A citation-based method for searching scientific literature

Xiaoyu Zhang, Junshi Yazaki, Ambika Sundaresan, Shawn Cokus, Simon W-L Chan, Huaming Chen, Ian R Henderson, Paul Shinn, Matteo Pellegrini, Steve E Jacobsen, Joseph R Ecker. Cell 2006
Times Cited: 1108







List of co-cited articles
948 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
437
38

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
33

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
880
28

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
28


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
420
22

Gene body DNA methylation in plants.
Adam J Bewick, Robert J Schmitz. Curr Opin Plant Biol 2017
145
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
516
21

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
564
20

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity.
Marjori A Matzke, Rebecca A Mosher. Nat Rev Genet 2014
754
20

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
518
17

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
231
17

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
461
15


Genome-wide evolutionary analysis of eukaryotic DNA methylation.
Assaf Zemach, Ivy E McDaniel, Pedro Silva, Daniel Zilberman. Science 2010
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
149
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

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

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
346
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
280
12

On the origin and evolutionary consequences of gene body DNA methylation.
Adam J Bewick, Lexiang Ji, Chad E Niederhuth, Eva-Maria Willing, Brigitte T Hofmeister, Xiuling Shi, Li Wang, Zefu Lu, Nicholas A Rohr, Benjamin Hartwig,[...]. Proc Natl Acad Sci U S A 2016
152
12

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
184
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
813
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
278
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
579
11

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
119
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
11

Gardening the genome: DNA methylation in Arabidopsis thaliana.
Simon W-L Chan, Ian R Henderson, Steven E Jacobsen. Nat Rev Genet 2005
561
10


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
10

BSMAP: whole genome bisulfite sequence MAPping program.
Yuanxin Xi, Wei Li. BMC Bioinformatics 2009
614
9

Epigenetic reprogramming in plant and animal development.
Suhua Feng, Steven E Jacobsen, Wolf Reik. Science 2010
702
9

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
739
9

Single-base-resolution methylomes of Populus trichocarpa reveal the association between DNA methylation and drought stress.
Dan Liang, Zhoujia Zhang, Honglong Wu, Chunyu Huang, Peng Shuai, Chu-Yu Ye, Sha Tang, Yunjie Wang, Ling Yang, Jun Wang,[...]. BMC Genet 2014
75
12

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
437
9

Active DNA demethylation: mechanism and role in plant development.
Yan Li, Suresh Kumar, Weiqiang Qian. Plant Cell Rep 2018
29
31

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
9

Human DNA methylomes at base resolution show widespread epigenomic differences.
Ryan Lister, Mattia Pelizzola, Robert H Dowen, R David Hawkins, Gary Hon, Julian Tonti-Filippini, Joseph R Nery, Leonard Lee, Zhen Ye, Que-Minh Ngo,[...]. Nature 2009
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
101
8

Regulation and function of DNA methylation in plants and animals.
Xin-Jian He, Taiping Chen, Jian-Kang Zhu. Cell Res 2011
262
8

DNA methylation: roles in mammalian development.
Zachary D Smith, Alexander Meissner. Nat Rev Genet 2013
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
88
9



Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape.
Ronan C O'Malley, Shao-Shan Carol Huang, Liang Song, Mathew G Lewsey, Anna Bartlett, Joseph R Nery, Mary Galli, Andrea Gallavotti, Joseph R Ecker. Cell 2016
482
8

Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation.
Olivier Mathieu, Jon Reinders, Marian Caikovski, Chotika Smathajitt, Jerzy Paszkowski. Cell 2007
262
8

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