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Peer-Reviewed

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         Differentiated human stem cells resemble fetal, not adult β cells
Sinisa Hrvatin, Charles W. O'Donnell, Francis Deng, Jeffrey R. Millman, Felicia Walton Pagliuca, Philip DiIorio, Alireza Rezania, David K. Gifford, Douglas A. Melton.
Proc. Natl. Acad. Sci., Published ahead of print, February 10, 2014.

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         MARIS: Method for Analyzing RNA following Intracellular Sorting
Sinisa Hrvatin, Francis Deng, Charles W. O'Donnell, David K. Gifford, Douglas A. Melton.
PLoS ONE, Volume 9, Issue 3, pp. e89459.

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         Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape
Richard I. Sherwood*, Tatsunori Hashimoto*, Charles W. O'Donnell*, Sophia Lewis, Amira A. Barkal, John Peter van Hoff, Vivek Karun, Tommi Jaakkola, David K. Gifford.
(*authors contributed equally)
Nature Biotechnology, Volume 32, pp. 171-178 (January 19, 2014)

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         Simultaneous Alignment and Folding of Multiple Protein Sequences
Jérôme Waldispühl*, Charles W. O'Donnell*, Sebastian Will*, Srinivas Devadas, Rolf Backofen, Bonnie Berger. (*authors contributed equally)
Journal of Computational Biology, Accepted, in press.

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         A global sampling approach to designing and reengineering RNA secondary structures
Alex Levin, Mieszko Lis, Yann Ponty, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger, Jérôme Waldispühl.
Nucleic Acids Research Volume 40, Issue 20, pp. 10041-10052 (August 31, 2012)

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         Lynx: A Programmatic SAT Solver for the RNA-folding Problem
Vijay Ganesh, Charles W. O'Donnell, Armando Solar-Lezama, Srinivas Devadas, Mate Soos, Martin Rinard,
15th International Conference on Theory and Applications of Satisfiability Testing
"SAT 2012," Trento, Italy (June 2012) Lecture Notes in Computer Science, 7317, pp. 143-156.

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         STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions
Allen W. Bryan, Jr., Charles W. O'Donnell, Matthew Menke, Lenore J. Cowen, Susan Lindquist, Bonnie Berger,
Proteins: Structure, Function, and Bioinformatics Volume 80, Issue 2, pp. 410-420 (February, 2012)

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         Opposing effects of glutamine and asparagine govern prion formation by intrinsically disordered proteins
Randal Halfmann, Simon Alberti, Rajaraman Krishnan, Nicholas Lyle, Charles W. O'Donnell, Oliver King, Bonnie Berger, Rohit V. Pappu, Susan Lindquist,
Molecular Cell, Volume 43, Issue 1, pp. 72-84 (July 8, 2011)

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         A method for probing the mutational landscape of amyloid structure
Charles W. O'Donnell, Jérôme Waldispühl. Mieszko Lis, Randal Halfmann, Srinivas Devadas, Susan Lindquist, Bonnie Berger,
19th Annual International Conference on Intelligent Systems for Molecular Biology & 10th European Conference on Computational Biology
"ISMB/ECCB 2011," Vienna, Austria (July 2011),
Bioinformatics Volume 27, Issue 13, pp. i34-i42 (July 1, 2011)

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         Efficient Traversal of Protein Folding Pathways using Ensemble Models
Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger, Jérôme Waldispühl.
15th Annual International Conference on Research in Computational Molecular Biology
"RECOMB 2011," Vancouver, BC, Canada (March 2011), Lecture Notes in Computer Science, 6577, pp. 408-423.

Extended version in Journal of Computational Biology. Volume 18, Issue 11, pp. 1635-1647 (November 10, 2011)

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         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)

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

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         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)

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         Memoization Attacks and Copy Protection in Partitioned Applications
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)

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         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)

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         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)

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         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)

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         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)

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         Information Leak in the Chord Lookup Protocol
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).


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         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).


Media Coverage

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             PIQ-ing into chromatin architecture
Nature Biotechnology News and Views highlighting our 2014 directional and non-directional pioneers / PIQ article (vol. 32, pp. 138-140), written by Sebastian Rieck & Christopher Wright, February 7, 2014

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             Understanding proteins - New model of protein folding helps researchers handle flood of genomic data
MIT News feature on our ensemble prediction methods, written by Larry Hardesty, March 22, 2011

[link]              MIT's Ensemble Approach Speeds Protein Folding with Minor Compromise in Accuracy
Genomeweb BioInform article on our ensemble prediction methods, written by Uduak Grace Thomas, March 25, 2011


Patents

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             Bacteriophages Expressing Amyloid Peptides and Uses Thereof
T. K. Lu, R. Krishnan, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger, J. J. Collins, Susan Lindquist
Provisional applications 61/229,703 (July 29, 2009), 61/233,697 (August 13, 2009).
International Serial Number: PCT/US2010/043770. Published February 3, 2011.
US Patent Application 20120301433. Published November 29, 2012.


Posters

         Predicting β-sheet Protein Folding Pathways Using Ensemble Models
Poster at "3DSIG 2011," Vienna, Austria (July 2011)


         A Method for Probing the Mutational Landscape of Amyloid Structure
Poster at 14th Annual International Conference on Research in Computational Molecular Biology
"RECOMB 2010," Lisbon, Portugal(August 2010)


         Hypothesis-Driven Ensemble Modeling of Amyloids
2010 GRC Conference on Protein Folding Dynamics
Ventura, CA, USA, (January 2010)


         Modeling Structure Ensembles of Conserved β-sheet Folds
2008 IMA Annual Program Year Workshop on Protein Folding
Minneapolis, MN, USA, (January 2008)


         Modeling Structure Ensembles of Conserved β-sheet Folds
2008 GRC Conference on Protein Folding Dynamics
Ventura, CA, USA, (January 2008)


         Modeling Ensembles of Transmembrane β-barrel Proteins
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)

           
         Learning Biophysically-Motivated Parameters for Alpha Helix Prediction
Poster at 10th Annual International Conference on Research in Computational Molecular Biology
"RECOMB 2006," Venice Lido, Italy (April 2006)


Other Reports

[thesis]          Modeling Ensembles of β-sheet Proteins (Ph.D. Thesis)
Charles W. O'Donnell
MIT EECS Ph.D. Thesis (May 2011)

[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
G. Edward Suh, Charles W. O'Donnell, Srinivas Devadas.
Elsevier Information Security Technical Report, Volume 10, Issue 2, pp. 63-73, 2005.

[article]          Proof of Freshness: How to efficiently use an online single secure clock to secure shared untrusted memory
Marten van Dijk, Luis F. G. Sarmenta, Charles W. O'Donnell, Srinivas Devadas.
MIT CSAIL CSG Technical Memo 496 (MIT-CSAIL-CSG-496), (2006).

[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
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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