Distributed simulation in Ada 95. - John A. Hamilton Jr.; David A. Cook; Udo W. Pooch (TRI-Ada, 1995)

A survey of object-oriented methodologies. - John A. Hamilton Jr.; Udo W. Pooch (TRI-Ada, 1995)

An Open Simulation Architecture for Force XXI. - John A. Hamilton Jr.; Udo W. Pooch (WSC, 1995)

AToolkit for Monitoring the Utilization and Performance of Computer Networks. - John A. Hamilton Jr.; Gary R. Ratterree; Udo W. Pooch (Simul., 1995)

PACKET tracing: a new paradigm for teaching computer network courses. - Willis F. Marti; Udo W. Pooch; John A. Hamilton Jr. (ITiCSE, 1996)

Ada Training and Education in the US Army and US Air Force. - John A. Hamilton Jr.; David A. Cook (TRI-Ada, 1996)

Public Domain Tools for Modeling and Simulating Computer Networks. - John A. Hamilton Jr.; Gary R. Ratterree; Paul C. Brutch; Udo W. Pooch (Simul., 1996)

A Comparison of Ada and Pascal in an Introductory Computer Science Course. - Jeanne L. Murtagh; John A. Hamilton Jr. (SIGAda, 1998)

The future of programming - are fundamental changes in computer science programs coming? (panel). - Hal Hart; James Caristi; Robert Dewar; Mark S. Gerhardt; J. A. Drew Hamilton Jr.; Christopher Haynes; Samuel A. Rebelsky (SIGCSE, 1998)

Tracking multiple objects in terrain. - Edward Sobiesk; John A. Hamilton Jr.; John A. Marin; Donald E. Brown; Maria L. Gini (SMC, 1998)

Software Process as a Foundation for Teaching, Learning and Accrediting. - David A. Umphress; John A. Hamilton Jr. (CSEE&T, 2002)

Security Vulnerabilities in Command and Control Interoperability. - John A. Hamilton Jr. (IAW, 2003)

On the current state of transport layer protocols in mobile ad hoc networks. - John Calagaz; Wade Chatam; Brian Eoff; John A. Hamilton Jr. (ACM Southeast Regional Conference, 2004)

Methods for the prevention, detection and removal of software security vulnerabilities. - Jay-Evan J. Tevis; John A. Hamilton Jr. (ACM Southeast Regional Conference, 2004)

Static analysis of anomalies and security vulnerabilities in executable files. - Jay-Evan J. Tevis; John A. Hamilton Jr. (ACM Southeast Regional Conference, 2006)

Integrating Ada 2005 into visual studio 2005. - Martin C. Carlisle; John A. Hamilton Jr. (SIGAda, 2006)

Impact of daily computer usage on GUI usage analysis. - Eric S. Imsand; John A. Hamilton Jr. (InfoSecCD, 2007)

Performance evaluation: running DSR and TORA routing protocols concurrently. - Suhair Hafez Amer; John A. Hamilton Jr. (SCSC, 2007)

Modeling unmanned aerial vehicle communications at the Auburn University Miss Center. - J. A. Drew Hamilton Jr.; Richard O. Chapman; David A. Umphress (SCSC, 2007)

Computer defense using artificial intelligence. - Winard Britt; Sundeep Gopalaswamy; John A. Hamilton Jr.; Gerry V. Dozier; Kai H. Chang (SpringSim (3), 2007)

A performance analysis of the spring protocol through simulation. - Kevin Richardson; John A. Hamilton Jr.; Martin C. Carlisle (SpringSim (3), 2007)

A security-centric ring-based software architecture. - Jay-Evan J. Tevis; John A. Hamilton Jr. (SpringSim (3), 2007)

Bowl championship series vulnerability analysis. - Caio Soares; George Page; Jonathan MacDonald; Sanjeev Baskiyar; John A. Hamilton Jr.; Gerry V. Dozier (Richard Tapia Celebration of Diversity in Computing Conference, 2007)

Simulation of army unmanned aerial vehicle communications. - Richard O. Chapman; J. A. Drew Hamilton Jr.; Daniel Box; Mark Kuhr; Jonathan MacDonald; Stephen Hamilton (WSC, 2007)

Validating a network simulation testbed for army UAVs. - Stephen Hamilton; Timothy Schmoyer; J. A. Drew Hamilton Jr. (WSC, 2007)

The TIGR Plant Transcript Assemblies database. - Kevin L. Childs; John P. Hamilton; Wei Zhu; Eugene Ly; Foo Cheung; Hank Wu; Pablo D. Rabinowicz; Christopher D. Town; C. Robin Buell; Agnes P. Chan (Nucleic Acids Res., 2007)

The TIGR Rice Genome Annotation Resource: improvements and new features. - Shu Ouyang; Wei Zhu; John A. Hamilton Jr.; Haining Lin; Matthew Campbell; Kevin L. Childs; Françoise Thibaud-Nissen; Renae L. Malek; Yuandan Lee; Li Zheng; Joshua Orvis; Brian Haas; et al. (Nucleic Acids Res., 2007)

DSR and TORA in fixed and mobile wireless networks. - Suhair Hafez Amer; John A. Hamilton Jr. (ACM Southeast Regional Conference, 2008)

Masquerade Detection through GUIID. - Eric S. Imsand; John A. Hamilton Jr. (GLOBECOM, 2008)

Understanding security architecture. - Suhair Hafez Amer; John A. Hamilton Jr. (SpringSim, 2008)

The importance of information security spending: an economic approach. - William R. Conkling; J. A. Drew Hamilton Jr. (SpringSim, 2008)

Building executable service-oriented architectures with the WS-Management specification. - Mark Kuhr; J. A. Drew Hamilton Jr. (SpringSim, 2008)

Supporting a service-oriented architecture. - Derek T. Sanders; John A. Hamilton Jr.; Richard A. MacDonald (SpringSim, 2008)

A Cloaking Algorithm Based on Spatial Networks for Location Privacy. - Po-Yi Li; Wen-Chih Peng; Tsung-Wei Wang; Wei-Shinn Ku; Jianliang Xu; John A. Hamilton Jr. (SUTC, 2008)

Panel discussion: What makes good research in modeling and simulation: Assessing the quality, success, and utility of M&S research. - Jeffrey S. Smith; John A. Hamilton Jr.; Richard E. Nance; Barry L. Nelson; George F. Riley; Lee W. Schruben (WSC, 2008)

User identification using GUI manipulation patterns and artificial neural networks. - Eric S. Imsand; Deon Garrett; John A. Hamilton Jr. (CICS, 2009)

A compiler classification framework for use in reverse engineering. - Stephen Torri; Winard Britt; John A. Hamilton Jr. (CICS, 2009)

DoDAF Modeling of a Unified Analysis Framework for Software Security. - Derek T. Sanders; Robert McGraw; John A. Hamilton Jr.; Aaron Corder; Teng K. Ooi (HSC, 2009)

Suggested improvements to the DoDAF for modeling architectural security. - William R. Conkling; John A. Hamilton Jr. (SpringSim, 2009)

Using software architecture to facilitate reuse in a product family. - Ryan O'Farrell; John A. Hamilton Jr. (SpringSim, 2009)

Building information assurance education partnerships with minority institutions. - J. A. Drew Hamilton Jr.; Robert Steven Owor; Khalil Dajani (Richard Tapia Celebration of Diversity in Computing Conference, 2009)

Enhanced expert field medical training simulations and their effect on the modern combat life saver training procedures. - Radha Kuskuntla; Eric S. Imsand; John A. Hamilton Jr. (SpringSim, 2010)

Information assurance modeling using the Department of Defense architecture framework. - Ryan O'Farrell; Sriharsha Banavara; Donald Folds; John A. Hamilton Jr. (SpringSim, 2010)

The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes. - John P. Hamilton; Eric C. Neeno-Eckwall; Bishwo N. Adhikari; Nicole T. Perna; Ned Tisserat; Jan Leach; C. André Lévesque; C. Robin Buell (Database J. Biol. Databases Curation, 2011)

An embedded system for real-time navigation and remote command of a trained canine. - Winard Britt; Jeffrey Miller; Paul Waggoner; David M. Bevly; John A. Hamilton Jr. (Pers. Ubiquitous Comput., 2011)

Constructing a Cloud-Based IDS by Merging VMI with FMA. - Christopher Harrison; Devin Cook; Robert McGraw; John A. Hamilton Jr. (TrustCom, 2012)

Architecture-based network simulation for cyber security. - John A. Hamilton Jr. (WSC, 2013)

We didn't start the fire: using an agent-directed thermal simulator to keep servers cool. - Jonathan Hood; Timothy Scott; Jiao Yu; Xiao Qin 001; Levent Yilmaz 001; J. A. Drew Hamilton Jr. (SpringSim (ADS), 2014)

Is there a Security Mindset and Can it be Taught? - Ambareen Siraj; Nigamanth Sridhar; John A. Drew Hamilton; Latifur Khan; Siddharth Kaza; Maanak Gupta; Sudip Mittal (CODASPY, 2021)

Automated Vulnerability Detection in Source Code Using Deep Representation Learning. - Christoforos Seas; Glenn Fitzpatrick; John A. Hamilton Jr.; Martin C. Carlisle (CCWC, 2024)

Covert penetrations: Analyzing and defending SCADA systems from stealth and Hijacking attacks. - Syed Wali; Yasir Ali Farrukh; Irfan Khan 001; John A. Hamilton Jr. (Comput. Secur., 2025)