A citation-based method for searching scientific literature

Youtaro Shibayama, Stephanie Fanucchi, Musa M Mhlanga. Methods Mol Biol 2017
Times Cited: 8







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



Times Cited
  Times     Co-cited
Similarity


Activating RNAs associate with Mediator to enhance chromatin architecture and transcription.
Fan Lai, Ulf A Orom, Matteo Cesaroni, Malte Beringer, Dylan J Taatjes, Gerd A Blobel, Ramin Shiekhattar. Nature 2013
599
75

An atlas of active enhancers across human cell types and tissues.
Robin Andersson, Claudia Gebhard, Irene Miguel-Escalada, Ilka Hoof, Jette Bornholdt, Mette Boyd, Yun Chen, Xiaobei Zhao, Christian Schmidl, Takahiro Suzuki,[...]. Nature 2014
62

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation.
Wenbo Li, Dimple Notani, Qi Ma, Bogdan Tanasa, Esperanza Nunez, Aaron Yun Chen, Daria Merkurjev, Jie Zhang, Kenneth Ohgi, Xiaoyuan Song,[...]. Nature 2013
638
50

Enhanced Identification of Transcriptional Enhancers Provides Mechanistic Insights into Diseases.
Yasuhiro Murakawa, Masahito Yoshihara, Hideya Kawaji, Miki Nishikawa, Hatem Zayed, Harukazu Suzuki, Fantom Consortium, Yoshihide Hayashizaki. Trends Genet 2016
58
37

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
37

Unlinking an lncRNA from Its Associated cis Element.
Vikram R Paralkar, Cristian C Taborda, Peng Huang, Yu Yao, Andrew V Kossenkov, Rishi Prasad, Jing Luan, James O J Davies, Jim R Hughes, Ross C Hardison,[...]. Mol Cell 2016
155
37

Enhancer transcripts mark active estrogen receptor binding sites.
Nasun Hah, Shino Murakami, Anusha Nagari, Charles G Danko, W Lee Kraus. Genome Res 2013
322
37

Enhancer RNAs and regulated transcriptional programs.
Michael T Y Lam, Wenbo Li, Michael G Rosenfeld, Christopher K Glass. Trends Biochem Sci 2014
331
37

eRNAs are required for p53-dependent enhancer activity and gene transcription.
Carlos A Melo, Jarno Drost, Patrick J Wijchers, Harmen van de Werken, Elzo de Wit, Joachim A F Oude Vrielink, Ran Elkon, Sónia A Melo, Nicolas Léveillé, Raghu Kalluri,[...]. Mol Cell 2013
377
37

RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity.
Evangelos Pefanis, Jiguang Wang, Gerson Rothschild, Junghyun Lim, David Kazadi, Jianbo Sun, Alexander Federation, Jaime Chao, Oliver Elliott, Zhi-Ping Liu,[...]. Cell 2015
272
37

Imaging individual mRNA molecules using multiple singly labeled probes.
Arjun Raj, Patrick van den Bogaard, Scott A Rifkin, Alexander van Oudenaarden, Sanjay Tyagi. Nat Methods 2008
37

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.
Erik Arner, Carsten O Daub, Kristoffer Vitting-Seerup, Robin Andersson, Berit Lilje, Finn Drabløs, Andreas Lennartsson, Michelle Rönnerblad, Olga Hrydziuszko, Morana Vitezic,[...]. Science 2015
359
37

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA.
Dong Wang, Ivan Garcia-Bassets, Chris Benner, Wenbo Li, Xue Su, Yiming Zhou, Jinsong Qiu, Wen Liu, Minna U Kaikkonen, Kenneth A Ohgi,[...]. Nature 2011
622
25

Identifying transcription start sites and active enhancer elements using BruUV-seq.
Brian Magnuson, Artur Veloso, Killeen S Kirkconnell, Leonardo Carmo de Andrade Lima, Michelle T Paulsen, Emily A Ljungman, Karan Bedi, Jayendra Prasad, Thomas E Wilson, Mats Ljungman. Sci Rep 2015
19
25

Noncoding transcription at enhancers: general principles and functional models.
Gioacchino Natoli, Jean-Christophe Andrau. Annu Rev Genet 2012
264
25

Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription.
Minna U Kaikkonen, Nathanael J Spann, Sven Heinz, Casey E Romanoski, Karmel A Allison, Joshua D Stender, Hyun B Chun, David F Tough, Rab K Prinjha, Christopher Benner,[...]. Mol Cell 2013
440
25

A large fraction of extragenic RNA pol II transcription sites overlap enhancers.
Francesca De Santa, Iros Barozzi, Flore Mietton, Serena Ghisletti, Sara Polletti, Betsabeh Khoramian Tusi, Heiko Muller, Jiannis Ragoussis, Chia-Lin Wei, Gioacchino Natoli. PLoS Biol 2010
573
25


Epstein-Barr virus super-enhancer eRNAs are essential for MYC oncogene expression and lymphoblast proliferation.
Jun Liang, Hufeng Zhou, Catherine Gerdt, Min Tan, Tyler Colson, Kenneth M Kaye, Elliott Kieff, Bo Zhao. Proc Natl Acad Sci U S A 2016
54
25

Alterations of androgen receptor-regulated enhancer RNAs (eRNAs) contribute to enzalutamide resistance in castration-resistant prostate cancer.
Jingwen Zhao, Yu Zhao, Liguo Wang, Jun Zhang, R Jeffrey Karnes, Manish Kohli, Guixia Wang, Haojie Huang. Oncotarget 2016
27
25

Identification of Transcribed Enhancers by Genome-Wide Chromatin Immunoprecipitation Sequencing.
Steven Blinka, Michael H Reimer, Kirthi Pulakanti, Luca Pinello, Guo-Cheng Yuan, Sridhar Rao. Methods Mol Biol 2017
12
25

Enhancer-associated RNAs as therapeutic targets.
Nicolas Léveillé, Carlos A Melo, Reuven Agami. Expert Opin Biol Ther 2015
18
25

Precise maps of RNA polymerase reveal how promoters direct initiation and pausing.
Hojoong Kwak, Nicholas J Fuda, Leighton J Core, John T Lis. Science 2013
434
25

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
25

Integrator mediates the biogenesis of enhancer RNAs.
Fan Lai, Alessandro Gardini, Anda Zhang, Ramin Shiekhattar. Nature 2015
161
25

Considerations when investigating lncRNA function in vivo.
Andrew R Bassett, Asifa Akhtar, Denise P Barlow, Adrian P Bird, Neil Brockdorff, Denis Duboule, Anne Ephrussi, Anne C Ferguson-Smith, Thomas R Gingeras, Wilfried Haerty,[...]. Elife 2014
248
25

Spatial partitioning of the regulatory landscape of the X-inactivation centre.
Elphège P Nora, Bryan R Lajoie, Edda G Schulz, Luca Giorgetti, Ikuhiro Okamoto, Nicolas Servant, Tristan Piolot, Nynke L van Berkum, Johannes Meisig, John Sedat,[...]. Nature 2012
25

RNA Binding to CBP Stimulates Histone Acetylation and Transcription.
Daniel A Bose, Greg Donahue, Danny Reinberg, Ramin Shiekhattar, Roberto Bonasio, Shelley L Berger. Cell 2017
201
25

RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells.
Kok Hao Chen, Alistair N Boettiger, Jeffrey R Moffitt, Siyuan Wang, Xiaowei Zhuang. Science 2015
851
25

Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency.
Yul W Yang, Ryan A Flynn, Yong Chen, Kun Qu, Bingbing Wan, Kevin C Wang, Ming Lei, Howard Y Chang. Elife 2014
133
25

RNA-Seq: a revolutionary tool for transcriptomics.
Zhong Wang, Mark Gerstein, Michael Snyder. Nat Rev Genet 2009
25

Initial sequencing and analysis of the human genome.
E S Lander, L M Linton, B Birren, C Nusbaum, M C Zody, J Baldwin, K Devon, K Dewar, M Doyle, W FitzHugh,[...]. Nature 2001
25

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
25

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
25

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
25

Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display.
David M Shechner, Ezgi Hacisuleyman, Scott T Younger, John L Rinn. Nat Methods 2015
190
25

Unique features of long non-coding RNA biogenesis and function.
Jeffrey J Quinn, Howard Y Chang. Nat Rev Genet 2016
25

Master transcription factors and mediator establish super-enhancers at key cell identity genes.
Warren A Whyte, David A Orlando, Denes Hnisz, Brian J Abraham, Charles Y Lin, Michael H Kagey, Peter B Rahl, Tong Ihn Lee, Richard A Young. Cell 2013
25

eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci.
Kambiz Mousavi, Hossein Zare, Stefania Dell'orso, Lars Grontved, Gustavo Gutierrez-Cruz, Assia Derfoul, Gordon L Hager, Vittorio Sartorelli. Mol Cell 2013
320
25

A promoter-level mammalian expression atlas.
Alistair R R Forrest, Hideya Kawaji, Michael Rehli, J Kenneth Baillie, Michiel J L de Hoon, Vanja Haberle, Timo Lassmann, Ivan V Kulakovskiy, Marina Lizio, Masayoshi Itoh,[...]. Nature 2014
25

Enhancers as non-coding RNA transcription units: recent insights and future perspectives.
Wenbo Li, Dimple Notani, Michael G Rosenfeld. Nat Rev Genet 2016
401
25

Targeting Oncogenic Super Enhancers in MYC-Dependent AML Using a Small Molecule Activator of NR4A Nuclear Receptors.
S Greg Call, Ryan P Duren, Anil K Panigrahi, Loc Nguyen, Pablo R Freire, Sandra L Grimm, Cristian Coarfa, Orla M Conneely. Sci Rep 2020
15
25

Enhancer RNAs in cancer: regulation, mechanisms and therapeutic potential.
Joo-Hyung Lee, Feng Xiong, Wenbo Li. RNA Biol 2020
30
25

Transcription factor trapping by RNA in gene regulatory elements.
Alla A Sigova, Brian J Abraham, Xiong Ji, Benoit Molinie, Nancy M Hannett, Yang Eric Guo, Mohini Jangi, Cosmas C Giallourakis, Phillip A Sharp, Richard A Young. Science 2015
257
25

Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation.
Chen-Lin Hsieh, Teng Fei, Yiwen Chen, Tiantian Li, Yanfei Gao, Xiaodong Wang, Tong Sun, Christopher J Sweeney, Gwo-Shu Mary Lee, Shaoyong Chen,[...]. Proc Natl Acad Sci U S A 2014
237
25

Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers.
Xiaoyang Zhang, Peter S Choi, Joshua M Francis, Marcin Imielinski, Hideo Watanabe, Andrew D Cherniack, Matthew Meyerson. Nat Genet 2016
212
25

RNAs interact with BRD4 to promote enhanced chromatin engagement and transcription activation.
Homa Rahnamoun, Jihoon Lee, Zhengxi Sun, Hanbin Lu, Kristen M Ramsey, Elizabeth A Komives, Shannon M Lauberth. Nat Struct Mol Biol 2018
73
25


Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA.
Nicolas Léveillé, Carlos A Melo, Koos Rooijers, Angel Díaz-Lagares, Sonia A Melo, Gozde Korkmaz, Rui Lopes, Farhad Akbari Moqadam, Ana R Maia, Patrick J Wijchers,[...]. Nat Commun 2015
128
25

TT-seq maps the human transient transcriptome.
Björn Schwalb, Margaux Michel, Benedikt Zacher, Katja Frühauf, Carina Demel, Achim Tresch, Julien Gagneur, Patrick Cramer. Science 2016
217
25


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.