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1

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression.

Ghavi-Helm Y, Jankowski A, Meiers S, Viales RR, Korbel JO, Furlong EEM. Ghavi-Helm Y, et al. Nat Genet. 2019 Aug;51(8):1272-1282. doi: 10.1038/s41588-019-0462-3. Epub 2019 Jul 15. Nat Genet. 2019. PMID: 31308546

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2

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

Ghavi-Helm Y, Klein FA, Pakozdi T, Ciglar L, Noordermeer D, Huber W, Furlong EE. Ghavi-Helm Y, et al. Nature. 2014 Aug 7;512(7512):96-100. doi: 10.1038/nature13417. Epub 2014 Jul 2. Nature. 2014. PMID: 25043061

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3

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

Ghavi-Helm Y, Zhao B, Furlong EE. Ghavi-Helm Y, et al. Methods Mol Biol. 2016;1478:263-277. doi: 10.1007/978-1-4939-6371-3_16. Methods Mol Biol. 2016. PMID: 27730588 Review.

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4

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

Ghavi-Helm Y, Klein FA, Pakozdi T, Ciglar L, Noordermeer D, Huber W, Furlong EE. Ghavi-Helm Y, et al. Nature. 2016 Sep 8;537(7619):254. doi: 10.1038/nature18962. Epub 2016 Jul 13. Nature. 2016. PMID: 27409805 No abstract available.

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5

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. Erceg J, et al. Among authors: Ghavi-Helm Y. Genes Dev. 2017 Mar 15;31(6):590-602. doi: 10.1101/gad.292870.116. Epub 2017 Apr 5. Genes Dev. 2017. PMID: 28381411 Free PMC article.

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6

FourCSeq: analysis of 4C sequencing data.

Klein FA, Pakozdi T, Anders S, Ghavi-Helm Y, Furlong EE, Huber W. Klein FA, et al. Among authors: Ghavi-Helm Y. Bioinformatics. 2015 Oct 1;31(19):3085-91. doi: 10.1093/bioinformatics/btv335. Epub 2015 Jun 1. Bioinformatics. 2015. PMID: 26034064 Free PMC article.

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7

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

Schauer T, Ghavi-Helm Y, Sexton T, Albig C, Regnard C, Cavalli G, Furlong EE, Becker PB. Schauer T, et al. Among authors: Ghavi-Helm Y. EMBO Rep. 2017 Aug 9;18(10):1854-68. doi: 10.15252/embr.201744292. Online ahead of print. EMBO Rep. 2017. PMID: 28794204 Free PMC article.

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8

Functional Consequences of Chromosomal Rearrangements on Gene Expression: Not So Deleterious After All?

Ghavi-Helm Y. Ghavi-Helm Y. J Mol Biol. 2020 Feb 7;432(3):665-675. doi: 10.1016/j.jmb.2019.09.010. Epub 2019 Oct 15. J Mol Biol. 2020. PMID: 31626801 Review.

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9

3D genome organisation in Drosophila.

Moretti C, Stévant I, Ghavi-Helm Y. Moretti C, et al. Among authors: Ghavi-Helm Y. Brief Funct Genomics. 2020 Mar 23;19(2):92-100. doi: 10.1093/bfgp/elz029. Brief Funct Genomics. 2020. PMID: 31796947

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10

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. Seyres D, et al. Among authors: Ghavi-Helm Y. Development. 2016 Dec 1;143(23):4533-4542. doi: 10.1242/dev.140822. Development. 2016. PMID: 27899510 Free article.

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