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Items: 20

1.

MeCP2-E1 isoform is a dynamically expressed, weakly DNA-bound protein with different protein and DNA interactions compared to MeCP2-E2.

Martínez de Paz A, Khajavi L, Martin H, Claveria-Gimeno R, Tom Dieck S, Cheema MS, Sanchez-Mut JV, Moksa MM, Carles A, Brodie NI, Sheikh TI, Freeman ME, Petrotchenko EV, Borchers CH, Schuman EM, Zytnicki M, Velazquez-Campoy A, Abian O, Hirst M, Esteller M, Vincent JB, Malnou CE, Ausió J.

Epigenetics Chromatin. 2019 Oct 10;12(1):63. doi: 10.1186/s13072-019-0298-1.

2.

Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish.

Dennenmoser S, Sedlazeck FJ, Schatz MC, Altmüller J, Zytnicki M, Nolte AW.

Mol Ecol. 2019 Mar;28(6):1491-1505. doi: 10.1111/mec.14969. Epub 2019 Feb 6.

PMID:
30520198
3.

The siRNA suppressor RTL1 is redox-regulated through glutathionylation of a conserved cysteine in the double-stranded-RNA-binding domain.

Charbonnel C, Niazi AK, Elvira-Matelot E, Nowak E, Zytnicki M, de Bures A, Jobet E, Opsomer A, Shamandi N, Nowotny M, Carapito C, Reichheld JP, Vaucheret H, Sáez-Vásquez J.

Nucleic Acids Res. 2017 Nov 16;45(20):11891-11907. doi: 10.1093/nar/gkx820.

4.

mmquant: how to count multi-mapping reads?

Zytnicki M.

BMC Bioinformatics. 2017 Sep 15;18(1):411. doi: 10.1186/s12859-017-1816-4.

5.

The Arabidopsis hnRNP-Q Protein LIF2 and the PRC1 Subunit LHP1 Function in Concert to Regulate the Transcription of Stress-Responsive Genes.

Molitor AM, Latrasse D, Zytnicki M, Andrey P, Houba-Hérin N, Hachet M, Battail C, Del Prete S, Alberti A, Quesneville H, Gaudin V.

Plant Cell. 2016 Sep;28(9):2197-2211. doi: 10.1105/tpc.16.00244. Epub 2016 Aug 5.

6.

Arabidopsis RNASE THREE LIKE2 Modulates the Expression of Protein-Coding Genes via 24-Nucleotide Small Interfering RNA-Directed DNA Methylation.

Elvira-Matelot E, Hachet M, Shamandi N, Comella P, Sáez-Vásquez J, Zytnicki M, Vaucheret H.

Plant Cell. 2016 Feb;28(2):406-25. doi: 10.1105/tpc.15.00540. Epub 2016 Jan 13.

7.

Plants Encode a General siRNA Suppressor That Is Induced and Suppressed by Viruses.

Shamandi N, Zytnicki M, Charbonnel C, Elvira-Matelot E, Bochnakian A, Comella P, Mallory AC, Lepère G, Sáez-Vásquez J, Vaucheret H.

PLoS Biol. 2015 Dec 22;13(12):e1002326. doi: 10.1371/journal.pbio.1002326. eCollection 2015 Dec.

8.

Post-transcriptional gene silencing triggered by sense transgenes involves uncapped antisense RNA and differs from silencing intentionally triggered by antisense transgenes.

Parent JS, Jauvion V, Bouché N, Béclin C, Hachet M, Zytnicki M, Vaucheret H.

Nucleic Acids Res. 2015 Sep 30;43(17):8464-75. doi: 10.1093/nar/gkv753. Epub 2015 Jul 24.

9.

Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation.

Willing EM, Rawat V, Mandáková T, Maumus F, James GV, Nordström KJ, Becker C, Warthmann N, Chica C, Szarzynska B, Zytnicki M, Albani MC, Kiefer C, Bergonzi S, Castaings L, Mateos JL, Berns MC, Bujdoso N, Piofczyk T, de Lorenzo L, Barrero-Sicilia C, Mateos I, Piednoël M, Hagmann J, Chen-Min-Tao R, Iglesias-Fernández R, Schuster SC, Alonso-Blanco C, Roudier F, Carbonero P, Paz-Ares J, Davis SJ, Pecinka A, Quesneville H, Colot V, Lysak MA, Weigel D, Coupland G, Schneeberger K.

Nat Plants. 2015 Feb 2;1:14023. doi: 10.1038/nplants.2014.23.

PMID:
27246759
10.

Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution.

Geering AD, Maumus F, Copetti D, Choisne N, Zwickl DJ, Zytnicki M, McTaggart AR, Scalabrin S, Vezzulli S, Wing RA, Quesneville H, Teycheney PY.

Nat Commun. 2014 Nov 10;5:5269. doi: 10.1038/ncomms6269.

11.

Tedna: a transposable element de novo assembler.

Zytnicki M, Akhunov E, Quesneville H.

Bioinformatics. 2014 Sep 15;30(18):2656-8. doi: 10.1093/bioinformatics/btu365. Epub 2014 Jun 3.

PMID:
24894500
12.

Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters.

Zanni V, Eymery A, Coiffet M, Zytnicki M, Luyten I, Quesneville H, Vaury C, Jensen S.

Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):19842-7. doi: 10.1073/pnas.1313677110. Epub 2013 Nov 18.

13.

RNA at 92 °C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi.

Toffano-Nioche C, Ott A, Crozat E, Nguyen AN, Zytnicki M, Leclerc F, Forterre P, Bouloc P, Gautheret D.

RNA Biol. 2013 Jul;10(7):1211-20. doi: 10.4161/rna.25567. Epub 2013 Jul 2.

14.

Detection of non-coding RNA in bacteria and archaea using the DETR'PROK Galaxy pipeline.

Toffano-Nioche C, Luo Y, Kuchly C, Wallon C, Steinbach D, Zytnicki M, Jacq A, Gautheret D.

Methods. 2013 Sep 1;63(1):60-5. doi: 10.1016/j.ymeth.2013.06.003. Epub 2013 Jun 25.

15.

Identification of a novel microRNA (miRNA) from rice that targets an alternatively spliced transcript of the Nramp6 (Natural resistance-associated macrophage protein 6) gene involved in pathogen resistance.

Campo S, Peris-Peris C, Siré C, Moreno AB, Donaire L, Zytnicki M, Notredame C, Llave C, San Segundo B.

New Phytol. 2013 Jul;199(1):212-27. doi: 10.1111/nph.12292. Epub 2013 Apr 29.

16.

Efficient comparison of sets of intervals with NC-lists.

Zytnicki M, Luo Y, Quesneville H.

Bioinformatics. 2013 Apr 1;29(7):933-9. doi: 10.1093/bioinformatics/btt070. Epub 2013 Feb 14.

PMID:
23413438
17.

Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis.

Schbath S, Martin V, Zytnicki M, Fayolle J, Loux V, Gibrat JF.

J Comput Biol. 2012 Jun;19(6):796-813. doi: 10.1089/cmb.2012.0022. Epub 2012 Apr 16.

18.

S-MART, a software toolbox to aid RNA-Seq data analysis.

Zytnicki M, Quesneville H.

PLoS One. 2011;6(10):e25988. doi: 10.1371/journal.pone.0025988. Epub 2011 Oct 6.

19.

BlastR--fast and accurate database searches for non-coding RNAs.

Bussotti G, Raineri E, Erb I, Zytnicki M, Wilm A, Beaudoing E, Bucher P, Notredame C.

Nucleic Acids Res. 2011 Sep 1;39(16):6886-95. doi: 10.1093/nar/gkr335. Epub 2011 May 30.

20.

Long noncoding RNAs with enhancer-like function in human cells.

Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, Guigo R, Shiekhattar R.

Cell. 2010 Oct 1;143(1):46-58. doi: 10.1016/j.cell.2010.09.001.

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