An Information Flow Tool for Gypsy. - John McHugh; Donald L. Good (S&P, 1985)

Ada verification using existing tools. - John McHugh; Karl A. Nyberg (ACM SIGSOFT Softw. Eng. Notes, 1985)

A Security Policy and Formal Top Level Specification for a Multi-Level Secure Local Area Network. - John McHugh; Andrew P. Moore (S&P, 1986)

Coding for a Believable Specification to Implementation Mapping. - William D. Young; John McHugh (S&P, 1987)

An Experience Using Two Covert Channel Analysis Techniques on a Real System Design. - J. Thomas Haigh; Richard A. Kemmerer; John McHugh; William D. Young (IEEE Trans. Software Eng., 1987)

A Formal Definition for Information Flow in the Gypsy Expression Language. - John McHugh (CSFW, 1988)

Multilevel security issues in distributed database management systems. - John McHugh; Bhavani M. Thuraisingham (Comput. Secur., 1988)

A risk driven process model for the development of trusted systems. - Ann B. Marmor-Squires; John McHugh; Martha A. Branstad; Bonnie P. Danner; Lou Nagy; Pat Rougeau; Daniel F. Sterne (ACSAC, 1989)

A prototype B3 trusted X Window System. - Jeremy Epstein; John McHugh; Rita Pascale; Hilarie K. Orman; Glenn S. Benson; Charles R. Martin; Ann B. Marmor-Squires; Bonnie P. Danner; Martha A. Branstad (ACSAC, 1991)

Heuristic authentication protocol for TCP/IP network applications under UNIX. - A. H. Wadaa; Hussein M. Abdel-Wahab; John McHugh (ACM Southeast Regional Conference, 1992)

A cautionary note on image downgrading. - Charles W. Kurak Jr.; John McHugh (ACSAC, 1992)

Ada 9X and Safety Critical/Secure Systems. - John McHugh (TRI-Ada, 1992)

Evolution of a trusted B3 window system prototype. - Jeremy Epstein; John McHugh; Rita Pascale; Charles R. Martin; D. Rothnie; Hilarie K. Orman; Ann B. Marmor-Squires; Martha A. Branstad; Bonnie P. Danner (S&P, 1992)

A High Assurance Window System Prototype. - Jeremy Epstein; John McHugh; Hilarie K. Orman; Rita Pascale; Ann B. Marmor-Squires; Bonnie P. Danner; Charles R. Martin; Martha A. Branstad; Glenn S. Benson; D. Rothnie (J. Comput. Secur., 1993)

Guest Editorial: Introduction to the Special Section. - John McHugh (IEEE Trans. Software Eng., 1996)

Chaffing at the Bit: Thoughts on a Note by Ronald Rivest. - John McHugh (Information Hiding, 1999)

Secure group management in large distributed systems: what is a group and what does it do? - John McHugh; James Bret Michael (NSPW, 1999)

The 1998 Lincoln Laboratory IDS Evaluation. - John McHugh (Recent Advances in Intrusion Detection, 2000)

Windows of Vulnerability: A Case Study Analysis. - William A. Arbaugh; William L. Fithen; John McHugh (Computer, 2000)

Defending Yourself: The Role of Intrusion Detection Systems. - John McHugh; Alan M. Christie; Julia Allen (IEEE Softw., 2000)

Testing Intrusion detection systems: a critique of the 1998 and 1999 DARPA intrusion detection system evaluations as performed by Lincoln Laboratory. - John McHugh (ACM Trans. Inf. Syst. Secur., 2000)

An Information Flow Tool for Gypsy. - John McHugh (ACSAC, 2001)

A Trend Analysis of Exploitations. - Hilary K. Browne; William A. Arbaugh; John McHugh; William L. Fithen (S&P, 2001)

Managing Software Development for Survivable Systems. - Nancy R. Mead; Richard C. Linger; John McHugh; Howard F. Lipson (Ann. Softw. Eng., 2001)

Intrusion and intrusion detection. - John McHugh (Int. J. Inf. Sec., 2001)

Hiding Intrusions: From the Abnormal to the Normal and Beyond. - Kymie M. C. Tan; John McHugh; Kevin S. Killourhy (Information Hiding, 2002)

Locality: a new paradigm for thinking about normal behavior and outsider threat. - John McHugh; Carrie Gates (NSPW, 2003)

Sets, Bags, and Rock and Roll: Analyzing Large Data Sets of Network Data. - John McHugh (ESORICS, 2004)

Software diversity: use of diversity as a defense mechanism. - John McHugh (NSPW, 2005)

Quality of protection: measuring the unmeasurable? - John McHugh (QoP, 2006)

Implementing and testing dynamic timeout adjustment as a dos counter-measure. - Daniel Boteanu; Edouard Reich; José M. Fernandez 001; John McHugh (QoP, 2007)

Queue Management as a DoS Counter-Measure? - Daniel Boteanu; José M. Fernandez 001; John McHugh; John Mullins (ISC, 2007)

NetBytes Viewer: An Entity-Based NetFlow Visualization Utility for Identifying Intrusive Behavior. - Teryl Taylor; Stephen Brooks; John McHugh (VizSEC, 2007)

The Contact Surface: A Technique for Exploring Internet Scale Emergent Behaviors. - Carrie Gates; John McHugh (DIMVA, 2008)

Structured Peer-to-Peer Overlay Networks: Ideal Botnets Command and Control Infrastructures?. - Carlton R. Davis; Stephen Neville; José M. Fernandez 001; Jean-Marc Robert 001; John McHugh (ESORICS, 2008)

Sybil attacks as a mitigation strategy against the Storm botnet. - Carlton R. Davis; José M. Fernandez 001; Stephen Neville; John McHugh (MALWARE, 2008)

Long term data storage issues for situational awareness. - John McHugh (CSIIRW, 2009)

DOE grass roots panel. - John McHugh; Robert C. Armstrong; Thomas A. Longstaff; Daniel Quinlan; Frederick T. Sheldon; Deborah A. Frincke (CSIIRW, 2009)

Over flow: An overview visualization for network analysis. - Joel Glanfield; Stephen Brooks; Teryl Taylor; Diana Paterson; Christopher Smith; Carrie Gates; John McHugh (VizSEC, 2009)

Progressive Internal Waves of Permanent Form. - John McHugh (SIAM J. Appl. Math., 2009)

Cuckoo bags for exploring multikey data. - John McHugh; Teryl Taylor; Jeff Janies (CSIIRW, 2010)

Why is there no science in cyber science?: a panel discussion at NSPW 2010. - Roy A. Maxion; Thomas A. Longstaff; John McHugh (NSPW, 2010)

Traffic classification using visual motifs: an empirical evaluation. - Wilson Lian; Fabian Monrose; John McHugh (VizSEC, 2010)

Verified workflow-based software development for infrastructure sensing and control applications. - Douglas A. Creager; John McHugh (CSIIRW, 2011)

Moving Forward, Building an Ethics Community (Panel Statements). - Erin Kenneally; Angelos Stavrou; John McHugh; Nicolas Christin (Financial Cryptography Workshops, 2011)

Toward Efficient Querying of Compressed Network Payloads. - Teryl Taylor; Scott E. Coull; Fabian Monrose; John McHugh (USENIX ATC, 2012)

Crossing the threshold: Detecting network malfeasance via sequential hypothesis testing. - Srinivas Krishnan; Teryl Taylor; Fabian Monrose; John McHugh (DSN, 2013)

An Anthropological Approach to Studying CSIRTs. - Sathya Chandran Sundaramurthy; John McHugh; Xinming Simon Ou; S. Raj Rajagopalan; Michael Wesch (IEEE Secur. Priv., 2014)

A Human Capital Model for Mitigating Security Analyst Burnout. - Sathya Chandran Sundaramurthy; Alexandru G. Bardas; Jacob Case; Xinming Ou; Michael Wesch; John McHugh; S. Raj Rajagopalan (SOUPS, 2015)

Turning Contradictions into Innovations or: How We Learned to Stop Whining and Improve Security Operations. - Sathya Chandran Sundaramurthy; John McHugh; Xinming Ou; Michael Wesch; Alexandru G. Bardas; S. Raj Rajagopalan (SOUPS, 2016)

Humans Are Dynamic - Our Tools Should Be Too. - Sathya Chandran Sundaramurthy; Michael Wesch; Xinming Ou; John McHugh; S. Raj Rajagopalan; Alexandru G. Bardas (IEEE Internet Comput., 2017)

Virtual Career Advisor System. - Tracey John; Dwaine Clarke; Daniel Coore; Fabian Monrose; John McHugh (MobiWIS, 2023)

Position Paper: Personal Experience in the Technology Opportunities and Associated Risks of Healthcare Challenges in a Continuing Care Retirement Community (CCRC). - John McHugh; William Yurcik (HealthSec@CCS, 2024)

"Function Extraction: A New Paradigm for Producing Secure Code". - Richard C. Linger; Mark G. Pleszkoch; Jack McGaughey; John McHugh; Wided Ghardallou; Ali Mili 001 (NSPW, 2024)

The Origins of Software Errors: Where Do They Come From? Where Do They Go? - John McHugh (Computer, 2025)