A citation-based method for searching scientific literature

Yuhao Chen, Xiaowei Wang. Nucleic Acids Res 2020
Times Cited: 661







List of co-cited articles
269 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
40

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
26

miRWalk: An online resource for prediction of microRNA binding sites.
Carsten Sticht, Carolina De La Torre, Alisha Parveen, Norbert Gretz. PLoS One 2018
481
17

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
16


miRBase: from microRNA sequences to function.
Ana Kozomara, Maria Birgaoanu, Sam Griffiths-Jones. Nucleic Acids Res 2019
12

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
11

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
8

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
8

NCBI GEO: archive for functional genomics data sets--update.
Tanya Barrett, Stephen E Wilhite, Pierre Ledoux, Carlos Evangelista, Irene F Kim, Maxim Tomashevsky, Kimberly A Marshall, Katherine H Phillippy, Patti M Sherman, Michelle Holko,[...]. Nucleic Acids Res 2013
8

The multilayered complexity of ceRNA crosstalk and competition.
Yvonne Tay, John Rinn, Pier Paolo Pandolfi. Nature 2014
8

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
8

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
422
7

A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?
Leonardo Salmena, Laura Poliseno, Yvonne Tay, Lev Kats, Pier Paolo Pandolfi. Cell 2011
7

DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts.
Maria D Paraskevopoulou, Ioannis S Vlachos, Dimitra Karagkouni, Georgios Georgakilas, Ilias Kanellos, Thanasis Vergoulis, Konstantinos Zagganas, Panayiotis Tsanakas, Evangelos Floros, Theodore Dalamagas,[...]. Nucleic Acids Res 2016
430
7

Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries.
Hyuna Sung, Jacques Ferlay, Rebecca L Siegel, Mathieu Laversanne, Isabelle Soerjomataram, Ahmedin Jemal, Freddie Bray. CA Cancer J Clin 2021
7

miRcode: a map of putative microRNA target sites in the long non-coding transcriptome.
Ashwini Jeggari, Debora S Marks, Erik Larsson. Bioinformatics 2012
449
7



Metascape provides a biologist-oriented resource for the analysis of systems-level datasets.
Yingyao Zhou, Bin Zhou, Lars Pache, Max Chang, Alireza Hadj Khodabakhshi, Olga Tanaseichuk, Christopher Benner, Sumit K Chanda. Nat Commun 2019
6

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
6


CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs.
Dawood B Dudekula, Amaresh C Panda, Ioannis Grammatikakis, Supriyo De, Kotb Abdelmohsen, Myriam Gorospe. RNA Biol 2016
586
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

The biochemical basis of microRNA targeting efficacy.
Sean E McGeary, Kathy S Lin, Charlie Y Shi, Thy M Pham, Namita Bisaria, Gina M Kelley, David P Bartel. Science 2019
141
6

KEGG: new perspectives on genomes, pathways, diseases and drugs.
Minoru Kanehisa, Miho Furumichi, Mao Tanabe, Yoko Sato, Kanae Morishima. Nucleic Acids Res 2017
5

Human MicroRNA targets.
Bino John, Anton J Enright, Alexei Aravin, Thomas Tuschl, Chris Sander, Debora S Marks. PLoS Biol 2004
5

WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
5

DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows.
Maria D Paraskevopoulou, Georgios Georgakilas, Nikos Kostoulas, Ioannis S Vlachos, Thanasis Vergoulis, Martin Reczko, Christos Filippidis, Theodore Dalamagas, A G Hatzigeorgiou. Nucleic Acids Res 2013
701
5

miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions.
Chih-Hung Chou, Sirjana Shrestha, Chi-Dung Yang, Nai-Wen Chang, Yu-Ling Lin, Kuang-Wen Liao, Wei-Chi Huang, Ting-Hsuan Sun, Siang-Jyun Tu, Wei-Hsiang Lee,[...]. Nucleic Acids Res 2018
5

The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
Damian Szklarczyk, Annika L Gable, Katerina C Nastou, David Lyon, Rebecca Kirsch, Sampo Pyysalo, Nadezhda T Doncheva, Marc Legeay, Tao Fang, Peer Bork,[...]. Nucleic Acids Res 2021
518
5

TIMER: A Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells.
Taiwen Li, Jingyu Fan, Binbin Wang, Nicole Traugh, Qianming Chen, Jun S Liu, Bo Li, X Shirley Liu. Cancer Res 2017
5

ceRNA in cancer: possible functions and clinical implications.
Xiaolong Qi, Da-Hong Zhang, Nan Wu, Jun-Hua Xiao, Xiang Wang, Wang Ma. J Med Genet 2015
649
5

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
Damian Szklarczyk, John H Morris, Helen Cook, Michael Kuhn, Stefan Wyder, Milan Simonovic, Alberto Santos, Nadezhda T Doncheva, Alexander Roth, Peer Bork,[...]. Nucleic Acids Res 2017
4

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
4

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
4

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Damian Szklarczyk, Annika L Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic, Nadezhda T Doncheva, John H Morris, Peer Bork,[...]. Nucleic Acids Res 2019
4

mirDIP 4.1-integrative database of human microRNA target predictions.
Tomas Tokar, Chiara Pastrello, Andrea E M Rossos, Mark Abovsky, Anne-Christin Hauschild, Mike Tsay, Richard Lu, Igor Jurisica. Nucleic Acids Res 2018
218
4

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
4

The Landscape of Circular RNA in Cancer.
Josh N Vo, Marcin Cieslik, Yajia Zhang, Sudhanshu Shukla, Lanbo Xiao, Yuping Zhang, Yi-Mi Wu, Saravana M Dhanasekaran, Carl G Engelke, Xuhong Cao,[...]. Cell 2019
671
4


circBase: a database for circular RNAs.
Petar Glažar, Panagiotis Papavasileiou, Nikolaus Rajewsky. RNA 2014
903
4

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
4

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
4

Gene regulation by long non-coding RNAs and its biological functions.
Luisa Statello, Chun-Jie Guo, Ling-Ling Chen, Maite Huarte. Nat Rev Mol Cell Biol 2021
609
4

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

The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.
Ethan Cerami, Jianjiong Gao, Ugur Dogrusoz, Benjamin E Gross, Selcuk Onur Sumer, Bülent Arman Aksoy, Anders Jacobsen, Caitlin J Byrne, Michael L Heuer, Erik Larsson,[...]. Cancer Discov 2012
4

Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.
Jianjiong Gao, Bülent Arman Aksoy, Ugur Dogrusoz, Gideon Dresdner, Benjamin Gross, S Onur Sumer, Yichao Sun, Anders Jacobsen, Rileen Sinha, Erik Larsson,[...]. Sci Signal 2013
4

Circbank: a comprehensive database for circRNA with standard nomenclature.
Ming Liu, Qian Wang, Jian Shen, Burton B Yang, Xiangming Ding. RNA Biol 2019
128
4

miRWalk database for miRNA-target interactions.
Harsh Dweep, Norbert Gretz, Carsten Sticht. Methods Mol Biol 2014
171
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.