Selected Publications
2010
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
pubmed
2009
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
The EMBO Journal. 2009 Oct 7;28(19):2959-70
pubmed
Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome.
Folkert van Werven, Hetty van Teeffelen, Frank Holstege, Marc Timmers
Nature Structural and Molecular Biology. 2009 Oct;16(10):1043-8
Redox-sensitive cysteines bridge p300/CBP-mediated acetylation and FoxO4 activity.
Tobias B. Dansen, Lydia M.M. Smits, Miranda H. van Triest, Peter L.J. de Keizer, Dik van Leenen, Marian Groot Koerkamp, Anna Szypowska, Amanda Meppelink, Arjan B. Brenkman, Junji Yodoi, Frank C.P. Holstege, Boudewijn M.T. Burgering
Nature Chemical Biology. 2009 Sep;5(9):664-72
pubmed
Adaptable gene-specific dye bias correction for two-channel DNA microarrays.
Thanasis Margaritis, Philip Lijnzaad, Dik van Leenen, Diane Bouwmeester, Patrick Kemmeren, Sander R. van Hooff and Frank C.P. Holstege
Molecular Systems Biology. 2009;5:266
pubmed
R package
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
pubmed
2008
Cooperative action of NC2 and Mot1p to regulate TATA-binding protein function across the genome.
Folkert J. van Werven, Harm van Bakel, Hetty A.A.M. van Teeffelen,
Maarten A.F. Altelaar, Marian J.A. Groot Koerkamp, Albert J.R. Heck,
Frank C.P. Holstege, Marc Th.M. Timmers
Genes & Development. 2008 Sep 1;22(17):2359-69
pubmed
Mediator-dependent recruitment of TFIIH modules in preinitiation complex.
Cyril Esnault, Yad Ghavi-Helm, Sylvain Brun, Julie Soutourina, Nynke van Berkum, Claire Boschiero, Frank Holstege and Michel Werner
Molecular Cell. 2008 Aug 8;31(3):337-46
pubmed
Poised RNA polymerase II gives pause for thought.
Thanasis Margaritis and Frank C.P. Holstege
Cell. 2008 May 16;133(4)581-4
pubmed
Structure-system correlation identifies a gene regulatory Mediator submodule.
Larivière L, Seizl M, van Wageningen S, Röther S, van de Pasch L, Feldmann H, Strässer K, Hahn S, Holstege FC, Cramer P
Genes & Development. 2008 Apr 1;22(7)872-7
pubmed
A tutorial for DNA microarray expression-profiling.
Harm van Bakel and Frank C.P. Holstege
Cell Press. 2008
pubmed
2007
Critical roles for a genetic code alteration in the evolution of the genus Candida.
Raquel M. Silva, João A. Paredes, Gabriela R. Moura, Bruno Manadas, Tatiana Lima-Costa, Rita Rocha, Isabel Miranda, Ana C. Gomes, Marian J. Groot Koerkamp, Michel Perrot, Frank C.P. Holstege, Hélian Boucherie and Manuel A.S. Santos
The EMBO Journal. 2007 Oct 31;26(21):4555-65
pubmed
Towards 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
pubmed
2006
Dissection of a Metastatic Gene Expression Signature into Distinct Components.
Paul Roepman, Erica de Koning, Dik van Leenen, J. Alain Kummer, Roel A. de Weger, Piet J. Slootweg, Frank C.P. Holstege
Genome Biology. 2006 Dec 11;7(12):R117
pubmed
Maintenance of head and neck tumor gene expression profiles upon lymph node metastasis.
Paul Roepman, Alike de Jager, Marian J.A. Groot Koerkamp, J. Alain Kummer, Piet J. Slootweg, Frank C.P. Holstege
Cancer Research. 2006 Dec 1;66(23):11110-4
pubmed
Genome-wide location of the coactivator Mediator: binding without activation and transient Cdk8 interaction on DNA.
Jean-Christophe Andrau, Loes van de Pasch, Philip Lijnzaad, Theo Bijma, Marian Groot Koerkamp, Jeroen van de Peppel, Michel Werner, Frank C.P. Holstege.
Molecular Cell. 2006 Apr 21;22(2):179-92
pubmed
Multiple Robust Signatures for Detecting Lymph Node Metastasis in Head and Neck Cancer.
Roepman P, Kemmeren P, Wessels LF, Slootweg PJ, Holstege FC.
Cancer Research. 2006 Feb 15;66(4):2361-2366
pubmed
Transcription factor target practice.
Holstege FC, Clevers H.
Cell. 2006 Jan 13;124(1):21-3
pubmed
2005
Expression-profiling of the Mediator transcription complex reveals an epistatic signal-transduction pathway with antagonistic submodules and highly specific downstream targets.
J. van de Peppel, N. Kettelarij, H. van Bakel, T.T.J.P. Kockelkorn, D. van Leenen, F.C.P. Holstege
Molecular Cell. 2005 Aug 19;19(4):511-22
pubmed
Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit.
M. Radonjic, J.C. Andrau, P. Lijnzaad, P. Kemmeren, T.T.J.P. Kockelkorn, D. van Leenen, N.L. van Berkum, F.C.P. Holstege
Molecular Cell. 2005 Apr 15;18(2):171-83
pubmed
Multifunctional genes. News & Views
J. van de Peppel, F.C.P. Holstege
Molecular Systems biology. doi:10.1038/msb4100006
Tumor profiling turmoil.
P. Roepman, F.C.P. Holstege
Cell Cycle. 2005 May 22;4(5):659-660
pubmed
An expression profile for diagnosis of lymph node metastases from primary head and neck squamous cell carcinomas.
P. Roepman, L.F.A. Wessels, N. Kettelarij, P. Kemmeren, A.J. Miles, P. Lijnzaad, M.G.J. Tilanus, R. Koole, G. Hordijk, P.C. van der Vliet, M.J.T. Reinders, P.J. Slootweg, F.C.P. Holstege
Nature Genetics. 2005 Feb;37(2):182-6
pubmed
2004
Predicting gene function through systematic analysis and quality assessment of high-throughput data.
P. Kemmeren, T.T.J.P. Kockelkorn, T. Bijma, R. Donders, F.C.P. Holstege
Bioinformatics. 2004 Nov 5 doi:10.1093/bioinformatics/bti103
pubmed - supplemental website
A high resolution protein interacton map of the yeast Mediator complex.
B. Guglielmi, N.L. van Berkum, B. Klapholz, T. Bijma, M. Boube, C. Boschiero, H.M. Bourbon, F.P. Holstege, M. Werner
Nucleic Acids Research. 2004 Oct 11;32(18):5379-91.
pubmed
In control: systematic assessment of microarray performance.
H. van Bakel, F.C.P. Holstege
EMBO Reports. 2004 Oct;5(10):964-9
pubmed
A unified nomenclature for protein subunits of Mediator complexes linking transcriptional regulators to RNA polymerase II.
H.M. Bourbon, A. Aguilera, A.Z. Ansari, F.J. Asturias, A.J. Berk, S. Bjorklund, T.K. Blackwell, T. Borggrefe, M. Carey , M. Carlson, J.W. Conaway, R.C. Conaway , S.W. Emmons, J.D. Fondell, L.P. Freedman, T. Fukasawa, C.M. Gustafsson, M. Han, X. He, P.K. Herman, A.G. Hinnebusch, S. Holmberg, F.C. Holstege, J.A. Jaehning, Y.J. Kim, L. Kuras, A. Leutz, J.T. Lis, M. Meisterernest, A.M. Naar, K. Nasmyth, J.D. Parvin, M. Ptashne, D. Reinberg, H. Ronne, I. Sadowski, H. Sakurai, M. Sipiczki, P.W. Sternberg, D.J. Stillman, R. Strich, K. Struhl, J.Q. Svejstrup, S. Tuck, F. Winston, R.G. Roeder, R.D. Kornberg.
Molecular Cell. 2004 Jun 4;14(5):553-7
pubmed
2003
Monitoring global mRNA changes with externally controlled microarray experiments.
J. van de Peppel, P. Kemmeren, H. van Bakel, M. Radonjic, D. van Leenen, F.C.P. Holstege
Embo Reports 4: 387-393 (2003)
pubmed - supplemental website
ArrayExpress -- a public repository for microarray gene expression data at the EBI.
A. Brazma, H. Parkinson, U. Sarkans, M. Shojatalab, J. Vilo, N. Abeygunawardena, E. Holloway, M. Kapushesky, P. Kemmeren, G. Garcia Lara, A. Oezcimen, P. Rocca-Serra, S. Sansone
Nucleic Acids Research. 31: 68-71 (2003)
pubmed
2002
Protein interaction verification and functional annotation by integrated analysis of genome-scale data.
P. Kemmeren, N.L. van Berkum, J. Vilo, T. Bijma, R. Donders, A. Brazma, F.C.P. Holstege
Molecular Cell 9: 1133-43 (2002)
pubmed - supplemental website
2001
Minimum information about a microarray experiment (miame) - toward standards for microarray data.
A. Brazma, P. Hingamp, J. Quackenbush, G. Sherlock, P. Spellman, C. Stoeckert, J. Aach, W. Ansorge, C.A. Ball, H.C. Causton, F.C.P. Holstege, et al.
Nature Genetics 29: 365-71 (2001)
pubmed
DNA microarrays: raising the profile.
N.L. van Berkum, F.C.P. Holstege
Current Opinion Biotechnology 12(1): 48-52 (2001)
pubmed