| 2016 | AMIA | Discovering representational differences between pathway knowledge bases for pathway resource merging. | Lucy Lu Wang, John H. Gennari, Neil F. Abernethy |
| 2015 | AMIA | The SDIDS System for Integrating Global Health Surveillance Data: An Example Application to Malaria Surveillance in Uganda. | Kate Zinszer, Anya Okhmatovskaia, Arash Shaban-Nejad, Lauren N. Carroll, Neil F. Abernethy, David L. Buckeridge |
| 2012 | AMIA | Timeliness and data element completeness of immunization data in Washington State in 2010: a comparison of data transfer methods. | Rebecca A. Hills, Debra Revere, Rita Altamore, Neil F. Abernethy, William B. Lober |
| 2012 | AMIA | Assessing the effective communication of pharmacogenomics knowledge embedded in the electronic health record for drug therapy individualization. | Casey Lynnette Overby, Emily Beth Devine, Neil F. Abernethy, Jeannine McCune, Peter Tarczy-Hornoch |
| 2012 | CIBCB | Assessing network characteristics of cancer associated genes in metabolic and signaling networks. | Deanna Petrochilos, Neil F. Abernethy |
| 2000 | ISMB | An Evaluation of Ontology Exchange Languages for Bioinformatics. | Robin McEntire, Peter D. Karp, Neil F. Abernethy, David Benton, Gregg Helt, Matt DeJongh, Robert Kent, Anthony Kosky, Suzanna Lewis, Dan Hodnett, Eric P. Neumann, Frank Olken, Dhiraj K. Pathak, Peter Tarczy-Hornoch, Luca Toldo, Thodoros Topaloglou |
| 1998 | AMIA | MHCWeb: converting a WWW database into a knowledge-based collaborative environment. | Lawrence S. Hon, Neil F. Abernethy, Vladimir Brusic, Jenny Chai, Russ B. Altman |
| 1997 | ISMB | Standardized Representations of the Literature: Combining Diverse Sources of Ribosomal Data. | Russ B. Altman, Neil F. Abernethy, Richard O. Chen |