A citation-based method for searching scientific literature

Mitchell Guttman, Ido Amit, Manuel Garber, Courtney French, Michael F Lin, David Feldser, Maite Huarte, Or Zuk, Bryce W Carey, John P Cassady, Moran N Cabili, Rudolf Jaenisch, Tarjei S Mikkelsen, Tyler Jacks, Nir Hacohen, Bradley E Bernstein, Manolis Kellis, Aviv Regev, John L Rinn, Eric S Lander. Nature 2009
Times Cited: 2906







List of co-cited articles
744 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
25

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
506
19

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
17

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
15

lincRNAs: genomics, evolution, and mechanisms.
Igor Ulitsky, David P Bartel. Cell 2013
14


Unique features of long non-coding RNA biogenesis and function.
Jeffrey J Quinn, Howard Y Chang. Nat Rev Genet 2016
13

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

Genome regulation by long noncoding RNAs.
John L Rinn, Howard Y Chang. Annu Rev Biochem 2012
12

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
11

Long Noncoding RNAs in Cancer Pathways.
Adam M Schmitt, Howard Y Chang. Cancer Cell 2016
11

Long non-coding RNAs: insights into functions.
Tim R Mercer, Marcel E Dinger, John S Mattick. Nat Rev Genet 2009
11

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
11

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
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



A long noncoding RNA mediates both activation and repression of immune response genes.
Susan Carpenter, Daniel Aiello, Maninjay K Atianand, Emiliano P Ricci, Pallavi Gandhi, Lisa L Hall, Meg Byron, Brian Monks, Meabh Henry-Bezy, Jeanne B Lawrence,[...]. Science 2013
646
10

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
10

Modular regulatory principles of large non-coding RNAs.
Mitchell Guttman, John L Rinn. Nature 2012
10

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
10

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
644
10


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
456
9

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

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

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
8

The multilayered complexity of ceRNA crosstalk and competition.
Yvonne Tay, John Rinn, Pier Paolo Pandolfi. Nature 2014
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
369
8

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

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
7

Long non-coding RNAs: new players in cell differentiation and development.
Alessandro Fatica, Irene Bozzoni. Nat Rev Genet 2014
7

On the classification of long non-coding RNAs.
Lina Ma, Vladimir B Bajic, Zhang Zhang. RNA Biol 2013
641
7

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
7

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
619
7

The Landscape of long noncoding RNA classification.
Georges St Laurent, Claes Wahlestedt, Philipp Kapranov. Trends Genet 2015
621
7

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
343
7

lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs.
Liuqing Yang, Chunru Lin, Chunyu Jin, Joy C Yang, Bogdan Tanasa, Wenbo Li, Daria Merkurjev, Kenneth A Ohgi, Da Meng, Jie Zhang,[...]. Nature 2013
464
6

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
193
6

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
6

Developmental dynamics of lncRNAs across mammalian organs and species.
Ioannis Sarropoulos, Ray Marin, Margarida Cardoso-Moreira, Henrik Kaessmann. Nature 2019
110
6

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
6

Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs.
Jasmina Ponjavic, Chris P Ponting, Gerton Lunter. Genome Res 2007
490
6

GENCODE reference annotation for the human and mouse genomes.
Adam Frankish, Mark Diekhans, Anne-Maud Ferreira, Rory Johnson, Irwin Jungreis, Jane Loveland, Jonathan M Mudge, Cristina Sisu, James Wright, Joel Armstrong,[...]. Nucleic Acids Res 2019
989
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
6

Non-coding RNA networks in cancer.
Eleni Anastasiadou, Leni S Jacob, Frank J Slack. Nat Rev Cancer 2018
733
6

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
107
6

Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome.
Timothy Ravasi, Harukazu Suzuki, Ken C Pang, Shintaro Katayama, Masaaki Furuno, Rie Okunishi, Shiro Fukuda, Kelin Ru, Martin C Frith, M Milena Gongora,[...]. Genome Res 2006
379
6

Long noncoding RNAs: past, present, and future.
Johnny T Y Kung, David Colognori, Jeannie T Lee. Genetics 2013
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.