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Items: 1 to 50 of 83

1.

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

Ghavi-Helm Y, Jankowski A, Meiers S, Viales RR, Korbel JO, Furlong EEM.

Nat Genet. 2019 Aug;51(8):1272-1282. doi: 10.1038/s41588-019-0462-3. Epub 2019 Jul 15.

PMID:
31308546
2.

BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity.

Khoueiry P, Ward Gahlawat A, Petretich M, Michon AM, Simola D, Lam E, Furlong EE, Benes V, Dawson MA, Prinjha RK, Drewes G, Grandi P.

Epigenetics Chromatin. 2019 Jul 2;12(1):39. doi: 10.1186/s13072-019-0286-5.

3.

The Role of Chromatin Accessibility in cis-Regulatory Evolution.

Peng PC, Khoueiry P, Girardot C, Reddington JP, Garfield DA, Furlong EEM, Sinha S.

Genome Biol Evol. 2019 Jul 1;11(7):1813-1828. doi: 10.1093/gbe/evz103.

4.

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 YH.

FEBS Lett. 2019 Jul;593(14):1698-1710. doi: 10.1002/1873-3468.13443. Epub 2019 May 29.

PMID:
31093969
5.

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

van Steensel B, Furlong EEM.

Nat Rev Mol Cell Biol. 2019 Jun;20(6):327-337. doi: 10.1038/s41580-019-0114-6. Review.

PMID:
30886333
6.

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

Schor IE, Bussotti G, Maleš M, Forneris M, Viales RR, Enright AJ, Furlong EEM.

Curr Biol. 2018 Nov 19;28(22):3547-3561.e9. doi: 10.1016/j.cub.2018.09.026. Epub 2018 Nov 1.

7.

Developmental enhancers and chromosome topology.

Furlong EEM, Levine M.

Science. 2018 Sep 28;361(6409):1341-1345. doi: 10.1126/science.aau0320. Review.

PMID:
30262496
8.

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

Gambetta MC, Furlong EEM.

Genetics. 2018 Sep;210(1):129-136. doi: 10.1534/genetics.118.301350. Epub 2018 Jul 18.

9.

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

Utharala R, Tseng Q, Furlong EEM, Merten CA.

Anal Chem. 2018 May 15;90(10):5982-5988. doi: 10.1021/acs.analchem.7b04689. Epub 2018 May 2.

10.

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 EEM.

Nature. 2018 Mar 22;555(7697):538-542. doi: 10.1038/nature25981. Epub 2018 Mar 14.

11.

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 EEM.

Genes Dev. 2018 Jan 1;32(1):42-57. doi: 10.1101/gad.308619.117. Epub 2018 Jan 29.

12.

A proteolytic fragment of histone deacetylase 4 protects the heart from failure by regulating the hexosamine biosynthetic pathway.

Lehmann LH, Jebessa ZH, Kreusser MM, Horsch A, He T, Kronlage M, Dewenter M, Sramek V, Oehl U, Krebs-Haupenthal J, von der Lieth AH, Schmidt A, Sun Q, Ritterhoff J, Finke D, Völkers M, Jungmann A, Sauer SW, Thiel C, Nickel A, Kohlhaas M, Schäfer M, Sticht C, Maack C, Gretz N, Wagner M, El-Armouche A, Maier LS, Londoño JEC, Meder B, Freichel M, Gröne HJ, Most P, Müller OJ, Herzig S, Furlong EEM, Katus HA, Backs J.

Nat Med. 2018 Jan;24(1):62-72. doi: 10.1038/nm.4452. Epub 2017 Dec 11.

PMID:
29227474
13.

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 EEM, Georgiev P.

Nucleic Acids Res. 2017 Dec 1;45(21):12285-12300. doi: 10.1093/nar/gkx840.

14.

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.

EMBO Rep. 2017 Aug 9. pii: e201744292. doi: 10.15252/embr.201744292. [Epub ahead of print]

15.

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.

Elife. 2017 Aug 9;6. pii: e28440. doi: 10.7554/eLife.28440.

16.

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

Pollex T, Furlong EEM.

Mol Cell. 2017 May 18;66(4):439-441. doi: 10.1016/j.molcel.2017.05.005.

17.

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.

Genes Dev. 2017 Mar 15;31(6):590-602. doi: 10.1101/gad.292870.116. Epub 2017 Apr 5.

18.

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

Monfort M, Furlong EEM, Girardot C.

Bioinformatics. 2017 Jul 15;33(14):2194-2196. doi: 10.1093/bioinformatics/btx141.

19.

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

Schor IE, Degner JF, Harnett D, Cannavò E, Casale FP, Shim H, Garfield DA, Birney E, Stephens M, Stegle O, Furlong EE.

Nat Genet. 2017 Apr;49(4):550-558. doi: 10.1038/ng.3791. Epub 2017 Feb 13.

PMID:
28191888
20.

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.

Nature. 2017 Jan 19;541(7637):402-406. doi: 10.1038/nature20802. Epub 2016 Dec 26.

PMID:
28024300
21.

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, Perrin L.

Development. 2016 Dec 1;143(23):4533-4542.

22.

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

Ghavi-Helm Y, Zhao B, Furlong EE.

Methods Mol Biol. 2016;1478:263-277. Review.

PMID:
27730588
23.

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

Girardot C, Scholtalbers J, Sauer S, Su SY, Furlong EE.

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

24.

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.

PLoS Comput Biol. 2016 Sep 6;12(9):e1005073. doi: 10.1371/journal.pcbi.1005073. eCollection 2016 Sep.

25.

Corrigendum: 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.

Nature. 2016 Sep 8;537(7619):254. doi: 10.1038/nature18962. Epub 2016 Jul 13. No abstract available.

PMID:
27409805
26.

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.

BMC Genomics. 2016 May 10;17:342. doi: 10.1186/s12864-016-2670-x.

27.

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.

Curr Biol. 2016 Jan 11;26(1):38-51. doi: 10.1016/j.cub.2015.11.034. Epub 2015 Dec 10.

28.

From Crisis to Crowd Control. Commentary: A Crisis in Comparative Psychology: Where Have All the Undergraduates Gone?

Furlong EE, AuBuchon S, Kraut J, Joiner N, Knowles J, Lewis K, Win M, Furlong J.

Front Psychol. 2015 Nov 10;6:1729. doi: 10.3389/fpsyg.2015.01729. eCollection 2015. No abstract available.

29.

FourCSeq: analysis of 4C sequencing data.

Klein FA, Pakozdi T, Anders S, Ghavi-Helm Y, Furlong EE, Huber W.

Bioinformatics. 2015 Oct 1;31(19):3085-91. doi: 10.1093/bioinformatics/btv335. Epub 2015 Jun 1.

30.

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.

Elife. 2015 Mar 17;4. doi: 10.7554/eLife.04837.

31.

Ultrasensitive proteome analysis using paramagnetic bead technology.

Hughes CS, Foehr S, Garfield DA, Furlong EE, Steinmetz LM, Krijgsveld J.

Mol Syst Biol. 2014 Oct 30;10:757. doi: 10.15252/msb.20145625.

32.

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.

Nature. 2014 Aug 7;512(7512):96-100. doi: 10.1038/nature13417. Epub 2014 Jul 2.

PMID:
25043061
33.

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

Ciglar L, Girardot C, Wilczyński B, Braun M, Furlong EE.

Development. 2014 Jul;141(13):2633-43. doi: 10.1242/dev.101956.

34.

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.

Genes Dev. 2014 Jan 15;28(2):167-81. doi: 10.1101/gad.230953.113. Epub 2014 Jan 8.

35.

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.

PLoS Genet. 2014 Jan;10(1):e1004060. doi: 10.1371/journal.pgen.1004060. Epub 2014 Jan 2.

36.

Logical modelling of Drosophila signalling pathways.

Mbodj A, Junion G, Brun C, Furlong EE, Thieffry D.

Mol Biosyst. 2013 Sep;9(9):2248-58. doi: 10.1039/c3mb70187e.

PMID:
23868318
37.

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

Wilczynski B, Liu YH, Yeo ZX, Furlong EE.

PLoS Comput Biol. 2012;8(12):e1002798. doi: 10.1371/journal.pcbi.1002798. Epub 2012 Dec 6.

38.

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.

Genome Res. 2013 Mar;23(3):568-79. doi: 10.1101/gr.142646.112. Epub 2012 Dec 6.

39.

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

Tseng Q, Lomonosov AM, Furlong EE, Merten CA.

Lab Chip. 2012 Nov 21;12(22):4677-82. doi: 10.1039/c2lc40595d.

PMID:
23014736
40.

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.

Genome Biol. 2012 Sep 28;13(9):R49. doi: 10.1186/gb-2012-13-9-r49.

41.

Transcription factors: from enhancer binding to developmental control.

Spitz F, Furlong EE.

Nat Rev Genet. 2012 Sep;13(9):613-26. doi: 10.1038/nrg3207. Epub 2012 Aug 7. Review.

PMID:
22868264
42.

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

Delhomme N, Padioleau I, Furlong EE, Steinmetz LM.

Bioinformatics. 2012 Oct 1;28(19):2532-3. Epub 2012 Jul 30.

43.

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.

Nat Protoc. 2012 Apr 26;7(5):978-94. doi: 10.1038/nprot.2012.049.

PMID:
22538849
44.

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.

Cell. 2012 Feb 3;148(3):473-86. doi: 10.1016/j.cell.2012.01.030.

45.

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.

Nat Genet. 2012 Jan 8;44(2):148-56. doi: 10.1038/ng.1064.

PMID:
22231485
46.

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

Ghavi-Helm Y, Furlong EE.

Methods Mol Biol. 2012;786:229-45. doi: 10.1007/978-1-61779-292-2_14.

PMID:
21938630
47.

Molecular biology: A fly in the face of genomics.

Furlong EE.

Nature. 2011 Mar 24;471(7339):458-9. doi: 10.1038/471458a. No abstract available.

PMID:
21430772
48.

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

Furlong EE.

Mol Biol Cell. 2010 Nov 15;21(22):3797-8. doi: 10.1091/mbc.E10-05-0436. No abstract available.

49.

Early development of spatial-numeric associations: evidence from spatial and quantitative performance of preschoolers.

Opfer JE, Thompson CA, Furlong EE.

Dev Sci. 2010 Sep 1;13(5):761-71. doi: 10.1111/j.1467-7687.2009.00934.x.

PMID:
20712742
50.

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.

PLoS Genet. 2010 Jul 1;6(7):e1001014. doi: 10.1371/journal.pgen.1001014.

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