Software Publications

Kruger R, Oler E, Saha S, Poelzer J, Han S, Punsalan MP, Green B, Bushra F, Kyes M, Disu F, Wakoli J, Woudstra R, Tejol E, Fakutan O, Wang F, Lee BL, Tian S, Torres-Calzada C, Berjanski M, MacKay S, Karu N, Kaddurah-Daouk R, Wishart DS. MiMeDB 2.0: An Expanded and Enriched Human Microbial Metabolome Database for 2026. Nucleic Acids Research 2026;54(D1), D623–D634. PMID 41273085

Wishart, D. S., Sajed, T., Pin, M., Poynton, E. F., Goel, B., Lee, B. L., Guo, A. C., Saha, S., Sayeeda, Z., Han, S., Berjanskii, M., Peters, H., Oler, E., Gautam, V., Jordan, T., Kim, J., Ledingham, B., Tretter, Z. M., Koller, J. T., Shreffler, H. A., Stillwell, L. R., Jystad, A. M., Govind, N., Bade, J. L., Sumner, L. W., Linington, R. G. and Cort, J. R. (2024). The Natural Products Magnetic Resonance Database (NP-MRD) for 2025. Nucleic Acids Res. 53(D1): D700-D708.

Jackson, H., Oler, E., Torres-Calzada, C., Kruger, R., Hira, A. S., López-Hernández, Y., Pandit, D., Wang, J., Yang, K., Fatokun, O., Berjanskii, M., MacKay, S., Sajed, T., Han, S., Woudstra, R., Sykes, G., Poelzer, J., Sivakumaran, A., Gautam, V., Wong, G. and Wishart, D. S. (2024). MarkerDB 2.0: a comprehensive molecular biomarker database for 2025. Nucleic Acids Res. 53(D1): D1415–D1426.

Knox, C., Wilson, M., Klinger, C.M., Franklin, M., Oler, E., Wilson, A., Pon, A., Cox, J., Chin, N.E., Strawbridge, S.A., Garcia-Patino, M., Kruger. R., Sivakumaran, A., Sandford, S., Doshi, R., Khetarpal, N., Fatokun, O., Doucet, D., Zubkowski, A., Rayat, D. Y., Jackson, H., Harford, K., Anjum, A., Zakir, M., Wang, F., Tian, S., Lee, B., Liigand, J., Peters, H., Wang, R. Q., Nguyen, T., So, D., Sharp, M., da Silva, R., Gabriel, C., Scantlebury, J., Jasinski, M., Ackerman, D., Jewison, T., Sajed, T., Gautam, V. and Wishart, D. S. (2024). Drugbank 6.0: the drugbank knowledgebase for 2024. Nucleic Acids Res. 52(D1): D1265-D1275.

Wishart, D.S., 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., Carin, L., Yee, K., Garros, C., Rayat, D. Y., Coleongco, J., Nandyala, T., Gautam, V. and Oler, E. (2024). PathBank 2.0—the pathway database for model organism metabolomics. Nucleic Acids Res. 52(D1): D654-D662.

Wishart, D.S. (2024) Knowledge translation and knowledge mobilization from the FoodBAll project. Appl. Physiol. Nutr. Metab. 49(9): 1279-1285.

Wishart, D. S., Oler, E., Peters, H., Guo, A., Girod, S., Han, S., Saha, S., Lui V. W., LeVatte, M., Gautam, V., Kaddurah-Daouk, R., Karu, N. (2023) MiMeDB: the Human Microbial Metabolome Database. Nucleic Acids Res. 51(D1): D611-D620.

Wishart, D. S., Girod, S., Peters, H., Oler, E., Jovel, J., Budinski, Z., Milford, R., Lui, V. W., Sayeeda, Z., Mah, R., Wei, W., Badran, H., Lo, E., Yamamoto, M., Djoumbou-Feunang, Y., Karu, N., Gautam, V. (2023) ChemFOnt: the chemical functional ontology resource. Nucleic Acids Res. 51(D1):

Wishart, D.S., Guo, A., Oler, E., Wang, F., Anjum, A., Peters, H., Dizon, R., Sayeeda, Z., Tian, S., Lee, B.L., Berjanskii, M., Mah, R., Yamamoto, M., Jovel, J., Torres-Calzada, C., Hiebert-Giesbrecht, M., Lui, V.W., Varshavi, D., Varshavi, D., Allen, D., Arndt, D., Khetarpal, N., Sivakumaran, A., Harford, K., Sanford, S., Yee, K., Cao, X., Budinski, Z., Liigand, J., Zhang, L., Zheng, J., Mandal, R., Karu, N., Dambrova, M., Schiöth, H.B., Greiner, R. and Gautam, V. (2022) HMDB 5.0: the Human Metabolome Database for 2022. Nucleic Acids Res. 50(D1): D622-D631.

Wishart, D.S., Sayeeda, Z., Budinski, Z., Guo, A., Lee, B.L., Berjanskii, M., Rout, M., Peters, H., Dizon, R., Mah, R., Torres-Calzada, C., Hiebert-Giesbrecht, M., Varshavi, D., Varshavi, D., Oler, E., Allen, D., Cao, X., Gautam, V., Maras, A., Poynton, E.F., Tavangar, P., Yang, V., van Santen, J.A., Ghosh, R., Sarma, S., Knutson, E., Sullivan, V., Jystad, A.M., Renslow, R., Sumner, L.W., Linington, R.G. and Cort, J.R. (2022) NP-MRD: the Natural Products Magnetic Resonance Database. Nucleic Acids Res. 50(D1):D665-D677.

Mohammed Taha, H., Aalizadeh, R., Alygizakis, N., Antignac, J. P., et al. (2022) The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry. Environ. Sci. Eur. 34(1):1-26,

Wishart, D.S., Bartok, B., Oler, E., Liang, K.Y.H., Budinski, Z., Berjanskii, M., Guo, A., Cao, X. and Wilson, M. (2021) MarkerDB: an online database of molecular biomarkers. Nucleic Acids Res. 49(D1): D1259-D1267.

Wishart, D.S., Li, C., Marcu, A., Badran, H., Pon, A., Budinski, Z., Patron, J., Lipton, D., Cao, X., Oler, E., Li, K., Paccoud, M., Hong, C., Guo, A.C., Chan, C., Wei, W. and Ramirez-Gaona, M. (2020) PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 48(D1):D470-D478.

Neveu, V., Nicolas, G., Salek, R.M., Wishart, D.S. and Scalbert. A. (2020) Exposome-Explorer 2.0: an update incorporating candidate dietary biomarkers and dietary associations with cancer risk. Nucleic Acids Res. 48(D1):D908-D912.

Zakir, M., LeVatte, M. A., & Wishart, D. S. (2025). RT-Pred: A web server for accurate, customized liquid chromatography retention time prediction of chemicals. Journal of chromatography. A, 1747, 465816.

Poelzer, J., Han, S., Saha, S., Oler, E., Kruger, R., Berjanskii, M., MacKay, S., & Wishart, D. S. (2025). BASys2: a next-generation bacterial genome annotation system. Nucleic acids research, 53(W1), W57–W67.

Kernick, K., Woudstra, R., Berjanskii, M., MacKay, S., & Wishart, D. S. (2025). Heatmapper2: web-enabled heat mapping made easy. Nucleic acids research, 53(W1), W316–W323.

Wakoli, J., Anjum, A., Sajed, T., Oler, E., Wang, F., Gautam, V., LeVatte, M. and Wishart, D.S. (2024) GCMS-ID: A webserver for identifying compounds from gas chromatography mass spectrometry experiments. Nucleic Acids Res. 52: W381-W389.

Pang, Z., Lu, Y., Zhou, G., Hui, F., Xu, L., Viau, C., Spigelman, A. F., MacDonald, P. E., Wishart, D. S., Li, S., and Xia, J. (2024). MetaboAnalyst 6.0: Towards a unified platform for metabolomics data processing, analysis and interpretation. Nucleic Acids Res.52:W398-W406.

Rout, M., Lipfert, M., Lee, B. L., Berjanskii, M., Assempour, N., Fresno, R.V., Cayuela, A.S., Dong, Y., Johnson, M., Shahin, H., Gautam, V., Sajed, T., Oler, E. Peters, H., Mandal, R., Wishart, D.S. (2023). MagMet: A fully automated web server for targeted nuclear magnetic resonance metabolomics of plasma and serum. Magn. Reson. Chem. 61(12): 681-704.

Wishart, D.S., Han, S., Saha, S., Oler, E., Peters, H., Grant, J.R., Stothard, P., Gautam, V. (2023) PHASTEST: faster than PHASTER, better than PHAST. Nucleic Acids Res. 51(W1): W443-W450.

Wishart, D.S., Ren, L., Leong-Sit, J., Saha, S., Grant, J.R., Stothard, P., Singh, U., Kropielnicki, A., Oler, E., Peters, H., Gautam, V. (2023) PlasMapper 3.0—a web server for generating, editing, annotating and visualizing publication quality plasmid maps. Nucleic Acids Res. 51(W1):W459-W467,

Wang, F., Allen, D., Tian, S., Oler, E., Gautam, V., Greiner, R., Metz, T.O. and Wishart, D.S. (2022) CFM-ID 4.0 - a web server for accurate MS-based metabolite identification. Nucleic Acids Res. 50(W1): W165-W174.

Wishart, D.S., Tian, S., Allen, D., Oler, E., Peters, H., Lui, V., Gautam, V., Djoumbou-Feunang, Y., Greiner, R. and Metz, T. (2022) BioTransformer 3.0—a Web Server for accurately predicting metabolic transformation products. Nucleic Acids Res. 50(W1):W115-W123.

Wang, F., Liigand, J., Tian, S., Arndt, D., Greiner, R. and Wishart, D.S. (2021) CFM-ID 4.0: More accurate ESI-MS/MS spectral prediction and compound identification. Anal. Chem. 93(34):11692-11700.

Kovur, P., Kovur, K. M., Rayat, D. Y., & Wishart, D. S. (2025). POC Sensor Systems and Artificial Intelligence-Where We Are Now and Where We Are Going?. Biosensors, 15(9), 589.

Jiang, S., Wallace, K., Yang, E., Roper, L., Aryal, G., Lee, D., Lodhi, R.J., Arnau, R., Isenberg, R., Green, B., Wishart, D. (2023) Logistic regression with machine learning sheds light on the problematic sexual behavior phenotype. J. Addict.Med.17(2):174-181.

Wang, K., Khoramjoo, M., Srinivasan, K., Mandal, R., Borchers, C., Wishart, D., Prasad, V. and Oudit, G. (2023). Machine learning analysis of long COVID multiomics reveals clinical phenotypes and prognostic biomarkers. Can. J. Diabetes 47(7): S1.

Wang, F., Pasin, D., Skinnider, M.A., Liigand, J., Kleis, J.N., Brown, D., Oler, E., Sajed, T., Gautam, V., Harrison, S., Greiner, R., Foster, L. J., Dalsgaard, P. W. and Wishart, D. S. (2023). Deep learning-enabled MS/MS spectrum prediction facilitates automated identification of novel psychoactive substances. Anal. Chem. 95(50): 18326-18334.

Suarez Suarez, R.G., Dijk, S.I., Zhang, Z., Focht, G., Navas-López, V., Koletzko, S., Griffiths, A., Wishart, D.S., Greiner, R., Turner, D. and Wine, E. (2022) A176 Utility of machine learning for serum metabolomic data analysis in pediatric Crohn Disease. J. Can. Assoc. Gastroenterol. 5 (1):56–57.