| 2018 | WAW | A Statistical Performance Analysis of Graph Clustering Algorithms. | Pierre Miasnikof, Alexander Y. Shestopaloff, Anthony J. Bonner, Yuri A. Lawryshyn |
| 2011 | IJCAI | Explaining Genetic Knock-Out Effects Using Cost-Based Abduction. | Emad A. M. Andrews, Anthony J. Bonner |
| 2010 | ICML | Deep Supervised t-Distributed Embedding. | Martin Renqiang Min, Laurens van der Maaten, Zineng Yuan, Anthony J. Bonner, Zhaolei Zhang |
| 2009 | ICDM | A Deep Non-linear Feature Mapping for Large-Margin kNN Classification. | Martin Renqiang Min, David A. Stanley, Zineng Yuan, Anthony J. Bonner, Zhaolei Zhang |
| 2009 | ICONIP | Finding MAPs Using High Order Recurrent Networks. | Emad A. M. Andrews, Anthony J. Bonner |
| 2009 | SDM | Learning Random-Walk Kernels for Protein Remote Homology Identification and Motif Discovery. | Martin Renqiang Min, Rui Kuang, Anthony J. Bonner, Zhaolei Zhang |
| 2007 | ICMLA | Modifying kernels using label information improves SVM classification performance. | Martin Renqiang Min, Anthony J. Bonner, Zhaolei Zhang |
| 2006 | ICONIP | Connectionist Approaches for Predicting Mouse Gene Function from Gene Expression. | Emad A. M. Andrews Shenouda, Quaid Morris, Anthony J. Bonner |
| 2006 | SDM | Towards the Prediction of Protein Abundance from Tandem Mass Spectrometry Data. | Anthony J. Bonner, Han Liu |
| 2004 | CIBCB | Comparison of discrimination methods for peptide classification in tandem mass spectrometry. | Anthony J. Bonner, Han Liu |
| 2004 | KDD | Clustering Labeled Data and Cross-Validation for Classification with Few Positives in Yeast. | Miles Trochesset, Anthony J. Bonner |
| 1999 | PODS | Workflow, Transactions, and Datalog. | Anthony J. Bonner |
| 1996 | EDBT | LabFlow-1: A Database Benchmark for High-Throughput Workflow Management. | Anthony J. Bonner, Adel Shrufi, Steve Rozen |
| 1996 | ICLP | Concurrency and Communication in Transaction Logic. | Anthony J. Bonner, Michael Kifer |
| 1996 | ISMB | Good Maps Are Straight. | Eric Harley, Anthony J. Bonner, Nathan Goodman |
| 1995 | PODS | Sequences, Datalog and Transducers. | Giansalvatore Mecca, Anthony J. Bonner |
| 1994 | ISMB | A Flexible Approach to Genome Map Assembly. | Eric Harley, Anthony J. Bonner |
| 1993 | ICLP | Transaction Logic Programming. | Anthony J. Bonner, Michael Kifer |
| 1992 | PODS | The Complexity of Reusing and Modifying Rulebases. | Anthony J. Bonner |
| 1991 | SIGMOD | Objects and Views. | Serge Abiteboul, Anthony J. Bonner |
| 1990 | EDBT | The Reuse and Modification of Rulebases by Predicate Substituation. | Anthony J. Bonner, Tomasz Imielinski |
| 1989 | PODS | Hypothetical Datalog: Negation and Linear Recursion. | Anthony J. Bonner |
| 1988 | AAAI | A Logic for Hypothetical Reasoning. | Anthony J. Bonner |
| 1988 | ICDT | Hypothetical Datalog: Complexity and Expressiblity. | Anthony J. Bonner |