A citation-based method for searching scientific literature

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, Lee Edsall, Jessica Antosiewicz-Bourget, Ron Stewart, Victor Ruotti, A Harvey Millar, James A Thomson, Bing Ren, Joseph R Ecker. Nature 2009
Times Cited: 2769







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



Times Cited
  Times     Co-cited
Similarity


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
17

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
17

The diverse roles of DNA methylation in mammalian development and disease.
Maxim V C Greenberg, Deborah Bourc'his. Nat Rev Mol Cell Biol 2019
340
16



Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
13

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
13



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
12


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
12

Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis.
Alexander Meissner, Andreas Gnirke, George W Bell, Bernard Ramsahoye, Eric S Lander, Rudolf Jaenisch. Nucleic Acids Res 2005
621
11



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
855
11

Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain.
Junjie U Guo, Yijing Su, Joo Heon Shin, Jaehoon Shin, Hongda Li, Bin Xie, Chun Zhong, Shaohui Hu, Thuc Le, Guoping Fan,[...]. Nat Neurosci 2014
413
11

DNA methylation: roles in mammalian development.
Zachary D Smith, Alexander Meissner. Nat Rev Genet 2013
10


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
10

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
10



Dynamic changes in the human methylome during differentiation.
Louise Laurent, Eleanor Wong, Guoliang Li, Tien Huynh, Aristotelis Tsirigos, Chin Thing Ong, Hwee Meng Low, Ken Wing Kin Sung, Isidore Rigoutsos, Jeanne Loring,[...]. Genome Res 2010
683
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

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
9

BSMAP: whole genome bisulfite sequence MAPping program.
Yuanxin Xi, Wei Li. BMC Bioinformatics 2009
538
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
678
8

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

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
8

The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape.
Daniel N Weinberg, Simon Papillon-Cavanagh, Haifen Chen, Yuan Yue, Xiao Chen, Kartik N Rajagopalan, Cynthia Horth, John T McGuire, Xinjing Xu, Hamid Nikbakht,[...]. Nature 2019
95
8

Role of TET enzymes in DNA methylation, development, and cancer.
Kasper Dindler Rasmussen, Kristian Helin. Genes Dev 2016
389
8

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

A bivalent chromatin structure marks key developmental genes in embryonic stem cells.
Bradley E Bernstein, Tarjei S Mikkelsen, Xiaohui Xie, Michael Kamal, Dana J Huebert, James Cuff, Ben Fry, Alex Meissner, Marius Wernig, Kathrin Plath,[...]. Cell 2006
7

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
7


Eukaryotic cytosine methyltransferases.
Mary Grace Goll, Timothy H Bestor. Annu Rev Biochem 2005
7

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
330
7

Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a.
B H Ramsahoye, D Biniszkiewicz, F Lyko, V Clark, A P Bird, R Jaenisch. Proc Natl Acad Sci U S A 2000
621
7

Chemistry. How are alkynes scrambled?
Uwe H F Bunz. Science 2005
918
7

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
7

Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome.
Wei Xie, Cathy L Barr, Audrey Kim, Feng Yue, Ah Young Lee, James Eubanks, Emma L Dempster, Bing Ren. Cell 2012
328
7

Gene body methylation can alter gene expression and is a therapeutic target in cancer.
Xiaojing Yang, Han Han, Daniel D De Carvalho, Fides D Lay, Peter A Jones, Gangning Liang. Cancer Cell 2014
559
7

DNA methylation loss in late-replicating domains is linked to mitotic cell division.
Wanding Zhou, Huy Q Dinh, Zachary Ramjan, Daniel J Weisenberger, Charles M Nicolet, Hui Shen, Peter W Laird, Benjamin P Berman. Nat Genet 2018
86
8

SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development.
Qianhua Xu, Yunlong Xiang, Qiujun Wang, Leyun Wang, Julie Brind'Amour, Aaron Blair Bogutz, Yu Zhang, Bingjie Zhang, Guang Yu, Weikun Xia,[...]. Nat Genet 2019
64
9

Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation.
Tuncay Baubec, Daniele F Colombo, Christiane Wirbelauer, Juliane Schmidt, Lukas Burger, Arnaud R Krebs, Altuna Akalin, Dirk Schübeler. Nature 2015
331
6

Charting a dynamic DNA methylation landscape of the human genome.
Michael J Ziller, Hongcang Gu, Fabian Müller, Julie Donaghey, Linus T-Y Tsai, Oliver Kohlbacher, Philip L De Jager, Evan D Rosen, David A Bennett, Bradley E Bernstein,[...]. Nature 2013
756
6

Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
6


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.