Bino John, Anton J Enright, Alexei Aravin, Thomas Tuschl, Chris Sander, Debora S Marks. PLoS Biol 2004
Times Cited: 2682
Times Cited: 2682
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
Vikram Agarwal, George W Bell, Jin-Wu Nam, David P Bartel. Elife 2015
22
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
17
The role of site accessibility in microRNA target recognition.
Michael Kertesz, Nicola Iovino, Ulrich Unnerstall, Ulrike Gaul, Eran Segal. Nat Genet 2007
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
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
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
Ana Kozomara, Maria Birgaoanu, Sam Griffiths-Jones. Nucleic Acids Res 2019
14
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets.
Benjamin P Lewis, Christopher B Burge, David P Bartel. Cell 2005
Benjamin P Lewis, Christopher B Burge, David P Bartel. Cell 2005
13
miRDB: an online database for prediction of functional microRNA targets.
Yuhao Chen, Xiaowei Wang. Nucleic Acids Res 2020
Yuhao Chen, Xiaowei Wang. Nucleic Acids Res 2020
11
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
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
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
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
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
Jun-Hao Li, Shun Liu, Hui Zhou, Liang-Hu Qu, Jian-Hua Yang. Nucleic Acids Res 2014
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
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
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
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
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
Marc R Friedländer, Sebastian D Mackowiak, Na Li, Wei Chen, Nikolaus Rajewsky. Nucleic Acids Res 2012
7
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
7
miRBase: tools for microRNA genomics.
Sam Griffiths-Jones, Harpreet Kaur Saini, Stijn van Dongen, Anton J Enright. Nucleic Acids Res 2008
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
Marc Rehmsmeier, Peter Steffen, Matthias Hochsmann, Robert Giegerich. RNA 2004
7
Rhabdovirus-Inducible MicroRNA-210 Modulates Antiviral Innate Immune Response via Targeting STING/MITA in Fish.
Tianjun Xu, Qing Chu, Junxia Cui. J Immunol 2018
Tianjun Xu, Qing Chu, Junxia Cui. J Immunol 2018
16
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
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
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
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
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
Petar Glažar, Panagiotis Papavasileiou, Nikolaus Rajewsky. RNA 2014
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
Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang, Xuegong Zhang. Bioinformatics 2010
6
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14.
R C Lee, R L Feinbaum, V Ambros. Cell 1993
R C Lee, R L Feinbaum, V Ambros. Cell 1993
6
miRBase: annotating high confidence microRNAs using deep sequencing data.
Ana Kozomara, Sam Griffiths-Jones. Nucleic Acids Res 2014
Ana Kozomara, Sam Griffiths-Jones. Nucleic Acids Res 2014
6
miR-122 involved in the regulation of toll-like receptor signaling pathway after Vibrio anguillarum infection by targeting TLR14 in miiuy croaker.
Junxia Cui, Qing Chu, Tianjun Xu. Fish Shellfish Immunol 2016
Junxia Cui, Qing Chu, Tianjun Xu. Fish Shellfish Immunol 2016
17
MicroRNA-216a Inhibits NF-κB-Mediated Inflammatory Cytokine Production in Teleost Fish by Modulating p65.
Tianjun Xu, Qing Chu, Junxia Cui, Ruixuan Huo. Infect Immun 2018
Tianjun Xu, Qing Chu, Junxia Cui, Ruixuan Huo. Infect Immun 2018
13
Inducible MicroRNA-3570 Feedback Inhibits the RIG-I-Dependent Innate Immune Response to Rhabdovirus in Teleost Fish by Targeting MAVS/IPS-1.
Tianjun Xu, Qing Chu, Junxia Cui, Dekun Bi. J Virol 2018
Tianjun Xu, Qing Chu, Junxia Cui, Dekun Bi. J Virol 2018
11
Inducible MicroRNA-217 Inhibits NF-κB- and IRF3-Driven Immune Responses in Lower Vertebrates through Targeting TAK1.
Lei Zhang, Qing Chu, Renjie Chang, Tianjun Xu. J Immunol 2020
Lei Zhang, Qing Chu, Renjie Chang, Tianjun Xu. J Immunol 2020
28
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
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
Mihaela Pertea, Geo M Pertea, Corina M Antonescu, Tsung-Cheng Chang, Joshua T Mendell, Steven L Salzberg. Nat Biotechnol 2015
5
Fast and accurate short read alignment with Burrows-Wheeler transform.
Heng Li, Richard Durbin. Bioinformatics 2009
Heng Li, Richard Durbin. Bioinformatics 2009
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
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
Robin C Friedman, Kyle Kai-How Farh, Christopher B Burge, David P Bartel. Genome Res 2009
5
miRWalk: An online resource for prediction of microRNA binding sites.
Carsten Sticht, Carolina De La Torre, Alisha Parveen, Norbert Gretz. PLoS One 2018
Carsten Sticht, Carolina De La Torre, Alisha Parveen, Norbert Gretz. PLoS One 2018
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
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
Martin Sturm, Michael Hackenberg, David Langenberger, Dmitrij Frishman. BMC Bioinformatics 2010
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
Ventsislav Rusinov, Vesselin Baev, Ivan Nikiforov Minkov, Martin Tabler. Nucleic Acids Res 2005
5
The inducible microRNA-203 in fish represses the inflammatory responses to Gram-negative bacteria by targeting IL-1 receptor-associated kinase 4.
Tianjun Xu, Qing Chu, Junxia Cui, Xueyan Zhao. J Biol Chem 2018
Tianjun Xu, Qing Chu, Junxia Cui, Xueyan Zhao. J Biol Chem 2018
12
Long noncoding RNA MARL regulates antiviral responses through suppression miR-122-dependent MAVS downregulation in lower vertebrates.
Qing Chu, Tianjun Xu, Weiwei Zheng, Renjie Chang, Lei Zhang. PLoS Pathog 2020
Qing Chu, Tianjun Xu, Weiwei Zheng, Renjie Chang, Lei Zhang. PLoS Pathog 2020
15
Long noncoding RNA IRL regulates NF-κB-mediated immune responses through suppression of miR-27c-3p-dependent IRAK4 downregulation in teleost fish.
Weiwei Zheng, Qing Chu, Tianjun Xu. J Biol Chem 2021
Weiwei Zheng, Qing Chu, Tianjun Xu. J Biol Chem 2021
29
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.