A citation-based method for searching scientific literature

Yimeng Yin, Ekaterina Morgunova, Arttu Jolma, Eevi Kaasinen, Biswajyoti Sahu, Syed Khund-Sayeed, Pratyush K Das, Teemu Kivioja, Kashyap Dave, Fan Zhong, Kazuhiro R Nitta, Minna Taipale, Alexander Popov, Paul A Ginno, Silvia Domcke, Jian Yan, Dirk Schübeler, Charles Vinson, Jussi Taipale. Science 2017
Times Cited: 398







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



Times Cited
  Times     Co-cited
Similarity


The diverse roles of DNA methylation in mammalian development and disease.
Maxim V C Greenberg, Deborah Bourc'his. Nat Rev Mol Cell Biol 2019
398
15


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
12

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
12

Transcription factors as readers and effectors of DNA methylation.
Heng Zhu, Guohua Wang, Jiang Qian. Nat Rev Genet 2016
236
12


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
11


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
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
865
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
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

Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming.
Abdenour Soufi, Meilin Fernandez Garcia, Artur Jaroszewicz, Nebiyu Osman, Matteo Pellegrini, Kenneth S Zaret. Cell 2015
352
9

CpG islands and the regulation of transcription.
Aimée M Deaton, Adrian Bird. Genes Dev 2011
9

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
9




Genome-wide methylation profiles reveal quantitative views of human aging rates.
Gregory Hannum, Justin Guinney, Ling Zhao, Li Zhang, Guy Hughes, SriniVas Sadda, Brandy Klotzle, Marina Bibikova, Jian-Bing Fan, Yuan Gao,[...]. Mol Cell 2013
8


DNA-binding specificities of human transcription factors.
Arttu Jolma, Jian Yan, Thomas Whitington, Jarkko Toivonen, Kazuhiro R Nitta, Pasi Rastas, Ekaterina Morgunova, Martin Enge, Mikko Taipale, Gonghong Wei,[...]. Cell 2013
661
8

A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
Suhas S P Rao, Miriam H Huntley, Neva C Durand, Elena K Stamenova, Ivan D Bochkov, James T Robinson, Adrian L Sanborn, Ido Machol, Arina D Omer, Eric S Lander,[...]. Cell 2014
8

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
7

DNA methylation: roles in mammalian development.
Zachary D Smith, Alexander Meissner. Nat Rev Genet 2013
7

Editing DNA Methylation in the Mammalian Genome.
X Shawn Liu, Hao Wu, Xiong Ji, Yonatan Stelzer, Xuebing Wu, Szymon Czauderna, Jian Shu, Daniel Dadon, Richard A Young, Rudolf Jaenisch. Cell 2016
557
7

Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues.
Gary C Hon, Nisha Rajagopal, Yin Shen, David F McCleary, Feng Yue, My D Dang, Bing Ren. Nat Genet 2013
295
7

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

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
7

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
7

Determination and inference of eukaryotic transcription factor sequence specificity.
Matthew T Weirauch, Ally Yang, Mihai Albu, Atina G Cote, Alejandro Montenegro-Montero, Philipp Drewe, Hamed S Najafabadi, Samuel A Lambert, Ishminder Mann, Kate Cook,[...]. Cell 2014
690
7

FIMO: scanning for occurrences of a given motif.
Charles E Grant, Timothy L Bailey, William Stafford Noble. Bioinformatics 2011
7

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

limma powers differential expression analyses for RNA-sequencing and microarray studies.
Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth. Nucleic Acids Res 2015
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
143
6

Competition between DNA methylation and transcription factors determines binding of NRF1.
Silvia Domcke, Anaïs Flore Bardet, Paul Adrian Ginno, Dominik Hartl, Lukas Burger, Dirk Schübeler. Nature 2015
234
6

Large conserved domains of low DNA methylation maintained by Dnmt3a.
Mira Jeong, Deqiang Sun, Min Luo, Yun Huang, Grant A Challen, Benjamin Rodriguez, Xiaotian Zhang, Lukas Chavez, Hui Wang, Rebecca Hannah,[...]. Nat Genet 2014
203
6


Diversity and complexity in DNA recognition by transcription factors.
Gwenael Badis, Michael F Berger, Anthony A Philippakis, Shaheynoor Talukder, Andrew R Gehrke, Savina A Jaeger, Esther T Chan, Genita Metzler, Anastasia Vedenko, Xiaoyu Chen,[...]. Science 2009
647
6

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
6


DNA methylation presents distinct binding sites for human transcription factors.
Shaohui Hu, Jun Wan, Yijing Su, Qifeng Song, Yaxue Zeng, Ha Nam Nguyen, Jaehoon Shin, Eric Cox, Hee Sool Rho, Crystal Woodard,[...]. Elife 2013
199
6

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
6

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.
Martin J Aryee, Andrew E Jaffe, Hector Corrada-Bravo, Christine Ladd-Acosta, Andrew P Feinberg, Kasper D Hansen, Rafael A Irizarry. Bioinformatics 2014
5

Repurposing the CRISPR-Cas9 system for targeted DNA methylation.
Aleksandar Vojta, Paula Dobrinić, Vanja Tadić, Luka Bočkor, Petra Korać, Boris Julg, Marija Klasić, Vlatka Zoldoš. Nucleic Acids Res 2016
362
5

An epigenetic biomarker of aging for lifespan and healthspan.
Morgan E Levine, Ake T Lu, Austin Quach, Brian H Chen, Themistocles L Assimes, Stefania Bandinelli, Lifang Hou, Andrea A Baccarelli, James D Stewart, Yun Li,[...]. Aging (Albany NY) 2018
443
5

Topological domains in mammalian genomes identified by analysis of chromatin interactions.
Jesse R Dixon, Siddarth Selvaraj, Feng Yue, Audrey Kim, Yan Li, Yin Shen, Ming Hu, Jun S Liu, Bing Ren. Nature 2012
5

DNA methylation age of blood predicts all-cause mortality in later life.
Riccardo E Marioni, Sonia Shah, Allan F McRae, Brian H Chen, Elena Colicino, Sarah E Harris, Jude Gibson, Anjali K Henders, Paul Redmond, Simon R Cox,[...]. Genome Biol 2015
525
5

DNA methylation-based measures of biological age: meta-analysis predicting time to death.
Brian H Chen, Riccardo E Marioni, Elena Colicino, Marjolein J Peters, Cavin K Ward-Caviness, Pei-Chien Tsai, Nicholas S Roetker, Allan C Just, Ellen W Demerath, Weihua Guan,[...]. Aging (Albany NY) 2016
411
5

The sva package for removing batch effects and other unwanted variation in high-throughput experiments.
Jeffrey T Leek, W Evan Johnson, Hilary S Parker, Andrew E Jaffe, John D Storey. Bioinformatics 2012
5


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.