afenley's library 83 articles Export

	A negatively charged residue in place of histone H3K56 supports chromatin assembly factor association but not genotoxic stress resistance. [My Copy] DNA repair (29 September 2009) by Judith A. Erkmann, Paul D. Kaufman posted to nucleosome chromatin by afenley on 2009-11-03 18:42:27 as
	Electrical Interaction Energy between Two Charged Entities in an Electrolyte Solution [My Copy] Journal of Colloid and Interface Science, Vol. 217, No. 2. (15 September 1999), pp. 219-236. by Jyh-Ping Hsu, Bo-Tau Liu posted to energy electrolyte_solution by afenley on 2009-10-29 18:24:59 as
	Exact Solution to the Linearized Poisson–Boltzmann Equation for Spheroidal Surfaces [My Copy] Journal of Colloid and Interface Science, Vol. 178, No. 2. (25 March 1996), pp. 785-788. by Jyh-Ping Hsu, Bo-Tau Liu posted to pb by afenley on 2009-10-29 18:20:54 as
	The flexibility of polyelectrolyte molecules [My Copy] The Journal of Chemical Physics, Vol. 76, No. 12. (1982), pp. 6346-6353. by Marshall Fixman posted to polyelectrolyte poisson-boltzmann by afenley on 2009-10-22 20:22:46 as along with 1 person Elena_Zubova
	Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome [My Copy] Science, Vol. 326, No. 5950. (9 October 2009), pp. 289-293. by Erez Lieberman-Aiden, Nynke L. van Berkum, Louise Williams, et al.Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R. Lajoie, Peter J. Sabo, Michael O. Dorschner, Richard Sandstrom, Bradley Bernstein, M. A. Bender, Mark Groudine, Andreas Gnirke, John Stamatoyannopoulos, Leonid A. Mirny, Eric S. Lander, Job Dekker posted to chromatin by afenley on 2009-10-12 19:35:58 as along with 32 people and 3 groups vingron pmcarlton alhufton psique qayub chvlyl TorstenWaldminghaus kintoki Garamonfok inesdesantiago NickFurnham DrRichardBadge roys rdiaz daveGerrard colinveal frohike nrk891 zwang timflutre kshameer polivares mgatmedsci diamantis flbarroso jdoconnell fenghezi daforerog bpcusack gjuggler gdb gbloeb JLab BergmanLab Journal picks
	Mechanism of Protein Access to Specific DNA Sequences in Chromatin: A Dynamic Equilibrium Model for Gene Regulation [My Copy] Journal of Molecular Biology, Vol. 254, No. 2. (24 November 1995), pp. 130-149. by K. Polach, J. Widom posted to unfolding nucleosome by afenley on 2009-10-09 23:39:09 as
	Rapid spontaneous accessibility of nucleosomal DNA [My Copy] Nature Structural & Molecular Biology, Vol. 12, No. 1. (05 December 2004), pp. 46-53. by Gu Li, Marcia Levitus, Carlos Bustamante, Jonathan Widom posted to unfolding nucleosome by afenley on 2009-10-09 23:37:39 as along with 2 people quanwang margaritis
	A small-RNA-mediated negative feedback loop controls quorum-sensing dynamics in Vibrio harveyi. [My Copy] Molecular microbiology, Vol. 70, No. 4. (18 November 2008), pp. 896-907. by Kimberly C. Tu, Christopher M. Waters, Sine L. Svenningsen, Bonnie L. Bassler posted to quorum-sensing harveyi by afenley on 2009-10-01 20:17:10 as along with 1 person erel10
	Requirements for Vibrio cholerae HapR Binding and Transcriptional Repression at the hapR Promoter Are Distinct from Those at the aphA Promoter [My Copy] J. Bacteriol., Vol. 187, No. 9. (1 May 2005), pp. 3013-3019. by Wei Lin, Gabriela Kovacikova, Karen Skorupski posted to hapr cholerae by afenley on 2009-09-30 21:12:41 as
	A quantitative comparison of sRNA-based and protein-based gene regulation [My Copy] Molecular Systems Biology, Vol. 4 (14 October 2008) by Pankaj Mehta, Sidhartha Goyal, Ned S. Wingreen posted to srna regulation by afenley on 2009-09-15 19:59:22 as along with 3 people brianb raik erel10
	A negative feedback loop involving small RNAs accelerates Vibrio cholerae’s transition out of quorum-sensing mode [My Copy] Genes & Development, Vol. 22, No. 2. (15 January 2008), pp. 226-238. by Sine L. Svenningsen, Christopher M. Waters, Bonnie L. Bassler posted to vibrio_cholerae srna quorum-sensing by afenley on 2009-09-01 19:15:35 as
	Regulation of virulence gene expression in <i>Vibrio cholerae</i> by quorum sensing: HapR functions at the <i>aphA</i> promoter [My Copy] Molecular Microbiology, Vol. 46, No. 4. (2002), pp. 1135-1147. by Gabriela Kovacikova, Karen Skorupski posted to vibrio_cholerae quorum-sensing apha by afenley on 2009-09-01 18:15:15 as
	<i>Vibrio cholerae</i> AphA uses a novel mechanism for virulence gene activation that involves interaction with the LysR-type regulator AphB at the <i>tcpPH</i> promoter [My Copy] Molecular Microbiology, Vol. 53, No. 1. (2004), pp. 129-142. by Gabriela Kovacikova, Wei Lin, Karen Skorupski posted to vibrio_cholerae apha by afenley on 2009-09-01 18:10:03 as
	Polyelectrolyte Solutions between Charged Surfaces [My Copy] EPL (Europhysics Letters), Vol. 32, No. 6. (1995), pp. 499-504. by I. Borukhov, D. Andelman, H. Orland posted to electrostatics by afenley on 2009-08-25 21:47:37 as
	Statistical mechanics of a Coulomb gas with finite size particles: A lattice field theory approach [My Copy] The Journal of Chemical Physics, Vol. 102, No. 11. (1995), pp. 4584-4594. by Rob D. Coalson, Alan M. Walsh, Anthony Duncan, Nir B. Tal posted to statistical_mechanics lattice coulomb by afenley on 2009-08-25 20:48:12 as along with 1 person and 1 group sobolevnrm baker-group
	Acetylation of histone H3 at the nucleosome dyad alters DNA-histone binding [My Copy] J. Biol. Chem. (11 June 2009), M109.003202. by Mridula Manohar, Alex M. Mooney, Justin A. North, et al.Robin J. Nakkula, Jonathan W. Picking, Annick Edon, Richard Fishel, Michael G. Poirier, Jennifer J. Ottesen posted to nucleosome histone by afenley on 2009-08-20 03:23:43 as
	Crystal structures of histone Sin mutant nucleosomes reveal altered protein–DNA interactions [My Copy] EMBO J., Vol. 23, No. 2. (28 January 2004), pp. 260-271. by Uma M. Muthurajan, Yunhe Bao, Lawrence J. Forsberg, et al.Rajeswari S. Edayathumangalam, Pamela N. Dyer, Cindy L. White, Karolin Luger posted to nucleosome histone by afenley on 2009-08-20 01:52:26 as
	Thermodynamically dominant hydration structures of aqueous ions [My Copy] The Journal of Chemical Physics, Vol. 130, No. 19. (2009), 195102. by Safir Merchant, D. Asthagiri posted to ionic_hydration by afenley on 2009-08-17 22:07:52 as along with 5 people and 1 group mikaellund flbarroso dlimmer agrossfield sobolevnrm baker-group
	Biophysical Journal - Ion Selectivity in the KcsA Potassium Channel from the Perspective of the Ion Binding Site [My Copy] Biophysical Journal, Vol. 96, No. 6. (March 2009), pp. 2138-2145. by P. D. Dixit, S. Merchant, D. Asthagiri posted to ionic_hydration by afenley on 2009-08-17 22:07:01 as
	A simple polarizable model of water based on classical Drude oscillators [My Copy] The Journal of Chemical Physics, Vol. 119, No. 10. (2003), pp. 5185-5197. by Guillaume Lamoureux, Jr, Benoît Roux posted to solvation polarization by afenley on 2009-08-15 22:58:17 as
	Dynamic features of gene expression control by small regulatory RNAs [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 26. (30 June 2009), pp. 10655-10659. by Namiko Mitarai, Julie-Anna M. Benjamin, Sandeep Krishna, et al.Szabolcs Semsey, Zsolt Csiszovszki, Eric Massé, Kim Sneppen posted to small_rnas by afenley on 2009-08-14 19:51:33 as
	Counting Nucleosomes in Living Cells with a Combination of Fluorescence Correlation Spectroscopy and Confocal Imaging [My Copy] Journal of Molecular Biology, Vol. 334, No. 2. (21 November 2003), pp. 229-240. by Thomas Weidemann, Malte Wachsmuth, Tobias A. Knoch, Gabriele Müller, Waldemar Waldeck, Jörg Langowski posted to no-tag by afenley on 2009-08-13 01:00:13 as
	Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms [My Copy] Proceedings of the National Academy of Sciences, Vol. 103, No. 22. (30 May 2006), pp. 8331-8336. by Jason A. Wagoner, Nathan A. Baker posted to implicit_solvation nonpolar_molecules by afenley on 2009-07-22 19:46:00 as along with 3 people ahmetbakan flbarroso rok
	On the free energy of ionic hydration [My Copy] (24 May 1995) by Gerhard Hummer, Lawrence R. Pratt, Angel E. Garcia posted to energy ionic_hydration by afenley on 2009-07-22 19:41:15 as
	Application of the level-set method to the implicit solvation of nonpolar molecules [My Copy] The Journal of Chemical Physics, Vol. 127, No. 8. (2007), 084503. by Li T. Cheng, Joachim Dzubiella, J. Andrew Mccammon, Bo Li posted to implicit_solvation nonpolar_molecules by afenley on 2009-07-22 19:33:07 as along with 2 people and 2 groups csrocha sobolevnrm structural_bioinformatics baker-group
	Coupling Hydrophobicity, Dispersion, and Electrostatics in Continuum Solvent Models [My Copy] Physical Review Letters, Vol. 96, No. 8. (2006), 087802. by J. Dzubiella, J. M. J. Swanson, J. A. Mccammon posted to electrostatics hydrophobic implicit_solvation by afenley on 2009-07-22 19:29:34 as
	Competition of hydrophobic and Coulombic interactions between nanosized solutes [My Copy] The Journal of Chemical Physics, Vol. 121, No. 11. (2004), pp. 5514-5530. by J. Dzubiella, J. P. Hansen posted to hydrophobic solvation by afenley on 2009-07-22 19:24:52 as
	Computational methods for biomolecular electrostatics. [My Copy] Methods in cell biology, Vol. 84 (2008), pp. 843-870. by F. Dong, B. Olsen, N. A. Baker posted to electrostatics by afenley on 2009-06-07 04:17:35 as along with 2 people flbarroso simone
	Multiscale Modeling of Nucleosome Dynamics [My Copy] Biophys. J., Vol. 92, No. 5. (1 March 2007), pp. 1457-1470. by Shantanu Sharma, Feng Ding, Nikolay V. Dokholyan posted to molecular_dynamics nucleosome by afenley on 2009-06-04 15:52:59 as along with 5 people and 9 groups aalibes shantanu choonpeng skoch3 phisics structural_bioinformatics MathBio Biostatistics Bioinformatics microRNA Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology Koch_Lab
	A test of implicit solvent models on the folding simulation of the GB1 peptide [My Copy] The Journal of Chemical Physics, Vol. 130, No. 19. (2009), 195104. by Qiang Shao, Lijiang Yang, Yi Q. Gao posted to generalized_born implicit_solvation molecular_dynamics by afenley on 2009-05-22 23:09:47 as along with 1 person dlimmer
	Small RNAs establish gene expression thresholds [My Copy] Current Opinion in Microbiology, Vol. 11, No. 6. (December 2008), pp. 574-579. by E. Levine, T. Hwa posted to gene_expression srna by afenley on 2009-05-09 21:05:22 as along with 2 people megraw lp2
	The tale beyond the tail: histone core domain modifications and the regulation of chromatin structure [My Copy] Nucleic Acids Research, Vol. 34, No. 9. (2006), pp. 2653-2662. by Mersfelder, L. Erica, Parthun, R. Mark posted to histone nucleosome by afenley on 2009-04-24 22:23:18 as
	Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach [My Copy] The Journal of Chemical Physics, Vol. 130, No. 10. (2009), 104110. by Jeremy Curuksu, Martin Zacharias posted to molecular_dynamics nucleic_acids by afenley on 2009-03-15 15:40:14 as
	3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. [My Copy] Nucleic Acids Res, Vol. 31, No. 17. (1 September 2003), pp. 5108-5121. by X. J. Lu, W. K. Olson posted to dna structure by afenley on 2009-03-14 23:24:15 as along with 2 people Elena_Zubova dna
	The Nucleosome Family: Dynamic and Growing [My Copy] Vol. 17, No. 2. (13 February 2009), pp. 160-171. by Jordanka Zlatanova, Thomas C. Bishop, Jean-Marc Victor, Vaughn Jackson, Ken van Holde posted to nucleosome structure by afenley on 2009-03-14 21:16:16 as
	Geometry of the Nucleosomal DNA Superhelix [My Copy] Vol. 95, No. 3. (1 August 2008), pp. 1007-1017. by Thomas C. Bishop posted to dna nucleosome by afenley on 2009-03-14 21:14:45 as
	Nucleosome Shape Dictates Chromatin Fiber Structure [My Copy] Biophysical Journal, Vol. 96, No. 3. (04 February 2009), pp. 777-784. by Martin Depken, Helmut Schiessel posted to chromatin nucleosome by afenley on 2009-03-14 14:59:49 as
	Multilevel summation of electrostatic potentials using graphics processing units☆ [My Copy] Parallel Computing (25 December 2008) by David J. Hardy, John E. Stone, Klaus Schulten posted to electrostatics gpu by afenley on 2009-02-16 19:03:33 as along with 1 person and 1 group sobolevnrm baker-group
	Enhanceosomes [My Copy] Current Opinion in Genetics & Development, Vol. 11, No. 2. (1 April 2001), pp. 205-208. by M. Merika posted to enhanceosomes by afenley on 2009-02-04 22:27:09 as along with 1 person lusk
	The Enhanceosome and Transcriptional Synergy [My Copy] Cell, Vol. 92, No. 1. (January 1998), pp. 5-8. by M. Carey posted to enhanceosomes by afenley on 2009-02-04 22:26:38 as
	Nucleosome Shape Dictates Chromatin Fiber Structure [My Copy] Biophysical Journal, Vol. 96, No. 3. (4 February 2009), pp. 777-784. by Martin Depken, Helmut Schiessel posted to chromatin nucleosome by afenley on 2009-02-04 22:05:57 as
	Histone structure and nucleosome stability. [My Copy] Expert Rev Proteomics, Vol. 2, No. 5. (October 2005), pp. 719-729. by L. Mariño-Ramírez, M. G. Kann, B. A. Shoemaker, D. Landsman posted to histone nucleosome by afenley on 2009-02-03 23:47:15 as along with 2 people aalibes onufriev
	Spontaneous access to DNA target sites in folded chromatin fibers. [My Copy] Journal of molecular biology, Vol. 379, No. 4. (13 June 2008), pp. 772-786. by M. G. Poirier, M. Bussiek, J. Langowski, J. Widom posted to chromatin dna nucleosome by afenley on 2009-02-03 23:46:02 as
	Nucleosome stability mediated by histone variants H3.3 and H2A.Z — Genes & Development [My Copy] Genes & Dev., Vol. 21 (2007), pp. 1519-1529. by Chunyuan Jin, Gary Felsenfeld posted to histone nucleosome by afenley on 2009-01-30 19:42:57 as
	Nucleosome destabilization in the epigenetic regulation of gene expression [My Copy] Nature Reviews Genetics, Vol. 9 (January 2008), pp. 15-26. by Steven Henikoff posted to nucleosome by afenley on 2009-01-20 04:04:18 as
	Electrostatic contributions to the binding free energy of the lambdacI repressor to DNA. [My Copy] Biophysical journal, Vol. 75, No. 5. (November 1998), pp. 2262-2273. by V. K. Misra, J. L. Hecht, A. S. Yang, B. Honig posted to electrostatics nlpb pb pka by afenley on 2009-01-19 22:42:25 as along with 1 person flbarroso
	A gamut of loops: meandering DNA. [My Copy] Trends Biochem Sci, Vol. 30, No. 6. (June 2005), pp. 334-341. by S. Semsey, K. Virnik, S. Adhya posted to dna by afenley on 2009-01-14 20:53:37 as along with 3 people boko4ikameto uz_labu_laimi mz2
	Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo [My Copy] The Journal of Chemical Physics, Vol. 126, No. 4. (2007) by Gaurav Arya, Tamar Schlick posted to chromatin monte_carlo by afenley on 2009-01-13 22:16:14 as
	Elastic origin of chiral selection in DNA wrapping [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 77, No. 2. (2008) by Tomohiro Yanao, Kenichi Yoshikawa posted to dna nucleosome by afenley on 2009-01-03 01:48:56 as
	Interplay of ion binding and attraction in DNA condensed by multivalent cations. [My Copy] Nucleic Acids Research, Vol. 36, No. 2. (February 2008), pp. 501-510. by Brian A. Todd, Donald C. Rau posted to dna by afenley on 2009-01-03 01:47:46 as

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nucleosome	26
electrostatics	16
histone	13
chromatin	12
dna	9
energy	8
unfolding	7
implicit_solvation	6
molecular_dynamics	6
srna	5
poisson-boltzmann	4
quorum-sensing	4
regulation	4
hydrophobic	3
ionic_hydration	3
structure	3
vibrio_cholerae	3
apha	2
charge_representation	2
cholerae	2
dielectric	2
enhanceosomes	2
gpu	2
nonpolar_molecules	2
parameter	2
pb	2
solvation	2
statistical_mechanics	2
tails	2
acetylation	1
biomolecule	1
coulomb	1
electrolyte_solution	1
entropy	1
feedback	1
force_field	1
gene_expression	1
generalized_born	1
h2az	1
hapr	1
harveyi	1
hfq	1
lattice	1
mechanical	1
modeling	1
monte_carlo	1
nlpb	1
nucleic_acids	1
nucleus	1
ph	1
pka	1
polarization	1
polyelectrolyte	1
sensitivity	1
small_rnas	1
space	1
systems_biology	1

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