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Full Text	Issue Date	Title	Author(s)
	2013	Transcriptome Analysis Using RNA-Seq	Hoeijmakers, W.A.M.; Bartfai, R.C.; Stunnenberg, H.
	2012	Comparioson of kuenenia genomes	Speth, D.R.; Hu, B.; Bosch, N.; Keltjens, J.; Stunnenberg, H.; Jetten, M.
	2012	ERG and FLI1 binding sites demarcate targets for aberrant epigenetic regulation by AML1-ETO in acute myeloid leukemia	Martens, J.H.A.; Mandoli, A.; Simmer, F.; Wierenga, B.-J.; Saeed, S.; Singh, A.A.; Altucci, L.; Vellenga, E.; Stunnenberg, H.G.
	2012	Uncovering Common Principles in Protein Export of Malaria Parasites	Grüring, C.; Heiber, A.; Kruse, F.; Flemming, S.; Franci, G.; Colombo, Sara F.; Fasana, E.; Schoeler, H.; Borgese, N.; Stunnenberg, Hendrik G.; Przyborski, Jude M.; Gilberger, T.-W.; Spielmann, T.
	2012	Plasmodium falciparum centromeres display a unique epigenetic makeup and cluster prior to and during schizogony	Hoeijmakers, W.A.M.; Flueck, C.; Francoijs, K.J.; Smits, A.H.; Wetzel, J.; Volz, J.C.; Cowman, A.F.; Voss, T.; Stunnenberg, H.G.; Bartfai, R.C.
	2012	Placing the Plasmodium falciparum epigenome on the map	Hoeijmakers, W.A.M.; Stunnenberg, H.G.; Bartfai, R.C.
	2012	BLUEPRINT to decode the epigenetic signature written in blood	Adams, D.; Martens, J.H.A.; Stunnenberg, H.G.; Willcocks, S.
	2012	SS18 Together with Animal-Specific Factors Defines Human BAF-Type SWI/SNF Complexes	Middeljans, E.H.; Wan, X.; Jansen, P. W.; Sharma, V.; Stunnenberg, H.G.; Logie, C.
	2012	CATCHprofiles: Clustering and Alignment Tool for ChIP Profiles	Nielsen, F. G. G.; Markus, K.G.; Friborg, R.M.; Favrholdt, L.M.; Stunnenberg, H.G.; Huynen, M.
	2012	Comparative genomics of two independently enriched “Candidatus Kuenenia stuttgartiensis” anammox bacteria	Speth, D.R.; Hu, B.; Bosch, N.; Keltjens, J.T.; Stunnenberg, H.; Jetten, M.
	2012	The human EKC/KEOPS complex is recruited to Cullin2 ubiquitin ligases by the human tumour antigen PRAME.	Costessi, A.; Mahrour, N.; Sharma, V.; Stunnenberg, R.; Stoel, M.A.; Tijchon, E.J.; Conaway, J.W.; Conaway, R.C.; Stunnenberg, H.G.
	2012	Indole-Derived Psammaplin A Analogues as Epigenetic Modulators with Multiple Inhibitory Activities	Pereira, R.; Benedetti, R.; Pérez-Rodríguez, S.; Nebbioso, A.; García-Rodríguez, J.; Carafa, V.; Stuhldreier, M.; Conte, M.; Rodríguez-Barrios, F.; Stunnenberg, H.G.; Gronemeyer, H.; Altucci, L.; Lera, Á.R. de
	2012	Chromatin accessibility, p300 and histone acetylation define PML-RARα and AML1-ETO binding sites in acute myeloid leukemia	Saeed, S.; Logie, C.; Francoijs, K.J.; Frigè, G.; Romanenghi, M.; Nielsen, F.G.; Raats, L.; Shahhoseini, M.; Huynen, M.; Altucci, L.; Minucci, S.; Martens, J.H.A.; Stunnenberg, H.G.
	2012	The chromatin remodeling complex NuRD establishes the poised state of rRNA genes characterized by bivalent histone modifications and altered nucleosome positions	Xie, W.; Ling, T.; Zhou, Y.; Feng, W.; Zhu, Q.; Stunnenberg, H.G.; Grummt, I.; Tao, W.
	2012	PfSET10, a Plasmodium falciparum Methyltransferase, Maintains the Active var Gene in a Poised State during Parasite Division	Volz, J.C.; Bartfai, R.C.; Petter, M.; Langer, C.; Josling, G.A.; Tsuboi, T.; Schwach, F.; Baum, J.; Rayner, J.C.; Stunnenberg, H.G.; Duffy, M.F.; Cowman, A.F.
	2012	Effect of oxygen on the anaerobic methanotroph 'Candidatus Methylomirabilis oxyfera': Kinetic and transcriptional analysis	Luesken, F.A.; Wu, M.L.; Camp, H.J.M. op den; Keltjens, J.T.; Stunnenberg, H.; Francoijs, K.J.; Strous, M.; Jetten, M.S.M.
	2012	Genome-Wide Profiling of Liver X Receptor, Retinoid X Receptor, and Peroxisome Proliferator-Activated Receptor alpha in Mouse Liver Reveals Extensive Sharing of Binding Sites	Boergesen, M.; Pedersen, T. A.; Gross, B.; Heeringen, S.J. van; Hagenbeek, D.; Bindesboll, C.; Caron, Sandrine; Lalloyer, F.; Steffensen, K.R.; Nebb, H.I.; Gustafsson, J.A.; Stunnenberg, H.G.; Staels, B.; Mandrup, S.
	2012	Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues	Simmer, F.; Brinkman, A.B.; Assenov, Y.; Matarese, F.; Kaan, A.; Sabatino, L.; Villanueva, A.; Huertas, D.; Esteller, M.; Lengauer, T.; Bock, C.; Colantuoni, V.; Altucci, L.; Stunnenberg, H.G.
	2012	The transcriptional and epigenomic foundations of ground state pluripotency	Marks, H.; Kalkan, T.; Smith, A.; Stunnenberg, H.G.; Menafra, R.; Denissov, S.; Jones, K.; Hofemeister, H.; Nichols, J.; Kranz, A.; Stewart, A.F.
	2012	Bacille Calmette-Guérin induces NOD2-dependent nonspecific protection from reinfection via epigenetic reprogramming of monocytes	Kleinnijenhuis, J.; Quintin, J.; Preijers, F.; Joosten, L.A.B.; Ifrim, D.C.; Saeed, S.; Jacobs, C; Loenhout, J. van; Jong, D. de; Stunnenberg, H.G.; Xavier, R.J.; Meer, J.W.M. van der; Crevel, R. van; Netea, M.G.
	2012	Draft genome sequence of the volcano-inhabiting thermoacidophilic methanotroph methylacidiphilum fumariolicum strain solv	Khadem, A.F.; Wieczorek, A.S.; Pol, A.; Vuilleumier, S.; Harhangi, H.R.; Dunfield, P.F.; Kalyuzhnaya, M.G.; Murrell, J.C.; Francoijs, K.J.; Stunnenberg, H.G.; Stein, L.Y.; DiSpirito, A.A.; Semrau, J.D.; Lajus, A.; Medigue, C.; Klotz, M.G.; Jetten, M.S.M.; Camp, H.J.M. op den
	2012	Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk	Brinkman, A.B.; Bartels, S.J.J.; Stunnenberg, H.G.; Gu, H.; Zhang, Y.; Matarese, F.; Simmer, F.; Marks, H.; Bock, C.; Gnirke, A.; Meissner, A.
	2012	The metagenome of the marine anammox bacterium 'Candidatus scalindua profunda' illustrates the versatility of this globally important nitrogen cycle bacterium	Vossenberg, J.L.C.M. van de; Woebken, D.; Maalcke, W.J.; Wessels, H.J.C.T.; Dutilh, B.E.; Kartal, B.; Janssen-Megens, E.M.; Roeselers, G.; Yan, J; Speth, D.; Gloerich, J.; Geerts, W.; Biezen, E. Van Der; Pluk, W.; Francoijs, K.J.; Russ, L.; Lam, P.; Malfatti, S.A.; Tringe, S.G.; Haaijer, S.C.M.; Camp, H.J.M. op den; Stunnenberg, H.G.; Amann, R.; Kuypers, M.M.M.; Jetten, M.S.M.
	2012	Candida albicans induces monocyte training via epigenetic reprogramming through a dectin-1-dependent pathway	Quintin, J.; Saeed, S.; Martens, J.H.A.; Giamarellos-Bourboulis, E.J.; Ifrim, D.C.; Logie, C.; Kullberg, B.J.; Joosten, L.A.B.; Xavier, R.J.; Stunnenberg, H.G.; Meer, J.W.M. van der; Netea, M.G.
	2012	Candida albicans Infection Affords Protection against Reinfection via Functional Reprogramming of Monocytes.	Quintin, J.; Saeed, S.; Martens, J.H.; Giamarellos-Bourboulis, E.J.; Ifrim, D.C.; Logie, C.; Jacobs, L.; Jansen, T.; Kullberg, B.J.; Wijmenga, C.; Joosten, L.A.B.; Xavier, R.J.; Meer, J.W.M. van der; Stunnenberg, H.G.; Netea, M.G.
	2012	Bacille Calmette-Guerin induces NOD2-dependent nonspecific protection from reinfection via epigenetic reprogramming of monocytes	Kleinnijenhuis, J.; Quintin, J.; Preyers, F.W.; Joosten, L.A.B.; Ifrim, D.C.; Saeed, S.; Jacobs, C.; Loenhout, J. van; de Jong, D.J.; Stunnenberg, H.G.; Xavier, R.J.; van der Meer, J.W.; van Crevel, R.; Netea, M.G.
	2011	Epigenome profiling of acute myeloid leukemia provides novel insight into transformation and block of differentiation	Stunnenberg, H.
	2011	The decade of the epigenomes?	Martens, J.H.A.; Stunnenberg, H.G.; Logie, C.
	2011	A model for the topology of active ribosomal RNA genes	Denissov, S.; Lessard, F.; Mayer, C.; Stefanovsky, V.; Driel, M. van; Grummt, I.; Moss, T.; Stunnenberg, H.G.
	2011	Genome-wide interplay of nuclear receptors with the epigenome	Martens, J.H.A.; Rao, N.A.S.; Stunnenberg, H.G.
	2011	Towards cracking the epigenetic code using a combination of high-throughput epigenomics and quantitative mass spectrometry-based proteomics	Stunnenberg, H.G.; Vermeulen, M.
	2011	RAD21 Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity	Nitzsche, A.; Paszkowski-Rogacz, M.; Matarese, F.; Janssen-Megens, E.M.; Hubner, N.C.; Schulz, H.; Vries, I. de; Ding, L.; Huebner, N.; Mann, M.; Stunnenberg, H.G.; Buchholz, F.
	2011	Evidence for a dynamic role of the histone variant H2A.Z in epigenetic regulation of normal/carcinoma switch	Shahhoseini, M.; Saeed, S.; Marks, H.; Stunnenberg, H.G.
	2011	Histone variant innovation in a rapidly evolving chordate lineage	Moosmann, A.; Campsteijn, C.; Jansen, P. W.; Nasrallah, C.; Raasholm, M.; Stunnenberg, H.G.; Thompson, E.M.
	2011	A SILAC-Based Screen for Methyl-CpG Binding Proteins Identifies RBP-J as a DNA Methylation and Sequence-Specific Binding Protein	Bartels, S.J.J.; Spruijt, C.G.; Brinkman, A.B.; Jansen, P.; Vermeulen, M.; Stunnenberg, H.G.
	2011	Coactivation of GR and NFKB alters the repertoire of their binding sites and target genes	Rao, N.A.S.; McCalman, M.T.; Moulos, P.; Francoijs, K.J.; Chatziioannou, A.; Kolisis, F.N.; Alexis, M.N.; Mitsiou, D. J.; Stunnenberg, H.G.
	2011	A model for the topology of active ribosomal RNA genes	Denissov, S.; Lessard, F.; Mayer, C.; Stefanovsky, V.; Driel, M. van; Grummt, I.; Moss, T.; Stunnenberg, H.G.
	2011	Linear amplification for deep sequencing	Hoeijmakers, W.A.M.; Bartfai, R.C.; Francoijs, K.J.; Stunnenberg, H.G.
	2011	Linear amplification for deep sequencing	Hoeijmakers, W.A.M.; Bartfai, R.C.; Francoijs, K.J.; Stunnenberg, H.G.
	2011	Genome-wide functions of PML-RAR alpha in acute promyelocytic leukaemia	Saeed, S.; Logie, C.; Stunnenberg, H.G.; Martens, J.H.A.
	2011	Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis	Bogdanovic, O.; Long, S.W.; Heeringen, S.J. van; Brinkman, A.B.; Gomez-Skarmeta, J.L.; Stunnenberg, H.G.; Jones, P.L.; Veenstra, G.J.C.
	2011	Role of p53 Serine 46 in p53 Target Gene Regulation	Smeenk, L.; Heeringen, S.J. van; Koeppel, M.; Gilbert, B.; Janssen-Megens, E.M.; Stunnenberg, H.G.; Lohrum, M.
	2011	Crosstalk between c-Jun and TAp73 alpha/beta contributes to the apoptosis-survival balance	Koeppel, M.; Heeringen, S.J. van; Kramer, D.; Smeenk, L.; Janssen-Megens, E.M.; Hartmann, M.; Stunnenberg, H.G.; Lohrum, M.
	2011	A Genome-wide Chromatin-associated Nuclear Peroxiredoxin from the Malaria Parasite Plasmodium falciparum	Richard, D.; Bartfai, R.C.; Volz, J.; Ralph, S.A.; Muller, S.; Stunnenberg, H.G.; Cowman, A. F.
	2011	The tumour antigen PRAME is a subunit of a Cul2 ubiquitin ligase and associates with active NFY promoters	Costessi, A.; Mahrour, N.; Tijchon, E.; Stunnenberg, R.; Stoel, M.A.; Jansen, P. W.; Sela, D.; Martin-Brown, S.; Washburn, M.P.; Florens, L.; Conaway, J.W.; Conaway, R.C.; Stunnenberg, H.G.
	2011	Coactivation of GR and NFKB alters the repertoire of their binding sites and target genes	Rao, N.A.S.; McCalman, M.T.; Moulos, P.; Francoijs, K.J.; Chatziioannou, A.; Kolisis, F.N.; Alexis, M.N.; Mitsiou, D. J.; Stunnenberg, H.G.
	2011	De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next-generation sequencing techniques	Angeloni, F.; Wagemaker, C.A.M.; Jetten, M.S.M.; Camp, H.J.M. op den; Janssen-Megens, E.M.; Francoijs, K.J.; Stunnenberg, H.G.; Ouborg, N.J.
	2011	Death receptor pathway activation and increase of ROS production by the triple epigenetic inhibitor, UVI5008	Nebbioso, A.; Pereira, R.; Khanwalkar, H.; Matarese, F.; Garcia-Rodriguez, J.; Miceli, M.; Logie, C.; Kedinger, V.; Ferrara, F.; Stunnenberg, H.G.; Lera, A.R. de; Gronemeyer, H.; Altucci, L.
	2011	Experimentally controlled downregulation of the histone chaperone FACT in Plasmodium berghei reveals that it is critical to male gamete fertility	Laurentino, E.C.; Taylor, S.; Mair, G.R.; Lasonder, E.; Bartfai, R.C.; Stunnenberg, H.G.; Kroeze, H.; Ramesar, J.; Franke-Fayard, B.; Khan, S.M.; Janse, C.J.; Waters, A.P.
	2011	An RNA-Seq Strategy to Detect the Complete Coding and Non-Coding Transcriptome Including Full-Length Imprinted Macro ncRNAs	Huang, R.; Jaritz, M.; Guenzl, P.; Vlatkovic, I.; Sommer, A.; Tamir, I.M.; Marks, H.; Klampfl, T.; Kralovics, R.; Stunnenberg, H.G.; Barlow, D. P.; Pauler, F. M.

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