A citation-based method for searching scientific literature

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
Times Cited: 2199







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



Times Cited
  Times     Co-cited
Similarity



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
20

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
18

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
18

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
659
17

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
121
16

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
784
16

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
16

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
16

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
14

DNA methylation: roles in mammalian development.
Zachary D Smith, Alexander Meissner. Nat Rev Genet 2013
14


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
584
13

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

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
342
12

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
92
11


The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing.
Yun Huang, William A Pastor, Yinghua Shen, Mamta Tahiliani, David R Liu, Anjana Rao. PLoS One 2010
505
10

BSMAP: whole genome bisulfite sequence MAPping program.
Yuanxin Xi, Wei Li. BMC Bioinformatics 2009
614
10

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.
Kasper D Hansen, Benjamin Langmead, Rafael A Irizarry. Genome Biol 2012
377
9

High sensitivity mapping of methylated cytosines.
S J Clark, J Harrison, C L Paul, M Frommer. Nucleic Acids Res 1994
9

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
563
9


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

DNA methylation and human disease.
Keith D Robertson. Nat Rev Genet 2005
9

Degradation of DNA by bisulfite treatment.
Kazuo Tanaka, Akimitsu Okamoto. Bioorg Med Chem Lett 2007
118
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


Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase.
Emily K Schutsky, Jamie E DeNizio, Peng Hu, Monica Yun Liu, Christopher S Nabel, Emily B Fabyanic, Young Hwang, Frederic D Bushman, Hao Wu, Rahul M Kohli. Nat Biotechnol 2018
74
10

Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome.
Miao Yu, Gary C Hon, Keith E Szulwach, Chun-Xiao Song, Liang Zhang, Audrey Kim, Xuekun Li, Qing Dai, Yin Shen, Beomseok Park,[...]. Cell 2012
684
8


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
813
8

Highly integrated single-base resolution maps of the epigenome in Arabidopsis.
Ryan Lister, Ronan C O'Malley, Julian Tonti-Filippini, Brian D Gregory, Charles C Berry, A Harvey Millar, Joseph R Ecker. Cell 2008
8

The diverse roles of DNA methylation in mammalian development and disease.
Maxim V C Greenberg, Deborah Bourc'his. Nat Rev Mol Cell Biol 2019
543
8

MethyLight: a high-throughput assay to measure DNA methylation.
C A Eads, K D Danenberg, K Kawakami, L B Saltz, C Blake, D Shibata, P V Danenberg, P W Laird. Nucleic Acids Res 2000
7

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
197
7

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
194
7

Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification.
Shinsuke Ito, Ana C D'Alessio, Olena V Taranova, Kwonho Hong, Lawrence C Sowers, Yi Zhang. Nature 2010
7

Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates.
Daniel Globisch, Martin Münzel, Markus Müller, Stylianos Michalakis, Mirko Wagner, Susanne Koch, Tobias Brückl, Martin Biel, Thomas Carell. PLoS One 2010
585
7


Genome-wide DNA methylation profiling using Infinium® assay.
Marina Bibikova, Jennie Le, Bret Barnes, Shadi Saedinia-Melnyk, Lixin Zhou, Richard Shen, Kevin L Gunderson. Epigenomics 2009
404
7

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
7

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging.
Fumihito Miura, Yusuke Enomoto, Ryo Dairiki, Takashi Ito. Nucleic Acids Res 2012
227
7

BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data.
Weilong Guo, Petko Fiziev, Weihong Yan, Shawn Cokus, Xueguang Sun, Michael Q Zhang, Pao-Yang Chen, Matteo Pellegrini. BMC Genomics 2013
223
7

Detection of significantly differentially methylated regions in targeted bisulfite sequencing data.
Katja Hebestreit, Martin Dugas, Hans-Ulrich Klein. Bioinformatics 2013
137
6

Strategies for analyzing bisulfite sequencing data.
Katarzyna Wreczycka, Alexander Gosdschan, Dilmurat Yusuf, Björn Grüning, Yassen Assenov, Altuna Akalin. J Biotechnol 2017
58
10


Genome-wide evolutionary analysis of eukaryotic DNA methylation.
Assaf Zemach, Ivy E McDaniel, Pedro Silva, Daniel Zilberman. Science 2010
6

Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine.
Miao Yu, Gary C Hon, Keith E Szulwach, Chun-Xiao Song, Peng Jin, Bing Ren, Chuan He. Nat Protoc 2012
148
6

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine.
Chun-Xiao Song, Keith E Szulwach, Ye Fu, Qing Dai, Chengqi Yi, Xuekun Li, Yujing Li, Chih-Hsin Chen, Wen Zhang, Xing Jian,[...]. Nat Biotechnol 2011
705
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.