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Kale, S., Sode, O., Dinner, A. R., & Weare, J. Finding chemical reaction paths with a multilevel preconditioning protocol. J. Chem. Theor. Comp. 10, 5467-5475.
Iyer-Biswas, S., Wright, C. S., Henry, J. T., Lo, K., Burov, S., Crooks, G. E., Crosson, S., Dinner, A. R. & Scherer, N. F. Scaling laws governing stochastic growth and division of single bacterial cells. Proc. Natl. Acad. Sci. USA 111, 15912-15917.
Iyer-Biswas, S., Crooks, G. E., Crosson, S., Scherer, N. F. & Dinner, A. R. Universality in stochastic exponential growth. Phys. Rev. Lett. 113, 028101.
Mathew, R., Mao, A., Chiang, A. H., Bertozzi-Villa, C., Bunker, J. J., Scanlon, S. T., McDonald, B. D., Constanides, M. G., Hollister, K., Singer, J. D., Dent, A. L., Dinner, A. R. & Bendelac, A. A negative feedback loop mediated by the Bcl6-cullin3 complex limits Tfh differentiation. J. Exp. Med. 211, 1137-1151.
Singh, H., Khan, A. A. & Dinner, A. R. Gene regulatory networks in the immune system. Trends Immunol. 35, 211-218.
Tempkin, J. O. B., Qi, B., Saunders, M. G., Roux, B., Dinner, A. R. & Weare, J. Using multiscale preconditioning to accelerate the convergence of iterative molecular calculations. J. Chem. Phys. 140, 184114.
Saunders, M. G., Tempkin, J., Weare, J., Dinner, A. R., Roux, B. & Voth, G. A. Nucleotide regulation of the structure and dynamics of G-actin. Biophys. J. 106, 1710- 1720.
Burov, S., Tabei, S. M. A., Huynh, T., Murrell, M. P., Philipson, L. H., Rice, S. A., Gardel, M. L., Scherer, N. F. & Dinner, A. R. Distribution of directional change as a signature of complex dynamics. Proc. Natl. Acad. Sci. USA 110, 19689-19694.
Xu, X., Rice, S. A. & Dinner, A. R. Influence of interlayer exchanges on vorticity-aligned colloidal string assembly in a simple shear flow. J. Phys. Chem. Lett. 4, 3310-3315.
Dama, J. F., Sinitskiy, A. V., McCullagh, M., Weare, J., Roux, B., Dinner, A. R. & Voth, G. A. The theory of ultra coarse-graining. I. General principles. J. Chem. Theor. Comp. 9, 2466-2480.
Ochiai, K., Maienschein-Cline, M., Simonetti, G., Chen, J., Rosenthal, R., Brink, R., Chong, A. S., Klein, U., Dinner, A. R., Singh, H. & Sciammas, R. Transcriptional regulation of germinal center B and plasma cell fates by dynamical control of IRF4. Immunity 38, 1-12.
Tabei, S. M. A., Burov, S., Kim, H. Y., Kuznetsov, A., Huynh, T., Jureller, J., Philipson, L. H., Dinner, A. R. & Scherer, N. F. Intracellular transport of insulin granules is a subordinated random walk. Proc. Natl. Acad. Sci. USA 110, 4911-4916.
Guttenberg, N., Dama, J. F., Saunders, M. G., Voth, G. A., Weare, J. & Dinner, A. R. Minimizing memory as an objective for coarse-graining. J. Chem. Phys. 138, 094111.
Xu, X., Rice, S. A. & Dinner, A. R. Relation between ordering and shear thinning in colloidal suspensions. Proc. Natl. Acad. Sci. USA 110, 3771-3776.
Lin, Y., Li, Y., Crosson, S., Dinner, A. R. & Scherer, N. F. Phase resetting reveals network dynamics underlying a bacterial cell cycle. PLoS Comp. Biol. 8, e1002778.
Maienschein-Cline, M., Dinner, A. R., Hlavacek, W. S. & Mu, F. Improved predictions of transcription factor binding sites using physicochemical features of DNA. Nuc. Acid Res. Advance Access.
Pesic, J., Xu, X., Terdik, J. Z., Lopez, A., Rice, S. A., Dinner, A. R. & Scherer, N. F. Structural responses of quasi-two-dimensional colloidal fluids to excitations elicited by nonequilibrium perturbations. Phys. Rev. E, 86, 031403.
Guttenberg, N., Dinner, A. R. & Weare, J. Steered transition path sampling. J. Chem. Phys. 136, 234103.
Yi, C., Chen, B., Qi, B., Zhang, W., Jia, G., Zhang, L., Li, C. Q., Dinner, A. R., Yang, C.-G. & He, C. Duplex interrogation by a direct DNA repair protein in search of base damage. Nature Struct. Mol. Biol. 19, 671-676.
Lenz, M., Thoresen, T., Gardel, M. L. & Dinner, A. R. F-actin buckling underlies the contraction of non-sarcomeric actomyosin bundles. Phys. Rev. Lett. 108, 238107.
Lenz, M., Gardel, M. L. & Dinner, A. R. Requirements for contractility in disordered cytoskeletal bundles. New J. Phys. 14, 033037.
Ochiai, K., Maienschein-Cline, M., Mandal, M., Triggs, J., Bertolino, E., Sciammas, R., Dinner, A. R., Clark, M. R. & Singh, H. A self-reinforcing regulatory network triggered by limiting IL-7 activates pre-BCR signaling and differentiation. Nature Immunol. 13, 300-307.
Maienschein-Cline, M., Zhou, J., White, K. P., Sciammas, R. & Dinner, A. R. Discovering transcription factor regulatory targets using gene expression and binding data. Bioinformatics 28, 206-213.
Tabei, S. M. A., Li, Y., Weigert, M. & Dinner, A. R. Model for competition from self during passive immunization, with application to broadly neutralizing antibodies for HIV. Vaccine 30, 607-613.
Cheng, X., Xu, X., Rice, S. A., Dinner, A. R. & Cohen, I. Assembly of vorticity-aligned hard-sphere colloidal strings in a simple shear flow. Proc. Natl. Acad. Sci. USA 109, 63-67.