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Reuse of public genome-wide gene expression data.
Rung J, Brazma A. Rung J, et al. Nat Rev Genet. 2013 Feb;14(2):89-99. doi: 10.1038/nrg3394. Epub 2012 Dec 27. Nat Rev Genet. 2013. PMID: 23269463 Review.
Predicting gene regulatory elements in silico on a genomic scale.
Brazma A, Jonassen I, Vilo J, Ukkonen E. Brazma A, et al. Genome Res. 1998 Nov;8(11):1202-15. doi: 10.1101/gr.8.11.1202. Genome Res. 1998. PMID: 9847082 Free PMC article.
We performed a systematic analysis of gene upstream regions in the yeast genome for occurrences of regular expression-type patterns with the goal of identifying potential regulatory elements. To achieve this goal, we have developed a new sequence pattern discovery a …
We performed a systematic analysis of gene upstream regions in the yeast genome for occurrences of regular expression-type patterns w …
One-stop shop for microarray data.
Brazma A, Robinson A, Cameron G, Ashburner M. Brazma A, et al. Nature. 2000 Feb 17;403(6771):699-700. doi: 10.1038/35001676. Nature. 2000. PMID: 10693778 No abstract available.
Gene expression data analysis.
Brazma A, Vilo J. Brazma A, et al. FEBS Lett. 2000 Aug 25;480(1):17-24. doi: 10.1016/s0014-5793(00)01772-5. FEBS Lett. 2000. PMID: 10967323 Review.
Mining for putative regulatory elements in the yeast genome using gene expression data.
Vilo J, Brazma A, Jonassen I, Robinson A, Ukkonen E. Vilo J, et al. Proc Int Conf Intell Syst Mol Biol. 2000;8:384-94. Proc Int Conf Intell Syst Mol Biol. 2000. PMID: 10977099
Our tool performs a rapid exhaustive search for a priori unknown statistically significant sequence patterns of unrestricted length. ...Automatically derived consensus patterns of these groups represent the results in a comprehensive way for a human in …
Our tool performs a rapid exhaustive search for a priori unknown statistically significant sequence patterns of unrestricted l …
Gene expression data analysis.
Brazma A, Vilo J. Brazma A, et al. Microbes Infect. 2001 Aug;3(10):823-9. doi: 10.1016/s1286-4579(01)01440-x. Microbes Infect. 2001. PMID: 11580977 Review.
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M. Brazma A, et al. Nat Genet. 2001 Dec;29(4):365-71. doi: 10.1038/ng1201-365. Nat Genet. 2001. PMID: 11726920
Microarray analysis has become a widely used tool for the generation of gene expression data on a genomic scale. Although many significant results have been derived from microarray studies, one limitation has been the lack of standards for presenting and exchanging …
Microarray analysis has become a widely used tool for the generation of gene expression data on a genomic scale. Although many …
Microarray data representation, annotation and storage.
Brazma A, Sarkans U, Robinson A, Vilo J, Vingron M, Hoheisel J, Fellenberg K. Brazma A, et al. Adv Biochem Eng Biotechnol. 2002;77:113-39. doi: 10.1007/3-540-45713-5_7. Adv Biochem Eng Biotechnol. 2002. PMID: 12227734
We describe the basic design of a microarray gene expression database to help microarray users and their informatics teams to set up their information services. We describe two data models--a simpler one called ArrayExpressB and the complete model ArrayExpressC, and …
We describe the basic design of a microarray gene expression database to help microarray users and their informatics teams to set up …
Building and analysing genome-wide gene disruption networks.
Rung J, Schlitt T, Brazma A, Freivalds K, Vilo J. Rung J, et al. Bioinformatics. 2002;18 Suppl 2:S202-10. doi: 10.1093/bioinformatics/18.suppl_2.s202. Bioinformatics. 2002. PMID: 12386004
RESULTS: We have built genome-wide disruption networks for yeast, using a representation of gene expression data as directed labelled graphs. ...We are interested in features of the resulting disruption networks that are robust over a range of significance cutoffs. …
RESULTS: We have built genome-wide disruption networks for yeast, using a representation of gene expression data as directed labelled …
The European Bioinformatics Institute's data resources.
Brooksbank C, Camon E, Harris MA, Magrane M, Martin MJ, Mulder N, O'Donovan C, Parkinson H, Tuli MA, Apweiler R, Birney E, Brazma A, Henrick K, Lopez R, Stoesser G, Stoehr P, Cameron G. Brooksbank C, et al. Nucleic Acids Res. 2003 Jan 1;31(1):43-50. doi: 10.1093/nar/gkg066. Nucleic Acids Res. 2003. PMID: 12519944 Free PMC article.
As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. ...But just as a cell would be useless if it couldn't transcribe DNA or translate RNA, our resource …
As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a
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