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Staff at EMBL

CP-60002540

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

Biography

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.

Publications

Total: 50 publication(s)

2014

Ghavi-Helm Y, Klein FA, Pakozdi T, Ciglar L, Noordermeer D, Huber W, Furlong EE. (2014)
Enhancer loops appear stable during development and are associated with paused polymerase
Nature doi:10.1038/nature13417
Europe PMC | doi

Ciglar L, Girardot C, Wilczyński B, Braun M, Furlong EE. (2014)
Coordinated repression and activation of two transcriptional programs stabilizes cell fate during myogenesis
Development 141(13):2633-2643. doi:10.1242/dev.101956
Europe PMC | doi

Rembold M, Ciglar L, Yáñez-Cuna JO, Zinzen RP, Girardot C, Jain A, Welte MA, Stark A, Leptin M, Furlong EE. (2014)
A conserved role for Snail as a potentiator of active transcription
Genes Dev. 28(2):167-181. doi:10.1101/gad.230953.113
Europe PMC | doi

Erceg J, Saunders TE, Girardot C, Devos DP, Hufnagel L, Furlong EE. (2014)
Subtle changes in motif positioning cause tissue-specific effects on robustness of an enhancer's activity
PLoS Genet. 10(1):e1004060. doi:10.1371/journal.pgen.1004060
Europe PMC | doi


2013

Mbodj A, Junion G, Brun C, Furlong EE, Thieffry D. (2013)
Logical modelling of Drosophila signalling pathways
Mol Biosyst 9(9):2248-2258. doi:10.1039/c3mb70187e
Europe PMC | doi

Zichner T, Garfield DA, Rausch T, Stütz AM, Cannavó E, Braun M, Furlong EE, Korbel JO. (2013)
Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing
Genome Res. 23(3):568-579. doi:10.1101/gr.142646.112
Europe PMC | doi


2012

Tseng Q, Lomonosov AM, Furlong EE, Merten CA. (2012)
Fragmentation of DNA in a sub-microliter microfluidic sonication device
Lab Chip 12(22):4677-4682. doi:10.1039/c2lc40595d
Europe PMC | doi

Delhomme N, Padioleau I, Furlong EE, Steinmetz LM. (2012)
easyRNASeq: a bioconductor package for processing RNA-Seq data
Bioinformatics 28(19):2532-2533. doi:10.1093/bioinformatics/bts477
Europe PMC | doi

Spitz F, Furlong EE. (2012)
Transcription factors: from enhancer binding to developmental control
Nat. Rev. Genet. 13(9):613-626. doi:10.1038/nrg3207
Europe PMC | doi

Bonn S, Zinzen RP, Perez-Gonzalez A, Riddell A, Gavin AC, Furlong EE. (2012)
Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP
Nat Protoc 7(5):978-994. doi:10.1038/nprot.2012.049
Europe PMC | doi

Junion G, Spivakov M, Girardot C, Braun M, Gustafson EH, Birney E, Furlong EE. (2012)
A transcription factor collective defines cardiac cell fate and reflects lineage history
Cell 148(3):473-486. doi:10.1016/j.cell.2012.01.030
Europe PMC | doi

Bonn S, Zinzen RP, Girardot C, Gustafson EH, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, Wilczyński B, Riddell A, Furlong EE. (2012)
Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development
Nat. Genet. 44(2):148-156. doi:10.1038/ng.1064
Europe PMC | doi

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

Ghavi-Helm Y, Furlong EE. (2012)
Analyzing transcription factor occupancy during embryo development using ChIP-seq
Methods Mol. Biol. 786:229-245. doi:10.1007/978-1-61779-292-2_14
Europe PMC | doi

Wilczynski B, Liu YH, Yeo ZX, Furlong EE. (2012)
Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state
PLoS Comput. Biol. 8(12):e1002798. doi:10.1371/journal.pcbi.1002798
Europe PMC | doi


2011

Furlong EE. (2011)
Molecular biology: A fly in the face of genomics
Nature 471(7339):458-459. doi:10.1038/471458a
Europe PMC | doi


2010

Furlong EE. (2010)
The importance of being specified: cell fate decisions and their role in cell biology
Mol. Biol. Cell 21(22):3797-3798. doi:10.1091/mbc.e10-05-0436
Europe PMC | doi

Cunha PM, Sandmann T, Gustafson EH, Ciglar L, Eichenlaub MP, Furlong EE. (2010)
Combinatorial binding leads to diverse regulatory responses: Lmd is a tissue-specific modulator of Mef2 activity
PLoS Genet. 6(7):e1001014. doi:10.1371/journal.pgen.1001014
Europe PMC | doi

Wilczyński B, Furlong EE. (2010)
Dynamic CRM occupancy reflects a temporal map of developmental progression
Mol. Syst. Biol. 6:383. doi:10.1038/msb.2010.35
Europe PMC | doi

Wilczynski B, Furlong EE. (2010)
Challenges for modeling global gene regulatory networks during development: insights from Drosophila
Dev. Biol. 340(2):161-169. doi:10.1016/j.ydbio.2009.10.032
Europe PMC | doi

Honkela A, Girardot C, Gustafson EH, Liu YH, Furlong EE, Lawrence ND, Rattray M. (2010)
Model-based method for transcription factor target identification with limited data
Proc. Natl. Acad. Sci. U.S.A. 107(17):7793-7798. doi:10.1073/pnas.0914285107
Europe PMC | doi


2009

Ciglar L, Furlong EE. (2009)
Conservation and divergence in developmental networks: a view from Drosophila myogenesis
Curr. Opin. Cell Biol. 21(6):754-760. doi:10.1016/j.ceb.2009.10.001
Europe PMC | doi

Zinzen RP, Girardot C, Gagneur J, Braun M, Furlong EE. (2009)
Combinatorial binding predicts spatio-temporal cis-regulatory activity
Nature 462(7269):65-70. doi:10.1038/nature08531
Europe PMC | doi

Liu YH, Jakobsen JS, Valentin G, Amarantos I, Gilmour DT, Furlong EE. (2009)
A systematic analysis of Tinman function reveals Eya and JAK-STAT signaling as essential regulators of muscle development
Dev. Cell 16(2):280-291. doi:10.1016/j.devcel.2009.01.006
Europe PMC | doi


2008

Bonn S, Furlong EE. (2008)
cis-Regulatory networks during development: a view of Drosophila
Curr. Opin. Genet. Dev. 18(6):513-520. doi:10.1016/j.gde.2008.09.005
Europe PMC | doi

Oktaba K, Gutiérrez L, Gagneur J, Girardot C, Sengupta AK, Furlong EE, Müller J. (2008)
Dynamic regulation by polycomb group protein complexes controls pattern formation and the cell cycle in Drosophila
Dev. Cell 15(6):877-889. doi:10.1016/j.devcel.2008.10.005
Europe PMC | doi

Furlong EE. (2008)
A topographical map of spatiotemporal patterns of gene expression
Dev. Cell 14(5):639-640. doi:10.1016/j.devcel.2008.04.007
Europe PMC | doi

Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T. (2008)
4DXpress: a database for cross-species expression pattern comparisons
Nucleic Acids Res. 36(Database issue):D847-53. doi:10.1093/nar/gkm797
Europe PMC | doi

Zinzen RP, Furlong EE. (2008)
Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis
Genome Biol. 9(11):240. doi:10.1186/gb-2008-9-11-240
Europe PMC | doi

Shah PK, Tripathi LP, Jensen LJ, Gahnim M, Mason C, Furlong EE, Rodrigues V, White KP, Bork P, Sowdhamini R. (2008)
Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families
Gene 407(1-2):199-215. doi:10.1016/j.gene.2007.10.012
Europe PMC | doi


2007

Jakobsen JS, Braun M, Astorga J, Gustafson EH, Sandmann T, Karzynski M, Carlsson P, Furlong EE. (2007)
Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network
Genes Dev. 21(19):2448-2460. doi:10.1101/gad.437607
Europe PMC | doi

Girardot C, Sklyar O, Grosz S, Huber W, Furlong EE. (2007)
CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data
Bioinformatics 23(6):771-773. doi:10.1093/bioinformatics/btl641
Europe PMC | doi

Sandmann T, Girardot C, Brehme M, Tongprasit W, Stolc V, Furlong EE. (2007)
A core transcriptional network for early mesoderm development in Drosophila melanogaster
Genes Dev. 21(4):436-449. doi:10.1101/gad.1509007
Europe PMC | doi

Hooper SD, Boué S, Krause R, Jensen LJ, Mason CE, Ghanim M, White KP, Furlong EE, Bork P. (2007)
Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis
Mol. Syst. Biol. 3:72. doi:10.1038/msb4100112
Europe PMC | doi


2006

Zimmermann G, Furlong EE, Suyama K, Scott MP. (2006)
Mes2, a MADF-containing transcription factor essential for Drosophila development
Dev. Dyn. 235(12):3387-3395. doi:10.1002/dvdy.20970
Europe PMC | doi

Spitz F, Furlong EE. (2006)
Genomics and development: Taking developmental biology to new heights
Dev. Cell 11(4):451-457. doi:10.1016/j.devcel.2006.09.013
Europe PMC | doi

Sandmann T, Jensen LJ, Jakobsen JS, Karzynski MM, Eichenlaub MP, Bork P, Furlong EE. (2006)
A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development
Dev. Cell 10(6):797-807. doi:10.1016/j.devcel.2006.04.009
Europe PMC | doi

Brandt A, Papagiannouli F, Wagner N, Wilsch-Bräuninger M, Braun M, Furlong EE, Loserth S, Wenzl C, Pilot F, Vogt N, Lecuit T, Krohne G, Grosshans J. (2006)
Developmental control of nuclear size and shape by Kugelkern and Kurzkern
Curr. Biol. 16(6):543-552. doi:10.1016/j.cub.2006.01.051
Europe PMC | doi

Sandmann T, Jakobsen JS, Furlong EE. (2006)
ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos
Nat Protoc 1(6):2839-2855. doi:10.1038/nprot.2006.383
Europe PMC | doi


2005

Furlong EE. (2005)
A functional genomics approach to identify new regulators of Wnt signaling
Dev. Cell 8(5):624-626. doi:10.1016/j.devcel.2005.04.006
Europe PMC | doi

Qiu F, Brendel S, Cunha PM, Astola N, Song B, Furlong EE, Leonard KR, Bullard B. (2005)
Myofilin, a protein in the thick filaments of insect muscle
J. Cell. Sci. 118(Pt 7):1527-1536. doi:10.1242/jcs.02281
Europe PMC | doi


2004

Hollich V, Johnson E, Furlong EE, Beckmann B, Carlson J, Celniker SE, Hoheisel JD. (2004)
Creation of a minimal tiling path of genomic clones for Drosophila: provision of a common resource
BioTechniques 37(2):282-284. doi:10.2144/3702A0282
Europe PMC | doi

Furlong EE. (2004)
Integrating transcriptional and signalling networks during muscle development
Curr. Opin. Genet. Dev. 14(4):343-350. doi:10.1016/j.gde.2004.06.011
Europe PMC | doi

Furlong EE. (2004)
Whole Genome Approaches to Studying Drosophila Muscle Development
In: Sink H (ed.), Muscle Development in Drosophila. Molecular Biology Intelligence Unit. Springer, New York. pp 157-168.Muscle Development in Drosophila 157-168. doi:10.1007/0-387-32963-3_13
doi


2003

Artero R, Furlong EE, Beckett K, Scott MP, Baylies M. (2003)
Notch and Ras signaling pathway effector genes expressed in fusion competent and founder cells during Drosophila myogenesis
Development 130(25):6257-6272. doi:10.1242/dev.00843
Europe PMC | doi


2002

Arbeitman MN, Furlong EE, Imam F, Johnson E, Null BH, Baker BS, Krasnow MA, Scott MP, Davis RW, White KP. (2002)
Gene expression during the life cycle of Drosophila melanogaster
Science 297(5590):2270-2275. doi:10.1126/science.1072152
Europe PMC | doi


2001

Furlong EE, Andersen EC, Null B, White KP, Scott MP. (2001)
Patterns of gene expression during Drosophila mesoderm development
Science 293(5535):1629-1633. doi:10.1126/science.1062660
Europe PMC | doi

Furlong EE, Profitt D, Scott MP. (2001)
Automated sorting of live transgenic embryos
Nat. Biotechnol. 19(2):153-156. doi:10.1038/84422
Europe PMC | doi


1996

Furlong EE, Keon NK, Thornton FD, Rein T, Martin F. (1996)
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
J. Biol. Chem. 271(47):29688-29697. doi:10.1074/jbc.271.47.29688
Europe PMC | doi

Furlong EE, Rein T, Martin F. (1996)
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
Mol. Cell. Biol. 16(10):5933-5945.
Europe PMC