A citation-based method for searching scientific literature

Assaf Zemach, Ivy E McDaniel, Pedro Silva, Daniel Zilberman. Science 2010
Times Cited: 973







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



Times Cited
  Times     Co-cited
Similarity


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
709
31



Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
14

DNA methylation landscapes: provocative insights from epigenomics.
Miho M Suzuki, Adrian Bird. Nat Rev Genet 2008
14


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
725
13


Eukaryotic cytosine methyltransferases.
Mary Grace Goll, Timothy H Bestor. Annu Rev Biochem 2005
12

Evolution of DNA Methylation across Insects.
Adam J Bewick, Kevin J Vogel, Allen J Moore, Robert J Schmitz. Mol Biol Evol 2017
126
12

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
11


Evolutionary patterns of genic DNA methylation vary across land plants.
Shohei Takuno, Jin-Hua Ran, Brandon S Gaut. Nat Plants 2016
104
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
858
10

The evolution of invertebrate gene body methylation.
Shrutii Sarda, Jia Zeng, Brendan G Hunt, Soojin V Yi. Mol Biol Evol 2012
115
10

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
205
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
391
10

The diverse roles of DNA methylation in mammalian development and disease.
Maxim V C Greenberg, Deborah Bourc'his. Nat Rev Mol Cell Biol 2019
420
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
393
9

Transposable elements and the epigenetic regulation of the genome.
R Keith Slotkin, Robert Martienssen. Nat Rev Genet 2007
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


Diversity of cytosine methylation across the fungal tree of life.
Adam J Bewick, Brigitte T Hofmeister, Rob A Powers, Stephen J Mondo, Igor V Grigoriev, Timothy Y James, Jason E Stajich, Robert J Schmitz. Nat Ecol Evol 2019
41
21

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
8

Dynamics and function of DNA methylation in plants.
Huiming Zhang, Zhaobo Lang, Jian-Kang Zhu. Nat Rev Mol Cell Biol 2018
341
8



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
532
8

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
8

Evolution of DNA Methylome Diversity in Eukaryotes.
Alex de Mendoza, Ryan Lister, Ozren Bogdanovic. J Mol Biol 2019
25
32

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
259
8

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
209
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

Single base-resolution methylome of the silkworm reveals a sparse epigenomic map.
Hui Xiang, Jingde Zhu, Quan Chen, Fangyin Dai, Xin Li, Muwang Li, Hongyu Zhang, Guojie Zhang, Dong Li, Yang Dong,[...]. Nat Biotechnol 2010
226
8

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
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
224
7

DNA methylation and its basic function.
Lisa D Moore, Thuc Le, Guoping Fan. Neuropsychopharmacology 2013
7

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
15
46

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg. Genome Biol 2009
7

DNA Methylation: Shared and Divergent Features across Eukaryotes.
Robert J Schmitz, Zachary A Lewis, Mary G Goll. Trends Genet 2019
47
14

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity.
Marjori A Matzke, Rebecca A Mosher. Nat Rev Genet 2014
702
7

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
284
7


Nutritional control of reproductive status in honeybees via DNA methylation.
R Kucharski, J Maleszka, S Foret, R Maleszka. Science 2008
607
7

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
7

Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome.
Michael Weber, Ines Hellmann, Michael B Stadler, Liliana Ramos, Svante Pääbo, Michael Rebhan, Dirk Schübeler. Nat Genet 2007
7

Gene body DNA methylation in plants.
Adam J Bewick, Robert J Schmitz. Curr Opin Plant Biol 2017
125
6

The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants.
Adam J Bewick, Chad E Niederhuth, Lexiang Ji, Nicholas A Rohr, Patrick T Griffin, Jim Leebens-Mack, Robert J Schmitz. Genome Biol 2017
65
9


DNA methylation regulates transcriptional homeostasis of algal endosymbiosis in the coral model Aiptasia.
Yong Li, Yi Jin Liew, Guoxin Cui, Maha J Cziesielski, Noura Zahran, Craig T Michell, Christian R Voolstra, Manuel Aranda. Sci Adv 2018
26
23


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.