A citation-based method for searching scientific literature

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
Times Cited: 137







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



Times Cited
  Times     Co-cited
Similarity


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
84
35

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
702
27

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
27

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
25

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
105
22

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
600
22

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
22

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

Degradation of DNA by bisulfite treatment.
Kazuo Tanaka, Akimitsu Okamoto. Bioorg Med Chem Lett 2007
122
20

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
18

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
375
16

DNA methylation: roles in mammalian development.
Zachary D Smith, Alexander Meissner. Nat Rev Genet 2013
16

Accurate targeted long-read DNA methylation and hydroxymethylation sequencing with TAPS.
Yibin Liu, Jingfei Cheng, Paulina Siejka-Zielińska, Carika Weldon, Hannah Roberts, Maria Lopopolo, Andrea Magri, Valentina D'Arienzo, James M Harris, Jane A McKeating,[...]. Genome Biol 2020
30
53

Mapping the epigenetic modifications of DNA and RNA.
Lin-Yong Zhao, Jinghui Song, Yibin Liu, Chun-Xiao Song, Chengqi Yi. Protein Cell 2020
77
20

Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale.
Bo Xia, Dali Han, Xingyu Lu, Zhaozhu Sun, Ankun Zhou, Qiangzong Yin, Hu Zeng, Menghao Liu, Xiang Jiang, Wei Xie,[...]. Nat Methods 2015
86
17

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
596
15

The diverse roles of DNA methylation in mammalian development and disease.
Maxim V C Greenberg, Deborah Bourc'his. Nat Rev Mol Cell Biol 2019
653
15



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
202
14

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
820
14

Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution.
Zhiyi Sun, Romualdas Vaisvila, Laura-Madison Hussong, Bo Yan, Chloé Baum, Lana Saleh, Mala Samaranayake, Shengxi Guan, Nan Dai, Ivan R Corrêa,[...]. Genome Res 2021
26
53

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
215
13

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
687
13

Bisulfite-Free, Nanoscale Analysis of 5-Hydroxymethylcytosine at Single Base Resolution.
Hu Zeng, Bo He, Bo Xia, Dongsheng Bai, Xingyu Lu, Jiabin Cai, Lei Chen, Ankun Zhou, Chenxu Zhu, Haowei Meng,[...]. J Am Chem Soc 2018
40
32

Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA.
Romualdas Vaisvila, V K Chaithanya Ponnaluri, Zhiyi Sun, Bradley W Langhorst, Lana Saleh, Shengxi Guan, Nan Dai, Matthew A Campbell, Brittany S Sexton, Katherine Marks,[...]. Genome Res 2021
31
41

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
721
12

Sensitive tumour detection and classification using plasma cell-free DNA methylomes.
Shu Yi Shen, Rajat Singhania, Gordon Fehringer, Ankur Chakravarthy, Michael H A Roehrl, Dianne Chadwick, Philip C Zuzarte, Ayelet Borgida, Ting Ting Wang, Tiantian Li,[...]. Nature 2018
366
12


DNA methylation and its basic function.
Lisa D Moore, Thuc Le, Guoping Fan. Neuropsychopharmacology 2013
11

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
11

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
11

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
453
10

Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming.
Chun-Xiao Song, Keith E Szulwach, Qing Dai, Ye Fu, Shi-Qing Mao, Li Lin, Craig Street, Yujing Li, Mickael Poidevin, Hao Wu,[...]. Cell 2013
378
10

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
511
10

Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution.
Yibin Liu, Zhiyuan Hu, Jingfei Cheng, Paulina Siejka-Zielińska, Jinfeng Chen, Masato Inoue, Ahmed Ashour Ahmed, Chun-Xiao Song. Nat Commun 2021
14
71


Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution.
Michael J Booth, Giovanni Marsico, Martin Bachman, Dario Beraldi, Shankar Balasubramanian. Nat Chem 2014
137
9

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
599
9

5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages.
Chun-Xiao Song, Senlin Yin, Li Ma, Amanda Wheeler, Yu Chen, Yan Zhang, Bin Liu, Junjie Xiong, Weihan Zhang, Jiankun Hu,[...]. Cell Res 2017
124
9


Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging.
Fumihito Miura, Yusuke Enomoto, Ryo Dairiki, Takashi Ito. Nucleic Acids Res 2012
239
9

Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data.
Qian Liu, Li Fang, Guoliang Yu, Depeng Wang, Chuan-Le Xiao, Kai Wang. Nat Commun 2019
114
8

Single-Cell 5-Formylcytosine Landscapes of Mammalian Early Embryos and ESCs at Single-Base Resolution.
Chenxu Zhu, Yun Gao, Hongshan Guo, Bo Xia, Jinghui Song, Xinglong Wu, Hu Zeng, Kehkooi Kee, Fuchou Tang, Chengqi Yi. Cell Stem Cell 2017
84
9

Dynamic DNA methylation: In the right place at the right time.
Chongyuan Luo, Petra Hajkova, Joseph R Ecker. Science 2018
266
8

DNA methylation in mammals.
En Li, Yi Zhang. Cold Spring Harb Perspect Biol 2014
472
8


BSMAP: whole genome bisulfite sequence MAPping program.
Yuanxin Xi, Wei Li. BMC Bioinformatics 2009
653
8

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
8



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.