A citation-based method for searching scientific literature

Peter A Jones. Nat Rev Genet 2012
Times Cited: 3476







List of co-cited articles
453 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
708
9

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

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
8



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

Dynamic DNA methylation: In the right place at the right time.
Chongyuan Luo, Petra Hajkova, Joseph R Ecker. Science 2018
278
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

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
7

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 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: roles in mammalian development.
Zachary D Smith, Alexander Meissner. Nat Rev Genet 2013
6

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
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


Role of TET enzymes in DNA methylation, development, and cancer.
Kasper Dindler Rasmussen, Kristian Helin. Genes Dev 2016
545
5

Regulation of chromatin by histone modifications.
Andrew J Bannister, Tony Kouzarides. Cell Res 2011
5

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
909
5


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
5

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
539
5

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
929
5

Translating the histone code.
T Jenuwein, C D Allis. Science 2001
5

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
5

WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
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
4


edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
4

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
675
4

Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling.
Ruth Pidsley, Elena Zotenko, Timothy J Peters, Mitchell G Lawrence, Gail P Risbridger, Peter Molloy, Susan Van Djik, Beverly Muhlhausler, Clare Stirzaker, Susan J Clark. Genome Biol 2016
559
4

Epigenetic modifications and human disease.
Anna Portela, Manel Esteller. Nat Biotechnol 2010
4

Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells.
Michael Weber, Jonathan J Davies, David Wittig, Edward J Oakeley, Michael Haase, Wan L Lam, Dirk Schübeler. Nat Genet 2005
4


Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
3


Targeting the cancer epigenome for therapy.
Peter A Jones, Jean-Pierre J Issa, Stephen Baylin. Nat Rev Genet 2016
650
3

Histone phosphorylation: a chromatin modification involved in diverse nuclear events.
Dorine Rossetto, Nikita Avvakumov, Jacques Côté. Epigenetics 2012
265
3

The emerging role of epigenetic therapeutics in immuno-oncology.
Michael J Topper, Michelle Vaz, Kristen A Marrone, Julie R Brahmer, Stephen B Baylin. Nat Rev Clin Oncol 2020
159
3

DNA methylation and cancer.
Marta Kulis, Manel Esteller. Adv Genet 2010
895
3

Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of α-ketoglutarate-dependent dioxygenases.
Wei Xu, Hui Yang, Ying Liu, Ying Yang, Ping Wang, Se-Hee Kim, Shinsuke Ito, Chen Yang, Pu Wang, Meng-Tao Xiao,[...]. Cancer Cell 2011
3


Epigenetic programming by maternal behavior.
Ian C G Weaver, Nadia Cervoni, Frances A Champagne, Ana C D'Alessio, Shakti Sharma, Jonathan R Seckl, Sergiy Dymov, Moshe Szyf, Michael J Meaney. Nat Neurosci 2004
3

TET2 Deficiency Causes Germinal Center Hyperplasia, Impairs Plasma Cell Differentiation, and Promotes B-cell Lymphomagenesis.
Pilar M Dominguez, Hussein Ghamlouch, Wojciech Rosikiewicz, Parveen Kumar, Wendy Béguelin, Lorena Fontán, Martín A Rivas, Patrycja Pawlikowska, Marine Armand, Enguerran Mouly,[...]. Cancer Discov 2018
87
3

The Polycomb group protein EZH2 directly controls DNA methylation.
Emmanuelle Viré, Carmen Brenner, Rachel Deplus, Loïc Blanchon, Mario Fraga, Céline Didelot, Lluis Morey, Aleyde Van Eynde, David Bernard, Jean-Marie Vanderwinden,[...]. Nature 2006
3

Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX.
Myunggon Ko, Jungeun An, Hozefa S Bandukwala, Lukas Chavez, Tarmo Aijö, William A Pastor, Matthew F Segal, Huiming Li, Kian Peng Koh, Harri Lähdesmäki,[...]. Nature 2013
255
3

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells.
Madeleine P Ball, Jin Billy Li, Yuan Gao, Je-Hyuk Lee, Emily M LeProust, In-Hyun Park, Bin Xie, George Q Daley, George M Church. Nat Biotechnol 2009
752
3


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.