A citation-based method for searching scientific literature

Sam Griffiths-Jones, Harpreet Kaur Saini, Stijn van Dongen, Anton J Enright. Nucleic Acids Res 2008
Times Cited: 3149







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



Times Cited
  Times     Co-cited
Similarity


miRBase: microRNA sequences, targets and gene nomenclature.
Sam Griffiths-Jones, Russell J Grocock, Stijn van Dongen, Alex Bateman, Anton J Enright. Nucleic Acids Res 2006
26

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
22

miRBase: integrating microRNA annotation and deep-sequencing data.
Ana Kozomara, Sam Griffiths-Jones. Nucleic Acids Res 2011
19

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades.
Marc R Friedländer, Sebastian D Mackowiak, Na Li, Wei Chen, Nikolaus Rajewsky. Nucleic Acids Res 2012
18

The microRNA Registry.
Sam Griffiths-Jones. Nucleic Acids Res 2004
17


miRBase: from microRNA sequences to function.
Ana Kozomara, Maria Birgaoanu, Sam Griffiths-Jones. Nucleic Acids Res 2019
17


miRBase: annotating high confidence microRNAs using deep sequencing data.
Ana Kozomara, Sam Griffiths-Jones. Nucleic Acids Res 2014
14


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
13

Rfam: an RNA family database.
Sam Griffiths-Jones, Alex Bateman, Mhairi Marshall, Ajay Khanna, Sean R Eddy. Nucleic Acids Res 2003
893
12

Predicting effective microRNA target sites in mammalian mRNAs.
Vikram Agarwal, George W Bell, Jin-Wu Nam, David P Bartel. Elife 2015
12

MicroRNA targets in Drosophila.
Anton J Enright, Bino John, Ulrike Gaul, Thomas Tuschl, Chris Sander, Debora S Marks. Genome Biol 2003
10

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
9

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
8

Most mammalian mRNAs are conserved targets of microRNAs.
Robin C Friedman, Kyle Kai-How Farh, Christopher B Burge, David P Bartel. Genome Res 2009
7

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

DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions.
Dimitra Karagkouni, Maria D Paraskevopoulou, Serafeim Chatzopoulos, Ioannis S Vlachos, Spyros Tastsoglou, Ilias Kanellos, Dimitris Papadimitriou, Ioannis Kavakiotis, Sofia Maniou, Giorgos Skoufos,[...]. Nucleic Acids Res 2018
398
7

Combinatorial microRNA target predictions.
Azra Krek, Dominic Grün, Matthew N Poy, Rachel Wolf, Lauren Rosenberg, Eric J Epstein, Philip MacMenamin, Isabelle da Piedade, Kristin C Gunsalus, Markus Stoffel,[...]. Nat Genet 2005
7

miRTarBase: a database curates experimentally validated microRNA-target interactions.
Sheng-Da Hsu, Feng-Mao Lin, Wei-Yun Wu, Chao Liang, Wei-Chih Huang, Wen-Ling Chan, Wen-Ting Tsai, Goun-Zhou Chen, Chia-Jung Lee, Chih-Min Chiu,[...]. Nucleic Acids Res 2011
822
7


Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
6

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
6

miRecords: an integrated resource for microRNA-target interactions.
Feifei Xiao, Zhixiang Zuo, Guoshuai Cai, Shuli Kang, Xiaolian Gao, Tongbin Li. Nucleic Acids Res 2009
995
6


Differential expression analysis for sequence count data.
Simon Anders, Wolfgang Huber. Genome Biol 2010
5

miRNA Target Prediction in Plants.
Noah Fahlgren, James C Carrington. Methods Mol Biol 2010
144
5

Real-time quantification of microRNAs by stem-loop RT-PCR.
Caifu Chen, Dana A Ridzon, Adam J Broomer, Zhaohui Zhou, Danny H Lee, Julie T Nguyen, Maura Barbisin, Nan Lan Xu, Vikram R Mahuvakar, Mark R Andersen,[...]. Nucleic Acids Res 2005
5

MicroRNA expression profiles classify human cancers.
Jun Lu, Gad Getz, Eric A Miska, Ezequiel Alvarez-Saavedra, Justin Lamb, David Peck, Alejandro Sweet-Cordero, Benjamin L Ebert, Raymond H Mak, Adolfo A Ferrando,[...]. Nature 2005
5

The functions of animal microRNAs.
Victor Ambros. Nature 2004
5

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
M Ashburner, C A Ball, J A Blake, D Botstein, H Butler, J M Cherry, A P Davis, K Dolinski, S S Dwight, J T Eppig,[...]. Nat Genet 2000
5

Functions of microRNAs in plant stress responses.
Ramanjulu Sunkar, Yong-Fang Li, Guru Jagadeeswaran. Trends Plant Sci 2012
466
5

psRNATarget: a plant small RNA target analysis server (2017 release).
Xinbin Dai, Zhaohong Zhuang, Patrick Xuechun Zhao. Nucleic Acids Res 2018
354
5

The role of site accessibility in microRNA target recognition.
Michael Kertesz, Nicola Iovino, Ulrich Unnerstall, Ulrike Gaul, Eran Segal. Nat Genet 2007
5

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
Mihaela Pertea, Geo M Pertea, Corina M Antonescu, Tsung-Cheng Chang, Joshua T Mendell, Steven L Salzberg. Nat Biotechnol 2015
5

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
4

Metazoan MicroRNAs.
David P Bartel. Cell 2018
4


Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.
Freddie Bray, Jacques Ferlay, Isabelle Soerjomataram, Rebecca L Siegel, Lindsey A Torre, Ahmedin Jemal. CA Cancer J Clin 2018
4

The microRNA.org resource: targets and expression.
Doron Betel, Manda Wilson, Aaron Gabow, Debora S Marks, Chris Sander. Nucleic Acids Res 2008
4

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Cole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, Lior Pachter. Nat Biotechnol 2010
4

Gene ontology analysis for RNA-seq: accounting for selection bias.
Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack. Genome Biol 2010
4

Pairing beyond the Seed Supports MicroRNA Targeting Specificity.
James P Broughton, Michael T Lovci, Jessica L Huang, Gene W Yeo, Amy E Pasquinelli. Mol Cell 2016
178
4


HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
4

DIANA-miRPath v3.0: deciphering microRNA function with experimental support.
Ioannis S Vlachos, Konstantinos Zagganas, Maria D Paraskevopoulou, Georgios Georgakilas, Dimitra Karagkouni, Thanasis Vergoulis, Theodore Dalamagas, Artemis G Hatzigeorgiou. Nucleic Acids Res 2015
949
4

RNAhybrid: microRNA target prediction easy, fast and flexible.
Jan Krüger, Marc Rehmsmeier. Nucleic Acids Res 2006
4

Overview of MicroRNA Biogenesis, Mechanisms of Actions, and Circulation.
Jacob O'Brien, Heyam Hayder, Yara Zayed, Chun Peng. Front Endocrinol (Lausanne) 2018
4

Oncomirs - microRNAs with a role in cancer.
Aurora Esquela-Kerscher, Frank J Slack. Nat Rev Cancer 2006
4


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.