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Items: 29

1.

Deciphering the mechanism of action of 089, a compound impairing the fungal cell cycle.

Stefanini I, Rizzetto L, Rivero D, Carbonell S, Gut M, Heath S, Gut IG, Trabocchi A, Guarna A, Ben Ghazzi N, Bowyer P, Kapushesky M, Cavalieri D.

Sci Rep. 2018 Apr 13;8(1):5964. doi: 10.1038/s41598-018-24341-y.

2.

Genomic and Phenotypic Variation in Morphogenetic Networks of Two Candida albicans Isolates Subtends Their Different Pathogenic Potential.

Cavalieri D, Di Paola M, Rizzetto L, Tocci N, De Filippo C, Lionetti P, Ardizzoni A, Colombari B, Paulone S, Gut IG, Berná L, Gut M, Blanc J, Kapushesky M, Pericolini E, Blasi E, Peppoloni S.

Front Immunol. 2018 Jan 19;8:1997. doi: 10.3389/fimmu.2017.01997. eCollection 2017.

3.

Correction: Mitochondrial Complex I Is a Global Regulator of Secondary Metabolism, Virulence and Azole Sensitivity in Fungi.

Bromley M, Johns A, Davies E, Fraczek M, Gilsenan JM, Kurbatova N, Keays M, Kapushesky M, Gut M, Gut I, Denning DW, Bowyer P.

PLoS One. 2017 Feb 2;12(2):e0171787. doi: 10.1371/journal.pone.0171787. eCollection 2017.

4.

Mitochondrial Complex I Is a Global Regulator of Secondary Metabolism, Virulence and Azole Sensitivity in Fungi.

Bromley M, Johns A, Davies E, Fraczek M, Mabey Gilsenan J, Kurbatova N, Keays M, Kapushesky M, Gut M, Gut I, Denning DW, Bowyer P.

PLoS One. 2016 Jul 20;11(7):e0158724. doi: 10.1371/journal.pone.0158724. eCollection 2016. Erratum in: PLoS One. 2017 Feb 2;12 (2):e0171787.

5.

Reversion of a fungal genetic code alteration links proteome instability with genomic and phenotypic diversification.

Bezerra AR, Simões J, Lee W, Rung J, Weil T, Gut IG, Gut M, Bayés M, Rizzetto L, Cavalieri D, Giovannini G, Bozza S, Romani L, Kapushesky M, Moura GR, Santos MA.

Proc Natl Acad Sci U S A. 2013 Jul 2;110(27):11079-84. doi: 10.1073/pnas.1302094110. Epub 2013 Jun 17.

6.

Low level genome mistranslations deregulate the transcriptome and translatome and generate proteotoxic stress in yeast.

Paredes JA, Carreto L, Simões J, Bezerra AR, Gomes AC, Santamaria R, Kapushesky M, Moura GR, Santos MA.

BMC Biol. 2012 Jun 20;10:55. doi: 10.1186/1741-7007-10-55.

7.

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures.

Culhane AC, Schröder MS, Sultana R, Picard SC, Martinelli EN, Kelly C, Haibe-Kains B, Kapushesky M, St Pierre AA, Flahive W, Picard KC, Gusenleitner D, Papenhausen G, O'Connor N, Correll M, Quackenbush J.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1060-6. doi: 10.1093/nar/gkr901. Epub 2011 Nov 21.

8.

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

Kapushesky M, Adamusiak T, Burdett T, Culhane A, Farne A, Filippov A, Holloway E, Klebanov A, Kryvych N, Kurbatova N, Kurnosov P, Malone J, Melnichuk O, Petryszak R, Pultsin N, Rustici G, Tikhonov A, Travillian RS, Williams E, Zorin A, Parkinson H, Brazma A.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1077-81. doi: 10.1093/nar/gkr913. Epub 2011 Nov 7.

9.

Systems biology of infectious diseases: a focus on fungal infections.

Santamaría R, Rizzetto L, Bromley M, Zelante T, Lee W, Cavalieri D, Romani L, Miller B, Gut I, Santos M, Pierre P, Bowyer P, Kapushesky M.

Immunobiology. 2011 Nov;216(11):1212-27. doi: 10.1016/j.imbio.2011.08.004. Epub 2011 Aug 16. Review.

PMID:
21889228
10.

ontoCAT: an R package for ontology traversal and search.

Kurbatova N, Adamusiak T, Kurnosov P, Swertz MA, Kapushesky M.

Bioinformatics. 2011 Sep 1;27(17):2468-70. doi: 10.1093/bioinformatics/btr375. Epub 2011 Jun 22.

PMID:
21697126
11.

OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript.

Adamusiak T, Burdett T, Kurbatova N, Joeri van der Velde K, Abeygunawardena N, Antonakaki D, Kapushesky M, Parkinson H, Swertz MA.

BMC Bioinformatics. 2011 May 29;12:218. doi: 10.1186/1471-2105-12-218.

12.

A pipeline for RNA-seq data processing and quality assessment.

Goncalves A, Tikhonov A, Brazma A, Kapushesky M.

Bioinformatics. 2011 Mar 15;27(6):867-9. doi: 10.1093/bioinformatics/btr012. Epub 2011 Jan 13.

13.

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.

14.

Modeling sample variables with an Experimental Factor Ontology.

Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H.

Bioinformatics. 2010 Apr 15;26(8):1112-8. doi: 10.1093/bioinformatics/btq099. Epub 2010 Mar 3.

15.

Gene expression atlas at the European bioinformatics institute.

Kapushesky M, Emam I, Holloway E, Kurnosov P, Zorin A, Malone J, Rustici G, Williams E, Parkinson H, Brazma A.

Nucleic Acids Res. 2010 Jan;38(Database issue):D690-8. doi: 10.1093/nar/gkp936. Epub 2009 Nov 11.

16.

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.

17.

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.

18.

Data storage and analysis in ArrayExpress and Expression Profiler.

Rustici G, Kapushesky M, Kolesnikov N, Parkinson H, Sarkans U, Brazma A.

Curr Protoc Bioinformatics. 2008 Sep;Chapter 7:Unit 7.13. doi: 10.1002/0471250953.bi0713s23.

PMID:
18819076
19.

4DXpress: a database for cross-species expression pattern comparisons.

Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T.

Nucleic Acids Res. 2008 Jan;36(Database issue):D847-53. Epub 2007 Oct 4.

20.

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.

21.

Data storage and analysis in ArrayExpress.

Brazma A, Kapushesky M, Parkinson H, Sarkans U, Shojatalab M.

Methods Enzymol. 2006;411:370-86. Review.

PMID:
16939801
22.

ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression.

Blake J, Schwager C, Kapushesky M, Brazma A.

Bioinformatics. 2006 Mar 15;22(6):765-7. Epub 2005 Dec 23.

PMID:
16377611
23.

A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings.

Torrente A, Kapushesky M, Brazma A.

Bioinformatics. 2005 Nov 1;21(21):3993-9. Epub 2005 Sep 1.

PMID:
16141251
24.

ArrayExpress--a public repository for microarray gene expression data at the EBI.

Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S, Coulson R, Farne A, Lara GG, Holloway E, Kapushesky M, Lilja P, Mukherjee G, Oezcimen A, Rayner T, Rocca-Serra P, Sharma A, Sansone S, Brazma A.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D553-5.

25.

The ArrayExpress gene expression database: a software engineering and implementation perspective.

Sarkans U, Parkinson H, Lara GG, Oezcimen A, Sharma A, Abeygunawardena N, Contrino S, Holloway E, Rocca-Serra P, Mukherjee G, Shojatalab M, Kapushesky M, Sansone SA, Farne A, Rayner T, Brazma A.

Bioinformatics. 2005 Apr 15;21(8):1495-501. Epub 2004 Nov 25.

PMID:
15564302
26.

Expression Profiler: next generation--an online platform for analysis of microarray data.

Kapushesky M, Kemmeren P, Culhane AC, Durinck S, Ihmels J, Körner C, Kull M, Torrente A, Sarkans U, Vilo J, Brazma A.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W465-70.

27.

ArrayExpress: a public database of gene expression data at EBI.

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.

C R Biol. 2003 Oct-Nov;326(10-11):1075-8.

PMID:
14744115
28.

Unraveling nature's networks.

Soinov L, Kapushesky M.

Genome Biol. 2003;4(10):341. Epub 2003 Sep 16.

29.

ArrayExpress--a public repository for microarray gene expression data at the EBI.

Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA.

Nucleic Acids Res. 2003 Jan 1;31(1):68-71.

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