A citation-based method for searching scientific literature

Sebastian Pott, Jason D Lieb. Nat Genet 2015
Times Cited: 371







List of co-cited articles
969 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
64

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
63

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
43

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
23

A Phase Separation Model for Transcriptional Control.
Denes Hnisz, Krishna Shrinivas, Richard A Young, Arup K Chakraborty, Phillip A Sharp. Cell 2017
770
19

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants.
Stephen C J Parker, Michael L Stitzel, D Leland Taylor, Jose Miguel Orozco, Michael R Erdos, Jennifer A Akiyama, Kelly Lammerts van Bueren, Peter S Chines, Narisu Narisu, Brian L Black,[...]. Proc Natl Acad Sci U S A 2013
428
18

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
17

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
17

Genetic dissection of the α-globin super-enhancer in vivo.
Deborah Hay, Jim R Hughes, Christian Babbs, James O J Davies, Bryony J Graham, Lars Hanssen, Mira T Kassouf, A Marieke Marieke Oudelaar, Jacqueline A Sharpe, Maria C Suciu,[...]. Nat Genet 2016
188
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
588
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
16

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
16


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
15

Super-Enhancer-Driven Transcriptional Dependencies in Cancer.
Satyaki Sengupta, Rani E George. Trends Cancer 2017
118
14

Dissecting super-enhancer hierarchy based on chromatin interactions.
Jialiang Huang, Kailong Li, Wenqing Cai, Xin Liu, Yuannyu Zhang, Stuart H Orkin, Jian Xu, Guo-Cheng Yuan. Nat Commun 2018
101
14

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
14

Hierarchy within the mammary STAT5-driven Wap super-enhancer.
Ha Youn Shin, Michaela Willi, Kyung HyunYoo, Xianke Zeng, Chaochen Wang, Gil Metser, Lothar Hennighausen. Nat Genet 2016
140
13

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
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


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
531
12

Long-range enhancer-promoter contacts in gene expression control.
Stefan Schoenfelder, Peter Fraser. Nat Rev Genet 2019
333
12

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
263
11

Developmental enhancers and chromosome topology.
Eileen E M Furlong, Michael Levine. Science 2018
207
11

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
11

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
10

A high-resolution map of the three-dimensional chromatin interactome in human cells.
Fulai Jin, Yan Li, Jesse R Dixon, Siddarth Selvaraj, Zhen Ye, Ah Young Lee, Chia-An Yen, Anthony D Schmitt, Celso A Espinoza, Bing Ren. Nature 2013
748
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

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
448
10

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

Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.
Guoliang Li, Xiaoan Ruan, Raymond K Auerbach, Kuljeet Singh Sandhu, Meizhen Zheng, Ping Wang, Huay Mei Poh, Yufen Goh, Joanne Lim, Jingyao Zhang,[...]. Cell 2012
809
10

Modification of enhancer chromatin: what, how, and why?
Eliezer Calo, Joanna Wysocka. Mol Cell 2013
799
10

NF-κB directs dynamic super enhancer formation in inflammation and atherogenesis.
Jonathan D Brown, Charles Y Lin, Qiong Duan, Gabriel Griffin, Alexander Federation, Ronald M Paranal, Steven Bair, Gail Newton, Andrew Lichtman, Andrew Kung,[...]. Mol Cell 2014
379
9

Is a super-enhancer greater than the sum of its parts?
Noah Dukler, Brad Gulko, Yi-Fei Huang, Adam Siepel. Nat Genet 2016
39
23

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
9

dbSUPER: a database of super-enhancers in mouse and human genome.
Aziz Khan, Xuegong Zhang. Nucleic Acids Res 2016
204
9

Expanded encyclopaedias of DNA elements in the human and mouse genomes.
Jill E Moore, Michael J Purcaro, Henry E Pratt, Charles B Epstein, Noam Shoresh, Jessika Adrian, Trupti Kawli, Carrie A Davis, Alexander Dobin, Rajinder Kaul,[...]. Nature 2020
357
9

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
487
9

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
9



Super-enhancer function and its application in cancer targeted therapy.
Faqing Tang, Zongbei Yang, Yuan Tan, Yuejin Li. NPJ Precis Oncol 2020
32
25

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution.
Hannah K Long, Sara L Prescott, Joanna Wysocka. Cell 2016
396
8

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
8

Transcription factor cooperativity in early adipogenic hotspots and super-enhancers.
Rasmus Siersbæk, Atefeh Rabiee, Ronni Nielsen, Simone Sidoli, Sofie Traynor, Anne Loft, Lars La Cour Poulsen, Adelina Rogowska-Wrzesinska, Ole N Jensen, Susanne Mandrup. Cell Rep 2014
157
8

YY1 Is a Structural Regulator of Enhancer-Promoter Loops.
Abraham S Weintraub, Charles H Li, Alicia V Zamudio, Alla A Sigova, Nancy M Hannett, Daniel S Day, Brian J Abraham, Malkiel A Cohen, Behnam Nabet, Dennis L Buckley,[...]. Cell 2017
399
8

Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor.
Wulan Deng, Jongjoo Lee, Hongxin Wang, Jeff Miller, Andreas Reik, Philip D Gregory, Ann Dean, Gerd A Blobel. Cell 2012
420
8

Enhancer redundancy provides phenotypic robustness in mammalian development.
Marco Osterwalder, Iros Barozzi, Virginie Tissières, Yoko Fukuda-Yuzawa, Brandon J Mannion, Sarah Y Afzal, Elizabeth A Lee, Yiwen Zhu, Ingrid Plajzer-Frick, Catherine S Pickle,[...]. Nature 2018
252
8


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.