A citation-based method for searching scientific literature

Pamela N Dyer, Raji S Edayathumangalam, Cindy L White, Yunhe Bao, Srinivas Chakravarthy, Uma M Muthurajan, Karolin Luger. Methods Enzymol 2004
Times Cited: 485







List of co-cited articles
823 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
46


Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
25

PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Paul D Adams, Pavel V Afonine, Gábor Bunkóczi, Vincent B Chen, Ian W Davis, Nathaniel Echols, Jeffrey J Headd, Li-Wei Hung, Gary J Kapral, Ralf W Grosse-Kunstleve,[...]. Acta Crystallogr D Biol Crystallogr 2010
24

UCSF Chimera--a visualization system for exploratory research and analysis.
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Gregory S Couch, Daniel M Greenblatt, Elaine C Meng, Thomas E Ferrin. J Comput Chem 2004
23

New tools for automated high-resolution cryo-EM structure determination in RELION-3.
Jasenko Zivanov, Takanori Nakane, Björn O Forsberg, Dari Kimanius, Wim Jh Hagen, Erik Lindahl, Sjors Hw Scheres. Elife 2018
22

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy.
Shawn Q Zheng, Eugene Palovcak, Jean-Paul Armache, Kliment A Verba, Yifan Cheng, David A Agard. Nat Methods 2017
18

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Ali Punjani, John L Rubinstein, David J Fleet, Marcus A Brubaker. Nat Methods 2017
17


CTFFIND4: Fast and accurate defocus estimation from electron micrographs.
Alexis Rohou, Nikolaus Grigorieff. J Struct Biol 2015
12

Coot: model-building tools for molecular graphics.
Paul Emsley, Kevin Cowtan. Acta Crystallogr D Biol Crystallogr 2004
12

Preparation of nucleosome core particle from recombinant histones.
K Luger, T J Rechsteiner, T J Richmond. Methods Enzymol 1999
510
12

Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units.
Feng Song, Ping Chen, Dapeng Sun, Mingzhu Wang, Liping Dong, Dan Liang, Rui-Ming Xu, Ping Zhu, Guohong Li. Science 2014
334
10

Mechanism of Cross-talk between H2B Ubiquitination and H3 Methylation by Dot1L.
Evan J Worden, Niklas A Hoffmann, Chad W Hicks, Cynthia Wolberger. Cell 2019
76
13

Nucleosome structure and function.
Robert K McGinty, Song Tan. Chem Rev 2015
201
10

Nucleosome structure and dynamics are coming of age.
Keda Zhou, Guillaume Gaullier, Karolin Luger. Nat Struct Mol Biol 2019
85
11

MolProbity: all-atom structure validation for macromolecular crystallography.
Vincent B Chen, W Bryan Arendall, Jeffrey J Headd, Daniel A Keedy, Robert M Immormino, Gary J Kapral, Laura W Murray, Jane S Richardson, David C Richardson. Acta Crystallogr D Biol Crystallogr 2010
9

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
9


UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Thomas D Goddard, Conrad C Huang, Elaine C Meng, Eric F Pettersen, Gregory S Couch, John H Morris, Thomas E Ferrin. Protein Sci 2018
996
9

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
337
9


Chromatin fiber folding: requirement for the histone H4 N-terminal tail.
Benedetta Dorigo, Thomas Schalch, Kerstin Bystricky, Timothy J Richmond. J Mol Biol 2003
366
8

SWISS-MODEL: homology modelling of protein structures and complexes.
Andrew Waterhouse, Martino Bertoni, Stefan Bienert, Gabriel Studer, Gerardo Tauriello, Rafal Gumienny, Florian T Heer, Tjaart A P de Beer, Christine Rempfer, Lorenza Bordoli,[...]. Nucleic Acids Res 2018
8


Histone exchange, chromatin structure and the regulation of transcription.
Swaminathan Venkatesh, Jerry L Workman. Nat Rev Mol Cell Biol 2015
476
8

Crystal structure of the human centromeric nucleosome containing CENP-A.
Hiroaki Tachiwana, Wataru Kagawa, Tatsuya Shiga, Akihisa Osakabe, Yuta Miya, Kengo Saito, Yoko Hayashi-Takanaka, Takashi Oda, Mamoru Sato, Sam-Yong Park,[...]. Nature 2011
263
8

Structure of RCC1 chromatin factor bound to the nucleosome core particle.
Ravindra D Makde, Joseph R England, Hemant P Yennawar, Song Tan. Nature 2010
265
8

Nucleosome-Chd1 structure and implications for chromatin remodelling.
Lucas Farnung, Seychelle M Vos, Christoph Wigge, Patrick Cramer. Nature 2017
114
8

Structure and dynamics of the yeast SWR1-nucleosome complex.
Oliver Willhoft, Mohamed Ghoneim, Chia-Liang Lin, Eugene Y D Chua, Martin Wilkinson, Yuriy Chaban, Rafael Ayala, Elizabeth A McCormack, Lorraine Ocloo, David S Rueda,[...]. Science 2018
75
10

Structural basis for ATP-dependent chromatin remodelling by the INO80 complex.
Sebastian Eustermann, Kevin Schall, Dirk Kostrewa, Kristina Lakomek, Mike Strauss, Manuela Moldt, Karl-Peter Hopfner. Nature 2018
99
8

Real-space refinement in PHENIX for cryo-EM and crystallography.
Pavel V Afonine, Billy K Poon, Randy J Read, Oleg V Sobolev, Thomas C Terwilliger, Alexandre Urzhumtsev, Paul D Adams. Acta Crystallogr D Struct Biol 2018
571
8

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
8

The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
8

New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?
Karolin Luger, Mekonnen L Dechassa, David J Tremethick. Nat Rev Mol Cell Biol 2012
382
8

Expression and purification of recombinant histones and nucleosome reconstitution.
K Luger, T J Rechsteiner, T J Richmond. Methods Mol Biol 1999
308
8

Histone octamer rearranges to adapt to DNA unwrapping.
Silvija Bilokapic, Mike Strauss, Mario Halic. Nat Struct Mol Biol 2018
75
10

Structural basis for histone H2B deubiquitination by the SAGA DUB module.
Michael T Morgan, Mahmood Haj-Yahya, Alison E Ringel, Prasanthi Bandi, Ashraf Brik, Cynthia Wolberger. Science 2016
126
7

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
7

Structural basis of nucleosome recognition and modification by MLL methyltransferases.
Han Xue, Tonghui Yao, Mi Cao, Guanjun Zhu, Yan Li, Guiyong Yuan, Yong Chen, Ming Lei, Jing Huang. Nature 2019
48
14

Inhibition of PRC2 activity by a gain-of-function H3 mutation found in pediatric glioblastoma.
Peter W Lewis, Manuel M Müller, Matthew S Koletsky, Francisco Cordero, Shu Lin, Laura A Banaszynski, Benjamin A Garcia, Tom W Muir, Oren J Becher, C David Allis. Science 2013
708
7

Structural Basis of Dot1L Stimulation by Histone H2B Lysine 120 Ubiquitination.
Marco Igor Valencia-Sánchez, Pablo De Ioannes, Miao Wang, Nikita Vasilyev, Ruoyu Chen, Evgeny Nudler, Jean-Paul Armache, Karim-Jean Armache. Mol Cell 2019
54
12

Organization of Chromatin by Intrinsic and Regulated Phase Separation.
Bryan A Gibson, Lynda K Doolittle, Maximillian W G Schneider, Liv E Jensen, Nathan Gamarra, Lisa Henry, Daniel W Gerlich, Sy Redding, Michael K Rosen. Cell 2019
242
7

Mechanism of DNA translocation underlying chromatin remodelling by Snf2.
Meijing Li, Xian Xia, Yuanyuan Tian, Qi Jia, Xiaoyu Liu, Ying Lu, Ming Li, Xueming Li, Zhucheng Chen. Nature 2019
51
13

Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome.
Felix R Wagner, Christian Dienemann, Haibo Wang, Alexandra Stützer, Dimitry Tegunov, Henning Urlaub, Patrick Cramer. Nature 2020
45
15

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
956
7

Expression and purification of recombinant human histones.
Yoshinori Tanaka, Maki Tawaramoto-Sasanuma, Shinichi Kawaguchi, Tsutomu Ohta, Kinya Yoda, Hitoshi Kurumizaka, Shigeyuki Yokoyama. Methods 2004
131
6

Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming.
Abdenour Soufi, Meilin Fernandez Garcia, Artur Jaroszewicz, Nebiyu Osman, Matteo Pellegrini, Kenneth S Zaret. Cell 2015
346
6

Genomic Nucleosome Organization Reconstituted with Pure Proteins.
Nils Krietenstein, Megha Wal, Shinya Watanabe, Bongsoo Park, Craig L Peterson, B Franklin Pugh, Philipp Korber. Cell 2016
109
6

Nucleosome positioning and gene regulation: advances through genomics.
Cizhong Jiang, B Franklin Pugh. Nat Rev Genet 2009
664
6


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.