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PeakForest: a multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management.
Paulhe N, Canlet C, Damont A, Peyriga L, Durand S, Deborde C, Alves S, Bernillon S, Berton T, Bir R, Bouville A, Cahoreau E, Centeno D, Costantino R, Debrauwer L, Delabrière A, Duperier C, Emery S, Flandin A, Hohenester U, Jacob D, Joly C, Jousse C, Lagree M, Lamari N, Lefebvre M, Lopez-Piffet C, Lyan B, Maucourt M, Migne C, Olivier MF, Rathahao-Paris E, Petriacq P, Pinelli J, Roch L, Roger P, Roques S, Tabet JC, Tremblay-Franco M, Traïkia M, Warnet A, Zhendre V, Rolin D, Jourdan F, Thévenot E, Moing A, Jamin E, Fenaille F, Junot C, Pujos-Guillot E, Giacomoni F. Paulhe N, et al. Among authors: roger p. Metabolomics. 2022 Jun 14;18(6):40. doi: 10.1007/s11306-022-01899-3. Metabolomics. 2022. PMID: 35699774 Free PMC article.
ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis.
Imbert A, Rompais M, Selloum M, Castelli F, Mouton-Barbosa E, Brandolini-Bunlon M, Chu-Van E, Joly C, Hirschler A, Roger P, Burger T, Leblanc S, Sorg T, Ouzia S, Vandenbrouck Y, Médigue C, Junot C, Ferro M, Pujos-Guillot E, de Peredo AG, Fenaille F, Carapito C, Herault Y, Thévenot EA. Imbert A, et al. Among authors: roger p. Sci Data. 2021 Dec 3;8(1):311. doi: 10.1038/s41597-021-01095-3. Sci Data. 2021. PMID: 34862403 Free PMC article.
PhenoMeNal: processing and analysis of metabolomics data in the cloud.
Peters K, Bradbury J, Bergmann S, Capuccini M, Cascante M, de Atauri P, Ebbels TMD, Foguet C, Glen R, Gonzalez-Beltran A, Günther UL, Handakas E, Hankemeier T, Haug K, Herman S, Holub P, Izzo M, Jacob D, Johnson D, Jourdan F, Kale N, Karaman I, Khalili B, Emami Khonsari P, Kultima K, Lampa S, Larsson A, Ludwig C, Moreno P, Neumann S, Novella JA, O'Donovan C, Pearce JTM, Peluso A, Piras ME, Pireddu L, Reed MAC, Rocca-Serra P, Roger P, Rosato A, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Selivanov V, Spjuth O, Schober D, Thévenot EA, Tomasoni M, van Rijswijk M, van Vliet M, Viant MR, Weber RJM, Zanetti G, Steinbeck C. Peters K, et al. Among authors: roger p. Gigascience. 2019 Feb 1;8(2):giy149. doi: 10.1093/gigascience/giy149. Gigascience. 2019. PMID: 30535405 Free PMC article.
ISA API: An open platform for interoperable life science experimental metadata.
Johnson D, Batista D, Cochrane K, Davey RP, Etuk A, Gonzalez-Beltran A, Haug K, Izzo M, Larralde M, Lawson TN, Minotto A, Moreno P, Nainala VC, O'Donovan C, Pireddu L, Roger P, Shaw F, Steinbeck C, Weber RJM, Sansone SA, Rocca-Serra P. Johnson D, et al. Among authors: roger p. Gigascience. 2021 Sep 16;10(9):giab060. doi: 10.1093/gigascience/giab060. Gigascience. 2021. PMID: 34528664 Free PMC article.
Interoperable and scalable data analysis with microservices: applications in metabolomics.
Emami Khoonsari P, Moreno P, Bergmann S, Burman J, Capuccini M, Carone M, Cascante M, de Atauri P, Foguet C, Gonzalez-Beltran AN, Hankemeier T, Haug K, He S, Herman S, Johnson D, Kale N, Larsson A, Neumann S, Peters K, Pireddu L, Rocca-Serra P, Roger P, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Schober D, Selivanov V, Thévenot EA, van Vliet M, Zanetti G, Steinbeck C, Kultima K, Spjuth O. Emami Khoonsari P, et al. Among authors: roger p. Bioinformatics. 2019 Oct 1;35(19):3752-3760. doi: 10.1093/bioinformatics/btz160. Bioinformatics. 2019. PMID: 30851093 Free PMC article.
Trends in mortality in people with HIV from 1999 to 2020: a multi-cohort collaboration.
Tusch E, Ryom L, Pelchen-Matthews A, Mocroft A, Elbirt D, Oprea C, Günthard HF, Staehelin C, Zangerle R, Suarez I, Vehreschild JJ, Wit F, Menozzi M, d'Arminio Monforte A, Spagnuolo V, Pradier C, Carlander C, Suanzes P, Wasmuth JC, Carr A, Petoumenos K, Borgans F, Bonnet F, De Wit S, El-Sadr W, Neesgaard B, Jaschinski N, Greenberg L, Hosein SR, Gallant J, Vannappagari V, Young L, Sabin C, Lundgren J, Peters L, Reekie J; D:A:D cohort study; RESPOND cohort study. Tusch E, et al. Clin Infect Dis. 2024 Apr 26:ciae228. doi: 10.1093/cid/ciae228. Online ahead of print. Clin Infect Dis. 2024. PMID: 38663013
Ventilator-associated pneumonia related to extended-spectrum beta-lactamase producing Enterobacterales during severe acute respiratory syndrome coronavirus 2 infection: risk factors and prognosis.
Razazi K, Luyt CE, Voiriot G, Rouzé A, Garnier M, Ferré A, Camous L, Heming N, Lapidus N, Charles-Nelson A, Mekontso-Dessap A; COVID-ICU Group on behalf of the REVA Network and the COVID-ICU Investigators. Razazi K, et al. Crit Care. 2024 Apr 20;28(1):131. doi: 10.1186/s13054-024-04906-2. Crit Care. 2024. PMID: 38641851 Free PMC article.
Salvage Therapy Including Foscarnet and Ibalizumab for Multidrug-Resistant Human Immunodeficiency Virus Type 2 Infection.
Bachelard A, Le Hingrat Q, Ferré VM, Lê M, Peytavin G, Damond F, Charpentier C, Fremont Goudot G, Goupil de Bouille J, Lariven S, Delobel P, Yazdanpanah Y, Descamps D, Matheron S, Ghosn J; ANRS CO05 VIH-2 cohort study group. Bachelard A, et al. Clin Infect Dis. 2024 Apr 10;78(4):1005-1010. doi: 10.1093/cid/ciad695. Clin Infect Dis. 2024. PMID: 38630945
Cardiac Adverse Events and Remdesivir in Hospitalized Patients with Coronavirus Disease 2019 (COVID-19): A Post Hoc Safety Analysis of the Randomized DisCoVeRy Trial.
Terzić V, Miantezila Basilua J, Billard N, de Gastines L, Belhadi D, Fougerou-Leurent C, Peiffer-Smadja N, Mercier N, Delmas C, Ferrane A, Dechanet A, Poissy J, Espérou H, Ader F, Hites M, Andrejak C, Greil R, Paiva JA, Staub T, Tacconelli E, Burdet C, Costagliola D, Mentré F, Yazdanpanah Y, Diallo A; DisCoVeRy study group. Terzić V, et al. Clin Infect Dis. 2024 Mar 29:ciae170. doi: 10.1093/cid/ciae170. Online ahead of print. Clin Infect Dis. 2024. PMID: 38552208
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