| 2014 | CBMS | Towards Using Probabilities and Logic to Model Regulatory Networks. | Antnio Gonalves, Irene M. Ong, Jeffrey A. Lewis, Vtor Santos Costa |
| 2014 | CBMS | Discovering Differentially Expressed Genes in Yeast Stress Data. | Antnio Gonalves, Irene M. Ong, Jeffrey A. Lewis, Vtor Santos Costa |
| 2012 | ILP | A Problog Model for Analyzing Gene Regulatory Networks. | Antnio Gonalves, Irene M. Ong, Jeffrey A. Lewis, Vtor Santos Costa |
| 2007 | IJCAI | Change of Representation for Statistical Relational Learning. | Jesse Davis, Irene M. Ong, Jan Struyf, Elizabeth S. Burnside, David Page, Vtor Santos Costa |
| 2006 | ILP | Inferring Regulatory Networks from Time Series Expression Data and Relational Data Via Inductive Logic Programming. | Irene M. Ong, Scott E. Topper, C. David Page Jr., Vtor Santos Costa |
| 2006 | PSB | Experimental Design of Time Series Data for Learning from Dynamic Bayesian Networks. | C. David Page Jr., Irene M. Ong |
| 2004 | ILP | FOIL-D: Efficiently Scaling FOIL for Multi-relational Data Mining of Large Datasets. | Joseph Bockhorst, Irene M. Ong |
| 2002 | ISMB | Modelling regulatory pathways in E. coli from time series expression profiles. | Irene M. Ong, Jeremy D. Glasner, David Page |