Kasper D Hansen, Benjamin Langmead, Rafael A Irizarry. Genome Biol 2012
Times Cited: 407
Times Cited: 407
Times Cited
Times Co-cited
Similarity
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.
Felix Krueger, Simon R Andrews. Bioinformatics 2011
Felix Krueger, Simon R Andrews. Bioinformatics 2011
69
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
Altuna Akalin, Matthias Kormaksson, Sheng Li, Francine E Garrett-Bakelman, Maria E Figueroa, Ari Melnick, Christopher E Mason. Genome Biol 2012
23
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
23
19
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
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
18
Detection and accurate false discovery rate control of differentially methylated regions from whole genome bisulfite sequencing.
Keegan Korthauer, Sutirtha Chakraborty, Yuval Benjamini, Rafael A Irizarry. Biostatistics 2019
Keegan Korthauer, Sutirtha Chakraborty, Yuval Benjamini, Rafael A Irizarry. Biostatistics 2019
28
Differential methylation analysis for BS-seq data under general experimental design.
Yongseok Park, Hao Wu. Bioinformatics 2016
Yongseok Park, Hao Wu. Bioinformatics 2016
17
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
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
16
Functions of DNA methylation: islands, start sites, gene bodies and beyond.
Peter A Jones. Nat Rev Genet 2012
Peter A Jones. Nat Rev Genet 2012
15
BEDTools: a flexible suite of utilities for comparing genomic features.
Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
14
Detection of significantly differentially methylated regions in targeted bisulfite sequencing data.
Katja Hebestreit, Martin Dugas, Hans-Ulrich Klein. Bioinformatics 2013
Katja Hebestreit, Martin Dugas, Hans-Ulrich Klein. Bioinformatics 2013
13
A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data.
Hao Feng, Karen N Conneely, Hao Wu. Nucleic Acids Res 2014
Hao Feng, Karen N Conneely, Hao Wu. Nucleic Acids Res 2014
13
MultiQC: summarize analysis results for multiple tools and samples in a single report.
Philip Ewels, Måns Magnusson, Sverker Lundin, Max Käller. Bioinformatics 2016
Philip Ewels, Måns Magnusson, Sverker Lundin, Max Käller. Bioinformatics 2016
13
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
Martin J Aryee, Andrew E Jaffe, Hector Corrada-Bravo, Christine Ladd-Acosta, Andrew P Feinberg, Kasper D Hansen, Rafael A Irizarry. Bioinformatics 2014
13
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
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
12
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
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
12
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
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
12
Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging.
Fumihito Miura, Yusuke Enomoto, Ryo Dairiki, Takashi Ito. Nucleic Acids Res 2012
Fumihito Miura, Yusuke Enomoto, Ryo Dairiki, Takashi Ito. Nucleic Acids Res 2012
11
Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
11
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
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
10
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
Deqiang Sun, Yuanxin Xi, Benjamin Rodriguez, Hyun Jung Park, Pan Tong, Mira Meong, Margaret A Goodell, Wei Li. Genome Biol 2014
10
MethylSig: a whole genome DNA methylation analysis pipeline.
Yongseok Park, Maria E Figueroa, Laura S Rozek, Maureen A Sartor. Bioinformatics 2014
Yongseok Park, Maria E Figueroa, Laura S Rozek, Maureen A Sartor. Bioinformatics 2014
10
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
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
10
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
Cory Y McLean, Dave Bristor, Michael Hiller, Shoa L Clarke, Bruce T Schaar, Craig B Lowe, Aaron M Wenger, Gill Bejerano. Nat Biotechnol 2010
10
DNA methylation: roles in mammalian development.
Zachary D Smith, Alexander Meissner. Nat Rev Genet 2013
Zachary D Smith, Alexander Meissner. Nat Rev Genet 2013
10
10
10
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
Frank Jühling, Helene Kretzmer, Stephan H Bernhart, Christian Otto, Peter F Stadler, Steve Hoffmann. Genome Res 2016
10
Strategies for analyzing bisulfite sequencing data.
Katarzyna Wreczycka, Alexander Gosdschan, Dilmurat Yusuf, Björn Grüning, Yassen Assenov, Altuna Akalin. J Biotechnol 2017
Katarzyna Wreczycka, Alexander Gosdschan, Dilmurat Yusuf, Björn Grüning, Yassen Assenov, Altuna Akalin. J Biotechnol 2017
15
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
Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth. Nucleic Acids Res 2015
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
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
9
Model-based analysis of ChIP-Seq (MACS).
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
9
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.
Yang Liao, Gordon K Smyth, Wei Shi. Bioinformatics 2014
Yang Liao, Gordon K Smyth, Wei Shi. Bioinformatics 2014
9
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
Weilong Guo, Petko Fiziev, Weihong Yan, Shawn Cokus, Xueguang Sun, Michael Q Zhang, Pao-Yang Chen, Matteo Pellegrini. BMC Genomics 2013
9
Software for computing and annotating genomic ranges.
Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin T Morgan, Vincent J Carey. PLoS Comput Biol 2013
Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin T Morgan, Vincent J Carey. PLoS Comput Biol 2013
9
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
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
8
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
Nelly Olova, Felix Krueger, Simon Andrews, David Oxley, Rebecca V Berrens, Miguel R Branco, Wolf Reik. Genome Biol 2018
8
Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex.
Chongyuan Luo, Christopher L Keown, Laurie Kurihara, Jingtian Zhou, Yupeng He, Junhao Li, Rosa Castanon, Jacinta Lucero, Joseph R Nery, Justin P Sandoval,[...]. Science 2017
Chongyuan Luo, Christopher L Keown, Laurie Kurihara, Jingtian Zhou, Yupeng He, Junhao Li, Rosa Castanon, Jacinta Lucero, Joseph R Nery, Justin P Sandoval,[...]. Science 2017
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
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
8
Fast and accurate short read alignment with Burrows-Wheeler transform.
Heng Li, Richard Durbin. Bioinformatics 2009
Heng Li, Richard Durbin. Bioinformatics 2009
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
Ryan Lister, Ronan C O'Malley, Julian Tonti-Filippini, Brian D Gregory, Charles C Berry, A Harvey Millar, Joseph R Ecker. Cell 2008
8
clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
7
Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain.
Junjie U Guo, Yijing Su, Joo Heon Shin, Jaehoon Shin, Hongda Li, Bin Xie, Chun Zhong, Shaohui Hu, Thuc Le, Guoping Fan,[...]. Nat Neurosci 2014
Junjie U Guo, Yijing Su, Joo Heon Shin, Jaehoon Shin, Hongda Li, Bin Xie, Chun Zhong, Shaohui Hu, Thuc Le, Guoping Fan,[...]. Nat Neurosci 2014
7
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
Alexander Meissner, Andreas Gnirke, George W Bell, Bernard Ramsahoye, Eric S Lander, Rudolf Jaenisch. Nucleic Acids Res 2005
7
LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor.
Nathan C Sheffield, Christoph Bock. Bioinformatics 2016
Nathan C Sheffield, Christoph Bock. Bioinformatics 2016
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
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
Complex heatmaps reveal patterns and correlations in multidimensional genomic data.
Zuguang Gu, Roland Eils, Matthias Schlesner. Bioinformatics 2016
Zuguang Gu, Roland Eils, Matthias Schlesner. Bioinformatics 2016
7
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.