Selected Papers from 109 Peer-Reviewed Publications
J.B. Rosen, K.A. Dill, A.T. Phillips. Protein structure
and energy landscape dependence on sequence using
a continuous energy function, J. Comp. Bio., 4, pp.
227-239, 1997.
K.A. Dill, A.T. Phillips & J.B. Rosen, "Protein Structure
Predication and Potential Energy Landscape
Analysis using Continuous Global Minimization,"
Proceedings of the First Annual International Conference
on Computational Molecular Biology, pp 109-117, 1997
A.T. Phillips, J.B. Rosen, K.A. Dill. Energy landscape
projections of molecular potential functions,
Optimization in Computational Chemistry and Molecular
Biology, C.A. Floudas, P.M. Pardalos, Eds.,
Kluwer, pp. 47-55, 1999
K.W. Foreman, A.T. Phillips, J.B. Rosen, K.A. Dill.
Comparing search strategies for finding global optima
on energy landscapes, J. Computational Chemistry, 20,
pp. 1527-1532, 1999.
Mitchell, J.C., Phillips, A.T., Posen, J.B. & Ten Eyck,
L., "Coupled optimization in protein docking,"
Proceedings of the Third Annual International Conference
on Computational Molecular Biology, pp. 108-
184, ACM Press, New York, 2000
J.C. Mitchell, A.T. Phillips, J.B. Rosen, L.T. Eyck. A
coupled scanning optimization scheme for analyzing
molecular interactions, Optimization in Computational
Chemistry and Molecular Biology, C.A. Floudas,
P.M. Pardalos, Eds., Kluwer, pp. 191-207, 2000.
K.A. Dill, A.T. Phillips, J.B. Rosen. Convex global
underestimation for molecular structures prediction.
From Local to Global Optimization, eds. P.M. Pardalos
et al. (Kluwer, Dordrecht), pp. 1-18, 2000.
J.B. Rosen, A.T. Phillips, S.Y. Oh, K.A. Dill. A method
for parameter optimization in computational
biology, Biophys. J., 79 (2000), pp. 2818-2824.
J.B. Rosen, H. Park, J. Glick. Signal identification
using a least L1 norm algorithm, Optimization and
Engineering, 1 (2000), pp. 51-65.
J.B. Rosen, H. Park, J. Glick, L. Zhang. Accurate
solution to overdetermined linear equations with errors
using L1 norm minimization. Computational Optimization
and Applications, 17 (2000), pp. 329-341.
J.B. Rosen, S.Y. Oh, K.A. Dill. Global minimization and
parameter estimation in computational biology,
Advances in Convexity and Global Optimization
(Hadjisavvas and Pardalos, Eds), Kluwer Academic Publ.,
pp.153-180, 2001.
C. Seok, J.B. Rosen, J.D. Chodera, K.A. Dill. MOPED:
method for optimizing physical energy parameters
using decoys, J. Computational Chemistry, 24 (2003), pp
89-97.
J.B. Rosen, R. Marcia. Convex Quadratic Approximation,
Computational Optimization and Applications.
Accepted for publication (2003).
R.H. Leary, J.B. Rosen, P. Jambeck. An optimal structure
discriminative amino acid index for protein fold
recognition, Biophysical J. 86(2004), 411-419.
e-mail: jbrosen@cs.ucsd.edu