| 2010 | ICASSP | An information retrieval perspective on visualization of gene expression data with ontological annotation. | Jaakko Peltonen, Helena Aidos, Nils Gehlenborg, Alvis Brazma, Samuel Kaski |
| 2008 | APBC | Preface. | Alvis Brazma, Satoru Miyano, Tatsuya Akutsu |
| 2008 | APBC | Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpress. | Yannick Haudry, Chuang Kee Ong, Laurence Ettwiller, Hugo Brub, Ivica Letunic, Misha Kapushesky, Paul-Daniel Weeber, Xi Wang, Julien Gagneur, Charles Girardot, Detlev Arendt, Peer Bork, Alvis Brazma, Eileen E. M. Furlong, Joachim Wittbrodt, Thorsten Henrich |
| 2005 | ECCB | Fusing microarray experiments with multivariate regression. | Walter R. Gilks, Brian D. M. Tom, Alvis Brazma |
| 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 |
| 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 |
| 1994 | ALT | Efficient Algorithm for Learning Simple Regular Expressions from Noisy Examples. | Alvis Brazma |
| 1994 | ALT | Efficient Learning of Regular Expressions from Good Examples. | Alvis Brazma, Karlis Cerans |
| 1994 | GD | A Simple Algorithm for Drawing Large Graphs on Small Screens. | Karlis Kaugars, Juris Reinfelds, Alvis Brazma |
| 1993 | COLT | Efficient Identification of Regular Expressions from Representative Examples. | Alvis Brazma |