Margus Lukk
I received my PhD in Bioinformatics from University of Helsinki in September 2010. Since then I've joned Duncan Odom lab at Cancer Research UK Cambridge Research Institute. If you would like to contact me please email firstname.lastname [thesign] cancer.org.uk.Research interests
- Bioinformatics and Computational Biology
- Functional genomics
- Gene regulation in disease and ageing.
Publications
Assessing affymetrix GeneChip microarray quality. McCall MN, Murakami PN, Lukk M, Huber W, Irizarry RA. BMC Bioinformatics. 2011 May 7;12:137.A user's guide to the encyclopedia of DNA elements (ENCODE). ENCODE Project Consortium, Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE, Gingeras TR, Kent WJ, Birney E, Wold B, Crawford GE. PLoS Biol. 2011 Apr;9(4):e1001046. Epub 2011 Apr 19.
ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments. Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A. Nucleic Acids Res. 2011 Jan;39(Database issue):D1002-4. Epub 2010 Nov 10.
A global map of human gene expression. Lukk M, Kapushesky M, Nikkilä J, Parkinson H, Goncalves A, Huber W, Ukkonen E, Brazma A. Nat Biotechnol. 2010 Apr;28(4):322-4.
Importing ArrayExpress datasets into R/Bioconductor. Kauffmann A, Rayner TF, Parkinson H, Kapushesky M, Lukk M, Brazma A, Huber W. Bioinformatics. 2009 Aug 15;25(16):2092-4. Epub 2009 Jun 8.
MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB. Rayner TF, Rezwan FI, Lukk M, Bradley XZ, Farne A, Holloway E, Malone J, Williams E, Parkinson H. Bioinformatics. 2009 Jan 15;25(2):279-80. Epub 2008 Nov 27.
ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. 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. Nucleic Acids Res. 2009 Jan;37(Database issue):D868-72. Epub 2008 Nov 10.
Systematic search for the best gene expression markers for melanoma micrometastasis detection. Soikkeli J, Lukk M, Nummela P, Virolainen S, Jahkola T, Katainen R, Harju L, Ukkonen E, Saksela O, Hölttä E. J Pathol. 2007 Oct;213(2):180-9.
ArrayExpress--a public database of microarray experiments and gene expression profiles. Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, Mani R, Rayner T, Sharma A, William E, Sarkans U, Brazma A. Nucleic Acids Res. 2007 Jan;35(Database issue):D747-50. Epub 2006 Nov 28.
Switch to an invasive growth phase in melanoma is associated with tenascin-C, fibronectin, and procollagen-I formi ng specific channel structures for invasion. Kääriäinen E, Nummela P, Soikkeli J, Yin M, Lukk M, Jahkola T, Virolainen S, Ora A, Ukkonen E, Saksela O, Hölttä E. J Pathol. 2006 Oct;210(2):181-91.
An MDL method for finding haplotype blocks and for estimating the strength of haplotype block boundaries. Koivisto M, Perola M, Varilo T, Hennah W, Ekelund J, Lukk M, Peltonen L, Ukkonen E, Mannila H. Pac Symp Biocomput. 2003:502-13.
Last modified: September 2011.