A citation-based method for searching scientific literature

Sarah Djebali, Carrie A Davis, Angelika Merkel, Alex Dobin, Timo Lassmann, Ali Mortazavi, Andrea Tanzer, Julien Lagarde, Wei Lin, Felix Schlesinger, Chenghai Xue, Georgi K Marinov, Jainab Khatun, Brian A Williams, Chris Zaleski, Joel Rozowsky, Maik Röder, Felix Kokocinski, Rehab F Abdelhamid, Tyler Alioto, Igor Antoshechkin, Michael T Baer, Nadav S Bar, Philippe Batut, Kimberly Bell, Ian Bell, Sudipto Chakrabortty, Xian Chen, Jacqueline Chrast, Joao Curado, Thomas Derrien, Jorg Drenkow, Erica Dumais, Jacqueline Dumais, Radha Duttagupta, Emilie Falconnet, Meagan Fastuca, Kata Fejes-Toth, Pedro Ferreira, Sylvain Foissac, Melissa J Fullwood, Hui Gao, David Gonzalez, Assaf Gordon, Harsha Gunawardena, Cedric Howald, Sonali Jha, Rory Johnson, Philipp Kapranov, Brandon King, Colin Kingswood, Oscar J Luo, Eddie Park, Kimberly Persaud, Jonathan B Preall, Paolo Ribeca, Brian Risk, Daniel Robyr, Michael Sammeth, Lorian Schaffer, Lei-Hoon See, Atif Shahab, Jorgen Skancke, Ana Maria Suzuki, Hazuki Takahashi, Hagen Tilgner, Diane Trout, Nathalie Walters, Huaien Wang, John Wrobel, Yanbao Yu, Xiaoan Ruan, Yoshihide Hayashizaki, Jennifer Harrow, Mark Gerstein, Tim Hubbard, Alexandre Reymond, Stylianos E Antonarakis, Gregory Hannon, Morgan C Giddings, Yijun Ruan, Barbara Wold, Piero Carninci, Roderic Guigó, Thomas R Gingeras. Nature 2012
Times Cited: 3315







List of co-cited articles
579 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
20

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
15

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
12


Molecular mechanisms of long noncoding RNAs.
Kevin C Wang, Howard Y Chang. Mol Cell 2011
11


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

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
9

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

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
8

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
8

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

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
543
8

Long non-coding RNAs: insights into functions.
Tim R Mercer, Marcel E Dinger, John S Mattick. Nat Rev Genet 2009
8


Non-coding RNA networks in cancer.
Eleni Anastasiadou, Leni S Jacob, Frank J Slack. Nat Rev Cancer 2018
862
7


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
6


lincRNAs: genomics, evolution, and mechanisms.
Igor Ulitsky, David P Bartel. Cell 2013
6

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
6

The multilayered complexity of ceRNA crosstalk and competition.
Yvonne Tay, John Rinn, Pier Paolo Pandolfi. Nature 2014
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
6

The Role of Non-coding RNAs in Oncology.
Frank J Slack, Arul M Chinnaiyan. Cell 2019
484
6

Non-coding RNAs in human disease.
Manel Esteller. Nat Rev Genet 2011
6

Widespread transcription at neuronal activity-regulated enhancers.
Tae-Kyung Kim, Martin Hemberg, Jesse M Gray, Allen M Costa, Daniel M Bear, Jing Wu, David A Harmin, Mike Laptewicz, Kellie Barbara-Haley, Scott Kuersten,[...]. Nature 2010
5

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
55
9

Linking Long Noncoding RNA Localization and Function.
Ling-Ling Chen. Trends Biochem Sci 2016
570
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

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

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Ewan Birney, John A Stamatoyannopoulos, Anindya Dutta, Roderic Guigó, Thomas R Gingeras, Elliott H Margulies, Zhiping Weng, Michael Snyder, Emmanouil T Dermitzakis, Robert E Thurman,[...]. Nature 2007
5

CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells.
S John Liu, Max A Horlbeck, Seung Woo Cho, Harjus S Birk, Martina Malatesta, Daniel He, Frank J Attenello, Jacqueline E Villalta, Min Y Cho, Yuwen Chen,[...]. Science 2017
390
5

Long non-coding RNAs: new players in cell differentiation and development.
Alessandro Fatica, Irene Bozzoni. Nat Rev Genet 2014
5

RNA-Seq: a revolutionary tool for transcriptomics.
Zhong Wang, Mark Gerstein, Michael Snyder. Nat Rev Genet 2009
5

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
5

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
5

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
5

FIMO: scanning for occurrences of a given motif.
Charles E Grant, Timothy L Bailey, William Stafford Noble. Bioinformatics 2011
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

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
5

The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells.
Tony Gutschner, Monika Hämmerle, Moritz Eissmann, Jeff Hsu, Youngsoo Kim, Gene Hung, Alexey Revenko, Gayatri Arun, Marion Stentrup, Matthias Gross,[...]. Cancer Res 2013
5

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
5

Natural RNA circles function as efficient microRNA sponges.
Thomas B Hansen, Trine I Jensen, Bettina H Clausen, Jesper B Bramsen, Bente Finsen, Christian K Damgaard, Jørgen Kjems. Nature 2013
4

Antisense transcription in the mammalian transcriptome.
S Katayama, Y Tomaru, T Kasukawa, K Waki, M Nakanishi, M Nakamura, H Nishida, C C Yap, M Suzuki, J Kawai,[...]. Science 2005
4

History, Discovery, and Classification of lncRNAs.
Julien Jarroux, Antonin Morillon, Marina Pinskaya. Adv Exp Med Biol 2017
434
4

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
4

Non-coding RNA.
John S Mattick, Igor V Makunin. Hum Mol Genet 2006
4

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
115
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.