| 2010 | ICAART | Development of Large Scientific Knowledge Bases. | Peter D. Karp |
| 2008 | ISMB | Annotation-based inference of transporter function. | Thomas J. Lee, Ian T. Paulsen, Peter D. Karp |
| 2007 | ISMB | Using genome-context data to identify specific types of functional associations in pathway/genome databases. | Michelle L. Green, Peter D. Karp |
| 2004 | PSB | An Evidence Ontology for Use in Pathway/Genome Databases. | Peter D. Karp, Suzanne M. Paley, Cynthia J. Krieger, Peifen Zhang |
| 2003 | PSB | Genome, Pathway, and Interaction Bioinformatics - Session Introduction. | Peter D. Karp, Eric P. Neumann, Alexander J. Hartemink, Pedro Romero |
| 2002 | ISMB | The Pathway Tools software. | Peter D. Karp, Suzanne M. Paley, Pedro Romero |
| 2002 | PSB | Genome, Pathway and Interaction Bioinformatics - Session Introduction. | Peter D. Karp, Pedro Romero, Eric P. Neumann |
| 2001 | PSB | Genome, Pathway and Interaction Bioinformatics - Session Introduction. | Peter D. Karp, Eric P. Neumann, Pedro Romero |
| 2001 | PSB | Nutrition-Related Analysis of Pathway/Genome Databases. | Pedro Romero, Peter D. Karp |
| 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 | AAAI | OKBC: A Programmatic Foundation for Knowledge Base Interoperability. | Vinay K. Chaudhri, Adam Farquhar, Richard Fikes, Peter D. Karp, James Rice |
| 1997 | AAAI | A Generic Knowledge-Base Browser and Editor. | Suzanne M. Paley, John D. Lowrance, Peter D. Karp |
| 1997 | ISMB | Prediction of Enzyme Classification from Protein Sequence without the Use of Sequence Similarity. | Marie desJardins, Peter D. Karp, Markus Krummenacker, Thomas J. Lee, Christos A. Ouzounis |
| 1996 | ISMB | HinCyc: A Knowledge Base of the Complete Genome and Metabolic Pathways of H. influenzae. | Peter D. Karp, Christos A. Ouzounis, Suzanne M. Paley |
| 1995 | IJCAI | The Generic Frame Protocol. | Peter D. Karp, Karen L. Myers, Thomas R. Gruber |
| 1995 | IJCAI | Knowledge Representation in the Large. | Peter D. Karp, Suzanne M. Paley |
| 1994 | CIKM | A Storage System for Scalable Knowledge Representation. | Peter D. Karp, Suzanne M. Paley, Ira B. Greenberg |
| 1994 | ISMB | Representations of Metabolic Knowledge: Pathways. | Peter D. Karp, Suzanne M. Paley |
| 1993 | ISMB | Representations of Metabolic Knowledge. | Peter D. Karp, Monica Riley |
| 1993 | SP | Detection and elimination of inference channels in multilevel relational database systems. | Xiaolei Qian, Mark E. Stickel, Peter D. Karp, Teresa F. Lunt, Thomas D. Garvey |