: S1532-0464(17)30065-5. doi: 10.1016/j.jbi.2017.03.016. [Epub ahead of print] PMID: 28359728.
  • Yang X, Bian J, Wu Y. Detecting Medications and Adverse Drug Events in Clinical Notes Using Recurrent Neural Networks. Proceedings (PMLR). 2018:90:1-6.
  • Wu Y, Xi Y, Bian J, Guo Y, Xu H, Hogan WR. Combine Factual Medical Knowledge and Distributed Word Representation to Improve Clinical Named Entity Recognition. AMIA Annual Symposium. 2018.