Alexe, G., G.S. Dalgin, R. Ramaswamy, C. Delisi, G. Bhanot.

“Data perturbation independent diagnosis and validation of breast cancer subtypes using clustering and patterns.”   Cancer Informatics 2:243-274 (2006)

Bhanot, G., G. Alexe, B. Venkataraghavan, A.J. Levine.

“A robust meta-classification strategy for cancer detection from MS data.”   Proteomics 6:592-604 (2006)

Chaves, M., E.D. Sontag, R. Albert.

“Methods of robustness analysis for Boolean models of gene control networks.”   IEE Proc. Systems Biology 153:154-167 (2006)

Czapla, L., D. Swigon, W.K. Olson.

“Sequence-dependent Monte Carlo Simulations of DNA Ring Closure.” J. Chem. Theor. Comp. 2, 685-695 (2006)

Enciso, G., E.D. Sontag.

“Global attractivity, I/O monotone small-gain theorems, and biological delay systems.'' Discrete and Continuous Dynamical Systems 14: 549-578  (2006)

Ibáñez-Ventoso, C., M. Yang, S. Guo, H. Robins, R.W. Padgett, M. Driscoll.

“Modulated microRNA expression during adult lifespan in C. elegans.” Aging Cell 5:235-246 (2006)

Kouranov, A, L. Xie, J. de la Cruz, L. Chen, J. Westbrook, P.E. Bourne, H.M. Berman.

"The RSCB PDB information portal for structural genomics." Nucleic Acids Res . 34(Database issue):D302-305 (2006)

Matsumoto, A., W.K. Olson.

“Effects of Sequence, Cyclization, and Superhelical Stress on the Internal Motions of DNA” in: Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems (Qiang Cui and Ivet Bahar , Eds.), Chapman & Hall/CRC Press, Boca Raton, FL, pp. 188-211 (2006)

Mohs, A., M. Popiel, Y. Li, J. Baum, B. Brodsky.

Conformational features of a natural break in the type IV collagen Gly-X-Y repeat.   J Biol Chem. 281:17197-17202 (2006)

Napoli, A.A., C.L. Lawson, R. H. Ebright, H.M. Berman.

"Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: Recognition of Pyrimidine-Purine and Purine-Purine Steps." J Mol Biol. 357:173-183 (2006)

Phadtare, S., V. Tadigotla, W.H. Shin, A. Sengupta, K. Severinov.

“Analysis of Escherichia coli global gene expression profiles in response to overexpression and deletion of CspC and CspE.”  J. Bacteriol. 188:2521-2527 (2006)

Ravindranathan, K.P., E. Gallicchio, R.A. Friesner, A.E. McDermott, R.M. Levy.

Conformational equilibrium of cytochrome P450 BM-3 complexed with N-Palmitoylglycine: A replica exchange molecular dynamics study.” J. Am. Chem. Soc., 128, 5786-5791 (2006)

Revyakin, A., C. Liu, R.H. Ebright, T.R. Strick.

“Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching.” Science 314:1139-43 (2006)

Swigon, D., B.D. Coleman, W.K. Olson.

“Modeling the Lac Repressor-operator Assembly. I. The Influence of DNA Looping on Lac Repressor Conformation.”  Proc. Natl. Acad. Sci., USA 103:9879-9884 (2006)

Szymczak, A., A. Stillman, A. Tannenbaum, K. Mischaikow.

"Coronary vessel trees from 3D imagery: A topological approach."  Med Image Anal. 10:548-559 (2006)

Tadigotla, V.R., D. O’Maoiléidigh, A.M. Sengupta, V. Epshtein, R.H. Ebright, E. Nudler, A.E. Ruckenstein.

"Thermodynamic and kinetic modeling of transcriptional pausing." Proc Natl Acad Sci USA. 103:4439-4444 (2006)

Van Riel, N.A.W., E.D. Sontag.

“Parameter estimation in models combining signal transduction and metabolic pathways: The dependent input approach.” IEE Proc. Systems Biology 153:263-274 (2006)