A citation-based method for searching scientific literature

Igor Ulitsky, David P Bartel. Cell 2013
Times Cited: 1796







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



Times Cited
  Times     Co-cited
Similarity


The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.
Thomas Derrien, Rory Johnson, Giovanni Bussotti, Andrea Tanzer, Sarah Djebali, Hagen Tilgner, Gregory Guernec, David Martin, Angelika Merkel, David G Knowles,[...]. Genome Res 2012
23


Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses.
Moran N Cabili, Cole Trapnell, Loyal Goff, Magdalena Koziol, Barbara Tazon-Vega, Aviv Regev, John L Rinn. Genes Dev 2011
14

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
828
12

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
12

The multilayered complexity of ceRNA crosstalk and competition.
Yvonne Tay, John Rinn, Pier Paolo Pandolfi. Nature 2014
12

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.
Mitchell Guttman, Ido Amit, Manuel Garber, Courtney French, Michael F Lin, David Feldser, Maite Huarte, Or Zuk, Bryce W Carey, John P Cassady,[...]. Nature 2009
11


A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?
Leonardo Salmena, Laura Poliseno, Yvonne Tay, Lev Kats, Pier Paolo Pandolfi. Cell 2011
10

Long non-coding RNAs: new players in cell differentiation and development.
Alessandro Fatica, Irene Bozzoni. Nat Rev Genet 2014
10

Unique features of long non-coding RNA biogenesis and function.
Jeffrey J Quinn, Howard Y Chang. Nat Rev Genet 2016
9

Local regulation of gene expression by lncRNA promoters, transcription and splicing.
Jesse M Engreitz, Jenna E Haines, Elizabeth M Perez, Glen Munson, Jenny Chen, Michael Kane, Patrick E McDonel, Mitchell Guttman, Eric S Lander. Nature 2016
698
9

A micropeptide encoded by a putative long noncoding RNA regulates muscle performance.
Douglas M Anderson, Kelly M Anderson, Chi-Lun Chang, Catherine A Makarewich, Benjamin R Nelson, John R McAnally, Prasad Kasaragod, John M Shelton, Jen Liou, Rhonda Bassel-Duby,[...]. Cell 2015
675
9

Landscape of transcription in human cells.
Sarah Djebali, Carrie A Davis, Angelika Merkel, Alex Dobin, Timo Lassmann, Ali Mortazavi, Andrea Tanzer, Julien Lagarde, Wei Lin, Felix Schlesinger,[...]. Nature 2012
9

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
9

Genome regulation by long noncoding RNAs.
John L Rinn, Howard Y Chang. Annu Rev Biochem 2012
8

Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins.
Sungyul Lee, Florian Kopp, Tsung-Cheng Chang, Anupama Sataluri, Beibei Chen, Sushama Sivakumar, Hongtao Yu, Yang Xie, Joshua T Mendell. Cell 2016
491
8

Evolution and functions of long noncoding RNAs.
Chris P Ponting, Peter L Oliver, Wolf Reik. Cell 2009
8

Long non-coding RNAs: insights into functions.
Tim R Mercer, Marcel E Dinger, John S Mattick. Nat Rev Genet 2009
7

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression.
Kevin C Wang, Yul W Yang, Bo Liu, Amartya Sanyal, Ryan Corces-Zimmerman, Yong Chen, Bryan R Lajoie, Angeline Protacio, Ryan A Flynn, Rajnish A Gupta,[...]. Nature 2011
7

Molecular mechanisms of long noncoding RNAs.
Kevin C Wang, Howard Y Chang. Mol Cell 2011
7

lincRNAs act in the circuitry controlling pluripotency and differentiation.
Mitchell Guttman, Julie Donaghey, Bryce W Carey, Manuel Garber, Jennifer K Grenier, Glen Munson, Geneva Young, Anne Bergstrom Lucas, Robert Ach, Laurakay Bruhn,[...]. Nature 2011
7

Long noncoding RNA as modular scaffold of histone modification complexes.
Miao-Chih Tsai, Ohad Manor, Yue Wan, Nima Mosammaparast, Jordon K Wang, Fei Lan, Yang Shi, Eran Segal, Howard Y Chang. Science 2010
7

Long Noncoding RNA and Cancer: A New Paradigm.
Arunoday Bhan, Milad Soleimani, Subhrangsu S Mandal. Cancer Res 2017
7

Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions.
Ci Chu, Kun Qu, Franklin L Zhong, Steven E Artandi, Howard Y Chang. Mol Cell 2011
850
6

A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells.
Ailone Tichon, Noa Gil, Yoav Lubelsky, Tal Havkin Solomon, Doron Lemze, Shalev Itzkovitz, Noam Stern-Ginossar, Igor Ulitsky. Nat Commun 2016
137
6

Cellular functions of long noncoding RNAs.
Run-Wen Yao, Yang Wang, Ling-Ling Chen. Nat Cell Biol 2019
657
6

Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals.
Stefan Washietl, Manolis Kellis, Manuel Garber. Genome Res 2014
252
6

The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3.
Colleen A McHugh, Chun-Kan Chen, Amy Chow, Christine F Surka, Christina Tran, Patrick McDonel, Amy Pandya-Jones, Mario Blanco, Christina Burghard, Annie Moradian,[...]. Nature 2015
689
6

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
6

Modular regulatory principles of large non-coding RNAs.
Mitchell Guttman, John L Rinn. Nature 2012
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

Endogenous microRNA sponges: evidence and controversy.
Daniel W Thomson, Marcel E Dinger. Nat Rev Genet 2016
6

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis.
Rajnish A Gupta, Nilay Shah, Kevin C Wang, Jeewon Kim, Hugo M Horlings, David J Wong, Miao-Chih Tsai, Tiffany Hung, Pedram Argani, John L Rinn,[...]. Nature 2010
6

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
6

A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response.
Maite Huarte, Mitchell Guttman, David Feldser, Manuel Garber, Magdalena J Koziol, Daniela Kenzelmann-Broz, Ahmad M Khalil, Or Zuk, Ido Amit, Michal Rabani,[...]. Cell 2010
6

The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation.
Vidisha Tripathi, Jonathan D Ellis, Zhen Shen, David Y Song, Qun Pan, Andrew T Watt, Susan M Freier, C Frank Bennett, Alok Sharma, Paula A Bubulya,[...]. Mol Cell 2010
5

Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs.
Margarita Schlackow, Takayuki Nojima, Tomas Gomes, Ashish Dhir, Maria Carmo-Fonseca, Nick J Proudfoot. Mol Cell 2017
139
5


Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters.
Tiffany Hung, Yulei Wang, Michael F Lin, Ashley K Koegel, Yojiro Kotake, Gavin D Grant, Hugo M Horlings, Nilay Shah, Christopher Umbricht, Pei Wang,[...]. Nat Genet 2011
854
5

The functions and unique features of long intergenic non-coding RNA.
Julia D Ransohoff, Yuning Wei, Paul A Khavari. Nat Rev Mol Cell Biol 2018
556
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

The evolution of lncRNA repertoires and expression patterns in tetrapods.
Anamaria Necsulea, Magali Soumillon, Maria Warnefors, Angélica Liechti, Tasman Daish, Ulrich Zeller, Julie C Baker, Frank Grützner, Henrik Kaessmann. Nature 2014
643
5

Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species.
Hadas Hezroni, David Koppstein, Matthew G Schwartz, Alexandra Avrutin, David P Bartel, Igor Ulitsky. Cell Rep 2015
364
5

Developmental dynamics of lncRNAs across mammalian organs and species.
Ioannis Sarropoulos, Ray Marin, Margarida Cardoso-Moreira, Henrik Kaessmann. Nature 2019
125
5

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
5

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
5


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.