Selected Publications
Journal Articles
Puig-Castellví F, Pacheco-Tapia R, Deslande M, et al.Puig-Castellví F, Pacheco-Tapia R, Deslande M, Jia M, Andrikopoulos P, Chechi K, Bonnefond A, Froguel P, Dumas ME close, 2023, Advances in the integration of metabolomics and metagenomics for human gut microbiome and their clinical applications, TRAC-Trends in Analytical Chemistry, Vol:167, ISSN:0165-9936
Andrikopoulos P, Aron-Wisnewsky J, Chakaroun R, et al.Andrikopoulos P, Aron-Wisnewsky J, Chakaroun R, Myridakis A, Forslund S, Nielsen T, Adriouch S, Holmes B, Chilloux J, Vieira-Silva S, Falony G, Salem J-E, Andreelli F, Belda E, Kieswich J, Chechi K, Puig-Castellvi F, Chevalier M, Le Chatelier E, Olanipekun M, Hoyles L, Alves R, Helft G, Isnard R, Køber L, Coelho LP, Rouault C, Gauguier D, Gøtze JP, Prifti E, Froguel P, The MetaCardis C, Zucker J-D, Bäckhed F, Vestergaard H, Hansen T, Oppert J-M, Blüher M, Nielsen J, Raes J, Bork P, Yaqoob M, Stumvoll M, Pedersen O, Ehrlich SD, Clément K, Dumas M-E close, 2023, Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide, Nature Communications, ISSN:2041-1723, Pages:1-20
Jones RE, Gruszczyk AV, Schmidt C, et al.Jones RE, Gruszczyk AV, Schmidt C, Hammersley DJ, Mach L, Lee M, Wong J, Yang M, Hatipoglu S, Lota AS, Barnett SN, Toscano-Rivalta R, Owen R, Raja S, De Robertis F, Smail H, De-Souza A, Stock U, Kellman P, Griffin J, Dumas M-E, Martin JL, Saeb-Parsy K, Vazir A, Cleland JGF, Pennell DJ, Bhudia SK, Halliday BP, Noseda M, Frezza C, Murphy MP, Prasad SK close, 2023, Assessment of left ventricular tissue mitochondrial bioenergetics in patients with stable coronary artery disease, Nature Cardiovascular Research, Vol:2, ISSN:2731-0590, Pages:733-745
Pairo-Castineira E, Rawlik K, Bretherick AD, et al.Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, GenOMICC Investigators, SCOURGE Consortium, ISARICC Investigators, 23andMe COVID-19 Team, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, Luchessi AD, Parra EJ, Cruz R, Carracedo A, Fawkes A, Murphy L, Rowan K, Pereira AC, Law A, Fairfax B, Hendry SC, Baillie JK close, 2023, GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19, Nature, Vol:617, ISSN:0028-0836, Pages:764-768
Belda E, Voland L, Tremaroli V, et al.Belda E, Voland L, Tremaroli V, Falony G, Adriouch S, Assmann KE, Prifiti E, Aron-Wisnewsky J, Debedat J, Le Roy T, Nielsen T, Amouyal C, Andre S, Andreelli F, Blueher M, Chakaroun R, Chilloux J, Coelho LP, Dao MC, Das P, Fellahi S, Forslund S, Galleron N, Hansen TH, Holmes B, Ji B, Pedersen HK, Phuong L, Le Chatelier E, Lewinter C, Manneras-Holm L, Marquet F, Myridakis A, Pelloux V, Pons N, Quinquis B, Rouault C, Roume H, Salem J-E, Sokolovska N, Sondertoft NB, Touch S, Vieira-Silva S, Galan P, Holst J, Gotze JP, Kober L, Vestergaard H, Hansen T, Hercberg S, Oppert J-M, Nielsen J, Letunic I, Dumas M-E, Stumvoll M, Pedersen OB, Bork P, Ehrlich SD, Zucker J-D, Baeckhed F, Raes J, Clement K close, 2022, Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism, Gut, Vol:71, ISSN:0017-5749, Pages:2463-2480
Serger E, Luengo-Gutierrez L, Chadwick JS, et al.Serger E, Luengo-Gutierrez L, Chadwick JS, Kong G, Zhou L, Crawford G, Danzi MC, Myridakis A, Brandis A, Bello AT, Muller F, Sanchez-Vassopoulos A, De Virgiliis F, Liddell P, Dumas ME, Strid J, Mani S, Dodd D, Di Giovanni S close, 2022, The gut metabolite indole-3 propionate promotes nerve regeneration and repair, Nature, Vol:607, ISSN:0028-0836, Pages:585-+
Talmor-Barkan Y, Bar N, Shaul AA, et al.Talmor-Barkan Y, Bar N, Shaul AA, Shahaf N, Godneva A, Bussi Y, Lotan-Pompan M, Weinberger A, Shechter A, Chezar-Azerrad C, Arow Z, Hammer Y, Chechi K, Forslund SK, Fromentin S, Dumas M-E, Ehrlich SD, Pedersen O, Kornowski R, Segal E close, 2022, Metabolomic and microbiome profiling reveals personalized risk factors for coronary artery disease, Nature Medicine, Vol:28, ISSN:1078-8956, Pages:295-+
Fromentin S, Forslund SK, Chechi K, et al.Fromentin S, Forslund SK, Chechi K, Aron-Wisnewsky J, Chakaroun R, Nielsen T, Tremaroli V, Ji B, Prifti E, Myridakis A, Chilloux J, Andrikopoulos P, Fan Y, Olanipekun MT, Alves R, Adiouch S, Bar N, Talmor-Barkan Y, Belda E, Caesar R, Coelho LP, Falony G, Fellahi S, Galan P, Galleron N, Helft G, Hoyles L, Isnard R, Le Chatelier E, Julienne H, Olsson L, Pedersen HK, Pons N, Quinquis B, Rouault C, Roume H, Salem J-E, Schmidt TSB, Vieira-Silva S, Li P, Zimmermann-Kogadeeva M, Lewinter C, Sondertoft NB, Hansen TH, Gauguier D, Gotze JP, Kober L, Kornowski R, Vestergaard H, Hansen T, Zucker J-D, Hercberg S, Letunic I, Backhed F, Oppert J-M, Nielsen J, Raes J, Bork P, Stumvoll M, Segal E, Clement K, Dumas M-E, Ehrlich SD, Pedersen O close, 2022, Microbiome and metabolome features of the cardiometabolic disease spectrum, Nature Medicine, Vol:28, ISSN:1078-8956, Pages:303-+
Dejnirattisai W, Huo J, Zhou D, et al.Dejnirattisai W, Huo J, Zhou D, Zahradník J, Supasa P, Liu C, Duyvesteyn HME, Ginn HM, Mentzer AJ, Tuekprakhon A, Nutalai R, Wang B, Dijokaite A, Khan S, Avinoam O, Bahar M, Skelly D, Adele S, Johnson SA, Amini A, Ritter TG, Mason C, Dold C, Pan D, Assadi S, Bellass A, Omo-Dare N, Koeckerling D, Flaxman A, Jenkin D, Aley PK, Voysey M, Costa Clemens SA, Naveca FG, Nascimento V, Nascimento F, Fernandes da Costa C, Resende PC, Pauvolid-Correa A, Siqueira MM, Baillie V, Serafin N, Kwatra G, Da Silva K, Madhi SA, Nunes MC, Malik T, Openshaw PJM, Baillie JK, Semple MG, Townsend AR, Huang K-YA, Tan TK, Carroll MW, Klenerman P, Barnes E, Dunachie SJ, Constantinides B, Webster H, Crook D, Pollard AJ, Lambe T, OPTIC Consortium, ISARIC4C Consortium, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Schreiber G, Stuart DI, Screaton GR close, 2022, SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses, Cell, Vol:185, ISSN:0092-8674, Pages:467-484.e15
Forslund SK, Chakaroun R, Zimmermann-Kogadeeva M, et al.Forslund SK, Chakaroun R, Zimmermann-Kogadeeva M, Marko L, Aron-Wisnewsky J, Nielsen T, Moitinho-Silva L, Schmidt TSB, Falony G, Vieira-Silva S, Adriouch S, Alves RJ, Assmann K, Bastard J-P, Birkner T, Caesar R, Chilloux J, Coelho LP, Fezeu L, Galleron N, Helft G, Isnard R, Ji B, Kuhn M, Le Chatelier E, Myridakis A, Olsson L, Pons N, Prifti E, Quinquis B, Roume H, Salem J-E, Sokolovska N, Tremaroli V, Valles-Colomer M, Lewinter C, Sondertoft NB, Pedersen HK, Hansen TH, Gotze JP, Kober L, Vestergaard H, Hansen T, Zucker J-D, Hercberg S, Oppert J-M, Letunic I, Nielsen J, Backhed F, Ehrlich SD, Dumas M-E, Raes J, Pedersen O, Clement K, Stumvoll M, Bork P close, 2021, Combinatorial, additive and dose-dependent drug-microbiome associations, Nature, Vol:600, ISSN:0028-0836, Pages:500-505
Wickenhagen A, Sugrue E, Lytras S, et al.Wickenhagen A, Sugrue E, Lytras S, Kuchi S, Noerenberg M, Turnbull ML, Loney C, Herder V, Allan J, Jarmson I, Cameron-Ruiz N, Varjak M, Pinto RM, Lee JY, Iselin L, Palmalux N, Stewart DG, Swingler S, Greenwood EJD, Crozier TWM, Gu Q, Davies EL, Clohisey S, Wang B, Maranhao Costa FT, Santana MF, de Lima Ferreira LC, Murphy L, Fawkes A, Meynert A, Grimes G, Filho JLDS, Marti M, Hughes J, Stanton RJ, Wang ECY, Ho A, Davis I, Jarrett RF, Castello A, Robertson DL, Semple MG, Openshaw PJM, Palmarini M, Lehner PJ, Baillie JK, Rihn SJ, Wilson SJ close, 2021, A prenylated dsRNA sensor protects against severe COVID-19, Science, Vol:374, ISSN:0036-8075, Pages:1-18
Drake TM, Riad AM, Fairfield CJ, et al.Drake TM, Riad AM, Fairfield CJ, Egan C, Knight SR, Pius R, Hardwick HE, Norman L, Shaw CA, McLean KA, Thompson AAR, Ho A, Swann OV, Sullivan M, Soares F, Holden KA, Merson L, Plotkin D, Sigfrid L, de Silva TI, Girvan M, Jackson C, Russell CD, Dunning J, Solomon T, Carson G, Olliaro P, Nguyen-Van-Tam JS, Turtle L, Docherty AB, Openshaw PJ, Baillie JK, Harrison EM, Semple MG, ISARIC4C investigators close, 2021, Characterisation of in-hospital complications associated with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol UK: a prospective, multicentre cohort study, The Lancet, Vol:398, ISSN:0140-6736, Pages:223-237
COVID-19 Host Genetics Initiative, 2021, Mapping the human genetic architecture of COVID-19, Nature, Vol:600, ISSN:0028-0836, Pages:472-477
Brial F, Chilloux J, Nielsen T, et al.Brial F, Chilloux J, Nielsen T, Vieira-Silva S, Falony G, Andrikopoulos P, Olanipekun M, Hoyles L, Djouadi F, Neves AL, Rodriguez-Martinez A, Mouawad GI, Pons N, Forslund S, Le-Chatelier E, Le Lay A, Nicholson J, Hansen T, Hyötyläinen T, Clément K, Oresic M, Bork P, Ehrlich SD, Raes J, Pedersen OB, Gauguier D, Dumas M-E close, 2021, Human and preclinical studies of the host-gut microbiome co-metabolite hippurate as a marker and mediator of metabolic health., Gut, Vol:70, ISSN:0017-5749, Pages:2105-2114
Molinaro A, Bel Lassen P, Henricsson M, et al.Molinaro A, Bel Lassen P, Henricsson M, Wu H, Adriouch S, Belda E, Chakaroun R, Nielsen T, Bergh P-O, Rouault C, Andre S, Marquet F, Andreelli F, Salem J-E, Assmann K, Bastard J-P, Forslund S, Le Chatelier E, Falony G, Pons N, Prifti E, Quinquis B, Roume H, Vieira-Silva S, Hansen TH, Pedersen HK, Lewinter C, Sonderskov NB, Kober L, Vestergaard H, Hansen T, Zucker J-D, Galan P, Dumas M-E, Raes J, Oppert J-M, Letunic I, Nielsen J, Bork P, Ehrlich SD, Stumvoll M, Pedersen O, Aron-Wisneswky J, Clement K, Backhed F close, 2020, Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology, Nature Communications, Vol:11, ISSN:2041-1723
Vieira-Silva S, Falony G, Belda E, et al.Vieira-Silva S, Falony G, Belda E, Nielsen T, Aron-Wisnewsky J, Chakaroun R, Forslund SK, Assmann K, Valles-Colomer M, Nguyen TTD, Proost S, Prifti E, Tremaroli V, Pons N, Le Chatelier E, Andreelli F, Bastard J-P, Coelho LP, Galleron N, Hansen TH, Hulot J-S, Lewinter C, Pedersen HK, Quinquis B, Rouault C, Roume H, Salem J-E, Sondertoft NB, Touch S, Dumas M-E, Ehrlich SD, Galan P, Gotze JP, Hansen T, Holst JJ, Kober L, Letunic I, Nielsen J, Oppert J-M, Stumvoll M, Vestergaard H, Zucker J-D, Bork P, Pedersen O, Backhed F, Clement K, Raes J close, 2020, Statin therapy is associated with lower prevalence of gut microbiota dysbiosis, Nature, Vol:581, ISSN:0028-0836, Pages:310-+
Hoyles L, Fernandez-Real J-M, Federici M, et al.Hoyles L, Fernandez-Real J-M, Federici M, Serino M, Abbott J, Charpentier J, Heymes C, Luque JL, Anthony E, Barton RH, Chilloux J, Myridakis A, Martinez-Gili L, Moreno-Navarrete JM, Benhamed F, Azalbert V, Blasco-Baque V, Puig J, Xifra G, Ricart W, Tomlinson C, Woodbridge M, Cardellini M, Davato F, Cardolini I, Porzio O, Gentileschi P, Lopez F, Foufelle F, Butcher SA, Holmes E, Nicholson JK, Postic C, Burcelin R, Dumas M-E close, 2018, Publisher Correction: Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women, Nature Medicine, Vol:24, ISSN:1078-8956, Pages:1628-1628
Hoyles L, Fernández-Real J-M, Federici M, et al.Hoyles L, Fernández-Real J-M, Federici M, Serino M, Abbott J, Charpentier J, Heymes C, Luque JL, Anthony E, Barton RH, Chilloux J, Myridakis A, Martinez-Gili L, Moreno-Navarrete JM, Benhamed F, Azalbert V, Blasco-Baque V, Puig J, Xifra G, Ricart W, Tomlinson C, Woodbridge M, Cardellini M, Davato F, Cardolini I, Porzio O, Gentileschi P, Lopez F, Foufelle F, Butcher SA, Holmes E, Nicholson JK, Postic C, Burcelin R, Dumas M-E close, 2018, Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women., Nat Med, Vol:24, Pages:1070-1080
Hoyles L, Jiménez-Pranteda MJ, Chilloux J, et al.Hoyles L, Jiménez-Pranteda MJ, Chilloux J, Brial F, Myridakis A, Aranias T, Magnan C, Gibson GR, Sanderson JD, Nicholson JK, Gauguier D, McCartney AL, Dumas ME close, 2018, Metabolic retroconversion of trimethylamine N-oxide and the gut microbiota, Microbiome, Vol:6, ISSN:2049-2618
Plovier H, Everard A, Depommier C, et al.Plovier H, Everard A, Depommier C, Van Hul M, Geurts L, Ottman N, Chilloux J, Duparc T, Lichtenstein L, Myridakis A, Delzenne NM, Klievink J, Bhattacharjee A, van der Ark KC, Aalvink S, Martinez LO, Dumas ME, Maiter D, Loumaye A, Hermans MP, Thissen JP, Belzer C, de Vos WM, Cani PD close, 2017, A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice, Nature Medicine, Vol:23, ISSN:1546-170X, Pages:107-113
Shoaie S, Ghaffari P, Kovatcheva-Datchary P, et al.Shoaie S, Ghaffari P, Kovatcheva-Datchary P, Mardinoglu A, Sen P, Pujos-Guillot E, de Wouters T, Juste C, Rizkalla S, Chilloux J, Hoyles L, Nicholson JK, MICRO-Obes consortium, Dore J, Dumas ME, Clement K, Bäckhed F, Nielsen J close, 2015, Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome, Cell Metabolism, Vol:22, ISSN:1932-7420, Pages:320-331
Venkatesh M, Mukherjee S, Wang H, et al.Venkatesh M, Mukherjee S, Wang H, Li H, Sun K, Benechet AP, Qiu Z, Maher L, Redinbo MR, Phillips RS, Fleet JC, Kortagere S, Mukherjee P, Fasano A, Le Ven J, Nicholson JK, Dumas ME, Khanna KM, Mani S close, 2014, Symbiotic bacterial metabolites regulate gastrointestinal barrier function via the Xenobiotic sensor PXR and toll-like receptor 4, Immunity, Vol:41, ISSN:1074-7613, Pages:296-310
Dumas ME, Wilder SP, Bihoreau MT, et al.Dumas ME, Wilder SP, Bihoreau MT, Barton RH, Fearnside JF, Argoud K, D'Amato L, Wallis RH, Blancher C, Keun HC, Baunsgaard D, Scott J, Sidelmann UG, Nicholson JK, Gauguier D close, 2007, Direct quantitative trait locus mapping of mammalian metabolic phenotypes in diabetic and normoglycemic rat models, Nature Genetics, Vol:39, ISSN:1061-4036, Pages:666-672
Dumas M-E, Barton RH, Toye A, et al.Dumas M-E, Barton RH, Toye A, Cloarec O, Blancher C, Rothwell A, Fearnside J, Tatoud R, Blanc V, Lindon JC, Mitchell SC, Holmes E, McCarthy MI, Scott J, Gauguier D, Nicholson J close, 2006, Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice, Proceedings of the National Academy of Sciences of the United States of America, Vol:103, ISSN:0027-8424, Pages:12511-12516
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