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Eileen E. M. Furlong, Ph.D. - Publications

Affiliations: 
Genome Biology European Molecular Biology 
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55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Sigalova OM, Shaeiri A, Forneris M, Furlong EE, Zaugg JB. Predictive features of gene expression variation reveal mechanistic link with differential expression. Molecular Systems Biology. 16: e9539. PMID 32767663 DOI: 10.15252/Msb.20209539  0.405
2017 Schauer T, Ghavi-Helm Y, Sexton T, Albig C, Regnard C, Cavalli G, Furlong EE, Becker PB. Chromosome topology guides the Drosophila Dosage Compensation Complex for target gene activation. Embo Reports. PMID 28794204 DOI: 10.15252/Embr.201744292  0.319
2017 Khoueiry P, Girardot C, Ciglar L, Peng PC, Gustafson EH, Sinha S, Furlong EE. Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity. Elife. 6. PMID 28792889 DOI: 10.7554/Elife.28440  0.448
2017 Erceg J, Pakozdi T, Marco-Ferreres R, Ghavi-Helm Y, Girardot C, Bracken AP, Furlong EE. Dual functionality of cis-regulatory elements as developmental enhancers and Polycomb response elements. Genes & Development. PMID 28381411 DOI: 10.1101/Gad.292870.116  0.457
2017 Schor IE, Degner JF, Harnett D, Cannavò E, Casale FP, Shim H, Garfield DA, Birney E, Stephens M, Stegle O, Furlong EE. Promoter shape varies across populations and affects promoter evolution and expression noise. Nature Genetics. PMID 28191888 DOI: 10.1038/Ng.3791  0.662
2016 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. Genetic variants regulating expression levels and isoform diversity during embryogenesis. Nature. PMID 28024300 DOI: 10.1038/Nature20802  0.687
2016 Seyres D, Ghavi-Helm Y, Junion G, Taghli-Lamallem O, Guichard C, Röder L, Girardot C, Furlong EE, Perrin L. Identification and in silico modeling of enhancers reveals new features of the cardiac differentiation network. Development (Cambridge, England). 143: 4533-4542. PMID 27899510 DOI: 10.1242/Dev.140822  0.428
2016 Ghavi-Helm Y, Zhao B, Furlong EE. Chromatin Immunoprecipitation for Analyzing Transcription Factor Binding and Histone Modifications in Drosophila. Methods in Molecular Biology (Clifton, N.J.). 1478: 263-277. PMID 27730588 DOI: 10.1007/978-1-4939-6371-3_16  0.449
2016 Girardot C, Scholtalbers J, Sauer S, Su SY, Furlong EE. Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers. Bmc Bioinformatics. 17: 419. PMID 27717304 DOI: 10.1186/S12859-016-1284-2  0.306
2016 Mbodj A, Gustafson EH, Ciglar L, Junion G, Gonzalez A, Girardot C, Perrin L, Furlong EE, Thieffry D. Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes. Plos Computational Biology. 12: e1005073. PMID 27599298 DOI: 10.1371/Journal.Pcbi.1005073  0.37
2016 Ghavi-Helm Y, Klein FA, Pakozdi T, Ciglar L, Noordermeer D, Huber W, Furlong EE. Corrigendum: Enhancer loops appear stable during development and are associated with paused polymerase. Nature. PMID 27409805 DOI: 10.1038/Nature18962  0.338
2016 Tica J, Lee E, Untergasser A, Meiers S, Garfield DA, Gokcumen O, Furlong EE, Park PJ, Stütz AM, Korbel JO. Next-generation sequencing-based detection of germline L1-mediated transductions. Bmc Genomics. 17: 342. PMID 27161561 DOI: 10.1186/S12864-016-2670-X  0.611
2015 Cannavò E, Khoueiry P, Garfield DA, Geeleher P, Zichner T, Gustafson EH, Ciglar L, Korbel JO, Furlong EE. Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks. Current Biology : Cb. PMID 26687625 DOI: 10.1016/J.Cub.2015.11.034  0.67
2015 Klein FA, Pakozdi T, Anders S, Ghavi-Helm Y, Furlong EE, Huber W. FourCSeq: analysis of 4C sequencing data. Bioinformatics (Oxford, England). PMID 26034064 DOI: 10.1093/Bioinformatics/Btv335  0.322
2015 Nitta KR, Jolma A, Yin Y, Morgunova E, Kivioja T, Akhtar J, Hens K, Toivonen J, Deplancke B, Furlong EE, Taipale J. Conservation of transcription factor binding specificities across 600 million years of bilateria evolution. Elife. 4. PMID 25779349 DOI: 10.7554/Elife.04837  0.439
2014 Hughes CS, Foehr S, Garfield DA, Furlong EE, Steinmetz LM, Krijgsveld J. Ultrasensitive proteome analysis using paramagnetic bead technology. Molecular Systems Biology. 10: 757. PMID 25358341 DOI: 10.15252/Msb.20145625  0.554
2014 Ghavi-Helm Y, Klein FA, Pakozdi T, Ciglar L, Noordermeer D, Huber W, Furlong EE. Enhancer loops appear stable during development and are associated with paused polymerase. Nature. 512: 96-100. PMID 25043061 DOI: 10.1038/Nature13417  0.474
2014 Ciglar L, Girardot C, WilczyÅ„ski B, Braun M, Furlong EE. Coordinated repression and activation of two transcriptional programs stabilizes cell fate during myogenesis. Development (Cambridge, England). 141: 2633-43. PMID 24961800 DOI: 10.1242/Jcs.158311  0.434
2014 Rembold M, Ciglar L, Yáñez-Cuna JO, Zinzen RP, Girardot C, Jain A, Welte MA, Stark A, Leptin M, Furlong EE. A conserved role for Snail as a potentiator of active transcription. Genes & Development. 28: 167-81. PMID 24402316 DOI: 10.1101/Gad.230953.113  0.735
2014 Erceg J, Saunders TE, Girardot C, Devos DP, Hufnagel L, Furlong EE. Subtle changes in motif positioning cause tissue-specific effects on robustness of an enhancer's activity. Plos Genetics. 10: e1004060. PMID 24391522 DOI: 10.1371/Journal.Pgen.1004060  0.504
2014 Hughes CS, Foehr S, Garfield DA, Furlong EE, Steinmetz LM, Krijgsveld J. Ultrasensitive proteome analysis using paramagnetic bead technology Molecular Systems Biology. 10. DOI: 10.15252/msb.20145625  0.538
2013 Zichner T, Garfield DA, Rausch T, Stütz AM, Cannavó E, Braun M, Furlong EE, Korbel JO. Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing. Genome Research. 23: 568-79. PMID 23222910 DOI: 10.1101/Gr.142646.112  0.637
2012 Wilczynski B, Liu YH, Yeo ZX, Furlong EE. Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state. Plos Computational Biology. 8: e1002798. PMID 23236268 DOI: 10.1371/Journal.Pcbi.1002798  0.47
2012 Spivakov M, Akhtar J, Kheradpour P, Beal K, Girardot C, Koscielny G, Herrero J, Kellis M, Furlong EE, Birney E. Analysis of variation at transcription factor binding sites in Drosophila and humans. Genome Biology. 13: R49. PMID 22950968 DOI: 10.1186/Gb-2012-13-9-R49  0.442
2012 Spitz F, Furlong EE. Transcription factors: from enhancer binding to developmental control. Nature Reviews. Genetics. 13: 613-26. PMID 22868264 DOI: 10.1038/Nrg3207  0.52
2012 Bonn S, Zinzen RP, Perez-Gonzalez A, Riddell A, Gavin AC, Furlong EE. Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP. Nature Protocols. 7: 978-94. PMID 22538849 DOI: 10.1038/Nprot.2012.049  0.713
2012 Junion G, Spivakov M, Girardot C, Braun M, Gustafson EH, Birney E, Furlong EE. A transcription factor collective defines cardiac cell fate and reflects lineage history. Cell. 148: 473-86. PMID 22304916 DOI: 10.1016/J.Cell.2012.01.030  0.413
2012 Bonn S, Zinzen RP, Girardot C, Gustafson EH, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, WilczyÅ„ski B, Riddell A, Furlong EE. Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Nature Genetics. 44: 148-56. PMID 22231485 DOI: 10.1038/Ng.1064  0.72
2012 Ghavi-Helm Y, Furlong EE. Analyzing transcription factor occupancy during embryo development using ChIP-seq. Methods in Molecular Biology (Clifton, N.J.). 786: 229-45. PMID 21938630 DOI: 10.1007/978-1-61779-292-2_14  0.476
2011 Furlong EE. Molecular biology: A fly in the face of genomics. Nature. 471: 458-9. PMID 21430772 DOI: 10.1038/471458A  0.386
2010 Cunha PM, Sandmann T, Gustafson EH, Ciglar L, Eichenlaub MP, Furlong EE. Combinatorial binding leads to diverse regulatory responses: Lmd is a tissue-specific modulator of Mef2 activity. Plos Genetics. 6: e1001014. PMID 20617173 DOI: 10.1371/Journal.Pgen.1001014  0.514
2010 WilczyÅ„ski B, Furlong EE. Dynamic CRM occupancy reflects a temporal map of developmental progression. Molecular Systems Biology. 6: 383. PMID 20571532 DOI: 10.1038/Msb.2010.35  0.418
2010 Honkela A, Girardot C, Gustafson EH, Liu YH, Furlong EE, Lawrence ND, Rattray M. Model-based method for transcription factor target identification with limited data. Proceedings of the National Academy of Sciences of the United States of America. 107: 7793-8. PMID 20385836 DOI: 10.1073/Pnas.0914285107  0.428
2010 Wilczynski B, Furlong EE. Challenges for modeling global gene regulatory networks during development: insights from Drosophila. Developmental Biology. 340: 161-9. PMID 19874814 DOI: 10.1016/J.Ydbio.2009.10.032  0.429
2009 Ciglar L, Furlong EE. Conservation and divergence in developmental networks: a view from Drosophila myogenesis. Current Opinion in Cell Biology. 21: 754-60. PMID 19896355 DOI: 10.1016/J.Ceb.2009.10.001  0.418
2009 Zinzen RP, Girardot C, Gagneur J, Braun M, Furlong EE. Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature. 462: 65-70. PMID 19890324 DOI: 10.1038/Nature08531  0.735
2009 Liu YH, Jakobsen JS, Valentin G, Amarantos I, Gilmour DT, Furlong EE. A systematic analysis of Tinman function reveals Eya and JAK-STAT signaling as essential regulators of muscle development. Developmental Cell. 16: 280-91. PMID 19217429 DOI: 10.1016/J.Devcel.2009.01.006  0.412
2008 Zinzen RP, Furlong EE. Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis. Genome Biology. 9: 240. PMID 19012800 DOI: 10.1186/Gb-2008-9-11-240  0.718
2008 Oktaba K, Gutiérrez L, Gagneur J, Girardot C, Sengupta AK, Furlong EE, Müller J. Dynamic regulation by polycomb group protein complexes controls pattern formation and the cell cycle in Drosophila. Developmental Cell. 15: 877-89. PMID 18993116 DOI: 10.1016/J.Devcel.2008.10.005  0.46
2008 Bonn S, Furlong EE. cis-Regulatory networks during development: a view of Drosophila. Current Opinion in Genetics & Development. 18: 513-20. PMID 18929653 DOI: 10.1016/J.Gde.2008.09.005  0.429
2008 Furlong EE. A topographical map of spatiotemporal patterns of gene expression. Developmental Cell. 14: 639-40. PMID 18477445 DOI: 10.1016/J.Devcel.2008.04.007  0.372
2008 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. 4DXpress: a database for cross-species expression pattern comparisons. Nucleic Acids Research. 36: D847-53. PMID 17916571 DOI: 10.1093/Nar/Gkm797  0.377
2007 Jakobsen JS, Braun M, Astorga J, Gustafson EH, Sandmann T, Karzynski M, Carlsson P, Furlong EE. Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network. Genes & Development. 21: 2448-60. PMID 17908931 DOI: 10.1101/Gad.437607  0.468
2007 Sandmann T, Girardot C, Brehme M, Tongprasit W, Stolc V, Furlong EE. A core transcriptional network for early mesoderm development in Drosophila melanogaster. Genes & Development. 21: 436-49. PMID 17322403 DOI: 10.1101/Gad.1509007  0.492
2007 Girardot C, Sklyar O, Grosz S, Huber W, Furlong EE. CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data. Bioinformatics (Oxford, England). 23: 771-3. PMID 17234641 DOI: 10.1093/Bioinformatics/Btl641  0.413
2007 Hooper SD, Boué S, Krause R, Jensen LJ, Mason CE, Ghanim M, White KP, Furlong EE, Bork P. Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis. Molecular Systems Biology. 3: 72. PMID 17224916 DOI: 10.1038/Msb4100112  0.443
2006 Sandmann T, Jakobsen JS, Furlong EE. ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos. Nature Protocols. 1: 2839-55. PMID 17406543 DOI: 10.1038/Nprot.2006.383  0.423
2006 Spitz F, Furlong EE. Genomics and development: Taking developmental biology to new heights. Developmental Cell. 11: 451-7. PMID 17051688 DOI: 10.1016/J.Devcel.2006.09.013  0.328
2006 Zimmermann G, Furlong EE, Suyama K, Scott MP. Mes2, a MADF-containing transcription factor essential for Drosophila development. Developmental Dynamics : An Official Publication of the American Association of Anatomists. 235: 3387-95. PMID 17029287 DOI: 10.1002/dvdy.20970  0.342
2006 Sandmann T, Jensen LJ, Jakobsen JS, Karzynski MM, Eichenlaub MP, Bork P, Furlong EE. A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development. Developmental Cell. 10: 797-807. PMID 16740481 DOI: 10.1016/J.Devcel.2006.04.009  0.507
2002 Arbeitman MN, Furlong EE, Imam F, Johnson E, Null BH, Baker BS, Krasnow MA, Scott MP, Davis RW, White KP. Gene expression during the life cycle of Drosophila melanogaster. Science (New York, N.Y.). 297: 2270-5. PMID 12351791 DOI: 10.1126/Science.1072152  0.408
2001 Furlong EE, Andersen EC, Null B, White KP, Scott MP. Patterns of gene expression during Drosophila mesoderm development. Science (New York, N.Y.). 293: 1629-33. PMID 11486054 DOI: 10.1126/Science.1062660  0.41
2001 Furlong EE, Profitt D, Scott MP. Automated sorting of live transgenic embryos. Nature Biotechnology. 19: 153-6. PMID 11175730 DOI: 10.1038/84422  0.349
1996 Furlong EE, Keon NK, Thornton FD, Rein T, Martin F. 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. The Journal of Biological Chemistry. 271: 29688-97. PMID 8939902 DOI: 10.1074/Jbc.271.47.29688  0.363
1996 Furlong EE, Rein T, Martin F. 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. Molecular and Cellular Biology. 16: 5933-45. PMID 8816507 DOI: 10.1128/Mcb.16.10.5933  0.39
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