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Journal articles Exploring the human small intestinal luminal microbiome via a newly developed ingestible sampling device Alexandre Tronel, Morgane Roger-Margueritat, Caroline Plazy, Salomé Biennier, Anthony Craspay, Ipsita Mohanty, Stéphanie Cools Portier, Manolo Laiola, Guus Roeselers, Nicolas Mathieu, Marianne Hupe, Pieter C Dorrestein, Jean-Pierre Alcaraz, Donald Martin, Philippe Cinquin, Anne-Sophie Silvent, Joris Giai, Marion Proust, Thomas Soranzo, Elena Buelow, Audrey Le Gouellec
ISME Communications, 2026, 5 (1), ⟨10.1093/ismeco/ycaf224⟩. ⟨hal-05467365⟩
Journal articles Penalized likelihood optimization for censored missing value imputation in proteomics Lucas Etourneau, Laura Fancello, Samuel Wieczorek, Nelle Varoquaux, Thomas Burger
Biostatistics, 2025, 26 (1), ⟨10.1093/biostatistics/kxaf006⟩. ⟨hal-05002295⟩
Conference papers Simulation-based inference of yeast centromeres Eloïse Touron, Pedro Luiz Coelho Rodrigues, Julyan Arbel, Nelle Varoquaux, Michael Arbel
NeurIPS 2025 - 39th Conference on Neural Information Processing Systems Workshop : The 3rd Workshop on Imageomics: Discovering Biological Knowledge from Images Using AI., Dec 2025, Copenhagen, Denmark. pp.1-13, ⟨10.48550/arXiv.2509.00200⟩. ⟨hal-05376939⟩
Preprints, Working Papers, ... Unwelcome guests: characterizing the ecological niche of insertion sequences within prokaryotic genomes Flora Gaudillière, Sophie Abby, Thomas Hindre, Ivan Junier
2025. ⟨hal-05394849⟩
Journal articles Screening of Carbapenemase-producing organisms and Vancomycin Resistant Enterococci by a molecular approach: impact and lessons learned Claire Dinh, Aurélie Hennebique, Mélanie Veloso, Nicolas Gonnet, Isabelle Pelloux, Sandra David-Tchouda, Caroline Landelle, Sandrine Boisset
Journal of Hospital Infection, 2025, Online ahead of print. ⟨10.1016/j.jhin.2025.11.044⟩. ⟨hal-05410938⟩
Journal articles Métabolomique clinique en biologie médicale : cartographie des pratiques, état de l’art et propositions du Groupe de Travail de la Société Française de Biologie Clinique Marie Lenski, Thibaud Lefebvre, Karim Chikh, Pierre-Edouard Grillet, Pascal Reynier, Estelle Pujos-Guillot, Hélène Blasco, François Fenaille, Raphael Thuillier-Duperrier, Audrey Le Gouellec
Annales de Biologie Clinique, 2025, 83 (5), pp.507-520. ⟨10.1684/abc.2025.1996⟩. ⟨hal-05441198⟩
Journal articles The Rechallenge Benefit Score: A Clinical Decision Tool for Patients Progressing After Immunotherapy Caroline Plazy, Mohamed Boussena, Linh Nguyen Phuong, Baptiste Assié Jean, Emmanuel Grolleau, Valerie Gounant, Nouha Chaabane, Chantal Decroisette, Eric Dansin, Hélène Babey, Catherine Daniel, Giroux Leprieur Etienne, David Planchard, Mariona Riuvadets, Anthony Canellas, Youssef Oulkhouir, Maurice Pérol, Anne-Claire Toffart, Sebastien Benzekry, Elisa Gobbini
European Journal of Cancer, 2025. ⟨hal-05240613v1⟩
Preprints, Working Papers, ... Global distribution of isoprenoid quinones across Bacteria Sophie-Carole Chobert, Suraj Kanwar, Olivier Lerouxel, Nelle Varoquaux, Julie Michaud, Ludovic Pelosi, Fabien Pierrel, Sophie S. Abby
2025. ⟨hal-05338460⟩
Journal articles Heterologous plastoquinone production using a newly identified O 2 ‐dependent cyanobacterial hydroxylase Morgane Roger-Margueritat, Margot Beltran, Juliette Schnoebelen, Laura Flandrin, Wafa Rezali, Eline Michel, Sophie S. Abby, Fabien Pierrel
FEBS Journal, 2025, ⟨10.1111/febs.70272⟩. ⟨hal-05302505⟩
Journal articles Studies of the membrane-bound flavocytochrome MsrQ flavin mononucleotide (FMN)-binding site reveal an unexpected ubiquinone cofactor Philippe Carpentier, Fabien Pierrel, Nicolas Duraffourg, Bruno Guigliarelli, Mahmoud Hajj Chehade, Laura Flandrin, Christian Basset, Christelle Caux, Stephane Torelli, Vincent Nivière
FEBS Journal, 2025, 292 (20), pp.5491-5505. ⟨10.1111/febs.70162⟩. ⟨hal-05106061⟩
Journal articles The Emergent Dynamics of Double-Folded Randomly Branching Ring Polymers Elham Ghobadpour, Max Kolb, Ivan Junier, Ralf Everaers
Macromolecules, 2025, 58 (19), pp.10632-10646. ⟨10.1021/acs.macromol.5c00697⟩. ⟨hal-05394796⟩
Journal articles Identification of an extraction protocol from dried blood spots for untargeted metabolomics: application to phenylketonuria Sébastien Vézirian, Valérie Cunin, Carlos Dias, Audrey Le Gouellec, Patrice Faure, Bertrand Toussaint, Christelle Corne, Caroline Plazy
Metabolomics, 2025, 21 (5), pp.141. ⟨10.1007/s11306-025-02338-9⟩. ⟨hal-05467410⟩
Preprints, Working Papers, ... Microbial computing: review and perspectives Paul Ahavi, Audrey Le Gouellec, Jean-Loup Faulon
2025. ⟨hal-05281013⟩
Preprints, Working Papers, ... DNA methylation and immune infiltration mediate the impact of tobacco exposure on pancreatic adenocarcinoma outcome: a high-dimensional mediation analysis Florence Pittion, Elise Amblard, Emilie Devijver, Adeline Samson, Nelle Varoquaux, Magali Richard
2025. ⟨hal-05262669⟩
Conference papers Contribution of multiblock methods for predicting the severity of COVID-19 from clinical, biochemical and metabolomic data Marion Brandolini-Bunlon, Benoit B. Jaillais, Audrey Le Gouellec, Jean-Michel J. -M. Roger, Estelle Pujos-Guillot
Colloquium Chemiometricum Mediterraneum (CCM2025), Société Française de Statistiques - groupe Chimiométrie, Sep 2025, Porquerolles, France. ⟨hal-05265568⟩
Journal articles The hospital sink drain biofilm resistome is independent of the corresponding microbiota, the environment and disinfection measures Aurélie Hennebique, Jostin Monge-Ruiz, Morgane Roger-Margueritat, Patrice Morand, Claire Terreaux-Masson, Max Maurin, Corinne Mercier, Caroline Landelle, Elena Buelow
Water Research, 2025, 284, pp.123902. ⟨10.1016/j.watres.2025.123902⟩. ⟨hal-05200256⟩
Journal articles A scaffold for quinone channeling between membrane and soluble bacterial oxidoreductases M. Broc, M. Cherrier, A. Uzel, R. Arias-Cartin, P. Arnoux, G. Brasseur, F. Seduk, B. Guigliarelli, P. Legrand, F. Pierrel, G. Schoehn, M. Maté, L. Martin, S. Grimaldi, Y. Nicolet, A. Magalon, A. Walburger
Nature Structural and Molecular Biology, 2025, 32, pp.2196-2202. ⟨10.1038/s41594-025-01607-4⟩. ⟨hal-05229188⟩
Software MacSyLib Bertrand Néron, Sophie Abby, Eduardo Rocha
2025, ⟨swh:1:dir:ab0579d9d9fea3b32750df4ccd076ddde3bbce6a;origin=https://github.com/gem-pasteur/macsylib;visit=swh:1:snp:12363be7b9e43518ba1945d24152d3b89b915f6d;anchor=swh:1:rel:54d76b45afdc0bbf3178753ce34003442b2a9afc⟩. ⟨hal-05421770⟩
Poster communications Characterization of swine influenza virus infections in pig herds: A machine learning approach identifying key environmental, physiological, immunological and virological determinants Hellec Elisabeth, Richard Gautier, Hervé Séverine, Fablet Christelle, Bougeard Stéphanie, Thiroux Sarah, Deblanc Céline, Andraud Mathieu, Hirchaud Edouard, Lucas Pierrick, Fonseca Roselyne, Barbier Nicolas, Gorin Stéphane, Quéguiner Stéphane, Eveno Eric, Eono Florent, Poulain Gilles, Kerphérique Stéphane, Blanchard Yannick, Rose Nicolas, Simon Gaëlle
Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jul 2025, Bordeaux, France. ⟨anses-05467801⟩
Journal articles Untargeted and semi-targeted metabolomics approach for profiling small intestinal and fecal metabolome using high-resolution mass spectrometry Alexandre Tronel, Morgane Roger-Margueritat, Caroline Plazy, Valérie Cunin, Ipsita Mohanty, Pieter Dorrestein, Thomas Soranzo, Audrey Le Gouellec
Metabolomics, 2025, 21 (4), pp.84. ⟨10.1007/s11306-025-02288-2⟩. ⟨hal-05467454⟩
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