| 2021 | AMIA | Improving PubMed Retrieval by Integrating Abstract and Full Text Search. | Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur, Zhiyong Lu |
| 2015 | EMNLP | Summarizing Topical Contents from PubMed Documents Using a Thematic Analysis. | Sun Kim, Lana Yeganova, W. John Wilbur |
| 2014 | AMIA | Extracting drug-drug interactions from literature using a rich feature-based linear kernel approach. | Sun Kim, Haibin Liu, Lana Yeganova, W. John Wilbur |
| 2014 | AMIA | Stochastic Gradient Descent and the Prediction of MeSH for PubMed Records. | W. John Wilbur, Won Kim |
| 2013 | AMIA | BioC: A Minimalist Approach to Interoperability for Biomedical Text Processing. | Donald C. Comeau, Rezarta Islamaj Dogan, W. John Wilbur |
| 2011 | ICMLA | An EM Clustering Algorithm which Produces a Dual Representation. | Sun Kim, W. John Wilbur |
| 2011 | ICMLA | Comparison of Two Methods for Finding Biomedical Categories in Medline. | Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur |
| 2010 | ICMLA | Improving a Gold Standard: Treating Human Relevance Judgments of MEDLINE Document Pairs. | Won Kim, W. John Wilbur |
| 2010 | ICMLA | Identifying Abbreviation Definitions Machine Learning with Naturally Labeled Data. | Lana Yeganova, Donald C. Comeau, W. John Wilbur |
| 2009 | AMIA | Finding Query Suggestions for PubMed. | Zhiyong Lu, W. John Wilbur, Johanna R. McEntyre, Alexey Iskhakov, Lee Szilagyi |
| 2008 | AMIA | Evaluating Relevance Ranking Strategies for MEDLINE Retrieval. | Zhiyong Lu, Won Kim, W. John Wilbur |
| 2007 | ICDM | Characterizing RNA Secondary-Structure Features and Their Effects on Splice-Site Prediction. | Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur |
| 2006 | AMIA | SemCat: Semantically Categorized Entities for Genomics. | Lorraine K. Tanabe, Lynne H. Thom, Wayne Matten, Donald C. Comeau, W. John Wilbur |
| 2005 | AMIA | A Strategy for Assigning New Concepts in the MEDLINE Database. | Won Kim, W. John Wilbur |
| 2005 | ISMB | MedTag: A Collection of Biomedical Annotations. | Lawrence H. Smith, Lorraine K. Tanabe, Thomas C. Rindflesch, W. John Wilbur |
| 2004 | CBMS | Using MEDLINE as a Knowledge Source for Disambiguating Abbreviations in Full-Text Biomedical Journal Articles. | Hong Yu, Won Kim, Vasileios Hatzivassiloglou, W. John Wilbur |
| 2003 | AMIA | The Dimensions of Indexing. | W. John Wilbur, Won Kim |
| 2002 | ACL | Tagging gene and protein names in full text articles. | Lorraine K. Tanabe, W. John Wilbur |
| 2002 | AMIA | DNA splice site detection: a comparison of specific and general methods. | Won Kim, W. John Wilbur |
| 2002 | AMIA | Automatic extraction of gene and protein synonyms from MEDLINE and journal articles. | Hong Yu, Vasileios Hatzivassiloglou, Carol Friedman, Andrey Rzhetsky, W. John Wilbur |
| 2002 | PSB | A Thematic Analysis of the AIDS Literature. | W. John Wilbur |
| 2001 | AMIA | Automatic MeSH term assignment and quality assessment. | Won Kim, Alan R. Aronson, W. John Wilbur |
| 2000 | AMIA | The NLM Indexing Initiative. | Alan R. Aronson, Olivier Bodenreider, Florence Chang, Susanne M. Humphrey, James G. Mork, Stuart J. Nelson, Thomas C. Rindflesch, W. John Wilbur |
| 2000 | AMIA | Boosting nave Bayesian learning on a large subset of MEDLINE. | W. John Wilbur |
| 2000 | ISMB | Genes, Themes, and Microarrays: Using Information Retrieval for Large-Scale Gene Analysis. | Hagit Shatkay, Stephen Edwards, W. John Wilbur, Mark Boguski |
| 1999 | AMIA | Automated Assignment of Medical Subject Headings. | Stuart J. Nelson, Alan R. Aronson, Tamas E. Doszkocs, W. John Wilbur, Olivier Bodenreider, H. Florence Chang, James G. Mork, Alexa T. McCray |
| 1999 | AMIA | Analysis of biomedical text for chemical names: a comparison of three methods. | W. John Wilbur, George F. Hazard Jr., Guy Divita, James G. Mork, Alan R. Aronson, Allen C. Browne |