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Items: 1 to 20 of 22

1.

Growth condition dependency is the major cause of non-responsiveness upon genetic perturbation.

Amini S, Holstege FC, Kemmeren P.

PLoS One. 2017 Mar 3;12(3):e0173432. doi: 10.1371/journal.pone.0173432. eCollection 2017.

2.

Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters.

de Jonge WJ, O'Duibhir E, Lijnzaad P, van Leenen D, Groot Koerkamp MJ, Kemmeren P, Holstege FC.

EMBO J. 2017 Feb 1;36(3):274-290. doi: 10.15252/embj.201695621. Epub 2016 Dec 15.

3.

An Evaluation of Active Learning Causal Discovery Methods for Reverse-Engineering Local Causal Pathways of Gene Regulation.

Ma S, Kemmeren P, Aliferis CF, Statnikov A.

Sci Rep. 2016 Mar 4;6:22558. doi: 10.1038/srep22558.

4.

A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions.

Sameith K, Amini S, Groot Koerkamp MJ, van Leenen D, Brok M, Brabers N, Lijnzaad P, van Hooff SR, Benschop JJ, Lenstra TL, Apweiler E, van Wageningen S, Snel B, Holstege FC, Kemmeren P.

BMC Biol. 2015 Dec 23;13:112. doi: 10.1186/s12915-015-0222-5.

5.

De-novo learning of genome-scale regulatory networks in S. cerevisiae.

Ma S, Kemmeren P, Gresham D, Statnikov A.

PLoS One. 2014 Sep 12;9(9):e106479. doi: 10.1371/journal.pone.0106479. eCollection 2014.

6.

The genomic landscape of compensatory evolution.

Szamecz B, Boross G, Kalapis D, Kovács K, Fekete G, Farkas Z, Lázár V, Hrtyan M, Kemmeren P, Groot Koerkamp MJ, Rutkai E, Holstege FC, Papp B, Pál C.

PLoS Biol. 2014 Aug 26;12(8):e1001935. doi: 10.1371/journal.pbio.1001935. eCollection 2014 Aug.

7.

Cell cycle population effects in perturbation studies.

O'Duibhir E, Lijnzaad P, Benschop JJ, Lenstra TL, van Leenen D, Groot Koerkamp MJ, Margaritis T, Brok MO, Kemmeren P, Holstege FC.

Mol Syst Biol. 2014 Jun 21;10:732. doi: 10.15252/msb.20145172.

8.

The role of Ctk1 kinase in termination of small non-coding RNAs.

Lenstra TL, Tudek A, Clauder S, Xu Z, Pachis ST, van Leenen D, Kemmeren P, Steinmetz LM, Libri D, Holstege FC.

PLoS One. 2013 Dec 4;8(12):e80495. doi: 10.1371/journal.pone.0080495. eCollection 2013.

9.

Yeast glucose pathways converge on the transcriptional regulation of trehalose biosynthesis.

Apweiler E, Sameith K, Margaritis T, Brabers N, van de Pasch L, Bakker LV, van Leenen D, Holstege FC, Kemmeren P.

BMC Genomics. 2012 Jun 14;13:239. doi: 10.1186/1471-2164-13-239.

10.

The specificity and topology of chromatin interaction pathways in yeast.

Lenstra TL, Benschop JJ, Kim T, Schulze JM, Brabers NA, Margaritis T, van de Pasch LA, van Heesch SA, Brok MO, Groot Koerkamp MJ, Ko CW, van Leenen D, Sameith K, van Hooff SR, Lijnzaad P, Kemmeren P, Hentrich T, Kobor MS, Buratowski S, Holstege FC.

Mol Cell. 2011 May 20;42(4):536-49. doi: 10.1016/j.molcel.2011.03.026.

11.

Functional overlap and regulatory links shape genetic interactions between signaling pathways.

van Wageningen S, Kemmeren P, Lijnzaad P, Margaritis T, Benschop JJ, de Castro IJ, van Leenen D, Groot Koerkamp MJ, Ko CW, Miles AJ, Brabers N, Brok MO, Lenstra TL, Fiedler D, Fokkens L, Aldecoa R, Apweiler E, Taliadouros V, Sameith K, van de Pasch LA, van Hooff SR, Bakker LV, Krogan NJ, Snel B, Holstege FC.

Cell. 2010 Dec 10;143(6):991-1004. doi: 10.1016/j.cell.2010.11.021.

12.

Epistatic relationships reveal the functional organization of yeast transcription factors.

Zheng J, Benschop JJ, Shales M, Kemmeren P, Greenblatt J, Cagney G, Holstege F, Li H, Krogan NJ.

Mol Syst Biol. 2010 Oct 5;6:420. doi: 10.1038/msb.2010.77.

13.

Cotranslational assembly of the yeast SET1C histone methyltransferase complex.

Halbach A, Zhang H, Wengi A, Jablonska Z, Gruber IM, Halbeisen RE, Dehé PM, Kemmeren P, Holstege F, Géli V, Gerber AP, Dichtl B.

EMBO J. 2009 Oct 7;28(19):2959-70. doi: 10.1038/emboj.2009.240. Epub 2009 Aug 27.

14.

A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system.

van Wijk SJ, de Vries SJ, Kemmeren P, Huang A, Boelens R, Bonvin AM, Timmers HT.

Mol Syst Biol. 2009;5:295. doi: 10.1038/msb.2009.55. Epub 2009 Aug 18. Erratum in: Mol Syst Biol. 2009;5:317.

15.

Adaptable gene-specific dye bias correction for two-channel DNA microarrays.

Margaritis T, Lijnzaad P, van Leenen D, Bouwmeester D, Kemmeren P, van Hooff SR, Holstege FC.

Mol Syst Biol. 2009;5:266. doi: 10.1038/msb.2009.21. Epub 2009 Apr 28.

16.

Functional organization of the S. cerevisiae phosphorylation network.

Fiedler D, Braberg H, Mehta M, Chechik G, Cagney G, Mukherjee P, Silva AC, Shales M, Collins SR, van Wageningen S, Kemmeren P, Holstege FC, Weissman JS, Keogh MC, Koller D, Shokat KM, Krogan NJ.

Cell. 2009 Mar 6;136(5):952-63. doi: 10.1016/j.cell.2008.12.039.

17.

CCR4/NOT complex associates with the proteasome and regulates histone methylation.

Laribee RN, Shibata Y, Mersman DP, Collins SR, Kemmeren P, Roguev A, Weissman JS, Briggs SD, Krogan NJ, Strahl BD.

Proc Natl Acad Sci U S A. 2007 Apr 3;104(14):5836-41. Epub 2007 Mar 26.

18.

GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases.

van Driel MA, Cuelenaere K, Kemmeren PP, Leunissen JA, Brunner HG, Vriend G.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W758-61.

19.

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.

20.

From microarray data to results. Workshop on genomic approaches to microarray data analysis.

Schlitt T, Kemmeren P.

EMBO Rep. 2004 May;5(5):459-63. Epub 2004 Apr 23. No abstract available.

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