Keywords

Co-authors

Researcher identifiers

Number of documents

57

Julie Aubert


Journal articles28 documents

  • Mariam Raliou, Doulaye Dembélé, Anna Düvel, Philippe Bolifraud, J. Aubert, et al.. Subclinical endometritis in dairy cattle is associated with distinct mRNA expression patterns in blood and endometrium. PLoS ONE, Public Library of Science, 2019, 14 (8), ⟨10.1371/journal.pone.0220244⟩. ⟨hal-02264367⟩
  • Reine Malek, Pascal Bonnarme, Francoise Irlinger, Pascale Frey-Klett, Djamila Onesime, et al.. Transcriptomic response of Debaryomyces hansenii during mixed culture in a liquid model cheese medium with Yarrowia lipolytica. International Journal of Food Microbiology, Elsevier, 2018, 264, pp.53-62. ⟨10.1016/j.ijfoodmicro.2017.10.026⟩. ⟨hal-01695894⟩
  • Héloïse Chassé, Julie Aubert, Sandrine Boulben, Gildas Le corguillé, Erwan Corre, et al.. Translatome analysis at the egg-to-embryo transition in sea urchin. Nucleic Acids Research, Oxford University Press, 2018, 46 (9), pp.4607 - 4621. ⟨10.1093/nar/gky258⟩. ⟨hal-01803500⟩
  • Tom La Chaise, Morgane Ourry, Lionel Lebreton, Anne-Yvonne Guillerm-Erckelboudt, Juliette Linglin, et al.. Can soil microbial diversity influence plant metabolites and life history traits of a rhizophagous insect?: A demonstration in oilseed rape.. Insect Science, Wiley, 2017, 24 (6), pp.1045-1056. ⟨10.1111/1744-7917.12478⟩. ⟨hal-01661250⟩
  • Eric Dugat-Bony, Cecile Straub, Aurélie Teissandier, Djamila Onesime, Valentin Loux, et al.. Overview of a surface-ripened cheese community functioning by meta-omics analyses. PLoS ONE, Public Library of Science, 2015, 10 (4), pp.e0124360. ⟨10.1371/journal.pone.0124360⟩. ⟨hal-01195505⟩
  • Jenny Veide Vilg, Nallani Vijay Kumar, Ewa Maciaszczyk-Dziubinska, Ewa Sloma, Djamila Onesime, et al.. Elucidating the response of Kluyveromyces lactis to arsenite and peroxide stress and the role of the transcription factor KlYap8. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms , Elsevier, 2014, 1839 (11), pp.1295 - 1306. ⟨10.1016/j.bbagrm.2014.09.004⟩. ⟨hal-01197637⟩
  • Marie-Agnès Dillies, Andrea Rau, Julie Aubert, Christelle Hennequet-Antier, Marine Jeanmougin, et al.. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Briefings in Bioinformatics, Oxford University Press (OUP), 2013, 14 (6), pp.671-683. ⟨10.1093/bib/bbs046⟩. ⟨hal-01521274⟩
  • Agnes Hebert, Marie-Pierre Forquin, Aurelie Roux, Julie Aubert, Christophe Junot, et al.. New insights into sulfur metabolism in yeasts as revealed by studies of yarrowia lipolytica. Applied and Environmental Microbiology, American Society for Microbiology, 2013, 79 (4), pp.1200 - 1211. ⟨10.1128/AEM.03259-12⟩. ⟨hal-01001589⟩
  • Marion Dalmasso, Julie Aubert, Sergine Even, Hélène Falentin, Marie-Bernadette Maillard, et al.. Accumulation of Intracellular Glycogen and Trehalose by Propionibacterium freudenreichii under Conditions Mimicking Cheese Ripening in the Cold. Applied and Environmental Microbiology, American Society for Microbiology, 2012, 78 (17), pp.6357-6364. ⟨10.1128/AEM.00561-12⟩. ⟨hal-02363390⟩
  • Marion Dalmasso, Julie Aubert, Sergine Even, Hélène Falentin, Marie-Bernadette Maillard, et al.. Accumulation of intracellular glycogen and trehalose by [i]Propionibacterium Freudenreichii[/i] under conditions mimicking cheese ripening in the cold. Applied and Environmental Microbiology, American Society for Microbiology, 2012, 78 (17), pp.6357-6364. ⟨10.1128/AEM.00561-12⟩. ⟨hal-01191223⟩
  • Marie-Agnès Dillies, Andrea Rau, Julie Aubert, Christelle Hennequet-Antier, Marine Jeanmougin, et al.. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Briefings in Bioinformatics, Oxford University Press (OUP), 2012, 14 (6), ⟨10.1093/bib/bbs046⟩. ⟨hal-00782486⟩
  • Marion Dalmasso, Julie Aubert, Valérie Briard-Bion, Victoria Chuat, Stéphanie-Marie Deutsch, et al.. Correction: A Temporal -omic Study of Propionibacterium freudenreichii CIRM-BIA1 T Adaptation Strategies in Conditions Mimicking Cheese Ripening in the Cold. PLoS ONE, Public Library of Science, 2012, 7 (4), ⟨10.1371/annotation/e0ff065d-a52d-44f2-8727-328393ed60b6⟩. ⟨hal-02363413⟩
  • Marion Dalmasso, Julie Aubert, Valérie Briard-Bion, Victoria Chuat, Stéphanie-Marie Deutsch, et al.. A Temporal -omic study of propionibacterium freudenreichii CIRM-BIA1T adaptation strategies in conditions mimicking cheese ripening in the cold. PLoS ONE, Public Library of Science, 2012, 7 (1), pp.e29083 (1-15). ⟨10.1371/journal.pone.0029083⟩. ⟨hal-01189567⟩
  • Agnes Hebert, Marie-Pierre Forquin-Gomez, Aurélie Roux, Julie Aubert, Christophe Junot, et al.. Exploration of sulfur metabolism in the yeast Kluyveromyces lactis. Applied Microbiology and Biotechnology, Springer Verlag, 2011, 91 (5), pp.1409-1423. ⟨10.1007/s00253-011-3481-2⟩. ⟨hal-01000029⟩
  • Marie-Pierre Forquin, Agnes Hebert, Aurélie Roux, Julie Aubert, Caroline Proux, et al.. Global regulation of the response to sulfur availability in the cheese-related bacterium Brevibacterium aurantiacum. Applied and Environmental Microbiology, American Society for Microbiology, 2011, 77 (4), pp.1449-1459. ⟨10.1128/AEM.01708-10⟩. ⟨hal-01000027⟩
  • Nathalie Ledée, Carine Munaut, Julie Aubert, Valérie Sérazin, Mona Rahmati, et al.. Specific and extensive endometrial deregulation is present before conception in IVF/ICSI repeated implantation failures (IF) or recurrent miscarriages. Journal of Pathology, Wiley, 2011, 225 (4), pp.554-564. ⟨10.1002/path.2948⟩. ⟨hal-01000290⟩
  • M. Abdelkarim, N. Vintonenko, A. Starzec, A. Robles, J. Aubert, et al.. Invading basement membrane matrix is sufficient for MDA-MB-231 breast cancer cells to develop a atable in vivo metastatic phenotype. PLoS ONE, Public Library of Science, 2011, 6 (8), pp.e23334. ⟨10.1371/journal.pone.0023334⟩. ⟨hal-00705949⟩
  • Felicie Faucon, Emmanuelle Rebours, Claudia Bevilacqua, Jean-Christophe Helbling, Julie Aubert, et al.. Terminal differentiation of goat mammary tissue during pregnancy requires the expression of genes involved in immune functions. Physiological Genomics, American Physiological Society, 2009, 40 (1), pp.61-82. ⟨10. 1152/ physiolgenomics. 00032. 2009⟩. ⟨hal-01193417⟩
  • Nadera Mansouri-Atiia, Julie Aubert, Pierrette Reinaud, Corinne Giraud-Delville, Geraldine Taghouti, et al.. Gene expression profiles of bovine caruncular and intercaruncular endometrium at implantation. Physiological Genomics, American Physiological Society, 2009, 39 (1), pp.14-27. ⟨10.1152/physiolgenomics.90404.2008⟩. ⟨hal-01197513⟩
  • Nadera Mansouri, Olivier Sandra, Julie Aubert, Severine Degrelle, Robin E. Everts, et al.. Endometrium as an early sensor of in vitro embryo manipulation technologies. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2009, 106 (14), pp.5687-5692. ⟨10.1073/pnas.0812722106⟩. ⟨hal-01197509⟩
  • N. Mansouri-Attia, Olivier Sandra, Julie Aubert, Séverine Degrelle, Robin Everts, et al.. Endometrium as an early sensor of in vitro embryo manipulation technologies. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2009, 106 (14), pp.5687-5692. ⟨10.1073/pnas.0812722106⟩. ⟨inserm-02440509⟩
  • Tristan Mary-Huard, Julie Aubert, Nadera Mansouri, Olivier Sandra, Jean-Jacques Daudin. Statistical methodology for the analysis of dye-switch microarray experiments. BMC Bioinformatics, BioMed Central, 2008, 9 (98), ⟨10.1186/1471-2105-9-98⟩. ⟨hal-01197510⟩
  • Marie-Laure Martin-Magniette, Julie Aubert, Avner Bar-Hen, Samira Elftieh, F. Magniette, et al.. Normalization for triple-target microarray experiments. BMC Bioinformatics, BioMed Central, 2008, 9, pp.216. ⟨hal-00270936⟩
  • Marie-Laure Magniette, Julie Aubert, Avner Bar-Hen, Samira Elftieh, Fréderic Magniette, et al.. Normalization for triple-target microarray experiments. BMC Bioinformatics, BioMed Central, 2008, 9, pp.article:216. ⟨10.1186/1471-2105-9-216⟩. ⟨hal-01197566⟩
  • Isabelle M. Frey, Isabel Rubio-Aliaga, Anne Siewert, Daniela Sailer, Aleksey Drobyshev, et al.. Profiling at mRNA, protein and metabolite level reveals alterations in renal amino acid handling and glutathione metabolism in kidney tissue of Pept2-I- mice. Physiological Genomics, American Physiological Society, 2007, 28 (3), pp.301-310. ⟨10.1152/physiolgenomics.00193.2006⟩. ⟨hal-01197531⟩
  • E. Aït Yahya-Graison, Julie Aubert, L. Dauphinot, Isabelle Rivals, Marguerite Prieur, et al.. Classification of variations of HSA21 gene expression in down syndrome lymphoblastoid cell lines : impact on disease phenotype. American Journal of Human Genetics, Elsevier (Cell Press), 2007, 81 (3), pp.475-491. ⟨hal-01208111⟩
  • E. Aït Yahya-Graison, Julie Aubert, Stephane Robin, L. Dauphinot, I. Rivals, et al.. Classification of human chromosome 21 gene-expression variations in down syndrome: Impact on disease phenotypes. American Journal of Human Genetics, Elsevier (Cell Press), 2007, 81 (3), pp.475-491. ⟨10.1086/520000⟩. ⟨hal-01197498⟩
  • Julie Aubert, Avner Bar-Hen, Jean-Jacques Daudin, Stephane Robin. Determination of the regulated genes in microarray experiments using local FDR. BMC Bioinformatics, BioMed Central, 2004, 5 (125), ⟨10.1186/1471-2105-5-125⟩. ⟨hal-01208107⟩

Conference papers20 documents

  • Julie Aubert, Xiaoqiang Wang, Émilie Lebarbier, Stephane Robin. CHMM : an R package for coupled Hidden Markov Models. R User Conference 2017, Jul 2017, Bruxelles, Belgium. ⟨hal-01661257⟩
  • Julie Aubert, Sophie Schbath, Stephane Robin. Latent Block Model for metagenomic data. 17. Journées Ouvertes Biologie Informatique Mathématiques (JOBIM 2016), Jun 2016, Lyon, France. ⟨hal-01661249⟩
  • Julie Aubert, Sophie Schbath, Christophe Mougel, Stephane Robin. Latent Block Model for ecological abundance data. 30. European Meeting of Statisticians, Jul 2015, Amsterdam, Netherlands. ⟨hal-01661254⟩
  • Julie Aubert. Latent Block Model for ecological abundance data. ISB Channel Network, Apr 2015, Nimègues, Netherlands. ⟨hal-01661253⟩
  • Julie Aubert, Sophie Schbath, Béatrice Laroche. Metagenomics data analysis using a latent block model: application to plant-microbial communities interactions in the rhizosphere .. ECMTB14 - European Conference on Mathematical and Theoretical Biology, Jun 2014, Gôteborg, Sweden. pp.1. ⟨hal-01197629⟩
  • Julie Aubert. Modèle à blocs latents pour l'analyse de données métagénomiques. 46. Journées de Statistique, Jun 2014, Rennes, France. ⟨hal-01197625⟩
  • Julie Aubert, Frédéric Fer, Jean-Marie Beckerich. Resilience in a cheese ecosystem. 14. Journées Ouvertes en Biologie, Informatique et Mathématiques - JOBIM 2013, Jul 2013, Toulouse, France. ⟨hal-01661259⟩
  • Xiaoqiang Wang, Émilie Lebarbier, Julie Aubert, Stephane Robin. A multivariate HMM with dependency structure for the detection of copy number variations . 45e Journées de Statistique de la SfDS, May 2013, Toulouse, France. ⟨hal-01589538⟩
  • Julie Aubert. An evaluation of normalization methods for the sequencing depth bias in comparative metagenomics studies. 5. Workshop Statistical Methods for Post-Genomic Data (SMPGD), Jan 2013, Amsterdam, Netherlands. ⟨hal-01661252⟩
  • Julie Aubert, Andrea Rau, Christelle Hennequet-Antier, Marine Jeanmougin, Marie-Agnes Dillies, et al.. Comprehensive evaluation of normalization methods for High-throughput rnaSequencing Data analysis. 4 Workshop of StatSeq COST Action TD0801, Apr 2012, Vérone, Italy. ⟨hal-01661260⟩
  • Julie Aubert, Jean-Jacques Daudin. On the use of the negative binomial regression model for comparing differential expression or abundance with ngs data. 12.Journées Ouvertes en Biologie, Informatique et Mathématiques - JOBIM 2011 , Jun 2011, Paris, France. ⟨hal-01661248⟩
  • Gérard Chaouat, Nathalie Rodde, Marie Petitbarat, Roberta Bulla, Mona Rahmati, et al.. An insight into normal and pathological pregnancies using large-scale microarrays: lessons from microarrays. 7. International Workshop on Reproductive Immunology, Immunological Tolerance and Immunology of Preeclampsia, Aug 2010, Tioman Island, Malaysia. ⟨10.1016/j.jri.2010.12.006⟩. ⟨hal-01239519⟩
  • Tristan Mary-Huard, Julie Aubert, Nadera Mansouri, Sandra Olivier, Jean-Jacques Daudin. Statistical methodology for the analysis of dye-switch microarray experiments. 24. International Biometric Conference, Jul 2008, Dublin, Ireland. 17 p. ⟨hal-01197571⟩
  • Felicie Faucon, Emmanuelle Rebours, Jean-Christophe Helbling, Claudia Bevilacqua, J. Aubert, et al.. Expression de gènes de l'immunité dans le tissu mammaire caprin gestant. Journées Scientifiques, Département de Génétique Animale, Apr 2008, Lacanau, France. ⟨hal-01193347⟩
  • Julie Aubert, Marie-Laure Martin-Magniette, Samira Elftieh, Avner Bar-Hen, Jean-Pierre Renou, et al.. Lowess extension to normalize three dyes cDNA microarray experiments. Journées Ouvertes Biologie Informatique Mathématiques, Jun 2008, Lille, France. ⟨hal-01197563⟩
  • Olivier Sandra, Nadera Mansouri, Julie Aubert, Pierrette Reinaud, Corinne Giraud-Delville, et al.. Impact du conceptus sur le transcriptome de l’endomètre bovin à l’implantation. 15. Rencontres autour des Recherches sur les Ruminants, Dec 2008, Paris, France. ⟨hal-01197538⟩
  • Nadera Mansouri, Laurent Galio, Isabelle Hue, Severine Degrelle, Xavier Vignon, et al.. Gene expression profiles in endometrium of cyclic and pregnant cows during the peri-implantation period. 3. EMBIC (EMBryo Implantation Control) Summer School, Sep 2007, Jena, Germany. ⟨hal-01197494⟩
  • Nadera Mansouri, Olivier Sandra, Julie Aubert, R. Everts, Laurent Galio, et al.. Analysis of gene expression profiles in the ruminant endometrium using a 13K microarray. 2. International Meeting on Mammalian Embryogenomics, Oct 2007, Paris, France. ⟨hal-01197493⟩
  • Jean-Jacques Daudin, Julie Aubert, Nadera Mansouri, G. Chaouat, Olivier Sandra, et al.. Statistical analysis for identifying differentially expressed genes in microarrays data, an overview. 2. International Meeting Mammalian Embryogenomics, Oct 2007, Paris, France. ⟨hal-01197495⟩
  • Nadera Mansouri, Julie Aubert, R.E. Everts, Laurent Galio, Yvan Heyman, et al.. Identification of genes involved in the implantation process in cattle. 3. EMBIC Summer School, Sep 2007, Jena, Germany. ⟨hal-01197496⟩

Poster communications7 documents

  • Julie Aubert, Sophie Schbath, Stephane Robin. Latent Block Model for metagenomic data. 15. European Conference on Computational Biology (ECCB 2016), Workshop "Recent Computational Advances in Metagenomics (RCAM)", Sep 2016, La Haye, Netherlands. 2016. ⟨hal-01661258⟩
  • Julie Aubert, Christelle Hennequet-Antier, Cyprien Guerin, Delphine Labourdette, Anne de la Foye, et al.. How to Design a good RNA-Seq experiment in an interdisciplinary context?. European conference on Computational Biology, Sep 2014, Strasbourg, France. 2014. ⟨hal-01462728⟩
  • Julie Aubert, Frédéric Fer, Jean-Marie Beckerich. Combining kinetic modeling and transcriptomic analysis to study the resilience 2014 on a model of microbial ecosystem. ECCB'14 : European Conference on Computational Biology, Sep 2014, Strasbourg, France. 2014. ⟨hal-01661256⟩
  • Clémentine Lepinay, Céline Faivre-Primot, Florence Deau, Julie Aubert, Sébastien Terrat, et al.. Soil microbial diversity effects on primary production and symbiotic interactions. 32. New Phytologist Symposium. Plant interactions with other organisms: molecules, ecology and evolution, Nov 2013, Buenos Aires, Argentina. 2013. ⟨hal-01197630⟩
  • A. Hébert, M.P. Forquin, J. Aubert, S. Luiggi, S. Landaud, et al.. Analyse de l’expression de Kluyveromyces lactis en interaction avec Brevibacterium aurantiacum . Journées des Microbiologistes de l’INRA, Nov 2012, L’Isle-sur-la-Sorgue, France. 2012. ⟨hal-01566447⟩
  • Marion Dalmasso, Julie Aubert, Stéphanie-Marie Deutsch, Hélène Falentin, J. Tanskanen, et al.. Adaptation and survival strategies of Propionibacterium freudenreichii under conditions mimicking cheese ripening in the cold. 6.IDF Cheese Ripening & Technology Symposium, May 2012, Madison, France. 2012. ⟨hal-01191245⟩
  • Marion Dalmasso, Julie Aubert, Stéphanie-Marie Deutsch, Hélène Falentin, J. Tanskanen, et al.. Stratégie d’adaptation et de survie de Propionibacterium freudenreichii dans des conditions simulant celle du fromage à basse température. Journéés des Microbiologistes de l'INRA 2012, Nov 2012, L'Isle sur la Sorgue, France. 2012. ⟨hal-01191287⟩

Book sections1 document

  • Pierre Peyret, Julie Aubert, Vincent Breton, François Enault, Line Le Gall, et al.. Qualité des données NGS : de la séquence aux bases de données. La génomique environnementale, ISTE Editions, 180 p., 2016, 978-1-78405-151-8. ⟨hal-01661251⟩

Theses1 document