Browse Data

The Furlong lab maintains several browsing instance of genome browsers (using JBrowse). Click on the thumbnails to access one.

Our browser instances runs with our in-house Dynamix plugin, for automated genome browsing. Learn more about it here.

The Furlong lab maintains and serves a genome browser instance where all of our public data is made available for browsing (with complementary datasets from other labs). Access the Furlong Browser.
The Furlong lab maintains and serves a genome browser instance where our 4C-seq data from Ghavi-Helm et al. 2014, Nature is available from browsing. Access the 4C Browser.

Shiny Apps

The Furlong lab maintains Shiny Apps to visualize complex results. Click on the thumbnails to access one.

Our Shiny App instances run on EMBL Shiny portal here.

The Shiny app allows for quick visualisation of the Basenji saturation scores calculated around the 175 top pAI and top AI variants in our publication “Contextualising transcription factor binding during embryogenesis using natural sequence variation“. You can select the variants from the table on top and visualise the corresponding saturation scores.


We provide the genotype information for the vasa-Cas9 line. This information can be used to design guide-RNAs and primers taking into account genetic variants specific to the vasa-Cas9 line. The variants were called using GATK short variant discovery pipeline. The pipeline focuses on SNPs and short INDELs. We also provide the personalized genome sequence of the vasa-Cas9 line based on the dm6 assembly. Finally, the liftOver chain files can be used to move the genomic coordinates from dm6 to vasa-Cas9 and vice-versa. The personalised genome is built using the unfiltered vcf to minimize false negative variant calls. Heterozygous variants are encoded using the IUPAC nucleotide code.

ReMap 2022 Drosophila coverage tracks

We provide all ReMap 2022 Drosophila tracks. The mapped bam files were provided by Fayrouz Hamal and Benoît Ballester and processed according to the ReMap analysis pipeline ( Hammal et al. 2022). According to the database annotation we were able to match 570 out of 1205 ChIP-seq samples with at least one corresponding ChIP input. All coverage tracks (ChIP samples and ChIP inputs) were generated using bamCoverage.

Publication Data

Our publication page allows you to access the data associated with our publications.

Enhancer–promoter interactions become more instructive in the transition from cell-fate specification to tissue differentiation

Pollex T, Rabinowitz A, Gambetta MC, Marco-Ferreres R, Viales RR, Jankowski A, Schaub C, Furlong EEM

Nature Genetics 2024 Mar. doi: 10.1038/s41588-024-01678-x | Nature Genetics | doi

See also Enhancer contacts during embryonic development show diverse interaction modes and modest yet significant increases upon gene activation

Chromatin gene-gene loops support the cross-regulation of genes with related function

Pollex T, Marco-Ferreres R, Ciglar L, Ghavi-Helm Y, Rabinowitz A, Viales RR, Schaub C, Jankowski A, Girardot C, Furlong EEM

Molecular Cell 2023 Dec. doi: 10.1016/j.molcel.2023.12.023 | Molecular Cell | doi

See also Chromatin loops facilitate co-regulation of paralogues and Role of gene–gene loops in fine-tuning cross-regulation

In Vivo Silencing of Regulatory Elements Using a Single AAV-CRISPRi Vector

Laurette P, Cao C, Ramanujam D, Schwaderer M, Lueneburg T, Kuss S, Weiss L, Dilshat R, Furlong EEM, Rezende F, Engelhardt S, Gilsbach R

Circulation Research 2024 Jan. doi: 10.1161/CIRCRESAHA.123.323854 | Circulation Research | doi

Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo

de Almeida BP, Schaub C, Pagani M, Secchia S, Furlong EEM, Stark A

Nature 2023 Dec. doi: 10.1038/s41586-023-06905-9 | Nature | doi

See also Designer enhancers for cell-type-specific gene regulation

CTCF, BEAF-32, and CP190 are not required for the establishment of TADs in early Drosophila embryos but have locus-specific roles

Cavalheiro GR, Girardot C, Viales RR, Pollex T, Ngoc Cao TB, Lacour P, Feng S, Rabinowitz A, Furlong EEM

Science Advances 2023 Feb. doi: 10.1126/sciadv.ade1085 | Science Advances | doi

Enhancers have more cofactor specificity than we think: A potential new way to classify enhancers based on their functional cofactor requirements

Pijuan-Sala B, Furlong EEM

Molecular Cell 2022 Aug. doi: 10.1016/j.molcel.2022.07.015 | Molecular Cell | doi

The continuum of Drosophila embryonic development at single-cell resolution

Calderon D, Blecher-Gonen R, Huang XF, Secchia S, Kentro J, Daza RM, Martin B, Dulja A, Schaub C, Trapnell C, Larschan E, O’Connor-Giles KM, Furlong EEM, Shendure J

Science 2022 Aug. doi: 10.1126/science.abn580 | Science | doi

Regulating specificity in enhancer-promoter communication

Galouzis CC, Furlong EEM

Current Opinion In Cell Biology 2022 Apr. doi: 10.1016/ | Current Opinion In Cell Biology | doi

Simultaneous cellular and molecular phenotyping of embryonic mutants using single-cell regulatory trajectories

Secchia S, Foneris M, Heinen T, Stegle O, Furlong EEM

Developmental Cell 2022 Feb. doi: 110.1016/j.devcel.2022.01.016 | Developmental Cell | doi

scDALI: modeling allelic heterogeneity in single cells reveals context-specific genetic regulation

Heinen T*, Secchia S*, Reddington JP, Zhao B, Furlong EEM, Stegle O

Genome Biology 2022 Jan. doi: 10.1186/s13059-021-02593-8 | Genome Biology | doi

* These authors contributed equally to this work.

Co-corresponding authors

Extremely rapid and reversible optogenetic perturbation of nuclear proteins in living embryos

Kögler AC, Kherdjemil Y, Bender K, Rabinowitz AH, Marco-Ferreres R, Furlong EEM

Developmental Cell 2021 Aug. doi: 10.1016/j.devcel.2021.07.011 | Developmental Cell | doi

The hourglass model of evolutionary conservation during embryogenesis extends to developmental enhancers with signatures of positive selection

Liu J, Viales RR, Khoueiry P, Reddington JP, Girardot C, Furlong EEM, Robinson-Rechavi M

Genome Research 2021 Jul. doi: 10.1101/gr.275212.121 | Genome Research | doi

To loop or not to loop: what is the role of TADs in enhancer function and gene regulation?

Cavalheiro GR, Pollex T, Furlong EEM

Current Opinion in Genetics & Development 2021 Apr. doi: 10.1016/j.gde.2020.12.015 | Current Opinion in Genetics & Development | doi

Chromatin accessibility profiling methods

Minnoye L, Marinov GK, Krausgruber T, Pan L, Marand AP, Secchia S, Greenleaf WJ, Furlong EEM, Zhao K, Schmitz RJ, Bock C, Aerts S

Nature Reviews Methods Primers 2021 Jan. doi: 10.1038/s43586-020-00008-9 | Nature Reviews Methods Primers | doi

Cis-acting variation is common across regulatory layers but is often buffered during embryonic development

Floc’hlay S*, Wong ES*, Zhao B*, Viales RR, Thomas-Chollier M, Thieffry D, Garfield DA, Furlong EEM

* These authors contributed equally to this work.

Co-corresponding authors

Genome Research 2020 Dec. doi: 10.1101/gr.266338.120 | Genome Research | doi

Lineage resolved enhancer and promoter usage during a time-course of embryogenesis

Reddington JP*, Garfield DA*, Sigalova O*, Calviello AK*, Marco-Ferreres R, Girardot C, Viales RR, Degner JF, Ohler U, Furlong EEM

* These authors contributed equally to this work.

Developmental Cell 2020 Dec. doi: 10.1016/j.devcel.2020.10.009 | Developmental Cell | doi

cover msb sigalova-et-al

Predictive features of gene expression variation reveal mechanistic link with differential expression.

Sigalova OM, Shaeiri A, Forneris M, Furlong EEM, Zaug JB (2020)

Molecular Systems Biology 2020 Aug. doi: 10.15252/msb.20209539 | Molecular Systems Biology | doi

Co-corresponding authors

cover nrg mcguire-et-al 2020

The road ahead in genetics and genomics

McGuire AL, Gabriel S, Tishkoff SA, Wonkam A, Chakravarti A, Furlong EEM, Treutlein B, Meissner A, Chang HY, Lopez-Bigas N, Segal E, Kim JS

Nature Review Genetics 2020 Aug; doi: 10.1038/s41576-020-0272-6 | Nature Review Genetics | doi

Characterization of button loci that promote homologous chromosome pairing and cell-type-specific interchromosomal gene regulation

Viets K, Sauria MEG, Chernoff C, Viales RR, Echterling M, Anderson C, Tran S, Dove A, Goyal R, Voortman L, Gordus A, Furlong EEM, Taylor J, Johnston RJ

Developmental Cell 2019 Nov; doi: 10.1016/j.devcel.2019.09.007 | Developmental Cell | doi

Chromatin topology, condensates and gene regulation: shifting paradigms or just a phase?

Mir M, Bickmore W, Furlong EEM, Narlikar G (2019)

Development 2019 Sep; 146. doi: 10.1242/dev.182766. | Development | doi

Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development

Zhou J, Schor IE, Yao V, Theesfeld CL, Marco-Ferreres R, Tadych A, Furlong EEM, Troyanskaya OG (2019)

PLOS Genetics 2019 Sep; doi: 10.1371/journal.pgen.1008382. | PLOS Genetics | doi

cover Ghavi-Helm-et-al-1019

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression.

Ghavi-Helm Y*, Jankowski A*, Meiers S*, Viales RR, Korbel JO, Furlong EEM (2019)

Nature Genetics 2019 Jul. doi: 10.1038/s41588-019-0462-3 | Nature Genetics | doi

* These authors contributed equally to this work.

Co-corresponding authors

See also A genome disconnect and Toppling TAD tenets

Expanding the mesodermal transcriptional network by genome-wide identification of Zinc finger homeodomain 1 (Zfh1) targets

Wu WH, Kuo TH, Kao CW, Girardot C, Hung SJ, Liu T, Furlong EEM, Liu YA (2019)

FEBS Letters 2019 May. doi: 10.1002/1873-3468.13443 | FEBS Letters | doi

Non-coding RNA expression, function and variation during Drosophila embryogenesis

Schor IE, Bussotti G, Males M, Forneris M, Viales RR, Enright AJ, Furlong EEM (2018)

Current Biology 2018 Oct. doi: 10.1016/j.cub.2018.09.026 | Current Biology | doi

Developmental enhancers and chromosome topology.

Furlong EEM, Levine M (2018)

Science 2018 Sep. doi: 10.1126/science.aau0320 | Science | doi

Co-corresponding authors

The Insulator Protein CTCF Is Required for Correct Hox Gene Expression, but Not for Embryonic Development in Drosophila.

Gambetta MC, Furlong EEM (2018)

Genetics 2018 Jul 18. doi: 10.1534/genetics.118.301350 | Europe PMC | doi

Co-corresponding authors

A Versatile, Low-Cost, Multiway Microfluidic Sorter for Droplets, Cells, and Embryos.

Utharala R, Tseng Q, Furlong EEM, Merten CA (2018)

Analytical Chem. 2018 May 15; 90(10):5982-5988. doi: 10.1021/acs.analchem.7b04689. | Europe PMC | doi

The cis-regulatory dynamics of embryonic development at single-cell resolution

Cusanovich DA*, Reddington JP*, Garfield DA*, Daza RM, Aghamirzaie D, Marco-Ferreres R, Pliner HA, Christiansen L, Qiu X, Steemers FJ, Trapnell C, Shendure J, Furlong EE (2018)

Nature Mar 14 [Epub ahead of print]. doi: 10.1038/nature25981 | Europe PMC | doi

* These authors contributed equally to this work.

Co-corresponding authors

cover genesdev mikhaylichenko-et-al 2018

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

Mikhaylichenko O*, Bondarenko V*, Harnett D, Schor IE, Males M, Viales RR, Furlong EE (2018)

Genes Dev. 32(1):42-57. doi: 10.1101/gad.292870.116 | Europe PMC | doi

* These authors contributed equally to this work.

See also and

Opbp is a new architectural/insulator protein required for ribosomal gene expression.

Zolotarev N, Maksimenko O, Kyrchanova O, Sokolinskaya E, Osadchiy I, Girardot C, Bonchuk A, Ciglar L, Furlong EE, Georgiev P (2017)

Nucleic Acids Res. 6, Aug. 2017. doi: 10.1093/nar/gkx840 | Europe PMC | doi

Co-corresponding authors

Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity

Khoueiry P, Girardot C, Ciglar L, Peng PC, Gustafson EH, Sinha S, Furlong EE (2017)

Elife 6, Aug. 2017. doi: 10.7554/eLife.28440 | Europe PMC | doi

Chromosome topology guides the Drosophila Dosage Compensation Complex for target gene activation

Schauer T, Ghavi-Helm Y, Sexton T, Albig C, Regnard C, Cavalli G, Furlong EE, Becker PB (2017)

EMBO Rep e201744292 , Aug. 2017. doi: 10.15252/embr.201744292 | Europe PMC | doi

Correlation Does Not Imply Causation: Histone Methyltransferases, but Not Histone Methylation, SET the Stage for Enhancer Activation

Pollex T, Furlong EE (2017)

Mol Cell 66(4):439-441. doi: 10.1016/j.molcel.2017.05.005 | Europe PMC | doi

cover genesdev erceg-et-al 2017

Dual functionality of cis-regulatory elements as developmental enhancers and Polycomb response elements

Erceg J*, Pakozdi T*, Marco-Ferreres R*, Ghavi-Helm Y, Girardot C, Bracken AP, Furlong EE (2017)

Genes Dev. 31(6):590-602. doi: 10.1101/gad.292870.116 | Europe PMC | doi

* These authors contributed equally to this work.

See also

Dynamix: dynamic visualization by automatic selection of informative tracks from hundreds of genomic datasets

Monfort M, Furlong EE, Girardot C (2017)

Bioinformatics 2017 Mar. 11. doi: 10.1093/bioinformatics/btx141 | Europe PMC | doi [Epub ahead of print]

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 49(4):550-558. 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

See also and

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

See also

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

See also

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/ | 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.

See also, and

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

See also

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</a

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