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Our publications in metabolomics research
Blood-Based Multiomics-Guided Detection of a Precancerous Pancreatic Tumor
Anwar MA, Keshteli AH, Yang H, Wang W, Li X, Messier HM, Cullis PR, Borchers CH, Fraser R, Wishart DS. (OMICS. 2024 Apr;28(4):182-192. doi: 10.1089/omi.2023.0278. Epub 2024 Apr 17. PMID: 38634790.)
MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation
Pang Z, Lu Y, Zhou G, Hui F, Xu L, Viau C, Spigelman AF, MacDonald PE, Wishart DS, Li S, Xia J. (Nucleic Acids Res. 2024 Jul 5;52(W1):W398-W406. doi: 10.1093/nar/gkae253. PMID: 38587201; PMCID: PMC11223798.)
Deep Learning-Enabled MS/MS Spectrum Prediction Facilitates Automated Identification Of Novel Psychoactive Substances.
Wang F, Pasin D, Skinnider MA, Liigand J, Kleis JN, Brown D, Oler E, Sajed T, Gautam V, Harrison S, Greiner R, Foster LJ, Dalsgaard PW, Wishart DS. (Anal Chem. 2023 Dec 19;95(50):18326-18334. doi: 10.1021/acs.analchem.3c02413. Epub 2023 Dec 4. PMID: 38048435; PMCID: PMC10733899.)
DrugBank 6.0: the DrugBank Knowledgebase for 2024
Knox C, Wilson M, Klinger CM, Franklin M, Oler E, Wilson A, Pon A, Cox J, Chin NEL, Strawbridge SA, Garcia-Patino M, Kruger R, Sivakumaran A, Sanford S, Doshi R, Khetarpal N, Fatokun O, Doucet D, Zubkowski A, Rayat DY, Jackson H, Harford K, Anjum A, Zakir M, Wang F, Tian S, Lee B, Liigand J, Peters H, Wang RQR, Nguyen T, So D, Sharp M, da Silva R, Gabriel C, Scantlebury J, Jasinski M, Ackerman D, Jewison T, Sajed T, Gautam V, Wishart DS. (Nucleic Acids Res. 2024 Jan 5;52(D1):D1265-D1275. doi: 10.1093/nar/gkad976. PMID: 37953279; PMCID: PMC10767804.)
Metabolome of Newborns with Perinatal Complications
López-Hernández Y, Lima-Rogel V, Mandal R, Zheng J, Zhang L, Oler E, García-López DA, Torres-Calzada C, Mejía-Elizondo AR, Poelsner J, López JA, Zubkowski A, Wishart DS. The Urinary (Metabolites. 2024 Jan 10;14(1):41. doi: 10.3390/metabo14010041. PMID: 38248844; PMCID: PMC10819924.)
Deep Learning-Enabled MS/MS Spectrum Prediction Facilitates Automated Identification Of Novel Psychoactive Substances.
Wang F, Pasin D, Skinnider MA, Liigand J, Kleis JN, Brown D, Oler E, Sajed T, Gautam V, Harrison S, Greiner R, Foster LJ, Dalsgaard PW, Wishart DS. (Anal Chem. 2023 Dec 19;95(50):18326-18334. doi: 10.1021/acs.analchem.3c02413. Epub 2023 Dec 4. PMID: 38048435; PMCID: PMC10733899.)
PathBank 2.0-the pathway database for model organism metabolomics
Wishart DS, Kruger R, Sivakumaran A, Harford K, Sanford S, Doshi R, Kehrtarpal N, Fatokun O, Doucet D, Zubkowski A, Jackson H, Sykes G, Ramirez-Gaona M, Marcu A, Li C, Yee K, Garros C, Rayat DY, Coleongco J, Nandyala T, Gautam V, Oler E. (Nucleic Acids Res. 2024 Jan 5;52(D1):D654-D662. doi: 10.1093/nar/gkad1041. Erratum in: Nucleic Acids Res. 2024 Apr 12;52(6):3486. doi: 10.1093/nar/gkae191. PMID: 37962386; PMCID: PMC10767802.)
Learning self-supervised molecular representations for drug–drug interaction prediction
R Kpanou, P Dallaire, E Rousseau, J Corbeil (BMC bioinformatics 25 (1), 47)
Sample Boosting Algorithm (SamBA)-An interpretable greedy ensemble classifier based on local expertise for fat data
Bauvin B et al. (PMLR 216:130–140, 2023)
Integrating and Reporting Full Multi-View Supervised Learning Experiments Using SuMMIT
Bauvin B et al. (PMRL 183:139–150, 2022)
Generative Flow Networks
Bengio Y. (Yoshua Bengio Web Page 2023)
Flexible protein database based on amino acid k-mers
Déraspe M. et al (Sci Rep 2022 Jun 1;12(1):9101)
HMDB 5.0: the Human Metabolome Database for 2022
Wishart D. et al (Nucleic Acids Res 2022 Jan 7;50(D1):D622-D631.
On the robustness of generalization of drug– drug interaction models
Kpanou R et al. (BMC Bioinformatic, 2021 Oct 4;22(1):477).
Machine learning analysis identifies genes differentiating triple negative breast cancers
Kothari C. et al. (Sci Rep, 2020 Jun 26;10(1):10464.)
Mass spectra alignment using virtual lock-masses
Brochu F. et al. (Sci Rep, 2019 Jun 11;9(1):8469)
Predicting Ion Mobility Collision Cross-Sections Using a Deep Neural Network: DeepCCS
Plante PL. et al. (Ana Chem, 2019 Apr 16;91(8):5191-5199)
Interpretable genotype-to-phenotype classifiers with performance guarantees
Drouin A. et al (Sci Rep, 2019 Mar 11;9(1):4071)