Staff at EMBL

Charles Girardot

Head of Genome Biology Computational Support

EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

Publications

Analysis of variation at transcription factor binding sites in Drosophila and humans. Spivakov, M., Akhtar, J., Kheradpour, P., Beal, K., Girardot, C., Koscielny, G., Herrero, J., Kellis, M., Furlong, E.E. & Birney, E. Genome Biol. 2012 Sep 28;13(9):R49. doi: 10.1186/gb-2012-13-9-r49. PubMed

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Bonn, S., Zinzen, R.P., Girardot, C., Gustafson, E.H., Perez-Gonzalez, A., Delhomme, N., Ghavi-Helm, Y., Wilczynski, B., Riddell, A. & Furlong, E.E. Nat Genet. 2012 Jan 8;44(2):148-56. doi: 10.1038/ng.1064. PubMed

A transcription factor collective defines cardiac cell fate and reflects lineage history. Junion, G.*, Spivakov, M.*, Girardot, C., Braun, M., Gustafson, E.H., Birney, E. & Furlong, E.E. Cell. 2012 Feb 3;148(3):473-86. PubMed

Model-based method for transcription factor target identification with limited data. Honkela, A., Girardot, C., Gustafson, E.H., Liu, Y.H., Furlong, E.E., Lawrence, N.D. & Rattray, M. Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7793-8. Epub 2010 Apr 12. PubMed

Combinatorial binding predicts spatio-temporal cis-regulatory activity. Zinzen, R.P., Girardot, C., Gagneur, J., Braun, M. & Furlong, E.E. Nature. 2009 Nov 5;462(7269):65-70. PubMed

Dynamic regulation by polycomb group protein complexes controls pattern formation and the cell cycle in Drosophila. Oktaba, K., Gutierrez, L., Gagneur, J., Girardot, C., Sengupta, A.K., Furlong, E.E. & Muller, J. Dev Cell. 2008 Dec;15(6):877-89. Epub 2008 Nov 6. PubMed

4DXpress: a database for cross-species expression pattern comparisons. Haudry, Y., Berube, H., Letunic, I., Weeber, P.D., Gagneur, J., Girardot, C., Kapushesky, M., Arendt, D., Bork, P., Brazma, A., Furlong, E., Wittbrodt, J. & Henrich, T. Nucleic Acids Res. 2007 Oct 4;. PubMed

CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data. Girardot, C., Sklyar, O., Grosz, S., Huber, W. & Furlong, E.E. Bioinformatics. 2007 Mar 15;23(6):771-3. Epub 2007 Jan 17. PubMed

A core transcriptional network for early mesoderm development in Drosophila melanogaster. Sandmann, T., Girardot, C., Brehme, M., Tongprasit, W., Stolc, V. & Furlong, E.E. Genes Dev. 2007 Feb 15;21(4):436-49. PubMed

Elucidation of an archaeal replication protein network to generate enhanced PCR enzymes. Motz, M., Kober, I., Girardot, C., Loeser, E., Bauer, U., Albers, M., Moeckel, G., Minch, E., Voss, H., Kilger, C. & Koegl, M. J Biol Chem. 2002 May 3;277(18):16179-88. Epub 2002 Jan 22. PubMed