For citations, please see my Google Scholar profile. Up to date as of May 12, 2022.

  1. Benjamin D. Lee, Michael A. Timony, and Pablo R. Ruiz. DNAvisualization.org: a serverless web tool for DNA sequence visualization. Nucleic Acids Research, 47(W1):W20–W25, July 2019. doi:10.1093/nar/gkz404. [bibtex] [pdf]
  2. Benjamin D. Lee. Python implementation of codon adaptation index. Journal of Open Source Software, 3(30):905, October 2018. doi:10.21105/joss.00905. [bibtex] [pdf]
  3. Benjamin D. Lee. Squiggle: a user-friendly two-dimensional DNA sequence visualization tool. Bioinformatics, 35(8):1425–1426, September 2018. doi:10.1093/bioinformatics/bty807. [bibtex] [pdf]
  4. Benjamin D. Lee. Ten simple rules for documenting scientific software. PLOS Computational Biology, 14(12):e1006561, December 2018. doi:10.1371/journal.pcbi.1006561. [bibtex] [pdf]
  5. Benjamin D. Lee, Uri Neri, Caleb J. Oh, Peter Simmonds, Eugene V. Koonin. ViroidDB: a database of viroids and viroid-like circular RNAs. Nucleic Acids Research, 50(D1):D432–D438, November 2021. doi:10.1093/nar/gkab974. [bibtex] [pdf]
  6. Benjamin D. Lee and Eugene V. Koonin. Viroids and viroid-like circular RNAs: Do they descend from primordial replicators? Life, 12(103), January 2021. doi:10.3390/life12010103. [bibtex] [pdf]
  7. Benjamin D. Lee, Anthony Gitter, Casey S. Greene, Sebastian Raschka, Finlay Maguire, Alexander J. Titus, Michael D. Kessler, Alexandra J. Lee, Marc G. Chevrette, Paul Allen Stewart, Thiago Britto-Borges, Evan M. Cofer, Kun-Hsing Yu, Juan Jose Carmona, Elana J. Fertig, Alexandr A. Kalinin, Brandon Signal, Benjamin J. Lengerich, Timothy J. Triche, Jr., and Simina M. Boca. Ten quick tips for deep learning in biology. PLOS Computational Biology, 18(3):e1009803, March 2022. doi:10.1371/journal.pcbi.1009803. [bibtex] [pdf]