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SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data
Varet, Hugo, Brillet-Guéguen, Loraine, Coppée, Jean-Yves, Dillies, Marie-Agnès
Published in PloS one (09.06.2016)
Published in PloS one (09.06.2016)
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Journal Article
Bacteriophages to reduce gut carriage of antibiotic resistant uropathogens with low impact on microbiota composition
Galtier, Matthieu, De Sordi, Luisa, Maura, Damien, Arachchi, Harindra, Volant, Stevenn, Dillies, Marie-Agnès, Debarbieux, Laurent
Published in Environmental microbiology (01.07.2016)
Published in Environmental microbiology (01.07.2016)
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Journal Article
Improvement of variables interpretability in kernel PCA
Briscik, Mitja, Dillies, Marie-Agnès, Déjean, Sébastien
Published in BMC bioinformatics (12.07.2023)
Published in BMC bioinformatics (12.07.2023)
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Journal Article
Bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection
Quereda, Juan J., Dussurget, Olivier, Nahori, Marie-Anne, Ghozlane, Amine, Volant, Stevenn, Dillies, Marie-Agnès, Regnault, Béatrice, Kennedy, Sean, Mondot, Stanislas, Villoing, Barbara, Cossart, Pascale, Pizarro-Cerda, Javier
Published in Proceedings of the National Academy of Sciences - PNAS (17.05.2016)
Published in Proceedings of the National Academy of Sciences - PNAS (17.05.2016)
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Journal Article
Identification and characterization of the genetic changes responsible for the characteristic smooth‐to‐rough morphotype alterations of clinically persistent Mycobacterium abscessus
Pawlik, Alexandre, Garnier, Guillaume, Orgeur, Mickael, Tong, Pin, Lohan, Amanda, Le Chevalier, Fabien, Sapriel, Guillaume, Roux, Anne‐Laure, Conlon, Kevin, Honoré, Nadine, Dillies, Marie‐Agnès, Ma, Laurence, Bouchier, Christiane, Coppée, Jean‐Yves, Gaillard, Jean‐Louis, Gordon, Stephen V., Loftus, Brendan, Brosch, Roland, Herrmann, Jean Louis
Published in Molecular microbiology (01.11.2013)
Published in Molecular microbiology (01.11.2013)
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Journal Article
Nonpathogenic SIV infection of African green monkeys induces a strong but rapidly controlled type I IFN response
Jacquelin, Béatrice, Mayau, Véronique, Targat, Brice, Liovat, Anne-Sophie, Kunkel, Désirée, Petitjean, Gaël, Dillies, Marie-Agnès, Roques, Pierre, Butor, Cécile, Silvestri, Guido, Giavedoni, Luis D., Lebon, Pierre, Barré-Sinoussi, Françoise, Benecke, Arndt, Müller-Trutwin, Michaela C.
Published in The Journal of clinical investigation (01.12.2009)
Published in The Journal of clinical investigation (01.12.2009)
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Journal Article
A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
Dillies, M.-A., Rau, A., Aubert, J., Hennequet-Antier, C., Jeanmougin, M., Servant, N., Keime, C., Marot, G., Castel, D., Estelle, J., Guernec, G., Jagla, B., Jouneau, L., Laloe, D., Le Gall, C., Schaeffer, B., Le Crom, S., Guedj, M., Jaffrezic, F.
Published in Briefings in bioinformatics (01.11.2013)
Published in Briefings in bioinformatics (01.11.2013)
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Journal Article
Lassa virus activates myeloid dendritic cells but suppresses their ability to stimulate T cells
Schaeffer, Justine, Carnec, Xavier, Reynard, Stéphanie, Mateo, Mathieu, Picard, Caroline, Pietrosemoli, Natalia, Dillies, Marie-Agnès, Baize, Sylvain
Published in PLoS pathogens (12.11.2018)
Published in PLoS pathogens (12.11.2018)
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Journal Article
Comparative analysis of viral RNA signatures on different RIG-I-like receptors
Sanchez David, Raul Y, Combredet, Chantal, Sismeiro, Odile, Dillies, Marie-Agnès, Jagla, Bernd, Coppée, Jean-Yves, Mura, Marie, Guerbois Galla, Mathilde, Despres, Philippe, Tangy, Frédéric, Komarova, Anastassia V
Published in eLife (24.03.2016)
Published in eLife (24.03.2016)
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Journal Article
MEMHDX: an interactive tool to expedite the statistical validation and visualization of large HDX-MS datasets
Hourdel, Véronique, Volant, Stevenn, O’Brien, Darragh P., Chenal, Alexandre, Chamot-Rooke, Julia, Dillies, Marie-Agnès, Brier, Sébastien
Published in Bioinformatics (Oxford, England) (15.11.2016)
Published in Bioinformatics (Oxford, England) (15.11.2016)
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Journal Article
GH16 and GH81 family β‐(1,3)‐glucanases in Aspergillus fumigatus are essential for conidial cell wall morphogenesis
Mouyna, Isabelle, Aimanianda, Vishukumar, Hartl, Lukas, Prevost, Marie‐christine, Sismeiro, Odile, Dillies, Marie‐Agnès, Jagla, Bernd, Legendre, Rachel, Coppee, Jean‐Yves, Latgé, Jean‐Paul
Published in Cellular microbiology (01.09.2016)
Published in Cellular microbiology (01.09.2016)
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Journal Article
Identification of the Virulence Landscape Essential for Entamoeba histolytica Invasion of the Human Colon
Thibeaux, Roman, Weber, Christian, Hon, Chung-Chau, Dillies, Marie-Agnès, Avé, Patrick, Coppée, Jean-Yves, Labruyère, Elisabeth, Guillén, Nancy
Published in PLoS pathogens (01.12.2013)
Published in PLoS pathogens (01.12.2013)
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Journal Article
Individual co-variation between viral RNA load and gene expression reveals novel host factors during early dengue virus infection of the Aedes aegypti midgut
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 neglected tropical diseases (19.12.2017)
Published in PLoS neglected tropical diseases (19.12.2017)
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Journal Article
Supervised multiple kernel learning approaches for multi-omics data integration
Briscik, Mitja, Tazza, Gabriele, Vidács, László, Dillies, Marie-Agnès, Déjean, Sébastien
Published in BioData mining (23.11.2024)
Published in BioData mining (23.11.2024)
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Journal Article
Virulence strategies for infecting phagocytes deduced from the in vivo transcriptional program of Legionella pneumophila
Brüggemann, Holger, Hagman, Arne, Jules, Matthieu, Sismeiro, Odile, Dillies, Marie‐Agnès, Gouyette, Catherine, Kunst, Frank, Steinert, Michael, Heuner, Klaus, Coppée, Jean‐Yves, Buchrieser, Carmen
Published in Cellular microbiology (01.08.2006)
Published in Cellular microbiology (01.08.2006)
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Journal Article
Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation
Krin, Evelyne, Pierlé, Sebastian Aguilar, Sismeiro, Odile, Jagla, Bernd, Dillies, Marie-Agnès, Varet, Hugo, Irazoki, Oihane, Campoy, Susana, Rouy, Zoé, Cruveiller, Stéphane, Médigue, Claudine, Coppée, Jean-Yves, Mazel, Didier
Published in BMC genomics (21.05.2018)
Published in BMC genomics (21.05.2018)
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Journal Article
Anti-Inflammatory Effect of Lactobacillus casei on Shigella-Infected Human Intestinal Epithelial Cells
Tien, Meng-Tsung, Girardin, Stephen E, Regnault, Beatrice, Le Bourhis, Lionel, Dillies, Marie-Agnes, Coppee, Jean-Yves, Bourdet-Sicard, Raphaelle, Sansonetti, Philippe J, Pedron, Thierry
Published in Journal of Immunology (15.01.2006)
Published in Journal of Immunology (15.01.2006)
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Journal Article
Docosahexaenoic Acid Inhibits Helicobacter pylori Growth In Vitro and Mice Gastric Mucosa Colonization
Correia, Marta, Michel, Valérie, Matos, António A., Carvalho, Patrícia, Oliveira, Maria J., Ferreira, Rui M., Dillies, Marie-Agnès, Huerre, Michel, Seruca, Raquel, Figueiredo, Ceu, Machado, Jose C., Touati, Eliette
Published in PloS one (17.04.2012)
Published in PloS one (17.04.2012)
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Journal Article
Metabolic plasticity of HIV-specific CD8+ T cells is associated with enhanced antiviral potential and natural control of HIV-1 infection
Angin, Mathieu, Volant, Stevenn, Passaes, Caroline, Lecuroux, Camille, Monceaux, Valérie, Dillies, Marie-Agnès, Valle-Casuso, José Carlos, Pancino, Gianfranco, Vaslin, Bruno, Le Grand, Roger, Weiss, Laurence, Goujard, Cecile, Meyer, Laurence, Boufassa, Faroudy, Müller-Trutwin, Michaela, Lambotte, Olivier, Sáez-Cirión, Asier
Published in Nature metabolism (01.07.2019)
Published in Nature metabolism (01.07.2019)
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Journal Article