Weilong Guo, Petko Fiziev, Weihong Yan, Shawn Cokus, Xueguang Sun, Michael Q Zhang, Pao-Yang Chen, Matteo Pellegrini. BMC Genomics 2013
Times Cited: 238
Times Cited: 238
Times Cited
Times Co-cited
Similarity
38
CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data.
Weilong Guo, Ping Zhu, Matteo Pellegrini, Michael Q Zhang, Xiangfeng Wang, Zhongfu Ni. Bioinformatics 2018
Weilong Guo, Ping Zhu, Matteo Pellegrini, Michael Q Zhang, Xiangfeng Wang, Zhongfu Ni. Bioinformatics 2018
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Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.
Felix Krueger, Simon R Andrews. Bioinformatics 2011
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The Sequence Alignment/Map format and SAMtools.
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methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles.
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Establishing, maintaining and modifying DNA methylation patterns in plants and animals.
Julie A Law, Steven E Jacobsen. Nat Rev Genet 2010
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BEDTools: a flexible suite of utilities for comparing genomic features.
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Fast and accurate short read alignment with Burrows-Wheeler transform.
Heng Li, Richard Durbin. Bioinformatics 2009
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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
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Trimmomatic: a flexible trimmer for Illumina sequence data.
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Assaf Zemach, Ivy E McDaniel, Pedro Silva, Daniel Zilberman. Science 2010
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Human DNA methylomes at base resolution show widespread epigenomic differences.
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BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.
Kasper D Hansen, Benjamin Langmead, Rafael A Irizarry. Genome Biol 2012
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Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
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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
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A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.
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BS Seeker: precise mapping for bisulfite sequencing.
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Functions of DNA methylation: islands, start sites, gene bodies and beyond.
Peter A Jones. Nat Rev Genet 2012
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BS-Seeker3: ultrafast pipeline for bisulfite sequencing.
Kevin Yu Yuan Huang, Yan-Jiun Huang, Pao-Yang Chen. BMC Bioinformatics 2018
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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
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Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley, Steven L Salzberg. Genome Biol 2013
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HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
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Highly integrated single-base resolution maps of the epigenome in Arabidopsis.
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The diverse roles of DNA methylation in mammalian development and disease.
Maxim V C Greenberg, Deborah Bourc'his. Nat Rev Mol Cell Biol 2019
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HISAT: a fast spliced aligner with low memory requirements.
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8
DNA methylation and its basic function.
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8
Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity.
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The GEM mapper: fast, accurate and versatile alignment by filtration.
Santiago Marco-Sola, Michael Sammeth, Roderic Guigó, Paolo Ribeca. Nat Methods 2012
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Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis.
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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
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Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis.
Hume Stroud, Truman Do, Jiamu Du, Xuehua Zhong, Suhua Feng, Lianna Johnson, Dinshaw J Patel, Steven E Jacobsen. Nat Struct Mol Biol 2014
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deepTools: a flexible platform for exploring deep-sequencing data.
Fidel Ramírez, Friederike Dündar, Sarah Diehl, Björn A Grüning, Thomas Manke. Nucleic Acids Res 2014
Fidel Ramírez, Friederike Dündar, Sarah Diehl, Björn A Grüning, Thomas Manke. Nucleic Acids Res 2014
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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
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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
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Profiling genome-wide DNA methylation.
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metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data.
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Frank Jühling, Helene Kretzmer, Stephan H Bernhart, Christian Otto, Peter F Stadler, Steve Hoffmann. Genome Res 2016
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Objective and comprehensive evaluation of bisulfite short read mapping tools.
Hong Tran, Jacob Porter, Ming-An Sun, Hehuang Xie, Liqing Zhang. Adv Bioinformatics 2014
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DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.
Manu J Dubin, Pei Zhang, Dazhe Meng, Marie-Stanislas Remigereau, Edward J Osborne, Francesco Paolo Casale, Philipp Drewe, André Kahles, Geraldine Jean, Bjarni Vilhjálmsson,[...]. Elife 2015
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The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
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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
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The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin.
Assaf Zemach, M Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor Eshed-Williams, Ka Thao, Stacey L Harmer, Daniel Zilberman. Cell 2013
Assaf Zemach, M Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor Eshed-Williams, Ka Thao, Stacey L Harmer, Daniel Zilberman. Cell 2013
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MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing.
Mark A Urich, Joseph R Nery, Ryan Lister, Robert J Schmitz, Joseph R Ecker. Nat Protoc 2015
Mark A Urich, Joseph R Nery, Ryan Lister, Robert J Schmitz, Joseph R Ecker. Nat Protoc 2015
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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
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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
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Sambamba: fast processing of NGS alignment formats.
Artem Tarasov, Albert J Vilella, Edwin Cuppen, Isaac J Nijman, Pjotr Prins. Bioinformatics 2015
Artem Tarasov, Albert J Vilella, Edwin Cuppen, Isaac J Nijman, Pjotr Prins. Bioinformatics 2015
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.