A citation-based method for searching scientific literature

Xin-Jian He, Taiping Chen, Jian-Kang Zhu. Cell Res 2011
Times Cited: 255







List of co-cited articles
727 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
39

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity.
Marjori A Matzke, Rebecca A Mosher. Nat Rev Genet 2014
742
28


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

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
19

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
17

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
17

DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation.
Mary Gehring, Jin Hoe Huh, Tzung-Fu Hsieh, Jon Penterman, Yeonhee Choi, John J Harada, Robert B Goldberg, Robert L Fischer. Cell 2006
456
17

Genome-wide evolutionary analysis of eukaryotic DNA methylation.
Assaf Zemach, Ivy E McDaniel, Pedro Silva, Daniel Zilberman. Science 2010
16

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
431
16


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
16

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

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
14

The methyl-CpG-binding protein MBD7 facilitates active DNA demethylation to limit DNA hyper-methylation and transcriptional gene silencing.
Zhaobo Lang, Mingguang Lei, Xingang Wang, Kai Tang, Daisuke Miki, Huiming Zhang, Satendra K Mangrauthia, Wenshan Liu, Wenfeng Nie, Guojie Ma,[...]. Mol Cell 2015
66
21

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
13

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
452
13

A DNA methylation reader complex that enhances gene transcription.
C Jake Harris, Marion Scheibe, Somsakul Pop Wongpalee, Wanlu Liu, Evan M Cornett, Robert M Vaughan, Xueqin Li, Wei Chen, Yan Xue, Zhenhui Zhong,[...]. Science 2018
99
13

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
116
13

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
144
12

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

Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are required for appropriate distribution of DNA methylation marks.
Ana Pilar Ortega-Galisteo, Teresa Morales-Ruiz, Rafael R Ariza, Teresa Roldán-Arjona. Plant Mol Biol 2008
143
12

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
305
12

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
12

Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription.
Daniel Zilberman, Mary Gehring, Robert K Tran, Tracy Ballinger, Steven Henikoff. Nat Genet 2007
878
11

A histone acetyltransferase regulates active DNA demethylation in Arabidopsis.
Weiqiang Qian, Daisuke Miki, Heng Zhang, Yunhua Liu, Xi Zhang, Kai Tang, Yunchao Kan, Honggui La, Xiaojie Li, Shaofang Li,[...]. Science 2012
141
10

Genome-wide demethylation of Arabidopsis endosperm.
Tzung-Fu Hsieh, Christian A Ibarra, Pedro Silva, Assaf Zemach, Leor Eshed-Williams, Robert L Fischer, Daniel Zilberman. Science 2009
412
10

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
99
9

A group of SUVH methyl-DNA binding proteins regulate expression of the DNA demethylase ROS1 in Arabidopsis.
Xinlong Xiao, Jieqiong Zhang, Tao Li, Xing Fu, Viswanathan Satheesh, Qingfeng Niu, Zhaobo Lang, Jian-Kang Zhu, Mingguang Lei. J Integr Plant Biol 2019
27
33

Methyl-CpG-binding domain protein MBD7 is required for active DNA demethylation in Arabidopsis.
Chunlei Wang, Xiaomei Dong, Dan Jin, Yusheng Zhao, Shaojun Xie, Xiaojie Li, Xinjian He, Zhaobo Lang, Jinsheng Lai, Jian-Kang Zhu,[...]. Plant Physiol 2015
36
25

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
9

BSMAP: whole genome bisulfite sequence MAPping program.
Yuanxin Xi, Wei Li. BMC Bioinformatics 2009
605
9

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
652
9



Epigenetic inheritance in plants.
Ian R Henderson, Steven E Jacobsen. Nature 2007
469
8

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
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

The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications.
Kai Tang, Zhaobo Lang, Heng Zhang, Jian-Kang Zhu. Nat Plants 2016
76
10

A pair of transposon-derived proteins function in a histone acetyltransferase complex for active DNA demethylation.
Cheng-Guo Duan, Xingang Wang, Shaojun Xie, Li Pan, Daisuke Miki, Kai Tang, Chuan-Chih Hsu, Mingguang Lei, Yingli Zhong, Yueh-Ju Hou,[...]. Cell Res 2017
42
19


DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases.
Teresa Morales-Ruiz, Ana Pilar Ortega-Galisteo, María Isabel Ponferrada-Marín, María Isabel Martínez-Macías, Rafael R Ariza, Teresa Roldán-Arjona. Proc Natl Acad Sci U S A 2006
219
8

Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation.
Fernanda Agius, Avnish Kapoor, Jian-Kang Zhu. Proc Natl Acad Sci U S A 2006
193
8

Local DNA hypomethylation activates genes in rice endosperm.
Assaf Zemach, M Yvonne Kim, Pedro Silva, Jessica A Rodrigues, Bradley Dotson, Matthew D Brooks, Daniel Zilberman. Proc Natl Acad Sci U S A 2010
218
8

Dynamic DNA Methylation in Plant Growth and Development.
Arthur Bartels, Qiang Han, Pooja Nair, Liam Stacey, Hannah Gaynier, Matthew Mosley, Qi Qing Huang, Jacob K Pearson, Tzung-Fu Hsieh, Yong-Qiang Charles An,[...]. Int J Mol Sci 2018
85
9

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

Transgenerational epigenetic instability is a source of novel methylation variants.
Robert J Schmitz, Matthew D Schultz, Mathew G Lewsey, Ronan C O'Malley, Mark A Urich, Ondrej Libiger, Nicholas J Schork, Joseph R Ecker. Science 2011
391
8

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
344
8

Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity.
Anjar Wibowo, Claude Becker, Gianpiero Marconi, Julius Durr, Jonathan Price, Jorg Hagmann, Ranjith Papareddy, Hadi Putra, Jorge Kageyama, Jorg Becker,[...]. Elife 2016
144
7


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.