| 2013 | ISI | Towards a network-of-networks framework for cyber security. | Mahantesh Halappanavar, Sutanay Choudhury, Emilie Hogan, Peter Hui, John R. Johnson, Indrajit Ray, Lawrence B. Holder |
| 2013 | ISI | Graph analytics for signature discovery. | Emilie Hogan, John R. Johnson, Mahantesh Halappanavar, Chaomei Lo |
| 2013 | ISI | A graph analytic metric for mitigating advanced persistent threat. | John R. Johnson, Emilie Hogan |
| 2002 | HPDC | Local Discovery of System Architecture - Application Parameter Sensitivity: An Empirical Technique for Adaptive Grid Applications. | Ivan Corey, John R. Johnson, Jeffrey S. Vetter |
| 1993 | SC | Efficient transposition algorithms for large matrices. | S. D. Kaushik, Chua-Huang Huang, John R. Johnson, Rodney W. Johnson, P. Sadayappan |
| 1992 | ICPP | Generating Parallel Programs from Tensor Product Formulas: A Case Study of Strassen's Matrix Multiplication Algorithm. | Chua-Huang Huang, John R. Johnson, Rodney W. Johnson |
| 1990 | SC | Multilinear algebra and parallel programming. | Rodney W. Johnson, Chua-Huang Huang, John R. Johnson |