• 2025
  Léa Deltourbe, Jamie Sugrue, Elizabeth Maloney, Florian Dubois, Anthony Jaquaniello, Jacob Bergstedt, Etienne Patin, Lluis Quintana-Murci, Molly Ingersoll, Darragh Duffy, Steroid hormone levels vary with sex, aging, lifestyle, and genetics, Science Advances , 2025, 11 (13), pp.eadu6094. ⟨10.1126/sciadv.adu6094⟩.
• 2024
  von Stemann JH, Dubois F, Saint-André V, Bondet V, Posseme C, Charbit B, Quintana-Murci L, Hansen MB, Ostrowski SR, Duffy D, Cytokine Autoantibodies Alter Gene Expression Profiles of Healthy Donors., Eur J Immunol 2025 Jan; 55(1): e202451211.
• 2024
  Bertrand A, Sugrue J, Lou T, Bourke NM, Quintana-Murci L, Saint-André V, O'Farrelly C, Duffy D, Impact of socioeconomic status on healthy immune responses in humans., Immunol Cell Biol 2024 Aug; 102(7): 618-629.
• 2024
  Dott T, Culina S, Chemali R, Mansour CA, Dubois F, Jagla B, Doisne JM, Rogge L, Huetz F, Jönsson F, Commere PH, Di Santo J, Terrier B, Quintana-Murci L, Duffy D, Hasan M, Standardized high-dimensional spectral cytometry protocol and panels for whole blood immune phenotyping in clinical and translational studies., Cytometry A 2024 Feb; 105(2): 124-138.
• 2023
  Delavy M, Sertour N, Patin E, Le Chatelier E, Cole N, Dubois F, Xie Z, Saint-André V, Manichanh C, Walker AW, Quintana-Murci L, Duffy D, d'Enfert C, Bougnoux ME, Consortium MI, Unveiling Candida albicans intestinal carriage in healthy volunteers: the role of micro- and mycobiota, diet, host genetics and immune response., Gut Microbes 2023 Dec; 15(2): 2287618.
• 2023
  José Lista M, Jousset A, Cheng M, SaintAndré V, Perrot E, Rodrigues M, Di Primo C, Gadelle D, Toccafondi E, Segeral E, BerliozTorrent C, Emiliani S, Mergny J, Lavigne M, Correction to: DNA topoisomerase 1 represses HIV-1 promoter activity through its interaction with a guanine quadruplex present in the LTR sequence., Retrovirology 2023 Jul; 20(1): 12.
• 2023
  María José Lista, Anne-Caroline Jousset, Mingpan Cheng, Violaine Saint-André, Elouan Perrot, Melissa Rodrigues, Carmelo Di Primo, Danielle Gadelle, Elenia Toccafondi, Emmanuel Segeral, Clarisse Berlioz-Torrent, Stéphane Emiliani, Jean-Louis Mergny, Marc Lavigne, DNA topoisomerase 1 represses HIV-1 promoter activity through its interaction with a guanine quadruplex present in the LTR sequence, Retrovirology, 2023, 20 (1), pp.10. ⟨10.1186/s12977-023-00625-8⟩.
• 2022
  Bergstedt J, Azzou SAK, Tsuo K, Jaquaniello A, Urrutia A, Rotival M, Lin DTS, MacIsaac JL, Kobor MS, Albert ML, Duffy D, Patin E, Quintana-Murci L, The immune factors driving DNA methylation variation in human blood., Nat Commun 2022 Oct; 13(1): 5895.
• 2022
  Posseme C, Llibre A, Charbit B, Bondet V, Rouilly V, Saint-André V, Boussier J, Bergstedt J, Smith N, Townsend L, Sugrue JA, Ní Cheallaigh C, Conlon N, Rotival M, Kobor MS, Mottez E, Pol S, Patin E, Albert ML, Quintana-Murci L, Duffy D, Early IFNβ secretion determines variable downstream IL-12p70 responses upon TLR4 activation., Cell Rep 2022 Jun; 39(13): 110989.
• 2022
  Trutschel D, Bost P, Mariette X, Bondet V, Llibre A, Posseme C, Charbit B, Thorball CW, Jonsson R, Lessard CJ, Felten R, Ng WF, Chatenoud L, Dumortier H, Sibilia J, Fellay J, Brokstad KA, Appel S, Tarn JR, Quintana-Murci L, Mingueneau M, Meyer N, Duffy D, Schwikowski B, Gottenberg JE, Variability of Primary Sjögren’s Syndrome Is Driven by Interferon-α and Interferon-α Blood Levels Are Associated With the Class II HLA-DQ Locus., Arthritis Rheumatol 2022 Dec; 74(12): 1991-2002.
• 2022
  Goncalves P, Doisne JM, Eri T, Charbit B, Bondet V, Posseme C, Llibre A, Casrouge A, Lenoir C, Neven B, Duffy D, Fischer A, Di Santo JP, Defects in mucosal immunity and nasopharyngeal dysbiosis in HSC-transplanted SCID patients with IL2RG/JAK3 deficiency., Blood 2022 Apr; 139(17): 2585-2600.
• 2022
  Sugrue JA, Smith M, Posseme C, Charbit B, , Bourke NM, Duffy D, O'Farrelly C, Rhesus negative males have an enhanced IFNγ-mediated immune response to influenza A virus., Genes Immun 2022 Apr; 23(2): 93-98.
• 2022
  Caron B, Patin E, Rotival M, Charbit B, Albert ML, Quintana-Murci L, Duffy D, Rausell A, Integrative genetic and immune cell analysis of plasma proteins in healthy donors identifies novel associations involving primary immune deficiency genes., Genome Med 2022 Mar; 14(1): 28.
• 2021
  Duffy D, Nemes E, Llibre A, Rouilly V, Musvosvi M, Smith N, Filander E, Africa H, Mabwe S, Jaxa L, Charbit B, Mulenga H, Tameris M, Walzl G, Malherbe S, Thomas S, Hatherill M, Bilek N, Scriba TJ, Albert ML, Immune Profiling Enables Stratification of Patients With Active Tuberculosis Disease or Mycobacterium tuberculosis Infection., Clin Infect Dis 2021 Nov; 73(9): e3398-e3408.
• 2021
  Bastard P, Gervais A, Le Voyer T, Rosain J, Philippot Q, Manry J, Michailidis E, Hoffmann HH, Eto S, Garcia-Prat M, Bizien L, Parra-Martínez A, Yang R, Haljasmägi L, Migaud M, Särekannu K, Maslovskaja J, de Prost N, Tandjaoui-Lambiotte Y, Luyt CE, Amador-Borrero B, Gaudet A, Poissy J, Morel P, Richard P, Cognasse F, Troya J, Trouillet-Assant S, Belot A, Saker K, Garçon P, Rivière JG, Lagier JC, Gentile S, Rosen LB, Shaw E, Morio T, Tanaka J, Dalmau D, Tharaux PL, Sene D, Stepanian A, Megarbane B, Triantafyllia V, Fekkar A, Heath JR, Franco JL, Anaya JM, Solé-Violán J, Imberti L, Biondi A, Bonfanti P, Castagnoli R, Delmonte OM, Zhang Y, Snow AL, Holland SM, Biggs C, Moncada-Vélez M, Arias AA, Lorenzo L, Boucherit S, Coulibaly B, Anglicheau D, Planas AM, Haerynck F, Duvlis S, Nussbaum RL, Ozcelik T, Keles S, Bousfiha AA, El Bakkouri J, Ramirez-Santana C, Paul S, Pan-Hammarström Q, Hammarström L, Dupont A, Kurolap A, Metz CN, Aiuti A, Casari G, Lampasona V, Ciceri F, Barreiros LA, Dominguez-Garrido E, Vidigal M, Zatz M, van de Beek D, Sahanic S, Tancevski I, Stepanovskyy Y, Boyarchuk O, Nukui Y, Tsumura M, Vidaur L, Tangye SG, Burrel S, Duffy D, Quintana-Murci L, Klocperk A, Kann NY, Shcherbina A, Lau YL, Leung D, Coulongeat M, Marlet J, Koning R, Reyes LF, Chauvineau-Grenier A, Venet F, Monneret G, Nussenzweig MC, Arrestier R, Boudhabhay I, Baris-Feldman H, Hagin D, Wauters J, Meyts I, Dyer AH, Kennelly SP, Bourke NM, Halwani R, Sharif-Askari NS, Dorgham K, Sallette J, Sedkaoui SM, AlKhater S, Rigo-Bonnin R, Morandeira F, Roussel L, Vinh DC, Ostrowski SR, Condino-Neto A, Prando C, Bonradenko A, Spaan AN, Gilardin L, Fellay J, Lyonnet S, Bilguvar K, Lifton RP, Mane S, , , , , , , , , , , , , , , , , , , , , Anderson MS, Boisson B, Béziat V, Zhang SY, Vandreakos E, Hermine O, Pujol A, Peterson P, Mogensen TH, Rowen L, Mond J, Debette S, de Lamballerie X, Duval X, Mentré F, Zins M, Soler-Palacin P, Colobran R, Gorochov G, Solanich X, Susen S, Martinez-Picado J, Raoult D, Vasse M, Gregersen PK, Piemonti L, Rodríguez-Gallego C, Notarangelo LD, Su HC, Kisand K, Okada S, Puel A, Jouanguy E, Rice CM, Tiberghien P, Zhang Q, Cobat A, Abel L, Casanova JL, Autoantibodies neutralizing type I IFNs are present in ~4% of uninfected individuals over 70 years old and account for ~20% of COVID-19 deaths., Sci Immunol 2021 Aug; 6(62): .
• 2021
  Menegatti S, Guillemot V, Latis E, Yahia-Cherbal H, Mittermüller D, Rouilly V, Mascia E, Rosine N, Koturan S, Millot GA, Leloup C, Duffy D, Gleizes A, Hacein-Bey-Abina S, , Sellam J, Berenbaum F, Miceli-Richard C, Dougados M, Bianchi E, Rogge L, Immune response profiling of patients with spondyloarthritis reveals signalling networks mediating TNF-blocker function in vivo., Ann Rheum Dis 2021 Apr; 80(4): 475-486.
• 2021
  Byrd AL, Liu M, Fujimura KE, Lyalina S, Nagarkar DR, Charbit B, Bergstedt J, Patin E, Harrison OJ, Quintana-Murci L, Mellman I, Duffy D, Albert ML, , , Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers., J Exp Med 2021 Jan; 218(1): .
• 2021
  Chansard A, Dubrulle N, Poujol de Molliens M, Falanga PB, Stephen T, Hasan M, van Zandbergen G, Aulner N, Shorte SL, David-Watine B, Corrigendum: Unveiling Interindividual Variability of Human Fibroblast Innate Immune Response Using Robust Cell-Based Protocols., Front Immunol 2021 ; 12(): 685768.
• 2021
  Saint-André V, , Computational biology approaches for mapping transcriptional regulatory networks., Comput Struct Biotechnol J 2021 ; 19(): 4884-4895.
• 2020
  Partula V, Deschasaux-Tanguy M, Mondot S, Victor-Bala A, Bouchemal N, Lécuyer L, Bobin-Dubigeon C, Torres MJ, Kesse-Guyot E, Charbit B, Patin E, Assmann KE, Latino-Martel P, Julia C, Galan P, Hercberg S, Quintana-Murci L, Albert ML, Duffy D, Lantz O, Savarin P, Triba MN, Touvier M, , , Associations between untargeted plasma metabolomic signatures and gut microbiota composition in the Milieu Intérieur population of healthy adults., Br J Nutr 2020 Dec; (): 1-11.
• 2020
  Goncalves P, Charbit B, Lenoir C, , Duffy D, Fischer A, Di Santo JP, , Antibody-coated microbiota in nasopharynx of healthy individuals and IVIg-treated patients with hypogammaglobulinemia., J Allergy Clin Immunol 2020 06; 145(6): 1686-1690.e4.
• 2020
  Partula V, Deschasaux M, Druesne-Pecollo N, Latino-Martel P, Desmetz E, Chazelas E, Kesse-Guyot E, Julia C, Fezeu LK, Galan P, Hercberg S, Mondot S, Lantz O, Quintana-Murci L, Albert ML, Duffy D, , Srour B, Touvier M, , Associations between consumption of dietary fibers and the risk of cardiovascular diseases, cancers, type 2 diabetes, and mortality in the prospective NutriNet-Santé cohort., Am. J. Clin. Nutr. 2020 May; (): .
• 2019
  Scepanovic P, Hodel F, Mondot S, Partula V, Byrd A, Hammer C, Alanio C, Bergstedt J, Patin E, Touvier M, Lantz O, Albert ML, Duffy D, Quintana-Murci L, Fellay J, A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals., Microbiome 2019 Sep; 7(1): 130.
• 2019
  Partula V, Mondot S, Torres MJ, Kesse-Guyot E, Deschasaux M, Assmann K, Latino-Martel P, Buscail C, Julia C, Galan P, Hercberg S, Rouilly V, Thomas S, Quintana-Murci L, Albert ML, Duffy D, Lantz O, Touvier M, , , Associations between usual diet and gut microbiota composition: results from the Milieu Intérieur cross-sectional study., Am J Clin Nutr 2019 May; 109(5): 1472-1483.
• 2018
  Clave E, Araujo IL, Alanio C, Patin E, Bergstedt J, Urrutia A, Lopez-Lastra S, Li Y, Charbit B, MacPherson CR, Hasan M, Melo-Lima BL, Douay C, Saut N, Germain M, Trégouët DA, Morange PE, Fontes M, Duffy D, Di Santo JP, Quintana-Murci L, Albert ML, Toubert A, , , Human thymopoiesis is influenced by a common genetic variant within the TCRA-TCRD locus., Sci Transl Med 2018 Sep; 10(457): .
• 2018
  Scepanovic P, Alanio C, Hammer C, Hodel F, Bergstedt J, Patin E, Thorball CW, Chaturvedi N, Charbit B, Abel L, Quintana-Murci L, Duffy D, Albert ML, Fellay J, , , Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccines., Genome Med 2018 Jul; 10(1): 59.
• 2018
  Patin E, Hasan M, Bergstedt J, Rouilly V, Libri V, Urrutia A, Alanio C, Scepanovic P, Hammer C, Jönsson F, Beitz B, Quach H, Lim YW, Hunkapiller J, Zepeda M, Green C, Piasecka B, Leloup C, Rogge L, Huetz F, Peguillet I, Lantz O, Fontes M, Di Santo JP, Thomas S, Fellay J, Duffy D, Quintana-Murci L, Albert ML, , , Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors., Nat Immunol 2018 Mar; 19(3): 302-314.
• 2018
  Kilens S, Meistermann D, Moreno D, Chariau C, Gaignerie A, Reignier A, Lelièvre Y, Casanova M, Vallot C, Nedellec S, Flippe L, Firmin J, Song J, Charpentier E, Lammers J, Donnart A, Marec N, Deb W, Bihouée A, Le Caignec C, Pecqueur C, Redon R, Barrière P, Bourdon J, Pasque V, Soumillon M, Mikkelsen TS, Rougeulle C, Fréour T, David L, , , Parallel derivation of isogenic human primed and naive induced pluripotent stem cells., Nat Commun 2018 Jan; 9(1): 360.
• 2018
  Piasecka B, Duffy D, Urrutia A, Quach H, Patin E, Posseme C, Bergstedt J, Charbit B, Rouilly V, MacPherson CR, Hasan M, Albaud B, Gentien D, Fellay J, Albert ML, Quintana-Murci L, , , Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges., Proc Natl Acad Sci U S A 2018 Jan; 115(3): E488-E497.
• 2016
  Urrutia A, Duffy D, Rouilly V, Posseme C, Djebali R, Illanes G, Libri V, Albaud B, Gentien D, Piasecka B, Hasan M, Fontes M, Quintana-Murci L, Albert ML, , , Standardized Whole-Blood Transcriptional Profiling Enables the Deconvolution of Complex Induced Immune Responses., Cell Rep 2016 Sep; 16(10): 2777-2791.
• 2015
  Chen X, Hasan M, Libri V, Urrutia A, Beitz B, Rouilly V, Duffy D, Patin É, Chalmond B, Rogge L, Quintana-Murci L, Albert ML, Schwikowski B, , , Automated flow cytometric analysis across large numbers of samples and cell types., Clin Immunol 2015 Apr; 157(2): 249-60.
• 2015
  Hasan M, Beitz B, Rouilly V, Libri V, Urrutia A, Duffy D, Cassard L, Di Santo JP, Mottez E, Quintana-Murci L, Albert ML, Rogge L, , , Semi-automated and standardized cytometric procedures for multi-panel and multi-parametric whole blood immunophenotyping., Clin Immunol 2015 Apr; 157(2): 261-76.
• 2015
  Thomas S, Rouilly V, Patin E, Alanio C, Dubois A, Delval C, Marquier LG, Fauchoux N, Sayegrih S, Vray M, Duffy D, Quintana-Murci L, Albert ML, , , The Milieu Intérieur study – an integrative approach for study of human immunological variance., Clin Immunol 2015 Apr; 157(2): 277-93.
• 2014
  Darragh Duffy, Vincent Rouilly, Valentina Libri, Milena Hasan, Benoit Beitz, Mikael David, Alejandra Urrutia, Aurélie Bisiaux, Samuel T Labrie, Annick Dubois, Ivo G Boneca, Cécile Delval, Stéphanie Thomas, Lars Rogge, Manfred Schmolz, Lluis Quintana-Murci, Matthew L Albert, Laurent Abel, Andres Alcover, Philippe Bousso, Ana Cumano, Marc Daëron, Caroline Demangel, Ludovic Deriano, James Di santo, Françoise Dromer, Gérard Eberl, Jost Enninga, Antonio Freitas, Ivo Gomperts-Boneca, Serge Hercberg, Olivier Lantz, Claude Leclerc, Hugo Mouquet, Sandra Pellegrini, Stanislas Pol, Anavaj Sakuntabhai, Olivier Schwartz, Benno Schwikowski, Spencer Shorte, Vassili Soumelis, Frédéric Tangy, Eric Tartour, Antoine Toubert, Marie-Noëlle Ungeheuer, Functional analysis via standardized whole-blood stimulation systems defines the boundaries of a healthy immune response to complex stimuli., Immunity, 2014, 40 (3), pp.436-50. ⟨10.1016/j.immuni.2014.03.002⟩.