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Refereed Journals and Conferences

[article]
[link]
          Simultaneous Alignment and Folding of Protein Sequences
         Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger.
13th Annual International Conference on Research in Computational Molecular Biology
"RECOMB 2009," Tucson, AZ, USA (May 2009)

[article]
[link]		          Modeling Ensembles of Transmembrane β-barrel Proteins
         Jérôme Waldispühl*, Charles W. O'Donnell*, Srinivas Devadas, Peter Clote, Bonnie Berger. (*authors equally contributed)
Proteins: Structure, Function, and Bioinformatics Volume 71, Issue 3, pp. 1097-1112 (15 May 2008, digitally published 14 November 2007)

[article]
[link]		          AEGIS: A Single-Chip Secure Processor
         G. Edward Suh, Charles W. O'Donnell, Srinivas Devadas.
IEEE Design & Test Volume 24, Issue 6, pp. 570-580 (November 2007)

[article]
[slides]		          Memoization Attacks and Copy Protection in Partitioned Applications (Presenter)
         Charles W. O'Donnell, G. Edward Suh, Marten van Dijk, Srinivas Devadas.
Proceedings of the 2007 IEEE Workshop on Information Assurance
"IAW 2007," United States Military Academy, West Point, NY, USA (June 2007)

[article]
[link]		          Learning Biophysically-Motivated Parameters for Alpha Helix Prediction
         Blaise Gassend, Charles W. O'Donnell, William Thies, Andrew Lee, Marten van Dijk, Srinivas Devadas.
BMC Bioinformatics Volume 8 (Supplement 5) p. S3 (24 May 2007)

[article]
[slides]		          Virtual Monotonic Counters and Count-Limited Objects using a TPM without a Trusted OS
         Luis F. G. Sarmenta, Marten van Dijk, Charles W. O'Donnell, Jonathan Rhodes, Srinivas Devadas.
Proceedings of the 2006 Workshop on Scalable Trusted Computing (held with the 13th ACM Conference on Computer and Communications Security)
"STC 2006," Fairfax, Virginia, USA (November 2006)
Extended version available as MIT CSAIL Technical Report 2006-064 (MIT-CSAIL-TR-2006-064)

[article]
[slides]		          Predicting Secondary Structure of All-Helical Proteins Using Hidden Markov Support Vector Machines
         Blaise Gassend, Charles W. O'Donnell, William Thies, Andrew Lee, Marten van Dijk, Srinivas Devadas.
Proceedings of the 2006 Workshop on Pattern Recognition in Bioinformatics, Volume 4146 of Lecture Notes in Computer Science, pp. 93-104, 2006
"PRIB 2006," Hong Kong, China (August 2006)
Extended version available as MIT LCS Technical Report 1003 (MIT-LCS-TR-1003)

[article]
[slides]		          Design and Implementation of the AEGIS Single-Chip Secure Processor Using Physical Random Functions
         G. Edward Suh, Charles W. O'Donnell, Ishan Sachdev, Srinivas Devadas.
Proceedings of the 32nd Annual International Symposium on Computer Architecture, pp. 25-36
"ISCA 2005," Madison, Wisconsin, USA (June 2005)
Updated version available as MIT CSAIL CSG Technical Memo 483 (MIT-CSAIL-CSG-483)

[article]
[slides]		          Information Leak in the Chord Lookup Protocol (Presenter)
         Charles W. O'Donnell, Vinod Vaikuntanathan.
Proceedings of 4th Annual IEEE International Conference on Peer-to-Peer Computing, pp. 28-35
"P2P 2004," Zurich, Switzerland (August 2004).

[article]
[slides]		          On the Existence of Hazard-Free Multi-Level Logic
         Steven M. Nowick, Charles W. O'Donnell.
Proceedings of the 9th Annual IEEE International Symposium on Advanced Research in Asynchronous Circuits and Systems, pp. 109-120
"ASYNC 2003," Vancouver, BC, Canada (May 2003).


Refereed Posters
[poster]
         Modeling Ensembles of Transmembrane β-barrel Proteins
         Jérôme Waldispühl* Charles W. O'Donnell*, Nathan Palmer, Srinivas Devadas, Peter Clote, Bonnie Berger. (*authors equally contributed)
Poster at 15th Annual International Conference on Intelligent Systems for Molecular Biology & 6th European Conference on Computational Biology
"ISMB/ECCB 2007," Vienna, Austria, (July 2007)

[poster]
[abstract]		          Learning Biophysically-Motivated Parameters for Alpha Helix Prediction (Presenter)
         Blaise Gassend, Charles W. O'Donnell, William Thies, Andrew Lee, Marten van Dijk, Srinivas Devadas.
Poster at 10th Annual International Conference on Research in Computational Molecular Biology
"RECOMB 2006," Venice Lido, Italy (April 2006)


Other Major Publications

[thesis]          Secure Application Partitioning for Intellectual Property Protection (Master's Thesis)
         Charles W. O'Donnell
MIT EECS Master's Thesis (August 2005)

[article]          AEGIS: A single-chip secure processor (Invited Journal Article)
         G. Edward Suh, Charles W. O'Donnell, Srinivas Devadas.
Elsevier Information Security Technical Report, Volume 10, Issue 2, pp. 63-73, 2005.

[article]          PUF-Based Random Number Generation
         Charles W. O'Donnell, G. Edward Suh, Srinivas Devadas.
MIT CSAIL CSG Technical Memo 481 (MIT-CSAIL-CSG-481), (November 2004).

[slides]          Program Partitioning for Secure Execution (Talk, Presenter)
         Charles W. O'Donnell, G. Edward Suh, Srinivas Devadas.
Presentation at the 4th Annual MIT CSAIL Computer Architecture Workshop
"CAW 2004," Ashland, Massachusetts (September 2004).



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