enviPath Publications

Documentation
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If you use enviPath in your research please cite:

  • Hafner, J., Lorsbach, T., Schmidt, S., Brydon, L., Dost, K., Zhang, K., Fenner, K., & Wicker, J (2024). Advancements in Biotransformation Pathway Prediction: Enhancements, Datasets, and Novel Functionalities in enviPath. Journal of Cheminformatics, 16, 93, https://doi.org/10.1186/s13321-024-00881-6

  • Wicker, J., Lorsbach, T., Gütlein, M., Schmid, E., Latino, D., Kramer, S., & Fenner, K. (2016). enviPath - The environmental contaminant biotransformation pathway resource. Nucleic Acids Research, 44(D1), D502–D508. https://doi.org/10.1093/nar/gkv1229

Additional literature related to enviPath is listed here

  • Gao, J., Ellis, L. B. M., & Wackett, L. P. (2009). The University of Minnesota Biocatalysis/Biodegradation Database: Improving public access. Nucleic Acids Research, 38, 488–491. https://doi.org/10.1093/nar/gkp771

  • Latino, D. A. R. S., Wicker, J., Gütlein, M., Schmid, E., Kramer, S., & Fenner, K. (2017). Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide soil biodegradation pathways and half-life data. Environmental Science. Processes & Impacts, 19(3), 449–464. https://doi.org/10.1039/c6em00697c

  • Tam, J.Y.C., Lorsbach, T., Schmidt, S., & Wicker,J. (2021). Holistic evaluation of biodegradation pathway prediction: assessing multi-step reactions and intermediate products. Journal of Cheminformatics 13, 63 (2021). https://doi.org/10.1186/s13321-021-00543-x

  • Trostel, L., Coll, C., Fenner, K., & Hafner, J. (2023). Combining predictive and analytical methods to elucidate pharmaceutical biotransformation in activated sludge. Environmental Science: Processes and Impacts, 25(8), 1322–1336. https://doi.org/10.1039/d3em00161j

  • Hafner, J., Fenner, K., & Scheidegger, A. (2023). Systematic Handling of Environmental Fate Data for Model Development─Illustrated for the Case of Biodegradation Half-Life Data. Environmental Science & Technology Letters, 10(10), 859–864. https://doi.org/10.1021/acs.estlett.3c00526

  • Hafner, J., Lorsbach, T., Schmidt, S., Brydon, L., Dost, K., Zhang, K., Fenner, K., & Wicker, J. S. (2023). Advancements in Biotransformation Pathway Prediction: Enhancements, Datasets, and Novel Functionalities in enviPath. https://doi.org/10.21203/rs.3.rs-3607847/v1

  • Zhang, K., & Fenner, K. (2023). enviRule: an end-to-end system for automatic extraction of reaction patterns from environmental contaminant biotransformation pathways. Bioinformatics, 39(7). https://doi.org/10.1093/bioinformatics/btad407

  • Karakurt-Fischer, S., Johnson, D. R., Fenner, K., & Hafner, J. (2023). Making waves: Enhancing pollutant biodegradation via rational engineering of microbial consortia. Water Research, 247, 120756. https://doi.org/10.1016/j.watres.2023.120756

  • Dost, K., Pullar-Strecker, Z., Brydon, L., Zhang, K., Hafner, J, Riddle, P., & Wicker, J (2023). Combatting over-specialization bias in growing chemical databases. Journal of Cheminformatics, 15, 53. https://doi.org/10.1186/s13321-023-00716-w