A citation-based method for searching scientific literature

Moran N Cabili, Cole Trapnell, Loyal Goff, Magdalena Koziol, Barbara Tazon-Vega, Aviv Regev, John L Rinn. Genes Dev 2011
Times Cited: 2352







List of co-cited articles
789 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
31

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
17

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
15

lincRNAs: genomics, evolution, and mechanisms.
Igor Ulitsky, David P Bartel. Cell 2013
15

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
14

Genome regulation by long noncoding RNAs.
John L Rinn, Howard Y Chang. Annu Rev Biochem 2012
13

Molecular mechanisms of long noncoding RNAs.
Kevin C Wang, Howard Y Chang. Mol Cell 2011
12


An atlas of human long non-coding RNAs with accurate 5' ends.
Chung-Chau Hon, Jordan A Ramilowski, Jayson Harshbarger, Nicolas Bertin, Owen J L Rackham, Julian Gough, Elena Denisenko, Sebastian Schmeier, Thomas M Poulsen, Jessica Severin,[...]. Nature 2017
521
12

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
12

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
10

Long Noncoding RNAs in Cancer Pathways.
Adam M Schmitt, Howard Y Chang. Cancer Cell 2016
10

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression.
Ahmad M Khalil, Mitchell Guttman, Maite Huarte, Manuel Garber, Arjun Raj, Dianali Rivea Morales, Kelly Thomas, Aviva Presser, Bradley E Bernstein, Alexander van Oudenaarden,[...]. Proc Natl Acad Sci U S A 2009
10

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
10

The landscape of long noncoding RNAs in the human transcriptome.
Matthew K Iyer, Yashar S Niknafs, Rohit Malik, Udit Singhal, Anirban Sahu, Yasuyuki Hosono, Terrence R Barrette, John R Prensner, Joseph R Evans, Shuang Zhao,[...]. Nat Genet 2015
9

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
9

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
9

HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
9

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
625
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

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.
Andrea Pauli, Eivind Valen, Michael F Lin, Manuel Garber, Nadine L Vastenhouw, Joshua Z Levin, Lin Fan, Albin Sandelin, John L Rinn, Aviv Regev,[...]. Genome Res 2012
553
8

Unique features of long non-coding RNA biogenesis and function.
Jeffrey J Quinn, Howard Y Chang. Nat Rev Genet 2016
8


Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs.
John L Rinn, Michael Kertesz, Jordon K Wang, Sharon L Squazzo, Xiao Xu, Samantha A Brugmann, L Henry Goodnough, Jill A Helms, Peggy J Farnham, Eran Segal,[...]. Cell 2007
8

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
350
8

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution.
Moran N Cabili, Margaret C Dunagin, Patrick D McClanahan, Andrew Biaesch, Olivia Padovan-Merhar, Aviv Regev, John L Rinn, Arjun Raj. Genome Biol 2015
378
8

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
130
8

A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?
Leonardo Salmena, Laura Poliseno, Yvonne Tay, Lev Kats, Pier Paolo Pandolfi. Cell 2011
8

On the classification of long non-coding RNAs.
Lina Ma, Vladimir B Bajic, Zhang Zhang. RNA Biol 2013
662
8

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
835
8

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
827
8

A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA.
Marcella Cesana, Davide Cacchiarelli, Ivano Legnini, Tiziana Santini, Olga Sthandier, Mauro Chinappi, Anna Tramontano, Irene Bozzoni. Cell 2011
8

MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer.
Ping Ji, Sven Diederichs, Wenbing Wang, Sebastian Böing, Ralf Metzger, Paul M Schneider, Nicola Tidow, Burkhard Brandt, Horst Buerger, Etmar Bulk,[...]. Oncogene 2003
7

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

Long noncoding RNAs and human disease.
Orly Wapinski, Howard Y Chang. Trends Cell Biol 2011
7

Single-cell analysis of long non-coding RNAs in the developing human neocortex.
Siyuan John Liu, Tomasz J Nowakowski, Alex A Pollen, Jan H Lui, Max A Horlbeck, Frank J Attenello, Daniel He, Jonathan S Weissman, Arnold R Kriegstein, Aaron A Diaz,[...]. Genome Biol 2016
207
7

WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
7

RNA maps reveal new RNA classes and a possible function for pervasive transcription.
Philipp Kapranov, Jill Cheng, Sujit Dike, David A Nix, Radharani Duttagupta, Aarron T Willingham, Peter F Stadler, Jana Hertel, Jörg Hackermüller, Ivo L Hofacker,[...]. Science 2007
7

Multiple knockout mouse models reveal lincRNAs are required for life and brain development.
Martin Sauvageau, Loyal A Goff, Simona Lodato, Boyan Bonev, Abigail F Groff, Chiara Gerhardinger, Diana B Sanchez-Gomez, Ezgi Hacisuleyman, Eric Li, Matthew Spence,[...]. Elife 2013
494
7

Developmental dynamics of lncRNAs across mammalian organs and species.
Ioannis Sarropoulos, Ray Marin, Margarida Cardoso-Moreira, Henrik Kaessmann. Nature 2019
118
7

The multilayered complexity of ceRNA crosstalk and competition.
Yvonne Tay, John Rinn, Pier Paolo Pandolfi. Nature 2014
7

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology.
Laura Poliseno, Leonardo Salmena, Jiangwen Zhang, Brett Carver, William J Haveman, Pier Paolo Pandolfi. Nature 2010
7

The transcriptional landscape of the mammalian genome.
P Carninci, T Kasukawa, S Katayama, J Gough, M C Frith, N Maeda, R Oyama, T Ravasi, B Lenhard, C Wells,[...]. Science 2005
7

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
7

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
7


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

High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity.
Kaia Mattioli, Pieter-Jan Volders, Chiara Gerhardinger, James C Lee, Philipp G Maass, Marta Melé, John L Rinn. Genome Res 2019
52
11

Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs.
Marta Melé, Kaia Mattioli, William Mallard, David M Shechner, Chiara Gerhardinger, John L Rinn. Genome Res 2017
110
6

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
6


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.