publications-ghavi-helm

This folder holds the following references to publications, sorted by year and author.

There are 20 references in this bibliography folder.

Alberti, B, Vincent, S, Stévant, I, Lajoignie, D, Tarayre, H, Villoutreix, P, and Ghavi-Helm, Y (2024).
Spatial reconstruction of single-cell enhancer activity in a multicellular organism
bioRxiv.

Zhang, J, Wencker, M, Marliac, Q, Berton, A, Hasan, U, Schneider, R, Laubreton, D, Cherrier, DE, Mathieu, AL, Rey, A, Jiang, W, Caramel, J, Genestier, L, Marçais, A, Marvel, J, Ghavi-Helm, Y, and Walzer, T (2020).
Zeb1 represses TCR signaling, promotes the proliferation of T cell progenitors and is essential for NK1.1+ T cell development
Cell Mol Immunol.

Ghavi-Helm, Y (2019).
Functional consequences of chromosomal rearrangements on gene expression: not so deleterious after all?
Journal of Molecular Biology.

Ghavi-Helm, Y, Jankowski, A, Meiers, S, Viales, RR, Korbel, JO, and Furlong, EEM (2019).
Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression
Nature Genetics.

Moretti, C, Stevant, I, and Ghavi-Helm, Y (2019).
3D genome organisation in Drosophila
Briefings in Functional Genomics.

Erceg, J, Pakozdi, T, Marco-Ferreres, R, Ghavi-Helm, Y, Girardot, C, Bracken, AP, and Furlong, EEM (2017).
Dual functionality of cis-regulatory elements as developmental enhancers and Polycomb response elements.
Genes Dev, 31(6):590-602.

Schauer, T, Ghavi-Helm, Y, Sexton, T, Albig, C, Regnard, C, Cavalli, G, Furlong, EE, and Becker, PB (2017).
Chromosome topology guides the Drosophila Dosage Compensation Complex for target gene activation
EMBO Rep.

Ghavi-Helm, Y, Klein, FA, Pakozdi, T, Ciglar, L, Noordermeer, D, Huber, W, and Furlong, EEM (2016).
Corrigendum: Enhancer loops appear stable during development and are associated with paused polymerase.
Nature, 537(7619):254.

Ghavi-Helm, Y, Zhao, B, and Furlong, EEM (2016).
Chromatin Immunoprecipitation for Analyzing Transcription Factor Binding and Histone Modifications in Drosophila.
Methods Mol Biol, 1478:263-277.

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

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

Ghavi-Helm, Y, Klein, FA, Pakozdi, T, Ciglar, L, Noordermeer, D, Huber, W, and Furlong, EEM (2014).
Enhancer loops appear stable during development and are associated with paused polymerase.
Nature, 512(7512):96-100.

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

Bonn, S, Zinzen, RP, Girardot, C, Gustafson, EH, Perez-Gonzalez, A, Delhomme, N, Ghavi-Helm, Y, Wilczynski, B, Riddell, A, and Furlong, EEM (2012).
Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development.
Nat Genet, 44(2):148-56.

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, and Werner, M (2012).
Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells.
Nucleic Acids Res, 40(1):270-83.

Ghavi-Helm, Y and Furlong, EEM (2012).
Analyzing transcription factor occupancy during embryo development using ChIP-seq.
Methods Mol Biol, 786:229-45.

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

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

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

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