EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany


Total: 25 publication(s)


Reddington JP, Garfield DA, Sigalova OM, Karabacak Calviello A, Marco-Ferreres R, Girardot C, Viales RR, Degner JF, Ohler U, Furlong EEM. (2020)

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

Dev Cell 55(5):648-664.e9. doi: 10.1016/j.devcel.2020.10.009
Europe PMC | doi


Peng PC, Khoueiry P, Girardot C, Reddington JP, Garfield DA, Furlong EEM, Sinha S. (2019)

The role of chromatin accessibility in cis-regulatory evolution.

Genome Biol Evol 11(7) doi: 10.1093/gbe/evz103
Europe PMC | doi

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

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

FEBS Lett. 593(14):1698-1710. doi: 10.1002/1873-3468.13443
Europe PMC | doi


Deliu E, Arecco N, Morandell J, Dotter CP, Contreras X, Girardot C, Käsper EL, Kozlova A, Kishi K, Chiaradia I, Noh KM, Novarino G. (2018)

Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.

Nat Neurosci 21(12) doi: 10.1038/s41593-018-0266-2
Europe PMC | doi


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

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

Nucleic Acids Res. 45(21):12285-12300. doi: 10.1093/nar/gkx840
Europe PMC | doi

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

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

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

Monfort M, Furlong EE, Girardot C. (2017)

Dynamix: Dynamic visualization by automatic selection of informative tracks from hundreds of genomic data sets.

Bioinformatics 33(14) doi: 10.1093/bioinformatics/btx141
Europe PMC | doi

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

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

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


Seyres D, Ghavi-Helm Y, Junion G, Taghli-Lamallem O, Guichard C, Röder L, Girardot C, Furlong EE, Perrin L. (2016)

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

Development 143(23):4533-4542. doi: 10.1242/dev.140822
Europe PMC | doi

Rafiee MR, Girardot C, Sigismondo G, Krijgsveld J. (2016)

Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins.

Mol. Cell 64(3):624-635. doi: 10.1016/j.molcel.2016.09.019
Europe PMC | doi

Girardot C, Scholtalbers J, Sauer S, Su SY, Furlong EE. (2016)

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

BMC Bioinformatics 17(1) doi: 10.1186/s12859-016-1284-2
Europe PMC | doi

Mbodj A, Gustafson EH, Ciglar L, Junion G, Gonzalez A, Girardot C, Perrin L, Furlong EE, Thieffry D. (2016)

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

PLoS Comput. Biol. 12(9) doi: 10.1371/journal.pcbi.1005073
Europe PMC | doi


Ciglar L, Girardot C, Wilczyński B, Braun M, Furlong EE. (2014)

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

Development 141(13):2633-2643. doi: 10.1242/dev.101956
Europe PMC | doi

Rembold M, Ciglar L, Yáñez-Cuna JO, Zinzen RP, Girardot C, Jain A, Welte MA, Stark A, Leptin M, Furlong EE. (2014)

A conserved role for Snail as a potentiator of active transcription

Genes Dev. 28(2):167-181. doi: 10.1101/gad.230953.113
Europe PMC | doi

Erceg J, Saunders TE, Girardot C, Devos DP, Hufnagel L, Furlong EE. (2014)

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

PLoS Genet. 10(1):e1004060. doi: 10.1371/journal.pgen.1004060
Europe PMC | doi


Bonn S, Zinzen RP, Girardot C, Gustafson EH, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, Wilczyński B, Riddell A, Furlong EE. (2012)

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

Nat. Genet. 44(2):148-156. doi: 10.1038/ng.1064
Europe PMC | doi

Junion G, Spivakov M, Girardot C, Braun M, Gustafson EH, Birney E, Furlong EE. (2012)

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

Cell 148(3):473-486. doi: 10.1016/j.cell.2012.01.030
Europe PMC | doi

Spivakov M, Akhtar J, Kheradpour P, Beal K, Girardot C, Koscielny G, Herrero J, Kellis M, Furlong EE, Birney E. (2012)

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

Genome Biol. 13(9):R49. doi: 10.1186/gb-2012-13-9-r49
Europe PMC | doi


Honkela A, Girardot C, Gustafson EH, Liu YH, Furlong EE, Lawrence ND, Rattray M. (2010)

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

Proc. Natl. Acad. Sci. U.S.A. 107(17):7793-7798. doi: 10.1073/pnas.0914285107
Europe PMC | doi


Zinzen RP, Girardot C, Gagneur J, Braun M, Furlong EE. (2009)

Combinatorial binding predicts spatio-temporal cis-regulatory activity

Nature 462(7269):65-70. doi: 10.1038/nature08531
Europe PMC | doi


Oktaba K, Gutiérrez L, Gagneur J, Girardot C, Sengupta AK, Furlong EE, Müller J. (2008)

Dynamic regulation by polycomb group protein complexes controls pattern formation and the cell cycle in Drosophila

Dev. Cell 15(6):877-889. doi: 10.1016/j.devcel.2008.10.005
Europe PMC | doi

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)

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

Nucleic Acids Res. 36(Database issue):D847-53. doi: 10.1093/nar/gkm797
Europe PMC | doi


Girardot C, Sklyar O, Grosz S, Huber W, Furlong EE. (2007)

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

Bioinformatics 23(6):771-773. doi: 10.1093/bioinformatics/btl641
Europe PMC | doi

Sandmann T, Girardot C, Brehme M, Tongprasit W, Stolc V, Furlong EE. (2007)

A core transcriptional network for early mesoderm development in Drosophila melanogaster

Genes Dev. 21(4):436-449. doi: 10.1101/gad.1509007
Europe PMC | doi


Motz M, Kober I, Girardot C, Loeser E, Bauer U, Albers M, Moeckel G, Minch E, Voss H, Kilger C, Koegl M. (2002)

Elucidation of an archaeal replication protein network to generate enhanced PCR enzymes

J. Biol. Chem. 277(18):16179-16188. doi: 10.1074/jbc.m107793200
Europe PMC | doi