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Aaron Dinner

TitleProfessor
InstitutionUniversity of Chicago
DepartmentChemistry
AddressChicago IL 60637
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Freedman SL, Suarez C, Winkelman JD, Kovar DR, Voth GA, Dinner AR, Hocky GM. Mechanical and kinetic factors drive sorting of F-actin cross-linkers on bundles. Proc Natl Acad Sci U S A. 2019 Aug 13; 116(33):16192-16197. PMID: 31346091.
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    2. Thiede EH, Giannakis D, Dinner AR, Weare J. Galerkin approximation of dynamical quantities using trajectory data. J Chem Phys. 2019 Jun 28; 150(24):244111. PMID: 31255053.
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    3. Xu F, Kula-Eversole E, Iwanaszko M, Hutchison AL, Dinner A, Allada R. Circadian Clocks Function in Concert with Heat Shock Organizing Protein to Modulate Mutant Huntingtin Aggregation and Toxicity. Cell Rep. 2019 Apr 02; 27(1):59-70.e4. PMID: 30943415.
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    4. Mayassi T, Ladell K, Gudjonson H, McLaren JE, Shaw DG, Tran MT, Rokicka JJ, Lawrence I, Grenier JC, van Unen V, Ciszewski C, Dimaano M, Sayegh HE, Kumar V, Wijmenga C, Green PHR, Gokhale R, Jericho H, Semrad CE, Guandalini S, Dinner AR, Kupfer SS, Reid HH, Barreiro LB, Rossjohn J, Price DA, Jabri B. Chronic Inflammation Permanently Reshapes Tissue-Resident Immunity in Celiac Disease. Cell. 2019 02 21; 176(5):967-981.e19. PMID: 30739797.
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    5. Karki S, Banerjee S, Mclean K, Dinner A, Clark MR. Transcription factories in Ig? allelic choice and diversity. Adv Immunol. 2019; 141:33-49. PMID: 30904132.
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    6. Leddy O, Lu Z, Dinner AR. Entropic constraints on the steady-state fitness of competing self-replicators. J Chem Phys. 2018 Dec 14; 149(22):224105. PMID: 30553248.
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    7. Hong L, Vani BP, Thiede EH, Rust MJ, Dinner AR. Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights. Proc Natl Acad Sci U S A. 2018 12 04; 115(49):E11475-E11484. PMID: 30442665.
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    8. Leypunskiy E, Kiciman E, Shah M, Walch OJ, Rzhetsky A, Dinner AR, Rust MJ. Geographically Resolved Rhythms in Twitter Use Reveal Social Pressures on Daily Activity Patterns. Curr Biol. 2018 12 03; 28(23):3763-3775.e5. PMID: 30449672.
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    9. Freedman SL, Hocky GM, Banerjee S, Dinner AR. Nonequilibrium phase diagrams for actomyosin networks. Soft Matter. 2018 Sep 26; 14(37):7740-7747. PMID: 30204203.
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    10. Karki S, Kennedy DE, Mclean K, Grzybowski AT, Maienschein-Cline M, Banerjee S, Xu H, Davis E, Mandal M, Labno C, Powers SE, Le Beau MM, Dinner AR, Singh H, Ruthenburg AJ, Clark MR. Regulated Capture of V? Gene Topologically Associating Domains by Transcription Factories. Cell Rep. 2018 08 28; 24(9):2443-2456. PMID: 30157436.
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    11. Hutchison AL, Allada R, Dinner AR. Bootstrapping and Empirical Bayes Methods Improve Rhythm Detection in Sparsely Sampled Data. J Biol Rhythms. 2018 08; 33(4):339-349. PMID: 30101659.
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    12. Boisclair Lachance JF, Webber JL, Hong L, Dinner AR, Rebay I. Cooperative recruitment of Yan via a high-affinity ETS supersite organizes repression to confer specificity and robustness to cardiac cell fate specification. Genes Dev. 2018 03 01; 32(5-6):389-401. PMID: 29535190.
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    13. Stam S, Freedman SL, Banerjee S, Weirich KL, Dinner AR, Gardel ML. Filament rigidity and connectivity tune the deformation modes of active biopolymer networks. Proc Natl Acad Sci U S A. 2017 11 21; 114(47):E10037-E10045. PMID: 29114058.
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    14. Scholz M, Dinner AR, Levine E, Biron D. Stochastic feeding dynamics arise from the need for information and energy. Proc Natl Acad Sci U S A. 2017 08 29; 114(35):9261-9266. PMID: 28802256.
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    15. Pekow J, Hutchison AL, Meckel K, Harrington K, Deng Z, Talasila N, Rubin DT, Hanauer SB, Hurst R, Umanskiy K, Fichera A, Hart J, Dinner AR, Bissonnette M. miR-4728-3p Functions as a Tumor Suppressor in Ulcerative Colitis-associated Colorectal Neoplasia Through Regulation of Focal Adhesion Signaling. Inflamm Bowel Dis. 2017 08; 23(8):1328-1337. PMID: 28594651.
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    16. Freedman SL, Banerjee S, Hocky GM, Dinner AR. A Versatile Framework for Simulating the Dynamic Mechanical Structure of Cytoskeletal Networks. Biophys J. 2017 Jul 25; 113(2):448-460. PMID: 28746855.
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    17. Banerjee S, Lo K, Daddysman MK, Selewa A, Kuntz T, Dinner AR, Scherer NF. Biphasic growth dynamics control cell division in Caulobacter crescentus. Nat Microbiol. 2017 Jul 24; 2:17116. PMID: 28737755.
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    18. Leypunskiy E, Lin J, Yoo H, Lee U, Dinner AR, Rust MJ. The cyanobacterial circadian clock follows midday in vivo and in vitro. Elife. 2017 07 07; 6. PMID: 28686160.
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    19. Burov S, Figliozzi P, Lin B, Rice SA, Scherer NF, Dinner AR. Single-pixel interior filling function approach for detecting and correcting errors in particle tracking. Proc Natl Acad Sci U S A. 2017 01 10; 114(2):221-226. PMID: 28028226.
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    20. Gibbons SM, Scholz M, Hutchison AL, Dinner AR, Gilbert JA, Coleman ML. Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System. MBio. 2016 12 20; 7(6). PMID: 27999158.
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    21. Reppert M, Roy AR, Tempkin JO, Dinner AR, Tokmakoff A. Refining Disordered Peptide Ensembles with Computational Amide I Spectroscopy: Application to Elastin-Like Peptides. J Phys Chem B. 2016 11 10; 120(44):11395-11404. PMID: 27736076.
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    22. Perera J, Zheng Z, Li S, Gudjonson H, Kalinina O, Benichou JIC, Block KE, Louzoun Y, Yin D, Chong AS, Dinner AR, Weigert M, Huang H. Self-Antigen-Driven Thymic B Cell Class Switching Promotes T Cell Central Tolerance. Cell Rep. 2016 10 04; 17(2):387-398. PMID: 27705788.
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    23. Thiede EH, Van Koten B, Weare J, Dinner AR. Eigenvector method for umbrella sampling enables error analysis. J Chem Phys. 2016 Aug 28; 145(8):084115. PMID: 27586912.
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    24. Liang WG, Triandafillou CG, Huang TY, Zulueta MM, Banerjee S, Dinner AR, Hung SC, Tang WJ. Structural basis for oligomerization and glycosaminoglycan binding of CCL5 and CCL3. Proc Natl Acad Sci U S A. 2016 May 03; 113(18):5000-5. PMID: 27091995.
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    25. Chen Y, Kale S, Weare J, Dinner AR, Roux B. Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics - Monte Carlo Canonical Propagation Algorithm. J Chem Theory Comput. 2016 Apr 12; 12(4):1449-1458. PMID: 26918826.
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    26. Banerjee S, Scherer NF, Dinner AR. Shape dynamics of growing cell walls. Soft Matter. 2016 Apr 14; 12(14):3442-50. PMID: 26953519.
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    27. Ishizuka IE, Chea S, Gudjonson H, Constantinides MG, Dinner AR, Bendelac A, Golub R. Single-cell analysis defines the divergence between the innate lymphoid cell lineage and lymphoid tissue-inducer cell lineage. Nat Immunol. 2016 Mar; 17(3):269-76. PMID: 26779601.
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    28. Peláez N, Gavalda-Miralles A, Wang B, Navarro HT, Gudjonson H, Rebay I, Dinner AR, Katsaggelos AK, Amaral LA, Carthew RW. Dynamics and heterogeneity of a fate determinant during transition towards cell differentiation. Elife. 2015 Nov 19; 4. PMID: 26583752.
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    29. Perelis M, Marcheva B, Ramsey KM, Schipma MJ, Hutchison AL, Taguchi A, Peek CB, Hong H, Huang W, Omura C, Allred AL, Bradfield CA, Dinner AR, Barish GD, Bass J. Pancreatic ß cell enhancers regulate rhythmic transcription of genes controlling insulin secretion. Science. 2015 Nov 06; 350(6261):aac4250. PMID: 26542580.
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    30. Flourakis M, Kula-Eversole E, Hutchison AL, Han TH, Aranda K, Moose DL, White KP, Dinner AR, Lear BC, Ren D, Diekman CO, Raman IM, Allada R. A Conserved Bicycle Model for Circadian Clock Control of Membrane Excitability. Cell. 2015 Aug 13; 162(4):836-48. PMID: 26276633.
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    31. Leone V, Gibbons SM, Martinez K, Hutchison AL, Huang EY, Cham CM, Pierre JF, Heneghan AF, Nadimpalli A, Hubert N, Zale E, Wang Y, Huang Y, Theriault B, Dinner AR, Musch MW, Kudsk KA, Prendergast BJ, Gilbert JA, Chang EB. Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism. Cell Host Microbe. 2015 May 13; 17(5):681-9. PMID: 25891358.
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    32. Constantinides MG, Gudjonson H, McDonald BD, Ishizuka IE, Verhoef PA, Dinner AR, Bendelac A. PLZF expression maps the early stages of ILC1 lineage development. Proc Natl Acad Sci U S A. 2015 Apr 21; 112(16):5123-8. PMID: 25838284.
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    33. Hutchison AL, Maienschein-Cline M, Chiang AH, Tabei SM, Gudjonson H, Bahroos N, Allada R, Dinner AR. Improved statistical methods enable greater sensitivity in rhythm detection for genome-wide data. PLoS Comput Biol. 2015 Mar; 11(3):e1004094. PMID: 25793520.
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    34. Wright CS, Banerjee S, Iyer-Biswas S, Crosson S, Dinner AR, Scherer NF. Intergenerational continuity of cell shape dynamics in Caulobacter crescentus. Sci Rep. 2015 Mar 17; 5:9155. PMID: 25778096.
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    35. Kale S, Sode O, Weare J, Dinner AR. Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol. J Chem Theory Comput. 2014 Dec 09; 10(12):5467-5475. PMID: 25516726.
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    36. Iyer-Biswas S, Wright CS, Henry JT, Lo K, Burov S, Lin Y, Crooks GE, Crosson S, Dinner AR, Scherer NF. Scaling laws governing stochastic growth and division of single bacterial cells. Proc Natl Acad Sci U S A. 2014 Nov 11; 111(45):15912-7. PMID: 25349411.
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    37. Iyer-Biswas S, Crooks GE, Scherer NF, Dinner AR. Universality in stochastic exponential growth. Phys Rev Lett. 2014 Jul 11; 113(2):028101. PMID: 25062238.
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    38. Mathew R, Mao AP, Chiang AH, Bertozzi-Villa C, Bunker JJ, Scanlon ST, McDonald BD, Constantinides MG, Hollister K, Singer JD, Dent AL, Dinner AR, Bendelac A. A negative feedback loop mediated by the Bcl6-cullin 3 complex limits Tfh cell differentiation. J Exp Med. 2014 Jun 02; 211(6):1137-51. PMID: 24863065.
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    39. Tempkin JO, Qi B, Saunders MG, Roux B, Dinner AR, Weare J. Using multiscale preconditioning to accelerate the convergence of iterative molecular calculations. J Chem Phys. 2014 May 14; 140(18):184114. PMID: 24832260.
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    40. Singh H, Khan AA, Dinner AR. Gene regulatory networks in the immune system. Trends Immunol. 2014 May; 35(5):211-8. PMID: 24768519.
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    41. Saunders MG, Tempkin J, Weare J, Dinner AR, Roux B, Voth GA. Nucleotide regulation of the structure and dynamics of G-actin. Biophys J. 2014 Apr 15; 106(8):1710-20. PMID: 24739170.
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    42. Burov S, Tabei SM, Huynh T, Murrell MP, Philipson LH, Rice SA, Gardel ML, Scherer NF, Dinner AR. Distribution of directional change as a signature of complex dynamics. Proc Natl Acad Sci U S A. 2013 Dec 03; 110(49):19689-94. PMID: 24248363.
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    43. Ochiai K, Maienschein-Cline M, Simonetti G, Chen J, Rosenthal R, Brink R, Chong AS, Klein U, Dinner AR, Singh H, Sciammas R. Transcriptional regulation of germinal center B and plasma cell fates by dynamical control of IRF4. Immunity. 2013 May 23; 38(5):918-29. PMID: 23684984.
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    44. Dama JF, Sinitskiy AV, McCullagh M, Weare J, Roux B, Dinner AR, Voth GA. The Theory of Ultra-Coarse-Graining. 1. General Principles. J Chem Theory Comput. 2013 May 14; 9(5):2466-80. PMID: 26583735.
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    45. Tabei SM, Burov S, Kim HY, Kuznetsov A, Huynh T, Jureller J, Philipson LH, Dinner AR, Scherer NF. Intracellular transport of insulin granules is a subordinated random walk. Proc Natl Acad Sci U S A. 2013 Mar 26; 110(13):4911-6. PMID: 23479621.
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    46. Guttenberg N, Dama JF, Saunders MG, Voth GA, Weare J, Dinner AR. Minimizing memory as an objective for coarse-graining. J Chem Phys. 2013 Mar 07; 138(9):094111. PMID: 23485281.
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    47. Xu X, Rice SA, Dinner AR. Relation between ordering and shear thinning in colloidal suspensions. Proc Natl Acad Sci U S A. 2013 Mar 05; 110(10):3771-6. PMID: 23431185.
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    48. Lin Y, Li Y, Crosson S, Dinner AR, Scherer NF. Phase resetting reveals network dynamics underlying a bacterial cell cycle. PLoS Comput Biol. 2012; 8(11):e1002778. PMID: 23209388.
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    49. Pesic J, Terdik JZ, Xu X, Tian Y, Lopez A, Rice SA, Dinner AR, Scherer NF. Structural responses of quasi-two-dimensional colloidal fluids to excitations elicited by nonequilibrium perturbations. Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Sep; 86(3 Pt 1):031403. PMID: 23030916.
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    50. Maienschein-Cline M, Dinner AR, Hlavacek WS, Mu F. Improved predictions of transcription factor binding sites using physicochemical features of DNA. Nucleic Acids Res. 2012 Dec; 40(22):e175. PMID: 22923524.
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    51. Guttenberg N, Dinner AR, Weare J. Steered transition path sampling. J Chem Phys. 2012 Jun 21; 136(23):234103. PMID: 22779577.
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    52. Lenz M, Thoresen T, Gardel ML, Dinner AR. Contractile units in disordered actomyosin bundles arise from F-actin buckling. Phys Rev Lett. 2012 Jun 08; 108(23):238107. PMID: 23003998.
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    53. Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ, Dinner AR, Yang CG, He C. Duplex interrogation by a direct DNA repair protein in search of base damage. Nat Struct Mol Biol. 2012 Jun 03; 19(7):671-6. PMID: 22659876.
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    54. Lenz M, Gardel ML, Dinner AR. Requirements for contractility in disordered cytoskeletal bundles. New J Phys. 2012 Mar 01; 14. PMID: 23155355.
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    55. Ochiai K, Maienschein-Cline M, Mandal M, Triggs JR, Bertolino E, Sciammas R, Dinner AR, Clark MR, Singh H. A self-reinforcing regulatory network triggered by limiting IL-7 activates pre-BCR signaling and differentiation. Nat Immunol. 2012 Jan 22; 13(3):300-7. PMID: 22267219.
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    56. Cheng X, Xu X, Rice SA, Dinner AR, Cohen I. Assembly of vorticity-aligned hard-sphere colloidal strings in a simple shear flow. Proc Natl Acad Sci U S A. 2012 Jan 03; 109(1):63-7. PMID: 22198839.
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    57. Dickson A, Tabei SM, Dinner AR. Entrainment of a driven oscillator as a dynamical phase transition. Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Dec; 84(6 Pt 1):061134. PMID: 22304067.
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    58. Ali Tabei SM, Li Y, Weigert M, Dinner AR. Model for competition from self during passive immunization, with application to broadly neutralizing antibodies for HIV. Vaccine. 2012 Jan 11; 30(3):607-13. PMID: 22119591.
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    59. Maienschein-Cline M, Zhou J, White KP, Sciammas R, Dinner AR. Discovering transcription factor regulatory targets using gene expression and binding data. Bioinformatics. 2012 Jan 15; 28(2):206-13. PMID: 22084256.
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    60. Mandal M, Powers SE, Maienschein-Cline M, Bartom ET, Hamel KM, Kee BL, Dinner AR, Clark MR. Epigenetic repression of the Igk locus by STAT5-mediated recruitment of the histone methyltransferase Ezh2. Nat Immunol. 2011 Oct 30; 12(12):1212-20. PMID: 22037603.
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    61. Zheng W, Qi B, Rohrdanz MA, Caflisch A, Dinner AR, Clementi C. Delineation of folding pathways of a ß-sheet miniprotein. J Phys Chem B. 2011 Nov 10; 115(44):13065-74. PMID: 21942785.
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    62. Guttenberg N, Tabei SM, Dinner AR. Short-time evolution in the adaptive immune system. Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Sep; 84(3 Pt 1):031932. PMID: 22060428.
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    63. Dickson A, Maienschein-Cline M, Tovo-Dwyer A, Hammond JR, Dinner AR. Flow-Dependent Unfolding and Refolding of an RNA by Nonequilibrium Umbrella Sampling. J Chem Theory Comput. 2011 Sep 13; 7(9):2710-20. PMID: 26605464.
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    64. Sciammas R, Li Y, Warmflash A, Song Y, Dinner AR, Singh H. An incoherent regulatory network architecture that orchestrates B cell diversification in response to antigen signaling. Mol Syst Biol. 2011 May 24; 7:495. PMID: 21613984.
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    65. Maienschein-Cline M, Warmflash A, Dinner AR. Defining cooperativity in gene regulation locally through intrinsic noise. IET Syst Biol. 2010 Nov; 4(6):379-92. PMID: 21073237.
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    66. Ren M, Guo Q, Guo L, Lenz M, Qian F, Koenen RR, Xu H, Schilling AB, Weber C, Ye RD, Dinner AR, Tang WJ. Polymerization of MIP-1 chemokine (CCL3 and CCL4) and clearance of MIP-1 by insulin-degrading enzyme. EMBO J. 2010 Dec 01; 29(23):3952-66. PMID: 20959807.
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    67. Graham TG, Tabei SM, Dinner AR, Rebay I. Modeling bistable cell-fate choices in the Drosophila eye: qualitative and quantitative perspectives. Development. 2010 Jul; 137(14):2265-78. PMID: 20570936.
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    68. Qi B, Muff S, Caflisch A, Dinner AR. Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet miniprotein. J Phys Chem B. 2010 May 27; 114(20):6979-89. PMID: 20438066.
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    69. Dickson A, Nasto A, Dinner AR. Incorporating friction and collective shear moves into a lattice gas. Phys Rev E Stat Nonlin Soft Matter Phys. 2010 May; 81(5 Pt 1):051111. PMID: 20866189.
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    70. Li Y, Bhimalapuram P, Dinner AR. Model for how retrograde actin flow regulates adhesion traction stresses. J Phys Condens Matter. 2010 May 19; 22(19):194113. PMID: 21386439.
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    71. Xu X, Lin B, Cui B, Dinner AR, Rice SA. Spreading of colloid clusters in a quasi-one-dimensional channel. J Chem Phys. 2010 Feb 28; 132(8):084902. PMID: 20192315.
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    72. Stewman SF, Jones-Rhoades M, Bhimalapuram P, Tchernookov M, Preuss D, Dinner AR. Mechanistic insights from a quantitative analysis of pollen tube guidance. BMC Plant Biol. 2010 Feb 22; 10:32. PMID: 20170550.
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    73. Tchernookov M, Warmflash A, Dinner AR. Field theoretic treatment of an effective action for a model of catalyzed autoamplification. Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Jan; 81(1 Pt 1):011112. PMID: 20365328.
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    74. Dickson A, Dinner AR. Enhanced sampling of nonequilibrium steady states. Annu Rev Phys Chem. 2010; 61:441-59. PMID: 20367083.
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    75. Dickson A, Warmflash A, Dinner AR. Separating forward and backward pathways in nonequilibrium umbrella sampling. J Chem Phys. 2009 Oct 21; 131(15):154104. PMID: 20568844.
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    76. Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M. CHARMM: the biomolecular simulation program. J Comput Chem. 2009 Jul 30; 30(10):1545-614. PMID: 19444816.
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    77. Li Y, Qu X, Ma A, Smith GJ, Scherer NF, Dinner AR. Models of single-molecule experiments with periodic perturbations reveal hidden dynamics in RNA folding. J Phys Chem B. 2009 May 28; 113(21):7579-90. PMID: 19415919.
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    78. Tchernookov M, Warmflash A, Dinner AR. Critical behavior of a model for catalyzed autoamplification. J Chem Phys. 2009 Apr 07; 130(13):134906. PMID: 19355779.
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    79. Lin Y, Zhao T, Jian X, Farooqui Z, Qu X, He C, Dinner AR, Scherer NF. Using the bias from flow to elucidate single DNA repair protein sliding and interactions with DNA. Biophys J. 2009 Mar 04; 96(5):1911-7. PMID: 19254550.
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    80. Dickson A, Warmflash A, Dinner AR. Nonequilibrium umbrella sampling in spaces of many order parameters. J Chem Phys. 2009 Feb 21; 130(7):074104. PMID: 19239281.
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    81. Zhao T, Li Y, Dinner AR. How focal adhesion size depends on integrin affinity. Langmuir. 2009 Feb 03; 25(3):1540-6. PMID: 19132823.
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    82. Warmflash A, Dinner AR. Signatures of combinatorial regulation in intrinsic biological noise. Proc Natl Acad Sci U S A. 2008 Nov 11; 105(45):17262-7. PMID: 18981421.
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    83. Chen H, Hu J, Chen PR, Lan L, Li Z, Hicks LM, Dinner AR, He C. The Pseudomonas aeruginosa multidrug efflux regulator MexR uses an oxidation-sensing mechanism. Proc Natl Acad Sci U S A. 2008 Sep 09; 105(36):13586-91. PMID: 18757728.
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    84. Warmflash A, Adamson DN, Dinner AR. How noise statistics impact models of enzyme cycles. J Chem Phys. 2008 Jun 14; 128(22):225101. PMID: 18554058.
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    85. Hu J, Ma A, Dinner AR. A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT. Proc Natl Acad Sci U S A. 2008 Mar 25; 105(12):4615-20. PMID: 18353991.
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    86. Li Y, Zhao T, Bhimalapuram P, Dinner AR. How the nature of an observation affects single-trajectory entropies. J Chem Phys. 2008 Feb 21; 128(7):074102. PMID: 18298135.
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    87. Warmflash A, Bhimalapuram P, Dinner AR. Umbrella sampling for nonequilibrium processes. J Chem Phys. 2007 Oct 21; 127(15):154112. PMID: 17949137.
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    88. Zhao T, Dinner AR. Apparent directional scanning for DNA repair. Biophys J. 2008 Jan 01; 94(1):47-52. PMID: 17827238.
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    89. Stewman SF, Dinner AR. Lattice model for self-assembly with application to the formation of cytoskeletal-like structures. Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Jul; 76(1 Pt 2):016103. PMID: 17677529.
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    90. Nag A, Zhao T, Dinner AR. Effects of nonproductive binding on the kinetics of enzymatic reactions with patterned substrates. J Chem Phys. 2007 Jan 21; 126(3):035103. PMID: 17249902.
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    91. Ma A, Hu J, Karplus M, Dinner AR. Implications of alternative substrate binding modes for catalysis by uracil-DNA glycosylase: an apparent discrepancy resolved. Biochemistry. 2006 Nov 21; 45(46):13687-96. PMID: 17105188.
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    92. Hu J, Ma A, Dinner AR. Bias annealing: a method for obtaining transition paths de novo. J Chem Phys. 2006 Sep 21; 125(11):114101. PMID: 16999460.
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    93. Warmflash A, Dinner AR. A model for TCR gene segment use. J Immunol. 2006 Sep 15; 177(6):3857-64. PMID: 16951348.
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    94. Laslo P, Spooner CJ, Warmflash A, Lancki DW, Lee HJ, Sciammas R, Gantner BN, Dinner AR, Singh H. Multilineage transcriptional priming and determination of alternate hematopoietic cell fates. Cell. 2006 Aug 25; 126(4):755-66. PMID: 16923394.
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    95. Hou P, Araujo E, Zhao T, Zhang M, Massenburg D, Veselits M, Doyle C, Dinner AR, Clark MR. B cell antigen receptor signaling and internalization are mutually exclusive events. PLoS Biol. 2006 Jul; 4(7):e200. PMID: 16719564.
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    96. Wylie DC, Hori Y, Dinner AR, Chakraborty AK. A hybrid deterministic-stochastic algorithm for modeling cell signaling dynamics in spatially inhomogeneous environments and under the influence of external fields. J Phys Chem B. 2006 Jun 29; 110(25):12749-65. PMID: 16800611.
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    97. Bitetti-Putzer R, Dinner AR, Yang W, Karplus M. Conformational sampling via a self-regulating effective energy surface. J Chem Phys. 2006 May 07; 124(17):174901. PMID: 16689598.
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    98. Ma A, Nag A, Dinner AR. Dynamic coupling between coordinates in a model for biomolecular isomerization. J Chem Phys. 2006 Apr 14; 124(14):144911. PMID: 16626249.
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    99. Hu J, Ma A, Dinner AR. Monte Carlo simulations of biomolecules: The MC module in CHARMM. J Comput Chem. 2006 Jan 30; 27(2):203-16. PMID: 16323162.
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    100. Nag A, Dinner AR. Enhancement of diffusion-controlled reaction rates by surface-induced orientational restriction. Biophys J. 2006 Feb 01; 90(3):896-902. PMID: 16299070.
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    101. Warmflash A, Weigert M, Dinner AR. Control of genotypic allelic inclusion through TCR surface expression. J Immunol. 2005 Nov 15; 175(10):6412-9. PMID: 16272293.
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    102. Ma A, Dinner AR. Automatic method for identifying reaction coordinates in complex systems. J Phys Chem B. 2005 Apr 14; 109(14):6769-79. PMID: 16851762.
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    103. Woo HJ, Dinner AR, Roux B. Grand canonical Monte Carlo simulations of water in protein environments. J Chem Phys. 2004 Oct 01; 121(13):6392-400. PMID: 15446937.
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    104. Li QJ, Dinner AR, Qi S, Irvine DJ, Huppa JB, Davis MM, Chakraborty AK. CD4 enhances T cell sensitivity to antigen by coordinating Lck accumulation at the immunological synapse. Nat Immunol. 2004 Aug; 5(8):791-9. PMID: 15247914.
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    105. Hagan MF, Dinner AR, Chandler D, Chakraborty AK. Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA. Proc Natl Acad Sci U S A. 2003 Nov 25; 100(24):13922-7. PMID: 14617777.
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    106. Lee KH, Dinner AR, Tu C, Campi G, Raychaudhuri S, Varma R, Sims TN, Burack WR, Wu H, Wang J, Kanagawa O, Markiewicz M, Allen PM, Dustin ML, Chakraborty AK, Shaw AS. The immunological synapse balances T cell receptor signaling and degradation. Science. 2003 Nov 14; 302(5648):1218-22. PMID: 14512504.
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    107. Sun S, Chandler D, Dinner AR, Oster G. Elastic energy storage in beta-sheets with application to F1-ATPase. Eur Biophys J. 2003 Dec; 32(8):676-83. PMID: 12955360.
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    108. Dinner AR, Karplus M. Comment on the Communication "The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State" by van Gunsteren et al. We thank Eugene Shakhnovich (Harvard University) for pointing out the references on lattice polymer simulations and very helpful discussions. We also thank Wilfred van Gunsteren for comments on the manuscript. A.R.D. is a Burroughs Wellcome Fund Hitchings-Elion Postdoctoral Fellow. The work done at Harvard was supported in part by the National Institutes of Health. Angew Chem Int Ed Engl. 2001 Dec 17; 40(24):4615-4616. PMID: 12404364.
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    109. Dinner AR, Blackburn GM, Karplus M. Uracil-DNA glycosylase acts by substrate autocatalysis. Nature. 2001 Oct 18; 413(6857):752-5. PMID: 11607036.
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    110. Dinner AR, Karplus M. The roles of stability and contact order in determining protein folding rates. Nat Struct Biol. 2001 Jan; 8(1):21-2. PMID: 11135664.
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    111. Dinner AR, Sali A, Smith LJ, Dobson CM, Karplus M. Understanding protein folding via free-energy surfaces from theory and experiment. Trends Biochem Sci. 2000 Jul; 25(7):331-9. PMID: 10871884.
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    112. Dinner AR, Verosub E, Karplus M. Use of a quantitative structure-property relationship to design larger model proteins that fold rapidly. Protein Eng. 1999 Nov; 12(11):909-17. PMID: 10585496.
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    113. Dinner AR, Karplus M. Is protein unfolding the reverse of protein folding? A lattice simulation analysis. J Mol Biol. 1999 Sep 17; 292(2):403-19. PMID: 10493884.
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    114. Dinner AR, Lazaridis T, Karplus M. Understanding beta-hairpin formation. Proc Natl Acad Sci U S A. 1999 Aug 03; 96(16):9068-73. PMID: 10430896.
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    115. Jasanoff A, Song S, Dinner AR, Wagner G, Wiley DC. One of two unstructured domains of Ii becomes ordered in complexes with MHC class II molecules. Immunity. 1999 Jun; 10(6):761-8. PMID: 10403651.
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    116. Dinner AR, Abkevich V, Shakhnovich E, Karplus M. Factors that affect the folding ability of proteins. Proteins. 1999 Apr 01; 35(1):34-40. PMID: 10090284.
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    117. Dinner AR, So SS, Karplus M. Use of quantitative structure-property relationships to predict the folding ability of model proteins. Proteins. 1998 Nov 01; 33(2):177-203. PMID: 9779787.
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    118. Dinner AR, Karplus M. A metastable state in folding simulations of a protein model. Nat Struct Biol. 1998 Mar; 5(3):236-41. PMID: 9501918.
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    119. Dinner AR, Sali A, Karplus M. The folding mechanism of larger model proteins: role of native structure. Proc Natl Acad Sci U S A. 1996 Aug 06; 93(16):8356-61. PMID: 8710875.
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    120. Dinner A, Fose JM. Industry's experience with worldwide regulation of biotechnology products. Bioprocess Technol. 1991; 13:371-82. PMID: 1367139.
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    121. Farid NA, Atkins LM, Becker GW, Dinner A, Heiney RE, Miner DJ, Riggin RM. Liquid chromatographic control of the identity, purity and "potency" of biomolecules used as drugs. J Pharm Biomed Anal. 1989; 7(2):185-8. PMID: 2488619.
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    122. Wikel JH, Paget CJ, DeLong DC, Nelson JD, Wu CY, Paschal JW, Dinner A, Templeton RJ, Chaney MO, Jones ND, Chamberlin JW. Synthesis of syn and anti isomers of 6-[[(hydroxyimino)phenyl]methyl]-1-[(1-methylethyl)sulfonyl]-1H-benzimidazol-2-amine. Inhibitors of rhinovirus multiplication. J Med Chem. 1980 Apr; 23(4):368-72. PMID: 6247489.
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    123. Bosin TR, Bickers RG, Dinner A. The metabolism of alpha-aminobenzo(b)thiophene-3-propionic acid (the sulfur analog of tryptophan) in the rat. Drug Metab Dispos. 1978 Jan-Feb; 6(1):31-7. PMID: 23271.
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    124. Indelicato JM, Dinner A, Peters LR, Wilham WL. Hydrolysis of 3-chloro-3-cephems. Intramolecular nucleophilic attack in cefaclor. J Med Chem. 1977 Jul; 20(7):961-3. PMID: 874971.
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    125. Dinner A. Cephalosporin degradations. J Med Chem. 1977 Jul; 20(7):963-5. PMID: 874972.
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    126. Dinner A, Farid KZ. Autoxidation of 24-R-ethylcholesterol. Lloydia. 1976 Mar-Jun; 39(2-3):144-6. PMID: 948240.
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    127. Souter RW, Dinner A. GLC determination of degradation of two related amine uptake inhibitors. J Pharm Sci. 1976 Mar; 65(3):457-9. PMID: 1263105.
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    128. Bosin TR, Campaigne E, Dinner A, Rogers RB, Maickel RP. Comparative toxicological studies of indole, benzo[b] thiophene, and 1-methylindole derivatives. J Toxicol Environ Health. 1976 Jan; 1(3):515-20. PMID: 1246091.
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    129. Bishara RH, Rutherford BS, Dinner A. GLC determination of 17 alpha-ethynylestriol 3-cyclopentyl ether. J Pharm Sci. 1975 Jul; 64(7):1210-3. PMID: 1151685.
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    130. Dinner A, Bishara RH, Rutherford BS. 3-Substituted 2',3'-dihydroestra-1,3,5(10)-trieno (16alpha, 17alpha-b)furan-17beta-ols as potential estrogens. J Med Chem. 1975 Mar; 18(3):314-5. PMID: 1133824.
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    131. Craig JC, Dinner A, Mulligan PJ. Simplified analogs of lysergic acid. V. Derivatives of N,N-diethyl-1-methyl-9H-indeno-1,2,3,9a-tetrahydro(2,1-b)pyridine-3-carboxamide. J Org Chem. 1974 Jun 14; 39(12):1669-76. PMID: 4854290.
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    132. Campaigne E, Dinner A. Benzo(b)thiophene derivatives. XVI. The sulfur isosteres of melatonin, bufotenine, 5-hydroxytryptophan, and related structures. J Med Chem. 1970 Nov; 13(6):1205-8. PMID: 5312307.
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