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Items: 47

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.

A multi-host approach to identify a transposon mutant of Pseudomonas aeruginosa LESB58 lacking full virulence.

Gagné-Thivierge C, Kukavica-Ibrulj I, Filion G, Dekimpe V, Tan SGE, Vincent AT, Déziel É, Levesque RC, Charette SJ.

BMC Res Notes. 2018 Mar 27;11(1):198. doi: 10.1186/s13104-018-3308-7.

7.

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.

8.

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.

9.

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.

10.

Parallel sequencing lives, or what makes large sequencing projects successful.

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

Gigascience. 2017 Nov 1;6(11):1-6. doi: 10.1093/gigascience/gix100.

11.

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.

12.

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.

13.

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.

14.

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
15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation.

Le Dily F, Baù D, Pohl A, Vicent GP, Serra F, Soronellas D, Castellano G, Wright RH, Ballare C, Filion G, Marti-Renom MA, Beato M.

Genes Dev. 2014 Oct 1;28(19):2151-62. doi: 10.1101/gad.241422.114.

21.

Assessing Pseudomonas aeruginosa virulence using a nonmammalian host: Dictyostelium discoideum.

Filion G, Charette SJ.

Methods Mol Biol. 2014;1149:671-80. doi: 10.1007/978-1-4939-0473-0_51.

PMID:
24818941
22.

Identification of dichloroacetic acid degrading Cupriavidus bacteria in a drinking water distribution network model.

Berthiaume C, Gilbert Y, Fournier-Larente J, Pluchon C, Filion G, Jubinville E, Sérodes JB, Rodriguez M, Duchaine C, Charette SJ.

J Appl Microbiol. 2014 Jan;116(1):208-21. doi: 10.1111/jam.12353. Epub 2013 Oct 17.

23.

Insertion sequence AS5 (IS AS5 ) is involved in the genomic plasticity of Aeromonas salmonicida.

Trudel MV, Tanaka KH, Filion G, Daher RK, Frenette M, Charette SJ.

Mob Genet Elements. 2013 May 1;3(3):e25640. Epub 2013 Jul 8.

24.

Lipid composition of multilamellar bodies secreted by Dictyostelium discoideum reveals their amoebal origin.

Paquet VE, Lessire R, Domergue F, Fouillen L, Filion G, Sedighi A, Charette SJ.

Eukaryot Cell. 2013 Oct;12(10):1326-34. doi: 10.1128/EC.00107-13. Epub 2013 Jun 7.

25.

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.

26.

Draft genome sequence of the virulent strain 01-B526 of the fish pathogen Aeromonas salmonicida.

Charette SJ, Brochu F, Boyle B, Filion G, Tanaka KH, Derome N.

J Bacteriol. 2012 Feb;194(3):722-3. doi: 10.1128/JB.06276-11.

27.

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
28.

Amoeba host model for evaluation of Streptococcus suis virulence.

Bonifait L, Charette SJ, Filion G, Gottschalk M, Grenier D.

Appl Environ Microbiol. 2011 Sep;77(17):6271-3. doi: 10.1128/AEM.00659-11. Epub 2011 Jul 8.

29.

Alteration of virulence factors and rearrangement of pAsa5 plasmid caused by the growth of Aeromonas salmonicida in stressful conditions.

Daher RK, Filion G, Tan SG, Dallaire-Dufresne S, Paquet VE, Charette SJ.

Vet Microbiol. 2011 Sep 28;152(3-4):353-60. doi: 10.1016/j.vetmic.2011.04.034. Epub 2011 May 6.

PMID:
21621930
30.

[The five colours of Drosophila chromatin].

Filion G.

Med Sci (Paris). 2011 Mar;27(3):246-8. doi: 10.1051/medsci/2011273246. Epub 2011 Mar 30. French. No abstract available.

31.

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.

32.

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
33.

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.

34.

Phase variation has a role in Burkholderia ambifaria niche adaptation.

Vial L, Groleau MC, Lamarche MG, Filion G, Castonguay-Vanier J, Dekimpe V, Daigle F, Charette SJ, Déziel E.

ISME J. 2010 Jan;4(1):49-60. doi: 10.1038/ismej.2009.95. Epub 2009 Aug 27.

PMID:
19710710
35.

The human protein kinase HIPK2 phosphorylates and downregulates the methyl-binding transcription factor ZBTB4.

Yamada D, Pérez-Torrado R, Filion G, Caly M, Jammart B, Devignot V, Sasai N, Ravassard P, Mallet J, Sastre-Garau X, Schmitz ML, Defossez PA.

Oncogene. 2009 Jul 9;28(27):2535-44. doi: 10.1038/onc.2009.109. Epub 2009 May 18.

PMID:
19448668
36.

In situ detection of antibiotic-resistance elements in single Bacillus cereus spores.

Laflamme C, Gendron L, Turgeon N, Filion G, Ho J, Duchaine C.

Syst Appl Microbiol. 2009 Aug;32(5):323-33. doi: 10.1016/j.syapm.2009.03.003. Epub 2009 May 14.

PMID:
19446419
37.

Permeabilization and hybridization protocols for rapid detection of Bacillus spores using fluorescence in situ hybridization.

Filion G, Laflamme C, Turgeon N, Ho J, Duchaine C.

J Microbiol Methods. 2009 Apr;77(1):29-36. doi: 10.1016/j.mimet.2008.12.009. Epub 2008 Dec 31. Erratum in: J Microbiol Methods. 2009 Nov;79(2):251.

PMID:
19159650
38.

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.

39.

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
40.

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
41.

[Epigenetics and cancer].

Filion GJ, Defossez PA.

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

42.

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.

43.

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.

44.

[Is it possible to sustain health promotion programs in private companies? The case of four Quebec private companies of blue collar workers].

Bilodeau A, Filion G, Labrie L, Bouteiller D, Perreault M.

Can J Public Health. 2005 Mar-Apr;96(2):114-20. French.

PMID:
15850031
45.

[Proteins binding to methylated DNA: interpreters of the epigenetic code].

Filion G, Defossez PA.

Med Sci (Paris). 2004 Jan;20(1):7-8. French. No abstract available.

46.

Feeding management of children with severe cerebral palsy and eating impairment: an exploratory study.

Gisel EG, Tessier MJ, Lapierre G, Seidman E, Drouin E, Filion G.

Phys Occup Ther Pediatr. 2003;23(2):19-44.

PMID:
12951786
47.

Quality of care in public health well child clinics: a neglected issue.

Infante-Rivard C, Filion G, Croteau N, Pineault R.

Child Health Care. 1987 Winter;15(3):178-82.

PMID:
10280038

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