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A global map of  human gene expression
Microarray Gene Expression Data Analysis - a beginner's guide


An essay on existentialism






Alvis on top of Peak Marx When I was young... Grand Canyon Rim to rim
 venice
Venice carnival
 Pyrenees
Pyrenees

Mont Blanc  		 Latvia
Home 1 - Latvia 		Cambridge
Home 2 - Cambridge
 Polar Adventures
matterhorn
Matterhorn on the third attempt
tibet
Cycling the roof of the World

Global warming in Gogmagog
Alaska

Favorite Quotes:

  • If it is good to have one foot in England, it is still better, or at least as good, to have the other one out of it – Henry James

  • The History of every major Galactic Civilization tends to pass through three distinct and recognizable phases, those of Survival, Inquiry and Sophistication, otherwise known as the How, Why, and Where phases. For instance, the first phase is characterized by the question ‘How can we eat?’, the second by the question ‘Why do we eat?’ and the third by the question, ‘Where shall we have lunch?’ – Douglas Adams, The Hitchhiker’s Guide to The Galaxy

  • All science is either physics or stamp collecting - Ernest Rutherford

  • Ask a computer scientist for a pint of milk, and he will start with setting up a dairy farm – Anonymous

  • Rowing harder doesn’t help if the boat is headed in the wrong direction – Kenichi Ohmae

  • Getting to the top is optional, but getting down is mandatory - Ed Viesturs


Selected publications:
Lukk M, Kapushesky M, Nikkilä J, Parkinson H, Goncalves A, Huber W, Ukkonen E, Brazma A. A global map of human gene expression. Nature Biotechnology. 2010 Apr;28(4):322-4.

Kapushesky M, Emam I, Holloway E, Kurnosov P, Zorin A, Malone J, Rustici G, Williams E, Parkinson H, Brazma A. Gene expression atlas at the European bioinformatics institute. Nucleic Acids Res. 2010 Jan;38 (Database issue):D690-8. 

Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A. ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression. (2008). Nucl. Acids Res. doi:10.1093/nar/gkn889
[PDF]

Alvis Brazma, Maria Krestyaninova and Ugis Sarkans. (2006). Standards for systems biology. Nat Rev Genet, 7, 593-605. [doi:10.1038/nrg1922]. [PDF]

Thomas Schlitt and Alvis Brazma. (2006). Modelling in molecular biology: describing transcription regulatory networks. Philosophical Transactions Royal Society B, 361 (1467), 483-494 [DOI: 10.1098/rstb.2005.1806]. [Abstract] [PDF - 385kb]

A. Torrente, M. Kapushesky and A. Brazma. A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings.  Bioinformatics, 2005, doi:10.1093/bioinformatics/bti644. [Abstract] [PDF] [Suppl. Info].

G. Rustici, J. Mata, K. Kivinen, P. Li󬠃.J. Penkett, G. Burns, J. Hayles, A. Brazma, P. Nurse and J. Baher. Periodic gene expression program of the fission yeast cell cycle. Nature Genetics, 2004, 36, 809-817 (doi:10.1038/ng1377). [Abstract] [PDF].

Schlitt, K. Palin, J. Rung, S. Dietmann, M. Lappe, E. Ukkonen, and A. Brazma. From Gene Networks to Gene Function. T Genome Research, 2003, 13: 2577-2587. [Abstract] [Full Text] [PDF]

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. [PDF]

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. [PubMed] [Abstract]

A Brazma, P Hingamp, J Quackenbush, G Sherlock, P Spellman, C Stoeckert, J Aach, W Ansorge, C A Ball, H C Causton, T Gaasterland, P Glenisson, F C P Holstege, I F Kim, V Markowitz, J C Matese, H Parkinson, A Robinson, U Sarkans, S Schulze-Kremer, J Stewart, R Taylor, J Vilo & M Vingron. Minimum information about a microarray experiment (MIAME)—toward standards for microarray data. Nature Genetics, vol 29 (December 2001), pp 365 - 371. [PDF] [PubMed]

Brazma, A., A. Robinson, G. Cameron, and M. Ashburner. One-stop shop for microarray data.  Commentary. Nature 403:699-700 (2000). [Nature] [PubMed]

Brazma, A., I. Jonassen, J. Vilo, and E. Ukkonen. Predicting Gene Regulatory Elements in Silico on a Genomic Scale. Genome Research Vol 8, 11:1202-1215 (1998). [Genome Research] [Pub Med]

Brazma, A., I. Jonassen, I. Eidhammer, and D. Gilbert. Approaches to Automatic Discovery of Patterns in Biosequences. Journal of Computational Biology 5:277-303 (1998) [Pub Med].

Brazma, A., J. Vilo, E. Ukkonen, and K. Valtonen. Data Mining for Regulatory Elements in Yeast Genome. In 'Proceedings of the Fifth International Conference Intelligent Systems for Molecular Biology' ISMB'97 , AAAI Press, pp. 65-74 (1997). [Pub Med]

A. Brazma, I. Jonassen, E. Ukkonen, J. Vilo. Discovering patterns and subfamilies in biosequences. In Proc. of 4th International Conference Intelligent Systems for Molecular Biology ISMB'96 , AAAI Press, 1996, p.34-43. [Pub Med]