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Items: 26

1.

Crisflash: open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation.

Jacquin ALS, Odom DT, Lukk M.

Bioinformatics. 2019 Sep 1;35(17):3146-3147. doi: 10.1093/bioinformatics/btz019.

2.

Worthy? Crowdfunding the Canadian Health Care and Education Sectors.

Lukk M, Schneiderhan E, Soares J.

Can Rev Sociol. 2018 Aug;55(3):404-424. doi: 10.1111/cars.12210. Epub 2018 Jul 9.

PMID:
29984886
3.

Mutational landscape of a chemically-induced mouse model of liver cancer.

Connor F, Rayner TF, Aitken SJ, Feig C, Lukk M, Santoyo-Lopez J, Odom DT.

J Hepatol. 2018 Oct;69(4):840-850. doi: 10.1016/j.jhep.2018.06.009. Epub 2018 Jun 26.

4.

Successful transmission and transcriptional deployment of a human chromosome via mouse male meiosis.

Ernst C, Pike J, Aitken SJ, Long HK, Eling N, Stojic L, Ward MC, Connor F, Rayner TF, Lukk M, Klose RJ, Kutter C, Odom DT.

Elife. 2016 Nov 18;5. pii: e20235. doi: 10.7554/eLife.20235.

5.

Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression.

Torrente A, Lukk M, Xue V, Parkinson H, Rung J, Brazma A.

PLoS One. 2016 Jun 20;11(6):e0157484. doi: 10.1371/journal.pone.0157484. eCollection 2016.

6.

Enhancer evolution across 20 mammalian species.

Villar D, Berthelot C, Aldridge S, Rayner TF, Lukk M, Pignatelli M, Park TJ, Deaville R, Erichsen JT, Jasinska AJ, Turner JM, Bertelsen MF, Murchison EP, Flicek P, Odom DT.

Cell. 2015 Jan 29;160(3):554-66. doi: 10.1016/j.cell.2015.01.006.

7.

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways.

Ballester B, Medina-Rivera A, Schmidt D, Gonzàlez-Porta M, Carlucci M, Chen X, Chessman K, Faure AJ, Funnell AP, Goncalves A, Kutter C, Lukk M, Menon S, McLaren WM, Stefflova K, Watt S, Weirauch MT, Crossley M, Marioni JC, Odom DT, Flicek P, Wilson MD.

Elife. 2014 Oct 3;3:e02626. doi: 10.7554/eLife.02626.

8.

Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders.

Blanco S, Dietmann S, Flores JV, Hussain S, Kutter C, Humphreys P, Lukk M, Lombard P, Treps L, Popis M, Kellner S, Hölter SM, Garrett L, Wurst W, Becker L, Klopstock T, Fuchs H, Gailus-Durner V, Hrabĕ de Angelis M, Káradóttir RT, Helm M, Ule J, Gleeson JG, Odom DT, Frye M.

EMBO J. 2014 Sep 17;33(18):2020-39. doi: 10.15252/embj.201489282. Epub 2014 Jul 25.

9.

AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation.

Aldridge S, Watt S, Quail MA, Rayner T, Lukk M, Bimson MF, Gaffney D, Odom DT.

Genome Biol. 2013 Nov 7;14(11):R124. doi: 10.1186/gb-2013-14-11-r124.

10.

Global gene expression profiling reveals SPINK1 as a potential hepatocellular carcinoma marker.

Marshall A, Lukk M, Kutter C, Davies S, Alexander G, Odom DT.

PLoS One. 2013;8(3):e59459. doi: 10.1371/journal.pone.0059459. Epub 2013 Mar 18.

11.

Latent regulatory potential of human-specific repetitive elements.

Ward MC, Wilson MD, Barbosa-Morais NL, Schmidt D, Stark R, Pan Q, Schwalie PC, Menon S, Lukk M, Watt S, Thybert D, Kutter C, Kirschner K, Flicek P, Blencowe BJ, Odom DT.

Mol Cell. 2013 Jan 24;49(2):262-72. doi: 10.1016/j.molcel.2012.11.013. Epub 2012 Dec 13.

12.

Antihypoxic and antioxidant effects of exogenous succinic acid and aminothiol succinate-containing antihypoxants.

Zarubina IV, Lukk MV, Shabanov PD.

Bull Exp Biol Med. 2012 Jul;153(3):336-9.

PMID:
22866305
13.

MageComet--web application for harmonizing existing large-scale experiment descriptions.

Xue V, Burdett T, Lukk M, Taylor J, Brazma A, Parkinson H.

Bioinformatics. 2012 May 15;28(10):1402-3. doi: 10.1093/bioinformatics/bts148. Epub 2012 Apr 2.

14.

Assessing affymetrix GeneChip microarray quality.

McCall MN, Murakami PN, Lukk M, Huber W, Irizarry RA.

BMC Bioinformatics. 2011 May 7;12:137. doi: 10.1186/1471-2105-12-137.

15.

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. doi: 10.1093/nar/gkq1040. Epub 2010 Nov 10.

16.

[Delayed effect of 2-amino-4-acetylthiazolo[5, 4-b]indole hydrobromide on physical capability in mice].

Marysheva VV, Lukk MV, Iunusov IA, Shabanov PD.

Eksp Klin Farmakol. 2010 Jul;73(7):19-22. Russian.

PMID:
20821975
17.

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. doi: 10.1038/nbt0410-322. No abstract available.

18.

[Comparison of the antihypoxic and antioxidant properties of aminothiol and triazinoindole derivatives].

Lukk MV, Zarubina IV, Shabanov PD.

Eksp Klin Farmakol. 2009 Jul-Aug;72(4):36-42. Russian.

PMID:
19803369
19.

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. doi: 10.1093/bioinformatics/btp354. Epub 2009 Jun 8.

20.

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. doi: 10.1093/bioinformatics/btn617. Epub 2008 Nov 27.

21.

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. doi: 10.1093/nar/gkn889. Epub 2008 Nov 10.

22.

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.

PMID:
17891747
23.

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.

24.

Switch to an invasive growth phase in melanoma is associated with tenascin-C, fibronectin, and procollagen-I forming 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.

PMID:
16924594
25.

Minimum description length block finder, a method to identify haplotype blocks and to compare the strength of block boundaries.

Mannila H, Koivisto M, Perola M, Varilo T, Hennah W, Ekelund J, Lukk M, Peltonen L, Ukkonen E.

Am J Hum Genet. 2003 Jul;73(1):86-94. Epub 2003 May 20. Retraction in: Warren S. Am J Hum Genet. 2003 Aug;73(2):444.

26.

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.

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