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Items: 48

1.

Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies.

Beaton A, Lood C, Cunningham-Oakes E, MacFadyen A, Mullins AJ, Bestawy WE, Botelho J, Chevalier S, Coleman S, Dalzell C, Dolan SK, Faccenda A, Ghequire MGK, Higgins S, Kutschera A, Murray J, Redway M, Salih T, da Silva AC, Smith BA, Smits N, Thomson R, Woodcock S, Welch M, Cornelis P, Lavigne R, van Noort V, Tucker NP.

FEMS Microbiol Lett. 2018 May 1;365(9). doi: 10.1093/femsle/fny069.

2.

Canonical germinant receptor is dispensable for spore germination in Clostridium botulinum group II strain NCTC 11219.

Clauwers C, Lood C, van Noort V, Michiels CW.

Sci Rep. 2017 Nov 13;7(1):15426. doi: 10.1038/s41598-017-15839-y.

3.

Catabolic task division between two near-isogenic subpopulations co-existing in a herbicide-degrading bacterial consortium: consequences for the interspecies consortium metabolic model.

Albers P, Lood C, Özturk B, Horemans B, Lavigne R, van Noort V, De Mot R, Marchal K, Sanchez-Rodriguez A, Springael D.

Environ Microbiol. 2018 Jan;20(1):85-96. doi: 10.1111/1462-2920.13994. Epub 2017 Dec 15.

PMID:
29124862
4.

Correlated duplications and losses in the evolution of palmitoylation writer and eraser families.

Wittouck S, van Noort V.

BMC Evol Biol. 2017 Mar 20;17(1):83. doi: 10.1186/s12862-017-0932-0.

5.

ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana.

Hazarika RR, De Coninck B, Yamamoto LR, Martin LR, Cammue BP, van Noort V.

BMC Bioinformatics. 2017 Jan 17;18(1):37. doi: 10.1186/s12859-016-1458-y.

6.

UV crosslinked mRNA-binding proteins captured from leaf mesophyll protoplasts.

Zhang Z, Boonen K, Ferrari P, Schoofs L, Janssens E, van Noort V, Rolland F, Geuten K.

Plant Methods. 2016 Nov 3;12:42. eCollection 2016.

7.

yMap: an automated method to map yeast variants to protein modifications and functional regions.

Arslan A, van Noort V.

Bioinformatics. 2017 Feb 15;33(4):571-573. doi: 10.1093/bioinformatics/btw658.

8.

Evolutionary conservation of Ebola virus proteins predicts important functions at residue level.

Arslan A, van Noort V.

Bioinformatics. 2017 Jan 15;33(2):151-154. doi: 10.1093/bioinformatics/btw610. Epub 2016 Sep 21.

9.

CART-a chemical annotation retrieval toolkit.

Deghou S, Zeller G, Iskar M, Driessen M, Castillo M, van Noort V, Bork P.

Bioinformatics. 2016 Sep 15;32(18):2869-71. doi: 10.1093/bioinformatics/btw233. Epub 2016 Jun 2.

10.

Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances.

Chen WH, van Noort V, Lluch-Senar M, Hennrich ML, Wodke JA, Yus E, Alibés A, Roma G, Mende DR, Pesavento C, Typas A, Gavin AC, Serrano L, Bork P.

Nucleic Acids Res. 2016 Feb 18;44(3):1192-202. doi: 10.1093/nar/gkw004. Epub 2016 Jan 14.

11.

Adaptation to High Ethanol Reveals Complex Evolutionary Pathways.

Voordeckers K, Kominek J, Das A, Espinosa-Cantú A, De Maeyer D, Arslan A, Van Pee M, van der Zande E, Meert W, Yang Y, Zhu B, Marchal K, DeLuna A, Van Noort V, Jelier R, Verstrepen KJ.

PLoS Genet. 2015 Nov 6;11(11):e1005635. doi: 10.1371/journal.pgen.1005635. eCollection 2015 Nov.

12.

Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains.

Vonkova I, Saliba AE, Deghou S, Anand K, Ceschia S, Doerks T, Galih A, Kugler KG, Maeda K, Rybin V, van Noort V, Ellenberg J, Bork P, Gavin AC.

Cell Rep. 2015 Sep 1;12(9):1519-30. doi: 10.1016/j.celrep.2015.07.054. Epub 2015 Aug 20.

13.

Discovery and validation of the antimetastatic activity of citalopram in colorectal cancer.

Iskar M, Bork P, van Noort V.

Mol Cell Oncol. 2015 Feb 11;2(2):e975080. doi: 10.4161/23723556.2014.975080. eCollection 2015 Apr-Jun.

14.

Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium.

Lluch-Senar M, Delgado J, Chen WH, Lloréns-Rico V, O'Reilly FJ, Wodke JA, Unal EB, Yus E, Martínez S, Nichols RJ, Ferrar T, Vivancos A, Schmeisky A, Stülke J, van Noort V, Gavin AC, Bork P, Serrano L.

Mol Syst Biol. 2015 Jan 21;11(1):780. doi: 10.15252/msb.20145558.

15.

An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.

Bock T, Chen WH, Ori A, Malik N, Silva-Martin N, Huerta-Cepas J, Powell ST, Kastritis PL, Smyshlyaev G, Vonkova I, Kirkpatrick J, Doerks T, Nesme L, Baßler J, Kos M, Hurt E, Carlomagno T, Gavin AC, Barabas O, Müller CW, van Noort V, Beck M, Bork P.

Nucleic Acids Res. 2014 Dec 16;42(22):13525-33. doi: 10.1093/nar/gku1147. Epub 2014 Nov 14.

16.

Comments on "Human dominant disease genes are enriched in paralogs originating from whole genome duplication".

Chen WH, Zhao XM, van Noort V, Bork P.

PLoS Comput Biol. 2014 Jul 31;10(7):e1003758. doi: 10.1371/journal.pcbi.1003758. eCollection 2014 Jul. No abstract available.

17.

Novel drug candidates for the treatment of metastatic colorectal cancer through global inverse gene-expression profiling.

van Noort V, Schölch S, Iskar M, Zeller G, Ostertag K, Schweitzer C, Werner K, Weitz J, Koch M, Bork P.

Cancer Res. 2014 Oct 15;74(20):5690-9. doi: 10.1158/0008-5472.CAN-13-3540. Epub 2014 Jul 18.

18.

Spike-in SILAC proteomic approach reveals the vitronectin as an early molecular signature of liver fibrosis in hepatitis C infections with hepatic iron overload.

Montaldo C, Mattei S, Baiocchini A, Rotiroti N, Del Nonno F, Pucillo LP, Cozzolino AM, Battistelli C, Amicone L, Ippolito G, van Noort V, Conigliaro A, Alonzi T, Tripodi M, Mancone C.

Proteomics. 2014 May;14(9):1107-15. doi: 10.1002/pmic.201300422.

PMID:
24616218
19.

Evolution and functional cross-talk of protein post-translational modifications.

Beltrao P, Bork P, Krogan NJ, van Noort V.

Mol Syst Biol. 2013 Dec 22;9:714. doi: 10.1002/msb.201304521. Print 2013. Review.

20.

A quantitative liposome microarray to systematically characterize protein-lipid interactions.

Saliba AE, Vonkova I, Ceschia S, Findlay GM, Maeda K, Tischer C, Deghou S, van Noort V, Bork P, Pawson T, Ellenberg J, Gavin AC.

Nat Methods. 2014 Jan;11(1):47-50. doi: 10.1038/nmeth.2734. Epub 2013 Nov 24.

PMID:
24270602
21.

Human monogenic disease genes have frequently functionally redundant paralogs.

Chen WH, Zhao XM, van Noort V, Bork P.

PLoS Comput Biol. 2013;9(5):e1003073. doi: 10.1371/journal.pcbi.1003073. Epub 2013 May 16.

22.

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding.

Iskar M, Zeller G, Blattmann P, Campillos M, Kuhn M, Kaminska KH, Runz H, Gavin AC, Pepperkok R, van Noort V, Bork P.

Mol Syst Biol. 2013;9:662. doi: 10.1038/msb.2013.20.

23.

Consistent mutational paths predict eukaryotic thermostability.

van Noort V, Bradatsch B, Arumugam M, Amlacher S, Bange G, Creevey C, Falk S, Mende DR, Sinning I, Hurt E, Bork P.

BMC Evol Biol. 2013 Jan 10;13:7. doi: 10.1186/1471-2148-13-7.

24.

Deciphering a global network of functionally associated post-translational modifications.

Minguez P, Parca L, Diella F, Mende DR, Kumar R, Helmer-Citterich M, Gavin AC, van Noort V, Bork P.

Mol Syst Biol. 2012 Jul 17;8:599. doi: 10.1038/msb.2012.31.

25.

Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins.

Doerks T, van Noort V, Minguez P, Bork P.

PLoS One. 2012;7(4):e34302. doi: 10.1371/journal.pone.0034302. Epub 2012 Apr 2.

26.

Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium.

van Noort V, Seebacher J, Bader S, Mohammed S, Vonkova I, Betts MJ, Kühner S, Kumar R, Maier T, O'Flaherty M, Rybin V, Schmeisky A, Yus E, Stülke J, Serrano L, Russell RB, Heck AJ, Bork P, Gavin AC.

Mol Syst Biol. 2012 Feb 28;8:571. doi: 10.1038/msb.2012.4.

27.

Prediction of drug combinations by integrating molecular and pharmacological data.

Zhao XM, Iskar M, Zeller G, Kuhn M, van Noort V, Bork P.

PLoS Comput Biol. 2011 Dec;7(12):e1002323. doi: 10.1371/journal.pcbi.1002323. Epub 2011 Dec 29.

28.

Drug discovery in the age of systems biology: the rise of computational approaches for data integration.

Iskar M, Zeller G, Zhao XM, van Noort V, Bork P.

Curr Opin Biotechnol. 2012 Aug;23(4):609-16. doi: 10.1016/j.copbio.2011.11.010. Epub 2011 Dec 5. Review.

PMID:
22153034
29.

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 DP, Arumugam M, Bork P, Hurt E.

Cell. 2011 Jul 22;146(2):277-89. doi: 10.1016/j.cell.2011.06.039.

30.

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. doi: 10.1371/journal.pone.0022187. Epub 2011 Jul 13.

31.

Drug-induced regulation of target expression.

Iskar M, Campillos M, Kuhn M, Jensen LJ, van Noort V, Bork P.

PLoS Comput Biol. 2010 Sep 9;6(9). pii: e1000925. doi: 10.1371/journal.pcbi.1000925.

32.

Transcriptome complexity in a genome-reduced bacterium.

Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, Serrano L.

Science. 2009 Nov 27;326(5957):1268-71. doi: 10.1126/science.1176951.

33.

Impact of genome reduction on bacterial metabolism and its regulation.

Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen WH, Wodke JA, Güell M, Martínez S, Bourgeois R, Kühner S, Raineri E, Letunic I, Kalinina OV, Rode M, Herrmann R, Gutiérrez-Gallego R, Russell RB, Gavin AC, Bork P, Serrano L.

Science. 2009 Nov 27;326(5957):1263-8. doi: 10.1126/science.1177263.

34.

Proteome organization in a genome-reduced bacterium.

Kühner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castaño-Diez D, Chen WH, Devos D, Güell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Böttcher B, Frangakis AS, Russell RB, Serrano L, Bork P, Gavin AC.

Science. 2009 Nov 27;326(5957):1235-40. doi: 10.1126/science.1176343.

35.

Repeatability of published microarray gene expression analyses.

Ioannidis JP, Allison DB, Ball CA, Coulibaly I, Cui X, Culhane AC, Falchi M, Furlanello C, Game L, Jurman G, Mangion J, Mehta T, Nitzberg M, Page GP, Petretto E, van Noort V.

Nat Genet. 2009 Feb;41(2):149-55. doi: 10.1038/ng.295. Epub 2008 Jan 28.

PMID:
19174838
36.

Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity.

Lasonder E, Janse CJ, van Gemert GJ, Mair GR, Vermunt AM, Douradinha BG, van Noort V, Huynen MA, Luty AJ, Kroeze H, Khan SM, Sauerwein RW, Waters AP, Mann M, Stunnenberg HG.

PLoS Pathog. 2008 Oct;4(10):e1000195. doi: 10.1371/journal.ppat.1000195. Epub 2008 Oct 31.

37.

Comparative genomics of the Rab protein family in Apicomplexan parasites.

Langsley G, van Noort V, Carret C, Meissner M, de Villiers EP, Bishop R, Pain A.

Microbes Infect. 2008 Apr;10(5):462-70. doi: 10.1016/j.micinf.2008.01.017. Epub 2008 Feb 8. Review.

38.
39.

Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution.

Kensche PR, van Noort V, Dutilh BE, Huynen MA.

J R Soc Interface. 2008 Feb 6;5(19):151-70. Review.

40.

Orthology prediction at scalable resolution by phylogenetic tree analysis.

van der Heijden RT, Snel B, van Noort V, Huynen MA.

BMC Bioinformatics. 2007 Mar 8;8:83.

41.

Assessment of phylogenomic and orthology approaches for phylogenetic inference.

Dutilh BE, van Noort V, van der Heijden RT, Boekhout T, Snel B, Huynen MA.

Bioinformatics. 2007 Apr 1;23(7):815-24. Epub 2007 Jan 19.

PMID:
17237036
42.

Combinatorial gene regulation in Plasmodium falciparum.

van Noort V, Huynen MA.

Trends Genet. 2006 Feb;22(2):73-8. Epub 2005 Dec 27. Review.

PMID:
16380193
43.

Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes.

Snel B, van Noort V, Huynen MA.

Nucleic Acids Res. 2004 Sep 7;32(16):4725-31. Print 2004.

44.

Comparative genomics for reliable protein-function prediction from genomic data.

Huynen MA, Snel B, van Noort V.

Trends Genet. 2004 Aug;20(8):340-4.

PMID:
15262404
45.
46.

Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome.

Kesmir C, van Noort V, de Boer RJ, Hogeweg P.

Immunogenetics. 2003 Oct;55(7):437-49. Epub 2003 Aug 30.

PMID:
12955356
47.

Strand misalignments lead to quasipalindrome correction.

van Noort V, Worning P, Ussery DW, Rosche WA, Sinden RR.

Trends Genet. 2003 Jul;19(7):365-9. No abstract available.

PMID:
12850440
48.

Predicting gene function by conserved co-expression.

van Noort V, Snel B, Huynen MA.

Trends Genet. 2003 May;19(5):238-42. Review.

PMID:
12711213

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