mmquant: how to count multi-mapping reads?

por Zytnicki, Matthias
Publicado en BMC Bioinformatics (2017)

S-MART, A Software Toolbox to Aid RNA-seq Data Analysis

por Zytnicki, Matthias, Quesneville, Hadi
Publicado 2011

mmannot: How to improve small–RNA annotation?

por Zytnicki, Matthias, Gaspin, Christine
Publicado en PLoS One (2020)

Mapping Reads on a Genomic Sequence: An Algorithmic Overview and a Practical Comparative Analysis

por Schbath, Sophie, Martin, Véronique, Zytnicki, Matthias, Fayolle, Julien, Loux, Valentin, Gibrat, Jean-François
Publicado 2012

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

por Parent, Jean-Sébastien, Jauvion, Vincent, Bouché, Nicolas, Béclin, Christophe, Hachet, Mélanie, Zytnicki, Matthias, Vaucheret, Hervé
Publicado en Nucleic Acids Res (2015)

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

por Bussotti, Giovanni, Raineri, Emanuele, Erb, Ionas, Zytnicki, Matthias, Wilm, Andreas, Beaudoing, Emmanuel, Bucher, Philipp, Notredame, Cedric
Publicado 2011

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

por Zanni, Vanessa, Eymery, Angéline, Coiffet, Michael, Zytnicki, Matthias, Luyten, Isabelle, Quesneville, Hadi, Vaury, Chantal, Jensen, Silke
Publicado 2013

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

por Elvira-Matelot, Emilie, Hachet, Mélanie, Shamandi, Nahid, Comella, Pascale, Sáez-Vásquez, Julio, Zytnicki, Matthias, Vaucheret, Hervé
Publicado en Plant Cell (2016)

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

por Toffano-Nioche, Claire, Ott, Alban, Crozat, Estelle, Nguyen, An N., Zytnicki, Matthias, Leclerc, Fabrice, Forterre, Patrick, Bouloc, Philippe, Gautheret, Daniel
Publicado 2013

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

por Shamandi, Nahid, Zytnicki, Matthias, Charbonnel, Cyril, Elvira-Matelot, Emilie, Bochnakian, Aurore, Comella, Pascale, Mallory, Allison C., Lepère, Gersende, Sáez-Vásquez, Julio, Vaucheret, Hervé
Publicado en PLoS Biol (2015)

Long non-coding RNAs with enhancer-like function in human

por Ørom, Ulf Andersson, Derrien, Thomas, Beringer, Malte, Gumireddy, Kiranmai, Gardini, Alessandro, Bussotti, Giovanni, Lai, Fan, Zytnicki, Matthias, Notredame, Cedric, Huang, Qihong, Guigo, Roderic, Shiekhattar, Ramin
Publicado 2010

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

por Molitor, Anne M., Latrasse, David, Zytnicki, Matthias, Andrey, Philippe, Houba-Hérin, Nicole, Hachet, Mélanie, Battail, Christophe, Del Prete, Stefania, Alberti, Adriana, Quesneville, Hadi, Gaudin, Valérie
Publicado en Plant Cell (2016)

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

por Geering, Andrew D. W., Maumus, Florian, Copetti, Dario, Choisne, Nathalie, Zwickl, Derrick J., Zytnicki, Matthias, McTaggart, Alistair R., Scalabrin, Simone, Vezzulli, Silvia, Wing, Rod A., Quesneville, Hadi, Teycheney, Pierre-Yves
Publicado en Nat Commun (2014)

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

por Charbonnel, Cyril, Niazi, Adnan K., Elvira-Matelot, Emilie, Nowak, Elżbieta, Zytnicki, Matthias, de Bures, Anne, Jobet, Edouard, Opsomer, Alisson, Shamandi, Nahid, Nowotny, Marcin, Carapito, Christine, Reichheld, Jean-Philippe, Vaucheret, Hervé, Sáez-Vásquez, Julio
Publicado en Nucleic Acids Res (2017)

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

por Martínez de Paz, Alexia, Khajavi, Leila, Martin, Hélène, Claveria-Gimeno, Rafael, Tom Dieck, Susanne, Cheema, Manjinder S., Sanchez-Mut, Jose V., Moksa, Malgorzata M., Carles, Annaick, Brodie, Nick I., Sheikh, Taimoor I., Freeman, Melissa E., Petrotchenko, Evgeniy V., Borchers, Christoph H., Schuman, Erin M., Zytnicki, Matthias, Velazquez-Campoy, Adrian, Abian, Olga, Hirst, Martin, Esteller, Manel, Vincent, John B., Malnou, Cécile E., Ausió, Juan
Publicado en Epigenetics Chromatin (2019)

Multi-species annotation of transcriptome and chromatin structure in domesticated animals

por Foissac, Sylvain, Djebali, Sarah, Munyard, Kylie, Vialaneix, Nathalie, Rau, Andrea, Muret, Kevin, Esquerré, Diane, Zytnicki, Matthias, Derrien, Thomas, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, Crisci, Elisa, Dhorne-Pollet, Sophie, Drouet, Françoise, Faraut, Thomas, Gonzalez, Ignacio, Goubil, Adeline, Lacroix-Lamandé, Sonia, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Momal-Leisenring, Raphaelle, Mompart, Florence, Quéré, Pascale, Robelin, David, Cristobal, Magali San, Tosser-Klopp, Gwenola, Vincent-Naulleau, Silvia, Fabre, Stéphane, der Laan, Marie-Hélène Pinard-Van, Klopp, Christophe, Tixier-Boichard, Michèle, Acloque, Hervé, Lagarrigue, Sandrine, Giuffra, Elisabetta
Publicado en BMC Biol (2019)