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, 2023

doi:10.1016/j.molcel.2023.12.023.

A stem cell zoo uncovers intracellular scaling of developmental tempo across mammals.

Lázaro J, Costanzo M, Sanaki-Matsumiya M, Girardot C, Hayashi M, Hayashi K, Diecke S, Hildebrandt TB, Lazzari G, Wu J, Petkov S, Behr R, Trivedi V, Matsuda M, Ebisuya M

Cell Stem Cell, 2023

doi:10.1016/j.stem.2023.05.014.

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, Cao TBN, Lacour P, Feng S, Rabinowitz A, Furlong EEM

Science advances, 2023

doi:10.1126/sciadv.ade1085.

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 E, Robinson-Rechavi M

Genome research, 2021

doi:10.1101/gr.275212.121.

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

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

Developmental cell, 2020

doi:10.1016/j.devcel.2020.10.009.

The role of chromatin accessibility in cis-regulatory evolution.

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

Genome biology and evolution, 2019

doi:10.1093/gbe/evz103.

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 letters, 2019

doi:10.1002/1873-3468.13443.

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

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

Nature neuroscience, 2018

doi:10.1038/s41593-018-0266-2.

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 research, 2017

doi:10.1093/nar/gkx840.

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

doi:10.7554/eLife.28440.

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

Monfort M, Furlong EE, Girardot C

Bioinformatics (Oxford, England), 2017

doi:10.1093/bioinformatics/btx141.

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 & development, 2017

doi:10.1101/gad.292870.116.

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 (Cambridge, England), 2016

doi:10.1242/dev.140822.

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

Rafiee MR, Girardot C, Sigismondo G, Krijgsveld J

Molecular cell, 2016

doi:10.1016/j.molcel.2016.09.019.

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

doi:10.1186/s12859-016-1284-2.

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 computational biology, 2016

doi:10.1371/journal.pcbi.1005073.

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

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

Development (Cambridge, England), 2014

doi:10.1242/dev.101956.

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 & development, 2014

doi:10.1101/gad.230953.113.

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 genetics, 2014

doi:10.1371/journal.pgen.1004060.

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

Nature genetics, 2012

doi:10.1038/ng.1064.

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

doi:10.1016/j.cell.2012.01.030.

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 biology, 2012

doi:10.1186/gb-2012-13-9-r49.

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

Proceedings of the National Academy of Sciences of the United States of America, 2010

doi:10.1073/pnas.0914285107.

Combinatorial binding predicts spatio-temporal cis-regulatory activity

Zinzen RP, Girardot C, Gagneur J, Braun M, Furlong EE

Nature, 2009

doi:10.1038/nature08531.

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

Developmental cell, 2008

doi:10.1016/j.devcel.2008.10.005.

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

Nucleic acids research, 2008

doi:10.1093/nar/gkm797.

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

Bioinformatics (Oxford, England), 2007

doi:10.1093/bioinformatics/btl641.

A core transcriptional network for early mesoderm development in Drosophila melanogaster

Sandmann T, Girardot C, Brehme M, Tongprasit W, Stolc V, Furlong EE

Genes & development, 2007

doi:10.1101/gad.1509007.

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

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

The Journal of biological chemistry, 2002

doi:10.1074/jbc.m107793200.