| 2022 | CIBCB | Predicting the specific substrate for transmembrane transport proteins using BERT language model. | Sima Ataei, Gregory Butler |
| 2022 | CIBCB | TooT-BERT-M: Discriminating Membrane Proteins from Non-Membrane Proteins using a BERT Representation of Protein Primary Sequences. | Hamed Ghazikhani, Gregory Butler |
| 2022 | DCAI | A Study on the Application of Protein Language Models in the Analysis of Membrane Proteins. | Hamed Ghazikhani, Gregory Butler |
| 2022 | PACBB | TooT-BERT-T: A BERT Approach on Discriminating Transport Proteins from Non-transport Proteins. | Hamed Ghazikhani, Gregory Butler |
| 2017 | BIBE | SynAPhy and SynAVal: Mining a Synteny-Similarity Graph to Resolve Orthology of Proteins in Fungal Genomes. | Christine Kehyayan, Gregory Butler |
| 2015 | ICSE | Computation for Genomics Knowledge Discovery. | Gregory Butler |
| 2013 | SAC | BenchDW: a generic framework for biological data warehouse benchmarking. | Thomas Triplet, Gregory Butler |
| 2012 | IDEAS | Untitled record | Jun Luo, Gregory Butler |
| 2010 | CIBCB | Issues with the PipeAlign phylogenomics toolkit in identifying protein subfamilies. | Christine Kehyayan, Gregory Butler |
| 2010 | CIBCB | A regression tree-based Gibbs sampler to learn the regulation programs in a transcription regulatory module network. | Jianlong Qi, Tom Michoel, Gregory Butler |
| 2006 | AI | Bayesian Learning for Feed-Forward Neural Network with Application to Proteomic Data: The Glycosylation Sites Detection of the Epidermal Growth Factor-Like Proteins Associated with Cancer as a Case Study. | Alireza Shaneh, Gregory Butler |
| 2004 | APSEC | Use Case Refactoring: A Tool and a Case Study. | Jian Xu, Wei Yu, Kexing Rui, Gregory Butler |
| 2002 | GPCE | Architectural Refactoring in Framework Evolution: A Case Study. | Gregory Butler |
| 2001 | ICSE | Generative Techniques for Product Lines. | Gregory Butler, Don S. Batory, Krzysztof Czarnecki, Ulrich W. Eisenecker |
| 2000 | SSDBM | Three Improvements to the BLASTP Search of Genome Databases. | Shawn Delaney, Gregory Butler, Clement W. H. Lam, Larry H. Thiel |
| 1999 | ADC | Towards OM - An Object-Oriented Implementation of Mantra. | Gregory Butler, T. Kharma, O. Tjandra |
| 1996 | AISC | Document Recognition, Semantics, and Symbolic Reasoning in Reverse Engineering of Software. | Gregory Butler, Peter Grogono, Rajjan Shinghal, Indra A. Tjandra |
| 1995 | DASFAA | Intelligent Mathematical Databases. | Gregory Butler |
| 1995 | ICDAR | Analyzing the logical structure of data flow diagrams in software documents. | Gregory Butler, Peter Grogono, Rajjan Shinghal, Indra A. Tjandra |
| 1994 | AISC | Datalog and TwoGroups and C++. | Gregory Butler |
| 1993 | ICCI | Specialised Theorem-Proving in an Intelligent Tutoring System for the Dijkstra-Gries Programming Methodology. | Frank Ng, Gregory Butler |
| 1992 | AISC | The Progress Towards an Intelligent Assistent - A Discussion Paper. | Gregory Butler |
| 1992 | ISSAC | Experimental Comparison of Algorithms for Sylow Subgroups. | Gregory Butler |
| 1991 | ISSAC | A Deductive Database of the Groups of Order Dividing 128. | Gregory Butler, Sridhar S. Iyer, Susan H. Ley |
| 1990 | SSDBM | Deductive Mathematical Databases - A Case Study. | Gregory Butler, Sridhar S. Iyer |
| 1988 | ISSAC | Cayley, Version 4: The User Language. | Gregory Butler, John J. Cannon |
| 1981 | ISSAC | Double cosets and searching small groups. | Gregory Butler |