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Items: 1 to 50 of 54

1.

Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures.

Borodavka A, Singaram SW, Stockley PG, Gelbart WM, Ben-Shaul A, Tuma R.

Biophys J. 2016 Nov 15;111(10):2077-2085. doi: 10.1016/j.bpj.2016.10.014.

2.

Biography of William M. Gelbart.

Ben-Shaul A, Knobler CM, Liu AJ.

J Phys Chem B. 2016 Jul 7;120(26):5789-93. doi: 10.1021/acs.jpcb.6b03370. No abstract available.

PMID:
27385353
3.

William M. Gelbart: An Appreciation.

Ben-Shaul A, Knobler CM, Liu AJ.

J Phys Chem B. 2016 Jul 7;120(26):5787-8. doi: 10.1021/acs.jpcb.6b03856. No abstract available.

PMID:
27385352
4.

A Prüfer-Sequence Based Algorithm for Calculating the Size of Ideal Randomly Branched Polymers.

Singaram SW, Gopal A, Ben-Shaul A.

J Phys Chem B. 2016 Jul 7;120(26):6231-7. doi: 10.1021/acs.jpcb.6b02258. Epub 2016 May 10.

PMID:
27104292
5.

Role of RNA Branchedness in the Competition for Viral Capsid Proteins.

Singaram SW, Garmann RF, Knobler CM, Gelbart WM, Ben-Shaul A.

J Phys Chem B. 2015 Nov 5;119(44):13991-4002. doi: 10.1021/acs.jpcb.5b06445. Epub 2015 Oct 19.

PMID:
26435053
6.

Viral ssRNAs are indeed compact.

Ben-Shaul A, Gelbart WM.

Biophys J. 2015 Jan 6;108(1):14-6. doi: 10.1016/j.bpj.2014.11.010. No abstract available.

7.

Viral RNAs are unusually compact.

Gopal A, Egecioglu DE, Yoffe AM, Ben-Shaul A, Rao AL, Knobler CM, Gelbart WM.

PLoS One. 2014 Sep 4;9(9):e105875. doi: 10.1371/journal.pone.0105875. eCollection 2014.

8.

Characterization of Viral Capsid Protein Self-Assembly around Short Single-Stranded RNA.

Comas-Garcia M, Garmann RF, Singaram SW, Ben-Shaul A, Knobler CM, Gelbart WM.

J Phys Chem B. 2014 Jul 10;118(27):7510-7519. doi: 10.1021/jp503050z. Epub 2014 Jun 30.

PMID:
24933579
9.

Reply to the comment by S. Harvey on "entropy, energy, and bending of DNA in viral capsids".

Ben-Shaul A.

Biophys J. 2014 Jan 21;106(2):493-6. doi: 10.1016/j.bpj.2013.11.4497.

10.

Entropy, energy, and bending of DNA in viral capsids.

Ben-Shaul A.

Biophys J. 2013 May 21;104(10):L15-7. doi: 10.1016/j.bpj.2013.04.006.

11.

Theory and simulations of adhesion receptor dimerization on membrane surfaces.

Wu Y, Honig B, Ben-Shaul A.

Biophys J. 2013 Mar 19;104(6):1221-9. doi: 10.1016/j.bpj.2013.02.009. Epub 2013 Mar 19.

12.

The size of RNA as an ideal branched polymer.

Fang LT, Gelbart WM, Ben-Shaul A.

J Chem Phys. 2011 Oct 21;135(15):155105. doi: 10.1063/1.3652763.

PMID:
22029339
13.

Transforming binding affinities from three dimensions to two with application to cadherin clustering.

Wu Y, Vendome J, Shapiro L, Ben-Shaul A, Honig B.

Nature. 2011 Jul 27;475(7357):510-3. doi: 10.1038/nature10183.

14.

A sequential folding model predicts length-independent secondary structure properties of long ssRNA.

Fang LT, Yoffe AM, Gelbart WM, Ben-Shaul A.

J Phys Chem B. 2011 Mar 31;115(12):3193-9. doi: 10.1021/jp110680e. Epub 2011 Mar 3.

PMID:
21370842
15.

The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins.

Harrison OJ, Jin X, Hong S, Bahna F, Ahlsen G, Brasch J, Wu Y, Vendome J, Felsovalyi K, Hampton CM, Troyanovsky RB, Ben-Shaul A, Frank J, Troyanovsky SM, Shapiro L, Honig B.

Structure. 2011 Feb 9;19(2):244-56. doi: 10.1016/j.str.2010.11.016.

16.

Cooperativity between trans and cis interactions in cadherin-mediated junction formation.

Wu Y, Jin X, Harrison O, Shapiro L, Honig BH, Ben-Shaul A.

Proc Natl Acad Sci U S A. 2010 Oct 12;107(41):17592-7. doi: 10.1073/pnas.1011247107. Epub 2010 Sep 27.

17.

The ends of a large RNA molecule are necessarily close.

Yoffe AM, Prinsen P, Gelbart WM, Ben-Shaul A.

Nucleic Acids Res. 2011 Jan;39(1):292-9. doi: 10.1093/nar/gkq642. Epub 2010 Sep 1.

18.

From branched networks of actin filaments to bundles.

Brill-Karniely Y, Ideses Y, Bernheim-Groswasser A, Ben-Shaul A.

Chemphyschem. 2009 Nov 9;10(16):2818-27. doi: 10.1002/cphc.200900615.

PMID:
19847840
19.

Linking molecular affinity and cellular specificity in cadherin-mediated adhesion.

Katsamba P, Carroll K, Ahlsen G, Bahna F, Vendome J, Posy S, Rajebhosale M, Price S, Jessell TM, Ben-Shaul A, Shapiro L, Honig BH.

Proc Natl Acad Sci U S A. 2009 Jul 14;106(28):11594-9. doi: 10.1073/pnas.0905349106. Epub 2009 Jun 24.

20.

Predicting the sizes of large RNA molecules.

Yoffe AM, Prinsen P, Gopal A, Knobler CM, Gelbart WM, Ben-Shaul A.

Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16153-8. doi: 10.1073/pnas.0808089105. Epub 2008 Oct 9.

21.

Arp2/3 branched actin network mediates filopodia-like bundles formation in vitro.

Ideses Y, Brill-Karniely Y, Haviv L, Ben-Shaul A, Bernheim-Groswasser A.

PLoS One. 2008 Sep 29;3(9):e3297. doi: 10.1371/journal.pone.0003297.

22.

The "electrostatic-switch" mechanism: Monte Carlo study of MARCKS-membrane interaction.

Tzlil S, Murray D, Ben-Shaul A.

Biophys J. 2008 Aug;95(4):1745-57. doi: 10.1529/biophysj.108.132522. Epub 2008 May 23.

23.

Modulation of the spontaneous curvature and bending rigidity of lipid membranes by interfacially adsorbed amphipathic peptides.

Zemel A, Ben-Shaul A, May S.

J Phys Chem B. 2008 Jun 12;112(23):6988-96. doi: 10.1021/jp711107y. Epub 2008 May 14.

PMID:
18479112
24.

Matrix formalism for site-specific binding of unstructured proteins to multicomponent lipid membranes.

Teif VB, Harries D, Lando DY, Ben-Shaul A.

J Pept Sci. 2008 Apr;14(4):368-73. doi: 10.1002/psc.994.

PMID:
18186025
25.

Reconstitution of the transition from lamellipodium to filopodium in a membrane-free system.

Haviv L, Brill-Karniely Y, Mahaffy R, Backouche F, Ben-Shaul A, Pollard TD, Bernheim-Groswasser A.

Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):4906-11. Epub 2006 Mar 20.

26.

Flexible charged macromolecules on mixed fluid lipid membranes: theory and Monte Carlo simulations.

Tzlil S, Ben-Shaul A.

Biophys J. 2005 Nov;89(5):2972-87. Epub 2005 Aug 26.

27.

Specificity of cell-cell adhesion by classical cadherins: Critical role for low-affinity dimerization through beta-strand swapping.

Chen CP, Posy S, Ben-Shaul A, Shapiro L, Honig BH.

Proc Natl Acad Sci U S A. 2005 Jun 14;102(24):8531-6. Epub 2005 Jun 3.

28.

Domain formation induced by the adsorption of charged proteins on mixed lipid membranes.

Mbamala EC, Ben-Shaul A, May S.

Biophys J. 2005 Mar;88(3):1702-14. Epub 2004 Dec 30.

29.

Perturbation of a lipid membrane by amphipathic peptides and its role in pore formation.

Zemel A, Ben-Shaul A, May S.

Eur Biophys J. 2005 May;34(3):230-42. Epub 2004 Dec 24.

PMID:
15619088
30.

Tilt modulus of a lipid monolayer.

May S, Kozlovsky Y, Ben-Shaul A, Kozlov MM.

Eur Phys J E Soft Matter. 2004 Jul;14(3):299-308.

PMID:
15338441
31.

Membrane perturbation induced by interfacially adsorbed peptides.

Zemel A, Ben-Shaul A, May S.

Biophys J. 2004 Jun;86(6):3607-19.

32.

A statistical-thermodynamic model of viral budding.

Tzlil S, Deserno M, Gelbart WM, Ben-Shaul A.

Biophys J. 2004 Apr;86(4):2037-48.

33.

Modeling of cationic lipid-DNA complexes.

May S, Ben-Shaul A.

Curr Med Chem. 2004 Jan;11(2):151-67. Review.

PMID:
14754414
34.

Osmotic shock and the strength of viral capsids.

Cordova A, Deserno M, Gelbart WM, Ben-Shaul A.

Biophys J. 2003 Jul;85(1):70-4.

35.

Energetics and self-assembly of amphipathic peptide pores in lipid membranes.

Zemel A, Fattal DR, Ben-Shaul A.

Biophys J. 2003 Apr;84(4):2242-55.

36.

Forces and pressures in DNA packaging and release from viral capsids.

Tzlil S, Kindt JT, Gelbart WM, Ben-Shaul A.

Biophys J. 2003 Mar;84(3):1616-27.

37.

Macroion-induced compositional instability of binary fluid membranes.

May S, Harries D, Ben-Shaul A.

Phys Rev Lett. 2002 Dec 23;89(26):268102. Epub 2002 Dec 9.

PMID:
12484858
38.

DNA packaging and ejection forces in bacteriophage.

Kindt J, Tzlil S, Ben-Shaul A, Gelbart WM.

Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13671-4. Epub 2001 Nov 13.

39.
40.

Association entropy in adsorption processes.

Ben-Tal N, Honig B, Bagdassarian CK, Ben-Shaul A.

Biophys J. 2000 Sep;79(3):1180-7.

41.

The phase behavior of cationic lipid-DNA complexes.

May S, Harries D, Ben-Shaul A.

Biophys J. 2000 Apr;78(4):1681-97.

42.
43.

Structure, stability, and thermodynamics of lamellar DNA-lipid complexes.

Harries D, May S, Gelbart WM, Ben-Shaul A.

Biophys J. 1998 Jul;75(1):159-73.

44.
45.
46.

Free-energy determinants of alpha-helix insertion into lipid bilayers.

Ben-Tal N, Ben-Shaul A, Nicholls A, Honig B.

Biophys J. 1996 Apr;70(4):1803-12.

48.
49.

Statistical-thermodynamic approach to fracture.

Selinger RL, Wang ZG, Gelbart WM, Ben-Shaul A.

Phys Rev A. 1991 Apr 15;43(8):4396-4400. No abstract available.

PMID:
9905543
50.

States of aggregation and phase transformations in mixtures of phosphatidylcholine and octyl glucoside.

Almog S, Litman BJ, Wimley W, Cohen J, Wachtel EJ, Barenholz Y, Ben-Shaul A, Lichtenberg D.

Biochemistry. 1990 May 15;29(19):4582-92.

PMID:
2372543

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