| 2025 | IJCNN | NanoHydra: Energy-Efficient Time-Series Classification at the Edge. | Cristian Cioflan, Jos Fonseca, Xiaying Wang, Luca Benini |
| 2023 | DSN | Using AI to Inject Vulnerabilities in Python Code. | C. G. Frdric Bogaerts, Naghmeh Ivaki, Jos Fonseca |
| 2018 | EDCC | Finding SQL Injection and Cross Site Scripting Vulnerabilities with Diverse Static Analysis Tools. | Areej Algaith, Paulo Jorge Costa Nunes, Jos Fonseca, Ilir Gashi, Marco Vieira |
| 2017 | EDCC | On Combining Diverse Static Analysis Tools for Web Security: An Empirical Study. | Paulo Jorge Costa Nunes, Iberia Medeiros, Jos Fonseca, Nuno Ferreira Neves, Miguel Correia, Marco Vieira |
| 2015 | DSN | phpSAFE: A Security Analysis Tool for OOP Web Application Plugins. | Paulo Jorge Costa Nunes, Jos Fonseca, Marco Vieira |
| 2010 | ISSRE | Comparing SQL Injection Detection Tools Using Attack Injection: An Experimental Study. | Ivano Alessandro Elia, Jos Fonseca, Marco Vieira |
| 2010 | ISSRE | The Web Attacker Perspective - A Field Study. | Jos Fonseca, Marco Vieira, Henrique Madeira |
| 2009 | DSN | Vulnerability & attack injection for web applications. | Jos Fonseca, Marco Vieira, Henrique Madeira |
| 2009 | ISSRE | Looking at Web Security Vulnerabilities from the Programming Language Perspective: A Field Study. | Nuno Seixas, Jos Fonseca, Marco Vieira, Henrique Madeira |
| 2008 | DSN | Mapping software faults with web security vulnerabilities. | Jos Fonseca, Marco Vieira |
| 2008 | PRDC | Training Security Assurance Teams Using Vulnerability Injection. | Jos Fonseca, Marco Vieira, Henrique Madeira |
| 2008 | SAC | Online detection of malicious data access using DBMS auditing. | Jos Fonseca, Marco Vieira, Henrique Madeira |
| 2007 | PRDC | Testing and Comparing Web Vulnerability Scanning Tools for SQL Injection and XSS Attacks. | Jos Fonseca, Marco Vieira, Henrique Madeira |
| 2007 | TrustBus | Detecting Malicious SQL. | Jos Fonseca, Marco Vieira, Henrique Madeira |
| 2006 | PRDC | Monitoring Database Application Behavior for Intrusion Detection. | Jos Fonseca, Marco Vieira, Henrique Madeira |
| 2001 | QUATIC | Contributos do Projecto ESSI na Melhoria do Desenvolvimento de Software. | Maria Clara Silveira, Jos Fonseca |