All 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
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Early host responses to avian influenza A virus are prolonged and enhanced at transcriptional level depending on maturation of the immune system.
Reemers SS, van Leenen D, Koerkamp MJ, van Haarlem D, van de Haar P, van Eden W, Vervelde L
Mol Immunol. 2010 May;47(9):1675-85
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Reduced immune reaction prevents immunopathology after challenge with avian influenza virus: A transcriptomics analysis of adjuvanted vaccines.
Reemers SS, Jansen C, Koerkamp MJ, van Haarlem D, van de Haar P, Degen WG, van Eden W, Vervelde L
Vaccine. 2010 Aug 31;28(38):6351-60
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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
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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
Gene expression profiles of progestin-induced canine mammary hyperplasia and spontaneous mammary tumors.
Rao NA, van Wolferen ME, Gracanin A, Bhatti SF, Krol M, Holstege FC, Mol JA
Journal Physiologycal Pharmacology. 2009 May;60 Suppl 1:73-84
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Tight control of MEK-ERK activation is essential in regulating proliferation, survival and cytokine production of CD34+ derived neutrophil progenitors.
Geest CR, Buitenhuis M, Groot Koerkamp MJ, Holstege FC, Vellenga E, Coffer PJ
Blood. 2009 Oct 15;114(16):3402-12
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Type I interferon receptor-independent and -dependent host transcriptional responses to mouse hepatitis coronavirus infection in vivo.
Raaben M, Groot Koerkamp MJ, Rottier PJ, de Haan CA
BMC Genomics. 2009 Aug 3;10:350
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Differential gene expression and host response profiles against avian influenza virus within the chicken lung due to anatomy and airflow.
Reemers SS, Van Haarlem DA, Groot Koerkamp MJ, Vervelde L
Journal of General Virology. 2009 Sep;90(Pt 9):2134-46
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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
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Cellular host transcriptional responses to Influenza A virus in chicken tracheal organ cultures differ from responses in in vivo infected trachea.
S. Reemers, M. Groot Koerkamp, F. Holstege, W. van Eden, L. Vervelde
Veterinary Immunology and Immunopathology. 2009 Dec 15;132(2-4):91-100
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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
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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
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High resolution genetic mapping of mammalian motor activity levels in mice.
Kas J.H. Martien, Annetrude de Mooij-van Malsen, Mariken de Krom,
Koen van Gassen, Hein van Lith, Berend Olivier, Hugo Oppelaar, Judith
Hendriks, Marina de Wit, Marjan Groot Koerkamp, Frank Holstege, Bernard
van Oost, Pierre de Graan
Genes, Brain and Behavior. 2009 Feb;8(1):13-22
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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
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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
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Improved microarray gene expression profiling of virus-infected cells after removal of viral RNA.
Raaben M, Whitley P, Bouwmeester D, Setterquist RA, Rottier PJ, de Haan CA
BMC Genomics. 2008 May 14;9(1):221
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Possible role of the innate immunity in temporal lobe epilepsy.
Koen L.I. van Gassen, Marina de Wit, Marian J.A. Grootkoerkamp,
Marije G.A. Rensen, Peter C. van Rijen, Frank C.P. Holstege, Dick
Lindhout and Pierre N.E. de Graan
Epilepsia. 2008 Jun;49(6):1055-65
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cDNA microarray profiles of canine mammary tumour cell lines reveal deregulated pathways pertaining to their phenotype.
Rao NA, van Wolferen ME, van den Ham R, van Leenen D, Groot Koerkamp MJ, Holstege FC, Mol JA
Anim Genet. 2008 Aug;39(4):333-45
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Poised RNA polymerase II gives pause for thought.
Thanasis Margaritis and Frank C.P. Holstege
Cell. 2008 May 16;133(4):581-4
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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
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A tutorial for DNA microarray expression-profiling.
Harm van Bakel and Frank C.P. Holstege
Cell Press. 2008
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On defining the dynamics of hydrophobic patches on protein surfaces.
P. Lijnzaad, K.A. Feenstra, J. Heringa, F.C.P. Holstege
Proteins: Structure, Function and Bioinformatics. 2008 Jan 10;72(1):105-114
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Improved genome-wide localization by ChIP-chip using double-round T7 RNA polymerase-based amplification.
Van Bakel, Harm, Van Werven, Folkert, Radonjic, Marijana, Brok, Mariel, Van Leenen, Dik, Holstege, Frank, Timmers, Marc
Nucleic Acids Research. 2008 Mar;36(4):e21
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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
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Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study.
Rustici G, van Bakel H, Lackner DH, Holstege F, Wijmenga C, Bahler J, Brazma A.
Genome Biology. 2007 May 3;8(5):R73
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Gene expression profiling of liver cells after copper overload in vivo and in vitro reveals new copper-regulated genes.
Muller P, van Bakel H, van de Sluis B, Holstege F, Wijmenga C, Klomp LW
J Biol Inorg Chem. 2007 May;12(4):495-507
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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 (epub 2007 Jan 2)
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Mouse hepatitis coronavirus replication induces host translational shutoff and mRNA decay, with concomitant formation of stress granules and processing bodies.
Raaben M, Koerkamp MJ, Rottier PJ, de Haan CA
Cell Microbiol. 2007 Sep 8;9(9):2218-29 (epub 2007 May 8)
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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
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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
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FOXO3A induces differentiation of BCR-ABL transformed cells through transcriptional down-regulation of ID1.
Birkenkamp KU, Essafi A, van der Vos KE, da Costa M, Hui RC, Holstege FC, Koenderman L, Lam EW, Coffer PJ.
J Biol Chem. 2006 Nov 27;
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Transcriptome-based identification of pro- and anti-oxidative 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. 2006 Oct 17
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Collagens are functional, high-affinity ligands for the inhibitory immune receptor LAIR-1.
Robert Jan Lebbink, Talitha de Ruiter, Jelle Adelmeijer, Arjan B. Brenkman, Joop M. van Helvoort, Manuel Koch, Richard W. Farndale, Ton Lisman, Arnoud Sonnenberg, Peter J. Lenting, and Linde Meyaard.
Journal of Experimental Medicine. 2006 Jun 12;203(6):1419-25
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Genexpressieprofielen en halskliermetastasen bij hoofd-halsplaveiselcelcarcinoom.
Slootweg PJ, Roepman P, Takes RP, Holstege FCP.
Ned Tijdschr Oncol. 2006 3:66-72
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
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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
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Wrestling with SUMO and bio-ontologies..
Stoeckert C, Ball C, Brazma A, Brinkman R, Causton H, Fan L, Fostel J, Fragoso G, Heiskanen M, Holstege F, Morrison N, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Sarkans U, Sherlock G, Stevens R, Taylor C, Taylor R, Whetzel P, White J..
Nat Biotechnol.. 2006 Jan;24(1):21-2; Correspondence
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Transcription factor target practice.
Holstege FC, Clevers H.
Cell. 2006 Jan 13;124(1):21-3
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2005
Differential Expression of Genes Involved in Skin Homing, Proliferation, and Apoptosis in CD4+ T Cells of Patients with Atopic Dermatitis.
Hijnen D, Nijhuis E, Bruin-Weller M, Holstege F, Koerkamp MG, Kok I, Bruijnzeel-Koomen C, Knol E
Journal of Investigative Dermatology. 2005 Dec;125(6):1149-55
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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
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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
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Gene expression profiling and phenotype analyses of S. cerevisiae inresponse to changing copper reveals six genes with new roles in copper and iron metabolism.
Van Bakel H, Strengman E, Wymenga C., Holstege F.C.,
Physiological Genomics. 2005 May 10
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Gene expression of energy and protein metabolism in hearts of hypertensive nitric oxide- or GSH-depleted mice.
Chon H, Bluyssen HA, Holstege FC, Koomans HA, Joles JA, Braam B.
European Journal of Pharmacology 2005 Apr 18;513(1-2):21-33
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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
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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
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Nitric oxide-dependent and independent transcriptional responses to high shear stress in edothelial cells.
B. Braam, R. de Roos, F. Holstege, P. Kemmeren, H. Bluyssen, J.A. Joles, H. Koomans
Hypertension, 2005 Feb 7
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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.
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In control: systematic assessment of microarray performance.
H. van Bakel, F.C.P. Holstege
EMBO Reports. 2004 Oct;5(10):964-9
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Nitric oxide donor induces temporal and dose-dependent reduction of gene expression in human edothelial cells.
B. Braam, R. de Roos R, A. Dijk, P. Boer, J.A. Post, P.P. Kemmeren, F.C. Holstege, H.A. Bluyssen, H.A. Koomans
American Journal Physiology Heart Circulatory Physiology.2004 Nov;287(5):H1977-86
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The use of external controls in microarray experiments.
J.M.L.M. van Helvoort, D. van Leenen, F.C.P. Holstege
In Genomics (P.F.R. Little, vol. ed.), from Genetics, Genomics, Proteomics and bioinformatics (J. Marsh, series ed.), Wiley & Sons Ltd, Chichester, in press
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
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A microarray screen for novel candidate genes in coeliac disease pathogenesis.
B. Diosdado, M.C. Wapenaar, L. Franke, K.J. Duran, M.J. Goerres, M. Hadithi, J.B.A. Crusius, J.W.R. Meijer, D.J. Duggan, C.J.J. Mulder, F.C.P. Holstege, C. Wijmenga
Gut. 2004 Jul;53(7):944-51
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Regulation of gene expression by dietary Ca2+ in kidneys of 25-hydroxyvitamin D3-1a-hydroxylase knockout mice.
J.G.J. Hoenderop, H. Chon, D. Gkika, H.A.R. Bluyssen, F.C.P. Holstege, R. St-Arnaud, B. Braam, R.J.M. Bindels
Kidney International. 65:531-539 (2004)
pubmed - supplemental data
Fibronectin is a hypoxia-independent target of the tumor suppressor VHL.
H.A.R. Bluyssen, M.P.J.K. Lolkema, M. van Beest, M. Boone, C.M.J.T. Snijckers, M. Los, M.F.B.G. Gebbink, B. Braam, F.C.P. Holstege, R.H. Giles, E.E. Voest
FEBS letters 556(1-3):137-42 (2004)
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2003
Integrating functional genomics data.
P. Kemmeren, F.C.P. Holstege
Biochemical Society Transactions. 31: 1484-87 (2003)
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Broadly altered gene expression in blood leukocytes in essential hypertension is absent during treatment.
H. Chon, C.A. Gaillard, B.B. van der Meijden, H.M. Dijstelbloem, R.J. Kraaijenhagen, D. van Leenen, F.C. Holstege, J.A. Joles, H.A. Bluyssen, H.A. Koomans, B. Braam
Hypertension. 2004 May;43(5):947-51. Epub 2004 Mar 08
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Regulation of gene expression by dietary Ca2+ in kidneys of 25-hydroxyvitamin D3-1 alpha-hydroxylase knockout mice.
J.G. Hoenderop, H. Chon, D. Gkika, H.A. Bluyssen, F.C. Holstege, R. St-Arnaud, B. Braam, R.J. Bindels
Kidney International. 2004 Feb;65(2):531-9
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Specific inhibition of gene expression using a stably integrated, inducible siRNA vector.
M. van de Wetering, I. Orving, V. Muncan, M. Tjon Pon Fong, H. Brantjes, D. van Leenen, F.C.P. Holstege, T.R. Brummelkamp, R. Agami, H. Clevers
Embo Reports 4(6): 609-15 (2003)
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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)
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2002
MOT1 is essential for TBP recruitment to selected promoters during in vivo gene activation.
J. Andrau, C.J.C. van Oevelen, H.A.A.M. van Teeffelen, A. Weil, F.C.P. Holstege, M.H.Th. Timmers
Embo Journal. 21: 5173-83 (2002)
pubmed - supplemental data
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)
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DNA microarrays: raising the profile.
N.L. van Berkum, F.C.P. Holstege
Current Opinion Biotechnology 12(1): 48-52 (2001)
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