SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data

by Varet, Hugo, Brillet-Guéguen, Loraine, Coppée, Jean-Yves, Dillies, Marie-Agnès
Published in PLoS One (2016)

Non-Pathogenic Mopeia Virus Induces More Robust Activation of Plasmacytoid Dendritic Cells than Lassa Virus

by Schaeffer, Justine, Reynard, Stéphanie, Carnec, Xavier, Pietrosemoli, Natalia, Dillies, Marie-Agnès, Baize, Sylvain
Published in Viruses (2019)

The Global Regulator CodY Regulates Toxin Gene Expression in Bacillus anthracis and Is Required for Full Virulence

by van Schaik, Willem, Château, Alice, Dillies, Marie-Agnès, Coppée, Jean-Yves, Sonenshein, Abraham L., Fouet, Agnès
Published 2009

Gene expression analysis in EBV-infected ataxia-telangiectasia cell lines by RNA-sequencing reveals protein synthesis defect and immune abnormalities

by Tatfi, Moussab, Perthame, Emeline, Hillion, Kenzo-Hugo, Dillies, Marie-Agnès, Menager, Hervé, Hermine, Olivier, Suarez, Felipe
Published in Orphanet J Rare Dis (2021)

Lassa virus activates myeloid dendritic cells but suppresses their ability to stimulate T cells

by Schaeffer, Justine, Carnec, Xavier, Reynard, Stéphanie, Mateo, Mathieu, Picard, Caroline, Pietrosemoli, Natalia, Dillies, Marie-Agnès, Baize, Sylvain
Published in PLoS Pathog (2018)

Genomic determinants for initiation and length of natural antisense transcripts in Entamoeba histolytica

by Mornico, Damien, Hon, Chung-Chau, Koutero, Mikael, Weber, Christian, Coppee, Jean-Yves, Dillies, Marie-Agnes, Guillen, Nancy
Published in Sci Rep (2020)

Overexpression of the Heterochromatinization Factor BAHD1 in HEK293 Cells Differentially Reshapes the DNA Methylome on Autosomes and X Chromosome

by Libertini, Emanuele, Lebreton, Alice, Lakisic, Goran, Dillies, Marie-Agnès, Beck, Stephan, Coppée, Jean-Yves, Cossart, Pascale, Bierne, Hélène
Published in Front Genet (2015)

MEMHDX: an interactive tool to expedite the statistical validation and visualization of large HDX-MS datasets

by Hourdel, Véronique, Volant, Stevenn, O’Brien, Darragh P., Chenal, Alexandre, Chamot-Rooke, Julia, Dillies, Marie-Agnès, Brier, Sébastien
Published in Bioinformatics (2016)

Identification of the Virulence Landscape Essential for Entamoeba histolytica Invasion of the Human Colon

by Thibeaux, Roman, Weber, Christian, Hon, Chung-Chau, Dillies, Marie-Agnès, Avé, Patrick, Coppée, Jean-Yves, Labruyère, Elisabeth, Guillén, Nancy
Published 2013

Extensive transcriptome analysis correlates the plasticity of Entamoeba histolytica pathogenesis to rapid phenotype changes depending on the environment

by Weber, Christian, Koutero, Mikael, Dillies, Marie-Agnes, Varet, Hugo, Lopez-Camarillo, Cesar, Coppée, Jean Yves, Hon, Chung-Chau, Guillén, Nancy
Published in Sci Rep (2016)

Expanding the RpoS/σ(S)-Network by RNA Sequencing and Identification of σ(S)-Controlled Small RNAs in Salmonella

by Lévi-Meyrueis, Corinne, Monteil, Véronique, Sismeiro, Odile, Dillies, Marie-Agnès, Monot, Marc, Jagla, Bernd, Coppée, Jean-Yves, Dupuy, Bruno, Norel, Françoise
Published 2014

Temporal transcriptomic response during arsenic stress in <it>Herminiimonas arsenicoxydans</it>

by Arsène-Ploetze Florence, Coppee Jean-Yves, Dillies Marie-Agnès, Proux Caroline, Fardeau Marie-Laure, Koechler Sandrine, Cleiss-Arnold Jessica, Bertin Philippe N
Published 2010-12-01

Transcriptome analysis of antigenic variation in Plasmodium falciparum - var silencing is not dependent on antisense RNA

by Ralph, Stuart A, Bischoff, Emmanuel, Mattei, Denise, Sismeiro, Odile, Dillies, Marie-Agnès, Guigon, Ghislaine, Coppee, Jean-Yves, David, Peter H, Scherf, Artur
Published 2005

Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans

by Cleiss-Arnold, Jessica, Koechler, Sandrine, Proux, Caroline, Fardeau, Marie-Laure, Dillies, Marie-Agnès, Coppee, Jean-Yves, Arsène-Ploetze, Florence, Bertin, Philippe N
Published 2010

Normal and Cystic Fibrosis Human Bronchial Epithelial Cells Infected with Pseudomonas aeruginosa Exhibit Distinct Gene Activation Patterns

by Balloy, Viviane, Varet, Hugo, Dillies, Marie-Agnès, Proux, Caroline, Jagla, Bernd, Coppée, Jean-Yves, Tabary, Olivier, Corvol, Harriet, Chignard, Michel, Guillot, Loïc
Published in PLoS One (2015)

Individual co-variation between viral RNA load and gene expression reveals novel host factors during early dengue virus infection of the Aedes aegypti midgut

by Raquin, Vincent, Merkling, Sarah Hélène, Gausson, Valérie, Moltini-Conclois, Isabelle, Frangeul, Lionel, Varet, Hugo, Dillies, Marie-Agnès, Saleh, Maria-Carla, Lambrechts, Louis
Published in PLoS Negl Trop Dis (2017)

A Putative Regulatory Genetic Locus Modulates Virulence in the Pathogen Leptospira interrogans

by Eshghi, Azad, Becam, Jérôme, Lambert, Ambroise, Sismeiro, Odile, Dillies, Marie-Agnès, Jagla, Bernd, Wunder, Elsio A., Ko, Albert I., Coppee, Jean-Yves, Goarant, Cyrille, Picardeau, Mathieu
Published 2014

Identification of RNA partners of viral proteins in infected cells

by Komarova, Anastassia V., Combredet, Chantal, Sismeiro, Odile, Dillies, Marie-Agnès, Jagla, Bernd, Sanchez David, Raul Yusef, Vabret, Nicolas, Coppée, Jean-Yves, Vidalain, Pierre-Olivier, Tangy, Frédéric
Published 2013

Endoplasmic Reticulum Stress-Sensing Mechanism Is Activated in Entamoeba histolytica upon Treatment with Nitric Oxide

by Santi-Rocca, Julien, Smith, Sherri, Weber, Christian, Pineda, Erika, Hon, Chung-Chau, Saavedra, Emma, Olivos-García, Alfonso, Rousseau, Sandrine, Dillies, Marie-Agnès, Coppée, Jean-Yves, Guillén, Nancy
Published 2012

Comparison of biofilm formation and motility processes in arsenic‐resistant Thiomonas spp. strains revealed divergent response to arsenite

by Farasin, Julien, Koechler, Sandrine, Varet, Hugo, Deschamps, Julien, Dillies, Marie‐Agnès, Proux, Caroline, Erhardt, Mathieu, Huber, Aline, Jagla, Bernd, Briandet, Romain, Coppée, Jean‐Yves, Arsène‐Ploetze, Florence
Published in Microb Biotechnol (2017)