A citation-based method for searching scientific literature

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, Chinweike Ukomadu, Kirsten C Sadler, Sriharsa Pradhan, Matteo Pellegrini, Steven E Jacobsen. Proc Natl Acad Sci U S A 2010
Times Cited: 774







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



Times Cited
  Times     Co-cited
Similarity


Genome-wide evolutionary analysis of eukaryotic DNA methylation.
Assaf Zemach, Ivy E McDaniel, Pedro Silva, Daniel Zilberman. Science 2010
55



DNA methylation landscapes: provocative insights from epigenomics.
Miho M Suzuki, Adrian Bird. Nat Rev Genet 2008
18

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
17

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
17

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
15

Dynamics and function of DNA methylation in plants.
Huiming Zhang, Zhaobo Lang, Jian-Kang Zhu. Nat Rev Mol Cell Biol 2018
564
15



Evolution of DNA Methylation across Insects.
Adam J Bewick, Kevin J Vogel, Allen J Moore, Robert J Schmitz. Mol Biol Evol 2017
158
14

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
256
13

The diverse roles of DNA methylation in mammalian development and disease.
Maxim V C Greenberg, Deborah Bourc'his. Nat Rev Mol Cell Biol 2019
708
13

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
12

DNA methylation and its basic function.
Lisa D Moore, Thuc Le, Guoping Fan. Neuropsychopharmacology 2013
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
909
12


Conserved role of intragenic DNA methylation in regulating alternative promoters.
Alika K Maunakea, Raman P Nagarajan, Mikhail Bilenky, Tracy J Ballinger, Cletus D'Souza, Shaun D Fouse, Brett E Johnson, Chibo Hong, Cydney Nielsen, Yongjun Zhao,[...]. Nature 2010
11

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
609
10

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
10

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity.
Marjori A Matzke, Rebecca A Mosher. Nat Rev Genet 2014
834
10

BSMAP: whole genome bisulfite sequence MAPping program.
Yuanxin Xi, Wei Li. BMC Bioinformatics 2009
661
10

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
469
10

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
10

Intragenic DNA methylation prevents spurious transcription initiation.
Francesco Neri, Stefania Rapelli, Anna Krepelova, Danny Incarnato, Caterina Parlato, Giulia Basile, Mara Maldotti, Francesca Anselmi, Salvatore Oliviero. Nature 2017
360
10

Genome-wide and caste-specific DNA methylomes of the ants Camponotus floridanus and Harpegnathos saltator.
Roberto Bonasio, Qiye Li, Jinmin Lian, Navdeep S Mutti, Lijun Jin, Hongmei Zhao, Pei Zhang, Ping Wen, Hui Xiang, Yun Ding,[...]. Curr Biol 2012
233
10

The honey bee epigenomes: differential methylation of brain DNA in queens and workers.
Frank Lyko, Sylvain Foret, Robert Kucharski, Stephan Wolf, Cassandra Falckenhayn, Ryszard Maleszka. PLoS Biol 2010
419
10

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
910
10

N6-methyladenine DNA modification in Drosophila.
Guoqiang Zhang, Hua Huang, Di Liu, Ying Cheng, Xiaoling Liu, Wenxin Zhang, Ruichuan Yin, Dapeng Zhang, Peng Zhang, Jianzhao Liu,[...]. Cell 2015
359
9

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
9


Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
9


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
264
9


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
544
8

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
507
8

CpG islands and the regulation of transcription.
Aimée M Deaton, Adrian Bird. Genes Dev 2011
8

The evolution of invertebrate gene body methylation.
Shrutii Sarda, Jia Zeng, Brendan G Hunt, Soojin V Yi. Mol Biol Evol 2012
132
8




Evolution of DNA Methylome Diversity in Eukaryotes.
Alex de Mendoza, Ryan Lister, Ozren Bogdanovic. J Mol Biol 2019
43
18

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

Signatures of DNA Methylation across Insects Suggest Reduced DNA Methylation Levels in Holometabola.
Panagiotis Provataris, Karen Meusemann, Oliver Niehuis, Sonja Grath, Bernhard Misof. Genome Biol Evol 2018
40
20

Transgenerational epigenetic inheritance: myths and mechanisms.
Edith Heard, Robert A Martienssen. Cell 2014
840
8

Convergent evolution of a vertebrate-like methylome in a marine sponge.
Alex de Mendoza, William L Hatleberg, Kevin Pang, Sven Leininger, Ozren Bogdanovic, Jahnvi Pflueger, Sam Buckberry, Ulrich Technau, Andreas Hejnol, Maja Adamska,[...]. Nat Ecol Evol 2019
27
29

DNA methylation: roles in mammalian development.
Zachary D Smith, Alexander Meissner. Nat Rev Genet 2013
7

DNA N6-Adenine Methylation in Arabidopsis thaliana.
Zhe Liang, Lisha Shen, Xuean Cui, Shengjie Bao, Yuke Geng, Guoliang Yu, Fan Liang, Shang Xie, Tiegang Lu, Xiaofeng Gu,[...]. Dev Cell 2018
117
7

CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize.
Jonathan I Gent, Nathanael A Ellis, Lin Guo, Alex E Harkess, Yingyin Yao, Xiaoyu Zhang, R Kelly Dawe. Genome Res 2013
199
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.