Publications

Promoter shape varies across populations and impacts promoter evolution and expression noise.

Schor IE, Degner JF, Harnett D, Cannavo E, Casale FP, Shim H, Garfield D, Birney E, Stephens M, Stegle O, Furlong EE (2017)

Nature Genetics 2017 Feb 13. doi: 10.1038/ng.3791 | Europe PMC | doi

Co-corresponding authors

Genetic variants regulating expression levels and isoform diversity during embryogenesis

Cannavò E*, Koelling N*, Harnett D, Garfield D, Casale FP, Ciglar L, Gustafson HE, Viales RR, Marco-Ferreres R, Degner JF, Zhao B, Stegle O, Birney E, Furlong EE (2016)

Nature 541(7637):402-406. doi: 10.1038/nature20802 | Europe PMC | doi

* These authors contributed equally to this work.

Co-corresponding authors

Identification and in silico modeling of enhancers reveals new features of the cardiac differentiation network

Seyres D, Ghavi-Helm Y*, Junion G*, Taghli-Lamallem O, Guichard C, Röder L, Girardot C, Furlong EE and Perrin L (2016)

Development 143(23):4533-4542. doi: 10.1242/dev.140822 | Europe PMC | doi

* These authors contributed equally to this work.

Co-corresponding authors

Chromatin Immunoprecipitation for Analyzing Transcription Factor Binding and Histone Modifications in Drosophila.

Ghavi-Helm Y, Zhao B, Furlong EE (2016)

Methods Mol. Biol. 1478:263-277. doi: 10.1007/978-1-4939-6371-3_16 | Europe PMC | doi

Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers.

Girardot C, Scholtalbers J, Sauer S, Su SY, Furlong EE (2016)

BMC Bioinformatics 17(1) doi: 10.1186/s12859-016-1284-2 | Europe PMC | doi

Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes.

Mbodj A, Gustafson EH, Ciglar L, Junion G, Gonzalez A, Girardot C, Perrin L, Furlong EE, Thieffry D (2016)

PLoS Comput. Biol. 12(9) doi: 10.1371/journal.pcbi.1005073 | Europe PMC | doi

Co-corresponding authors

Next-generation sequencing-based detection of germline L1-mediated transductions.

Tica J*, Lee E*, Untergasser A, Meiers S, Garfield DA, Gokcumen O, Furlong EE, Park PJ, Stütz AM*,‡, Korbel JO*,‡ (2016)

BMC Genomics 17(1) doi: 10.1186/s12864-016-2670-x | Europe PMC | doi

* These authors contributed equally to this work.

Co-corresponding authors

Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks.

Cannavò E, Khoueiry P, Garfield DA, Geeleher P, Zichner T, Gustafson EH, Ciglar L, Korbel JO, Furlong EE (2016)

Curr. Biol. 26(1):38-51. doi: 10.1016/j.cub.2015.11.034 | Europe PMC | doi

FourCSeq: Analysis of 4C sequencing data.

Klein FA, Pakozdi T, Anders S, Ghavi-Helm Y, Furlong EE, Huber W (2015)

Bioinformatics 31(19):3085-3091. doi: 10.1093/bioinformatics/btv335 | Europe PMC | doi

Conservation of transcription factor binding specificities across 600 million years of bilateria evolution.

Nitta KR, Jolma A, Yin Y, Morgunova E, Kivioja T, Akhtar J, Hens K, Toivonen J, Deplancke B, Furlong EE, Taipale J (2015)

Elife 4 doi: 10.7554/elife.04837 | Europe PMC | doi

Ultrasensitive proteome analysis using paramagnetic bead technology.

Hughes CS, Foehr S, Garfield DA, Furlong EE, Steinmetz LM, Krijgsveld J (2014)

Mol. Syst. Biol. 10(10) doi: 10.15252/msb.20145625 | Europe PMC | doi

Enhancer loops appear stable during development and are associated with paused polymerase

Ghavi-Helm Y, Klein FA, Pakozdi T, Ciglar L, Noordermeer D, Huber W, Furlong EE (2014)

Nature 512(7512):96-100. doi: 10.1038/nature13417 | Europe PMC | doi

Coordinated repression and activation of two transcriptional programs stabilizes cell fate during myogenesis

Ciglar L, Girardot C, Wilczyński B, Braun M, Furlong EE (2014)

Development 141:2633-2643. doi: 10.1242/dev.101956 | Europe PMC | doi

Subtle changes in motif positioning cause tissue-specific effects on robustness of an enhancer’s activity

Erceg J, Saunders TE, Girardot C, Devos DP, Hufnagel L, Furlong EE (2014)

PLoS Genet. 10(1):e1004060. doi: 10.1371/journal.pgen.1004060 | Europe PMC | doi

A conserved role for Snail as a potentiator of active transcription

Rembold M*, Ciglar L*, Yáñez-Cuna JO, Zinzen RP, Girardot C, Jain A, Welte MA, Stark A, Leptin M, Furlong EE (2014)

Genes Dev. 28:167-181. doi: 10.1101/gad.230953.113 | Europe PMC | doi

* These authors contributed equally to this work.

Co-corresponding authors

Logical modelling of Drosophila signalling pathways

Mbodj A, Junion G, Brun C, Furlong EE, Thieffry D (2013)

Mol Biosyst 9(9):2248-2258. doi: 10.1039/c3mb70187e | Europe PMC | doi

Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing

Zichner T, Garfield DA, Rausch T, Stütz AM, Cannavó E, Braun M, Furlong EE, Korbel JO (2013)

Genome Res. 23(3):568-579. doi: 10.1101/gr.142646.112 | Europe PMC | doi

Fragmentation of DNA in a sub-microliter microfluidic sonication device

Tseng Q, Lomonosov AM, Furlong EE, Merten CA (2012)

Lab Chip 12(22):4677-4682. doi: 10.1039/c2lc40595d | Europe PMC | doi

easyRNASeq: a bioconductor package for processing RNA-Seq data

Delhomme N, Padioleau I, Furlong EE, Steinmetz LM (2012)

Bioinformatics 28(19):2532-2533. doi: 10.1093/bioinformatics/bts477 | Europe PMC | doi

Transcription factors: from enhancer binding to developmental control

Spitz F, Furlong EE (2012)

Nat. Rev. Genet. 13(9):613-626. doi: 10.1038/nrg3207 | Europe PMC | doi

Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP

Bonn S, Zinzen RP, Perez-Gonzalez A, Riddell A, Gavin AC, Furlong EE (2012)

Nat Protoc 7(5):978-994. doi: 10.1038/nprot.2012.049 | Europe PMC | doi

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

Bonn S*, Zinzen RP*, Girardot C*, Gustafson EH, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, Wilczyński B, Riddell A, Furlong EE (2012)

Nat. Genet. 44(2):148-156. doi: 10.1038/ng.1064 | Europe PMC | doi

* These authors contributed equally to this work.

A transcription factor collective defines cardiac cell fate and reflects lineage history

Junion G*, Spivakov M*, Girardot C, Braun M, Gustafson EH, Birney E, Furlong EE (2012)

Cell 148(3):473-486. doi: 10.1016/j.cell.2012.01.030 | Europe PMC | doi

* These authors contributed equally to this work.

Analyzing transcription factor occupancy during embryo development using ChIP-seq

Ghavi-Helm Y, Furlong EE (2012)

Methods Mol. Biol. 786:229-245. doi: 10.1007/978-1-61779-292-2_14 | Europe PMC | doi

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 EE, Birney E (2012)

Genome Biol. 13(9):R49. doi: 10.1186/gb-2012-13-9-r49 | Europe PMC | doi

Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state

Wilczyński B, Liu YH, Yeo ZX, Furlong EE (2012)

PLoS Comput. Biol. 8(12):e1002798. doi: 10.1371/journal.pcbi.1002798 | Europe PMC | doi

Molecular biology: A fly in the face of genomics

Furlong EE (2011)

Nature 471(7339):458-459. doi: 10.1038/471458a | Europe PMC | doi

The importance of being specified: cell fate decisions and their role in cell biology

Furlong EE (2010)

Mol. Biol. Cell 21(22):3797-3798. doi: 10.1091/mbc.e10-05-0436 | Europe PMC | doi

Combinatorial binding leads to diverse regulatory responses: Lmd is a tissue-specific modulator of Mef2 activity

Cunha PM*, Sandmann T*, Gustafson EH, Ciglar L, Eichenlaub MP, Furlong EE (2010)

PLoS Genet. 6(7):e1001014. doi: 10.1371/journal.pgen.1001014 | Europe PMC | doi

* These authors contributed equally to this work.

Dynamic CRM occupancy reflects a temporal map of developmental progression

Wilczyński B, Furlong EE (2010)

Mol. Syst. Biol. 6:383. doi: 10.1038/msb.2010.35 | Europe PMC | doi

Model-based method for transcription factor target identification with limited data

Honkela A, Girardot C, Gustafson EH, Liu YH, Furlong EE, Lawrence ND, Rattray M (2010)

Proc. Natl. Acad. Sci. U.S.A. 107(17):7793-7798. doi: 10.1073/pnas.0914285107 | Europe PMC | doi

Challenges for modeling global gene regulatory networks during development: insights from Drosophila

Wilczyński B, Furlong EE (2010)

Dev. Biol. 340(2):161-169. doi: 10.1016/j.ydbio.2009.10.032 | Europe PMC | doi

Conservation and divergence in developmental networks: a view from Drosophila myogenesis

Ciglar L, Furlong EE (2009)

Curr. Opin. Cell Biol. 21(6):754-760. doi: 10.1016/j.ceb.2009.10.001 | Europe PMC | doi

Combinatorial binding predicts spatio-temporal cis-regulatory activity

Zinzen RP*, Girardot C*, Gagneur J*, Braun M, Furlong EE (2009)

Nature 462(7269):65-70. doi: 10.1038/nature08531 | Europe PMC | doi

* These authors contributed equally to this work.

A systematic analysis of Tinman function reveals Eya and JAK-STAT signaling as essential regulators of muscle development

Liu YH, Jakobsen JS, Valentin G, Amarantos I, Gilmour DT, Furlong EE (2009)

Dev. Cell 16(2):280-291. doi: 10.1016/j.devcel.2009.01.006 | Europe PMC | doi

cis-Regulatory networks during development: a view of Drosophila

Bonn S, Furlong EE (2008)

Curr. Opin. Genet. Dev. 18(6):513-520. doi: 10.1016/j.gde.2008.09.005 | Europe PMC | doi

Dynamic regulation by polycomb group protein complexes controls pattern formation and the cell cycle in Drosophila

Oktaba K, Gutiérrez L, Gagneur J, Girardot C, Sengupta AK, Furlong EE, Müller J (2008)

Dev. Cell 15(6):877-889. doi: 10.1016/j.devcel.2008.10.005 | Europe PMC | doi

A topographical map of spatiotemporal patterns of gene expression

Furlong EE (2008)

Dev. Cell 14(5):639-640. doi: 10.1016/j.devcel.2008.04.007 | Europe PMC | doi

4DXpress: a database for cross-species expression pattern comparisons

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)

Nucleic Acids Res. 36(Database issue):D847-53. doi: 10.1093/nar/gkm797 | Europe PMC | doi

Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families

Shah PK, Tripathi LP, Jensen LJ, Gahnim M, Mason C, Furlong EE, Rodrigues V, White KP, Bork P, Sowdhamini R (2008)

Gene 407(1-2):199-215. doi: 10.1016/j.gene.2007.10.012 | Europe PMC | doi

Divergence in cis-regulatory networks: taking the ‘species’ out of cross-species analysis

Zinzen RP, Furlong EE (2008)

Genome Biol. 9(11):240. doi: 10.1186/gb-2008-9-11-240 | Europe PMC | doi

Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network

Jakobsen JS, Braun M, Astorga J, Gustafson EH, Sandmann T, Karzynski M, Carlsson P, Furlong EE (2007)

Genes Dev. 21(19):2448-2460. doi: 10.1101/gad.437607 | Europe PMC | doi

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 EE (2007)

Bioinformatics 23(6):771-773. doi: 10.1093/bioinformatics/btl641 | Europe PMC | doi

A core transcriptional network for early mesoderm development in Drosophila melanogaster

Sandmann T, Girardot C, Brehme M, Tongprasit W, Stolc V, Furlong EE (2007)

Genes Dev. 21(4):436-449. doi: 10.1101/gad.1509007 | Europe PMC | doi

Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis

Hooper SD, Boué S, Krause R, Jensen LJ, Mason CE, Ghanim M, White KP, Furlong EE, Bork P (2007)

Mol. Syst. Biol. 3:72. doi: 10.1038/msb4100112 | Europe PMC | doi

Mes2, a MADF-containing transcription factor essential for Drosophila development

Zimmermann G, Furlong EE, Suyama K, Scott MP (2006)

Dev. Dyn. 235(12):3387-3395. doi: 10.1002/dvdy.20970 | Europe PMC | doi

Genomics and development: Taking developmental biology to new heights

Spitz F, Furlong EE (2006)

Dev. Cell 11(4):451-457. doi: 10.1016/j.devcel.2006.09.013 | Europe PMC | doi

A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development

Sandmann T, Jensen LJ, Jakobsen JS, Karzynski MM, Eichenlaub MP, Bork P, Furlong EE (2006)

Dev. Cell 10(6):797-807. doi: 10.1016/j.devcel.2006.04.009 | Europe PMC | doi

Developmental control of nuclear size and shape by Kugelkern and Kurzkern

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)

Curr. Biol. 16(6):543-552. doi: 10.1016/j.cub.2006.01.051 | Europe PMC | doi

ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos

Sandmann T, Jakobsen JS, Furlong EE (2006)

Nat Protoc 1(6):2839-2855. doi: 10.1038/nprot.2006.383 | Europe PMC | doi

A functional genomics approach to identify new regulators of Wnt signaling

Furlong EE (2005)

Dev. Cell 8(5):624-626. doi: 10.1016/j.devcel.2005.04.006 | Europe PMC | doi

Myofilin, a protein in the thick filaments of insect muscle

Qiu F, Brendel S, Cunha PM, Astola N, Song B, Furlong EE, Leonard KR, Bullard B (2005)

J. Cell. Sci. 118(Pt 7):1527-1536. doi: 10.1242/jcs.02281 | Europe PMC | doi

Integrating transcriptional and signalling networks during muscle development

Furlong EE (2004)

Curr. Opin. Genet. Dev. 14(4):343-350. doi: 10.1016/j.gde.2004.06.011 | Europe PMC | doi

Creation of a minimal tiling path of genomic clones for Drosophila: provision of a common resource

Hollich V, Johnson E, Furlong EE, Beckmann B, Carlson J, Celniker SE, Hoheisel JD (2004)

BioTechniques 37(2):282-284. doi: 10.2144/3702A0282 | Europe PMC | doi

Notch and Ras signaling pathway effector genes expressed in fusion competent and founder cells during Drosophila myogenesis

Artero R, Furlong EE, Beckett K, Scott MP, Baylies M (2003)

Development 130(25):6257-6272. doi: 10.1242/dev.00843 | Europe PMC | doi

Gene expression during the life cycle of Drosophila melanogaster

Arbeitman MN, Furlong EE, Imam F, Johnson E, Null BH, Baker BS, Krasnow MA, Scott MP, Davis RW, White KP (2002)

Science 297(5590):2270-2275. doi: 10.1126/science.1072152 | Europe PMC | doi

Patterns of gene expression during Drosophila mesoderm development

Furlong EE, Andersen EC, Null B, White KP, Scott MP (2001)

Science 293(5535):1629-1633. doi: 10.1126/science.1062660 | Europe PMC | doi

Automated sorting of live transgenic embryos

Furlong EE, Profitt D, Scott MP (2001)

Nat. Biotechnol. 19(2):153-156. doi: 10.1038/84422 | Europe PMC | doi