LW Yang, A.J. Rader, X. Liu, C.J. Jursa, S.C. Chen, H.A. Karimi, and I. Bahar
"oGNM: online computation of structural dynamics using the Gaussian Network Model" Nucleic Acids Res 34, W24-31, 2006.

C. Chennubhotla and I. Bahar.
"Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES" Mol Syst Biol 2:36, 2006

E. Z. Bagci, Y. Vodovotz, T. R. Billiar, G. B. Ermentrout, and I. Bahar
"Bistability in Apoptosis: Roles of Bax, Bcl-2, and Mitochondrial Permeability Transition Pores" Biophys J 90, 1546-1559, March 2006

I. H. Shrivastava and I. Bahar.
"Common Mechanism of Pore Opening Shared by Five Different Potassium Channels" Biophys J 90, 3929-3940, 2006.

A.J. Rader, C. Chennubhotla, L-W. Yang, and I. Bahar.
"The Gaussian Network Model: Theory and Applications" in "Normal Mode Analysis. Theory and Applications to Biological and Chemical Systems" Eds Qiang Cui and I Bahar, Chapman & Hall / CRC Mathematical and Computational Biology Series, CRC Press, Taylor & Francis Group, 41-64, 2006.

R. Munshi, R.D. Coalson, G.B. Ermentrout, J.D. Madura, H. Meirovitch, J.R. Stiles, and I. Bahar.
"An Introduction to Simulation and Visualization of Biological Systems at Multiple Scales: A Summer Training Program for Interdisciplinary Research" Biotechnology Progress 22, 179-185, 2006.

C. Chennubhotla and I. Bahar.
"Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics" RECOMB'06, accepted.  Lecture Notes in Computer Science 3909, 379-393, 2006

D. Tobi and I. Bahar.
"Optimal Design of Protein Docking Potentials: Efficiency and Limitations" Proteins: Structure, Function, and Bioinformatics, 62, 970-981, 2006

C. Chennubhotla, A.J. Rader, L-W. Yang, and I. Bahar.
"Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies" Physical Biology 2, S173-S180, 2005.

D. Tobi and I. Bahar.
"Structural Changes Involved in Protein Binding Correlate with Motions of Proteins in the Unbound State" Proc. Natl. Acad. Sci. USA 102, 18908-18913, 2005.

I. Bahar and A.J. Rader.
"Coarse-grained normal mode analysis in structural biology" Current Opinion in Structural Biology 15, 1-7, 2005.

L-W. Yang, X. Liu, C.J. Jursa, M. Holliman, H.A. Karimi, and I. Bahar.
"iGNM: A Database of Protein Functional Motions Based on Gaussian Network Model" Bioinformatics 21, 2978-2987, 2005

L-W. Yang and I. Bahar.
"Coupling between Catalytic Site and Collective Dynamics: A requirement for Mechanochemical Activity of Enzymes" Structure 13, 893-904, 2005.

J. Berberich, L-W. Yang, I. Bahar, and A.J. Russell.
"Analysis of the impact of silver ions on creatine amidinohydrolase" ACTA Biomateriala 1, 183-191, 2005.

J. Berberich, L-W. Yang, J.D. Madura, I. Bahar, and A.J. Russell.
"A Stable Three Enzyme Creatinine Biosensor Impact of structure, function and environment on PEGylated and immobilized sarcosine oxidase" ACTA Biomateriala 1, 173-181, 2005.

A.J. Rader, D. Vlad, and I. Bahar.
"Maturation Dynamics of Bacteriophage HK97 Capsid" Structure (Camb) 13, 413-21, 2005.

A. Ramaswamy, I. Bahar, and I. Ioshikhes.
"Structural Dynamics of Nucleosome Core Particle: Comparison with Nucleosomes Containing Histone Variants" Proteins: Structure, Function and Bioinformatics 58, 683-696, 2005.

M. Seki, C. Masutani, L-W. Yang, A. Schuffert, S. Iwai, I. Bahar, and R.D. Wood.
"High efficiency bypass of DNA damage by a single human DNA polymerase" EMBO Journal 23, 4484-4494, 2004.

X. Liu, H. Karimi, L-W. Yang, and I. Bahar.
"Protein Functional Motion Query and Visualization" IEEE Proceedings, 28th Annual International Computer Software and Applications Conference - (COMPSAC'04), 2004.

M. Brisson, T. Nguyen, A. Vogt, J. Yalowich, A. Giorgianni, D. Tobi, I. Bahar, C.R.J. Stephenson, P. Wipf, and J.S. Lazo.
"Discovery and characterization of novel small molecule inhibitors of human Cdc25B dual specificity phosphatase" Molecular Pharmacology 66, 824-833, 2004.

J.K. Vries  R. Munshi, D. Tobi J. Klein-Seetharaman, P.V. Benos, and I. Bahar.
"A Sequence Alignment-Independent Method For Protein Classification" Applied Bioinformatics 3, 137-48, 2004.

N.A. Temiz, E. Meirovitch, and I. Bahar.
"E. coli Adenylate Kinase Dynamics: Comparison of Elastic Network Model Modes with Mode-Coupling 15N-NMR Relaxation Data." Proteins, Structure, Function and Bioinformatics 57, 468-480, 2004.

N. Sluis-Cremer, N.A. Temiz, and I. Bahar.
"Conformational changes in HIV-1 reverse transcriptase induced by nonnucleoside reverse transcriptase inhibitor binding." , Current Research in HIV 2, 323-32, 2004.

Y. Wang, A.J. Rader, I. Bahar, and R.L. Jernigan.
"Global Ribosome Motions Revealed with Elastic Network Model" Journal of Structural Biology 147, 302-314, 2004.

A.J. Rader, G. Anderson, B. Isin, H. G. Khorana, I. Bahar and J. Klein-Seetharaman
"Identification of core amino acids stabilizing rhodopsin" Proc. Natl. Acad. Sci. USA 101, 7246-7251, 2004.

A.J. Rader and I. Bahar
"Folding Core Predictions from Network Models of Proteins" Polymer 45, 659-668, 2004.

Y. Vodovotz, P. Kim, E.Z. Bagci, G.B. Ermentrout, C.C. Chow, I. Bahar, and T.R. Billiar.
"Inflammatory Modulation of Hepatocyte Apoptosis by Nitric Oxide: In Vivo, In Vitro, and In Silico Studies." Current Molecular Medicine 4, 753-762, 2004.

S.-C. Chen and I. Bahar.
"Mining frequent patterns in proteins: A study of serine proteinases” Bioinformatics 20 Suppl. 1, i77-i85, 2004.

C. Xu, D. Tobi, and I. Bahar,
"Allosteric Changes in Protein Structure Computed by a Simple Mechanical Model: Hemoglobin T --> R2 Transition" Journal of Molecular Biology 333, 153–168, 2003.

E.Z. Bagci, A. Kloczkowski, R.L. Jernigan, and I. Bahar
"The Origin and Extent of Coarse-Grained Regularities in Protein Internal Packing" , PROTEINS 53, 56-67, 2003.

S.B. Ozkan, K.A. Dill, and I. Bahar.
"Computing the Transition State Populations in Simple Protein Models" Biopolymers 68, 35-46, 2003.