| 2020 | AMIA | The Impact of Model and Tokenization Method Selection on a Deep Learning Classifier on Medical Text. | Juan D. Irizarry-Cole, Stephen B. Johnson, Zane Dennis |
| 2019 | AMIA | Educational Communities in the Academic Forum: Sharing Knowledge and Promoting Standards. | Stephen B. Johnson, Saif S. Khairat, Suzanne Austin Boren, Vishnu Mohan, Eva LaVerne Manos, William R. Hersh |
| 2018 | AMIA | Ascertaining Depression Severity by Extracting Patient Health Questionnaire-9 (PHQ-9) Scores from Clinical Notes. | Prakash Adekkanattu, Evan Sholle, Joseph J. DeFerio, Jyotishman Pathak, Stephen B. Johnson, Thomas R. Campion Jr. |
| 2017 | AMIA | Secondary Use of Patients' Electronic Records (SUPER): An Approach for Meeting Specific Data Needs of Clinical and Translational Researchers. | Evan Sholle, Joseph Kabariti, Stephen B. Johnson, John P. Leonard, Jyotishman Pathak, Vinay I. Varughese, Curtis L. Cole, Thomas R. Campion Jr. |
| 2016 | AMIA | Designing an evaluation methods course in health informatics. | Jessica S. Ancker, Stephen B. Johnson |
| 2015 | AMIA | Health Informatics Graduate Program Accreditation: CAHIIM Process and Standards Update. | Judith J. Warren, Stephen B. Johnson, Suzanne Austin Boren, Stuart M. Speedie, Gnter Tusch |
| 2014 | AMIA | An Institutional Strategy to Support Clinical Research with Centrally Managed Custom Data Repositories. | Stephen B. Johnson, Thomas R. Campion Jr., Nonie E. Pegoraro, Leon Rozenblit, Charles Tirrell, Curt Cole |
| 2012 | AMIA | Barriers to and Facilitators of Community-Based Health Information Technology Implementation. | Thomas R. Campion Jr., Lisa M. Kern, Alison Edwards, Renny Thomas, Stephen B. Johnson, Rainu Kaushal |
| 2009 | AMIA | Evaluation of a Prototype Search and Visualization System for Exploring Scientific Communities. | Michael E. Bales, David R. Kaufman, Stephen B. Johnson |
| 2008 | AMIA | Re-engineering Opportunities in Clinical Research using Workflow Analysis in Community Practice Settings. | Sharib A. Khan, Rita Kukafka, J. Thomas Bigger, Stephen B. Johnson |
| 2008 | AMIA | Content and Structure of Clinical Problem Lists: A Corpus Analysis. | Tielman Van Vleck, Adam B. Wilcox, Peter D. Stetson, Stephen B. Johnson, Nomie Elhadad |
| 2007 | AMIA | Signout: A Collaborative Document with Implications for the Future of Clinical Information Systems. | Daniel M. Stein, Jesse O. Wrenn, Stephen B. Johnson, Peter D. Stetson |
| 2007 | AMIA | Assessing Data Relevance For Automated Generation Of A Clinical Summary. | Tielman Van Vleck, Daniel M. Stein, Peter D. Stetson, Stephen B. Johnson |
| 2007 | AMIA | An Unsupervised Machine Learning Approach to Segmentation of Clinician-Entered Free Text. | Jesse O. Wrenn, Peter D. Stetson, Stephen B. Johnson |
| 2006 | AMIA | Heuristic Evaluation of eNote: an Electronic Notes System. | Tiffani J. Bright, Suzanne Bakken, Stephen B. Johnson |
| 2006 | AMIA | Modeling Clinical Trials Workflow in Community Practice Settings. | Sharib A. Khan, Philip R. O. Payne, Stephen B. Johnson, J. Thomas Bigger, Rita Kukafka |
| 2005 | AMIA | Clinicians' Perceptions of Usability of eNote. | Janet P. Haas, Suzanne Bakken, Tiffani J. Bright, Genevieve B. Melton, Peter D. Stetson, Stephen B. Johnson |
| 2005 | AMIA | Analyzing the Structure and Content of Public Health Messages. | Frances P. Morrison, Rita Kukafka, Stephen B. Johnson |
| 2005 | AMIA | Document Ontology: Supporting Narrative Documents in Electronic Health Records. | Jason S. Shapiro, Suzanne Bakken, Sookyung Hyun, Genevieve B. Melton, Cara Schlegel, Stephen B. Johnson |
| 2003 | AMIA | Natural Language Processing Challenges in HIV/AIDS Clinic Notes. | Sookyung Hyun, Suzanne Bakken, Carol Friedman, Stephen B. Johnson |
| 2003 | AMIA | A Framework for the Biomedical Informatics Curriculum. | Stephen B. Johnson |
| 2003 | AMIA | A Native XML Database Design for Clinical Document Research. | Stephen B. Johnson, David A. Campbell, Michael Krauthammer, P. Karina Tulipano, Eneida A. Mendona, Carol Friedman, George Hripcsak |
| 2003 | AMIA | Automatic Learning of the Morphology of Medical Language using Information Compression. | Shamim Mollah, Stephen B. Johnson |
| 2002 | ACL | A transformational-based learner for dependency grammars in discharge summaries. | David A. Campbell, Stephen B. Johnson |
| 2002 | ACL | Analyzing the Semantics of patient data to rank records of literature retrieval. | Eneida A. Mendona, Stephen B. Johnson, Yoon-Ho Seol, James J. Cimino |
| 2002 | AMIA | Representing nested semantic information in a linear string of text using XML. | Michael Krauthammer, Stephen B. Johnson, George Hripcsak, David A. Campbell, Carol Friedman |
| 2002 | AMIA | Using Patient Data to Rank Records of Literature Retrieval. | Eneida A. Mendona, James J. Cimino, Stephen B. Johnson |
| 2002 | AMIA | Knowledge Acquisition of Generic Queries for Information Retrieval. | Yoon-Ho Seol, Stephen B. Johnson, James J. Cimino |
| 2002 | AMIA | The sublanguage of cross-coverage. | Peter D. Stetson, Stephen B. Johnson, Matthew Scotch, George Hripcsak |
| 2002 | AMIA | The cognitive demands of an innovative query user interface. | Di Wang, David R. Kaufman, Eneida A. Mendona, Yoon-Ho Seol, Stephen B. Johnson, James J. Cimino |
| 2001 | AMIA | Comparing syntactic complexity in medical and non-medical corpora. | David A. Campbell, Stephen B. Johnson |
| 2001 | AMIA | Evaluating the UMLS as a source of lexical knowledge for medical language processing. | Carol Friedman, Hongfang Liu, Lyudmila Shagina, Stephen B. Johnson, George Hripcsak |
| 2001 | AMIA | Using narrative reports to support a digital library. | Eneida A. Mendona, James J. Cimino, Stephen B. Johnson |
| 2001 | AMIA | Conceptual Guidance in Information Retrieval. | Yoon-Ho Seol, Stephen B. Johnson, James J. Cimino |
| 2000 | AMIA | Generic data modeling for home telemonitoring of chronically ill patients. | Jinsong Cai, Stephen B. Johnson, George Hripcsak |
| 2000 | AMIA | Knowledge Sharing in the Construction of an Anatomical Navigational Ontology. | Michael Krauthammer, Nina Wacholder, Stephen B. Johnson, Gai Elhanan, Pat Molholt |
| 1999 | AMIA | Security architecture for multi-site patient records research. | Fred M. Behlen, Stephen B. Johnson |
| 1999 | AMIA | A technique for semantic classification of unknown words using UMLS resources. | David A. Campbell, Stephen B. Johnson |
| 1999 | AMIA | Extended SQL for manipulating clinical warehouse data. | Stephen B. Johnson, Damianos Chatziantoniou |
| 1999 | AMIA | Use of the Extensible Stylesheet Language (XSL) for medical data transformation. | Yoon-Ho Seol, Stephen B. Johnson, Justin B. Starren |
| 1999 | AMIA | New Dogs for Old Tricks: Finite State Modeling and XML for Access to Legacy Systems. | Justin Starren, Stephen B. Johnson |
| 1997 | AMIA | Generic database design for patient management information. | Stephen B. Johnson, T. Paul, A. Khenina |
| 1995 | AISTATS | Two Applications of Statistical Modelling to Natural Language Processing. | William DuMouchel, Carol Friedman, George Hripcsak, Stephen B. Johnson, Paul D. Clayton |