A citation-based method for searching scientific literature

Kevin Yu Yuan Huang, Yan-Jiun Huang, Pao-Yang Chen. BMC Bioinformatics 2018
Times Cited: 21







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



Times Cited
  Times     Co-cited
Similarity



BSMAP: whole genome bisulfite sequence MAPping program.
Yuanxin Xi, Wei Li. BMC Bioinformatics 2009
653
76

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
42

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
233
38

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
33

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.
Kasper D Hansen, Benjamin Langmead, Rafael A Irizarry. Genome Biol 2012
399
33

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
33

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
33

BS Seeker: precise mapping for bisulfite sequencing.
Pao-Yang Chen, Shawn J Cokus, Matteo Pellegrini. BMC Bioinformatics 2010
158
28

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
885
28

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg. Genome Biol 2009
28

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
28

Profiling genome-wide DNA methylation.
Wai-Shin Yong, Fei-Man Hsu, Pao-Yang Chen. Epigenetics Chromatin 2016
142
28

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
28

MOABS: model based analysis of bisulfite sequencing data.
Deqiang Sun, Yuanxin Xi, Benjamin Rodriguez, Hyun Jung Park, Pan Tong, Mira Meong, Margaret A Goodell, Wei Li. Genome Biol 2014
164
23


Bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data.
Osvaldo Graña, Hugo López-Fernández, Florentino Fdez-Riverola, David González Pisano, Daniel Glez-Peña. Bioinformatics 2018
13
38

Human body epigenome maps reveal noncanonical DNA methylation variation.
Matthew D Schultz, Yupeng He, John W Whitaker, Manoj Hariharan, Eran A Mukamel, Danny Leung, Nisha Rajagopal, Joseph R Nery, Mark A Urich, Huaming Chen,[...]. Nature 2015
376
23

DNA methylation and its basic function.
Lisa D Moore, Thuc Le, Guoping Fan. Neuropsychopharmacology 2013
23

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
23

CpG islands and the regulation of transcription.
Aimée M Deaton, Adrian Bird. Genes Dev 2011
19


Methodological aspects of whole-genome bisulfite sequencing analysis.
Swarnaseetha Adusumalli, Mohd Feroz Mohd Omar, Richie Soong, Touati Benoukraf. Brief Bioinform 2015
50
19

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
19

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
19


METHimpute: imputation-guided construction of complete methylomes from WGBS data.
Aaron Taudt, David Roquis, Amaryllis Vidalis, René Wardenaar, Frank Johannes, Maria Colomé-Tatché. BMC Genomics 2018
14
28

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging.
Fumihito Miura, Yusuke Enomoto, Ryo Dairiki, Takashi Ito. Nucleic Acids Res 2012
239
19

Single-cell DNA methylome sequencing of human preimplantation embryos.
Ping Zhu, Hongshan Guo, Yixin Ren, Yu Hou, Ji Dong, Rong Li, Ying Lian, Xiaoying Fan, Boqiang Hu, Yun Gao,[...]. Nat Genet 2018
151
19

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
137
19

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
19


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

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR.
Yunshun Chen, Bhupinder Pal, Jane E Visvader, Gordon K Smyth. F1000Res 2017
35
14

Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis.
Pan Du, Xiao Zhang, Chiang-Ching Huang, Nadereh Jafari, Warren A Kibbe, Lifang Hou, Simon M Lin. BMC Bioinformatics 2010
14


MethylCoder: software pipeline for bisulfite-treated sequences.
Brent Pedersen, Tzung-Fu Hsieh, Christian Ibarra, Robert L Fischer. Bioinformatics 2011
48
14

Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing.
Hongshan Guo, Ping Zhu, Fan Guo, Xianlong Li, Xinglong Wu, Xiaoying Fan, Lu Wen, Fuchou Tang. Nat Protoc 2015
100
14

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
14

DNA methylome analysis using short bisulfite sequencing data.
Felix Krueger, Benjamin Kreck, Andre Franke, Simon R Andrews. Nat Methods 2012
219
14

Role for DNA methylation in genomic imprinting.
E Li, C Beard, R Jaenisch. Nature 1993
14

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
14


WALT: fast and accurate read mapping for bisulfite sequencing.
Haifeng Chen, Andrew D Smith, Ting Chen. Bioinformatics 2016
37
14

Patterns of population epigenomic diversity.
Robert J Schmitz, Matthew D Schultz, Mark A Urich, Joseph R Nery, Mattia Pelizzola, Ondrej Libiger, Andrew Alix, Richard B McCosh, Huaming Chen, Nicholas J Schork,[...]. Nature 2013
338
14

BRAT-nova: fast and accurate mapping of bisulfite-treated reads.
Elena Y Harris, Rachid Ounit, Stefano Lonardi. Bioinformatics 2016
8
37

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing.
Michael J Ziller, Kasper D Hansen, Alexander Meissner, Martin J Aryee. Nat Methods 2015
155
14

DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts.
Marco Catoni, Jonathan Mf Tsang, Alessandro P Greco, Nicolae Radu Zabet. Nucleic Acids Res 2018
34
14

DNA Methylation Analysis: Choosing the Right Method.
Sergey Kurdyukov, Martyn Bullock. Biology (Basel) 2016
314
14

CpG islands in vertebrate genomes.
M Gardiner-Garden, M Frommer. J Mol Biol 1987
14


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.