| 2011 | CIKM | Fast fully dynamic landmark-based estimation of shortest path distances in very large graphs. | Konstantin Tretyakov, Abel Armas-Cervantes, Luciano Garca-Bauelos, Jaak Vilo, Marlon Dumas |
| 2010 | LREC | Information Retrieval of Word Form Variants in Spoken Language Corpora Using Generalized Edit Distance. | Siim Orasmaa, Reina Krik, Jaak Vilo, Tiit Hennoste |
| 2008 | LREC | Strengthening the Estonian Language Technology. | Einar Meister, Jaak Vilo |
| 2002 | ECCB | Correlating gene promoters and expression in gene disruption experiments. | Kimmo Palin, Esko Ukkonen, Alvis Brazma, Jaak Vilo |
| 2002 | ECCB | Building and analysing genome-wide gene disruption networks. | Johan Rung, Thomas Schlitt, Alvis Brazma, Karlis Freivalds, Jaak Vilo |
| 2001 | ISMB | Prediction of the coupling specificity of G protein coupled receptors to their G proteins. | Steffen Mller, Jaak Vilo, Michael D. R. Croning |
| 2000 | ISMB | Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data. | Jaak Vilo, Alvis Brazma, Inge Jonassen, Alan J. Robinson, Esko Ukkonen |
| 1997 | ISMB | Data Mining for Regulatory Elements in Yeast Genome. | Alvis Brazma, Jaak Vilo, Esko Ukkonen, Kimmo Valtonen |
| 1996 | ISAAC | Discovering Unbounded Unions of Regular Pattern Languages from Positive Examples (Extended Abstract). | Alvis Brazma, Esko Ukkonen, Jaak Vilo |
| 1996 | ISMB | Discovering Patterns and Subfamilies in Biosequences. | Alvis Brazma, Inge Jonassen, Esko Ukkonen, Jaak Vilo |