A citation-based method for searching scientific literature

Preston R Arnold, Andrew D Wells, Xian C Li. Front Cell Dev Biol 2020
Times Cited: 60







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



Times Cited
  Times     Co-cited
Similarity


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
43

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
33

A Phase Separation Model for Transcriptional Control.
Denes Hnisz, Krishna Shrinivas, Richard A Young, Arup K Chakraborty, Phillip A Sharp. Cell 2017
711
26

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
221
25

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
23

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
23

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
23

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
21

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
20

Enhancer RNAs are an important regulatory layer of the epigenome.
Vittorio Sartorelli, Shannon M Lauberth. Nat Struct Mol Biol 2020
63
20

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
18

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
18

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
18

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
16


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

Developmental enhancers and chromosome topology.
Eileen E M Furlong, Michael Levine. Science 2018
195
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

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
16

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
16

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
16

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

Enhancer RNAs and regulated transcriptional programs.
Michael T Y Lam, Wenbo Li, Michael G Rosenfeld, Christopher K Glass. Trends Biochem Sci 2014
315
15

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus.
Sofia A Quinodoz, Noah Ollikainen, Barbara Tabak, Ali Palla, Jan Marten Schmidt, Elizabeth Detmar, Mason M Lai, Alexander A Shishkin, Prashant Bhat, Yodai Takei,[...]. Cell 2018
310
15

Topological domains in mammalian genomes identified by analysis of chromatin interactions.
Jesse R Dixon, Siddarth Selvaraj, Feng Yue, Audrey Kim, Yan Li, Yin Shen, Ming Hu, Jun S Liu, Bing Ren. Nature 2012
15

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
15

Enhancers as non-coding RNA transcription units: recent insights and future perspectives.
Wenbo Li, Dimple Notani, Michael G Rosenfeld. Nat Rev Genet 2016
376
13

Genome-wide quantitative enhancer activity maps identified by STARR-seq.
Cosmas D Arnold, Daniel Gerlach, Christoph Stelzer, Łukasz M Boryń, Martina Rath, Alexander Stark. Science 2013
507
13

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
13

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Erez Lieberman-Aiden, Nynke L van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R Lajoie, Peter J Sabo, Michael O Dorschner,[...]. Science 2009
13

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution.
Hannah K Long, Sara L Prescott, Joanna Wysocka. Cell 2016
375
13

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
17

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
13

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
13

Modification of enhancer chromatin: what, how, and why?
Eliezer Calo, Joanna Wysocka. Mol Cell 2013
779
13


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
11

Long-range enhancer-promoter contacts in gene expression control.
Stefan Schoenfelder, Peter Fraser. Nat Rev Genet 2019
295
11

Formation of Chromosomal Domains by Loop Extrusion.
Geoffrey Fudenberg, Maxim Imakaev, Carolyn Lu, Anton Goloborodko, Nezar Abdennur, Leonid A Mirny. Cell Rep 2016
766
11

A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
Suhas S P Rao, Miriam H Huntley, Neva C Durand, Elena K Stamenova, Ivan D Bochkov, James T Robinson, Adrian L Sanborn, Ido Machol, Arina D Omer, Eric S Lander,[...]. Cell 2014
11

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
11

CUT&Tag for efficient epigenomic profiling of small samples and single cells.
Hatice S Kaya-Okur, Steven J Wu, Christine A Codomo, Erica S Pledger, Terri D Bryson, Jorja G Henikoff, Kami Ahmad, Steven Henikoff. Nat Commun 2019
341
11

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
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
10

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates.
Won-Ki Cho, Jan-Hendrik Spille, Micca Hecht, Choongman Lee, Charles Li, Valentin Grube, Ibrahim I Cisse. Science 2018
488
10

Liquid-liquid phase separation in biology.
Anthony A Hyman, Christoph A Weber, Frank Jülicher. Annu Rev Cell Dev Biol 2014
10

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates.
Yang Eric Guo, John C Manteiga, Jonathan E Henninger, Benjamin R Sabari, Alessandra Dall'Agnese, Nancy M Hannett, Jan-Hendrik Spille, Lena K Afeyan, Alicia V Zamudio, Krishna Shrinivas,[...]. Nature 2019
209
10

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development.
Stefan Bonn, Robert P Zinzen, Charles Girardot, E Hilary Gustafson, Alexis Perez-Gonzalez, Nicolas Delhomme, Yad Ghavi-Helm, Bartek Wilczyński, Andrew Riddell, Eileen E M Furlong. Nat Genet 2012
326
10

An oestrogen-receptor-alpha-bound human chromatin interactome.
Melissa J Fullwood, Mei Hui Liu, You Fu Pan, Jun Liu, Han Xu, Yusoff Bin Mohamed, Yuriy L Orlov, Stoyan Velkov, Andrea Ho, Poh Huay Mei,[...]. Nature 2009
10

Enhancer Features that Drive Formation of Transcriptional Condensates.
Krishna Shrinivas, Benjamin R Sabari, Eliot L Coffey, Isaac A Klein, Ann Boija, Alicia V Zamudio, Jurian Schuijers, Nancy M Hannett, Phillip A Sharp, Richard A Young,[...]. Mol Cell 2019
118
10


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.