Eileen E Furlong

Eileen E Furlong

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Eileen E Furlong

Eileen E Furlong

Publications by authors named "Eileen E Furlong"

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

PLoS Genet 2019 09 25;15(9):e1008382. Epub 2019 Sep 25.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1008382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6779412PMC
September 2019

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

Development 2019 Sep 25;146(19). Epub 2019 Sep 25.

Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.

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http://dx.doi.org/10.1242/dev.182766DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6803379PMC
September 2019

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

Nat Genet 2019 08 15;51(8):1272-1282. Epub 2019 Jul 15.

European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.

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http://dx.doi.org/10.1038/s41588-019-0462-3DOI Listing
August 2019

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

FEBS Lett 2019 Jul 29;593(14):1698-1710. Epub 2019 May 29.

Department of Life Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan.

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http://dx.doi.org/10.1002/1873-3468.13443DOI Listing
July 2019

The role of transcription in shaping the spatial organization of the genome.

Nat Rev Mol Cell Biol 2019 Jun;20(6):327-337

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.

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http://www.nature.com/articles/s41580-019-0114-6
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http://dx.doi.org/10.1038/s41580-019-0114-6DOI Listing
June 2019

Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis.

Curr Biol 2018 11 1;28(22):3547-3561.e9. Epub 2018 Nov 1.

Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09609822183122
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http://dx.doi.org/10.1016/j.cub.2018.09.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6264527PMC
November 2018

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

Genetics 2018 09 18;210(1):129-136. Epub 2018 Jul 18.

European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany

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http://www.genetics.org/lookup/doi/10.1534/genetics.118.3013
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http://dx.doi.org/10.1534/genetics.118.301350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116963PMC
September 2018

Developmental enhancers and chromosome topology.

Science 2018 09;361(6409):1341-1345

Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ 08540, USA.

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http://dx.doi.org/10.1126/science.aau0320DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986801PMC
September 2018

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

Anal Chem 2018 05 2;90(10):5982-5988. Epub 2018 May 2.

European Molecular Biology Laboratory (EMBL) , Genome Biology Unit , Heidelberg , Germany 69117.

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http://dx.doi.org/10.1021/acs.analchem.7b04689DOI Listing
May 2018

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

Methods Mol Biol 2016 ;1478:263-277

European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, D-69117, Germany.

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http://dx.doi.org/10.1007/978-1-4939-6371-3_16DOI Listing
January 2018

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

Genes Dev 2018 01 29;32(1):42-57. Epub 2018 Jan 29.

Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany.

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http://dx.doi.org/10.1101/gad.308619.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5828394PMC
January 2018

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

Bioinformatics 2017 Jul;33(14):2194-2196

European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btx141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870560PMC
July 2017

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

Mol Cell 2017 May;66(4):439-441

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg 69117, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2017.05.005DOI Listing
May 2017

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

Nat Genet 2017 Apr 13;49(4):550-558. Epub 2017 Feb 13.

European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany.

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http://dx.doi.org/10.1038/ng.3791DOI Listing
April 2017

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

Genes Dev 2017 03 5;31(6):590-602. Epub 2017 Apr 5.

Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg D69117, Germany.

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http://dx.doi.org/10.1101/gad.292870.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5393054PMC
March 2017

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

Development 2016 12;143(23):4533-4542

Inserm UMR_S 1090, TAGC, Parc Scientifique de Luminy, Case 908, Cedex 9, Marseille 13288, France

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http://dx.doi.org/10.1242/dev.140822DOI Listing
December 2016

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

BMC Bioinformatics 2016 Oct 8;17(1):419. Epub 2016 Oct 8.

European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, D-69117, Germany.

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http://dx.doi.org/10.1186/s12859-016-1284-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5055726PMC
October 2016

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

PLoS Comput Biol 2016 09 6;12(9):e1005073. Epub 2016 Sep 6.

Computational Systems Biology team, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), INSERM, Ecole Normale Supérieure, PSL Research University, Paris, France.

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http://dx.doi.org/10.1371/journal.pcbi.1005073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5012701PMC
September 2016

FourCSeq: analysis of 4C sequencing data.

Bioinformatics 2015 Oct 1;31(19):3085-91. Epub 2015 Jun 1.

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btv335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4576695PMC
October 2015

Ultrasensitive proteome analysis using paramagnetic bead technology.

Mol Syst Biol 2014 Oct 30;10:757. Epub 2014 Oct 30.

European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299378PMC
http://dx.doi.org/10.15252/msb.20145625DOI Listing
October 2014

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

Nature 2014 Aug 2;512(7512):96-100. Epub 2014 Jul 2.

European Molecular Biology Laboratory, Genome Biology Unit, D-69117 Heidelberg, Germany.

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http://www.nature.com/articles/nature13417
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http://dx.doi.org/10.1038/nature13417DOI Listing
August 2014

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

Development 2014 Jul;141(13):2633-43

European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg 69117, Germany

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http://dx.doi.org/10.1242/dev.101956DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4146391PMC
July 2014

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

PLoS Genet 2014 Jan 2;10(1):e1004060. Epub 2014 Jan 2.

Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.

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http://dx.doi.org/10.1371/journal.pgen.1004060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3879207PMC
January 2014

Logical modelling of Drosophila signalling pathways.

Mol Biosyst 2013 Sep;9(9):2248-58

Technological Advances for Genomics and Clinics (TAGC), INSERM UMR_S 1090, Aix-Marseille Université, Marseille, France.

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http://dx.doi.org/10.1039/c3mb70187eDOI Listing
September 2013

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

PLoS Comput Biol 2012 6;8(12):e1002798. Epub 2012 Dec 6.

Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1002798DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516547PMC
May 2013

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

Genome Res 2013 Mar 6;23(3):568-79. Epub 2012 Dec 6.

Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1101/gr.142646.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3589545PMC
March 2013

Fragmentation of DNA in a sub-microliter microfluidic sonication device.

Lab Chip 2012 Nov;12(22):4677-82

Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany.

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http://dx.doi.org/10.1039/c2lc40595dDOI Listing
November 2012

easyRNASeq: a bioconductor package for processing RNA-Seq data.

Bioinformatics 2012 Oct 30;28(19):2532-3. Epub 2012 Jul 30.

Genome Biology Computational Support, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bts477DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463124PMC
October 2012

Transcription factors: from enhancer binding to developmental control.

Nat Rev Genet 2012 Sep 7;13(9):613-26. Epub 2012 Aug 7.

Developmental Biology Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany.

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http://dx.doi.org/10.1038/nrg3207DOI Listing
September 2012

Analysis of variation at transcription factor binding sites in Drosophila and humans.

Genome Biol 2012 Sep 28;13(9):R49. Epub 2012 Sep 28.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.

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http://dx.doi.org/10.1186/gb-2012-13-9-r49DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491393PMC
September 2012

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

Nat Protoc 2012 Apr 26;7(5):978-94. Epub 2012 Apr 26.

Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1038/nprot.2012.049DOI Listing
April 2012

Analyzing transcription factor occupancy during embryo development using ChIP-seq.

Methods Mol Biol 2012 ;786:229-45

Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1007/978-1-61779-292-2_14DOI Listing
February 2012

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

Cell 2012 Feb;148(3):473-86

Genome Biology Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.cell.2012.01.030DOI Listing
February 2012

Molecular biology: A fly in the face of genomics.

Nature 2011 Mar;471(7339):458-9

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http://dx.doi.org/10.1038/471458aDOI Listing
March 2011

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

Authors:
Eileen E Furlong

Mol Biol Cell 2010 Nov;21(22):3797-8

European Molecular Biology Laboratory, Genome Biology Unit, Myerhofstrasse, Heidelberg BW D69117, Germany.

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http://dx.doi.org/10.1091/mbc.E10-05-0436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2982138PMC
November 2010

Dynamic CRM occupancy reflects a temporal map of developmental progression.

Mol Syst Biol 2010 Jun;6:383

Department of Genome Biology, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.

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http://dx.doi.org/10.1038/msb.2010.35DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913398PMC
June 2010

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

Dev Biol 2010 Apr 27;340(2):161-9. Epub 2009 Oct 27.

European Molecular Biology Laboratory, D-69117 Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.ydbio.2009.10.032DOI Listing
April 2010

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

Proc Natl Acad Sci U S A 2010 Apr 12;107(17):7793-8. Epub 2010 Apr 12.

Department of Information and Computer Science, Aalto University School of Science and Technology, Helsinki, Finland.

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http://dx.doi.org/10.1073/pnas.0914285107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2867914PMC
April 2010

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

Curr Opin Cell Biol 2009 Dec 4;21(6):754-60. Epub 2009 Nov 4.

European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.ceb.2009.10.001DOI Listing
December 2009

Combinatorial binding predicts spatio-temporal cis-regulatory activity.

Nature 2009 Nov;462(7269):65-70

European Molecular Biology Laboratory, D-69117 Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature08531DOI Listing
November 2009

Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis.

Genome Biol 2008 4;9(11):240. Epub 2008 Nov 4.

European Molecular Biology Laboratory, D-69117 Heidelberg, Germany.

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http://dx.doi.org/10.1186/gb-2008-9-11-240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614484PMC
February 2009

cis-Regulatory networks during development: a view of Drosophila.

Curr Opin Genet Dev 2008 Dec 16;18(6):513-20. Epub 2008 Oct 16.

European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.gde.2008.09.005DOI Listing
December 2008

A topographical map of spatiotemporal patterns of gene expression.

Dev Cell 2008 May;14(5):639-40

European Molecular Biology Laboratory, D-69117 Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.devcel.2008.04.007DOI Listing
May 2008

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

Nucleic Acids Res 2008 Jan 4;36(Database issue):D847-53. Epub 2007 Oct 4.

European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1093/nar/gkm797DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238840PMC
January 2008

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

Nat Protoc 2006 ;1(6):2839-55

EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1038/nprot.2006.383DOI Listing
November 2007

CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data.

Bioinformatics 2007 Mar 17;23(6):771-3. Epub 2007 Jan 17.

European Molecular Biology Laboratory, D-69117 Heidelberg, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btl641DOI Listing
March 2007

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

Dev Dyn 2006 Dec;235(12):3387-95

Department of Developmental Biology, Howard Hughes Medical Institute, Clark Center West W252, Stanford University School of Medicine, Stanford, California 94305-5439, USA.

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http://dx.doi.org/10.1002/dvdy.20970DOI Listing
December 2006

Genomics and development: Taking developmental biology to new heights.

Dev Cell 2006 Oct;11(4):451-7

Developmental Biology Programme, EMBL, Heidelberg 69117, Germany.

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http://dx.doi.org/10.1016/j.devcel.2006.09.013DOI Listing
October 2006

Developmental control of nuclear size and shape by Kugelkern and Kurzkern.

Curr Biol 2006 Mar 2;16(6):543-52. Epub 2006 Feb 2.

Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.cub.2006.01.051DOI Listing
March 2006

A functional genomics approach to identify new regulators of Wnt signaling.

Authors:
Eileen E Furlong

Dev Cell 2005 May;8(5):624-6

Developmental Biology Programme and Gene Expression Programme, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.devcel.2005.04.006DOI Listing
May 2005

Myofilin, a protein in the thick filaments of insect muscle.

J Cell Sci 2005 Apr 15;118(Pt 7):1527-36. Epub 2005 Mar 15.

European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1242/jcs.02281DOI Listing
April 2005

Integrating transcriptional and signalling networks during muscle development.

Authors:
Eileen E Furlong

Curr Opin Genet Dev 2004 Aug;14(4):343-50

Developmental Biology and Gene Expression Programmes, EMBL, Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.gde.2004.06.011DOI Listing
August 2004

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

Development 2003 Dec 5;130(25):6257-72. Epub 2003 Nov 5.

Developmental Biology Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA.

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http://furlonglab.embl.de/extras/Artero_Furlong_2003_Develop
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http://dev.biologists.org/cgi/doi/10.1242/dev.00843
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http://dx.doi.org/10.1242/dev.00843DOI Listing
December 2003