SyBoSS - Systems Biology of Stem Cells and Reprogramming

Supported by the EU Seventh Research Framework Programme (FP7).

SyBoSS funded publications

Publications from the lab of Francis Stewart

Bird AW, Erler A, Fu J, Hériché J-K, Maresca M, Zhang Y, Hyman AA and Stewart AF. (2012) High efficiency counterselection recombineering for site-directed mutagenesis in bacterial artificial chromosomes. Nature Methods, 9, 103-109.


Marks H, Denissov S, Menafra R, Kalkan T, Jones K, Hofemeister H, Nichols J, Kranz A, Stewart AF, Smith A and Stunnenberg H. The permissive epigenomic landscape of naïve pluripotency (2012) Cell, 149, 590-604.

Publications from the Choudhary lab


Global phosphoproteome profiling reveals unanticipated networks responsive to cisplatin treatment of embryonic stem cells. Pines A, Kelstrup CD, Vrouwe MG, Puigvert JC, Typas D, Misovic B, de Groot A, von Stechow L, van de Water B, Danen EH, Vrieling H, Mullenders LH, Olsen JV. Mol Cell Biol. 2011 Dec;31(24):4964-77.


A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C. Mol Cell Proteomics. 2011 Oct;10(10):M111.013284.


Publications from Andreas Beyer's lab


Davey, N. E.; Van Roey, K.; Weatheritt, R. J.; Toedt, G.; Uyar, B.; Altenberg, B.; Budd, A.; Diella, F. et al. (2012). "Attributes of short linear motifs". Molecular BioSystems. PMID 21909575.

Elefsinioti A, Saraç ÖS, Hegele A, Plake C, Hubner NC, Poser I, Sarov M, Hyman A, Mann M, Schroeder M, Stelzl U, Beyer A. (2011) 

“Large-scale de novo prediction of physical protein-protein association.” Mol Cell Proteomics. 10(11):M111.010629.

Publications from Frank Grosveld's lab

doi: 10.1038/emboj.2011.450

EMBO J. 2011 Dec 13;31(4):986-99. doi: 10.1038/emboj.2011.450.

Dynamic long-range chromatin interactions control Myb protooncogene transcription during erythroid development


Genome-wide analysis shows that Ldb1 controls essential hematopoietic genes/pathways in mouse early development and reveals novel players in hematopoiesis Running title: The role of Ldb1 in hemangioblast development Athina Mylona, Charlotte Andrieu-Soler, Supat Thongjuea, Andrea Martella, Eric Soler, Ruud Jorna, Jun Hou, Christel Kockx, Wilfred van Ijcken, Boris Lenhard and Frank Grosveld

Blood (in press)

Publications from the Mann lab

K. T. G. Rigbolt, T. A. Prokhorova, V. Akimov, J. Henningsen, P. T. Johansen, I. Kratchmarova, M. Kassem, M. Mann, J. V. Olsen and B. Blagoev. (2011) System-Wide Temporal Characterization of the Proteome and Phosphoproteome of Human Embryonic Stem Cell Differentiation. Sci. Signal. 4, rs3.

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