A citation-based method for searching scientific literature

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, Eirene Markenscoff-Papadimitriou, Dietmar Kuhl, Haruhiko Bito, Paul F Worley, Gabriel Kreiman, Michael E Greenberg. Nature 2010
Times Cited: 1543







List of co-cited articles
1137 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


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
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
562
33

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
254
28

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
622
24

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
22

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
228
22

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
20

Enhancers as non-coding RNA transcription units: recent insights and future perspectives.
Wenbo Li, Dimple Notani, Michael G Rosenfeld. Nat Rev Genet 2016
386
19

Model-based analysis of ChIP-Seq (MACS).
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
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
347
18

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
359
17

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
189
17


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
16

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
15


The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
15

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
371
15

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
15

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
78
19

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
246
14


Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
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
13

Enhancer transcripts mark active estrogen receptor binding sites.
Nasun Hah, Shino Murakami, Anusha Nagari, Charles G Danko, W Lee Kraus. Genome Res 2013
315
13

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
13

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
72
18

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
160
13

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
12

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
12

A unique chromatin signature uncovers early developmental enhancers in humans.
Alvaro Rada-Iglesias, Ruchi Bajpai, Tomek Swigut, Samantha A Brugmann, Ryan A Flynn, Joanna Wysocka. Nature 2011
12

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
12

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
12

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
853
12

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
586
12

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
422
11

deepTools2: a next generation web server for deep-sequencing data analysis.
Fidel Ramírez, Devon P Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S Richter, Steffen Heyne, Friederike Dündar, Thomas Manke. Nucleic Acids Res 2016
11

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
312
11

Determinants of enhancer and promoter activities of regulatory elements.
Robin Andersson, Albin Sandelin. Nat Rev Genet 2020
163
11

A Phase Separation Model for Transcriptional Control.
Denes Hnisz, Krishna Shrinivas, Richard A Young, Arup K Chakraborty, Phillip A Sharp. Cell 2017
746
11

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
429
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
212
10

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
608
10

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
10

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
208
10


Noncoding transcription at enhancers: general principles and functional models.
Gioacchino Natoli, Jean-Christophe Andrau. Annu Rev Genet 2012
261
10

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
115
10

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
383
10

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
9


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.