2009

Lezon TR, Sali A, Bahar I. (2009) "Global motions of the nuclear pore complex: insights from elastic network models." PLoS Comput Biol. 9:e1000496 (Abstract)

Yang Z, Bahar I, Widom M. (2009) "Vibrational dynamics of icosahedrally symmetric biomolecular assemblies compared with predictions based on continuum elasticity." Biophys J. 96: 4438-48. (Abstract)

Molina G, Vogt A, Bakan A, Dai W, Queiroz de Oliveira P, Znosko W, Smithgall TE, Bahar I, Lazo JS, Day BW, Tsang M. (2009) "Zebrafish chemical screening reveals an inhibitor of Dusp6 that expands cardiac cell lineages." Nat Chem Biol. 5:680-7 (Abstract)

Liu L, Koharudin LM, Gronenborn AM, Bahar I (2009)"A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations." Proteins, in press. (Abstract)

Lezon TR, Sali A, Bahar I (2009) "Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models". PLoS Comput Biol 5(9): e1000496. (PDF)

Bakan, A; Bahar, I (2009) "The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding" ,Proc Natl Acad Sci USA 106, 14349-14354 (PDF)

Brower-Sinning R, Carter DM, Crevar CJ, Ghedin E, Ross TM, Benos PV. (2009) “The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus.” Genome Biol 10, R18. (PDF)

Corcoran DL, Pandit KV, Gordon B, Bhattacharjee A, Kaminski N, Benos PV. (2009) “Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data.” PLoS One 4, e5279. (PDF)

Faeder JR, Blinov ML, Hlavacek WS. (2009) “Rule-based modeling of biochemical systems with BioNetGen.” Methods Mol Biol 500, 113-67. (PDF)

Gu Y, Shrivastava IH, Amara SG, Bahar I. (2009) “Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter.” PNAS 106, 2589-94. (PDF)

Kim MJ, Maly IV. (2009) “Deterministic mechanical model of T-killer cell polarization reproduces the wandering of aim between simultaneously engaged targets.” PLoS Comput Biol 5, e1000260. (PDF)

Maly IV. (2009) “Introduction: a practical guide to the systems approach in biology.” Methods Mol Biol 500, 3-13. (PDF)

Mamonov AB, Bhatt D, Cashman DJ, Ding Y, Zuckerman DM. (2009) “General Library-Based Monte Carlo Technique Enables Equilibrium Sampling of Semi-atomistic Protein Models.” J Phys Chem B 113, 10891-10904. (PDF)

Meirovitch H. (2009) “Methods for calculating the absolute entropy and free energy of biological systems based on ideas from polymer physics.” J Mol Recognit [Epub ahead of print]

Meirovitch H, Cheluvaraja S, White RP (2009) “Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding.” Curr Protein Pept Sci 10, 229-43. (PDF)

Mihailescu M, Meirovitch H. (2009) “Absolute free energy and entropy of a mobile loop of the enzyme acetylcholinesterase.” J Phys Chem B 113, 7950-64. (PDF)

Molina G, Vogt A, Bakan A, Dai W, de Oliveira PQ, Znosko W, Smithgall TE, Bahar I, Lazo JS, Day BW, Tsang M. (2009) “Zebrafish chemical screening reveals an inhibitor of Dusp6 that expands cardiac cell lineages.” Nat Chem Biol In Press. (PDF)

Mustata G, Follis AV, Hammoudeh DI, Metallo SJ, Wang H, Prochownik EV, Lazo JS, Bahar I. (2009) “Discovery of Novel Myc-Max Heterodimer Disruptors with a Three-Dimensional Pharmacophore Model.” J Med Chem 52, 1247-50. (PDF)

Tastan O, Klein-Seetharaman J, Meirovitch H. (2009) “The effect of loops on the structural organization of alpha-helical membrane proteins” Biophys J 96, 2299-312. (PDF)

Temiz NA, Camacho CJ. (2009) “Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface.” Nucleic Acids Res 37, 4076-88. (PDF)

Yang LW, Eyal E, Bahar I, Kitao A. (2009) “Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics.” Bioinformatics 25, 606-14. (PDF) (Abstract)

Yang Z, Bahar I, Widom M. (2009) “Vibrational dynamics of icosahedrally symmetric biomolecular assemblies compared with predictions based on continuum elasticity.” Biophys J 96, 4438-48. (PDF)

Yang, Z; Ma´jek, P; Bahar, I (2009) "Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL." PLoS Comput Biol 5(4): e1000360. (PDF)

2008

An, G; Faeder, J; Vodovotz, Y, (2008) “Translational Systems Biology: Introduction of an Engineering Approach to the Pathophysiology of the Burn Patient” Journal of Burn Care & Research 29, 277-285. (Abstract)

Arkhipov, S.N.; Maly, I.V., (2008) “Retractile processes in T lymphocyte orientation on a stimulatory substrate: morphology and dynamics” Physical Biology 5, 016006. (HTML)

Bagci EZ, Vodovotz Y, Billiar TR, Ermentrout B, Bahar I. (2008) “Computational insights on the competing effects of nitric oxide in regulating apoptosis.” PLoS ONE, 3, e2249. (PDF)

Baratt A, Arkhipov SN, Maly IV. (2008) “An experimental and computational study of effects of microtubule stabilization on T-cell polarity” PLoS One 3, e3861. (PDF)

Barua, D; Faeder, JR; Haugh, JM, (2008) “Computational models of tandem Src homology 2 domain interactions and application to phosphoinositide 3-kinase” Journal of Biological Chemistry 283, 7338-7345. (PDF)

Bueno, M; Camacho, CJ; Randhawa, PS, (2008) “A molecular modeling approach to develop compounds with anti-BK virus activity” American Journal of Transplantation, 8, Suppl. 2, 284-285.

Camacho CJ. (2008) “Quantitative modeling of currents from a voltage gated ion channel undergoing fast inactivation” PLoS One 3, e3342. (PDF)

Camacho CJ, Katsumata Y, Ascherman DP. (2008) “Structural and thermodynamic approach to peptide immunogenicity” PLoS Comput Biol 4, e1000231. (PDF)

Cheluvaraja, S; Meirovitch, H, (2008) “Stability of the free and bound microstates of a mobile loop of alpha-amylase obtained from the absolute entropy and free energy” Journal of Chemical Theory and Computation, 4, 192-208.

Cheluvaraja, S; Mihailescu, M; Meirovitch, H (2008) “Entropy and free energy of a mobile protein loop in explicit water” Journal of Physical Chemistry B , 112, 9512-9522. (PDF)

Chennubhotla, C; Yang, Z; Bahar, I (2008) “Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL” Molecular Biosystems 4, 287-292. (PDF)

Engen JR, Wales TE, Hochrein JM, Meyn MA 3rd, Ozkan, SB, Bahar I, Smithgall TE. (2008) “Structure and dynamic regulation of Src-family kinases.”  Cell Mol Life Sci. Jun 20. (PDF)

Eyal, E; Bahar, I, (2008) “Toward a molecular understanding of the anisotropic response of proteins to external forces: Insights from elastic network models” Biophysical Journal 94, 3424-3435. (PDF)

Faeder J. R., M. L. Blinov, & W. S. Hlavacek (2008) “Rule-Based Modeling of Biochemical Systems with BioNetGen.” In Methods in Molecular Biology: Systems Biology, Ed. I. V. Maly, Humana Press, Totowa, NJ, in press. (PDF)

Goldstein B., Coombs D., Faeder J. R. & Hlavacek W. S.. (2008) “Kinetic Proofreading Model.” In Multichain Immune Recognition Receptor Signaling: From Spatiotemporal Organization to Human Disease, Ed. A. B. Sigalov. Landes Bioscience, Austin, TX.

Isin, B; Schulten, K; Tajkhorshid, E; Bahar, I, (2008) “Mechanism of signal propagation upon retinal isomerization: Insights from molecular dynamics simulations of rhodopsin restrained by normal modes” Biophysical Journal 95, 789-803. (PDF)

Liu, Y; Eyal, E; Bahar, I, (2008) “Analysis of correlated mutations in HIV-1 protease using spectral clustering” Bioinformatics 24, 1243- 1250. (PDF)

Shrivastava IH, Jiang J, Amara SG, Bahar I. (2008) “Time-resolved mechanism of extracellular gate opening and substrate binding in a glutamate transporter” J Biol Chem 283, 28680-90.

Vorobjev I.A. and Maly I.V. On the relation of the microtubule length and dynamics: boundary effect and properties of an extended radial array. Cell Tissue Biol. (in press).

Vries, JK; Liu, X, (2008) “Subfamily specific conservation profiles for proteins based on n-gram patterns” BMC Bioinformatics 9, 72. (PDF)

White, RP; Meirovitch, H, (2008) “Minimalist explicit solvation models for surface loops in proteins” Journal of Chemical Theory and Computation 4, 216. (PDF)

Ytreberg, FM; Zuckerman, DM (2008) “A black-box re-weighting analysis can correct flawed simulation data” Proceedings of the National Academy of Sciences, USA 105, 7982-7987. (PDF)

DM Zuckerman, “Principles and Practicalities of Canonical Mixed-Resolution Sampling of Biomolecules,” to appear in Coarse-Graining of Condensed Phase and Biomolecular Systems, edited by GA Voth (Taylor and Francis).

2007

Arkhipov, S.N. and Maly, I.V. (2007) “A model for the interplay of receptor recycling and receptor-mediated contact in T cells” PLoS ONE, 2, e633. (PDF)

Bahar, I; Chennubhotla, C; Tobi, D (2007) “Intrinsic Enzyme Motions in the Unbound State and Relation to Allosteric Regulation” Current Opinion in Structural Biology 17, 633-640. (Abstract)

Bahar, I., Chennubhotla, C., and Erman, B. (2007) "Reply to comment on elastic network models and proteins" Physical Biology 4, 64-65. (PDF)

Barua, D., Faeder, J.R. and Haugh, J.M. (2007) “Structure-based Kinetic Models of Modular Signaling Protein Function: Focus on Shp2” Biophys. J. 92, 2290-2300. (PDF)

Benos, P. V., Corcoran, D. L., and Feingold, E. (2007). "Footer: Web-Based Identification of Evolutionary Conserved DNA cis-regulatory Elements" Methods in Molecular Biology/Comparative Genomics, edited by N. Bergman, Totowa, New Jersey: Humana Press, Inc.

Bueno, M and Camacho CJ (2007) “Acidic groups docked to well defined wetted pockets at the core of the binding interface: a tale of scoring and missing protein interactions in CAPRI” Proteins: Structure, Function, and Bioinformatics,69, 786-792 (PDF).

Bueno M, Camacho CJ, Sancho J. (2007) “SIMPLE estimate of the free energy change due to aliphatic mutations: superior predictions based on first principles” Proteins 68, 850-62. (PDF)

Champ PC, Camacho CJ. (2007) “FastContact: a free energy scoring tool for protein-protein complex structures” Nucleic Acids Res. 35 (Web Server issue), W556-60. Epub 2007 May 30. (PDF)

Chennubhotla, C. and Bahar, I (2007) “Signal Propagation in Proteins and Relation to Equilibrium Fluctuations” PLoS Computational Biology, 3, 1716-1726. (PDF)

Chennubhotla C, Bahar I. (2007) “Markov methods for hierarchical coarse-graining of large protein dynamics” J Comput Biol.14, 765-76. (PDF)

Edwards, JS; Faeder, JR; Hlavacek, WS; Jiang, Y; Nemenman, I; Wall, ME (2007) “q-bio 2007: a watershed moment in modern biology” Molecular Systems Biology 3, 148. (PDF)

Eyal, E., Chennubhotla, C., Yang, L. W., and Bahar, I. (2007) “Anisotropic fluctuations of amino acids in protein structures: Insights from X-ray crystallography and elastic network models” Bioinformatics 23, i175-i184. (PDF)

Eyal E, Pietrokovski S, Bahar I.(2007) “Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices” Bioinformatics 23, 1837-9. (PDF)

Faeder, JR; Hlavacek, WS; An, G (2007) “BioNetGen: A tool for formal knowledge representation of intracellular pathways” Shock 27, Suppl. 1, 31.

H. Feng, J.L. Taylor, P.V. Benos, R. Newton, R. Downing, K. Waddell, Y. Chang, P.S. Moore, (2007) “Human Transcriptome Subtraction by Using Short Sequence Tags To Search for Tumor Viruses in Conjunctival Carcinoma
”, J Virol 81: 11332- 11340. (PDF)

Grigoriev, I. , Splinter, D., Keijzer, N., Wulf, P.S., Demmers, J., Ohtsuka, T., Modesti, M., Maly, I.V., Grosveld, F., Hoogenraad, C.C., and Akhmanova, A.  (2007) “Rab6 regulates transport and targeting of exocytotic carriers” Dev. Cell, 13, 305–314. (Abstract)

Grigoriev, I. , Splinter, D., Keijzer, N., Wulf, P.S., Demmers, J., Ohtsuka, T., Modesti, M., Maly, I.V., Grosveld, F., Hoogenraad, C.C., and Akhmanova, A..  (2007) “Rab6 regulates transport and targeting of exocytotic carriers” Dev. Cell, 13, 305–314. (PDF)

Iyer AK, Tran KT, Borysenko CW, Cascio M, Camacho CJ, Blair HC, Bahar I, Wells A. (2007) “Tenascin cytotactin epidermal growth factor-like repeat binds epidermal growth factor receptor with low affinity” J Cell Physiol. 211, 748-58. (PDF)

Katsumata, Y., Ridgway, W. M., Oriss, T., Gu, X. Y., Chin, D., Wu, Y. H., Fertig, N., Oury, T., Vandersteen, D., Clemens, P., Camacho, C. J., Weinberg, A., & Ascherman, D. P. (2007) "Species-specific immune responses generated by histidyl-tRNA synthetase immunization are associated with muscle and lung inflammation" Journal of Autoimmunity 29, 174-186. (PDF)

Lazo, J.S., Skoko, J.J., Werner, S., Mitasev, B., Bakan, A., Koizumi, F, Yellow-Duke, A., Bahar, I, Brummond, K.M. (2007) “Structurally unique inhibitors of human mitogen-activated protein kinase phosphatase-1 identified in a pyrrole carboxamide library” J Pharmacol Exp Ther. 322 940-7. (PDF)

Lee, J., Li, Z., Brower-Sinning, R., John, B. (2007) “Regulatory circuit of human microRNA biogenesis” PLoS Comput Biol. 3, 721-732. (PDF)

Lu, Y., Mahony, S., Benos, P.V., Rosenfeld, R., Simon, I., Breeden, L., Bar-Joseph, Z. (2007) “Combined analysis reveals a core set of cycling genes” Genome Biol. 8, R146. (PDF)

Lyman, E. and Zuckerman, D.M. (2007) "Annealed importance sampling of peptides" J. Chem. Phys., 127, 065101. (PDF)

Lyman, E; Zuckerman, DM (2007) “On the structural convergence of biomolecular simulations by determination of the effective sample size” Journal of Physical Chemistry B 111, 12876-12882. (PDF)

Mahony, S; Benos, PV (2007) “STAMP: a web tool for exploring DNA-binding motif similarities” Nucleic Acids Research 35, Suppl. S, W253-W258. (PDF)

Mahony, S; Corcoran, DL; Feingold, E; Benos, PV (2007) “Regulatory conservation of protein coding and miRNA genes in vertebrates: lessons from the opossum genome” Genome Biology 8, r84. (PDF)

Mahony, S., Auron, P. E., and Benos, P. V. (2007) "DNA Famililial binding profiles made easy:Comparison of various motif alignment and clustering strategies" PloS Comput Biology 3, e61. (PDF)

Mahony, S., Auron, P.E., Benos, P.V. (2007) “Inferring protein-DNA dependencies using motif alignments and mutual information” Bioinformatics 23, i297-i304. (PDF)

Meirovitch H. (2007) “Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation” Curr Opin Struct Biol. 17, 181-6. (Abstract)

Mikkelsen, T.S. and et al. [Benos, P.V.] (2007) "Genome of the marsupial Monodelphia domestica reveals innovation in on-coding sequences" Nature 447, 167-177. (PDF)

Mu, FP; Williams, RF; Unkefer, CJ; Unkefer, PJ; Faeder, JR; Hlavacek, WS (2007) “Carbon-fate maps for metabolic reactions” Bioinformatics 23, 3193-3199. (PDF)

Prasad, J. C., Goldstone, J. V., Camacho, C. J., Vajda, S., and Stegeman, J. J. (2007) "Ensemble modeling of substrate binding to cytochromes p450: Analysis of catalytic differences between CYP1A orthologs" Biochemistry 46, 2640-2654. (PDF)

Ringquist, S., Pecoraro, C., Lu, Y., Styche, A., Rudert, W. A., Benos, P. V., and Trucco, M. (2007). “Web-based primer design software for genome scale SNP mapping by pyrosequencing” Humana Press, Inc., Totowa, New Jersey.

Tobi D, Bahar I. (2007) “Recruitment of rare 3-grams at functional sites: Is this a mechanism for increasing enzyme specificity?” BMC Bioinformatics 8, 226. (PDF)

Torigoe, C., Faeder, J.R., Oliver, J.M. and Goldstein, B. (2007) “Kinetic proofreading of ligand-FcεRI interactions may persist beyond LAT phosphorylation” J. Immunol. 178, 3530-3535. (PDF)

Vries, J. K., Liu, X., and Bahar, I. (2007) "Relationship between n-gram patterns and secondary structure" Proteins-Structure Function and Bioinformatics 68, 830-838. (PDF)

Yang LW, Eyal E, Chennubhotla C, Jee J, Gronenborn AM, Bahar I. (2007) “Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions” Structure. 15, 741-9. (Abstract)

Yasuhiro, K et al. [Camacho, CJ] (2007) “Species-specific immune responses generated by histidyl-tRNA synthetase immunization are associated with muscle and lung inflammation” Journal of Autoimmunity, 29, 174-186. (Abstract)

Ytreberg, F.M., Aroutiounian, S.Kh., and Zuckerman, D.M. (2007) "Demonstrated convergence of the equilibrium ensemble for a fast united-residue protein model" J. Chem. Theory Comp., 3, 1860-1866. (PDF)

Zhang, Bin W., Jasnow, David, and Zuckerman, Daniel M. (2007) "Efficient and verified simulation of a path-ensemble for conformational change in a united-residue model of calmodulin," Proc. Nat. Acad. Sci. USA 104:18043-18048 (2007).(Abstract) (PDF)

Zhang, B. W., Jasnow, D., & Zuckerman, D. M. (2007) "Transition-event durations in one-dimensional activated processes" Journal of Chemical Physics 126, 074504 (Abstract)

2006

Arkhipov, S. N. and Maly, I. V. (2006) "Contribution of whole-cell optimization via cell body rolling to polarization of T cells" Physical Biology 3, 209-219. (PDF)

Arkhipov, S. N. and Maly, I. V. (2006) "Quantitative analysis of the role of receptor recycling in T cell polarization" Biophysical Journal 91, 4306-4316. (PDF)

Bagci, E. Z., Vodovotz, Y., Billiar, T. R., Ermentrout, G. B., and Bahar, I. (2006) "Bistability in apoptosis: roles of Bax, Bcl-2, and mitochondrial permeability transition pores" Biophysical Journal 90, 1546-1559. (PDF)

Belov, K., Deakin, J. E., Papenfuss, A. T., Baker, M. L., Melman, S. D., Siddle, H. V., Gouin, N., Goode, D. L., Sargeant, T. J., Robinson, M. D., Wakefield, M. J., Mahony, S., Cross, J. G. R., Benos, P. V., Samollow, P. B., Speed, T. P., Graves, J. A. M., and Miller, R. D. (2006) "Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex" PloS Biology 4, 317-328. (PDF) (Supplementary Material)

Blinov, M.L., Faeder, J.R., Goldstein, B. and Hlavacek, W.S. (2006) “A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity” Biosystems 83, 136-151. (Abstract)

Blinov, M.L., Yang, J., Faeder, J.R. and Hlavacek, W.S. (2006) “Graph theory for rule-based modeling of biochemical networks” Lec. Notes Comput. Sci. 4230, 89-106. (PDF)

Blinov, M.L., Yang, J., Faeder, J.R. and Hlavacek, W.S. (2006) “Depicting signaling cascades” Nat. Biotechnol. 24, 137-138. (PDF)

Camacho, C. J., Ma, H., and Champ, P. C. (2006) "Scoring a diverse set of high-quality docked conformations: A metascore based on electrostatic and desolvation interactions" Proteins-Structure Function and Bioinformatics 63, 868-877. (PDF)

Chennubhotla, C. and Bahar, I. “Markov Propagation of Allosteric Effects in Biomolecular Systems” Molecular Systems Biology, 2, 36, 2006. (PDF) (Supplementary Material)

Chennubhotla, Chakra and Bahar, Ivet. (2006) Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics. RECOMB’06, accepted.  Lecture Notes in Computer Science 3909, 379-393. (PDF)

Cheluvaraja, S. and Meirovitch, H. (2006) "Calculation of the entropy and free energy of peptides by molecular dynamics simulations using the hypothetical scanning molecular dynamics method" Journal of Chemical Physics 125 024905. (Abstract)

Cui, Q & Bahar, Ivet (Eds). Normal Mode Analysis. Theory and Applications to Biological and Chemical Systems, Chapman & Hall / CRC Mathematical and Computational Biology Series, CRC Press, Taylor & Francis Group, 2006.

Eyal, E., Yang, L. W., and Bahar, I. (2006) "Anisotropic network model: systematic evaluation and a new web interface" Bioinformatics 22, 2619-2627. (PDF)

Farkas, I. J., Wu, C., Chennubhotla, C., Bahar, I., and Oltvai, Z. N. (2006) "Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae" BMC Bioinformatics 7. Published online 2006 October 28. (PDF) (Supplementary Material)

William S. Hlavacek, James R. Faeder, Michael L. Blinov, Richard G. Posner, Michael Hucka, Walter Fontana (2006) “Rules for modeling signal-transduction systems” Science STKE, re6. (PDF)

Isin, B., Rader, A. J., Dhiman, H. K., Klein-Seetharaman, J., and Bahar, I. (2006) "Predisposition of the dark state of rhodopsin to functional changes in structure" Proteins-Structure Function and Bioinformatics 65, 970-983. (PDF)

John, B., Sander, C., and Marks, D. S. (2006) "Prediction of human MicroRNA targets" Methods in Molecular Biology 342, 101-113. (Abstract)

Lyman, E. and Zuckerman, D. M. (2006) "Ensemble-based convergence analysis of biomolecular trajectories" Biophysical Journal 91, 164-172. (PDF)

Lyman, E. and Zuckerman, D. M. (2006) "Resolution exchange simulation with incremental coarsening" Journal of Chemical Theory and Computation 2, 656-666. (PDF)

Lyman, E., Ytreberg, F.M. and Zuckerman, D. M., Resolution Exchange Simulation, Phys. Rev. Lett. 96:028105 (2006). (Abstract)

Lyman, E. and Zuckerman, D. M. (2006) "A second look at canonical sampling of biomolecules using replica exchange simulation" Journal of Chemical Theory and Computation 2, 1200-1202. (PDF)

Mahony, S., Benos, P. V., Smith, T. J., and Golden, A. (2006) "Self-organizing neural networks to support the discovery of DNA-binding motifs" Neural Networks 19, 950-962. (Abstract)

Munshi, R., Coalson, R. D., Ermentrout, G. B., Madura, J. D., Meirovitch, H., Stiles, J. R., and Bahar, I. (2006) "An introduction to simulation and visualization of biological systems at multiple scales: A summer training program for interdisciplinary research" Biotechnology Progress 22, 179-185. (PDF)

Rader, AJ, Chennubhotla, Chakra, Yang, Lee-Wei and Bahar, Ivet. 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.

Shrivastava, I. H. and Bahar, I. (2006) "Common mechanism of pore opening shared by five different potassium channels" Biophysical Journal 90, 3929-3940. (PDF)

Szarecka, A. and Meirovitch, H. (2006) "Optimization of the GB/SA solvation model for predicting the structure of surface loops in proteins" Journal of Physical Chemistry B 110, 2869-2880. (PDF)

Tobi, D. and Bahar, I. (2006) "Optimal design of protein docking potentials: Efficiency and limitations" Proteins-Structure Function and Bioinformatics 62, 970-981. (PDF)

White, R. P. and Meirovitch, H. (2006) "Minimalist explicit solvation models for surface loops in proteins" Journal of Chemical Theory and Computation 2, 1135-1151. (PDF)

White, R. P. and Meirovitch, H. (2006) "Free volume hypothetical scanning molecular dynamics method for the absolute free energy of liquids" Journal of Chemical Physics 124 204108. (PDF)

Yang, L. W., Rader, A., Liu, X., Jursa, C. J., Chen, S. C., Karimi, H. A., and Bahar, I. (2006) "oGNM: online computation of structural dynamics using the Gaussian Network Model" Nucleic Acids Research 34, 24-31. (PDF) (Supplementary Material)

Ytreberg, F.M., Swendsen, R.H. and Zuckerman, D.M. (2006) "Comparison of free energy methods for molecular systems," J. Chem. Phys 125, 184114. (PDF)

Ytreberg, F.M. and Zuckerman, D.M. (2006) "BlackBox Reweighting" arXiv:physics/0609194v1 [physics.comp-ph]. (PDF)

Ytreberg, F. M. and Zuckerman, D. M. (2006) "Simple estimation of absolute free energies for biomolecules" Journal of Chemical Physics 124 104105. (PDF)