Publications IGFL

Spatial reconstruction of single-cell enhancer activity in a multicellular organism: Author(s) : Alberti B, Vincent S, Stévant I, Lajoignie D, Tarayre H, Villoutreix P, Ghavi-Helm Y,; Journal : bioRxiv; 2024
Enhancer-promoter interactions form independently of genomic distance and are functional across TAD boundaries: Author(s) : Borges Pinto P, Grasso A, Balasubramanian D, Vincent S, Tarayre H, Lajoignie D, Ghavi-Helm Y,; Journal : NAR; 2023
Zeb1 represses TCR signaling, promotes the proliferation of T cell progenitors and is essential for NK1.1+ T cell development: Author(s) : Zhang J, Wencker M, Marliac Q, Berton A, Hasan U, Schneider R, Laubreton D, Cherrier D, Mathieu A, Rey A, Jiang W, Caramel J, Genestier L, Marçais A, Marvel J, Ghavi-Helm Y, Walzer T,; Journal : Cell Mol Immunol; 2020
3D genome organisation in Drosophila: Author(s) : Moretti C, Stevant I, Ghavi-Helm Y,; Journal : Briefings in Functional Genomics; 2019
Functional consequences of chromosomal rearrangements on gene expression: not so deleterious after all?: Author(s) : Ghavi-Helm Y,; Journal : Journal of Molecular Biology; 2019
Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression: Author(s) : Ghavi-Helm Y, Jankowski A, Meiers S, Viales R, Korbel J, Furlong E,; Journal : Nature Genetics; 2019
Chromosome topology guides the Drosophila Dosage Compensation Complex for target gene activation: Author(s) : Schauer T, Ghavi-Helm Y, Sexton T, Albig C, Regnard C, Cavalli G, Furlong E, Becker P,; Journal : EMBO Rep; 2017
Dual functionality of cis-regulatory elements as developmental enhancers and Polycomb response elements.: Author(s) : Erceg J, Pakozdi T, Marco-Ferreres R, Ghavi-Helm Y, Girardot C, Bracken A, Furlong E,; Journal : Genes Dev; 2017
Corrigendum: Enhancer loops appear stable during development and are associated with paused polymerase.: Author(s) : Ghavi-Helm Y, Klein F, Pakozdi T, Ciglar L, Noordermeer D, Huber W, Furlong E,; Journal : Nature; 2016
Chromatin Immunoprecipitation for Analyzing Transcription Factor Binding and Histone Modifications in Drosophila.: Author(s) : Ghavi-Helm Y, Zhao B, Furlong E,; Journal : Methods Mol Biol; 2016
Identification and in silico modeling of enhancers reveals new features of the cardiac differentiation network.: Author(s) : Seyres D, Ghavi-Helm Y, Junion G, Taghli-Lamallem O, Guichard C, Roder L, Girardot C, Furlong E, Perrin L,; Journal : Development; 2016
FourCSeq: analysis of 4C sequencing data.: Author(s) : Klein F, Pakozdi T, Anders S, Ghavi-Helm Y, Furlong E, Huber W,; Journal : Bioinformatics; 2015
PHD and TFIIS-Like domains of the Bye1 transcription factor determine its multivalent genomic distribution.: Author(s) : Pinskaya M, Ghavi-Helm Y, Mariotte-Labarre S, Morillon A, Soutourina J, Werner M,; Journal : PLoS One; 2014
Enhancer loops appear stable during development and are associated with paused polymerase.: Author(s) : Ghavi-Helm Y, Klein F, Pakozdi T, Ciglar L, Noordermeer D, Huber W, Furlong E,; Journal : Nature; 2014
Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells.: Author(s) : Carriere L, Graziani S, Alibert O, Ghavi-Helm Y, Boussouar F, Humbertclaude H, Jounier S, Aude J, Keime C, Murvai J, Foglio M, Gut M, Gut I, Lathrop M, Soutourina J, Gerard M, Werner M,; Journal : Nucleic Acids Res; 2012
Analyzing transcription factor occupancy during embryo development using ChIP-seq.: Author(s) : Ghavi-Helm Y, Furlong E,; Journal : Methods Mol Biol; 2012
Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development.: Author(s) : Bonn S, Zinzen R, Girardot C, Gustafson E, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, Wilczynski B, Riddell A, Furlong E,; Journal : Nat Genet; 2012
Multigenome analysis identifies a worldwide distributed epidemic Legionella pneumophila clone that emerged within a highly diverse species.: Author(s) : Cazalet C, Jarraud S, Ghavi-Helm Y, Kunst F, Glaser P, Etienne J, Buchrieser C,; Journal : Genome Res; 2008
Genome-wide location analysis reveals a role of TFIIS in RNA polymerase III transcription.: Author(s) : Ghavi-Helm Y, Michaut M, Acker J, Aude J, Thuriaux P, Werner M, Soutourina J,; Journal : Genes Dev; 2008
Mediator-dependent recruitment of TFIIH modules in preinitiation complex.: Author(s) : Esnault C, Ghavi-Helm Y, Brun S, Soutourina J, Van Berkum N, Boschiero C, Holstege F, Werner M,; Journal : Mol Cell; 2008
Mutations of RNA polymerase II activate key genes of the nucleoside triphosphate biosynthetic pathways.: Author(s) : Kwapisz M, Wery M, Despres D, Ghavi-Helm Y, Soutourina J, Thuriaux P, Lacroute F,; Journal : EMBO J; 2008

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Publications IGFL

Spatial reconstruction of single-cell enhancer activity in a multicellular organism

Enhancer-promoter interactions form independently of genomic distance and are functional across TAD boundaries

Zeb1 represses TCR signaling, promotes the proliferation of T cell progenitors and is essential for NK1.1+ T cell development

3D genome organisation in Drosophila

Functional consequences of chromosomal rearrangements on gene expression: not so deleterious after all?

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

Chromosome topology guides the Drosophila Dosage Compensation Complex for target gene activation

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

Corrigendum: Enhancer loops appear stable during development and are associated with paused polymerase.

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

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

FourCSeq: analysis of 4C sequencing data.

PHD and TFIIS-Like domains of the Bye1 transcription factor determine its multivalent genomic distribution.

Enhancer loops appear stable during development and are associated with paused polymerase.

Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells.

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

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

Multigenome analysis identifies a worldwide distributed epidemic Legionella pneumophila clone that emerged within a highly diverse species.

Genome-wide location analysis reveals a role of TFIIS in RNA polymerase III transcription.

Mediator-dependent recruitment of TFIIH modules in preinitiation complex.

Mutations of RNA polymerase II activate key genes of the nucleoside triphosphate biosynthetic pathways.

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