Altuna Akalin, Matthias Kormaksson, Sheng Li, Francine E Garrett-Bakelman, Maria E Figueroa, Ari Melnick, Christopher E Mason. Genome Biol 2012
Times Cited: 909
Times Cited: 909
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
66
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
27
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
22
20
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
17
Dynamics and function of DNA methylation in plants.
Huiming Zhang, Zhaobo Lang, Jian-Kang Zhu. Nat Rev Mol Cell Biol 2018
Huiming Zhang, Zhaobo Lang, Jian-Kang Zhu. Nat Rev Mol Cell Biol 2018
16
Genomation: a toolkit to summarize, annotate and visualize genomic intervals.
Altuna Akalin, Vedran Franke, Kristian Vlahoviček, Christopher E Mason, Dirk Schübeler. Bioinformatics 2015
Altuna Akalin, Vedran Franke, Kristian Vlahoviček, Christopher E Mason, Dirk Schübeler. Bioinformatics 2015
13
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
12
Establishing, maintaining and modifying DNA methylation patterns in plants and animals.
Julie A Law, Steven E Jacobsen. Nat Rev Genet 2010
Julie A Law, Steven E Jacobsen. Nat Rev Genet 2010
12
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
11
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
11
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
10
SLIM: a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures.
Hong-Qiang Wang, Lindsey K Tuominen, Chung-Jui Tsai. Bioinformatics 2011
Hong-Qiang Wang, Lindsey K Tuominen, Chung-Jui Tsai. Bioinformatics 2011
10
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
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
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
9
9
HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
8
fastp: an ultra-fast all-in-one FASTQ preprocessor.
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. Bioinformatics 2018
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. Bioinformatics 2018
8
BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.
Kasper D Hansen, Benjamin Langmead, Rafael A Irizarry. Genome Biol 2012
Kasper D Hansen, Benjamin Langmead, Rafael A Irizarry. Genome Biol 2012
7
Differential methylation analysis for BS-seq data under general experimental design.
Yongseok Park, Hao Wu. Bioinformatics 2016
Yongseok Park, Hao Wu. Bioinformatics 2016
7
Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening.
Silin Zhong, Zhangjun Fei, Yun-Ru Chen, Yi Zheng, Mingyun Huang, Julia Vrebalov, Ryan McQuinn, Nigel Gapper, Bao Liu, Jenny Xiang,[...]. Nat Biotechnol 2013
Silin Zhong, Zhangjun Fei, Yun-Ru Chen, Yi Zheng, Mingyun Huang, Julia Vrebalov, Ryan McQuinn, Nigel Gapper, Bao Liu, Jenny Xiang,[...]. Nat Biotechnol 2013
7
Widespread natural variation of DNA methylation within angiosperms.
Chad E Niederhuth, Adam J Bewick, Lexiang Ji, Magdy S Alabady, Kyung Do Kim, Qing Li, Nicholas A Rohr, Aditi Rambani, John M Burke, Joshua A Udall,[...]. Genome Biol 2016
Chad E Niederhuth, Adam J Bewick, Lexiang Ji, Magdy S Alabady, Kyung Do Kim, Qing Li, Nicholas A Rohr, Aditi Rambani, John M Burke, Joshua A Udall,[...]. Genome Biol 2016
7
A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics.
Qiang Song, Benjamin Decato, Elizabeth E Hong, Meng Zhou, Fang Fang, Jianghan Qu, Tyler Garvin, Michael Kessler, Jun Zhou, Andrew D Smith. PLoS One 2013
Qiang Song, Benjamin Decato, Elizabeth E Hong, Meng Zhou, Fang Fang, Jianghan Qu, Tyler Garvin, Michael Kessler, Jun Zhou, Andrew D Smith. PLoS One 2013
7
DNA methylation and its basic function.
Lisa D Moore, Thuc Le, Guoping Fan. Neuropsychopharmacology 2013
Lisa D Moore, Thuc Le, Guoping Fan. Neuropsychopharmacology 2013
7
Downregulation of RdDM during strawberry fruit ripening.
Jingfei Cheng, Qingfeng Niu, Bo Zhang, Kunsong Chen, Ruihua Yang, Jian-Kang Zhu, Yijing Zhang, Zhaobo Lang. Genome Biol 2018
Jingfei Cheng, Qingfeng Niu, Bo Zhang, Kunsong Chen, Ruihua Yang, Jian-Kang Zhu, Yijing Zhang, Zhaobo Lang. Genome Biol 2018
9
Single-base methylome analysis reveals dynamic epigenomic differences associated with water deficit in apple.
Jidi Xu, Shasha Zhou, Xiaoqing Gong, Yi Song, Steve van Nocker, Fengwang Ma, Qingmei Guan. Plant Biotechnol J 2018
Jidi Xu, Shasha Zhou, Xiaoqing Gong, Yi Song, Steve van Nocker, Fengwang Ma, Qingmei Guan. Plant Biotechnol J 2018
8
Fast and accurate short read alignment with Burrows-Wheeler transform.
Heng Li, Richard Durbin. Bioinformatics 2009
Heng Li, Richard Durbin. Bioinformatics 2009
6
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
6
ViewBS: a powerful toolkit for visualization of high-throughput bisulfite sequencing data.
Xiaosan Huang, Shaoling Zhang, Kongqing Li, Jyothi Thimmapuram, Shaojun Xie, Jonathan Wren. Bioinformatics 2018
Xiaosan Huang, Shaoling Zhang, Kongqing Li, Jyothi Thimmapuram, Shaojun Xie, Jonathan Wren. Bioinformatics 2018
27
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
6
A DEMETER-like DNA demethylase governs tomato fruit ripening.
Ruie Liu, Alexandre How-Kit, Linda Stammitti, Emeline Teyssier, Dominique Rolin, Anne Mortain-Bertrand, Stefanie Halle, Mingchun Liu, Junhua Kong, Chaoqun Wu,[...]. Proc Natl Acad Sci U S A 2015
Ruie Liu, Alexandre How-Kit, Linda Stammitti, Emeline Teyssier, Dominique Rolin, Anne Mortain-Bertrand, Stefanie Halle, Mingchun Liu, Junhua Kong, Chaoqun Wu,[...]. Proc Natl Acad Sci U S A 2015
6
DNA methylation of the gonadal aromatase (cyp19a) promoter is involved in temperature-dependent sex ratio shifts in the European sea bass.
Laia Navarro-Martín, Jordi Viñas, Laia Ribas, Noelia Díaz, Arantxa Gutiérrez, Luciano Di Croce, Francesc Piferrer. PLoS Genet 2011
Laia Navarro-Martín, Jordi Viñas, Laia Ribas, Noelia Díaz, Arantxa Gutiérrez, Luciano Di Croce, Francesc Piferrer. PLoS Genet 2011
6
DNA methylation: roles in mammalian development.
Zachary D Smith, Alexander Meissner. Nat Rev Genet 2013
Zachary D Smith, Alexander Meissner. Nat Rev Genet 2013
6
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
6
ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization.
Guangchuang Yu, Li-Gen Wang, Qing-Yu He. Bioinformatics 2015
Guangchuang Yu, Li-Gen Wang, Qing-Yu He. Bioinformatics 2015
5
Statistical and integrative system-level analysis of DNA methylation data.
Andrew E Teschendorff, Caroline L Relton. Nat Rev Genet 2018
Andrew E Teschendorff, Caroline L Relton. Nat Rev Genet 2018
5
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
Helga Thorvaldsdóttir, James T Robinson, Jill P Mesirov. Brief Bioinform 2013
Helga Thorvaldsdóttir, James T Robinson, Jill P Mesirov. Brief Bioinform 2013
5
Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.
K J Livak, T D Schmittgen. Methods 2001
K J Livak, T D Schmittgen. Methods 2001
5
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
5
5
Epigenetic modification and inheritance in sexual reversal of fish.
Changwei Shao, Qiye Li, Songlin Chen, Pei Zhang, Jinmin Lian, Qiaomu Hu, Bing Sun, Lijun Jin, Shanshan Liu, Zongji Wang,[...]. Genome Res 2014
Changwei Shao, Qiye Li, Songlin Chen, Pei Zhang, Jinmin Lian, Qiaomu Hu, Bing Sun, Lijun Jin, Shanshan Liu, Zongji Wang,[...]. Genome Res 2014
5
DNA methylation landscapes: provocative insights from epigenomics.
Miho M Suzuki, Adrian Bird. Nat Rev Genet 2008
Miho M Suzuki, Adrian Bird. Nat Rev Genet 2008
5
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
5
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
Hongcang Gu, Zachary D Smith, Christoph Bock, Patrick Boyle, Andreas Gnirke, Alexander Meissner. Nat Protoc 2011
5
ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase.
Zhizhong Gong, Teresa Morales-Ruiz, Rafael R Ariza, Teresa Roldán-Arjona, Lisa David, Jian Kang Zhu. Cell 2002
Zhizhong Gong, Teresa Morales-Ruiz, Rafael R Ariza, Teresa Roldán-Arjona, Lisa David, Jian Kang Zhu. Cell 2002
5
Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit.
Zhaobo Lang, Yihai Wang, Kai Tang, Dengguo Tang, Tatsiana Datsenka, Jingfei Cheng, Yijing Zhang, Avtar K Handa, Jian-Kang Zhu. Proc Natl Acad Sci U S A 2017
Zhaobo Lang, Yihai Wang, Kai Tang, Dengguo Tang, Tatsiana Datsenka, Jingfei Cheng, Yijing Zhang, Avtar K Handa, Jian-Kang Zhu. Proc Natl Acad Sci U S A 2017
5
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
5
Widespread dynamic DNA methylation in response to biotic stress.
Robert H Dowen, Mattia Pelizzola, Robert J Schmitz, Ryan Lister, Jill M Dowen, Joseph R Nery, Jack E Dixon, Joseph R Ecker. Proc Natl Acad Sci U S A 2012
Robert H Dowen, Mattia Pelizzola, Robert J Schmitz, Ryan Lister, Jill M Dowen, Joseph R Nery, Jack E Dixon, Joseph R Ecker. Proc Natl Acad Sci U S A 2012
5
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nucleic Acids Res 2009
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nucleic Acids Res 2009
5
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.