Works Cited

The following is a list of all references cited throughout the documentation.


Saugat Poudel, Hannah Tsunemoto, Yara Seif, Anand V. Sastry, Richard Szubin, Sibei Xu, Henrique Machado, Connor A. Olson, Amitesh Anand, Joe Pogliano, Victor Nizet, and Bernhard O. Palsson. Revealing 29 sets of independently modulated genes inStaphylococcus aureus, their regulators, and role in key physiological response. Proceedings of the National Academy of Sciences, 117(29):17228–17239, July 2020. URL:, doi:10.1073/pnas.2008413117.


Kevin Rychel, Katherine Decker, Anand V Sastry, Patrick V Phaneuf, Saugat Poudel, and Bernhard O Palsson. iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning. Nucleic Acids Research, 49(D1):D112–D120, October 2020. URL:, doi:10.1093/nar/gkaa810.


Kevin Rychel, Anand V. Sastry, and Bernhard O. Palsson. Machine learning uncovers independently regulated modules in the bacillus subtilis transcriptome. Nature Communications, December 2020. URL:, doi:10.1038/s41467-020-20153-9.


Anand V. Sastry, Ye Gao, Richard Szubin, Ying Hefner, Sibei Xu, Donghyuk Kim, Kumari Sonal Choudhary, Laurence Yang, Zachary A. King, and Bernhard O. Palsson. The escherichia coli transcriptome mostly consists of independently regulated modules. Nature Communications, December 2019. URL:, doi:10.1038/s41467-019-13483-w.