A citation-based method for searching scientific literature

Hongcang Gu, Zachary D Smith, Christoph Bock, Patrick Boyle, Andreas Gnirke, Alexander Meissner. Nat Protoc 2011
Times Cited: 461







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



Times Cited
  Times     Co-cited
Similarity



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
31

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
695
29

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
18

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
16

BSMAP: whole genome bisulfite sequence MAPping program.
Yuanxin Xi, Wei Li. BMC Bioinformatics 2009
661
14

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
14

Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling.
Patrick Boyle, Kendell Clement, Hongcang Gu, Zachary D Smith, Michael Ziller, Jennifer L Fostel, Laurie Holmes, Jim Meldrim, Fontina Kelley, Andreas Gnirke,[...]. Genome Biol 2012
170
12

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
12


Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
12

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
11

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
11


Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution.
Yibin Liu, Paulina Siejka-Zielińska, Gergana Velikova, Ying Bi, Fang Yuan, Marketa Tomkova, Chunsen Bai, Lei Chen, Benjamin Schuster-Böckler, Chun-Xiao Song. Nat Biotechnol 2019
146
10

Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine.
Michael J Booth, Tobias W B Ost, Dario Beraldi, Neil M Bell, Miguel R Branco, Wolf Reik, Shankar Balasubramanian. Nat Protoc 2013
203
10

Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution.
Michael J Booth, Miguel R Branco, Gabriella Ficz, David Oxley, Felix Krueger, Wolf Reik, Shankar Balasubramanian. Science 2012
605
10

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
10

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
10

CpG islands and the regulation of transcription.
Aimée M Deaton, Adrian Bird. Genes Dev 2011
10

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
9

Quantitative comparison of genome-wide DNA methylation mapping technologies.
Christoph Bock, Eleni M Tomazou, Arie B Brinkman, Fabian Müller, Femke Simmer, Hongcang Gu, Natalie Jäger, Andreas Gnirke, Hendrik G Stunnenberg, Alexander Meissner. Nat Biotechnol 2010
412
9

Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands.
J G Herman, J R Graff, S Myöhänen, B D Nelkin, S B Baylin. Proc Natl Acad Sci U S A 1996
9

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
9

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
9


DNA methylation: roles in mammalian development.
Zachary D Smith, Alexander Meissner. Nat Rev Genet 2013
8


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

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity.
Sébastien A Smallwood, Heather J Lee, Christof Angermueller, Felix Krueger, Heba Saadeh, Julian Peat, Simon R Andrews, Oliver Stegle, Wolf Reik, Gavin Kelsey. Nat Methods 2014
610
8

Degradation of DNA by bisulfite treatment.
Kazuo Tanaka, Akimitsu Okamoto. Bioorg Med Chem Lett 2007
127
7

Direct detection of DNA methylation during single-molecule, real-time sequencing.
Benjamin A Flusberg, Dale R Webster, Jessica H Lee, Kevin J Travers, Eric C Olivares, Tyson A Clark, Jonas Korlach, Stephen W Turner. Nat Methods 2010
834
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

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
7

Enhanced reduced representation bisulfite sequencing for assessment of DNA methylation at base pair resolution.
Francine E Garrett-Bakelman, Caroline K Sheridan, Thadeous J Kacmarczyk, Jennifer Ishii, Doron Betel, Alicia Alonso, Christopher E Mason, Maria E Figueroa, Ari M Melnick. J Vis Exp 2015
76
9

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.
Kasper D Hansen, Benjamin Langmead, Rafael A Irizarry. Genome Biol 2012
407
7

Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias.
Shalima S Nair, Marcel W Coolen, Clare Stirzaker, Jenny Z Song, Aaron L Statham, Dario Strbenac, Mark D Robinson, Susan J Clark. Epigenetics 2011
142
7

DNA methylation and human disease.
Keith D Robertson. Nat Rev Genet 2005
7

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging.
Fumihito Miura, Yusuke Enomoto, Ryo Dairiki, Takashi Ito. Nucleic Acids Res 2012
242
7

Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data.
Nelly Olova, Felix Krueger, Simon Andrews, David Oxley, Rebecca V Berrens, Miguel R Branco, Wolf Reik. Genome Biol 2018
111
7

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
7

epiGBS: reference-free reduced representation bisulfite sequencing.
Thomas P van Gurp, Niels C A M Wagemaker, Björn Wouters, Philippine Vergeer, Joop N J Ouborg, Koen J F Verhoeven. Nat Methods 2016
57
12

Mapping DNA methylation with high-throughput nanopore sequencing.
Arthur C Rand, Miten Jain, Jordan M Eizenga, Audrey Musselman-Brown, Hugh E Olsen, Mark Akeson, Benedict Paten. Nat Methods 2017
226
6

Detecting DNA cytosine methylation using nanopore sequencing.
Jared T Simpson, Rachael E Workman, P C Zuzarte, Matei David, L J Dursi, Winston Timp. Nat Methods 2017
401
6

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.
Thomas A Down, Vardhman K Rakyan, Daniel J Turner, Paul Flicek, Heng Li, Eugene Kulesha, Stefan Gräf, Nathan Johnson, Javier Herrero, Eleni M Tomazou,[...]. Nat Biotechnol 2008
430
6

Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome.
Juan Sandoval, Holger Heyn, Sebastian Moran, Jordi Serra-Musach, Miguel A Pujana, Marina Bibikova, Manel Esteller. Epigenetics 2011
705
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




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.