2004

• 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, Web Server issue W465 W470
  [NAR:Web] [PubMed:Abstract] [DOI:10.1093/nar/gkh470] [Local PDF copy]
  

2003

• 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.
  [Accompanying web page] [Amazon UK] [Amazon.com]
  
• 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.
  [Abstract] [PDF]
  
• 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.
  PMID:14744115

2002

• 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)
  [Abstract] [PDF in E-Thesis] [local]
  
  
• 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.
  [Abstract]
  
• 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
  [Abstract] [Abstract in Nature]
  
• 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)
  [Abstract (PubMed)] [PDF]
• 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)
  [Abstract (PubMed)] [PDF]
• 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
  [Abstract] [PubMed]
• 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
  [PubMed]

2001

• 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.
  [Abstract] [PDF] [MGED]
• Alvis Brazma, Alan Robinson and Jaak Vilo
  Gene Expression Data Mining and Analysis pp. 106-129.
  Book chapter: B. Jordan (editor): DNA Microarrays: Gene Expression Applications Springer-Verlag ISBN:3-540-41508-4 (Amazon)
• Alvis Brazma and Jaak Vilo
  Gene Expression Data Analysis
  Microbes and Infection Volume 3, Issue 10, August 2001, Pages 823-829. [ScienceDirect] [Abstract]
• 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. [PubMed:Abstract]  [PDF]
• 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.
  [Abstract] [Print PDF] [Screen PDF]   [Local PDF] [Local Postscript]
  Supplement: Pattern visualisation for G-protein specific GPCR sequence motifs found and reported in the paper.

2000

• Alvis Brazma and Jaak Vilo
  Gene Expression Data Analysis
  FEBS Letters Volume 480, Issue 1, pp. 17-24.
  [Abstract] [Article Online] [Article PDF] [PostScript]
• 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. [PostScript] [PDF]

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 . (local pdf)
• 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.
• Jaak Vilo
  Discovering Frequent Patterns from Strings.
  Technical Report C-1998-9 (pp. 20) May 1998. Department of Computer Science, University of Helsinki.

1997

• Alvis Brazma, Jaak Vilo and Esko Ukkonen
  Finding Transcription Factor Binding Site Combinations in Yeast Genome (Extended Abstract).
  Computer Science and Biology, Proceedings of the German Conference on Bioinformatics GCB '97 D. Frishman and H.W. Mewes (ed.) (pp. 57-59) September 1997. Münchener Informationszentrum f. Proteinsequenzen. MIPS-GSF Am Max-Planck Institut f. Biochemie; 82152 Martinsried.
• 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. [PostScript] [PDF]

1996

• 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.
• Alvis Brazma, Inge Jonassen, Esko Ukkonen and Jaak Vilo
  Poster: Automatic Discovery of Patterns and Subfamilies in Biosequences
  International Symposium on Theoretical and Computational Genome Research, held March 24-27, 1996, in Heidelberg, Germany.
• Jaak Vilo
  Arvutiteadusega bioloogia probleemide kallale
  Proceedings of Schola Biotheoretica XXII, Elu Keeled (pp 71-76). Teaduste Akadeemia Kirjastus, Tartu-Tallinn, 1996.

1995

• Alvis Brazma, Esko Ukkonen and Jaak Vilo
  Finding a Good Collection of Patterns Covering a Set of Sequences.
  Report C-1995-60 Dec 1995. Department of Computer Science, University of Helsinki. CR: I.2.6, F.2.2, J.3
  

1994

• 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.

1992

• 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.
• Jaak Vilo
  Attribute Grammars and Computational Models as Combined Language Development Tools
  Institute of Cybernetics, Tallinn (15 pp). Research Report No. CS-43/92, 1992
• Jaan Penjam, Merik Meriste and Jaak Vilo
  Specification and Implementation of Languages
  Report on Research project no. 9100. Institute of Cybernetics, Tallinn (44 pp.) (in Estonian), 1992

1991

• Jaak Vilo
  Attribute Grammars and Computational Models
  Dipl. thesis, Faculty of Mathematics, University of Tartu, 1991.
• Jaak Vilo
  Eksperimentaalne Atribuutgrammatikate realiseerimise süsteem. Kasutamisjuhend. (User Manual)
  Institute of Cybernetics, Tallinn (10 pp, in Estonian). Research Report No. CS-22/91, 1991