metabolomics-practical

Literature

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Kutmon, M., van Iersel, M. P., Bohler, A., Kelder, T., Nunes, N., Pico, A. R., & Evelo, C. T. (2015). PathVisio 3: An Extendable Pathway Analysis Toolbox. PLOS Computational Biology, 11(2), e1004085. https://doi.org/10.1371/journal.pcbi.1004085
Yurekten, O., Payne, T., Tejera, N., Amaladoss, F. X., Martin, C., Williams, M., & O’Donovan, C. (2023). MetaboLights: open data repository for metabolomics. Nucleic Acids Research, 52(D1), D640–D646. https://doi.org/10.1093/nar/gkad1045
Malik, A., Arsalan, M., Moreno, C., Mosquera, J., Félix, E., Kizilören, T., Muthukrishnan, V., Zdrazil, B., Leach, A. R., & O’Boyle, N. M. (2025). ChEBI: re-engineered for a sustainable future. Nucleic Acids Research, 54(D1), D1768–D1778. https://doi.org/10.1093/nar/gkaf1271
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., … Gautam, V. (2021). HMDB 5.0: the Human Metabolome Database for 2022. Nucleic Acids Research, 50(D1), D622–D631. https://doi.org/10.1093/nar/gkab1062
Conroy, M. J., Andrews, R. M., Andrews, S., Cockayne, L., Dennis, E. A., Fahy, E., Gaud, C., Griffiths, W. J., Jukes, G., Kolchin, M., Mendivelso, K., Lopez-Clavijo, A. F., Ready, C., Subramaniam, S., & O’Donnell, V. B. (2023). LIPID MAPS: update to databases and tools for the lipidomics community. Nucleic Acids Research, 52(D1), D1677–D1682. https://doi.org/10.1093/nar/gkad896
Rutz, A., Sorokina, M., Galgonek, J., Mietchen, D., Willighagen, E., Gaudry, A., Graham, J. G., Stephan, R., Page, R., Vondrášek, J., Steinbeck, C., Pauli, G. F., Wolfender, J.-L., Bisson, J., & Allard, P.-M. (2022). The LOTUS initiative for open knowledge management in natural products research. eLife, 11. https://doi.org/10.7554/elife.70780
Williams, A. J., Grulke, C. M., Edwards, J., McEachran, A. D., Mansouri, K., Baker, N. C., Patlewicz, G., Shah, I., Wambaugh, J. F., Judson, R. S., & Richard, A. M. (2017). The CompTox Chemistry Dashboard: a community data resource for environmental chemistry. Journal of Cheminformatics, 9(1). https://doi.org/10.1186/s13321-017-0247-6
Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J., & Bolton, E. E. (2022). PubChem 2023 update. Nucleic Acids Research, 51(D1), D1373–D1380. https://doi.org/10.1093/nar/gkac956
Agrawal, A., Balcı, H., Hanspers, K., Coort, S. L., Martens, M., Slenter, D. N., Ehrhart, F., Digles, D., Waagmeester, A., Wassink, I., Abbassi-Daloii, T., Lopes, E. N., Iyer, A., Acosta, J. M., Willighagen, L. G., Nishida, K., Riutta, A., Basaric, H., Evelo, C. T., … Pico, A. R. (2023). WikiPathways 2024: next generation pathway database. Nucleic Acids Research, 52(D1), D679–D689. https://doi.org/10.1093/nar/gkad960
Jacobs, A., Williams, D., Hickey, K., Patrick, N., Williams, A. J., Chalk, S., McEwen, L., Willighagen, E., Walker, M., Bolton, E., Sinclair, G., & Sanford, A. (2022). CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community. Journal of Chemical Information and Modeling, 62(11), 2737–2743. https://doi.org/10.1021/acs.jcim.2c00268
Neumann, S., Meier, R., Wenk, M., Elapavalore, A., Nishioka, T., Schulze, T., Stravs, M., Tsugawa, H., Matsuda, F., & Schymanski, E. L. (2025). MassBank: an open and FAIR mass spectral data resource. Nucleic Acids Research, 54(D1), D601–D606. https://doi.org/10.1093/nar/gkaf1193
McKay, B. D., Yirik, M. A., & Steinbeck, C. (2022). Surge: a fast open-source chemical graph generator. Journal of Cheminformatics, 14(1). https://doi.org/10.1186/s13321-022-00604-9
Willighagen, E. L., Mayfield, J. W., Alvarsson, J., Berg, A., Carlsson, L., Jeliazkova, N., Kuhn, S., Pluskal, T., Rojas-Chertó, M., Spjuth, O., Torrance, G., Evelo, C. T., Guha, R., & Steinbeck, C. (2017). The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. Journal of Cheminformatics, 9(1). https://doi.org/10.1186/s13321-017-0220-4

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