How to Cite enviPath
If you use enviPath in your research, please cite our work. Citations help us demonstrate the impact of our platform and support continued development and maintenance.
Quick Reference
Main Platform Citation
If you use the enviPath platform in general, please cite:
Advancements in biotransformation pathway prediction: enhancements, datasets, and novel functionalities in enviPath
Authors: Hafner, J., Lorsbach, T., Schmidt, S.,
Brydon, L., Dost, K., Zhang, K., Fenner, K., and Wicker, J.
Journal: Journal of Cheminformatics, 16(1), 93
Year: 2024
DOI:
10.1186/s13321-024-00881-6
@ARTICLE{Hafner2024enviPath,
title = "Advancements in biotransformation pathway prediction:
enhancements, datasets, and novel functionalities in enviPath",
author = "Hafner, Jasmin and Lorsbach, Tim and Schmidt, Sebastian and
Brydon, Liam and Dost, Katharina and Zhang, Kunyang and Fenner,
Kathrin and Wicker, J{\"o}rg",
journal = "J. Cheminform.",
publisher = "Springer Science and Business Media LLC",
volume = 16,
number = 1,
pages = "93",
month = aug,
year = 2024,
doi = "10.1186/s13321-024-00881-6"
}enviPath – The environmental contaminant biotransformation pathway resource
Authors: Wicker, J., Lorsbach, T., Gütlein, M.,
Schmid, E., Latino, D., Kramer, S., Fenner, K.
Journal: Nucleic Acids Research, 44(D1),
D502-D508
Year: 2016
DOI:
10.1093/nar/gkv1229
@ARTICLE{Wicker2016enviPath,
title = "enviPath – The environmental contaminant biotransformation pathway resource",
author = "Wicker, J{\"o}rg and Lorsbach, Tim and Gütlein, Martin and Schmid,
Emanuel and Latino, Diogo and Kramer, Stefan and Fenner, Kathrin",
journal = "Nucleic Acids Research",
volume = 44,
number = "D1",
pages = "D502-D508",
year = 2016,
month = jan,
doi = "10.1093/nar/gkv1229"
}Pathway Prediction System
If you use the pathway prediction functionality, please also cite:
A Hybrid Machine Learning and Knowledge Based Approach to Limit Combinatorial Explosion in Biodegradation Prediction
Authors: Wicker, J., Fenner, K., Kramer, S.
Book: Computational Sustainability, 75-97
Year: 2016
DOI:
10.1007/978-3-319-31858-5_5
@INBOOK{Wicker2016ML,
title="A Hybrid Machine Learning and Knowledge Based Approach to
Limit Combinatorial Explosion in Biodegradation Prediction",
author="Wicker, J{\"o}rg and Fenner, Kathrin and Kramer, Stefan",
editor="L{\"a}ssig, J{\"o}rg and Kersting, Kristian and Morik, Katharina",
bookTitle="Computational Sustainability",
year=2016,
publisher="Springer International Publishing",
pages="75--97",
doi="10.1007/978-3-319-31858-5_5"
}Predictive modeling of biodegradation pathways using transformer architectures
Authors: Brydon, L., Zhang, K., Dobbie, G.,
Taškova, K., and Wicker, J.
Journal: Journal of Cheminformatics, 17(1), 21
Year: 2025
DOI:
10.1186/s13321-025-00969-7
@article{Brydon2025Transformer,
title = "Predictive modeling of biodegradation pathways using transformer architectures",
author = "Brydon, Liam and Zhang, Kunyang and Dobbie, Gillian and
Ta\v{s}kova, Katerina and Wicker, J{\"o}rg Simon",
journal = "Journal of Cheminformatics",
volume = 17,
number = 1,
pages = "1--16",
year = 2025,
month = feb,
doi = "10.1186/s13321-025-00969-7",
}Machine Learning Models
Relative Reasoning Models
For relative reasoning and machine learning approaches, please cite:
Predicting biodegradation products and pathways: a hybrid knowledge- and machine learning-based approach
Authors: Wicker, J., Fenner, K., Ellis, L.,
Wackett, L., Kramer, S.
Journal: Bioinformatics, 26(6), 814-821
Year: 2010
DOI:
10.1093/bioinformatics/btq024
@ARTICLE{Wicker2010,
title = "Predicting biodegradation products and pathways:
a hybrid knowledge- and machine learning-based approach",
author = "Wicker, J{\"o}rg and Fenner, Kathrin and Ellis, Lynda and Wackett, Larry and Kramer, Stefan",
journal = "Bioinformatics",
volume = 26,
number = 6,
pages = "814-821",
year = 2010,
month = jan,
doi = "10.1093/bioinformatics/btq024"
}Data-driven extraction of relative reasoning rules to limit combinatorial explosion in biodegradation pathway prediction
Authors: Fenner, K., Junfeng, G., Kramer, S.,
Ellis, L., Wackett, L.
Journal: Bioinformatics, 26(18), 2079-2085
Year: 2008
DOI:
10.1093/bioinformatics/btn378
@ARTICLE{Fenner2008Reason,
title = "Data-driven extraction of relative reasoning rules to
limit combinatorial explosion in biodegradation pathway prediction",
author = "Fenner, Kathrin and Gao, Junfeng and Kramer, Stefan and Ellis, Lynda and Wackett, Larry",
journal = "Bioinformatics",
volume = 24,
number = 18,
pages = "2079-2085",
year = 2008,
month = 07,
doi = "10.1093/bioinformatics/btn378"
}Package-Specific Citations
If you use data from a specific package within enviPath, please also acknowledge the package creators and cite any relevant publications associated with that package. Package-specific citation information is available on each package's detail page.
Example Acknowledgment Text
You may use the following text in your acknowledgments section:
"Biotransformation pathway predictions were performed using enviPath (https://envipath.org), a database and prediction system for microbial biotransformation of organic environmental contaminants."
Additional Resources
For a complete list of publications related to enviPath, please visit:
Thank You!
Questions?
If you're unsure which papers to cite or have questions about citations, please contact us or ask on our community forums.