A citation-based method for searching scientific literature

Bino John, Anton J Enright, Alexei Aravin, Thomas Tuschl, Chris Sander, Debora S Marks. PLoS Biol 2004
Times Cited: 2682







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



Times Cited
  Times     Co-cited
Similarity


Predicting effective microRNA target sites in mammalian mRNAs.
Vikram Agarwal, George W Bell, Jin-Wu Nam, David P Bartel. Elife 2015
22


The role of site accessibility in microRNA target recognition.
Michael Kertesz, Nicola Iovino, Ulrich Unnerstall, Ulrike Gaul, Eran Segal. Nat Genet 2007
17

RNAhybrid: microRNA target prediction easy, fast and flexible.
Jan Krüger, Marc Rehmsmeier. Nucleic Acids Res 2006
16

Prediction of mammalian microRNA targets.
Benjamin P Lewis, I-hung Shih, Matthew W Jones-Rhoades, David P Bartel, Christopher B Burge. Cell 2003
15

miRBase: from microRNA sequences to function.
Ana Kozomara, Maria Birgaoanu, Sam Griffiths-Jones. Nucleic Acids Res 2019
14




Natural RNA circles function as efficient microRNA sponges.
Thomas B Hansen, Trine I Jensen, Bettina H Clausen, Jesper B Bramsen, Bente Finsen, Christian K Damgaard, Jørgen Kjems. Nature 2013
11

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
10


edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
9

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
9

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data.
Jun-Hao Li, Shun Liu, Hui Zhou, Liang-Hu Qu, Jian-Hua Yang. Nucleic Acids Res 2014
9

The functions of animal microRNAs.
Victor Ambros. Nature 2004
9

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
8

MicroRNA targets in Drosophila.
Anton J Enright, Bino John, Ulrike Gaul, Thomas Tuschl, Chris Sander, Debora S Marks. Genome Biol 2003
8

Circular RNAs are a large class of animal RNAs with regulatory potency.
Sebastian Memczak, Marvin Jens, Antigoni Elefsinioti, Francesca Torti, Janna Krueger, Agnieszka Rybak, Luisa Maier, Sebastian D Mackowiak, Lea H Gregersen, Mathias Munschauer,[...]. Nature 2013
8

A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?
Leonardo Salmena, Laura Poliseno, Yvonne Tay, Lev Kats, Pier Paolo Pandolfi. Cell 2011
8

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
7


miRBase: tools for microRNA genomics.
Sam Griffiths-Jones, Harpreet Kaur Saini, Stijn van Dongen, Anton J Enright. Nucleic Acids Res 2008
7

Fast and effective prediction of microRNA/target duplexes.
Marc Rehmsmeier, Peter Steffen, Matthias Hochsmann, Robert Giegerich. RNA 2004
7

Regulation of microRNA biogenesis.
Minju Ha, V Narry Kim. Nat Rev Mol Cell Biol 2014
7


miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database.
Hsi-Yuan Huang, Yang-Chi-Dung Lin, Jing Li, Kai-Yao Huang, Sirjana Shrestha, Hsiao-Chin Hong, Yun Tang, Yi-Gang Chen, Chen-Nan Jin, Yuan Yu,[...]. Nucleic Acids Res 2020
386
7

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
6

The biogenesis, biology and characterization of circular RNAs.
Lasse S Kristensen, Maria S Andersen, Lotte V W Stagsted, Karoline K Ebbesen, Thomas B Hansen, Jørgen Kjems. Nat Rev Genet 2019
6

circBase: a database for circular RNAs.
Petar Glažar, Panagiotis Papavasileiou, Nikolaus Rajewsky. RNA 2014
903
6

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.
Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang, Xuegong Zhang. Bioinformatics 2010
6


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

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


Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs.
Qiupeng Zheng, Chunyang Bao, Weijie Guo, Shuyi Li, Jie Chen, Bing Chen, Yanting Luo, Dongbin Lyu, Yan Li, Guohai Shi,[...]. Nat Commun 2016
5

Most mammalian mRNAs are conserved targets of microRNAs.
Robin C Friedman, Kyle Kai-How Farh, Christopher B Burge, David P Bartel. Genome Res 2009
5

MicroRNA signatures in human cancers.
George A Calin, Carlo M Croce. Nat Rev Cancer 2006
5

miRWalk: An online resource for prediction of microRNA binding sites.
Carsten Sticht, Carolina De La Torre, Alisha Parveen, Norbert Gretz. PLoS One 2018
481
5

A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes.
Kevin C Miranda, Tien Huynh, Yvonne Tay, Yen-Sin Ang, Wai-Leong Tam, Andrew M Thomson, Bing Lim, Isidore Rigoutsos. Cell 2006
5

TargetSpy: a supervised machine learning approach for microRNA target prediction.
Martin Sturm, Michael Hackenberg, David Langenberger, Dmitrij Frishman. BMC Bioinformatics 2010
103
5

MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence.
Ventsislav Rusinov, Vesselin Baev, Ivan Nikiforov Minkov, Martin Tabler. Nucleic Acids Res 2005
192
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.