Citing BioMASS

If you use BioMASS in your research, please cite the following paper:

• Arakane, K., Imoto, H., Ormersbach, F. & Okada, M. Extending BioMASS to construct mathematical models from external knowledge. Bioinformatics Advances 4, vbae042 (2024). https://doi.org/10.1093/bioadv/vbae042

In BibTeX format:

@article{10.1093/bioadv/vbae042,
  author  = {Arakane, Kiwamu and Imoto, Hiroaki and Ormersbach, Fabian and Okada, Mariko},
  title   = "{Extending BioMASS to construct mathematical models from external knowledge}",
  journal = {Bioinformatics Advances},
  volume  = {4},
  number  = {1},
  pages   = {vbae042},
  year    = {2024},
  month   = {04},
  issn    = {2635-0041},
  doi     = {10.1093/bioadv/vbae042},
  url     = {https://doi.org/10.1093/bioadv/vbae042},
  eprint  = {https://academic.oup.com/bioinformaticsadvances/advance-article-pdf/doi/10.1093/bioadv/vbae042/57163215/vbae042.pdf},
}

If you construct a mathematical model using biomass.construction.text2model.Text2Model, please also cite the Pasmopy paper:

• Imoto, H., Yamashiro, S. & Okada, M. A text-based computational framework for patient -specific modeling for classification of cancers. iScience 25, 103944 (2022). https://doi.org/10.1016/j.isci.2022.103944

In BibTeX format:

@article{imoto2022text,
  title     = {A text-based computational framework for patient-specific modeling for classification of cancers},
  author    = {Imoto, Hiroaki and Yamashiro, Sawa and Okada, Mariko},
  journal   = {iScience},
  volume    = {25},
  number    = {3},
  pages     = {103944},
  year      = {2022},
  publisher = {Elsevier},
  doi       = {10.1016/ j.isci.2022.103944},
  url       = {https://www.cell.com/iscience/fulltext/S2589-0042(22)00214-0}
}

When presenting work that uses BioMASS, feel free to use the logo.