A citation-based method for searching scientific literature

Ana Kozomara, Maria Birgaoanu, Sam Griffiths-Jones. Nucleic Acids Res 2019
Times Cited: 882







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



Times Cited
  Times     Co-cited
Similarity



Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
16

Predicting effective microRNA target sites in mammalian mRNAs.
Vikram Agarwal, George W Bell, Jin-Wu Nam, David P Bartel. Elife 2015
15


Regulation of microRNA biogenesis.
Minju Ha, V Narry Kim. Nat Rev Mol Cell Biol 2014
12

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
11


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
11

miRBase: annotating high confidence microRNAs using deep sequencing data.
Ana Kozomara, Sam Griffiths-Jones. Nucleic Acids Res 2014
9

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


Regulation of microRNA function in animals.
Luca F R Gebert, Ian J MacRae. Nat Rev Mol Cell Biol 2019
659
9

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
9

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 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
8

The role of MicroRNAs in human cancer.
Yong Peng, Carlo M Croce. Signal Transduct Target Ther 2016
746
8

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
914
7

Metazoan MicroRNAs.
David P Bartel. Cell 2018
7

Overview of MicroRNA Biogenesis, Mechanisms of Actions, and Circulation.
Jacob O'Brien, Heyam Hayder, Yara Zayed, Chun Peng. Front Endocrinol (Lausanne) 2018
808
7

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
6

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

ViennaRNA Package 2.0.
Ronny Lorenz, Stephan H Bernhart, Christian Höner Zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F Stadler, Ivo L Hofacker. Algorithms Mol Biol 2011
6

Circulating microRNAs as stable blood-based markers for cancer detection.
Patrick S Mitchell, Rachael K Parkin, Evan M Kroh, Brian R Fritz, Stacia K Wyman, Era L Pogosova-Agadjanyan, Amelia Peterson, Jennifer Noteboom, Kathy C O'Briant, April Allen,[...]. Proc Natl Acad Sci U S A 2008
6

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
149
6

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
6

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
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
5


GENCODE: the reference human genome annotation for The ENCODE Project.
Jennifer Harrow, Adam Frankish, Jose M Gonzalez, Electra Tapanari, Mark Diekhans, Felix Kokocinski, Bronwen L Aken, Daniel Barrell, Amonida Zadissa, Stephen Searle,[...]. Genome Res 2012
5

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
303
5

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.
Mihaela Pertea, Daehwan Kim, Geo M Pertea, Jeffrey T Leek, Steven L Salzberg. Nat Protoc 2016
5

Towards a molecular understanding of microRNA-mediated gene silencing.
Stefanie Jonas, Elisa Izaurralde. Nat Rev Genet 2015
900
5

The widespread regulation of microRNA biogenesis, function and decay.
Jacek Krol, Inga Loedige, Witold Filipowicz. Nat Rev Genet 2010
5

LNCipedia 5: towards a reference set of human long non-coding RNAs.
Pieter-Jan Volders, Jasper Anckaert, Kenneth Verheggen, Justine Nuytens, Lennart Martens, Pieter Mestdagh, Jo Vandesompele. Nucleic Acids Res 2019
153
5

microRNA functions.
Natascha Bushati, Stephen M Cohen. Annu Rev Cell Dev Biol 2007
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
623
5

Ensembl 2020.
Andrew D Yates, Premanand Achuthan, Wasiu Akanni, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Andrey G Azov, Ruth Bennett,[...]. Nucleic Acids Res 2020
426
5

The nuclear RNase III Drosha initiates microRNA processing.
Yoontae Lee, Chiyoung Ahn, Jinju Han, Hyounjeong Choi, Jaekwang Kim, Jeongbin Yim, Junho Lee, Patrick Provost, Olof Rådmark, Sunyoung Kim,[...]. Nature 2003
5

psRNATarget: a plant small RNA target analysis server (2017 release).
Xinbin Dai, Zhaohong Zhuang, Patrick Xuechun Zhao. Nucleic Acids Res 2018
267
5

MicroRNA-373 induces expression of genes with complementary promoter sequences.
Robert F Place, Long-Cheng Li, Deepa Pookot, Emily J Noonan, Rajvir Dahiya. Proc Natl Acad Sci U S A 2008
841
5

The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
5

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
174
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

Circular RNAs are abundant, conserved, and associated with ALU repeats.
William R Jeck, Jessica A Sorrentino, Kai Wang, Michael K Slevin, Christin E Burd, Jinze Liu, William F Marzluff, Norman E Sharpless. RNA 2013
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
853
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


Treatment of HCV infection by targeting microRNA.
Harry L A Janssen, Hendrik W Reesink, Eric J Lawitz, Stefan Zeuzem, Maribel Rodriguez-Torres, Keyur Patel, Adriaan J van der Meer, Amy K Patick, Alice Chen, Yi Zhou,[...]. N Engl J Med 2013
4

How close are miRNAs from clinical practice? A perspective on the diagnostic and therapeutic market.
E Bonneau, B Neveu, E Kostantin, G J Tsongalis, V De Guire. EJIFCC 2019
81
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.