A citation-based method for searching scientific literature

Chen-Lin Hsieh, Teng Fei, Yiwen Chen, Tiantian Li, Yanfei Gao, Xiaodong Wang, Tong Sun, Christopher J Sweeney, Gwo-Shu Mary Lee, Shaoyong Chen, Steven P Balk, Xiaole Shirley Liu, Myles Brown, Philip W Kantoff. Proc Natl Acad Sci U S A 2014
Times Cited: 221







List of co-cited articles
1082 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


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
610
66

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
56

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
44

Enhancer RNA facilitates NELF release from immediate early genes.
Katie Schaukowitch, Jae-Yeol Joo, Xihui Liu, Jonathan K Watts, Carlos Martinez, Tae-Kyung Kim. Mol Cell 2014
242
43

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
582
40

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
308
36

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
557
35

Enhancer transcripts mark active estrogen receptor binding sites.
Nasun Hah, Shino Murakami, Anusha Nagari, Charles G Danko, W Lee Kraus. Genome Res 2013
312
31

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
367
31

Enhancers as non-coding RNA transcription units: recent insights and future perspectives.
Wenbo Li, Dimple Notani, Michael G Rosenfeld. Nat Rev Genet 2016
376
31

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
345
30

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
182
30

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
28

Super-enhancers in the control of cell identity and disease.
Denes Hnisz, Brian J Abraham, Tong Ihn Lee, Ashley Lau, Violaine Saint-André, Alla A Sigova, Heather A Hoke, Richard A Young. Cell 2013
27


Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription.
Michael T Y Lam, Han Cho, Hanna P Lesch, David Gosselin, Sven Heinz, Yumiko Tanaka-Oishi, Christopher Benner, Minna U Kaikkonen, Aneeza S Kim, Mika Kosaka,[...]. Nature 2013
380
25

A Muscle-Specific Enhancer RNA Mediates Cohesin Recruitment and Regulates Transcription In trans.
Pei-Fang Tsai, Stefania Dell'Orso, Joseph Rodriguez, Karinna O Vivanco, Kyung-Dae Ko, Kan Jiang, Aster H Juan, Aishe A Sarshad, Laura Vian, Michelle Tran,[...]. Mol Cell 2018
67
37

Coactivator condensation at super-enhancers links phase separation and gene control.
Benjamin R Sabari, Alessandra Dall'Agnese, Ann Boija, Isaac A Klein, Eliot L Coffey, Krishna Shrinivas, Brian J Abraham, Nancy M Hannett, Alicia V Zamudio, John C Manteiga,[...]. Science 2018
809
24

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
602
24

Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters.
Frederic Koch, Romain Fenouil, Marta Gut, Pierre Cauchy, Thomas K Albert, Joaquin Zacarias-Cabeza, Salvatore Spicuglia, Albane Lamy de la Chapelle, Martin Heidemann, Corinna Hintermair,[...]. Nat Struct Mol Biol 2011
211
22

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
239
22

Transcriptional landscape and clinical utility of enhancer RNAs for eRNA-targeted therapy in cancer.
Zhao Zhang, Joo-Hyung Lee, Hang Ruan, Youqiong Ye, Joanna Krakowiak, Qingsong Hu, Yu Xiang, Jing Gong, Bingying Zhou, Li Wang,[...]. Nat Commun 2019
68
32

Noncoding transcription at enhancers: general principles and functional models.
Gioacchino Natoli, Jean-Christophe Andrau. Annu Rev Genet 2012
258
21

Histone H3K27ac separates active from poised enhancers and predicts developmental state.
Menno P Creyghton, Albert W Cheng, G Grant Welstead, Tristan Kooistra, Bryce W Carey, Eveline J Steine, Jacob Hanna, Michael A Lodato, Garrett M Frampton, Phillip A Sharp,[...]. Proc Natl Acad Sci U S A 2010
21

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription.
Olga Mikhaylichenko, Vladyslav Bondarenko, Dermot Harnett, Ignacio E Schor, Matilda Males, Rebecca R Viales, Eileen E M Furlong. Genes Dev 2018
110
21

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
419
20

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
19

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
60
31

A Phase Separation Model for Transcriptional Control.
Denes Hnisz, Krishna Shrinivas, Richard A Young, Arup K Chakraborty, Phillip A Sharp. Cell 2017
711
18

The long-range interaction landscape of gene promoters.
Amartya Sanyal, Bryan R Lajoie, Gaurav Jain, Job Dekker. Nature 2012
950
17

Mediator and cohesin connect gene expression and chromatin architecture.
Michael H Kagey, Jamie J Newman, Steve Bilodeau, Ye Zhan, David A Orlando, Nynke L van Berkum, Christopher C Ebmeier, Jesse Goossens, Peter B Rahl, Stuart S Levine,[...]. Nature 2010
17

RNA transcribed from a distal enhancer is required for activating the chromatin at the promoter of the gonadotropin α-subunit gene.
Lilach Pnueli, Sergei Rudnizky, Yahav Yosefzon, Philippa Melamed. Proc Natl Acad Sci U S A 2015
62
27

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
260
17

Activation of P-TEFb by Androgen Receptor-Regulated Enhancer RNAs in Castration-Resistant Prostate Cancer.
Yu Zhao, Liguo Wang, Shancheng Ren, Lan Wang, Patrick R Blackburn, Melissa S McNulty, Xu Gao, Meng Qiao, Robert L Vessella, Manish Kohli,[...]. Cell Rep 2016
63
25

The Super-Enhancer-Derived alncRNA-EC7/Bloodlinc Potentiates Red Blood Cell Development in trans.
Juan R Alvarez-Dominguez, Marko Knoll, Austin A Gromatzky, Harvey F Lodish. Cell Rep 2017
46
34


Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains.
Ann Boija, Isaac A Klein, Benjamin R Sabari, Alessandra Dall'Agnese, Eliot L Coffey, Alicia V Zamudio, Charles H Li, Krishna Shrinivas, John C Manteiga, Nancy M Hannett,[...]. Cell 2018
529
16

Widespread transcriptional pausing and elongation control at enhancers.
Telmo Henriques, Benjamin S Scruggs, Michiko O Inouye, Ginger W Muse, Lucy H Williams, Adam B Burkholder, Christopher A Lavender, David C Fargo, Karen Adelman. Genes Dev 2018
157
16

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
52
28

Integrator mediates the biogenesis of enhancer RNAs.
Fan Lai, Alessandro Gardini, Anda Zhang, Ramin Shiekhattar. Nature 2015
148
15

Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly.
Sreejith J Nair, Lu Yang, Dario Meluzzi, Soohwan Oh, Feng Yang, Meyer J Friedman, Susan Wang, Tom Suter, Ibraheem Alshareedah, Amir Gamliel,[...]. Nat Struct Mol Biol 2019
122
15

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.
Leighton J Core, André L Martins, Charles G Danko, Colin T Waters, Adam Siepel, John T Lis. Nat Genet 2014
354
15

Diversity and Emerging Roles of Enhancer RNA in Regulation of Gene Expression and Cell Fate.
Preston R Arnold, Andrew D Wells, Xian C Li. Front Cell Dev Biol 2020
60
25

Selective inhibition of tumor oncogenes by disruption of super-enhancers.
Jakob Lovén, Heather A Hoke, Charles Y Lin, Ashley Lau, David A Orlando, Christopher R Vakoc, James E Bradner, Tong Ihn Lee, Richard A Young. Cell 2013
14

Enhancer RNAs and regulated transcriptional programs.
Michael T Y Lam, Wenbo Li, Michael G Rosenfeld, Christopher K Glass. Trends Biochem Sci 2014
315
14

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.
Nathaniel D Heintzman, Rhona K Stuart, Gary Hon, Yutao Fu, Christina W Ching, R David Hawkins, Leah O Barrera, Sara Van Calcar, Chunxu Qu, Keith A Ching,[...]. Nat Genet 2007
14

HPSE enhancer RNA promotes cancer progression through driving chromatin looping and regulating hnRNPU/p300/EGR1/HPSE axis.
Wanju Jiao, Yajun Chen, Huajie Song, Dan Li, Hong Mei, Feng Yang, Erhu Fang, Xiaojing Wang, Kai Huang, Liduan Zheng,[...]. Oncogene 2018
44
29

Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus.
Jian-Feng Xiang, Qing-Fei Yin, Tian Chen, Yang Zhang, Xiao-Ou Zhang, Zheng Wu, Shaofeng Zhang, Hai-Bin Wang, Junhui Ge, Xuhua Lu,[...]. Cell Res 2014
440
12

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples.
Han Chen, Chunyan Li, Xinxin Peng, Zhicheng Zhou, John N Weinstein, Han Liang. Cell 2018
116
12

A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells.
Nasun Hah, Charles G Danko, Leighton Core, Joshua J Waterfall, Adam Siepel, John T Lis, W Lee Kraus. Cell 2011
341
12


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.