A citation-based method for searching scientific literature

Marjori A Matzke, Rebecca A Mosher. Nat Rev Genet 2014
Times Cited: 702







List of co-cited articles
1068 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
341
35

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
532
21


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
391
18

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
489
17

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
489
16

Non-canonical RNA-directed DNA methylation.
Diego Cuerda-Gil, R Keith Slotkin. Nat Plants 2016
110
14

DNA methylation pathways and their crosstalk with histone methylation.
Jiamu Du, Lianna M Johnson, Steven E Jacobsen, Dinshaw J Patel. Nat Rev Mol Cell Biol 2015
420
14

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
14

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
14

The expanding world of small RNAs in plants.
Filipe Borges, Robert A Martienssen. Nat Rev Mol Cell Biol 2015
396
14

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

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
13


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
562
12

Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA.
Joseph P Calarco, Filipe Borges, Mark T A Donoghue, Frédéric Van Ex, Pauline E Jullien, Telma Lopes, Rui Gardner, Frédéric Berger, José A Feijó, Jörg D Becker,[...]. Cell 2012
320
12


Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes.
Christian A Ibarra, Xiaoqi Feng, Vera K Schoft, Tzung-Fu Hsieh, Rie Uzawa, Jessica A Rodrigues, Assaf Zemach, Nina Chumak, Adriana Machlicova, Toshiro Nishimura,[...]. Science 2012
277
11

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
211
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

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
149
11

Epigenetic inheritance in plants.
Ian R Henderson, Steven E Jacobsen. Nature 2007
460
10

Transposable elements and the epigenetic regulation of the genome.
R Keith Slotkin, Robert Martienssen. Nat Rev Genet 2007
10


RNA polymerase V transcription guides ARGONAUTE4 to chromatin.
Andrzej T Wierzbicki, Thomas S Ream, Jeremy R Haag, Craig S Pikaard. Nat Genet 2009
284
10

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
725
10

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
169
10

Regulation and function of DNA methylation in plants and animals.
Xin-Jian He, Taiping Chen, Jian-Kang Zhu. Cell Res 2011
243
10

Epigenetic reprogramming and small RNA silencing of transposable elements in pollen.
R Keith Slotkin, Matthew Vaughn, Filipe Borges, Milos Tanurdzić, Jörg D Becker, José A Feijó, Robert A Martienssen. Cell 2009
639
9

Silencing in sperm cells is directed by RNA movement from the surrounding nurse cell.
Germán Martínez, Kaushik Panda, Claudia Köhler, R Keith Slotkin. Nat Plants 2016
108
9

Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit.
Zhaobo Lang, Yihai Wang, Kai Tang, Dengguo Tang, Tatsiana Datsenka, Jingfei Cheng, Yijing Zhang, Avtar K Handa, Jian-Kang Zhu. Proc Natl Acad Sci U S A 2017
126
9

Widespread natural variation of DNA methylation within angiosperms.
Chad E Niederhuth, Adam J Bewick, Lexiang Ji, Magdy S Alabady, Kyung Do Kim, Qing Li, Nicholas A Rohr, Aditi Rambani, John M Burke, Joshua A Udall,[...]. Genome Biol 2016
205
9

Gene body DNA methylation in plants.
Adam J Bewick, Robert J Schmitz. Curr Opin Plant Biol 2017
125
9

RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome.
Qing Li, Jonathan I Gent, Greg Zynda, Jawon Song, Irina Makarevitch, Cory D Hirsch, Candice N Hirsch, R Kelly Dawe, Thelma F Madzima, Karen M McGinnis,[...]. Proc Natl Acad Sci U S A 2015
105
9


Regulatory link between DNA methylation and active demethylation in Arabidopsis.
Mingguang Lei, Huiming Zhang, Russell Julian, Kai Tang, Shaojun Xie, Jian-Kang Zhu. Proc Natl Acad Sci U S A 2015
110
9

Methylation-sensitive expression of a DNA demethylase gene serves as an epigenetic rheostat.
Ben P Williams, Daniela Pignatta, Steven Henikoff, Mary Gehring. PLoS Genet 2015
92
9

Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis.
James Walker, Hongbo Gao, Jingyi Zhang, Billy Aldridge, Martin Vickers, James D Higgins, Xiaoqi Feng. Nat Genet 2018
74
12

BSMAP: whole genome bisulfite sequence MAPping program.
Yuanxin Xi, Wei Li. BMC Bioinformatics 2009
573
9

ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase.
Zhizhong Gong, Teresa Morales-Ruiz, Rafael R Ariza, Teresa Roldán-Arjona, Lisa David, Jian Kang Zhu. Cell 2002
417
9

Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements.
David Secco, Chuang Wang, Huixia Shou, Matthew D Schultz, Serge Chiarenza, Laurent Nussaume, Joseph R Ecker, James Whelan, Ryan Lister. Elife 2015
169
9

Arabidopsis MET1 cytosine methyltransferase mutants.
Mark W Kankel, Douglas E Ramsey, Trevor L Stokes, Susan K Flowers, Jeremy R Haag, Jeffrey A Jeddeloh, Nicole C Riddle, Michelle L Verbsky, Eric J Richards. Genetics 2003
328
9

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
198
9

DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV.
Heng Zhang, Ze-Yang Ma, Liang Zeng, Kaori Tanaka, Cui-Jun Zhang, Jun Ma, Ge Bai, Pengcheng Wang, Su-Wei Zhang, Zhang-Wei Liu,[...]. Proc Natl Acad Sci U S A 2013
102
9

Genetic and functional diversification of small RNA pathways in plants.
Zhixin Xie, Lisa K Johansen, Adam M Gustafson, Kristin D Kasschau, Andrew D Lellis, Daniel Zilberman, Steven E Jacobsen, James C Carrington. PLoS Biol 2004
8


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
262
8

DNA demethylation in the Arabidopsis genome.
Jon Penterman, Daniel Zilberman, Jin Hoe Huh, Tracy Ballinger, Steven Henikoff, Robert L Fischer. Proc Natl Acad Sci U S A 2007
295
8

Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense.
Agnès Yu, Gersende Lepère, Florence Jay, Jingyu Wang, Laure Bapaume, Yu Wang, Anne-Laure Abraham, Jon Penterman, Robert L Fischer, Olivier Voinnet,[...]. Proc Natl Acad Sci U S A 2013
223
8


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.