A citation-based method for searching scientific literature

Dirk Schübeler. Nature 2015
Times Cited: 941







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



Times Cited
  Times     Co-cited
Similarity




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
13

DNA methylation: roles in mammalian development.
Zachary D Smith, Alexander Meissner. Nat Rev Genet 2013
11



The diverse roles of DNA methylation in mammalian development and disease.
Maxim V C Greenberg, Deborah Bourc'his. Nat Rev Mol Cell Biol 2019
378
10

Genome-wide evolutionary analysis of eukaryotic DNA methylation.
Assaf Zemach, Ivy E McDaniel, Pedro Silva, Daniel Zilberman. Science 2010
965
9

Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1.
Mamta Tahiliani, Kian Peng Koh, Yinghua Shen, William A Pastor, Hozefa Bandukwala, Yevgeny Brudno, Suneet Agarwal, Lakshminarayan M Iyer, David R Liu, L Aravind,[...]. Science 2009
9

Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine.
Shinsuke Ito, Li Shen, Qing Dai, Susan C Wu, Leonard B Collins, James A Swenberg, Chuan He, Yi Zhang. Science 2011
9

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

Impact of cytosine methylation on DNA binding specificities of human transcription factors.
Yimeng Yin, Ekaterina Morgunova, Arttu Jolma, Eevi Kaasinen, Biswajyoti Sahu, Syed Khund-Sayeed, Pratyush K Das, Teemu Kivioja, Kashyap Dave, Fan Zhong,[...]. Science 2017
388
9

Dynamic DNA methylation: In the right place at the right time.
Chongyuan Luo, Petra Hajkova, Joseph R Ecker. Science 2018
176
8

DNA-binding factors shape the mouse methylome at distal regulatory regions.
Michael B Stadler, Rabih Murr, Lukas Burger, Robert Ivanek, Florian Lienert, Anne Schöler, Erik van Nimwegen, Christiane Wirbelauer, Edward J Oakeley, Dimos Gaidatzis,[...]. Nature 2011
863
8

Active DNA demethylation at enhancers during the vertebrate phylotypic period.
Ozren Bogdanović, Arne H Smits, Elisa de la Calle Mustienes, Juan J Tena, Ethan Ford, Ruth Williams, Upeka Senanayake, Matthew D Schultz, Saartje Hontelez, Ila van Kruijsbergen,[...]. Nat Genet 2016
125
7

The molecular hallmarks of epigenetic control.
C David Allis, Thomas Jenuwein. Nat Rev Genet 2016
913
7

CpG islands and the regulation of transcription.
Aimée M Deaton, Adrian Bird. Genes Dev 2011
7


Role of TET enzymes in DNA methylation, development, and cancer.
Kasper Dindler Rasmussen, Kristian Helin. Genes Dev 2016
408
6

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
6

DNA methylation aging clocks: challenges and recommendations.
Christopher G Bell, Robert Lowe, Peter D Adams, Andrea A Baccarelli, Stephan Beck, Jordana T Bell, Brock C Christensen, Vadim N Gladyshev, Bastiaan T Heijmans, Steve Horvath,[...]. Genome Biol 2019
137
6

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
708
6



DNA methylation landscapes: provocative insights from epigenomics.
Miho M Suzuki, Adrian Bird. Nat Rev Genet 2008
6

The hallmarks of aging.
Carlos López-Otín, Maria A Blasco, Linda Partridge, Manuel Serrano, Guido Kroemer. Cell 2013
6

Global epigenomic reconfiguration during mammalian brain development.
Ryan Lister, Eran A Mukamel, Joseph R Nery, Mark Urich, Clare A Puddifoot, Nicholas D Johnson, Jacinta Lucero, Yun Huang, Andrew J Dwork, Matthew D Schultz,[...]. Science 2013
6

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
6


Histone H3K27ac separates active from poised enhancers and predicts developmental state.
Menno P Creyghton, Albert W Cheng, G Grant Welstead, Tristan Kooistra, Bryce W Carey, Eveline J Steine, Jacob Hanna, Michael A Lodato, Garrett M Frampton, Phillip A Sharp,[...]. Proc Natl Acad Sci U S A 2010
6

MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing.
Mark A Urich, Joseph R Nery, Ryan Lister, Robert J Schmitz, Joseph R Ecker. Nat Protoc 2015
134
5

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
5

Transcription factors as readers and effectors of DNA methylation.
Heng Zhu, Guohua Wang, Jiang Qian. Nat Rev Genet 2016
231
5

Direct detection of DNA methylation during single-molecule, real-time sequencing.
Benjamin A Flusberg, Dale R Webster, Jessica H Lee, Kevin J Travers, Eric C Olivares, Tyson A Clark, Jonas Korlach, Stephen W Turner. Nat Methods 2010
740
5

Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA.
Yu-Fei He, Bin-Zhong Li, Zheng Li, Peng Liu, Yang Wang, Qingyu Tang, Jianping Ding, Yingying Jia, Zhangcheng Chen, Lin Li,[...]. Science 2011
5

Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates.
Hao Wu, Tianlei Xu, Hao Feng, Li Chen, Ben Li, Bing Yao, Zhaohui Qin, Peng Jin, Karen N Conneely. Nucleic Acids Res 2015
121
5

Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data.
Nelly Olova, Felix Krueger, Simon Andrews, David Oxley, Rebecca V Berrens, Miguel R Branco, Wolf Reik. Genome Biol 2018
70
7


Global delay in nascent strand DNA methylation.
Jocelyn Charlton, Timothy L Downing, Zachary D Smith, Hongcang Gu, Kendell Clement, Ramona Pop, Veronika Akopian, Sven Klages, David P Santos, Alexander M Tsankov,[...]. Nat Struct Mol Biol 2018
25
20

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity.
Sébastien A Smallwood, Heather J Lee, Christof Angermueller, Felix Krueger, Heba Saadeh, Julian Peat, Simon R Andrews, Oliver Stegle, Wolf Reik, Gavin Kelsey. Nat Methods 2014
503
5


Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
5

DNA methylation in mammals.
En Li, Yi Zhang. Cold Spring Harb Perspect Biol 2014
376
5

The accessible chromatin landscape of the human genome.
Robert E Thurman, Eric Rynes, Richard Humbert, Jeff Vierstra, Matthew T Maurano, Eric Haugen, Nathan C Sheffield, Andrew B Stergachis, Hao Wang, Benjamin Vernot,[...]. Nature 2012
5

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
407
4

Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands.
J G Herman, J R Graff, S Myöhänen, B D Nelkin, S B Baylin. Proc Natl Acad Sci U S A 1996
4

Retention of paternal DNA methylome in the developing zebrafish germline.
Ksenia Skvortsova, Katsiaryna Tarbashevich, Martin Stehling, Ryan Lister, Manuel Irimia, Erez Raz, Ozren Bogdanovic. Nat Commun 2019
33
12

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
4

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
273
4

Crystal structure of the nucleosome core particle at 2.8 A resolution.
K Luger, A W Mäder, R K Richmond, D F Sargent, T J Richmond. Nature 1997
4


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.