Furlong GroupPublications
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. PubMed
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. 2012 Dec 6. PubMed
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
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. PubMed
Fragmentation of DNA in a sub-microliter microfluidic sonication device.
Tseng, Q., Lomonosov, A.M., Furlong, E.E. & Merten, C.A.
Lab Chip. 2012 Sep 26. PubMed
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. 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
Analyzing transcription factor occupancy during embryo development using ChIP-seq.
Ghavi-Helm, Y. & Furlong, E.E.
Methods Mol Biol. 2012;786:229-45. PubMed
Molecular biology: A fly in the face of genomics.
Furlong, E.E.
Nature. 2011 Mar 24;471(7339):458-9. PubMed
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. PubMed
Dynamic CRM occupancy reflects a temporal map of developmental progression.
Wilczynski, B. & Furlong, E.E.
Mol Syst Biol. 2010 Jun 22;6:383. 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 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. PubMed
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. 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
Challenges for modeling global gene regulatory networks during development: Insights from Drosophila.
Wilczynski, B. & Furlong, E.E.
Dev Biol. 2009 Oct 27. PubMed
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. 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
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. PubMed
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. PubMed
A topographical map of spatiotemporal patterns of gene expression.
Furlong, E.E.
Dev Cell. 2008 May;14(5):639-40. PubMed
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. 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
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. 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
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. PubMed
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. PubMed
Genomics and development: Taking developmental biology to new heights.
Spitz, F. & Furlong, E.E.
Dev Cell. 2006 Oct;11(4):451-7. PubMed
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. PubMed
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. PubMed
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. PubMed
A functional genomics approach to identify new regulators of Wnt signaling.
Furlong, E.E.
Dev Cell 2005 May;8(5):624-6. PubMed
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. PubMed
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. PubMed
Integrating transcriptional and signalling networks during muscle development.
Furlong, E.E.
Curr Opin Genet Dev 2004 Aug;14(4):343-50. PubMed
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. PubMed
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. PubMed
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. PubMed
Automated sorting of live transgenic embryos.
Furlong, E.E., Profitt, D. & Scott, M.P.
Nat Biotechnol 2001 Feb;19(2):153-6. PubMed
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. PubMed
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. PubMed
