A citation-based method for searching scientific literature

Ryan Lister, Ronan C O'Malley, Julian Tonti-Filippini, Brian D Gregory, Charles C Berry, A Harvey Millar, Joseph R Ecker. Cell 2008
Times Cited: 1535







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



Times Cited
  Times     Co-cited
Similarity


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
40



Dynamics and function of DNA methylation in plants.
Huiming Zhang, Zhaobo Lang, Jian-Kang Zhu. Nat Rev Mol Cell Biol 2018
437
23

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
22

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
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
516
19

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
18

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity.
Marjori A Matzke, Rebecca A Mosher. Nat Rev Genet 2014
754
18

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
18

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
15

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

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
14

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

Genome-wide evolutionary analysis of eukaryotic DNA methylation.
Assaf Zemach, Ivy E McDaniel, Pedro Silva, Daniel Zilberman. Science 2010
13

BSMAP: whole genome bisulfite sequence MAPping program.
Yuanxin Xi, Wei Li. BMC Bioinformatics 2009
614
12

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
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

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
11

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
11

The transcriptional landscape of the yeast genome defined by RNA sequencing.
Ugrappa Nagalakshmi, Zhong Wang, Karl Waern, Chong Shou, Debasish Raha, Mark Gerstein, Michael Snyder. Science 2008
10

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
10

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
146
10

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
294
10

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
10

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
9

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
9


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
309
9

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
415
9

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
9


Mapping and quantifying mammalian transcriptomes by RNA-Seq.
Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer, Barbara Wold. Nat Methods 2008
8

Epigenetic inheritance in plants.
Ian R Henderson, Steven E Jacobsen. Nature 2007
471
8

Non-canonical RNA-directed DNA methylation.
Diego Cuerda-Gil, R Keith Slotkin. Nat Plants 2016
123
8

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
457
8

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
240
8

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
479
8


DNA Methylation Signatures of the Plant Chromomethyltransferases.
Quentin Gouil, David C Baulcombe. PLoS Genet 2016
81
9

Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA.
Joseph P Calarco, Filipe Borges, Mark T A Donoghue, Frédéric Van Ex, Pauline E Jullien, Telma Lopes, Rui Gardner, Frédéric Berger, José A Feijó, Jörg D Becker,[...]. Cell 2012
332
8

Epigenetic reprogramming in plant sexual reproduction.
Tomokazu Kawashima, Frédéric Berger. Nat Rev Genet 2014
148
8

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
657
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
388
8

Role of transposable elements in heterochromatin and epigenetic control.
Zachary Lippman, Anne-Valérie Gendrel, Michael Black, Matthew W Vaughn, Neilay Dedhia, W Richard McCombie, Kimberly Lavine, Vivek Mittal, Bruce May, Kristin D Kasschau,[...]. Nature 2004
797
8

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
8

A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.
M Frommer, L E McDonald, D S Millar, C M Collis, F Watt, G W Grigg, P L Molloy, C L Paul. Proc Natl Acad Sci U S A 1992
8

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging.
Fumihito Miura, Yusuke Enomoto, Ryo Dairiki, Takashi Ito. Nucleic Acids Res 2012
227
8

Differential expression analysis for sequence count data.
Simon Anders, Wolfgang Huber. Genome Biol 2010
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.