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Items: 1 to 20 of 35

1.

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.

2.

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(1):112. doi: 10.1186/s12915-015-0222-5.

3.

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.

4.

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.

5.

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.

6.

Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors.

Kemmeren P, Sameith K, van de Pasch LA, Benschop JJ, Lenstra TL, Margaritis T, O'Duibhir E, Apweiler E, van Wageningen S, Ko CW, van Heesch S, Kashani MM, Ampatziadis-Michailidis G, Brok MO, Brabers NA, Miles AJ, Bouwmeester D, van Hooff SR, van Bakel H, Sluiters E, Bakker LV, Snel B, Lijnzaad P, van Leenen D, Groot Koerkamp MJ, Holstege FC.

Cell. 2014 Apr 24;157(3):740-52. doi: 10.1016/j.cell.2014.02.054.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

A consensus of core protein complex compositions for Saccharomyces cerevisiae.

Benschop JJ, Brabers N, van Leenen D, Bakker LV, van Deutekom HW, van Berkum NL, Apweiler E, Lijnzaad P, Holstege FC, Kemmeren P.

Mol Cell. 2010 Jun 25;38(6):916-28. doi: 10.1016/j.molcel.2010.06.002.

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.

Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae.

Collins SR, Kemmeren P, Zhao XC, Greenblatt JF, Spencer F, Holstege FC, Weissman JS, Krogan NJ.

Mol Cell Proteomics. 2007 Mar;6(3):439-50. Epub 2007 Jan 2.

19.

Transcriptome-based identification of pro- and antioxidative gene expression in kidney cortex of nitric oxide-depleted rats.

Wesseling S, Joles JA, van Goor H, Bluyssen HA, Kemmeren P, Holstege FC, Koomans HA, Braam B.

Physiol Genomics. 2007 Jan 17;28(2):158-67. Epub 2006 Oct 17.

20.

Multiple robust signatures for detecting lymph node metastasis in head and neck cancer.

Roepman P, Kemmeren P, Wessels LF, Slootweg PJ, Holstege FC.

Cancer Res. 2006 Feb 15;66(4):2361-6.

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