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Items: 1 to 50 of 108

1.

Cooperative recruitment of Yan via a high-affinity ETS supersite organizes repression to confer specificity and robustness to cardiac cell fate specification.

Boisclair Lachance JF, Webber JL, Hong L, Dinner AR, Rebay I.

Genes Dev. 2018 Mar 1;32(5-6):389-401. doi: 10.1101/gad.307132.117. Epub 2018 Mar 13.

PMID:
29535190
2.

Filament rigidity and connectivity tune the deformation modes of active biopolymer networks.

Stam S, Freedman SL, Banerjee S, Weirich KL, Dinner AR, Gardel ML.

Proc Natl Acad Sci U S A. 2017 Nov 21;114(47):E10037-E10045. doi: 10.1073/pnas.1708625114. Epub 2017 Nov 7.

3.

Stochastic feeding dynamics arise from the need for information and energy.

Scholz M, Dinner AR, Levine E, Biron D.

Proc Natl Acad Sci U S A. 2017 Aug 29;114(35):9261-9266. doi: 10.1073/pnas.1703958114. Epub 2017 Aug 11.

4.

A Versatile Framework for Simulating the Dynamic Mechanical Structure of Cytoskeletal Networks.

Freedman SL, Banerjee S, Hocky GM, Dinner AR.

Biophys J. 2017 Jul 25;113(2):448-460. doi: 10.1016/j.bpj.2017.06.003.

PMID:
28746855
5.

Biphasic growth dynamics control cell division in Caulobacter crescentus.

Banerjee S, Lo K, Daddysman MK, Selewa A, Kuntz T, Dinner AR, Scherer NF.

Nat Microbiol. 2017 Jul 24;2:17116. doi: 10.1038/nmicrobiol.2017.116.

PMID:
28737755
6.

The cyanobacterial circadian clock follows midday in vivo and in vitro.

Leypunskiy E, Lin J, Yoo H, Lee U, Dinner AR, Rust MJ.

Elife. 2017 Jul 7;6. pii: e23539. doi: 10.7554/eLife.23539.

7.

miR-4728-3p Functions as a Tumor Suppressor in Ulcerative Colitis-associated Colorectal Neoplasia Through Regulation of Focal Adhesion Signaling.

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.

Inflamm Bowel Dis. 2017 Aug;23(8):1328-1337. doi: 10.1097/MIB.0000000000001104.

PMID:
28594651
8.

Single-pixel interior filling function approach for detecting and correcting errors in particle tracking.

Burov S, Figliozzi P, Lin B, Rice SA, Scherer NF, Dinner AR.

Proc Natl Acad Sci U S A. 2017 Jan 10;114(2):221-226. doi: 10.1073/pnas.1619104114. Epub 2016 Dec 27.

9.

Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System.

Gibbons SM, Scholz M, Hutchison AL, Dinner AR, Gilbert JA, Coleman ML.

MBio. 2016 Dec 20;7(6). pii: e01372-16. doi: 10.1128/mBio.01372-16.

10.

Refining Disordered Peptide Ensembles with Computational Amide I Spectroscopy: Application to Elastin-Like Peptides.

Reppert M, Roy AR, Tempkin JO, Dinner AR, Tokmakoff A.

J Phys Chem B. 2016 Nov 10;120(44):11395-11404. Epub 2016 Oct 27.

11.

Self-Antigen-Driven Thymic B Cell Class Switching Promotes T Cell Central Tolerance.

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.

Cell Rep. 2016 Oct 4;17(2):387-398. doi: 10.1016/j.celrep.2016.09.011.

12.

Eigenvector method for umbrella sampling enables error analysis.

Thiede EH, Van Koten B, Weare J, Dinner AR.

J Chem Phys. 2016 Aug 28;145(8):084115. doi: 10.1063/1.4960649.

13.

Structural basis for oligomerization and glycosaminoglycan binding of CCL5 and CCL3.

Liang WG, Triandafillou CG, Huang TY, Zulueta MM, Banerjee S, Dinner AR, Hung SC, Tang WJ.

Proc Natl Acad Sci U S A. 2016 May 3;113(18):5000-5. doi: 10.1073/pnas.1523981113. Epub 2016 Apr 18.

14.

Shape dynamics of growing cell walls.

Banerjee S, Scherer NF, Dinner AR.

Soft Matter. 2016 Apr 14;12(14):3442-50. doi: 10.1039/c5sm02991k. Epub 2016 Mar 8.

PMID:
26953519
15.

Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics - Monte Carlo Canonical Propagation Algorithm.

Chen Y, Kale S, Weare J, Dinner AR, Roux B.

J Chem Theory Comput. 2016 Apr 12;12(4):1449-1458. doi: 10.1021/acs.jctc.5b00706. Epub 2016 Mar 25.

16.

Single-cell analysis defines the divergence between the innate lymphoid cell lineage and lymphoid tissue-inducer cell lineage.

Ishizuka IE, Chea S, Gudjonson H, Constantinides MG, Dinner AR, Bendelac A, Golub R.

Nat Immunol. 2016 Mar;17(3):269-76. doi: 10.1038/ni.3344. Epub 2016 Jan 18.

17.

Dynamics and heterogeneity of a fate determinant during transition towards cell differentiation.

Peláez N, Gavalda-Miralles A, Wang B, Navarro HT, Gudjonson H, Rebay I, Dinner AR, Katsaggelos AK, Amaral LA, Carthew RW.

Elife. 2015 Nov 19;4. pii: e08924. doi: 10.7554/eLife.08924.

18.

Pancreatic β cell enhancers regulate rhythmic transcription of genes controlling insulin secretion.

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.

Science. 2015 Nov 6;350(6261):aac4250. doi: 10.1126/science.aac4250.

19.

A Conserved Bicycle Model for Circadian Clock Control of Membrane Excitability.

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.

Cell. 2015 Aug 13;162(4):836-48. doi: 10.1016/j.cell.2015.07.036.

20.

Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism.

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.

Cell Host Microbe. 2015 May 13;17(5):681-9. doi: 10.1016/j.chom.2015.03.006. Epub 2015 Apr 16.

21.

PLZF expression maps the early stages of ILC1 lineage development.

Constantinides MG, Gudjonson H, McDonald BD, Ishizuka IE, Verhoef PA, Dinner AR, Bendelac A.

Proc Natl Acad Sci U S A. 2015 Apr 21;112(16):5123-8. doi: 10.1073/pnas.1423244112. Epub 2015 Apr 2.

22.

Improved statistical methods enable greater sensitivity in rhythm detection for genome-wide data.

Hutchison AL, Maienschein-Cline M, Chiang AH, Tabei SM, Gudjonson H, Bahroos N, Allada R, Dinner AR.

PLoS Comput Biol. 2015 Mar 20;11(3):e1004094. doi: 10.1371/journal.pcbi.1004094. eCollection 2015 Mar.

23.

Intergenerational continuity of cell shape dynamics in Caulobacter crescentus.

Wright CS, Banerjee S, Iyer-Biswas S, Crosson S, Dinner AR, Scherer NF.

Sci Rep. 2015 Mar 17;5:9155. doi: 10.1038/srep09155.

24.

Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol.

Kale S, Sode O, Weare J, Dinner AR.

J Chem Theory Comput. 2014 Dec 9;10(12):5467-5475. Epub 2014 Nov 7.

25.

Scaling laws governing stochastic growth and division of single bacterial cells.

Iyer-Biswas S, Wright CS, Henry JT, Lo K, Burov S, Lin Y, Crooks GE, Crosson S, Dinner AR, Scherer NF.

Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):15912-7. doi: 10.1073/pnas.1403232111. Epub 2014 Oct 27.

26.

Universality in stochastic exponential growth.

Iyer-Biswas S, Crooks GE, Scherer NF, Dinner AR.

Phys Rev Lett. 2014 Jul 11;113(2):028101. Epub 2014 Jul 7.

PMID:
25062238
27.

A negative feedback loop mediated by the Bcl6-cullin 3 complex limits Tfh cell differentiation.

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.

J Exp Med. 2014 Jun 2;211(6):1137-51. doi: 10.1084/jem.20132267. Epub 2014 May 26.

28.

Using multiscale preconditioning to accelerate the convergence of iterative molecular calculations.

Tempkin JO, Qi B, Saunders MG, Roux B, Dinner AR, Weare J.

J Chem Phys. 2014 May 14;140(18):184114. doi: 10.1063/1.4872021.

PMID:
24832260
29.

Gene regulatory networks in the immune system.

Singh H, Khan AA, Dinner AR.

Trends Immunol. 2014 May;35(5):211-8. doi: 10.1016/j.it.2014.03.006. Epub 2014 Apr 23. Review.

PMID:
24768519
30.

Nucleotide regulation of the structure and dynamics of G-actin.

Saunders MG, Tempkin J, Weare J, Dinner AR, Roux B, Voth GA.

Biophys J. 2014 Apr 15;106(8):1710-20. doi: 10.1016/j.bpj.2014.03.012.

31.

Distribution of directional change as a signature of complex dynamics.

Burov S, Tabei SM, Huynh T, Murrell MP, Philipson LH, Rice SA, Gardel ML, Scherer NF, Dinner AR.

Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):19689-94. doi: 10.1073/pnas.1319473110. Epub 2013 Nov 18.

32.

Transcriptional regulation of germinal center B and plasma cell fates by dynamical control of IRF4.

Ochiai K, Maienschein-Cline M, Simonetti G, Chen J, Rosenthal R, Brink R, Chong AS, Klein U, Dinner AR, Singh H, Sciammas R.

Immunity. 2013 May 23;38(5):918-29. doi: 10.1016/j.immuni.2013.04.009. Epub 2013 May 16.

33.

The Theory of Ultra-Coarse-Graining. 1. General Principles.

Dama JF, Sinitskiy AV, McCullagh M, Weare J, Roux B, Dinner AR, Voth GA.

J Chem Theory Comput. 2013 May 14;9(5):2466-80. doi: 10.1021/ct4000444. Epub 2013 Apr 10.

PMID:
26583735
34.

Minimizing memory as an objective for coarse-graining.

Guttenberg N, Dama JF, Saunders MG, Voth GA, Weare J, Dinner AR.

J Chem Phys. 2013 Mar 7;138(9):094111. doi: 10.1063/1.4793313.

PMID:
23485281
35.

Intracellular transport of insulin granules is a subordinated random walk.

Tabei SM, Burov S, Kim HY, Kuznetsov A, Huynh T, Jureller J, Philipson LH, Dinner AR, Scherer NF.

Proc Natl Acad Sci U S A. 2013 Mar 26;110(13):4911-6. doi: 10.1073/pnas.1221962110. Epub 2013 Mar 11.

36.

Relation between ordering and shear thinning in colloidal suspensions.

Xu X, Rice SA, Dinner AR.

Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3771-6. doi: 10.1073/pnas.1301055110. Epub 2013 Feb 19.

37.

Phase resetting reveals network dynamics underlying a bacterial cell cycle.

Lin Y, Li Y, Crosson S, Dinner AR, Scherer NF.

PLoS Comput Biol. 2012;8(11):e1002778. doi: 10.1371/journal.pcbi.1002778. Epub 2012 Nov 29.

38.

Requirements for contractility in disordered cytoskeletal bundles.

Lenz M, Gardel ML, Dinner AR.

New J Phys. 2012 Mar 1;14. pii: 033037. Epub 2012 Mar 28.

39.

Structural responses of quasi-two-dimensional colloidal fluids to excitations elicited by nonequilibrium perturbations.

Pesic J, Terdik JZ, Xu X, Tian Y, Lopez A, Rice SA, Dinner AR, Scherer NF.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Sep;86(3 Pt 1):031403. Epub 2012 Sep 28.

PMID:
23030916
40.

Contractile units in disordered actomyosin bundles arise from F-actin buckling.

Lenz M, Thoresen T, Gardel ML, Dinner AR.

Phys Rev Lett. 2012 Jun 8;108(23):238107. Epub 2012 Jun 8.

41.

Improved predictions of transcription factor binding sites using physicochemical features of DNA.

Maienschein-Cline M, Dinner AR, Hlavacek WS, Mu F.

Nucleic Acids Res. 2012 Dec;40(22):e175. doi: 10.1093/nar/gks771. Epub 2012 Aug 25.

42.

Steered transition path sampling.

Guttenberg N, Dinner AR, Weare J.

J Chem Phys. 2012 Jun 21;136(23):234103. doi: 10.1063/1.4724301.

PMID:
22779577
43.

Duplex interrogation by a direct DNA repair protein in search of base damage.

Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ, Dinner AR, Yang CG, He C.

Nat Struct Mol Biol. 2012 Jun 3;19(7):671-6. doi: 10.1038/nsmb.2320.

44.

Entrainment of a driven oscillator as a dynamical phase transition.

Dickson A, Tabei SM, Dinner AR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Dec;84(6 Pt 1):061134. Epub 2011 Dec 20.

PMID:
22304067
45.

A self-reinforcing regulatory network triggered by limiting IL-7 activates pre-BCR signaling and differentiation.

Ochiai K, Maienschein-Cline M, Mandal M, Triggs JR, Bertolino E, Sciammas R, Dinner AR, Clark MR, Singh H.

Nat Immunol. 2012 Jan 22;13(3):300-7. doi: 10.1038/ni.2210.

46.

Assembly of vorticity-aligned hard-sphere colloidal strings in a simple shear flow.

Cheng X, Xu X, Rice SA, Dinner AR, Cohen I.

Proc Natl Acad Sci U S A. 2012 Jan 3;109(1):63-7. doi: 10.1073/pnas.1118197108. Epub 2011 Dec 23.

47.

Model for competition from self during passive immunization, with application to broadly neutralizing antibodies for HIV.

Ali Tabei SM, Li Y, Weigert M, Dinner AR.

Vaccine. 2012 Jan 11;30(3):607-13. doi: 10.1016/j.vaccine.2011.11.048. Epub 2011 Nov 23.

PMID:
22119591
48.

Discovering transcription factor regulatory targets using gene expression and binding data.

Maienschein-Cline M, Zhou J, White KP, Sciammas R, Dinner AR.

Bioinformatics. 2012 Jan 15;28(2):206-13. doi: 10.1093/bioinformatics/btr628. Epub 2011 Nov 13.

49.

Short-time evolution in the adaptive immune system.

Guttenberg N, Tabei SM, Dinner AR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Sep;84(3 Pt 1):031932. Epub 2011 Sep 30.

PMID:
22060428
50.

Epigenetic repression of the Igk locus by STAT5-mediated recruitment of the histone methyltransferase Ezh2.

Mandal M, Powers SE, Maienschein-Cline M, Bartom ET, Hamel KM, Kee BL, Dinner AR, Clark MR.

Nat Immunol. 2011 Oct 30;12(12):1212-20. doi: 10.1038/ni.2136.

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