In response to "On E-value for tandem MS scoring schemes". - Jainab Khatun; Morgan C. Giddings (Bioinform., 2008)

Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification. - Jainab Khatun; Eric Hamlett; Morgan C. Giddings (Bioinform., 2008)

On the Process of Becoming a Great Scientist. - Morgan C. Giddings (PLoS Comput. Biol., 2008)

Ultra-Structure database design methodology for managing systems biology data and analyses. - Christopher W. Maier; Jeffrey G. Long; Bradley M. Hemminger; Morgan C. Giddings (BMC Bioinform., 2009)

Baking a mass-spectrometry data PIE with McMC and simulated annealing: predicting protein post-translational modifications from integrated top-down and bottom-up data. - Stuart R. Jefferys; Morgan C. Giddings (Bioinform., 2011)