| 2017 | AMIA | Detection of adverse drug reactions using medical named entities on Twitter. | Andrew MacKinlay, Hafsah Aamer, Antonio Jimeno-Yepes |
| 2017 | IJCNLP | Named Entity Recognition with Stack Residual LSTM and Trainable Bias Decoding. | Quan Tran, Andrew MacKinlay, Antonio Jimeno-Yepes |
| 2015 | CIKM | Identification and Analysis of Medical Entity Co-occurrences in Twitter. | Andrew MacKinlay, Antonio Jimeno-Yepes, Bo Han |
| 2014 | COLING | Integrating UIMA with Alveo, a human communication science virtual laboratory. | Dominique Estival, Steve Cassidy, Karin Verspoor, Andrew MacKinlay, Denis Burnham |
| 2013 | IJCNLP | How Noisy Social Media Text, How Diffrnt Social Media Sources? | Timothy Baldwin, Paul Cook, Marco Lui, Andrew MacKinlay, Li Wang |
| 2013 | PSB | Detection of Protein Catalytic Sites in the Biomedical Literature. | Karin Verspoor, Andrew MacKinlay, Judith D. Cohn, Michael E. Wall |
| 2011 | IJCNLP | Treeblazing: Using External Treebanks to Filter Parse Forests for Parse Selection and Treebanking. | Andrew MacKinlay, Rebecca Dridan, Dan Flickinger, Stephan Oepen, Timothy Baldwin |
| 2006 | LREC | Reconsidering Language Identification for Written Language Resources. | Baden Hughes, Timothy Baldwin, Steven Bird, Jeremy Nicholson, Andrew MacKinlay |