2008

Eyal E, Bahar I. Toward a molecular understanding of the anisotropic response of proteins to external forces: Insights from elastic network models. Biophys J (2008)(Abstract)

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

John K Vries and Xiong Liu, Subfamily specific conservation profiles for proteins based on n-gram patterns BMC Bioinformatics 2008, 9:72 (Abstract)

F. Marty Ytreberg and Daniel M. Zuckerman, A "black-box" re-weighting analysis can correct flawed simulation data, after the fact, Proc. Nat. Acad. Sci. USA (in press).

2007

Mahony, S. and Benos, P. V. STAMP; a web tool for exploring DNA-binding motif similarities Nucleic Acids Research, 35(Web Server issue), W253-W258 (2007)

An, G., Faeder, J. and Vodovotz, Y. (2007) “Translational Systems Biology: Introduction of an Engineering Approach to the Pathophysiology of the Burn Patient” Journal of Burn Care and Research (in press).

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. and D. Tobi (2007) “Intrinsic Enzyme Motions in the Unbound State and Relation to Allosteric Regulation” Current Opinion Structural Biology, 17(5) (in press)

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)

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 22, 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)

Feng, H. C., Taylor, J. L., Benos, P. V., Newton, R., Waddell, K., Lucas, S. B., Chang, Y., & Moore, P. S. (2007) "Human transcriptome subtraction by using short sequence tags to search for tumor viruses in conjunctival carcinoma" Journal of Virology 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. (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. and Zuckerman, D.M. (2007) “On the convergence of biomolecular simulations: Determining the effective sample size" J. Phys. Chem. B, (PDF).

Mahony, S. and Benos, P. V. (2007) "STAMP; a web tool for exploring DNA-binding motif similarities" Nucleic Acids Research. (PDF)

Mahony, S., Corcoran, D. L., Feingold, E., and Benos, P. V. (2007) "Regulatory conservation of protein coding and miRNA genes in vertebrates: lessons from the opossum genome" Genome Biology, 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)

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)

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, C., Bahar, I. (2006) "Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics" 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. and Bahar, I. (2006). “Normal Mode Analysis,Theory and Applications to Biological and Chemical Systems” CRC Press, Taylor and Francis Group. Chapman and Hall/CRC Mathematical and Computational Biology Series.

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. (2006) "Resolution exchange simulation" Physical Review Letters 96. (PDF)

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, A., Chennubhotla, C., Yang, L. W., and Bahar, I. (2006) “The Gaussian Network Model: Theory and Applications, Normal Mode Analysis,Theory and Applications to Biological and Chemical Systems,” edited by Q. Cio and I. Bahar, pp. 41-64. CRC Press, Taylor and Francis Group, Chapman and Hall/CRC Mathematical and Computational Biology Series. (PDF)

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)