A citation-based method for searching scientific literature

Marc R Friedländer, Sebastian D Mackowiak, Na Li, Wei Chen, Nikolaus Rajewsky. Nucleic Acids Res 2012
Times Cited: 1517

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

Times Cited
  Times     Co-cited

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

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

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

Gene ontology analysis for RNA-seq: accounting for selection bias.
Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack. Genome Biol 2010

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

Integrated profiling of microRNAs and mRNAs: microRNAs located on Xq27.3 associate with clear cell renal cell carcinoma.
Liang Zhou, Jiahao Chen, Zhizhong Li, Xianxin Li, Xueda Hu, Yi Huang, Xiaokun Zhao, Chaozhao Liang, Yong Wang, Liang Sun,[...]. PLoS One 2010

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

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012

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

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

HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015

KEGG for linking genomes to life and the environment.
Minoru Kanehisa, Michihiro Araki, Susumu Goto, Masahiro Hattori, Mika Hirakawa, Masumi Itoh, Toshiaki Katayama, Shuichi Kawashima, Shujiro Okuda, Toshiaki Tokimatsu,[...]. Nucleic Acids Res 2008

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

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

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

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

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

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

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts.
Liang Sun, Haitao Luo, Dechao Bu, Guoguang Zhao, Kuntao Yu, Changhai Zhang, Yuanning Liu, Runsheng Chen, Yi Zhao. Nucleic Acids Res 2013

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases.
Chen Xie, Xizeng Mao, Jiaju Huang, Yang Ding, Jianmin Wu, Shan Dong, Lei Kong, Ge Gao, Chuan-Yun Li, Liping Wei. Nucleic Acids Res 2011

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

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014

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

Metazoan MicroRNAs.
David P Bartel. Cell 2018

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Cole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, Lior Pachter. Nat Biotechnol 2010

Rfam: an RNA family database.
Sam Griffiths-Jones, Alex Bateman, Mhairi Marshall, Ajay Khanna, Sean R Eddy. Nucleic Acids Res 2003

Analyzing real-time PCR data by the comparative C(T) method.
Thomas D Schmittgen, Kenneth J Livak. Nat Protoc 2008

fastp: an ultra-fast all-in-one FASTQ preprocessor.
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. Bioinformatics 2018

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
Cole Trapnell, Adam Roberts, Loyal Goff, Geo Pertea, Daehwan Kim, David R Kelley, Harold Pimentel, Steven L Salzberg, John L Rinn, Lior Pachter. Nat Protoc 2012

Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines.
Clotilde Théry, Kenneth W Witwer, Elena Aikawa, Maria Jose Alcaraz, Johnathon D Anderson, Ramaroson Andriantsitohaina, Anna Antoniou, Tanina Arab, Fabienne Archer, Georgia K Atkin-Smith,[...]. J Extracell Vesicles 2018

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

CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.
Lei Kong, Yong Zhang, Zhi-Qiang Ye, Xiao-Qiao Liu, Shu-Qi Zhao, Liping Wei, Ge Gao. Nucleic Acids Res 2007

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

Differential expression analysis for sequence count data.
Simon Anders, Wolfgang Huber. Genome Biol 2010

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

Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites.
Doron Betel, Anjali Koppal, Phaedra Agius, Chris Sander, Christina Leslie. Genome Biol 2010

The multiMiR R package and database: integration of microRNA-target interactions along with their disease and drug associations.
Yuanbin Ru, Katerina J Kechris, Boris Tabakoff, Paula Hoffman, Richard A Radcliffe, Russell Bowler, Spencer Mahaffey, Simona Rossi, George A Calin, Lynne Bemis,[...]. Nucleic Acids Res 2014

DIANA-miRPath v3.0: deciphering microRNA function with experimental support.
Ioannis S Vlachos, Konstantinos Zagganas, Maria D Paraskevopoulou, Georgios Georgakilas, Dimitra Karagkouni, Thanasis Vergoulis, Theodore Dalamagas, Artemis G Hatzigeorgiou. Nucleic Acids Res 2015

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

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

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

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.