Julie AUBERT

Identifiants chercheurs

IdHAL :

julie-aubert

ORCID :

0000-0001-5203-5748

IdRef :

203352173

Présentation

Publications

Article dans une revue (33)

A new scenario of pathogen-microbiota interactions involving the oomycete Plasmopara viticola Paola Fournier,Lucile Pellan,Julie Aubert,Patrice This,Corinne Vacher FEMS Microbiology Ecology, 2025, 101 (12), pp.fiaf111. ⟨10.1093/femsec/fiaf111⟩ Article dans une revue hal-05369425v1
Global genotype by environment prediction competition reveals that diverse modeling strategies can deliver satisfactory maize yield estimates Jacob Washburn,José Ignacio Varela,Alencar Xavier,Qiuyue Chen,David Ertlet al. Genetics, 2025, 229 (2), ⟨10.1093/genetics/iyae195⟩ Article dans une revue hal-05201508v1
Medicago truncatula genotype drives the plant nutritional strategy and its associated rhizosphere bacterial communities Anouk Zancarini,Christine Le Signor,Sébastien Terrat,Julie Aubert,Christophe Salonet al. New Phytologist, 2025, 245 (2), pp.767-784. ⟨10.1111/nph.20272⟩ Article dans une revue hal-04835437v1
Unraveling negative biotic interactions determining soil microbial community assembly and functioning Sana Romdhane,Aymé Spor,Julie Aubert,David Bru,Marie-Christine Breuilet al. The International Society of Microbiologial Ecology Journal, 2022, 16 (1), pp.296-306. ⟨10.1038/s41396-021-01076-9⟩ Article dans une revue hal-03604836v1
Model‐based biclustering for overdispersed count data with application in microbial ecology Julie Aubert,Sophie Schbath,Stéphane Robin Methods in Ecology and Evolution, 2021, 12 (6), pp.1050-1061. ⟨10.1111/2041-210X.13582⟩ Article dans une revue hal-03323318v1
Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions E. Lejal,J. Chiquet,J. Aubert,S. Robin,A. Estrada-Peñaet al. Microbiome, 2021, 9 (1), pp.153. ⟨10.1186/s40168-021-01051-8⟩ Article dans une revue hal-03287263v1
Fine-Tuning of Process Parameters Modulates Specific Metabolic Bacterial Activities and Aroma Compound Production in Semi-Hard Cheese Wenfan Cao,Julie Aubert,Marie-Bernadette Maillard,Francoise Boissel,Arlette Leducet al. Journal of Agricultural and Food Chemistry, 2021, ⟨10.1021/acs.jafc.1c01634⟩ Article dans une revue hal-03313075v1
Variational inference for coupled hidden markov models applied to the joint detection of copy number variations Xiaoqiang Wang,Émilie Lebarbier,Julie Aubert,Stephane Robin The international journal of biostatistics, 2019, 15 (1), ⟨10.1515/ijb-2018-0023⟩ Article dans une revue hal-02626026v1
Subclinical endometritis in dairy cattle is associated with distinct mRNA expression patterns in blood and endometrium Mariam Raliou,Doulaye Dembélé,Anna Düvel,Philippe Bolifraud,J. Aubertet al. PLoS ONE, 2019, 14 (8), ⟨10.1371/journal.pone.0220244⟩ Article dans une revue hal-02264367v1
Transcriptomic response of Debaryomyces hansenii during mixed culture in a liquid model cheese medium with Yarrowia lipolytica Reine Malek,Pascal Bonnarme,Francoise Irlinger,Pascale Frey-Klett,Djamila Onesimeet al. International Journal of Food Microbiology, 2018, 264, pp.53-62. ⟨10.1016/j.ijfoodmicro.2017.10.026⟩ Article dans une revue hal-01695894v1
Translatome analysis at the egg-to-embryo transition in sea urchin Héloïse Chassé,Julie Aubert,Sandrine Boulben,Gildas Le corguillé,Erwan Correet al. Nucleic Acids Research, 2018, 46 (9), pp.4607 - 4621. ⟨10.1093/nar/gky258⟩ Article dans une revue hal-01803500v1
Can soil microbial diversity influence plant metabolites and life history traits of a rhizophagous insect? Tom Lachaise,Morgane Ourry,Lionel Lebreton,Anne-Yvonne Guillerm-Erckelboudt,Juliette Linglinet al. Insect Science, 2017, 24 (6), pp.1045-1056. ⟨10.1111/1744-7917.12478⟩ Article dans une revue hal-01661250v1
Overview of a surface-ripened cheese community functioning by meta-omics analyses Eric Dugat-Bony,Cecile Straub,Aurélie Teissandier,Djamila Onesime,Valentin Louxet al. PLoS ONE, 2015, 10 (4), pp.e0124360. ⟨10.1371/journal.pone.0124360⟩ Article dans une revue hal-01195505v1
Elucidating the response of Kluyveromyces lactis to arsenite and peroxide stress and the role of the transcription factor KlYap8 Jenny Veide Vilg,Nallani Vijay Kumar,Ewa Maciaszczyk-Dziubinska,Ewa Sloma,Djamila Onesimeet al. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms , 2014, 1839 (11), pp.1295 - 1306. ⟨10.1016/j.bbagrm.2014.09.004⟩ Article dans une revue istex hal-01197637v1
New insights into sulfur metabolism in yeasts as revealed by studies of yarrowia lipolytica Agnes A. Hebert,Marie-Pierre M.-P. Forquin,Aurelie A. Roux,Julie J. Aubert,Christophe C. Junotet al. Applied and Environmental Microbiology, 2013, 79 (4), pp.1200 - 1211. ⟨10.1128/AEM.03259-12⟩ Article dans une revue hal-01001589v1
A Temporal -omic study of propionibacterium freudenreichii CIRM-BIA1T adaptation strategies in conditions mimicking cheese ripening in the cold Marion Dalmasso,Julie Aubert,Valérie Briard-Bion,Victoria Chuat,Stéphanie-Marie Deutschet al. PLoS ONE, 2012, 7 (1), pp.e29083 (1-15). ⟨10.1371/journal.pone.0029083⟩ Article dans une revue hal-01189567v1
Accumulation of intracellular glycogen and trehalose by [i]Propionibacterium Freudenreichii[/i] under conditions mimicking cheese ripening in the cold Marion Dalmasso,Julie Aubert,Sergine Even,Hélène Falentin,Marie-Bernadette Maillardet al. Applied and Environmental Microbiology, 2012, 78 (17), pp.6357-6364. ⟨10.1128/AEM.00561-12⟩ Article dans une revue hal-01191223v1
Accumulation of Intracellular Glycogen and Trehalose by Propionibacterium freudenreichii under Conditions Mimicking Cheese Ripening in the Cold Marion Dalmasso,Julie Aubert,Sergine Even,Hélène Falentin,Marie-Bernadette Maillardet al. Applied and Environmental Microbiology, 2012, 78 (17), pp.6357-6364. ⟨10.1128/AEM.00561-12⟩ Article dans une revue hal-02363390v1
A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis Marie-Agnès Dillies,Andrea Rau,Julie Aubert,Christelle Hennequet-Antier,Marine Jeanmouginet al. Briefings in Bioinformatics, 2012, 14 (6), pp.671-683. ⟨10.1093/bib/bbs046⟩ Article dans une revue hal-00782486v1
Correction: A Temporal -omic Study of Propionibacterium freudenreichii CIRM-BIA1 T Adaptation Strategies in Conditions Mimicking Cheese Ripening in the Cold Marion Dalmasso,Julie Aubert,Valérie Briard-Bion,Victoria Chuat,Stéphanie-Marie Deutschet al. PLoS ONE, 2012, 7 (4), ⟨10.1371/annotation/e0ff065d-a52d-44f2-8727-328393ed60b6⟩ Article dans une revue hal-02363413v1
Specific and extensive endometrial deregulation is present before conception in IVF/ICSI repeated implantation failures (IF) or recurrent miscarriages Nathalie N. Ledée,Carine C. Munaut,Julie J. Aubert,Valérie V. Sérazin,Mona M. Rahmatiet al. Journal of Pathology, 2011, 225 (4), pp.554-564. ⟨10.1002/path.2948⟩ Article dans une revue hal-01000290v1
Exploration of sulfur metabolism in the yeast Kluyveromyces lactis Agnes A. Hebert,Marie-Pierre Forquin Forquin-Gomez,Aurélie A. Roux,Julie J. Aubert,Christophe C. Junotet al. Applied Microbiology and Biotechnology, 2011, 91 (5), pp.1409-1423. ⟨10.1007/s00253-011-3481-2⟩ Article dans une revue istex hal-01000029v1
Invading basement membrane matrix is sufficient for MDA-MB-231 breast cancer cells to develop a atable in vivo metastatic phenotype M. Abdelkarim,N. Vintonenko,A. Starzec,A. Robles,J. Aubertet al. PLoS ONE, 2011, 6 (8), pp.e23334. ⟨10.1371/journal.pone.0023334⟩ Article dans une revue hal-00705949v1
Global regulation of the response to sulfur availability in the cheese-related bacterium Brevibacterium aurantiacum Marie-Pierre M.-P. Forquin,Agnes A. Hebert,Aurélie A. Roux,Julie J. Aubert,Caroline C. Prouxet al. Applied and Environmental Microbiology, 2011, 77 (4), pp.1449-1459. ⟨10.1128/AEM.01708-10⟩ Article dans une revue hal-01000027v1
Gene expression profiles of bovine caruncular and intercaruncular endometrium at implantation Nadera Mansouri-Atiia,Julie Aubert,Pierrette Reinaud,Corinne Giraud-Delville,Geraldine Taghoutiet al. Physiological Genomics, 2009, 39 (1), pp.14-27. ⟨10.1152/physiolgenomics.90404.2008⟩ Article dans une revue hal-01197513v1
Endometrium as an early sensor of in vitro embryo manipulation technologies N. Mansouri-Attia,Olivier Sandra,Julie J. Aubert,Séverine Degrelle,Robin E Evertset al. Proceedings of the National Academy of Sciences of the United States of America, 2009, 106 (14), pp.5687-5692. ⟨10.1073/pnas.0812722106⟩ Article dans une revue inserm-02440509v1
Terminal differentiation of goat mammary tissue during pregnancy requires the expression of genes involved in immune functions Felicie Faucon,Emmanuelle Rebours,Claudia Bevilacqua,Jean-Christophe Helbling,Julie Aubertet al. Physiological Genomics, 2009, 40 (1), pp.61-82 Article dans une revue hal-01193417v1
Statistical methodology for the analysis of dye-switch microarray experiments Tristan Mary-Huard,Julie Aubert,Nadera Mansouri,Olivier Sandra,Jean-Jacques Daudin BMC Bioinformatics, 2008, 9 (98), ⟨10.1186/1471-2105-9-98⟩ Article dans une revue hal-01197510v1
Normalization for triple-target microarray experiments Marie-Laure Magniette,Julie Aubert,Avner Bar-Hen,Samira Elftieh,Fréderic Magnietteet al. BMC Bioinformatics, 2008, 9, pp.216. ⟨10.1186/1471-2105-9-216⟩ Article dans une revue hal-01197566v1
Classification of variations of HSA21 gene expression in down syndrome lymphoblastoid cell lines : impact on disease phenotype E. Aït Yahya-Graison,Julie Aubert,L. Dauphinot,Isabelle Rivals,Marguerite Prieuret al. American Journal of Human Genetics, 2007, 81 (3), pp.475-491 Article dans une revue hal-01208111v1
Profiling at mRNA, protein and metabolite level reveals alterations in renal amino acid handling and glutathione metabolism in kidney tissue of Pept2-I- mice Isabelle M. Frey,Isabel Rubio-Aliaga,Anne Siewert,Daniela Sailer,Aleksey Drobyshevet al. Physiological Genomics, 2007, 28 (3), pp.301-310. ⟨10.1152/physiolgenomics.00193.2006⟩ Article dans une revue hal-01197531v1
Classification of human chromosome 21 gene-expression variations in down syndrome: Impact on disease phenotypes E. Aït Yahya-Graison,Julie Aubert,Stephane Robin,L. Dauphinot,I. Rivalset al. American Journal of Human Genetics, 2007, 81 (3), pp.475-491. ⟨10.1086/520000⟩ Article dans une revue hal-01197498v1
Determination of the regulated genes in microarray experiments using local FDR Julie Aubert,Avner Bar-Hen,Jean-Jacques Daudin,Stephane Robin BMC Bioinformatics, 2004, 5 (125), ⟨10.1186/1471-2105-5-125⟩ Article dans une revue hal-01208107v1

Thèse (1)

Analyse statistique de données biologiques à haut débit Julie Aubert Statistiques [math.ST]. Université Paris Saclay (COmUE), 2017. Français. ⟨NNT : 2017SACLS048⟩ Thèse tel-01721318v1

Chapitre d'ouvrage (2)

Chapter 6: Using Latent Block Models to Detect Structure in Ecological Networks Julie J. Aubert,Pierre M Barbillon,Sophie Donnet,Vincent Miele Statistical Approaches for Hidden Variables in Ecology., Wiley, pp.117-134, 2022, ⟨10.1002/9781119902799.ch6⟩ Chapitre d'ouvrage hal-03811607v1
Qualité des données NGS : de la séquence aux bases de données Pierre Peyret,Julie Aubert,Vincent Breton,François Enault,Line Le Gallet al. La génomique environnementale, ISTE Editions, 180 p., 2016, 978-1-78405-151-8 Chapitre d'ouvrage hal-01661251v1

Pré-publication, Document de travail (3)

Integration of Proxy Intermediate Omics traits into a Nonlinear Two-Step model for accurate phenotypic prediction Hayato Yoshioka,Tristan Mary-Huard,Julie Aubert,Yusuke Toda,Yoshihiro Ohmoriet al. 2025 Pré-publication, Document de travail (preprint/prepublication) hal-05292871v1
Ridge Redundancy Analysis for High-Dimensional Omics Data Hayato Yoshioka,Julie Aubert,Hiroyoshi Iwata,Tristan Mary-Huard 2025 Pré-publication, Document de travail (preprint/prepublication) hal-05292867v1
Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling Maxime Lecomte,Wenfan Cao,Julie J. Aubert,David James Sherman,Hélène Falentinet al. 2023 Pré-publication, Document de travail hal-04088301v2

Logiciel (4)

TANGO models: numerical multi-omics reconciliation of bacterial fermentation in cheese production Julie Aubert,Hélène Falentin,Clémence Frioux,Simon Labarthe,Maxime Lecomteet al. 2024, ⟨swh:1:dir:0a1da28c523c2f32e1214b5d1c1a60ac17ec29df;origin=https://forgemia.inra.fr/tango/tango_models.git;visit=swh:1:snp:722365d9bf1004d05edfe63717763283d4adf26f;anchor=swh:1:rev:bc0bd9895942ed6d82faa9553c1f0a32f60cbbef⟩ Logiciel hal-04562266v1
shinySbm Théodore Vanrenterghem,Julie J. Aubert,Saint-Clair Chabert-Liddell 2023, ⟨swh:1:dir:1445449338afa5a1399ec8ddf5a24a9cf9671fd3;origin=https://cran.r-project.org/package%3DshinySbm;visit=swh:1:snp:56c5c23f21cf91de166ffc887dd3a1ea0ea40122;anchor=swh:1:rel:7bc4498b353dfb5bb55be365356c0a1fe11d3287⟩ Logiciel hal-04206080v1
cobiclust: Biclustering via Latent Block Model Adapted to Overdispersed Count Data Julie Aubert 2018, ⟨swh:1:dir:b76ffd82ce2f270ad548bf4df9ab9f46ca53a3bf;origin=https://cran.r-project.org/package%3Dcobiclust;visit=swh:1:snp:b65946d4ccbf2ce41b8c9f2fe68f9b23f2bc2c0e;anchor=swh:1:rel:1b4d5f893e459e3c922581321f112decf6c807ae⟩ Logiciel hal-04532764v1
CHMM: Coupled Hidden Markov Models Julie Aubert,Xiaoqiang Wang 2017, ⟨swh:1:dir:931f86746bd8648062f8c78ac1cbe52864f3eeb2;origin=https://cran.r-project.org/package%3DCHMM;visit=swh:1:snp:a71f470404d95f6dfa1d172fd23c8ad7728347c1;anchor=swh:1:rel:cd36fa2bc45e5211ef524cdf219350e358a40713⟩ Logiciel hal-04532830v1