A Systematic Method for Specifying Effective Value Models. - Benjamin D. Lee; William R. Binder; Christiaan J. J. Paredis (CSER, 2014)

Python Implementation of Codon Adaptation Index. - Benjamin D. Lee (J. Open Source Softw., 2018)

Ten simple rules for documenting scientific software. - Benjamin D. Lee (PLoS Comput. Biol., 2018)

Squiggle: a user-friendly two-dimensional DNA sequence visualization tool. - Benjamin D. Lee (Bioinform., 2019)

DNAvisualization.org: a serverless web tool for DNA sequence visualization. - Benjamin D. Lee; Michael A. Timony; Pablo Ruiz 005 (Nucleic Acids Res., 2019)

Rule-Based Dispatching of Microgrids with Coupled Electricity and Heat Power Systems. - Martin Seydenschwanz; Corinna Gottschalk; Benjamin D. Lee; Dino Ablakovic (ISGT-Europe, 2020)

Ten Quick Tips for Deep Learning in Biology. - 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; et al. (CoRR, 2021)

ViroidDB: a database of viroids and viroid-like circular RNAs. - Benjamin D. Lee; Uri Neri; Caleb J. Oh; Peter Simmonds; Eugene V. Koonin (Nucleic Acids Res., 2022)

Ten quick tips for deep learning in biology. - 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; et al. (PLoS Comput. Biol., 2022)