A citation-based method for searching scientific literature

Qi Ma, Feng Yang, Carlos Mackintosh, Ranveer Singh Jayani, Soohwan Oh, Chunyu Jin, Sreejith Janardhanan Nair, Daria Merkurjev, Wubin Ma, Stephanie Allen, Dong Wang, Angels Almenar-Queralt, Ivan Garcia-Bassets. Cell Rep 2020
Times Cited: 19







List of co-cited articles
109 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
36

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
31

Chemotherapy-Induced Distal Enhancers Drive Transcriptional Programs to Maintain the Chemoresistant State in Ovarian Cancer.
Stephen Shang, Jiekun Yang, Amir A Jazaeri, Alexander James Duval, Turan Tufan, Natasha Lopes Fischer, Mouadh Benamar, Fadila Guessous, Inyoung Lee, Robert M Campbell,[...]. Cancer Res 2019
20
31

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
26

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
881
21

A Phase Separation Model for Transcriptional Control.
Denes Hnisz, Krishna Shrinivas, Richard A Young, Arup K Chakraborty, Phillip A Sharp. Cell 2017
770
21

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
21

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
21

Modification of enhancer chromatin: what, how, and why?
Eliezer Calo, Joanna Wysocka. Mol Cell 2013
799
21

A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations.
Sreenath V Sharma, Diana Y Lee, Bihua Li, Margaret P Quinlan, Fumiyuki Takahashi, Shyamala Maheswaran, Ultan McDermott, Nancy Azizian, Lee Zou, Michael A Fischbach,[...]. Cell 2010
21

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
21

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
21

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



CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes.
Luke A Gilbert, Matthew H Larson, Leonardo Morsut, Zairan Liu, Gloria A Brar, Sandra E Torres, Noam Stern-Ginossar, Onn Brandman, Evan H Whitehead, Jennifer A Doudna,[...]. Cell 2013
15

Super-enhancers in cancer.
Palaniraja Thandapani. Pharmacol Ther 2019
35
15

BET Inhibitors Suppress ALDH Activity by Targeting ALDH1A1 Super-Enhancer in Ovarian Cancer.
Yuhki Yokoyama, Hengrui Zhu, Jeong Heon Lee, Andrew V Kossenkov, Sherry Y Wu, Jayamanna M Wickramasinghe, Xiangfan Yin, Katherine C Palozola, Alessandro Gardini, Louise C Showe,[...]. Cancer Res 2016
82
15

Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer.
Shaokun Shu, Charles Y Lin, Housheng Hansen He, Robert M Witwicki, Doris P Tabassum, Justin M Roberts, Michalina Janiszewska, Sung Jin Huh, Yi Liang, Jeremy Ryan,[...]. Nature 2016
356
15

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
15

Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia.
Charles C Bell, Katie A Fennell, Yih-Chih Chan, Florian Rambow, Miriam M Yeung, Dane Vassiliadis, Luis Lara, Paul Yeh, Luciano G Martelotto, Aljosja Rogiers,[...]. Nat Commun 2019
74
15

Adaptive Chromatin Remodeling Drives Glioblastoma Stem Cell Plasticity and Drug Tolerance.
Brian B Liau, Cem Sievers, Laura K Donohue, Shawn M Gillespie, William A Flavahan, Tyler E Miller, Andrew S Venteicher, Christine H Hebert, Christopher D Carey, Scott J Rodig,[...]. Cell Stem Cell 2017
223
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

The novel BET bromodomain inhibitor BI 894999 represses super-enhancer-associated transcription and synergizes with CDK9 inhibition in AML.
Daniel Gerlach, Ulrike Tontsch-Grunt, Anke Baum, Johannes Popow, Dirk Scharn, Marco H Hofmann, Harald Engelhardt, Onur Kaya, Janina Beck, Norbert Schweifer,[...]. Oncogene 2018
45
15

Enhancer Reprogramming Promotes Pancreatic Cancer Metastasis.
Jae-Seok Roe, Chang-Il Hwang, Tim D D Somerville, Joseph P Milazzo, Eun Jung Lee, Brandon Da Silva, Laura Maiorino, Hervé Tiriac, C Megan Young, Koji Miyabayashi,[...]. Cell 2017
206
15

Enhancer reprogramming driven by high-order assemblies of transcription factors promotes phenotypic plasticity and breast cancer endocrine resistance.
Mingjun Bi, Zhao Zhang, Yi-Zhou Jiang, Pengya Xue, Hu Wang, Zhao Lai, Xiaoyong Fu, Carmine De Angelis, Yue Gong, Zhen Gao,[...]. Nat Cell Biol 2020
35
15

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
588
10

Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
10

Combinatorial function of transcription factors and cofactors.
Franziska Reiter, Sebastian Wienerroither, Alexander Stark. Curr Opin Genet Dev 2017
137
10

Discovery and saturation analysis of cancer genes across 21 tumour types.
Michael S Lawrence, Petar Stojanov, Craig H Mermel, James T Robinson, Levi A Garraway, Todd R Golub, Matthew Meyerson, Stacey B Gabriel, Eric S Lander, Gad Getz. Nature 2014
10

p53 regulates enhancer accessibility and activity in response to DNA damage.
Scott T Younger, John L Rinn. Nucleic Acids Res 2017
29
10

Long-range enhancer-promoter contacts in gene expression control.
Stefan Schoenfelder, Peter Fraser. Nat Rev Genet 2019
333
10

Control of p53-dependent transcription and enhancer activity by the p53 family member p63.
Gizem Karsli Uzunbas, Faraz Ahmed, Morgan A Sammons. J Biol Chem 2019
13
15

iRegulon: from a gene list to a gene regulatory network using large motif and track collections.
Rekin's Janky, Annelien Verfaillie, Hana Imrichová, Bram Van de Sande, Laura Standaert, Valerie Christiaens, Gert Hulselmans, Koen Herten, Marina Naval Sanchez, Delphine Potier,[...]. PLoS Comput Biol 2014
457
10

Transcription factors: from enhancer binding to developmental control.
François Spitz, Eileen E M Furlong. Nat Rev Genet 2012
10

The accessible chromatin landscape of the human genome.
Robert E Thurman, Eric Rynes, Richard Humbert, Jeff Vierstra, Matthew T Maurano, Eric Haugen, Nathan C Sheffield, Andrew B Stergachis, Hao Wang, Benjamin Vernot,[...]. Nature 2012
10

Genome engineering using the CRISPR-Cas9 system.
F Ann Ran, Patrick D Hsu, Jason Wright, Vineeta Agarwala, David A Scott, Feng Zhang. Nat Protoc 2013
10

RNA-guided human genome engineering via Cas9.
Prashant Mali, Luhan Yang, Kevin M Esvelt, John Aach, Marc Guell, James E DiCarlo, Julie E Norville, George M Church. Science 2013
10

Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations.
Charles P Fulco, Joseph Nasser, Thouis R Jones, Glen Munson, Drew T Bergman, Vidya Subramanian, Sharon R Grossman, Rockwell Anyoha, Benjamin R Doughty, Tejal A Patwardhan,[...]. Nat Genet 2019
199
10

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
366
10

FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription.
Mathieu Lupien, Jérôme Eeckhoute, Clifford A Meyer, Qianben Wang, Yong Zhang, Wei Li, Jason S Carroll, X Shirley Liu, Myles Brown. Cell 2008
680
10

The role of enhancers in cancer.
Inderpreet Sur, Jussi Taipale. Nat Rev Cancer 2016
192
10

CDK7 Inhibition Suppresses Castration-Resistant Prostate Cancer through MED1 Inactivation.
Reyaz Ur Rasool, Ramakrishnan Natesan, Qu Deng, Shweta Aras, Priti Lal, Samuel Sander Effron, Erick Mitchell-Velasquez, Jessica M Posimo, Shannon Carskadon, Sylvan C Baca,[...]. Cancer Discov 2019
33
10

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
255
10

Selective inhibition of BET bromodomains.
Panagis Filippakopoulos, Jun Qi, Sarah Picaud, Yao Shen, William B Smith, Oleg Fedorov, Elizabeth M Morse, Tracey Keates, Tyler T Hickman, Ildiko Felletar,[...]. Nature 2010
10

SEdb: a comprehensive human super-enhancer database.
Yong Jiang, Fengcui Qian, Xuefeng Bai, Yuejuan Liu, Qiuyu Wang, Bo Ai, Xiaole Han, Shanshan Shi, Jian Zhang, Xuecang Li,[...]. Nucleic Acids Res 2019
79
10

Selective inhibition of the BD2 bromodomain of BET proteins in prostate cancer.
Emily J Faivre, Keith F McDaniel, Daniel H Albert, Srinivasa R Mantena, Joshua P Plotnik, Denise Wilcox, Lu Zhang, Mai H Bui, George S Sheppard, Le Wang,[...]. Nature 2020
143
10


Darolutamide antagonizes androgen signaling by blocking enhancer and super-enhancer activation.
Simon J Baumgart, Ekaterina Nevedomskaya, Ralf Lesche, Richard Newman, Dominik Mumberg, Bernard Haendler. Mol Oncol 2020
11
18


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.