Deniss Sudak, MSc, 2005, juh. Jaak Vilo. Design of universal dictionary editor. Tartu Ülikool

Meelis Kull, MSc, 2004, juh. Jaak Vilo. Fast Clustering in Metric Spaces. Tartu Ülikool

Meelis Kull, Jaak Vilo: Clustering in metric spaces US60/633,006 UNITED STATES PATENT AND TRADEMARK OFFICE (USPTO)

Misha Kapushesky, Patrick Kemmeren, Aedín C. Culhane, Steffen Durinck, Jan Ihmels, Christine Körner, Meelis Kull, Aurora Torrente, Ugis Sarkans, Jaak Vilo, Alvis Brazma. Expression Profiler: next generation - an online platform for analysis of microarray data. Nucleic Acids Research, 2004, Vol. 32, W465-W470

A. Brazma, H. Parkinson, U. Sarkans, M. Shojatalab, J. Vilo, N. Abeygunawardena, E. Holloway, M. Kapushesky, P. Kemmeren, G.G. Lara, A. Oezcimen, P. Rocca-Serra and S. Sansone. ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Research, 2003, 31: 68-71.

Jaak Vilo, Misha Kapushesky, Patrick Kemmeren, Ugis Sarkans, Alvis Brazma. Expression Profiler. In Parmigiani,G., Garrett,E.S., Irizarry,R. and Zeger,S.L. (eds), The Analysis of Gene Expression Data: Methods and Software, Springer Verlag, 2003, New York, NY.

Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M, Contrino S, Vilo J, Abeygunawardena N, Mukherjee G, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Sansone SA. ArrayExpress: a public database of gene expression data at EBI. Comptes Rendus Biologies Volume 326, Issues 10-11 , 2003 Oct-Nov;326(10-11):1075-8.

Alvis Brazma, Ugis Sarkans, Alan Robinson, Jaak Vilo, Martin Vingron, Jorg Hoheisel, and Kurt Fellenberg Microarray Data Representation, Annotation and Storage. Advances in Biochemical Engineering/Biotechnology, 2002, Vol.77(Chip Technology): pp. 113-139.

Elisabeth Dawson, Goncalo R. Abecasis, Suzannah Bumpstead, Yuan Chen, Sarah Hunt, David M. Beare, Jagjit Pabial, Thomas Dibling, Emma Tinsley, Susan Kirby, David Carter, Marianna Papaspyridonos, Simon Livingstone, Rocky Ganskek, Elin Lohmussaar, Jana Zernant, Neeme Tonisson, Maido Remm, Reedik Magi, Tarmo Puurand, Jaak Vilo, Ants Kurg, Kate Rice, Panos Deloukas, Richard Mott, Andres Metspalu, David R. Bentley, Lon R. Cardon & Ian Dunham A first-generation linkage disequilibrium map of human chromosome 22. Nature 2002, Aug 1, 418(6897):544-8

Jaak Vilo Pattern Discovery from Biosequences. PhD Thesis, Department of Computer Science, University of Helsinki, Finland. Series of Publications A, Report A-2002-3 Helsinki, November 2002, 149 pages. ISSN 1238-8645; ISBN 952-10-0792-3 (paperback); ISBN 952-10-0819-9 (PDF)

Johan Rung, Thomas Schlitt, Alvis Brazma, Karlis Freivalds, Jaak Vilo Building and analysing genome-wide gene disruption networks. Bioinformatics 2002 Oct;18 Suppl 2:S202-210 European Conference on Computational Biology (ECCB 2002)

Kimmo Palin, Esko Ukkonen, Alvis Brazma, Jaak Vilo Correlating gene promoters and expression in gene disruption experiments Bioinformatics 2002 Oct;18 Suppl 2:S172-180; European Conference on Computational Biology (ECCB, 2002)

Patrick Kemmeren, Nynke L. van Berkum, Jaak Vilo, Theo Bijma, Rogier Donders, Alvis Brazma, and Frank C.P. Holstege Protein Interaction Verification and Functional Annotation by Integrated Analysis of Genome-Scale Data. Molecular Cell 2002, May 24; 9(5) pp. 1133-1143

Renata Almeida, Alan Norrish, Mark Levick, David Vetrie, Tom Freeman, Jaak Vilo, Alasdair Ivens, Uta Lange, Carmel Stober, Sharon McCann, Jenefer M. Blackwell From genomes to vaccines: Leishmania as a model. Philos Trans R Soc Lond B Biol Sci 2002 Jan 29;357(1417):5-11

Alvis Brazma, Alan Robinson and Jaak Vilo Gene Expression Data Mining and Analysis (2001) pp. 106-129. Book chapter: B. Jordan (editor): DNA Microarrays: Gene Expression Applications Springer-Verlag ISBN:3-540-41508-4

Alvis Brazma and Jaak Vilo Gene Expression Data Analysis Microbes and Infection Volume 3, Issue 10, August 2001, Pages 823-829.

Alvis Brazma, Pascal Hingamp, John Quackenbush, Gavin Sherlock, Paul Spellman, Chris Stoeckert, John Aach, Wilhelm Ansorge, Catherine A. Ball, Helen C. Causton, Terry Gaasterland, Patrick Glenisson, Frank C.P. Holstege, Irene F. Kim, Victor Markowitz, John C. Matese, Helen Parkinson, Alan Robinson, Ugis Sarkans, Steffen Schulze-Kremer, Jason Stewart, Ronald Taylor, Jaak Vilo & Martin Vingron Minimum information about a microarray experiment (MIAME) toward standards for microarray data. Nature Genetics volume 29 no. 4, December 2001, pp. 365--371.

Jaak Vilo and Katja Kivinen Regulatory sequence analysis: application to interpretation of gene expression. European Neuropsychopharmacology, Volume 11, Issue 6, December 2001, Pages 399-411.

Steffen Möller, Jaak Vilo, Michael D.R. Croning Prediction of the coupling specificity of G protein coupled receptors to their G proteins. ISMB-2001 July 2001. Bioinformatics 2001 17: S174-S181.

Alvis Brazma and Jaak Vilo Gene Expression Data Analysis. (2000) FEBS Letters Volume 480, Issue 1, pp. 17-24.

Jaak Vilo, Alvis Brazma, Inge Jonassen, Alan Robinson, and Esko Ukkonen Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data. ISMB-2000 August 2000. AAAI press. pages 384-394.

Alvis Brazma, Inge Jonassen, Jaak Vilo and Esko Ukkonen Pattern Discovery in Biosequences. Proceedings of Fourth International Colloquium on Grammatical Inference (ICGI-98) (1433) (pp. 255--270) July 1998. Springer.

Alvis Brazma, Inge Jonassen, Jaak Vilo, and Esko Ukkonen Predicting Gene Regulatory Elements from their Expression Data in the Complete Yeast Genome (Extended Abstract). GCB 98, German Conference on Bioinformatics 1998.

Alvis Brazma, Inge Jonassen, Jaak Vilo, and Esko Ukkonen Predicting Gene Regulatory Elements in Silico on a Genomic Scale. Genome Research Vol. 8, Issue 11 (pp. 1202-1215) November 1998. Cold Spring Harbor Laboratory Press .

Alvis Brazma, Jaak Vilo, Esko Ukkonen and Kimmo Valtonen Data Mining for Regulatory Elements in Yeast Genome. Fifth International Conference on Intelligent Systems for Molecular Biology, ISMB-97 (pp. 65-74) June, 1997. AAAI Press.

Alvis Brazma, Esko Ukkonen, and Jaak Vilo Discovering unbounded unions of regular pattern languages from positive example. 7th International symposium, ISAAC'96. T. Asano, Y. Igarashi, H. Nagamochi, S: Miyano and S. Suri (ed.) (pp. 95-104) Springer-Verlag. Dec 1996. Osaka, Japan.

Alvis Brazma, Inge Jonassen, Esko Ukkonen and Jaak Vilo Discovering Patterns and Subfamilies in Biosequences. Proceedings of Fourth International Conference on Intelligent Systems for Molecular Biology ISMB-96 (pp. 34-43) AAAI Press. June 12-15 1996 . Wahington University, St. Louis, MO.

Jyrki Kivinen, Heikki Mannila, Esko Ukkonen and Jaak Vilo An algorithm for learning hierarchical classifiers. Machine Learning: ECML-94, Proc. Seventh European Conference on Machine Learning F. Bergadano and L. De Raedt (ed.) (pp. 375--378) Lecture Notes in Computer Science 784, Springer-Verlag. 1994.

Jaak Vilo Implementing Attribute Grammars by Computational Models. Proceedings of 4th International Symposium on Programming Language Implementation and Logic Programming (PLILP'92) Bruynooghe, M. and Wirsing, M. (eds.) (pp. 485--486) Springer-Verlag, Lecture Notes in Computer Science vol. 631, 1992.

Deniss Sudak, MSc, 2005, superv. Jaak Vilo. Design of universal dictionary editor. Tartu Ülikool

Meelis Kull, MSc, 2004, superv. Jaak Vilo. Fast Clustering in Metric Spaces. Tartu Ülikool

Meelis Kull, Jaak Vilo: Clustering in metric spaces US60/633,006 UNITED STATES PATENT AND TRADEMARK OFFICE (USPTO)

Misha Kapushesky, Patrick Kemmeren, Aedín C. Culhane, Steffen Durinck, Jan Ihmels, Christine Körner, Meelis Kull, Aurora Torrente, Ugis Sarkans, Jaak Vilo, Alvis Brazma. Expression Profiler: next generation - an online platform for analysis of microarray data. Nucleic Acids Research, 2004, Vol. 32, W465-W470

A. Brazma, H. Parkinson, U. Sarkans, M. Shojatalab, J. Vilo, N. Abeygunawardena, E. Holloway, M. Kapushesky, P. Kemmeren, G.G. Lara, A. Oezcimen, P. Rocca-Serra and S. Sansone. ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Research, 2003, 31: 68-71.

Jaak Vilo, Misha Kapushesky, Patrick Kemmeren, Ugis Sarkans, Alvis Brazma. Expression Profiler. In Parmigiani,G., Garrett,E.S., Irizarry,R. and Zeger,S.L. (eds), The Analysis of Gene Expression Data: Methods and Software, Springer Verlag, 2003, New York, NY.

Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M, Contrino S, Vilo J, Abeygunawardena N, Mukherjee G, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Sansone SA. ArrayExpress: a public database of gene expression data at EBI. Comptes Rendus Biologies Volume 326, Issues 10-11 , 2003 Oct-Nov;326(10-11):1075-8.

Alvis Brazma, Ugis Sarkans, Alan Robinson, Jaak Vilo, Martin Vingron, Jorg Hoheisel, and Kurt Fellenberg Microarray Data Representation, Annotation and Storage. Advances in Biochemical Engineering/Biotechnology, 2002, Vol.77(Chip Technology): pp. 113-139.

Elisabeth Dawson, Goncalo R. Abecasis, Suzannah Bumpstead, Yuan Chen, Sarah Hunt, David M. Beare, Jagjit Pabial, Thomas Dibling, Emma Tinsley, Susan Kirby, David Carter, Marianna Papaspyridonos, Simon Livingstone, Rocky Ganskek, Elin Lohmussaar, Jana Zernant, Neeme Tonisson, Maido Remm, Reedik Magi, Tarmo Puurand, Jaak Vilo, Ants Kurg, Kate Rice, Panos Deloukas, Richard Mott, Andres Metspalu, David R. Bentley, Lon R. Cardon & Ian Dunham A first-generation linkage disequilibrium map of human chromosome 22. Nature 2002, Aug 1, 418(6897):544-8

Jaak Vilo Pattern Discovery from Biosequences. PhD Thesis, Department of Computer Science, University of Helsinki, Finland. Series of Publications A, Report A-2002-3 Helsinki, November 2002, 149 pages. ISSN 1238-8645; ISBN 952-10-0792-3 (paperback); ISBN 952-10-0819-9 (PDF)

Johan Rung, Thomas Schlitt, Alvis Brazma, Karlis Freivalds, Jaak Vilo Building and analysing genome-wide gene disruption networks. Bioinformatics 2002 Oct;18 Suppl 2:S202-210 European Conference on Computational Biology (ECCB 2002)

Kimmo Palin, Esko Ukkonen, Alvis Brazma, Jaak Vilo Correlating gene promoters and expression in gene disruption experiments Bioinformatics 2002 Oct;18 Suppl 2:S172-180; European Conference on Computational Biology (ECCB, 2002)

Patrick Kemmeren, Nynke L. van Berkum, Jaak Vilo, Theo Bijma, Rogier Donders, Alvis Brazma, and Frank C.P. Holstege Protein Interaction Verification and Functional Annotation by Integrated Analysis of Genome-Scale Data. Molecular Cell 2002, May 24; 9(5) pp. 1133-1143

Renata Almeida, Alan Norrish, Mark Levick, David Vetrie, Tom Freeman, Jaak Vilo, Alasdair Ivens, Uta Lange, Carmel Stober, Sharon McCann, Jenefer M. Blackwell From genomes to vaccines: Leishmania as a model. Philos Trans R Soc Lond B Biol Sci 2002 Jan 29;357(1417):5-11

Alvis Brazma, Alan Robinson and Jaak Vilo Gene Expression Data Mining and Analysis (2001) pp. 106-129. Book chapter: B. Jordan (editor): DNA Microarrays: Gene Expression Applications Springer-Verlag ISBN:3-540-41508-4

Alvis Brazma and Jaak Vilo Gene Expression Data Analysis Microbes and Infection Volume 3, Issue 10, August 2001, Pages 823-829.

Alvis Brazma, Pascal Hingamp, John Quackenbush, Gavin Sherlock, Paul Spellman, Chris Stoeckert, John Aach, Wilhelm Ansorge, Catherine A. Ball, Helen C. Causton, Terry Gaasterland, Patrick Glenisson, Frank C.P. Holstege, Irene F. Kim, Victor Markowitz, John C. Matese, Helen Parkinson, Alan Robinson, Ugis Sarkans, Steffen Schulze-Kremer, Jason Stewart, Ronald Taylor, Jaak Vilo & Martin Vingron Minimum information about a microarray experiment (MIAME) toward standards for microarray data. Nature Genetics volume 29 no. 4, December 2001, pp. 365--371.

Jaak Vilo and Katja Kivinen Regulatory sequence analysis: application to interpretation of gene expression. European Neuropsychopharmacology, Volume 11, Issue 6, December 2001, Pages 399-411.

Steffen Möller, Jaak Vilo, Michael D.R. Croning Prediction of the coupling specificity of G protein coupled receptors to their G proteins. ISMB-2001 July 2001. Bioinformatics 2001 17: S174-S181.

Alvis Brazma and Jaak Vilo Gene Expression Data Analysis. (2000) FEBS Letters Volume 480, Issue 1, pp. 17-24.

Jaak Vilo, Alvis Brazma, Inge Jonassen, Alan Robinson, and Esko Ukkonen Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data. ISMB-2000 August 2000. AAAI press. pages 384-394.

Alvis Brazma, Inge Jonassen, Jaak Vilo and Esko Ukkonen Pattern Discovery in Biosequences. Proceedings of Fourth International Colloquium on Grammatical Inference (ICGI-98) (1433) (pp. 255--270) July 1998. Springer.

Alvis Brazma, Inge Jonassen, Jaak Vilo, and Esko Ukkonen Predicting Gene Regulatory Elements from their Expression Data in the Complete Yeast Genome (Extended Abstract). GCB 98, German Conference on Bioinformatics 1998.

Alvis Brazma, Inge Jonassen, Jaak Vilo, and Esko Ukkonen Predicting Gene Regulatory Elements in Silico on a Genomic Scale. Genome Research Vol. 8, Issue 11 (pp. 1202-1215) November 1998. Cold Spring Harbor Laboratory Press .

Alvis Brazma, Jaak Vilo, Esko Ukkonen and Kimmo Valtonen Data Mining for Regulatory Elements in Yeast Genome. Fifth International Conference on Intelligent Systems for Molecular Biology, ISMB-97 (pp. 65-74) June, 1997. AAAI Press.

Alvis Brazma, Esko Ukkonen, and Jaak Vilo Discovering unbounded unions of regular pattern languages from positive example. 7th International symposium, ISAAC'96. T. Asano, Y. Igarashi, H. Nagamochi, S: Miyano and S. Suri (ed.) (pp. 95-104) Springer-Verlag. Dec 1996. Osaka, Japan.

Alvis Brazma, Inge Jonassen, Esko Ukkonen and Jaak Vilo Discovering Patterns and Subfamilies in Biosequences. Proceedings of Fourth International Conference on Intelligent Systems for Molecular Biology ISMB-96 (pp. 34-43) AAAI Press. June 12-15 1996 . Wahington University, St. Louis, MO.

Jyrki Kivinen, Heikki Mannila, Esko Ukkonen and Jaak Vilo An algorithm for learning hierarchical classifiers. Machine Learning: ECML-94, Proc. Seventh European Conference on Machine Learning F. Bergadano and L. De Raedt (ed.) (pp. 375--378) Lecture Notes in Computer Science 784, Springer-Verlag. 1994.

Jaak Vilo Implementing Attribute Grammars by Computational Models. Proceedings of 4th International Symposium on Programming Language Implementation and Logic Programming (PLILP'92) Bruynooghe, M. and Wirsing, M. (eds.) (pp. 485--486) Springer-Verlag, Lecture Notes in Computer Science vol. 631, 1992.