Computational Biology

Jerome Waldispuhl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, and Bonnie Berger, "Simultaneous Alignment and Folding of Protein Sequences", Journal of Computational Biology, April 2014.

Alex Levin; Mieszko Lis; Yann Ponty; Charles W. O'Donnell; Srinivas Devadas; Bonnie Berger; Jerome Waldispuhl"A global sampling approach to designing and reengineering RNA secondary structures", Nucleic Acids Research, 2012.

V. Ganesh, C. W. O'Donnell, M. Soos, S. Devadas, M. Rinard, and A. Solar-Lezama"Lynx: A Programmatic SAT Solver for the RNA-folding Problem", 15th International Conference on Satisfiability Testing (SAT), June 2012.

Charles W. O'Donnell, Jerome Waldispuhl, Mieszko Lis, Randall Halfmann, Srinivas Devadas, Susan Lindquist, Bonnie Berger "A method for probing the mutational landscape of amyloid structure", ISMB/ECCB 2011, July 2011.

Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Jerome Waldispuhl, "Efficient traversal of protein folding pathways using ensemble models", RECOMB 2011, March 2011.

M. Artomov, M. Lis, S. Devadas, M. Davis and A. Chakraborty, "CD4 and CD8 binding to MHC molecules primarily acts to enhance Lck delivery", Proceedings of the Nat'l Academy of Science, September 2010.

M. Lis, M. Artomov, S. Devadas, and A. Chakraborty, "Efficient stochastic simulation of reaction-diffusion processes via direct compilation", Bioinformatics, 25(17), pages 2289-2291, 2009.

Jerome Waldispuhl, Srinivas Devadas, Bonnie Berger, and Peter Clote, "RNAmutants: a web server to explore the mutational landscape of RNA secondary structures", Nucleic Acids Research 37, June 2009.

Jerome Waldispuhl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, and Bonnie Berger, "Simultaneous Alignment and Folding of Proteins", RECOMB 2009, March 2009.

Jerome Waldispuhl, Srinivas Devadas, Bonnie Berger, and Peter Clote, "Efficient Algorithms for Probing the RNA Mutation Landscape", PLoS: Computational Biology, August 2008.

Jerome Waldispuhl, Charles. W. O'Donnell, Srinivas Devadas, Peter Clote, and Bonnie Berger, "Modeling Ensembles of Transmembrane β-barrel Proteins, Proteins: Structure, Function, and Bioinformatics, Volume 71, Issue 3, pp. 1097-1112 (15 May 2008, digitally published 14 November 2007)

Blaise Gassend, Charles W. O'Donnell, William Thies, Andrew Lee, Marten van Dijk, and Srinivas Devadas, "Learning Biophysically-Motivated Parameters for Alpha Helix Prediction", BMC Bioinformatics, May 2007.

Blaise Gassend, Charles W. O'Donnell, William Thies, Andrew Lee, Marten van Dijk, and Srinivas Devadas, "Learning Biophysically-Motivated Parameters for Alpha Helix Prediction", RECOMB 2006 Poster , April 2006.