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Items: 39

1.

The clinical implementation of copy number detection in the age of next-generation sequencing.

Hehir-Kwa JY, Tops BBJ, Kemmeren P.

Expert Rev Mol Diagn. 2018 Oct;18(10):907-915. doi: 10.1080/14737159.2018.1523723. Epub 2018 Sep 27.

PMID:
30221560
2.

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.

3.

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.

4.

Proteome-wide Changes in Protein Turnover Rates in C. elegans Models of Longevity and Age-Related Disease.

Visscher M, De Henau S, Wildschut MHE, van Es RM, Dhondt I, Michels H, Kemmeren P, Nollen EA, Braeckman BP, Burgering BMT, Vos HR, Dansen TB.

Cell Rep. 2016 Sep 13;16(11):3041-3051. doi: 10.1016/j.celrep.2016.08.025.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

PMID:
17047089
24.

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.

25.

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.

26.

Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit.

Radonjic M, Andrau JC, Lijnzaad P, Kemmeren P, Kockelkorn TT, van Leenen D, van Berkum NL, Holstege FC.

Mol Cell. 2005 Apr 15;18(2):171-83.

27.

Nitric oxide-dependent and nitric oxide-independent transcriptional responses to high shear stress in endothelial cells.

Braam B, de Roos R, Bluyssen H, Kemmeren P, Holstege F, Joles JA, Koomans H.

Hypertension. 2005 Apr;45(4):672-80. Epub 2005 Feb 7.

PMID:
15699468
28.

An expression profile for diagnosis of lymph node metastases from primary head and neck squamous cell carcinomas.

Roepman P, Wessels LF, Kettelarij N, Kemmeren P, Miles AJ, Lijnzaad P, Tilanus MG, Koole R, Hordijk GJ, van der Vliet PC, Reinders MJ, Slootweg PJ, Holstege FC.

Nat Genet. 2005 Feb;37(2):182-6. Epub 2005 Jan 9.

PMID:
15640797
29.

Predicting gene function through systematic analysis and quality assessment of high-throughput data.

Kemmeren P, Kockelkorn TT, Bijma T, Donders R, Holstege FC.

Bioinformatics. 2005 Apr 15;21(8):1644-52. Epub 2004 Nov 5.

PMID:
15531615
30.

Nitric oxide donor induces temporal and dose-dependent reduction of gene expression in human endothelial cells.

Braam B, de Roos R, Dijk A, Boer P, Post JA, Kemmeren PP, Holstege FC, Bluysen HA, Koomans HA.

Am J Physiol Heart Circ Physiol. 2004 Nov;287(5):H1977-86. Epub 2004 Jul 8.

31.

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.

32.

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.

33.

ArrayExpress: a public database of gene expression data at EBI.

Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M, Contrino S, Vilo J, Abeygunawardena N, Mukherjee G, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Sansone SA.

C R Biol. 2003 Oct-Nov;326(10-11):1075-8.

PMID:
14744115
34.

Integrating functional genomics data.

Kemmeren P, Holstege FC.

Biochem Soc Trans. 2003 Dec;31(Pt 6):1484-7. Review.

PMID:
14641095
35.

Monitoring global messenger RNA changes in externally controlled microarray experiments.

van de Peppel J, Kemmeren P, van Bakel H, Radonjic M, van Leenen D, Holstege FC.

EMBO Rep. 2003 Apr;4(4):387-93.

36.

A new web-based data mining tool for the identification of candidate genes for human genetic disorders.

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

Eur J Hum Genet. 2003 Jan;11(1):57-63.

37.

ArrayExpress--a public repository for microarray gene expression data at the EBI.

Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA.

Nucleic Acids Res. 2003 Jan 1;31(1):68-71.

38.

Protein interaction verification and functional annotation by integrated analysis of genome-scale data.

Kemmeren P, van Berkum NL, Vilo J, Bijma T, Donders R, Brazma A, Holstege FC.

Mol Cell. 2002 May;9(5):1133-43.

39.

Acute-phase protein haptoglobin is a cell migration factor involved in arterial restructuring.

de Kleijn DP, Smeets MB, Kemmeren PP, Lim SK, Van Middelaar BJ, Velema E, Schoneveld A, Pasterkamp G, Borst C.

FASEB J. 2002 Jul;16(9):1123-5. Epub 2002 May 21.

PMID:
12039846

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