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Items: 28

1.

Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration.

Lucic B, Chen HC, Kuzman M, Zorita E, Wegner J, Minneker V, Wang W, Fronza R, Laufs S, Schmidt M, Stadhouders R, Roukos V, Vlahovicek K, Filion GJ, Lusic M.

Nat Commun. 2019 Sep 6;10(1):4059. doi: 10.1038/s41467-019-12046-3.

2.

Transcription factors and 3D genome conformation in cell-fate decisions.

Stadhouders R, Filion GJ, Graf T.

Nature. 2019 May;569(7756):345-354. doi: 10.1038/s41586-019-1182-7. Epub 2019 May 15. Review.

PMID:
31092938
3.

An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape.

Pokusaeva VO, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan KS, Mishin AS, Bogatyreva NS, Ivankov DN, Akopyan AV, Avvakumov SY, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov FA.

PLoS Genet. 2019 Apr 10;15(4):e1008079. doi: 10.1371/journal.pgen.1008079. eCollection 2019 Apr.

4.

Using Barcoded HIV Ensembles (B-HIVE) for Single Provirus Transcriptomics.

Chen HC, Zorita E, Filion GJ.

Curr Protoc Mol Biol. 2018 Apr;122(1):e56. doi: 10.1002/cpmb.56.

PMID:
29851299
5.

Theoretical principles of transcription factor traffic on folded chromatin.

Cortini R, Filion GJ.

Nat Commun. 2018 Apr 30;9(1):1740. doi: 10.1038/s41467-018-04130-x.

6.

OneD: increasing reproducibility of Hi-C samples with abnormal karyotypes.

Vidal E, le Dily F, Quilez J, Stadhouders R, Cuartero Y, Graf T, Marti-Renom MA, Beato M, Filion GJ.

Nucleic Acids Res. 2018 May 4;46(8):e49. doi: 10.1093/nar/gky064.

7.

A New Quinoline BRD4 Inhibitor Targets a Distinct Latent HIV-1 Reservoir for Reactivation from Other "Shock" Drugs.

Abner E, Stoszko M, Zeng L, Chen HC, Izquierdo-Bouldstridge A, Konuma T, Zorita E, Fanunza E, Zhang Q, Mahmoudi T, Zhou MM, Filion GJ, Jordan A.

J Virol. 2018 Apr 27;92(10). pii: e02056-17. doi: 10.1128/JVI.02056-17. Print 2018 May 15.

8.

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming.

Stadhouders R, Vidal E, Serra F, Di Stefano B, Le Dily F, Quilez J, Gomez A, Collombet S, Berenguer C, Cuartero Y, Hecht J, Filion GJ, Beato M, Marti-Renom MA, Graf T.

Nat Genet. 2018 Feb;50(2):238-249. doi: 10.1038/s41588-017-0030-7. Epub 2018 Jan 15.

9.

Methylation of DNA Ligase 1 by G9a/GLP Recruits UHRF1 to Replicating DNA and Regulates DNA Methylation.

Ferry L, Fournier A, Tsusaka T, Adelmant G, Shimazu T, Matano S, Kirsh O, Amouroux R, Dohmae N, Suzuki T, Filion GJ, Deng W, de Dieuleveult M, Fritsch L, Kudithipudi S, Jeltsch A, Leonhardt H, Hajkova P, Marto JA, Arita K, Shinkai Y, Defossez PA.

Mol Cell. 2017 Aug 17;67(4):550-565.e5. doi: 10.1016/j.molcel.2017.07.012. Epub 2017 Aug 10.

10.

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors.

Serra F, Baù D, Goodstadt M, Castillo D, Filion GJ, Marti-Renom MA.

PLoS Comput Biol. 2017 Jul 19;13(7):e1005665. doi: 10.1371/journal.pcbi.1005665. eCollection 2017 Jul.

11.

Clustering of Drosophila housekeeping promoters facilitates their expression.

Corrales M, Rosado A, Cortini R, van Arensbergen J, van Steensel B, Filion GJ.

Genome Res. 2017 Jul;27(7):1153-1161. doi: 10.1101/gr.211433.116. Epub 2017 Apr 18.

12.

Position effects influence HIV latency reversal.

Chen HC, Martinez JP, Zorita E, Meyerhans A, Filion GJ.

Nat Struct Mol Biol. 2017 Jan;24(1):47-54. doi: 10.1038/nsmb.3328. Epub 2016 Nov 21.

PMID:
27870832
13.

Zerone: a ChIP-seq discretizer for multiple replicates with built-in quality control.

Cuscó P, Filion GJ.

Bioinformatics. 2016 Oct 1;32(19):2896-902. doi: 10.1093/bioinformatics/btw336. Epub 2016 Jun 10.

14.

Machine Learning: How Much Does It Tell about Protein Folding Rates?

Corrales M, Cuscó P, Usmanova DR, Chen HC, Bogatyreva NS, Filion GJ, Ivankov DN.

PLoS One. 2015 Nov 25;10(11):e0143166. doi: 10.1371/journal.pone.0143166. eCollection 2015.

15.

3D genome structure. Organization of the nucleus in space and time.

Filion GJ, Beato M.

FEBS Lett. 2015 Oct 7;589(20 Pt A):2867-8. doi: 10.1016/j.febslet.2015.09.003. Epub 2015 Sep 9. No abstract available.

16.

The signed Kolmogorov-Smirnov test: why it should not be used.

Filion GJ.

Gigascience. 2015 Feb 27;4:9. doi: 10.1186/s13742-015-0048-7. eCollection 2015.

17.

Starcode: sequence clustering based on all-pairs search.

Zorita E, Cuscó P, Filion GJ.

Bioinformatics. 2015 Jun 15;31(12):1913-9. doi: 10.1093/bioinformatics/btv053. Epub 2015 Jan 31.

18.

A network model of the molecular organization of chromatin in Drosophila.

van Bemmel JG, Filion GJ, Rosado A, Talhout W, de Haas M, van Welsem T, van Leeuwen F, van Steensel B.

Mol Cell. 2013 Feb 21;49(4):759-71. doi: 10.1016/j.molcel.2013.01.040.

19.

The inner nuclear membrane proteins Man1 and Ima1 link to two different types of chromatin at the nuclear periphery in S. pombe.

Steglich B, Filion GJ, van Steensel B, Ekwall K.

Nucleus. 2012 Jan-Feb;3(1):77-87.

PMID:
22156748
20.

Systematic protein location mapping reveals five principal chromatin types in Drosophila cells.

Filion GJ, van Bemmel JG, Braunschweig U, Talhout W, Kind J, Ward LD, Brugman W, de Castro IJ, Kerkhoven RM, Bussemaker HJ, van Steensel B.

Cell. 2010 Oct 15;143(2):212-24. doi: 10.1016/j.cell.2010.09.009. Epub 2010 Sep 30. Erratum in: Cell. 2011 Apr 1;145(1):160.

21.

Reassessing the abundance of H3K9me2 chromatin domains in embryonic stem cells.

Filion GJ, van Steensel B.

Nat Genet. 2010 Jan;42(1):4; author reply 5-6. doi: 10.1038/ng0110-4. No abstract available.

PMID:
20037608
22.

Bayesian network analysis of targeting interactions in chromatin.

van Steensel B, Braunschweig U, Filion GJ, Chen M, van Bemmel JG, Ideker T.

Genome Res. 2010 Feb;20(2):190-200. doi: 10.1101/gr.098822.109. Epub 2009 Dec 9.

23.

Sensing X chromosome pairs before X inactivation via a novel X-pairing region of the Xic.

Augui S, Filion GJ, Huart S, Nora E, Guggiari M, Maresca M, Stewart AF, Heard E.

Science. 2007 Dec 7;318(5856):1632-6.

24.

Using reverse electrophoretic mobility shift assay to measure and compare protein-DNA binding affinities.

Filion GJ, Fouvry L, Defossez PA.

Anal Biochem. 2006 Oct 1;357(1):156-8. Epub 2006 Aug 4. No abstract available.

PMID:
16914111
25.

Transmission and immunity: the importance of heterogeneity in the fight against malaria.

Filion GJ, Paul RE, Robert V.

Trends Parasitol. 2006 Aug;22(8):345-8. Epub 2006 Jun 22. Review.

PMID:
16797234
26.

[Epigenetics and cancer].

Filion GJ, Defossez PA.

Bull Cancer. 2006 Apr;93(4):343-7. French.

27.

A family of human zinc finger proteins that bind methylated DNA and repress transcription.

Filion GJ, Zhenilo S, Salozhin S, Yamada D, Prokhortchouk E, Defossez PA.

Mol Cell Biol. 2006 Jan;26(1):169-81.

28.

The human enhancer blocker CTC-binding factor interacts with the transcription factor Kaiso.

Defossez PA, Kelly KF, Filion GJ, Pérez-Torrado R, Magdinier F, Menoni H, Nordgaard CL, Daniel JM, Gilson E.

J Biol Chem. 2005 Dec 30;280(52):43017-23. Epub 2005 Oct 17.

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