Publications

• Pang, Z., Xu, L., Viau, C., Lu, Y., Salavati, R., Basu, N., and Xia, J. (2024) MetaboAnalystR 4.0: a unified LC-MS workflow for global metabolomics Nature Communications (doi: 10.1038/s41467-024-48009-6)
• Pang, Z., Lu, Y., Zhou, G., Hui, F., Xu, L., Viau, C., Spigelman, A., MacDonald, P., Wishart, D., Li, S., and Xia, J. (2024) MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation Nucleic Acids Research (doi: 10.1093/nar/gkae253)
• Ewald J., Zhou, G., Lu, Y., Kolic, J., Ellis, C., Johnson, J.D., Macdonald P.E. and Xia, J. (2024) Web-based multi-omics integration using the Analyst software suite Nature Protocols (doi: 10.1038/s41596-023-00950-4)
• Lu, Y., Pang, Z., and Xia, J. (2023) Comprehensive investigation of pathway enrichment methods for functional interpretation of LC-MS global metabolomics data Briefings In Bioinformatics (doi: 10.1093/bib/bbac553)
• Pang, Z., Zhou, G., Ewald, J., Chang, L., Hacariz, O., Basu, N., and Xia, J. (2022) Using MetaboAnalyst 5.0 for LC-HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data Nature Protocols (doi: 10.1038/s41596-022-00710-w)
• Pang, Z., Chong, J., Zhou, G., Morais D., Chang, L., Barrette, M., Gauthier, C., Jacques, PE., Li, S., and Xia, J. (2021) MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights Nucl. Acids Res. (doi: 10.1093/nar/gkab382)
• Pang, Z., Zhou, G., Chong, J. and Xia, J. (2021) Comprehensive Meta-Analysis of COVID-19 Global Metabolomics Datasets Metabolites 11(1), 44 (Functional meta-analysis)
• Pang, Z., Chong, J., Li, S. and Xia, J. (2020) MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics. Metabolites 10(5) 186 (R code underlying MetaboAnalyst web server)
• Chong, J., Wishart, D.S. and Xia, J. (2019) Using MetaboAnalyst 4.0 for Comprehensive and Integrative Metabolomics Data Analysis. Current Protocols in Bioinformatics 68, e86 (128 pages)
• Chong, J., Yamamoto M. and Xia, J. (2019) MetaboAnalystR 2.0: From Raw Spectra to Biological Insights. Metabolites, 9(3), 57. (R code underlying MetaboAnalyst web server)
• Chong, J. and Xia, J. (2018) MetaboAnalystR: an R package for flexible and reproducible analysis of metabolomics data. Bioinformatics, 27 4313–4314. (R code underlying MetaboAnalyst web server)
• Chong, J., Soufan, O., Li, C., Caraus, I., Li, S., Bourque, G., Wishart, D.S. and Xia, J. (2018) MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis. Nucl. Acids Res. 46, W486-494.
• Xia, J. and Wishart, D.S. (2016) Using MetaboAnalyst 3.0 for Comprehensive Metabolomics Data Analysis Current Protocols in Bioinformatics, 55:14.10.1-14.10.91.
• Xia, J., Sinelnikov, I., Han, B., and Wishart, D.S. (2015) MetaboAnalyst 3.0 - making metabolomics more meaningful . Nucl. Acids Res. 43, W251-257.
• Xia, J., Broadhurst, D., Wilson, M. and Wishart, D. (2013) Translational biomarker discovery in clinical metabolomics: an introductory tutorial. Metabolomics, 9, 280-299. (biomarker analysis)
• Xia, J., Mandal, R., Sinelnikov, I., Broadhurst, D., and Wishart, D.S. (2012) MetaboAnalyst 2.0 - a comprehensive server for metabolomic data analysis . Nucl. Acids Res. 40, W127-133.
• Xia, J., Sinelnikov, I., and Wishart, D.S. (2011) MetATT - a web-based metabolomic tool for analyzing time-series and two-factor data sets. Bioinformatics, 27, 2455-2456 (time-series and two-factor analysis)
• Xia, J. and Wishart, D.S. (2011) Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst Nature Protocols 6 (6), 743-760.
• Xia, J. and Wishart, D.S. (2011) Metabolomic data processing, analysis, and interpretation using MetaboAnalyst Current Protocols in Bioinformatics, 14.10.1-14.10.48.
• Xia, J. and Wishart, D.S. (2010) MetPA: a web-based metabolomics tool for pathway analysis and visualization. Bioinformatics, 26, 2342-2344 (metabolic pathway analysis)
• Xia, J. and Wishart, D.S. (2010) MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data. Nucleic Acids Research, 38, W71-77 (metabolite set enrichment analysis)
• Xia, J., Psychogios, N., Young, N. and Wishart, D.S. (2009) MetaboAnalyst: a web server for metabolomic data analysis and interpretation. Nucl. Acids Res. 37, W652-660.