A citation-based method for searching scientific literature

Joshua Lequieu, David C Schwartz, Juan J de Pablo. Proc Natl Acad Sci U S A 2017
Times Cited: 32







List of co-cited articles
399 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Crystal structure of the nucleosome core particle at 2.8 A resolution.
K Luger, A W Mäder, R K Richmond, D F Sargent, T J Richmond. Nature 1997
81

Exploring the Free Energy Landscape of Nucleosomes.
Bin Zhang, Weihua Zheng, Garegin A Papoian, Peter G Wolynes. J Am Chem Soc 2016
63
59

Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution.
Curt A Davey, David F Sargent, Karolin Luger, Armin W Maeder, Timothy J Richmond. J Mol Biol 2002
954
59


DNA shape dominates sequence affinity in nucleosome formation.
Gordon S Freeman, Joshua P Lequieu, Daniel M Hinckley, Jonathan K Whitmer, Juan J de Pablo. Phys Rev Lett 2014
49
46

Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions.
Alexey K Shaytan, Grigoriy A Armeev, Alexander Goncearenco, Victor B Zhurkin, David Landsman, Anna R Panchenko. J Mol Biol 2016
80
43


Tension-Dependent Free Energies of Nucleosome Unwrapping.
Joshua Lequieu, Andrés Córdoba, David C Schwartz, Juan J de Pablo. ACS Cent Sci 2016
33
43

Chromatin dynamics: nucleosomes go mobile through twist defects.
I M Kulić, H Schiessel. Phys Rev Lett 2003
56
40

Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations.
Toru Niina, Giovanni B Brandani, Cheng Tan, Shoji Takada. PLoS Comput Biol 2017
24
54

DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations.
Giovanni B Brandani, Toru Niina, Cheng Tan, Shoji Takada. Nucleic Acids Res 2018
34
40

Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility.
Thuy T M Ngo, Qiucen Zhang, Ruobo Zhou, Jaya G Yodh, Taekjip Ha. Cell 2015
149
37

The structure of DNA in the nucleosome core.
Timothy J Richmond, Curt A Davey. Nature 2003
766
34

Rapid spontaneous accessibility of nucleosomal DNA.
Gu Li, Marcia Levitus, Carlos Bustamante, Jonathan Widom. Nat Struct Mol Biol 2005
441
34


Coarse-grained modeling of DNA curvature.
Gordon S Freeman, Daniel M Hinckley, Joshua P Lequieu, Jonathan K Whitmer, Juan J de Pablo. J Chem Phys 2014
50
28

Polymer reptation and nucleosome repositioning.
H Schiessel, J Widom, R F Bruinsma, W M Gelbart. Phys Rev Lett 2001
80
28


High-resolution dynamic mapping of histone-DNA interactions in a nucleosome.
Michael A Hall, Alla Shundrovsky, Lu Bai, Robert M Fulbright, John T Lis, Michelle D Wang. Nat Struct Mol Biol 2009
249
28

Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study.
Rosana Collepardo-Guevara, Guillem Portella, Michele Vendruscolo, Daan Frenkel, Tamar Schlick, Modesto Orozco. J Am Chem Soc 2015
74
28



A genomic code for nucleosome positioning.
Eran Segal, Yvonne Fondufe-Mittendorf, Lingyi Chen, AnnChristine Thåström, Yair Field, Irene K Moore, Ji-Ping Z Wang, Jonathan Widom. Nature 2006
25

Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes.
Cedric R Clapier, Janet Iwasa, Bradley R Cairns, Craig L Peterson. Nat Rev Mol Cell Biol 2017
326
25


The role of DNA sequence in nucleosome breathing.
Jamie Culkin, Lennart de Bruin, Marco Tompitak, Rob Phillips, Helmut Schiessel. Eur Phys J E Soft Matter 2017
15
53

Dissecting DNA-histone interactions in the nucleosome by molecular dynamics simulations of DNA unwrapping.
Ramona Ettig, Nick Kepper, Rene Stehr, Gero Wedemann, Karsten Rippe. Biophys J 2011
59
25

Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA.
Brent D Brower-Toland, Corey L Smith, Richard C Yeh, John T Lis, Craig L Peterson, Michelle D Wang. Proc Natl Acad Sci U S A 2002
302
25

Molecular Mechanism of Spontaneous Nucleosome Unraveling.
David Winogradoff, Aleksei Aksimentiev. J Mol Biol 2019
27
29


Nucleosomes facilitate their own invasion.
Gu Li, Jonathan Widom. Nat Struct Mol Biol 2004
253
21


Determinants of nucleosome positioning.
Kevin Struhl, Eran Segal. Nat Struct Mol Biol 2013
357
21

Using DNA mechanics to predict in vitro nucleosome positions and formation energies.
Alexandre V Morozov, Karissa Fortney, Daria A Gaykalova, Vasily M Studitsky, Jonathan Widom, Eric D Siggia. Nucleic Acids Res 2009
132
21

Poly(dA:dT) tracts: major determinants of nucleosome organization.
Eran Segal, Jonathan Widom. Curr Opin Struct Biol 2009
272
21

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
21

DNA sequence-dependent deformability deduced from protein-DNA crystal complexes.
W K Olson, A A Gorin, X J Lu, L M Hock, V B Zhurkin. Proc Natl Acad Sci U S A 1998
753
21

Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure.
Xiaoyu Liu, Meijing Li, Xian Xia, Xueming Li, Zhucheng Chen. Nature 2017
117
21

Nucleosome dynamics: Sequence matters.
Behrouz Eslami-Mossallam, Helmut Schiessel, John van Noort. Adv Colloid Interface Sci 2016
35
21


CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work.
Hiroo Kenzaki, Nobuyasu Koga, Naoto Hori, Ryo Kanada, Wenfei Li, Kei-Ichi Okazaki, Xin-Qiu Yao, Shoji Takada. J Chem Theory Comput 2011
97
18

Mobile nucleosomes--a general behavior.
G Meersseman, S Pennings, E M Bradbury. EMBO J 1992
240
18

Nucleosome sliding mechanisms: new twists in a looped history.
Felix Mueller-Planitz, Henrike Klinker, Peter B Becker. Nat Struct Mol Biol 2013
62
18

Nucleosomes in solution exist as a mixture of twist-defect states.
Rajeswari S Edayathumangalam, Philipp Weyermann, Peter B Dervan, Joel M Gottesfeld, Karolin Luger. J Mol Biol 2005
44
18

Structural rearrangements of the histone octamer translocate DNA.
Silvija Bilokapic, Mike Strauss, Mario Halic. Nat Commun 2018
36
18

Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core.
Yujie Chen, Joshua M Tokuda, Traci Topping, Steve P Meisburger, Suzette A Pabit, Lisa M Gloss, Lois Pollack. Proc Natl Acad Sci U S A 2017
53
18

Nucleosome accessibility governed by the dimer/tetramer interface.
Vera Böhm, Aaron R Hieb, Andrew J Andrews, Alexander Gansen, Andrea Rocker, Katalin Tóth, Karolin Luger, Jörg Langowski. Nucleic Acids Res 2011
132
18

Dynamics of nucleosome invasion by DNA binding proteins.
Hannah S Tims, Kaushik Gurunathan, Marcia Levitus, Jonathan Widom. J Mol Biol 2011
84
18

Molecular dynamics simulations of a nucleosome and free DNA.
Thomas C Bishop. J Biomol Struct Dyn 2005
45
18

The mechanics behind DNA sequence-dependent properties of the nucleosome.
Eugene Y D Chua, Dileep Vasudevan, Gabriela E Davey, Bin Wu, Curt A Davey. Nucleic Acids Res 2012
102
18


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.