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2017

Erceg J*, Pakozdi T*, Marco-Ferreres R*, Ghavi-Helm Y, Girardot C, Bracken AP, and Furlong EEM. Dual functionality of cis-regulatory elements as developmental enhancers and polycomb response elements.  Genes and Development. 2017 Apr 5.

2016

Seyres D, Ghavi-Helm Y, Junion G, Taghli-Lamalhem O, Guichard C, Roder L, Girardot C, Furlong EE, Perrin L. Identification and in silico modeling of enhancers reveals new features of the cardiac differentiation network. Development. 2016 Dec 1;143(23):4533-4542.

Ghavi-Helm Y, Zhao B, Furlong EE. Chromatin immunoprecipitation for analyzing transcription factor binding and histone modifications in Drosophila. Methods in Molecular Biology. 2016;1478:263-277.

2015

Klein FA, Pakozdi T, Anders S, Ghavi-Helm Y, Furlong EE, Huber W. FourCSeq: analysis of 4C sequencing data. Bioinformatics. 2015 Oct 1;31(19):3085-91.

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. 2014 Aug 7;512(7512):96-100.

Pinskaya M, Ghavi-Helm Y, Mariotte-Labarre S, Morillon A, Soutourina J, Werner M. PHD and TFIIS-like domains of the Bye1 transcription factor determine its multivalent genomic distribution. PLoS One. 2014 Jul 16;9(7):e102464.

2012

Bonn S, Zinzen RP, Girardot C, Gustafson EH, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, Wilczyński B, Riddell A, Furlong EE. Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Nature Genetics. 2012 Jan 8;44(2):148-56.

Carrière L, Graziani S, Alibert O, Ghavi-Helm Y, Boussouar F, Humbertclaude H, Jounier S, Aude JC, Keime C, Murvai J, Foglio M, Gut M, Gut I, Lathrop M, Soutourina J, Gérard M, Werner M. Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells. Nucleic Acids Research. 2012 Jan;40(1):270-83.

2008

Ghavi-Helm Y, Furlong EE. Analyzing transcription factor occupancy during embryo development using ChIP-seq. Methods in Molecular Biology. 2012;786:229-45.2008

Ghavi-Helm Y, Michaut M, Acker J, Aude J-C, Thuriaux P, Werner M, Soutourina J. Genome-wide location analysis reveals a role of TFIIS in RNA polymerase III transcription. Genes and Development. 2008 Jul 15;22(14):1934-47.

Esnault C, Ghavi-Helm Y, Brun S, Soutourina J, Van Berkum N, Boschiero C, Holstege F and Werner M. Mediator-dependent recruitment of TFIIH modules in preinitiation complex. Molecular Cell. 2008 Aug 8;31(3):337-46.

Kwapisz M, Wery M, Després D, Ghavi-Helm Y, Soutourina J, Thuriaux P and Lacroute F. Mutations of RNA polymerase II activate key genes of the nucleoside triphosphate biosynthetic pathways. The EMBO Journal. 2008 Sep 17;27(18):2411-21.

Cazalet C, Jarraud S, Ghavi-Helm Y, Kunst F, Glaser P, Etienne J, Buchrieser C. Multigenome analysis identifies a worldwide distributed epidemic Legionella pneumophila clone that emerged within a highly diverse species. Genome Research. 2008 Mar;18(3):431-41.