A citation-based method for searching scientific literature

Raymond G Cavalcante, Maureen A Sartor. Bioinformatics 2017
Times Cited: 92







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



Times Cited
  Times     Co-cited
Similarity



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
22

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

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
17

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
16

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
15

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
15

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
15


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
14

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
13


Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
11

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
10


BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.
Kasper D Hansen, Benjamin Langmead, Rafael A Irizarry. Genome Biol 2012
344
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
9

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
8


regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.
Bernat Gel, Anna Díez-Villanueva, Eduard Serra, Marcus Buschbeck, Miguel A Peinado, Roberto Malinverni. Bioinformatics 2016
143
8


MultiQC: summarize analysis results for multiple tools and samples in a single report.
Philip Ewels, Måns Magnusson, Sverker Lundin, Max Käller. Bioinformatics 2016
7

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
7

Enhanced reduced representation bisulfite sequencing for assessment of DNA methylation at base pair resolution.
Francine E Garrett-Bakelman, Caroline K Sheridan, Thadeous J Kacmarczyk, Jennifer Ishii, Doron Betel, Alicia Alonso, Christopher E Mason, Maria E Figueroa, Ari M Melnick. J Vis Exp 2015
64
10

The NIEHS TaRGET II Consortium and environmental epigenomics.
Ting Wang, Erica C Pehrsson, Deepak Purushotham, Daofeng Li, Xiaoyu Zhuo, Bo Zhang, Heather A Lawson, Michael A Province, Christopher Krapp, Yemin Lan,[...]. Nat Biotechnol 2018
33
21



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
7


ChIP-Enrich: gene set enrichment testing for ChIP-seq data.
Ryan P Welch, Chee Lee, Paul M Imbriano, Snehal Patil, Terry E Weymouth, R Alex Smith, Laura J Scott, Maureen A Sartor. Nucleic Acids Res 2014
61
9



Editing DNA Methylation in the Mammalian Genome.
X Shawn Liu, Hao Wu, Xiong Ji, Yonatan Stelzer, Xuebing Wu, Szymon Czauderna, Jian Shu, Daniel Dadon, Richard A Young, Rudolf Jaenisch. Cell 2016
549
6

An atlas of active enhancers across human cell types and tissues.
Robin Andersson, Claudia Gebhard, Irene Miguel-Escalada, Ilka Hoof, Jette Bornholdt, Mette Boyd, Yun Chen, Xiaobei Zhao, Christian Schmidl, Takahiro Suzuki,[...]. Nature 2014
6

deepTools2: a next generation web server for deep-sequencing data analysis.
Fidel Ramírez, Devon P Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S Richter, Steffen Heyne, Friederike Dündar, Thomas Manke. Nucleic Acids Res 2016
6

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
33
18

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
6


Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling.
Ruth Pidsley, Elena Zotenko, Timothy J Peters, Mitchell G Lawrence, Gail P Risbridger, Peter Molloy, Susan Van Djik, Beverly Muhlhausler, Clare Stirzaker, Susan J Clark. Genome Biol 2016
378
5

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
5

BSMAP: whole genome bisulfite sequence MAPping program.
Yuanxin Xi, Wei Li. BMC Bioinformatics 2009
552
5

DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos.
Daniel M Messerschmidt, Barbara B Knowles, Davor Solter. Genes Dev 2014
353
5

Comprehensive analysis of DNA methylation data with RnBeads.
Yassen Assenov, Fabian Müller, Pavlo Lutsik, Jörn Walter, Thomas Lengauer, Christoph Bock. Nat Methods 2014
365
5

Longitudinal Effects of Developmental Bisphenol A Exposure on Epigenome-Wide DNA Hydroxymethylation at Imprinted Loci in Mouse Blood.
Joseph J Kochmanski, Elizabeth H Marchlewicz, Raymond G Cavalcante, Bambarendage P U Perera, Maureen A Sartor, Dana C Dolinoy. Environ Health Perspect 2018
16
31

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing.
Michael J Ziller, Kasper D Hansen, Alexander Meissner, Martin J Aryee. Nat Methods 2015
136
5

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
5

A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
Suhas S P Rao, Miriam H Huntley, Neva C Durand, Elena K Stamenova, Ivan D Bochkov, James T Robinson, Adrian L Sanborn, Ido Machol, Arina D Omer, Eric S Lander,[...]. Cell 2014
5



Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling.
Patrick Boyle, Kendell Clement, Hongcang Gu, Zachary D Smith, Michael Ziller, Jennifer L Fostel, Laurie Holmes, Jim Meldrim, Fontina Kelley, Andreas Gnirke,[...]. Genome Biol 2012
156
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.