A citation-based method for searching scientific literature

Jiamu Du, Lianna M Johnson, Steven E Jacobsen, Dinshaw J Patel. Nat Rev Mol Cell Biol 2015
Times Cited: 452







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



Times Cited
  Times     Co-cited
Similarity



Dynamics and function of DNA methylation in plants.
Huiming Zhang, Zhaobo Lang, Jian-Kang Zhu. Nat Rev Mol Cell Biol 2018
413
24

The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin.
Assaf Zemach, M Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor Eshed-Williams, Ka Thao, Stacey L Harmer, Daniel Zilberman. Cell 2013
557
21

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity.
Marjori A Matzke, Rebecca A Mosher. Nat Rev Genet 2014
742
20

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis.
Hume Stroud, Truman Do, Jiamu Du, Xuehua Zhong, Suhua Feng, Lianna Johnson, Dinshaw J Patel, Steven E Jacobsen. Nat Struct Mol Biol 2014
415
18

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
17


Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome.
Hume Stroud, Maxim V C Greenberg, Suhua Feng, Yana V Bernatavichute, Steven E Jacobsen. Cell 2013
511
15

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
13

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.
Shawn J Cokus, Suhua Feng, Xiaoyu Zhang, Zugen Chen, Barry Merriman, Christian D Haudenschild, Sriharsa Pradhan, Stanley F Nelson, Matteo Pellegrini, Steven E Jacobsen. Nature 2008
13

HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
12

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
12

Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis.
Xiaoyu Zhang, Junshi Yazaki, Ambika Sundaresan, Shawn Cokus, Simon W-L Chan, Huaming Chen, Ian R Henderson, Paul Shinn, Matteo Pellegrini, Steve E Jacobsen,[...]. Cell 2006
12

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
11

Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants.
Jiamu Du, Xuehua Zhong, Yana V Bernatavichute, Hume Stroud, Suhua Feng, Elena Caro, Ajay A Vashisht, Jolyon Terragni, Hang Gyeong Chin, Andy Tu,[...]. Cell 2012
275
11

Widespread dynamic DNA methylation in response to biotic stress.
Robert H Dowen, Mattia Pelizzola, Robert J Schmitz, Ryan Lister, Jill M Dowen, Joseph R Nery, Jack E Dixon, Joseph R Ecker. Proc Natl Acad Sci U S A 2012
508
11

Highly integrated single-base resolution maps of the epigenome in Arabidopsis.
Ryan Lister, Ronan C O'Malley, Julian Tonti-Filippini, Brian D Gregory, Charles C Berry, A Harvey Millar, Joseph R Ecker. Cell 2008
11

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
10

The molecular hallmarks of epigenetic control.
C David Allis, Thomas Jenuwein. Nat Rev Genet 2016
9

UHRF1 plays a role in maintaining DNA methylation in mammalian cells.
Magnolia Bostick, Jong Kyong Kim, Pierre-Olivier Estève, Amander Clark, Sriharsa Pradhan, Steven E Jacobsen. Science 2007
856
9


SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation.
Lianna M Johnson, Jiamu Du, Christopher J Hale, Sylvain Bischof, Suhua Feng, Ramakrishna K Chodavarapu, Xuehua Zhong, Giuseppe Marson, Matteo Pellegrini, David J Segal,[...]. Nature 2014
176
9


Gene body DNA methylation in plants.
Adam J Bewick, Robert J Schmitz. Curr Opin Plant Biol 2017
138
8


Conservation and divergence of methylation patterning in plants and animals.
Suhua Feng, Shawn J Cokus, Xiaoyu Zhang, Pao-Yang Chen, Magnolia Bostick, Mary G Goll, Jonathan Hetzel, Jayati Jain, Steven H Strauss, Marnie E Halpern,[...]. Proc Natl Acad Sci U S A 2010
734
8

Genome-wide evolutionary analysis of eukaryotic DNA methylation.
Assaf Zemach, Ivy E McDaniel, Pedro Silva, Daniel Zilberman. Science 2010
8

Molecular mechanism of action of plant DRM de novo DNA methyltransferases.
Xuehua Zhong, Jiamu Du, Christopher J Hale, Javier Gallego-Bartolome, Suhua Feng, Ajay A Vashisht, Joanne Chory, James A Wohlschlegel, Dinshaw J Patel, Steven E Jacobsen. Cell 2014
160
8



Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase.
James P Jackson, Anders M Lindroth, Xiaofeng Cao, Steven E Jacobsen. Nature 2002
856
8

Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation.
A M Lindroth, X Cao, J P Jackson, D Zilberman, C M McCallum, S Henikoff, S E Jacobsen. Science 2001
577
8

Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1.
Julie A Law, Jiamu Du, Christopher J Hale, Suhua Feng, Krzysztof Krajewski, Ana Marie S Palanca, Brian D Strahl, Dinshaw J Patel, Steven E Jacobsen. Nature 2013
205
8

DNA methylation and its basic function.
Lisa D Moore, Thuc Le, Guoping Fan. Neuropsychopharmacology 2013
7

Mechanism of DNA methylation-directed histone methylation by KRYPTONITE.
Jiamu Du, Lianna M Johnson, Martin Groth, Suhua Feng, Christopher J Hale, Sisi Li, Ajay A Vashisht, James A Wohlschlegel, Dinshaw J Patel, Steven E Jacobsen. Mol Cell 2014
100
7

Transposable elements and the epigenetic regulation of the genome.
R Keith Slotkin, Robert Martienssen. Nat Rev Genet 2007
7

BSMAP: whole genome bisulfite sequence MAPping program.
Yuanxin Xi, Wei Li. BMC Bioinformatics 2009
605
7

Regulation of chromatin by histone modifications.
Andrew J Bannister, Tony Kouzarides. Cell Res 2011
7


Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
7

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
7



methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles.
Altuna Akalin, Matthias Kormaksson, Sheng Li, Francine E Garrett-Bakelman, Maria E Figueroa, Ari Melnick, Christopher E Mason. Genome Biol 2012
783
7

Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation.
Xueqin Li, C Jake Harris, Zhenhui Zhong, Wei Chen, Rui Liu, Bei Jia, Zonghua Wang, Sisi Li, Steven E Jacobsen, Jiamu Du. Proc Natl Acad Sci U S A 2018
48
14

The SET domain proteins SUVH2 and SUVH9 are required for Pol V occupancy at RNA-directed DNA methylation loci.
Zhang-Wei Liu, Chang-Rong Shao, Cui-Jun Zhang, Jin-Xing Zhou, Su-Wei Zhang, Lin Li, She Chen, Huan-Wei Huang, Tao Cai, Xin-Jian He. PLoS Genet 2014
109
7

Non-canonical RNA-directed DNA methylation.
Diego Cuerda-Gil, R Keith Slotkin. Nat Plants 2016
117
7

ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation.
Daniel Zilberman, Xiaofeng Cao, Steven E Jacobsen. Science 2003
720
6

deepTools: a flexible platform for exploring deep-sequencing data.
Fidel Ramírez, Friederike Dündar, Sarah Diehl, Björn A Grüning, Thomas Manke. Nucleic Acids Res 2014
6

RNA-Directed DNA Methylation: The Evolution of a Complex Epigenetic Pathway in Flowering Plants.
Marjori A Matzke, Tatsuo Kanno, Antonius J M Matzke. Annu Rev Plant Biol 2015
225
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.