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Items: 17

1.

Predicting gene function from uncontrolled expression variation among individual wild-type Arabidopsis plants.

Bhosale R, Jewell JB, Hollunder J, Koo AJ, Vuylsteke M, Michoel T, Hilson P, Goossens A, Howe GA, Browse J, Maere S.

Plant Cell. 2013 Aug;25(8):2865-77. doi: 10.1105/tpc.113.112268. Epub 2013 Aug 13.

2.

Comparative transcriptomics as a tool for the identification of root branching genes in maize.

Jansen L, Hollunder J, Roberts I, Forestan C, Fonteyne P, Van Quickenborne C, Zhen RG, McKersie B, Parizot B, Beeckman T.

Plant Biotechnol J. 2013 Dec;11(9):1092-102. doi: 10.1111/pbi.12104. Epub 2013 Aug 14.

3.

CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations.

De Bodt S, Hollunder J, Nelissen H, Meulemeester N, Inzé D.

New Phytol. 2012 Aug;195(3):707-20. doi: 10.1111/j.1469-8137.2012.04184.x. Epub 2012 May 31.

4.

The progeny of Arabidopsis thaliana plants exposed to salt exhibit changes in DNA methylation, histone modifications and gene expression.

Bilichak A, Ilnystkyy Y, Hollunder J, Kovalchuk I.

PLoS One. 2012;7(1):e30515. doi: 10.1371/journal.pone.0030515. Epub 2012 Jan 23.

5.

Specific impact of tobamovirus infection on the Arabidopsis small RNA profile.

Hu Q, Hollunder J, Niehl A, Kørner CJ, Gereige D, Windels D, Arnold A, Kuiper M, Vazquez F, Pooggin M, Heinlein M.

PLoS One. 2011 May 10;6(5):e19549. doi: 10.1371/journal.pone.0019549.

6.

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana.

Van Leene J, Hollunder J, Eeckhout D, Persiau G, Van De Slijke E, Stals H, Van Isterdael G, Verkest A, Neirynck S, Buffel Y, De Bodt S, Maere S, Laukens K, Pharazyn A, Ferreira PC, Eloy N, Renne C, Meyer C, Faure JD, Steinbrenner J, Beynon J, Larkin JC, Van de Peer Y, Hilson P, Kuiper M, De Veylder L, Van Onckelen H, Inzé D, Witters E, De Jaeger G.

Mol Syst Biol. 2010 Aug 10;6:397. doi: 10.1038/msb.2010.53.

7.

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL.

Laukens K, Hollunder J, Dang TH, De Jaeger G, Kuiper M, Witters E, Verschoren A, Van Leemput K.

BMC Bioinformatics. 2010 Jul 1;11:360. doi: 10.1186/1471-2105-11-360.

8.

Functional modules in the Arabidopsis core cell cycle binary protein-protein interaction network.

Boruc J, Van den Daele H, Hollunder J, Rombauts S, Mylle E, Hilson P, Inzé D, De Veylder L, Russinova E.

Plant Cell. 2010 Apr;22(4):1264-80. doi: 10.1105/tpc.109.073635. Epub 2010 Apr 20.

9.

Transgenerational adaptation of Arabidopsis to stress requires DNA methylation and the function of Dicer-like proteins.

Boyko A, Blevins T, Yao Y, Golubov A, Bilichak A, Ilnytskyy Y, Hollunder J, Meins F Jr, Kovalchuk I.

PLoS One. 2010 Mar 3;5(3):e9514. doi: 10.1371/journal.pone.0009514. Erratum in: PLoS One. 2010;5(4). doi: 10.1371/annotation/726f31b5-99c4-44e9-9cd6-b8d66b3f6038. Hollander, Jens [corrected to Hollunder, Jens].

10.

DASS-GUI: a user interface for identification and analysis of significant patterns in non-sequential data.

Hollunder J, Friedel M, Kuiper M, Wilhelm T.

Bioinformatics. 2010 Apr 1;26(7):987-9. doi: 10.1093/bioinformatics/btq071. Epub 2010 Feb 19.

11.

CORNET: a user-friendly tool for data mining and integration.

De Bodt S, Carvajal D, Hollunder J, Van den Cruyce J, Movahedi S, Inzé D.

Plant Physiol. 2010 Mar;152(3):1167-79. doi: 10.1104/pp.109.147215. Epub 2010 Jan 6.

12.

Protein subcomplexes--molecular machines with highly specialized functions.

Hollunder J, Beyer A, Wilhelm T.

IEEE Trans Nanobioscience. 2007 Mar;6(1):86-93.

PMID:
17393854
13.

DASS: efficient discovery and p-value calculation of substructures in unordered data.

Hollunder J, Friedel M, Beyer A, Workman CT, Wilhelm T.

Bioinformatics. 2007 Jan 1;23(1):77-83. Epub 2006 Oct 10.

PMID:
17032678
14.

Integrated assessment and prediction of transcription factor binding.

Beyer A, Workman C, Hollunder J, Radke D, Möller U, Wilhelm T, Ideker T.

PLoS Comput Biol. 2006 Jun 16;2(6):e70. Epub 2006 Jun 16.

15.

Common patterns in type II restriction enzyme binding sites.

Nikolajewa S, Beyer A, Friedel M, Hollunder J, Wilhelm T.

Nucleic Acids Res. 2005 May 11;33(8):2726-33. Print 2005.

16.

Identification and characterization of protein subcomplexes in yeast.

Hollunder J, Beyer A, Wilhelm T.

Proteomics. 2005 May;5(8):2082-9.

PMID:
15832363
17.

Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale.

Beyer A, Hollunder J, Nasheuer HP, Wilhelm T.

Mol Cell Proteomics. 2004 Nov;3(11):1083-92. Epub 2004 Aug 23.

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