A citation-based method for searching scientific literature

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, Gustavo Turecki, Allen Delaney, Richard Varhol, Nina Thiessen, Ksenya Shchors, Vivi M Heine, David H Rowitch, Xiaoyun Xing, Chris Fiore, Maximiliaan Schillebeeckx, Steven J M Jones, David Haussler, Marco A Marra, Martin Hirst, Ting Wang, Joseph F Costello. Nature 2010
Times Cited: 1067







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



Times Cited
  Times     Co-cited
Similarity




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
563
16

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
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
11

DNA methylation landscapes: provocative insights from epigenomics.
Miho M Suzuki, Adrian Bird. Nat Rev Genet 2008
10


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
10

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
692
9

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
626
9

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
9

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
269
9

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
9



Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells.
Matthew C Lorincz, David R Dickerson, Mike Schmitt, Mark Groudine. Nat Struct Mol Biol 2004
335
8

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing.
Sanjeev Shukla, Ersen Kavak, Melissa Gregory, Masahiko Imashimizu, Bojan Shutinoski, Mikhail Kashlev, Philipp Oberdoerffer, Rickard Sandberg, Shalini Oberdoerffer. Nature 2011
618
8

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
686
8

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
696
8

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling.
Hongcang Gu, Zachary D Smith, Christoph Bock, Patrick Boyle, Andreas Gnirke, Alexander Meissner. Nat Protoc 2011
408
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


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

Genome-wide evolutionary analysis of eukaryotic DNA methylation.
Assaf Zemach, Ivy E McDaniel, Pedro Silva, Daniel Zilberman. Science 2010
957
7





Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.
R Alan Harris, Ting Wang, Cristian Coarfa, Raman P Nagarajan, Chibo Hong, Sara L Downey, Brett E Johnson, Shaun D Fouse, Allen Delaney, Yongjun Zhao,[...]. Nat Biotechnol 2010
442
7

The alternative role of DNA methylation in splicing regulation.
Galit Lev Maor, Ahuvi Yearim, Gil Ast. Trends Genet 2015
252
6

Dynamic DNA methylation across diverse human cell lines and tissues.
Katherine E Varley, Jason Gertz, Kevin M Bowling, Stephanie L Parker, Timothy E Reddy, Florencia Pauli-Behn, Marie K Cross, Brian A Williams, John A Stamatoyannopoulos, Gregory E Crawford,[...]. Genome Res 2013
437
6

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
860
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

Conservation and divergence of methylation patterning in plants and animals.
Suhua Feng, Shawn J Cokus, Xiaoyu Zhang, Pao-Yang Chen, Magnolia Bostick, Mary G Goll, Jonathan Hetzel, Jayati Jain, Steven H Strauss, Marnie E Halpern,[...]. Proc Natl Acad Sci U S A 2010
691
6

DNA methylation and its basic function.
Lisa D Moore, Thuc Le, Guoping Fan. Neuropsychopharmacology 2013
925
6


High density DNA methylation array with single CpG site resolution.
Marina Bibikova, Bret Barnes, Chan Tsan, Vincent Ho, Brandy Klotzle, Jennie M Le, David Delano, Lu Zhang, Gary P Schroth, Kevin L Gunderson,[...]. Genomics 2011
6

A data-driven approach to preprocessing Illumina 450K methylation array data.
Ruth Pidsley, Chloe C Y Wong, Manuela Volta, Katie Lunnon, Jonathan Mill, Leonard C Schalkwyk. BMC Genomics 2013
491
6

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
6

Association of a History of Child Abuse With Impaired Myelination in the Anterior Cingulate Cortex: Convergent Epigenetic, Transcriptional, and Morphological Evidence.
Pierre-Eric Lutz, Arnaud Tanti, Alicja Gasecka, Sarah Barnett-Burns, John J Kim, Yi Zhou, Gang G Chen, Marina Wakid, Meghan Shaw, Daniel Almeida,[...]. Am J Psychiatry 2017
63
7


DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA.
Steen K T Ooi, Chen Qiu, Emily Bernstein, Keqin Li, Da Jia, Zhe Yang, Hediye Erdjument-Bromage, Paul Tempst, Shau-Ping Lin, C David Allis,[...]. Nature 2007
952
5

Genetic-epigenetic interactions in cis: a major focus in the post-GWAS era.
Catherine Do, Alyssa Shearer, Masako Suzuki, Mary Beth Terry, Joel Gelernter, John M Greally, Benjamin Tycko. Genome Biol 2017
65
7

CpG islands and the regulation of transcription.
Aimée M Deaton, Adrian Bird. Genes Dev 2011
5

Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis.
Xiaoyu Zhang, Junshi Yazaki, Ambika Sundaresan, Shawn Cokus, Simon W-L Chan, Huaming Chen, Ian R Henderson, Paul Shinn, Matteo Pellegrini, Steve E Jacobsen,[...]. Cell 2006
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

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores.
Rafael A Irizarry, Christine Ladd-Acosta, Bo Wen, Zhijin Wu, Carolina Montano, Patrick Onyango, Hengmi Cui, Kevin Gabo, Michael Rongione, Maree Webster,[...]. Nat Genet 2009
5

Genome-scale DNA methylation maps of pluripotent and differentiated cells.
Alexander Meissner, Tarjei S Mikkelsen, Hongcang Gu, Marius Wernig, Jacob Hanna, Andrey Sivachenko, Xiaolan Zhang, Bradley E Bernstein, Chad Nusbaum, David B Jaffe,[...]. Nature 2008
5

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
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.