A citation-based method for searching scientific literature

Huiming Zhang, Zhaobo Lang, Jian-Kang Zhu. Nat Rev Mol Cell Biol 2018
Times Cited: 413







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



Times Cited
  Times     Co-cited
Similarity



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

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
19


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
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

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
15

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
15

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
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
452
13

The mechanism and function of active DNA demethylation in plants.
Ruie Liu, Zhaobo Lang. J Integr Plant Biol 2020
38
34

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
12

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

Gene body DNA methylation in plants.
Adam J Bewick, Robert J Schmitz. Curr Opin Plant Biol 2017
138
12

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
12

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
12

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions.
Taiji Kawakatsu, Shao-Shan Carol Huang, Florian Jupe, Eriko Sasaki, Robert J Schmitz, Mark A Urich, Rosa Castanon, Joseph R Nery, Cesar Barragan, Yupeng He,[...]. Cell 2016
275
11

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
11

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
11

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
11

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
223
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
783
10


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
10

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
10

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
10

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
10

Epigenetic regulation of stress responses in plants.
Viswanathan Chinnusamy, Jian-Kang Zhu. Curr Opin Plant Biol 2009
523
9

An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress.
Hidetaka Ito, Hervé Gaubert, Etienne Bucher, Marie Mirouze, Isabelle Vaillant, Jerzy Paszkowski. Nature 2011
340
9


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
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
9

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

The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications.
Kai Tang, Zhaobo Lang, Heng Zhang, Jian-Kang Zhu. Nat Plants 2016
76
11

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
290
9

A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening.
Kenneth Manning, Mahmut Tör, Mervin Poole, Yiguo Hong, Andrew J Thompson, Graham J King, James J Giovannoni, Graham B Seymour. Nat Genet 2006
644
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
275
8


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
8

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
81
9

A Role for Epigenetic Regulation in the Adaptation and Stress Responses of Non-model Plants.
Flávia Thiebaut, Adriana Silva Hemerly, Paulo Cavalcanti Gomes Ferreira. Front Plant Sci 2019
47
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
8

Regulation and function of DNA methylation in plants and animals.
Xin-Jian He, Taiping Chen, Jian-Kang Zhu. Cell Res 2011
255
8

Epigenetic regulation in plant abiotic stress responses.
Ya-Nan Chang, Chen Zhu, Jing Jiang, Huiming Zhang, Jian-Kang Zhu, Cheng-Guo Duan. J Integr Plant Biol 2020
82
9

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
8

Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening.
Silin Zhong, Zhangjun Fei, Yun-Ru Chen, Yi Zheng, Mingyun Huang, Julia Vrebalov, Ryan McQuinn, Nigel Gapper, Bao Liu, Jenny Xiang,[...]. Nat Biotechnol 2013
383
7

Epigenetic inheritance in plants.
Ian R Henderson, Steven E Jacobsen. Nature 2007
469
7

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
7

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
233
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.