On the exact maximum likelihood estimation of Gaussian autoregressive processes. - Bruno Cernuschi-Frías; John D. Rogers (IEEE Trans. Acoust. Speech Signal Process., 1988)

The Isomorphism Conjecture Holds and One-Way Functions Exist Relative to an Oracle. - John D. Rogers (SCT, 1995)

The Isomorphism Conjecture Holds and One-Way Functions Exists Relative to an Oracle. - John D. Rogers (J. Comput. Syst. Sci., 1997)

A Hierarchy Based on Output Multiplicity. - Ashish V. Naik; John D. Rogers; James S. Royer; Alan L. Selman (Theor. Comput. Sci., 1998)

Complexity Limitations on Quantum Computation. - Lance Fortnow; John D. Rogers (J. Comput. Syst. Sci., 1999)

Separability and one-way functions. - Lance Fortnow; John D. Rogers (Comput. Complex., 2002)

Inverting onto functions. - Stephen A. Fenner; Lance Fortnow; Ashish V. Naik; John D. Rogers (Inf. Comput., 2003)

Foreword. - André Berthiaume; John D. Rogers (Theor. Comput. Sci., 2003)

Inverting onto functions might not be hard. - Harry Buhrman; Lance Fortnow; Michal Koucký 001; John D. Rogers; Nikolai K. Vereshchagin (Electron. Colloquium Comput. Complex., 2006)

Inverting Onto Functions and Polynomial Hierarchy. - Harry Buhrman; Lance Fortnow; Michal Koucký 001; John D. Rogers; Nikolai K. Vereshchagin (CSR, 2007)

Review of "The Art of Computer Programming, Volume 4, Fascicles 2, 3, and 4 by Donald E. Knuth, " Pearson Education (Addison-Wesley), 2005. - John D. Rogers (SIGACT News, 2008)

Does the Polynomial Hierarchy Collapse if Onto Functions are Invertible? - Harry Buhrman; Lance Fortnow; Michal Koucký 001; John D. Rogers; Nikolai K. Vereshchagin (Theory Comput. Syst., 2010)

Review of the art of computer programming: volume 4a by Donald E. Knuth. - John D. Rogers (SIGACT News, 2013)

Combinatorial Game Complexity: An Introduction with Poset Games. - Stephen A. Fenner; John D. Rogers (Bull. EATCS, 2015)

Using Quartets to Compare the NCD and MCMC Methods for Constructing Phylogenetic Trees. - John D. Rogers (BIBM, 2018)

Review of The Art of Computer Programming Fascicle 6 'Satisfiability' by Donald E. Knuth. - John D. Rogers (SIGACT News, 2018)

Evaluating Compression-Based Phylogeny Estimation in the Presence of Incomplete Lineage Sorting. - DeAngelo Wilson; John D. Rogers (J. Comput. Biol., 2023)