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The Furlong Laboratory
The Furlong Laboratory

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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.

Furlong Browser

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.

4C 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.

Basenjii Saturation Scores

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.

vasa-Cas9

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.

Genotype of the Drosophila vasa-Cas9 line
VCF: Genome Sequence:

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.

To explore the dataset: To download some or all of the coverage tracks:

Publication Data

Chip (Ldb1) is a putative cofactor of Zelda forming a functional bridge to CBP during zygotic genome activation
Galouzis CC, Kherdjemil Y, Forneris M, Viales RR, Marco-Ferreres R, Furlong EEM – Molecular Cell
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Integrating
Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
Sigalova O*, Forneris M*, Stojanovska F, Zhao B, Viales RR, Rabinowitz A, Hamal F, Ballester B, Zaugg JB, Furlong EEM – Genome Research
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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
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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
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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
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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
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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
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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
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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
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Regulating specificity in enhancer-promoter communication
Galouzis CC, Furlong EEM – Current Opinion In Cell Biology
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Simultaneous cellular and molecular phenotyping of embryonic mutants using single-cell regulatory trajectories
Secchia S, Forneris M, Heinen T, Stegle O, Furlong EEM – Developmental Cell
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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
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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
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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
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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
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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
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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‡ – Genome Research
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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 – Developmental Cell
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Predictive features of gene expression variation reveal mechanistic link with differential expression.
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
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The road ahead in genetics and genomics
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
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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…
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Chromatin topology, condensates and gene regulation: shifting paradigms or just a phase?
Mir M, Bickmore W, Furlong EEM, Narlikar G (2019) – Development
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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
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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
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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
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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
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Developmental enhancers and chromosome topology.
Furlong EEM‡, Levine M‡ (2018) – Science
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The Insulator Protein CTCF Is Required for Correct Hox Gene Expression, but Not for Embryonic Development in Drosophila.
Gambetta MC‡, Furlong EEM‡ (2018) – Genetics
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A Versatile, Low-Cost, Multiway Microfluidic Sorter for Droplets, Cells, and Embryos.
Utharala R, Tseng Q, Furlong EEM, Merten CA (2018) – Analytical Chem
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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
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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
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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
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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
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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
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Correlation Does Not Imply Causation: Histone Methyltransferases, but Not Histone Methylation, SET the Stage for Enhancer Activation
Pollex T, Furlong EE (2017) – Mol Cell
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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
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Dynamix: dynamic visualization by automatic selection of informative tracks from hundreds of genomic datasets
Monfort M, Furlong EE, Girardot C (2017) – Bioinformatics
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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
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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) –…
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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
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Chromatin Immunoprecipitation for Analyzing Transcription Factor Binding and Histone Modifications in Drosophila
Ghavi-Helm Y, Zhao B, Furlong EE (2016) – Methods Mol. Biol.
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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
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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.
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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
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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.
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FourCSeq: Analysis of 4C sequencing data
Klein FA, Pakozdi T, Anders S, Ghavi-Helm Y, Furlong EE, Huber W (2015) – Bioinformatics
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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
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Ultrasensitive proteome analysis using paramagnetic bead technology
Hughes CS, Foehr S, Garfield DA, Furlong EE, Steinmetz LM, Krijgsveld J (2014) – Mol. Syst. Biol.
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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
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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
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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
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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.
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Logical modelling of Drosophila signalling pathways
Mbodj A, Junion G, Brun C, Furlong EE, Thieffry D (2013) – Mol Biosyst
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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.
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Fragmentation of DNA in a sub-microliter microfluidic sonication device
Tseng Q, Lomonosov AM, Furlong EE, Merten CA (2012) – Lab Chip
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easyRNASeq: a bioconductor package for processing RNA-Seq data
Delhomme N, Padioleau I, Furlong EE, Steinmetz LM (2012) – Bioinformatics
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Transcription factors: from enhancer binding to developmental control
Spitz F, Furlong EE (2012) – Nat. Rev. Genet.
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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
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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.
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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
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Analyzing transcription factor occupancy during embryo development using ChIP-seq
Ghavi-Helm Y, Furlong EE (2012) – Methods Mol. Biol
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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.
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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.
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Molecular biology: A fly in the face of genomics
Furlong EE (2011) – Nature
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The importance of being specified: cell fate decisions and their role in cell biology
Furlong EE (2010) – Mol. Biol. Cell
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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
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Dynamic CRM occupancy reflects a temporal map of developmental progression
Wilczyński B, Furlong EE (2010) – Mol. Syst. Biol.
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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.
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Challenges for modeling global gene regulatory networks during development: insights from Drosophila
Wilczyński B, Furlong EE (2010) – Dev. Biol.
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Conservation and divergence in developmental networks: a view from Drosophila myogenesis
Ciglar L, Furlong EE (2009) – Curr. Opin. Cell Biol.
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Combinatorial binding predicts spatio-temporal cis-regulatory activit
Zinzen RP*, Girardot C*, Gagneur J*, Braun M, Furlong EE (2009) – Nature
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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
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cis-Regulatory networks during development: a view of Drosophila
Bonn S, Furlong EE (2008) – Curr. Opin. Genet. Dev.
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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
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A topographical map of spatiotemporal patterns of gene expression
Furlong EE (2008) Dev. Cell 1
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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…
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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
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Divergence in cis-regulatory networks: taking the ‘species’ out of cross-species analysis
Zinzen RP, Furlong EE (2008) – Genome Biol.
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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
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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
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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
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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.
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Mes2, a MADF-containing transcription factor essential for Drosophila development
Zimmermann G, Furlong EE, Suyama K, Scott MP (2006) – Dev. Dyn.
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Genomics and development: Taking developmental biology to new heights
Spitz F, Furlong EE (2006) – Dev. Cell
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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
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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
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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
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A functional genomics approach to identify new regulators of Wnt signaling
Furlong EE (2005) – Dev. Cell
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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.
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Integrating transcriptional and signalling networks during muscle development
Furlong EE (2004) – Curr. Opin. Genet. Dev.
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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
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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
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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
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Patterns of gene expression during Drosophila mesoderm development
Furlong EE, Andersen EC, Null B, White KP, Scott MP (2001) – Science
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Automated sorting of live transgenic embryos
Furlong EE, Profitt D, Scott MP (2001) – Nat. Biotechnol.
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