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Staff at EMBL

Dr. Eileen Furlong

Head of Unit and Senior Scientist
Genome Biology Furlong Group

EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

E-mail: send a mail


PhD 1996, University College Dublin.
Postdoctoral research at Stanford University.
Group leader at EMBL since September 2002.
Senior Scientist since 2009.
Joint Head of Genome Biology Unit 2009-13.
Head of Genome Biology Unit since 2013.
ERC Advanced Investigator since 2013.
Elected EMBO Member since 2013.


Enhancer loops appear stable during development and are associated with paused polymerase. Ghavi-Helm, Y., Klein, F.A., Pakozdi, T., Ciglar, L., Noordermeer, D., Huber, W. & Furlong, E.E. Nature. 2014 Jul 2. doi: 10.1038/nature13417. Europe PMC

Coordinated repression and activation of two transcriptional programs stabilizes cell fate during myogenesis. Ciglar, L., Girardot, C., Wilczynski, B., Braun, M. & Furlong, E.E. Development. 2014 Jul;141(13):2633-43. doi: 10.1242/dev.101956. Europe PMC

Subtle changes in motif positioning cause tissue-specific effects on robustness of an enhancer's activity. Erceg, J., Saunders, T.E., Girardot, C., Devos, D.P., Hufnagel, L. & Furlong, E.E. PLoS Genet. 2014 Jan;10(1):e1004060. doi: 10.1371/journal.pgen.1004060. Epub 2014Jan 2. Europe PMC

A conserved role for Snail as a potentiator of active transcription. Rembold, M., Ciglar, L., Yanez-Cuna, J.O., Zinzen, R.P., Girardot, C., Jain, A., Welte, M.A., Stark, A., Leptin, M. & Furlong, E.E. Genes Dev. 2014 Jan 15;28(2):167-81. doi: 10.1101/gad.230953.113. Epub 2014 Jan8. Europe PMC

Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing. Zichner, T., Garfield, D.A., Rausch, T., Stutz, A.M., Cannavo, E., Braun, M., Furlong, E.E. & Korbel, J.O. Genome Res. 2013 Mar;23(3):568-79. doi: 10.1101/gr.142646.112. Epub 2012 Dec 6. Europe PMC

Logical modelling of Drosophila signalling pathways. Mbodj, A., Junion, G., Brun, C., Furlong, E.E. & Thieffry, D. Mol Biosyst. 2013 Jul 30;9(9):2248-58. doi: 10.1039/c3mb70187e. Europe PMC

Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state. Wilczynski, B., Liu, Y.H., Yeo, Z.X. & Furlong, E.E. PLoS Comput Biol. 2012 Dec;8(12):e1002798. doi: 10.1371/journal.pcbi.1002798.Epub 2012 Dec 6. Europe PMC

Fragmentation of DNA in a sub-microliter microfluidic sonication device. Tseng, Q., Lomonosov, A.M., Furlong, E.E. & Merten, C.A. Lab Chip. 2012 Nov 21;12(22):4677-82. doi: 10.1039/c2lc40595d. Europe PMC

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. Europe PMC

Transcription factors: from enhancer binding to developmental control. Spitz, F. & Furlong, E.E. Nat Rev Genet. 2012 Sep;13(9):613-26. doi: 10.1038/nrg3207. Epub 2012 Aug 7. Europe PMC

Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP. Bonn, S., Zinzen, R.P., Perez-Gonzalez, A., Riddell, A., Gavin, A.C. & Furlong, E.E. Nat Protoc. 2012 Apr 26;7(5):978-94. doi: 10.1038/nprot.2012.049. Europe PMC

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. Europe PMC

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. Europe PMC

Analyzing transcription factor occupancy during embryo development using ChIP-seq. Ghavi-Helm, Y. & Furlong, E.E. Methods Mol Biol. 2012;786:229-45. Europe PMC

Molecular biology: A fly in the face of genomics. Furlong, E.E. Nature. 2011 Mar 24;471(7339):458-9. doi: 10.1038/471458a. Europe PMC

The importance of being specified: cell fate decisions and their role in cell biology. Furlong, E.E. Mol Biol Cell. 2010 Nov 15;21(22):3797-8. doi: 10.1091/mbc.E10-05-0436. Europe PMC

Dynamic CRM occupancy reflects a temporal map of developmental progression. Wilczynski, B. & Furlong, E.E. Mol Syst Biol. 2010 Jun 22;6:383. Europe PMC

Challenges for modeling global gene regulatory networks during development: insights from Drosophila. Wilczynski, B. & Furlong, E.E. Dev Biol. 2010 Apr 15;340(2):161-9. doi: 10.1016/j.ydbio.2009.10.032. Epub 2009Oct 27. Europe PMC

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. Europe PMC

Combinatorial binding leads to diverse regulatory responses: Lmd is a tissue-specific modulator of Mef2 activity. Cunha, P.M.*, Sandmann, T.*, Gustafson, E.H., Ciglar, L., Eichenlaub, M.P. & Furlong, E.E. PLoS Genet. 2010 Jul 1;6:e1001014. Europe PMC

Conservation and divergence in developmental networks: a view from Drosophila myogenesis. Ciglar, L. & Furlong, E.E. Curr Opin Cell Biol. 2009 Dec;21(6):754-60. Epub 2009 Nov 4. Europe PMC

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. Europe PMC

A systematic analysis of Tinman function reveals Eya and JAK-STAT signaling as essential regulators of muscle development. Liu, Y.H., Jakobsen, J.S., Valentin, G., Amarantos, I., Gilmour, D.T. & Furlong, E.E. Dev Cell. 2009 Feb;16(2):280-91. Europe PMC

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. doi: 10.1016/j.devcel.2008.10.005. Epub 2008 Nov6. Europe PMC

cis-Regulatory networks during development: a view of Drosophila. Bonn, S. & Furlong, E.E. Curr Opin Genet Dev. 2008 Dec;18(6):513-20. Epub 2008 Oct 16. Europe PMC

Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis. Zinzen, R.P. & Furlong, E.E. Genome Biol. 2008 Nov 4;9(11):240. Europe PMC

A topographical map of spatiotemporal patterns of gene expression. Furlong, E.E. Dev Cell. 2008 May;14(5):639-40. Europe PMC

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.E., Wittbrodt, J. & Henrich, T. Nucleic Acids Res. 2008 Jan;36(Database issue):D847-53. Epub 2007 Oct 4. Europe PMC

Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families. Shah, P.K., Tripathi, L.P., Jensen, L.J., Gahnim, M., Mason, C., Furlong, E.E., Rodrigues, V., White, K.P., Bork, P. & Sowdhamini, R. Gene. 2008 Jan 15;407(1-2):199-215. Epub 2007 Oct 15. Europe PMC

Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network. Jakobsen, J.S., Braun, M., Astorga, J., Gustafson, E.H., Sandmann, T., Karzynski, M., Carlsson, P. & Furlong, E.E. Genes Dev. 2007 Oct 1;21(19):2448-60. Europe PMC

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. Europe PMC

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. Europe PMC

Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis. Hooper, S.D., Boue, S., Krause, R., Jensen, L.J., Mason, C.E., Ghanim, M., White, K.P., Furlong, E.E. & Bork, P. Mol Syst Biol. 2007;3:72. Epub 2007 Jan 16. Europe PMC

Mes2, a MADF-containing transcription factor essential for Drosophila development. Zimmermann, G., Furlong, E.E., Suyama, K. & Scott, M.P. Dev Dyn. 2006 Dec;235(12):3387-95. Europe PMC

Genomics and development: Taking developmental biology to new heights. Spitz, F. & Furlong, E.E. Dev Cell. 2006 Oct;11(4):451-7. Europe PMC

A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development. Sandmann, T., Jensen, L.J., Jakobsen, J.S., Karzynski, M.M., Eichenlaub, M.P., Bork, P. & Furlong, E.E. Dev Cell. 2006 Jun;10(6):797-807. Europe PMC

Developmental control of nuclear size and shape by Kugelkern and Kurzkern. Brandt, A., Papagiannouli, F., Wagner, N., Wilsch-Brauninger, M., Braun, M., Furlong, E.E., Loserth, S., Wenzl, C., Pilot, F., Vogt, N., Lecuit, T., Krohne, G. & Grosshans, J. Curr Biol. 2006 Mar 21;16(6):543-52. Epub 2006 Feb 2. Europe PMC

ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos. Sandmann, T., Jakobsen, J.S. & Furlong, E.E. Nat Protoc. 2006;1(6):2839-55. Europe PMC

A functional genomics approach to identify new regulators of Wnt signaling. Furlong, E.E. Dev Cell 2005 May;8(5):624-6. Europe PMC

Myofilin, a protein in the thick filaments of insect muscle. Qiu, F., Brendel, S., Cunha, P.M., Astola, N., Song, B., Furlong, E.E., Leonard, K.R. & Bullard, B. J Cell Sci 2005 Apr 1;118(Pt 7):1527-36. Epub 2005 Mar 15. Europe PMC

Creation of a minimal tiling path of genomic clones for Drosophila: provision of a common resource. Hollich, V., Johnson, E., Furlong, E.E., Beckmann, B., Carlson, J., Celniker, S.E. & Hoheisel, J.D. Biotechniques 2004 Aug;37(2):282-4. Europe PMC

Integrating transcriptional and signalling networks during muscle development. Furlong, E.E. Curr Opin Genet Dev 2004 Aug;14(4):343-50. Europe PMC

Obtaining a Global View of Drosophila Muscle Development. Furlong, E.E. Book chapter. In “Muscle Development in Drosophila” by Landes Bioscience Publishing, 2004.

Notch and Ras signaling pathway effector genes expressed in fusion competent and founder cells during Drosophila myogenesis. Artero, R., Furlong, E.E., Beckett, K., Scott, M.P. & Baylies, M. Development 2003 Dec;130(25):6257-72. Europe PMC

Gene expression during the life cycle of Drosophila melanogaster. Arbeitman, M.N., Furlong, E.E., Imam, F., Johnson, E., Null, B.H., Baker, B.S., Krasnow, M.A., Scott, M.P., Davis, R.W. & White, K.P. Science 2002 Sep 27;297(5590):2270-5. Europe PMC

Patterns of gene expression during Drosophila mesoderm development. Furlong, E.E., Andersen, E.C., Null, B., White, K.P. & Scott, M.P. Science 2001 Aug 31;293(5535):1629-33. Europe PMC

Automated sorting of live transgenic embryos. Furlong, E.E., Profitt, D. & Scott, M.P. Nat Biotechnol 2001 Feb;19(2):153-6. Europe PMC

Expression of a 74-kDa nuclear factor 1 (NF1) protein is induced in mouse mammary gland involution. Involution-enhanced occupation of a twin NF1 binding element in the testosterone-repressed prostate message-2/clusterin promoter. Furlong, E.E., Keon, N.K., Thornton, F.D., Rein, T. & Martin, F. J Biol Chem. 1996 Nov 22;271(47):29688-97. Europe PMC

YY1 and NF1 both activate the human p53 promoter by alternatively binding to a composite element, and YY1 and E1A cooperate to amplify p53 promoter activity. Furlong, E.E., Rein, T. & Martin, F. Mol Cell Biol. 1996 Oct;16(10):5933-45. Europe PMC