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Here are some links to various papers/research projects that somehow relate to Qubes.
Attacks on Intel TXT
- Attacking Intel® Trusted Execution Technology by Rafal Wojtczuk, Joanna Rutkowska
- ACPI: Design Principles and Concerns by Loic Duflot, Olivier Levillain, and Benjamin Morin
- Another Way to Circumvent Intel® Trusted Execution Technology by Rafal Wojtczuk, Joanna Rutkowska, Alex Tereshkin
- Attacking Intel TXT® via SINIT code execution hijacking by Rafal Wojtczuk and Joanna Rutkowska
Software attacks coming through devices
- Can you still trust your network card? by Loïc Duflot, Yves-Alexis Perez and others
- Remotely Attacking Network Cards (or why we do need VT-d and TXT) by Joanna Rutkowska
- On Formally Verified Microkernels (and on attacking them) by Joanna Rutkowska
- Following the White Rabbit: Software Attacks against Intel® VT-d by Rafal Wojtczuk and Joanna Rutkowska
Application-level security
- Virtics: A System for Privilege Separation of Legacy Desktop Applications by Matt Piotrowski
VMM/Xen disagregation
- [http://tjd.phlegethon.org/words/sosp11-xoar.pdf "Breaking Up is Hard to Do: Security and Functionality in a Commodity Hypervisor] by Patrick Colp at el. (Also see this thread on xen-devel)