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Publications
All supplementary data is available in the Download section2009
Robert P. Zinzen*, Charles Girardot*, Julien Gagneur*, Martina Braun and Eileen E. M. Furlong.
Combinatorial binding predicts spatio-temporal cis-regulatory activity.
Nature 462, 65-70 (5 November 2009).
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*Co-first authors, reverse alphabetical order
Research highlight in Molecular Systems biology. Nov 2009. 5 Article 329
Research highlight in Nature Biotechnology. ChIPs and regulatory bits (Feb 2010)
Lucia Ciglar and Eileen EM Furlong. Conservation and divergence in developmental networks: a view from Drosophila myogenesis. Curr Opin Cell Biol. Curr Opin Cell Biol. 2009 Nov 4. ( Abstract )
Wilczynski B and Furlong EE. Challenges for modeling global gene regulatory networks during development: Insights from Drosophila. Dev Biol. 2009 Oct 27. ( Abstract )
Ya-Hsin Liu, Janus S. Jakobsen, Guillaume Valentin, Ioannis Amarantos, Darren T. Gilmour and Eileen E.M. Furlong. A Systematic Analysis of Tinman Function Reveals Eya and JAK-STAT Signaling as Essential Regulators of Muscle Development. Developmental Cell. 2009 Feb 17; 16(2):280-291. ( Abstract )
2008
Zinzen RP, Furlong EE. Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis. Genome Biol. 2008 Nov 4;9(11):240. ( Abstract )
Oktaba K, Gutierrez L, Gagneur J, Girardot C, Sengupta AK, Furlong EE, Mueller J. Dynamic Regulation by Polycomb Group Protein Complexes Controls Pattern Formation and the Cell Cycle in Drosophila. Dev Cell. 2008 Nov 5. ( Abstract )
Bonn S, Furlong EE. cis-Regulatory networks during development: a view of Drosophila. Curr Opin Genet Dev. 2008 Oct 16. ( Abstract )
Furlong EE. A topographical map of spatiotemporal patterns of gene expression. Dev Cell. 2008 May;14(5):639-40. ( Abstract )
Shah PK, Tripathi LP, Jensen LJ, Gahnim M, Mason C, Furlong EE, Rodrigues V, White KP, Bork P, Sowdhamini R. Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families. Gene. 2008 Jan 15;407(1-2):199-215. Epub 2007 Oct 15. ( Abstract )
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 . 4DXpress: a database for cross-species expression pattern comparisons. Nucleic Acids Research. 2008 Jan; 36(Database issue):D847-D853. Epub Oct 4, 2007 doi: 10.1093/nar/gkm797 ( Abstract )
2007
Jakobsen JS, Braun M, Astorga J, Gustafson EH, Sandmann T, Karzynski M, Carlsson P, and Furlong EE . Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network. Genes & Development. 2007 Oct 3; 21: 2448-2460. ( Abstract )
Sandmann T, Girardot C, Brehme M, Tongprasit W, Stolc V, and Furlong EE . A core transcriptional network for early mesoderm development in Drosophila melanogaster. Genes & Development. 2007 Feb 15;21: 436-449. ( Abstract )
Research highlight in Nature Reviews Genetics. April 2007, pg 249
Girardot C, Sklyar O, Grosz S, Huber W, Furlong EE CoCo: A web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data. Bioinformatics. 2007 23: 771-773 ( Abstract )
Hooper SD, Boue S, Krause R, Jensen LJ, Mason CE, Ghanim M, White KP, Furlong EE, Bork P . Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis. Mol Syst Biol. 2007;3:72. Epub 2007 Jan 16. ( Abstract )
Sandmann T, Jakobsen JS and Furlong EE. ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos. Nature Prot Jan1(6): 2839-2855 ( Abstract )
2006
Spitz F, Furlong EE .Genomics and development: Taking developmental biology to new heights. Dev Cell. 2006 Oct;11(4):451-7. ( Abstract )
Zimmermann G, Furlong EE, Suyama K, Scott MP . Mes2, a MADF-containing transcription factor essential for Drosophila development. Dev Dyn. Dec 2006;235(12):3387-95. ( Abstract )
Sandmann T, Jensen LJ, Jakobsen JS, Karzynski MM, Eichenlaub MP, Bork P, Furlong EE . A temporal map of transcription factor activity: Mef2 directly regulates target genes at all stages of muscle development Dev Cell, June 2006; 10(6): 797-807. ( PDF, Abstract )
2005
Furlong, EE. A functional genomics approach to identify new regulators of Wnt signaling. Dev Cell, May 2005; 8(5): 624-6. ( PDF, Abstract )
Furlong, EE. Obtaining a Global View of Drosophila Muscle Development. Book chapter. In “Muscle Development in Drosophila.” Edited by Helen Sink, Landes Bioscience Publishing.
Qiu F, Brendel S, Cunha PM, Astola N, Song B, Furlong EE, Leonard KR, Bullard B. Myofilin, a protein in the thick filaments of insect muscle. J Cell Sci,2005 Apr 1;118 (Pt 7): 1527-36. ( PDF, Abstract )
2004
Furlong, EE. Integrating transcriptional and signalling networks during muscle development. Curr Opin Genet Dev, Aug 2004; 14(4): 343-50. ( PDF, Abstract )
Hollich V, Johnson E, Furlong EE, Beckmann B, Carlson J, Celniker SE, Hoheisel JD. Creation of a minimal tiling path of genomic clones for Drosophila: provision of a common resource. Biotechniques, 2004 Aug; 37(2): 282-4. ( PDF, Abstract )
2003
Artero R*, Furlong EE*, Beckett K, Scott MP, Baylies M.
Notch and Ras signaling pathway effector genes expressed in fusion competent and founder cells during Drosophila myogenesis.
Development, Dec 2003;130(25): 6257-72
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* Co-first authors, listed alphabetically
2002
Arbeitman MN*, Furlong EE*, Imam F*, Johnson E*, Null BH*, Baker BS, Krasnow MA, Scott MP, Davis RW and White KP.
Gene expression during the life cycle of Drosophila melanogaster. Science, 2002 Sep 27; 297(5590): 2270-5.
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* Co-first authors, listed alphabetically
2001
Furlong EE, Andersen EC, Null B, White KP and Scott MP. Patterns of gene expression during Drosophila mesoderm development. Science, 2001 Aug 31; 293(5535): 1629-33. ( PDF, Abstract )
Furlong EE, Profitt D and Scott MP. Automated Sorting of Live Transgenic Embryos. Nature Biotechnology, Feb 2001; 19(2): 153-6. ( PDF, Abstract )
