A citation-based method for searching scientific literature

Yongseok Park, Hao Wu. Bioinformatics 2016
Times Cited: 122







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



Times Cited
  Times     Co-cited
Similarity




Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates.
Hao Wu, Tianlei Xu, Hao Feng, Li Chen, Ben Li, Bing Yao, Zhaohui Qin, Peng Jin, Karen N Conneely. Nucleic Acids Res 2015
121
34

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.
Kasper D Hansen, Benjamin Langmead, Rafael A Irizarry. Genome Biol 2012
344
26

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
708
23


Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
21

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
20

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
19

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
17

MethylSig: a whole genome DNA methylation analysis pipeline.
Yongseok Park, Maria E Figueroa, Laura S Rozek, Maureen A Sartor. Bioinformatics 2014
106
14

Detection of significantly differentially methylated regions in targeted bisulfite sequencing data.
Katja Hebestreit, Martin Dugas, Hans-Ulrich Klein. Bioinformatics 2013
129
13


Gene ontology analysis for RNA-seq: accounting for selection bias.
Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack. Genome Biol 2010
12


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
140
11

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
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
9

metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data.
Frank Jühling, Helene Kretzmer, Stephan H Bernhart, Christian Otto, Peter F Stadler, Steve Hoffmann. Genome Res 2016
128
9

BSMAP: whole genome bisulfite sequence MAPping program.
Yuanxin Xi, Wei Li. BMC Bioinformatics 2009
552
9

Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
9

GREAT improves functional interpretation of cis-regulatory regions.
Cory Y McLean, Dave Bristor, Michael Hiller, Shoa L Clarke, Bruce T Schaar, Craig B Lowe, Aaron M Wenger, Gill Bejerano. Nat Biotechnol 2010
9


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
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
632
8

Genome-wide evolutionary analysis of eukaryotic DNA methylation.
Assaf Zemach, Ivy E McDaniel, Pedro Silva, Daniel Zilberman. Science 2010
965
8


clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
8

annotatr: genomic regions in context.
Raymond G Cavalcante, Maureen A Sartor. Bioinformatics 2017
92
8

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
7

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
7

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
7

HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
7

Epigenetics: a landscape takes shape.
Aaron D Goldberg, C David Allis, Emily Bernstein. Cell 2007
7

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
7

CpG islands and the regulation of transcription.
Aimée M Deaton, Adrian Bird. Genes Dev 2011
6

Reversible switching between epigenetic states in honeybee behavioral subcastes.
Brian R Herb, Florian Wolschin, Kasper D Hansen, Martin J Aryee, Ben Langmead, Rafael Irizarry, Gro V Amdam, Andrew P Feinberg. Nat Neurosci 2012
181
6

Genome-wide and caste-specific DNA methylomes of the ants Camponotus floridanus and Harpegnathos saltator.
Roberto Bonasio, Qiye Li, Jinmin Lian, Navdeep S Mutti, Lijun Jin, Hongmei Zhao, Pei Zhang, Ping Wen, Hui Xiang, Yun Ding,[...]. Curr Biol 2012
208
6

The honey bee epigenomes: differential methylation of brain DNA in queens and workers.
Frank Lyko, Sylvain Foret, Robert Kucharski, Stephan Wolf, Cassandra Falckenhayn, Ryszard Maleszka. PLoS Biol 2010
387
6

Evolution of DNA Methylation across Insects.
Adam J Bewick, Kevin J Vogel, Allen J Moore, Robert J Schmitz. Mol Biol Evol 2017
118
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
284
6

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
6

DNA methylation: roles in mammalian development.
Zachary D Smith, Alexander Meissner. Nat Rev Genet 2013
6


HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
6


Comprehensive analysis of DNA methylation data with RnBeads.
Yassen Assenov, Fabian Müller, Pavlo Lutsik, Jörn Walter, Thomas Lengauer, Christoph Bock. Nat Methods 2014
365
6

Dose-dependent incidence of hepatic tumors in adult mice following perinatal exposure to bisphenol A.
Caren Weinhouse, Olivia S Anderson, Ingrid L Bergin, David J Vandenbergh, Joseph P Gyekis, Marc A Dingman, Jingyun Yang, Dana C Dolinoy. Environ Health Perspect 2014
89
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.