A citation-based method for searching scientific literature

James E Bradner, Denes Hnisz, Richard A Young. Cell 2017
Times Cited: 474







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



Times Cited
  Times     Co-cited
Similarity


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

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
20

Targeting transcription regulation in cancer with a covalent CDK7 inhibitor.
Nicholas Kwiatkowski, Tinghu Zhang, Peter B Rahl, Brian J Abraham, Jessica Reddy, Scott B Ficarro, Anahita Dastur, Arnaud Amzallag, Sridhar Ramaswamy, Bethany Tesar,[...]. Nature 2014
480
17

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
15

Transcriptional amplification in tumor cells with elevated c-Myc.
Charles Y Lin, Jakob Lovén, Peter B Rahl, Ronald M Paranal, Christopher B Burge, James E Bradner, Tong Ihn Lee, Richard A Young. Cell 2012
956
12

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
12

CDK7-dependent transcriptional addiction in triple-negative breast cancer.
Yubao Wang, Tinghu Zhang, Nicholas Kwiatkowski, Brian J Abraham, Tong Ihn Lee, Shaozhen Xie, Haluk Yuzugullu, Thanh Von, Heyuan Li, Ziao Lin,[...]. Cell 2015
250
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

Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element.
Marc R Mansour, Brian J Abraham, Lars Anders, Alla Berezovskaya, Alejandro Gutierrez, Adam D Durbin, Julia Etchin, Lee Lawton, Stephen E Sallan, Lewis B Silverman,[...]. Science 2014
443
10

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
10

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
10

Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
9

Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers.
Denes Hnisz, Jurian Schuijers, Charles Y Lin, Abraham S Weintraub, Brian J Abraham, Tong Ihn Lee, James E Bradner, Richard A Young. Mol Cell 2015
260
9

Covalent targeting of remote cysteine residues to develop CDK12 and CDK13 inhibitors.
Tinghu Zhang, Nicholas Kwiatkowski, Calla M Olson, Sarah E Dixon-Clarke, Brian J Abraham, Ann K Greifenberg, Scott B Ficarro, Jonathan M Elkins, Yanke Liang, Nancy M Hannett,[...]. Nat Chem Biol 2016
156
9

Selective gene dependencies in MYCN-amplified neuroblastoma include the core transcriptional regulatory circuitry.
Adam D Durbin, Mark W Zimmerman, Neekesh V Dharia, Brian J Abraham, Amanda Balboni Iniguez, Nina Weichert-Leahey, Shuning He, John M Krill-Burger, David E Root, Francisca Vazquez,[...]. Nat Genet 2018
92
9

CDK7 inhibition suppresses super-enhancer-linked oncogenic transcription in MYCN-driven cancer.
Edmond Chipumuro, Eugenio Marco, Camilla L Christensen, Nicholas Kwiatkowski, Tinghu Zhang, Clark M Hatheway, Brian J Abraham, Bandana Sharma, Caleb Yeung, Abigail Altabef,[...]. Cell 2014
358
9

Cancer statistics, 2020.
Rebecca L Siegel, Kimberly D Miller, Ahmedin Jemal. CA Cancer J Clin 2020
9

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
9


The Human Transcription Factors.
Samuel A Lambert, Arttu Jolma, Laura F Campitelli, Pratyush K Das, Yimeng Yin, Mihai Albu, Xiaoting Chen, Jussi Taipale, Timothy R Hughes, Matthew T Weirauch. Cell 2018
715
8

Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells.
Robin M Meyers, Jordan G Bryan, James M McFarland, Barbara A Weir, Ann E Sizemore, Han Xu, Neekesh V Dharia, Phillip G Montgomery, Glenn S Cowley, Sasha Pantel,[...]. Nat Genet 2017
668
8

Targeting super-enhancer-associated oncogenes in oesophageal squamous cell carcinoma.
Yan-Yi Jiang, De-Chen Lin, Anand Mayakonda, Masaharu Hazawa, Ling-Wen Ding, Wen-Wen Chien, Liang Xu, Ye Chen, Jin-Fen Xiao, William Senapedis,[...]. Gut 2017
115
8

The Mediator complex: a central integrator of transcription.
Benjamin L Allen, Dylan J Taatjes. Nat Rev Mol Cell Biol 2015
472
8

Super-Enhancer-Driven Transcriptional Dependencies in Cancer.
Satyaki Sengupta, Rani E George. Trends Cancer 2017
116
8

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
8

c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells.
Zuqin Nie, Gangqing Hu, Gang Wei, Kairong Cui, Arito Yamane, Wolfgang Resch, Ruoning Wang, Douglas R Green, Lino Tessarollo, Rafael Casellas,[...]. Cell 2012
704
7

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
7

Development of a Selective CDK7 Covalent Inhibitor Reveals Predominant Cell-Cycle Phenotype.
Calla M Olson, Yanke Liang, Alan Leggett, Woojun D Park, Lianbo Li, Caitlin E Mills, Selma Z Elsarrag, Scott B Ficarro, Tinghu Zhang, Robert Düster,[...]. Cell Chem Biol 2019
55
12


Discovery and Characterization of SY-1365, a Selective, Covalent Inhibitor of CDK7.
Shanhu Hu, Jason J Marineau, Nisha Rajagopal, Kristin B Hamman, Yoon Jong Choi, Darby R Schmidt, Nan Ke, Liv Johannessen, Michael J Bradley, David A Orlando,[...]. Cancer Res 2019
54
12

CDK7 Inhibition Potentiates Genome Instability Triggering Anti-tumor Immunity in Small Cell Lung Cancer.
Hua Zhang, Camilla L Christensen, Ruben Dries, Matthew G Oser, Jiehui Deng, Brian Diskin, Fei Li, Yuanwang Pan, Xuzhu Zhang, Yandong Yin,[...]. Cancer Cell 2020
78
8

The history and future of targeting cyclin-dependent kinases in cancer therapy.
Uzma Asghar, Agnieszka K Witkiewicz, Nicholas C Turner, Erik S Knudsen. Nat Rev Drug Discov 2015
891
7

ICEC0942, an Orally Bioavailable Selective Inhibitor of CDK7 for Cancer Treatment.
Hetal Patel, Manikandan Periyasamy, Georgina P Sava, Alexander Bondke, Brian W Slafer, Sebastian H B Kroll, Marion Barbazanges, Richard Starkey, Silvia Ottaviani, Alison Harrod,[...]. Mol Cancer Ther 2018
50
14

Targeting transcriptional addictions in small cell lung cancer with a covalent CDK7 inhibitor.
Camilla L Christensen, Nicholas Kwiatkowski, Brian J Abraham, Julian Carretero, Fatima Al-Shahrour, Tinghu Zhang, Edmond Chipumuro, Grit S Herter-Sprie, Esra A Akbay, Abigail Altabef,[...]. Cancer Cell 2014
274
7

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
565
7

BET bromodomain inhibition as a therapeutic strategy to target c-Myc.
Jake E Delmore, Ghayas C Issa, Madeleine E Lemieux, Peter B Rahl, Junwei Shi, Hannah M Jacobs, Efstathios Kastritis, Timothy Gilpatrick, Ronald M Paranal, Jun Qi,[...]. Cell 2011
7

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
7

The role of enhancers in cancer.
Inderpreet Sur, Jussi Taipale. Nat Rev Cancer 2016
187
6

Small-molecule targeting of brachyury transcription factor addiction in chordoma.
Tanaz Sharifnia, Mathias J Wawer, Ting Chen, Qing-Yuan Huang, Barbara A Weir, Ann Sizemore, Matthew A Lawlor, Amy Goodale, Glenn S Cowley, Francisca Vazquez,[...]. Nat Med 2019
61
9

Cyclin-dependent kinases.
Marcos Malumbres. Genome Biol 2014
667
6

THZ1 Reveals Roles for Cdk7 in Co-transcriptional Capping and Pausing.
Kyle A Nilson, Jiannan Guo, Michael E Turek, John E Brogie, Elizabeth Delaney, Donal S Luse, David H Price. Mol Cell 2015
98
6

Preclinical Efficacy and Molecular Mechanism of Targeting CDK7-Dependent Transcriptional Addiction in Ovarian Cancer.
Zhenfeng Zhang, Huixin Peng, Xiaojie Wang, Xia Yin, Pengfei Ma, Ying Jing, Mei-Chun Cai, Jin Liu, Meiying Zhang, Shengzhe Zhang,[...]. Mol Cancer Ther 2017
40
15

Therapeutic Targeting of CDK12/CDK13 in Triple-Negative Breast Cancer.
Victor Quereda, Simon Bayle, Francesca Vena, Sylvia M Frydman, Andrii Monastyrskyi, William R Roush, Derek R Duckett. Cancer Cell 2019
89
6

What are super-enhancers?
Sebastian Pott, Jason D Lieb. Nat Genet 2015
365
6

Next-generation characterization of the Cancer Cell Line Encyclopedia.
Mahmoud Ghandi, Franklin W Huang, Judit Jané-Valbuena, Gregory V Kryukov, Christopher C Lo, E Robert McDonald, Jordi Barretina, Ellen T Gelfand, Craig M Bielski, Haoxin Li,[...]. Nature 2019
903
6

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
6


The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.
Jordi Barretina, Giordano Caponigro, Nicolas Stransky, Kavitha Venkatesan, Adam A Margolin, Sungjoon Kim, Christopher J Wilson, Joseph Lehár, Gregory V Kryukov, Dmitriy Sonkin,[...]. Nature 2012
6

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg. Genome Biol 2009
6

Mediator kinase inhibition further activates super-enhancer-associated genes in AML.
Henry E Pelish, Brian B Liau, Ioana I Nitulescu, Anupong Tangpeerachaikul, Zachary C Poss, Diogo H Da Silva, Brittany T Caruso, Alexander Arefolov, Olugbeminiyi Fadeyi, Amanda L Christie,[...]. Nature 2015
217
6


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.