A citation-based method for searching scientific literature

Julie A Law, Steven E Jacobsen. Nat Rev Genet 2010
Times Cited: 2155







List of co-cited articles
877 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
547
33

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity.
Marjori A Matzke, Rebecca A Mosher. Nat Rev Genet 2014
822
23


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
604
19

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
464
18

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
18

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
14

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
14

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

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
901
12


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
255
12

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
362
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
599
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
460
11

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
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
177
10


DNA methylation: roles in mammalian development.
Zachary D Smith, Alexander Meissner. Nat Rev Genet 2013
10

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
541
10

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
175
10

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
541
10

fastp: an ultra-fast all-in-one FASTQ preprocessor.
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. Bioinformatics 2018
9


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
500
9

DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in arabidopsis.
Yeonhee Choi, Mary Gehring, Lianna Johnson, Mike Hannon, John J Harada, Robert B Goldberg, Steven E Jacobsen, Robert L Fischer. Cell 2002
498
9

BSMAP: whole genome bisulfite sequence MAPping program.
Yuanxin Xi, Wei Li. BMC Bioinformatics 2009
656
9

Downregulation of RdDM during strawberry fruit ripening.
Jingfei Cheng, Qingfeng Niu, Bo Zhang, Kunsong Chen, Ruihua Yang, Jian-Kang Zhu, Yijing Zhang, Zhaobo Lang. Genome Biol 2018
71
12

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
130
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
416
8

Regulation and function of DNA methylation in plants and animals.
Xin-Jian He, Taiping Chen, Jian-Kang Zhu. Cell Res 2011
278
8

The diverse roles of DNA methylation in mammalian development and disease.
Maxim V C Greenberg, Deborah Bourc'his. Nat Rev Mol Cell Biol 2019
677
8

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

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
253
8

Single-base methylome analysis reveals dynamic epigenomic differences associated with water deficit in apple.
Jidi Xu, Shasha Zhou, Xiaoqing Gong, Yi Song, Steve van Nocker, Fengwang Ma, Qingmei Guan. Plant Biotechnol J 2018
87
9

HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
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
132
8

Genome-wide evolutionary analysis of eukaryotic DNA methylation.
Assaf Zemach, Ivy E McDaniel, Pedro Silva, Daniel Zilberman. Science 2010
7


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
7


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
198
7

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
469
7

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
7

Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression.
Xin Li, Jingde Zhu, Fengyi Hu, Song Ge, Mingzhi Ye, Hui Xiang, Guojie Zhang, Xiaoming Zheng, Hongyu Zhang, Shilai Zhang,[...]. BMC Genomics 2012
183
7

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
908
7

Dynamics of DNA Methylation and Its Functions in Plant Growth and Development.
Suresh Kumar, Trilochan Mohapatra. Front Plant Sci 2021
30
23

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
160
7

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.
Manu J Dubin, Pei Zhang, Dazhe Meng, Marie-Stanislas Remigereau, Edward J Osborne, Francesco Paolo Casale, Philipp Drewe, André Kahles, Geraldine Jean, Bjarni Vilhjálmsson,[...]. Elife 2015
261
7

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
166
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.