Staff at EMBL
Vera Van Noort
Staff Scientist
Bork Group
EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| E-mail: | send a mail |
|---|
Publications
Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding. Iskar, M., Zeller, G., Blattmann, P., Campillos, M., Kuhn, M., Kaminska, K.H., Runz, H., Gavin, A.C., Pepperkok, R., van Noort, V. & Bork, P. Mol Syst Biol. 2013 Apr 30;9:662. doi: 10.1038/msb.2013.20. PubMed
Consistent mutational paths predict eukaryotic thermostability. van Noort, V., Bradatsch, B., Arumugam, M., Amlacher, S., Bange, G., Creevey, C., Falk, S., Mende, D.R., Sinning, I., Hurt, E. & Bork, P. BMC Evol Biol. 2013 Jan 10;13:7. doi: 10.1186/1471-2148-13-7. PubMed
Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. van Noort, V., Seebacher, J., Bader, S., Mohammed, S., Vonkova, I., Betts, M.J., Kuhner, S., Kumar, R., Maier, T., O'Flaherty, M., Rybin, V., Schmeisky, A., Yus, E., Stulke, J., Serrano, L., Russell, R.B., Heck, A.J., Bork, P. & Gavin, A.C. Mol Syst Biol. 2012 Feb 28;8:571. doi: 10.1038/msb.2012.4. PubMed
Deciphering a global network of functionally associated post-translational modifications. Minguez, P., Parca, L., Diella, F., Mende, D.R., Kumar, R., Helmer-Citterich, M., Gavin, A.C., van Noort, V. & Bork, P. Mol Syst Biol. 2012 Jul 17;8:599. doi: 10.1038/msb.2012.31. PubMed
Drug discovery in the age of systems biology: the rise of computational approaches for data integration. Iskar, M., Zeller, G., Zhao, X.M., van Noort, V. & Bork, P. Curr Opin Biotechnol. 2011 Dec 5. PubMed
Prediction of drug combinations by integrating molecular and pharmacological data. Zhao, X.M., Iskar, M., Zeller, G., Kuhn, M., Noort, V. & Bork, P. PLoS Comput Biol. 2011 Dec;7(12):e1002323. Epub 2011 Dec 29. PubMed
Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile. Amlacher, S., Sarges, P., Flemming, D., van Noort, V., Kunze, R., Devos, D.P., Arumugam, M., Bork, P. & Hurt, E. Cell. 2011 Jul 22;146(2):277-89. PubMed
Network neighbors of drug targets contribute to drug side-effect similarity. Brouwers, L., Iskar, M., Zeller, G., van Noort, V. & Bork, P. PLoS One. 2011;6(7):e22187. Epub 2011 Jul 13. PubMed
Drug-induced regulation of target expression. Iskar, M., Campillos, M., Kuhn, M., Jensen, L.J., van Noort, V. & Bork, P. PLoS Comput Biol. 2010 Sep 9;6(9). pii: e1000925. PubMed
Impact of genome reduction on bacterial metabolism and its regulation. Yus, E., Maier, T., Michalodimitrakis, K., van Noort, V., Yamada, T., Chen, W.H., Wodke, J.A., Guell, M., Martinez, S., Bourgeois, R., Kuhner, S., Raineri, E., Letunic, I., Kalinina, O.V., Rode, M., Herrmann, R., Gutierrez-Gallego, R., Russell, R.B., Gavin, A.C., Bork, P. & Serrano, L. Science. 2009 Nov 27;326(5957):1263-8. PubMed
Transcriptome complexity in a genome-reduced bacterium. Guell, M., van Noort, V., Yus, E., Chen, W.H., Leigh-Bell, J., Michalodimitrakis, K., Yamada, T., Arumugam, M., Doerks, T., Kuhner, S., Rode, M., Suyama, M., Schmidt, S., Gavin, A.C., Bork, P. & Serrano, L. Science. 2009 Nov 27;326(5957):1268-71. PubMed
Repeatability of published microarray gene expression analyses. Ioannidis, J.P., Allison, D.B., Ball, C.A., Coulibaly, I., Cui, X., Culhane, A.C., Falchi, M., Furlanello, C., Game, L., Jurman, G., Mangion, J., Mehta, T., Nitzberg, M., Page, G.P., Petretto, E. & van Noort, V. Nat Genet. 2009 Feb;41(2):149-55. Epub 2008 Jan 28. PubMed
Proteome organization in a genome-reduced bacterium.
Kühner S., van Noort V., Betts M.J., Leo-Macias A., Batisse C., Rode M., Yamada T., Maier T., Bader S., Beltran-Alvarez P., Castaño-Diez D., Chen W.H., Devos D., Güell Cargol M., Norambuena T., Racke I., Rybin V., Schmidt A., Yus E., Aebersold R., Herrmann R., Böttcher B., Frangakis A.S., Russell R.B., Serrano L., Bork, P. and Gavin, A.C.
Science, 2009, 326, 1235-1240
Full text
Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity. Lasonder, E., Janse, C.J., van Gemert, G.J., Mair, G.R., Vermunt, A.M., Douradinha, B.G., van Noort, V., Huynen, M.A., Luty, A.J., Kroeze, H., Khan, S.M., Sauerwein, R.W., Waters, A.P., Mann, M. & Stunnenberg, H.G. PLoS Pathog. 2008 Oct;4(10):e1000195. Epub 2008 Oct 31. PubMed
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. Kensche, P.R., van Noort, V., Dutilh, B.E. & Huynen, M.A. J R Soc Interface. 2008 Apr 22;5(19):151-70. PubMed
Comparative genomics of the Rab protein family in Apicomplexan parasites. Langsley, G., van Noort, V., Carret, C., Meissner, M., de Villiers, E.P., Bishop, R. & Pain, A. Microbes Infect. 2008 Apr;10(5):462-70. Epub 2008 Feb 8. PubMed
Assessment of phylogenomic and orthology approaches for phylogenetic inference. Dutilh, B.E., van Noort, V., van der Heijden, R.T., Boekhout, T., Snel, B. & Huynen, M.A. Bioinformatics. 2007 Apr 1;23(7):815-24. Epub 2007 Jan 19. PubMed
Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions. van Noort, V., Snel, B. & Huynen, M.A. Genome Biol. 2007;8(9):R197. PubMed
Orthology prediction at scalable resolution by phylogenetic tree analysis. van der Heijden, R.T., Snel, B., van Noort, V. & Huynen, M.A. BMC Bioinformatics. 2007 Mar 8;8:83. PubMed
Combinatorial gene regulation in Plasmodium falciparum. van Noort, V. & Huynen, M.A. Trends Genet. 2006 Feb;22(2):73-8. Epub 2005 Dec 27. PubMed
Comparative genomics for reliable protein-function prediction from genomic data. Huynen, M.A., Snel, B. & van Noort, V. Trends Genet. 2004 Aug;20(8):340-4. PubMed
The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model. van Noort, V., Snel, B. & Huynen, M.A. EMBO Rep. 2004 Mar;5(3):280-4. Epub 2004 Feb 13. PubMed
Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes. Snel, B., van Noort, V. & Huynen, M.A. Nucleic Acids Res. 2004 Sep 7;32(16):4725-31. Print 2004. PubMed
Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome. Kesmir, C., van Noort, V., de Boer, R.J. & Hogeweg, P. Immunogenetics. 2003 Oct;55(7):437-49. Epub 2003 Aug 30. PubMed
Strand misalignments lead to quasipalindrome correction. van Noort, V., Worning, P., Ussery, D.W., Rosche, W.A. & Sinden, R.R. Trends Genet. 2003 Jul;19(7):365-9. PubMed
Predicting gene function by conserved co-expression. van Noort, V., Snel, B. & Huynen, M.A. Trends Genet. 2003 May;19(5):238-42. PubMed