A citation-based method for searching scientific literature

Chongyuan Luo, Petra Hajkova, Joseph R Ecker. Science 2018
Times Cited: 209







List of co-cited articles
653 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
504
27





DNA methylation: roles in mammalian development.
Zachary D Smith, Alexander Meissner. Nat Rev Genet 2013
9

DNA methylation and its basic function.
Lisa D Moore, Thuc Le, Guoping Fan. Neuropsychopharmacology 2013
9


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

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
448
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
8

DNA Methylation: Shared and Divergent Features across Eukaryotes.
Robert J Schmitz, Zachary A Lewis, Mary G Goll. Trends Genet 2019
54
14



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
8

Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex.
Chongyuan Luo, Christopher L Keown, Laurie Kurihara, Jingtian Zhou, Yupeng He, Junhao Li, Rosa Castanon, Jacinta Lucero, Joseph R Nery, Justin P Sandoval,[...]. Science 2017
207
7

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
7

Transcription factors as readers and effectors of DNA methylation.
Heng Zhu, Guohua Wang, Jiang Qian. Nat Rev Genet 2016
266
7


Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
7

DNA Methylation Clocks in Aging: Categories, Causes, and Consequences.
Adam E Field, Neil A Robertson, Tina Wang, Aaron Havas, Trey Ideker, Peter D Adams. Mol Cell 2018
189
7



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
195
6


Role of TET enzymes in DNA methylation, development, and cancer.
Kasper Dindler Rasmussen, Kristian Helin. Genes Dev 2016
469
6

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
112
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

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
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 in mammals.
En Li, Yi Zhang. Cold Spring Harb Perspect Biol 2014
415
6


The molecular hallmarks of epigenetic control.
C David Allis, Thomas Jenuwein. Nat Rev Genet 2016
5

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
793
5

Human body epigenome maps reveal noncanonical DNA methylation variation.
Matthew D Schultz, Yupeng He, John W Whitaker, Manoj Hariharan, Eran A Mukamel, Danny Leung, Nisha Rajagopal, Joseph R Nery, Mark A Urich, Huaming Chen,[...]. Nature 2015
356
5

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
5

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
5

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
310
5

Spatiotemporal DNA methylome dynamics of the developing mouse fetus.
Yupeng He, Manoj Hariharan, David U Gorkin, Diane E Dickel, Chongyuan Luo, Rosa G Castanon, Joseph R Nery, Ah Young Lee, Yuan Zhao, Hui Huang,[...]. Nature 2020
34
14

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
587
5

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nat Protoc 2009
5


On the origin and evolutionary consequences of gene body DNA methylation.
Adam J Bewick, Lexiang Ji, Chad E Niederhuth, Eva-Maria Willing, Brigitte T Hofmeister, Xiuling Shi, Li Wang, Zefu Lu, Nicholas A Rohr, Benjamin Hartwig,[...]. Proc Natl Acad Sci U S A 2016
149
5

Epigenomic analysis of multilineage differentiation of human embryonic stem cells.
Wei Xie, Matthew D Schultz, Ryan Lister, Zhonggang Hou, Nisha Rajagopal, Pradipta Ray, John W Whitaker, Shulan Tian, R David Hawkins, Danny Leung,[...]. Cell 2013
485
5

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
5


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
5

deepTools2: a next generation web server for deep-sequencing data analysis.
Fidel Ramírez, Devon P Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S Richter, Steffen Heyne, Friederike Dündar, Thomas Manke. Nucleic Acids Res 2016
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.