A citation-based method for searching scientific literature

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, Men-Yee Chiew, Chun-San Tai, Ting-Yen Wei, Tzi-Ren Tsai, Hsin-Tzu Huang, Chung-Yu Wang, Hsin-Yi Wu, Shu-Yi Ho, Pin-Rong Chen, Cheng-Hsun Chuang, Pei-Jung Hsieh, Yi-Shin Wu, Wen-Liang Chen, Meng-Ju Li, Yu-Chun Wu, Xin-Yi Huang, Fung Ling Ng, Waradee Buddhakosai, Pei-Chun Huang, Kuan-Chun Lan, Chia-Yen Huang, Shun-Long Weng, Yeong-Nan Cheng, Chao Liang, Wen-Lian Hsu, Hsien-Da Huang. Nucleic Acids Res 2018
Times Cited: 1052







List of co-cited articles
303 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
29

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
22

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
19

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
18

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
16


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
14


HMDD v3.0: a database for experimentally supported human microRNA-disease associations.
Zhou Huang, Jiangcheng Shi, Yuanxu Gao, Chunmei Cui, Shan Zhang, Jianwei Li, Yuan Zhou, Qinghua Cui. Nucleic Acids Res 2019
233
13

A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?
Leonardo Salmena, Laura Poliseno, Yvonne Tay, Lev Kats, Pier Paolo Pandolfi. Cell 2011
12

miRBase: from microRNA sequences to function.
Ana Kozomara, Maria Birgaoanu, Sam Griffiths-Jones. Nucleic Acids Res 2019
11

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
10

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
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

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
9

miRBase: annotating high confidence microRNAs using deep sequencing data.
Ana Kozomara, Sam Griffiths-Jones. Nucleic Acids Res 2014
8

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
8

miRWalk: An online resource for prediction of microRNA binding sites.
Carsten Sticht, Carolina De La Torre, Alisha Parveen, Norbert Gretz. PLoS One 2018
441
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

DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants.
Janet Piñero, Àlex Bravo, Núria Queralt-Rosinach, Alba Gutiérrez-Sacristán, Jordi Deu-Pons, Emilio Centeno, Javier García-García, Ferran Sanz, Laura I Furlong. Nucleic Acids Res 2017
866
7

Most mammalian mRNAs are conserved targets of microRNAs.
Robin C Friedman, Kyle Kai-How Farh, Christopher B Burge, David P Bartel. Genome Res 2009
6


DrugBank 5.0: a major update to the DrugBank database for 2018.
David S Wishart, Yannick D Feunang, An C Guo, Elvis J Lo, Ana Marcu, Jason R Grant, Tanvir Sajed, Daniel Johnson, Carin Li, Zinat Sayeeda,[...]. Nucleic Acids Res 2018
6

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nat Protoc 2009
6

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
6


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




TransmiR v2.0: an updated transcription factor-microRNA regulation database.
Zhan Tong, Qinghua Cui, Juan Wang, Yuan Zhou. Nucleic Acids Res 2019
104
5


cytoHubba: identifying hub objects and sub-networks from complex interactome.
Chia-Hao Chin, Shu-Hwa Chen, Hsin-Hung Wu, Chin-Wen Ho, Ming-Tat Ko, Chung-Yen Lin. BMC Syst Biol 2014
5

Inferring tumour purity and stromal and immune cell admixture from expression data.
Kosuke Yoshihara, Maria Shahmoradgoli, Emmanuel Martínez, Rahulsimham Vegesna, Hoon Kim, Wandaliz Torres-Garcia, Victor Treviño, Hui Shen, Peter W Laird, Douglas A Levine,[...]. Nat Commun 2013
5

GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses.
Zefang Tang, Chenwei Li, Boxi Kang, Ge Gao, Cheng Li, Zemin Zhang. Nucleic Acids Res 2017
5

miRcode: a map of putative microRNA target sites in the long non-coding transcriptome.
Ashwini Jeggari, Debora S Marks, Erik Larsson. Bioinformatics 2012
443
5

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
418
5

lncRNASNP2: an updated database of functional SNPs and mutations in human and mouse lncRNAs.
Ya-Ru Miao, Wei Liu, Qiong Zhang, An-Yuan Guo. Nucleic Acids Res 2018
122
5

dbDEMC 2.0: updated database of differentially expressed miRNAs in human cancers.
Zhen Yang, Liangcai Wu, Anqiang Wang, Wei Tang, Yi Zhao, Haitao Zhao, Andrew E Teschendorff. Nucleic Acids Res 2017
145
5

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
353
5

Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs.
David M Garcia, Daehyun Baek, Chanseok Shin, George W Bell, Andrew Grimson, David P Bartel. Nat Struct Mol Biol 2011
667
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

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

circBase: a database for circular RNAs.
Petar Glažar, Panagiotis Papavasileiou, Nikolaus Rajewsky. RNA 2014
875
4

miR2Disease: a manually curated database for microRNA deregulation in human disease.
Qinghua Jiang, Yadong Wang, Yangyang Hao, Liran Juan, Mingxiang Teng, Xinjun Zhang, Meimei Li, Guohua Wang, Yunlong Liu. Nucleic Acids Res 2009
888
4

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
4

Complex heatmaps reveal patterns and correlations in multidimensional genomic data.
Zuguang Gu, Roland Eils, Matthias Schlesner. Bioinformatics 2016
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.