A citation-based method for searching scientific literature

Cornelia G Spruijt, Felix Gnerlich, Arne H Smits, Toni Pfaffeneder, Pascal W T C Jansen, Christina Bauer, Martin Münzel, Mirko Wagner, Markus Müller, Fariha Khan, H Christian Eberl, Anneloes Mensinga, Arie B Brinkman, Konstantin Lephikov, Udo Müller, Jörn Walter, Rolf Boelens, Hugo van Ingen, Heinrich Leonhardt, Thomas Carell, Michiel Vermeulen. Cell 2013
Times Cited: 677







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



Times Cited
  Times     Co-cited
Similarity


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
42

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
40

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
36


5-Hydroxymethylcytosine is a predominantly stable DNA modification.
Martin Bachman, Santiago Uribe-Lewis, Xiaoping Yang, Michael Williams, Adele Murrell, Shankar Balasubramanian. Nat Chem 2014
300
23

A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation.
Mario Iurlaro, Gabriella Ficz, David Oxley, Eun-Ang Raiber, Martin Bachman, Michael J Booth, Simon Andrews, Shankar Balasubramanian, Wolf Reik. Genome Biol 2013
210
22



Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification.
Shinsuke Ito, Ana C D'Alessio, Olena V Taranova, Kwonho Hong, Lawrence C Sowers, Yi Zhang. Nature 2010
18

5-Formylcytosine can be a stable DNA modification in mammals.
Martin Bachman, Santiago Uribe-Lewis, Xiaoping Yang, Heather E Burgess, Mario Iurlaro, Wolf Reik, Adele Murrell, Shankar Balasubramanian. Nat Chem Biol 2015
157
16


Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome.
Miao Yu, Gary C Hon, Keith E Szulwach, Chun-Xiao Song, Liang Zhang, Audrey Kim, Xuekun Li, Qing Dai, Yin Shen, Beomseok Park,[...]. Cell 2012
682
15

Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics.
Li Shen, Hao Wu, Dinh Diep, Shinpei Yamaguchi, Ana C D'Alessio, Ho-Lim Fung, Kun Zhang, Yi Zhang. Cell 2013
342
14

MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system.
Marian Mellén, Pinar Ayata, Scott Dewell, Skirmantas Kriaucionis, Nathaniel Heintz. Cell 2012
623
13

Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2.
Myunggon Ko, Yun Huang, Anna M Jankowska, Utz J Pape, Mamta Tahiliani, Hozefa S Bandukwala, Jungeun An, Edward D Lamperti, Kian Peng Koh, Rebecca Ganetzky,[...]. Nature 2010
936
13

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine.
Chun-Xiao Song, Keith E Szulwach, Ye Fu, Qing Dai, Chengqi Yi, Xuekun Li, Yujing Li, Chih-Hsin Chen, Wen Zhang, Xing Jian,[...]. Nat Biotechnol 2011
701
13

The discovery of 5-formylcytosine in embryonic stem cell DNA.
Toni Pfaffeneder, Benjamin Hackner, Matthias Truss, Martin Münzel, Markus Müller, Christian A Deiml, Christian Hagemeier, Thomas Carell. Angew Chem Int Ed Engl 2011
346
13

Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates.
Daniel Globisch, Martin Münzel, Markus Müller, Stylianos Michalakis, Mirko Wagner, Susanne Koch, Tobias Brückl, Martin Biel, Thomas Carell. PLoS One 2010
584
13

Biochemical reconstitution of TET1-TDG-BER-dependent active DNA demethylation reveals a highly coordinated mechanism.
Alain R Weber, Claudia Krawczyk, Adam B Robertson, Anna Kuśnierczyk, Cathrine B Vågbø, David Schuermann, Arne Klungland, Primo Schär. Nat Commun 2016
115
13


DNA methylation: roles in mammalian development.
Zachary D Smith, Alexander Meissner. Nat Rev Genet 2013
12

Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation.
Gabriella Ficz, Miguel R Branco, Stefanie Seisenberger, Fátima Santos, Felix Krueger, Timothy A Hore, C Joana Marques, Simon Andrews, Wolf Reik. Nature 2011
802
11

Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation.
Kelly Moran-Crusio, Linsey Reavie, Alan Shih, Omar Abdel-Wahab, Delphine Ndiaye-Lobry, Camille Lobry, Maria E Figueroa, Aparna Vasanthakumar, Jay Patel, Xinyang Zhao,[...]. Cancer Cell 2011
824
11

Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming.
Chun-Xiao Song, Keith E Szulwach, Qing Dai, Ye Fu, Shi-Qing Mao, Li Lin, Craig Street, Yujing Li, Mickael Poidevin, Hao Wu,[...]. Cell 2013
370
11

Crystal structure of TET2-DNA complex: insight into TET-mediated 5mC oxidation.
Lulu Hu, Ze Li, Jingdong Cheng, Qinhui Rao, Wei Gong, Mengjie Liu, Yujiang Geno Shi, Jiayu Zhu, Ping Wang, Yanhui Xu. Cell 2013
232
11

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
11

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
10

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
10

Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution.
Michael J Booth, Miguel R Branco, Gabriella Ficz, David Oxley, Felix Krueger, Wolf Reik, Shankar Balasubramanian. Science 2012
583
10

Nucleosome-interacting proteins regulated by DNA and histone methylation.
Till Bartke, Michiel Vermeulen, Blerta Xhemalce, Samuel C Robson, Matthias Mann, Tony Kouzarides. Cell 2010
399
10

Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence.
Hideharu Hashimoto, Yusuf Olatunde Olanrewaju, Yu Zheng, Geoffrey G Wilson, Xing Zhang, Xiaodong Cheng. Genes Dev 2014
80
12

5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription.
Matthew W Kellinger, Chun-Xiao Song, Jenny Chong, Xing-Yu Lu, Chuan He, Dong Wang. Nat Struct Mol Biol 2012
161
10

Role of TET enzymes in DNA methylation, development, and cancer.
Kasper Dindler Rasmussen, Kristian Helin. Genes Dev 2016
469
9

The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA.
Jafar Sharif, Masahiro Muto, Shin-ichiro Takebayashi, Isao Suetake, Akihiro Iwamatsu, Takaho A Endo, Jun Shinga, Yoko Mizutani-Koseki, Tetsuro Toyoda, Kunihiro Okamura,[...]. Nature 2007
808
9

UHRF1 plays a role in maintaining DNA methylation in mammalian cells.
Magnolia Bostick, Jong Kyong Kim, Pierre-Olivier Estève, Amander Clark, Sriharsa Pradhan, Steven E Jacobsen. Science 2007
856
9

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription.
William A Pastor, L Aravind, Anjana Rao. Nat Rev Mol Cell Biol 2013
551
9

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells.
William A Pastor, Utz J Pape, Yun Huang, Hope R Henderson, Ryan Lister, Myunggon Ko, Erin M McLoughlin, Yevgeny Brudno, Sahasransu Mahapatra, Philipp Kapranov,[...]. Nature 2011
573
9

The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes.
Tian-Peng Gu, Fan Guo, Hui Yang, Hai-Ping Wu, Gui-Fang Xu, Wei Liu, Zhi-Guo Xie, Linyu Shi, Xinyi He, Seung-gi Jin,[...]. Nature 2011
731
9

Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation.
Hideharu Hashimoto, Yiwei Liu, Anup K Upadhyay, Yanqi Chang, Shelley B Howerton, Paula M Vertino, Xing Zhang, Xiaodong Cheng. Nucleic Acids Res 2012
292
9

TET-mediated oxidation of methylcytosine causes TDG or NEIL glycosylase dependent gene reactivation.
Udo Müller, Christina Bauer, Michael Siegl, Andrea Rottach, Heinrich Leonhardt. Nucleic Acids Res 2014
60
15

5-Formylcytosine organizes nucleosomes and forms Schiff base interactions with histones in mouse embryonic stem cells.
Eun-Ang Raiber, Guillem Portella, Sergio Martínez Cuesta, Robyn Hardisty, Pierre Murat, Zhe Li, Mario Iurlaro, Wendy Dean, Julia Spindel, Dario Beraldi,[...]. Nat Chem 2018
50
18

TET2 promotes histone O-GlcNAcylation during gene transcription.
Qiang Chen, Yibin Chen, Chunjing Bian, Ryoji Fujiki, Xiaochun Yu. Nature 2013
343
9

Model-based analysis of ChIP-Seq (MACS).
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
9


Tet and TDG mediate DNA demethylation essential for mesenchymal-to-epithelial transition in somatic cell reprogramming.
Xiao Hu, Lei Zhang, Shi-Qing Mao, Zheng Li, Jiekai Chen, Run-Rui Zhang, Hai-Ping Wu, Juan Gao, Fan Guo, Wei Liu,[...]. Cell Stem Cell 2014
204
8

5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging.
Keith E Szulwach, Xuekun Li, Yujing Li, Chun-Xiao Song, Hao Wu, Qing Dai, Hasan Irier, Anup K Upadhyay, Marla Gearing, Allan I Levey,[...]. Nat Neurosci 2011
550
8

TET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS.
Rachel Deplus, Benjamin Delatte, Marie K Schwinn, Matthieu Defrance, Jacqui Méndez, Nancy Murphy, Mark A Dawson, Michael Volkmar, Pascale Putmans, Emilie Calonne,[...]. EMBO J 2013
332
8

Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase.
Eun-Ang Raiber, Dario Beraldi, Gabriella Ficz, Heather E Burgess, Miguel R Branco, Pierre Murat, David Oxley, Michael J Booth, Wolf Reik, Shankar Balasubramanian. Genome Biol 2012
161
8


Tet proteins connect the O-linked N-acetylglucosamine transferase Ogt to chromatin in embryonic stem cells.
Pietro Vella, Andrea Scelfo, Sriganesh Jammula, Fulvio Chiacchiera, Kristine Williams, Alessandro Cuomo, Alessandra Roberto, Jesper Christensen, Tiziana Bonaldi, Kristian Helin,[...]. Mol Cell 2013
221
8


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.