A citation-based method for searching scientific literature

Takashi Fukaya, Bomyi Lim, Michael Levine. Cell 2016
Times Cited: 330







List of co-cited articles
1602 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping.
Caroline R Bartman, Sarah C Hsu, Chris C-S Hsiung, Arjun Raj, Gerd A Blobel. Mol Cell 2016
176
38

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
36

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
34

Dynamic interplay between enhancer-promoter topology and gene activity.
Hongtao Chen, Michal Levo, Lev Barinov, Miki Fujioka, James B Jaynes, Thomas Gregor. Nat Genet 2018
172
29

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation.
Nezha S Benabdallah, Iain Williamson, Robert S Illingworth, Lauren Kane, Shelagh Boyle, Dipta Sengupta, Graeme R Grimes, Pierre Therizols, Wendy A Bickmore. Mol Cell 2019
112
29

Cohesin Loss Eliminates All Loop Domains.
Suhas S P Rao, Su-Chen Huang, Brian Glenn St Hilaire, Jesse M Engreitz, Elizabeth M Perez, Kyong-Rim Kieffer-Kwon, Adrian L Sanborn, Sarah E Johnstone, Gavin D Bascom, Ivan D Bochkov,[...]. Cell 2017
769
29

Genomic encoding of transcriptional burst kinetics.
Anton J M Larsson, Per Johnsson, Michael Hagemann-Jensen, Leonard Hartmanis, Omid R Faridani, Björn Reinius, Åsa Segerstolpe, Chloe M Rivera, Bing Ren, Rickard Sandberg. Nature 2019
171
28

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
27

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
27

Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity.
Jeffrey M Alexander, Juan Guan, Bingkun Li, Lenka Maliskova, Michael Song, Yin Shen, Bo Huang, Stavros Lomvardas, Orion D Weiner. Elife 2019
104
27

Developmental enhancers and chromosome topology.
Eileen E M Furlong, Michael Levine. Science 2018
207
27

A Phase Separation Model for Transcriptional Control.
Denes Hnisz, Krishna Shrinivas, Richard A Young, Arup K Chakraborty, Phillip A Sharp. Cell 2017
770
26

Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.
Elphège P Nora, Anton Goloborodko, Anne-Laure Valton, Johan H Gibcus, Alec Uebersohn, Nezar Abdennur, Job Dekker, Leonid A Mirny, Benoit G Bruneau. Cell 2017
725
24

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
24

Imaging dynamic and selective low-complexity domain interactions that control gene transcription.
Shasha Chong, Claire Dugast-Darzacq, Zhe Liu, Peng Dong, Gina M Dailey, Claudia Cattoglio, Alec Heckert, Sambashiva Banala, Luke Lavis, Xavier Darzacq,[...]. Science 2018
405
23

Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions.
Darío G Lupiáñez, Katerina Kraft, Verena Heinrich, Peter Krawitz, Francesco Brancati, Eva Klopocki, Denise Horn, Hülya Kayserili, John M Opitz, Renata Laxova,[...]. Cell 2015
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
22

Stochastic mRNA synthesis in mammalian cells.
Arjun Raj, Charles S Peskin, Daniel Tranchina, Diana Y Vargas, Sanjay Tyagi. PLoS Biol 2006
22

Visualization of Transvection in Living Drosophila Embryos.
Bomyi Lim, Tyler Heist, Michael Levine, Takashi Fukaya. Mol Cell 2018
81
27

Formation of Chromosomal Domains by Loop Extrusion.
Geoffrey Fudenberg, Maxim Imakaev, Carolyn Lu, Anton Goloborodko, Nezar Abdennur, Leonid A Mirny. Cell Rep 2016
816
22

Two independent modes of chromatin organization revealed by cohesin removal.
Wibke Schwarzer, Nezar Abdennur, Anton Goloborodko, Aleksandra Pekowska, Geoffrey Fudenberg, Yann Loe-Mie, Nuno A Fonseca, Wolfgang Huber, Christian H Haering, Leonid Mirny,[...]. Nature 2017
503
20

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
20

Long-range enhancer-promoter contacts in gene expression control.
Stefan Schoenfelder, Peter Fraser. Nat Rev Genet 2019
333
20

Spatial partitioning of the regulatory landscape of the X-inactivation centre.
Elphège P Nora, Bryan R Lajoie, Edda G Schulz, Luca Giorgetti, Ikuhiro Okamoto, Nicolas Servant, Tristan Piolot, Nynke L van Berkum, Johannes Meisig, John Sedat,[...]. Nature 2012
19

Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding.
Tsung-Han S Hsieh, Claudia Cattoglio, Elena Slobodyanyuk, Anders S Hansen, Oliver J Rando, Robert Tjian, Xavier Darzacq. Mol Cell 2020
134
19

Transcription in Living Cells: Molecular Mechanisms of Bursting.
Joseph Rodriguez, Daniel R Larson. Annu Rev Biochem 2020
50
36

Mammalian genes are transcribed with widely different bursting kinetics.
David M Suter, Nacho Molina, David Gatfield, Kim Schneider, Ueli Schibler, Felix Naef. Science 2011
517
17

Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes.
Jill M Dowen, Zi Peng Fan, Denes Hnisz, Gang Ren, Brian J Abraham, Lyndon N Zhang, Abraham S Weintraub, Jurian Schujiers, Tong Ihn Lee, Keji Zhao,[...]. Cell 2014
546
17

Enhancer loops appear stable during development and are associated with paused polymerase.
Yad Ghavi-Helm, Felix A Klein, Tibor Pakozdi, Lucia Ciglar, Daan Noordermeer, Wolfgang Huber, Eileen E M Furlong. Nature 2014
307
17

Real-time dynamics of RNA polymerase II clustering in live human cells.
Ibrahim I Cisse, Ignacio Izeddin, Sebastien Z Causse, Lydia Boudarene, Adrien Senecal, Leila Muresan, Claire Dugast-Darzacq, Bassam Hajj, Maxime Dahan, Xavier Darzacq. Science 2013
261
16

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
16

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression.
Yad Ghavi-Helm, Aleksander Jankowski, Sascha Meiers, Rebecca R Viales, Jan O Korbel, Eileen E M Furlong. Nat Genet 2019
135
16

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
16

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
233
16

Intrinsic Dynamics of a Human Gene Reveal the Basis of Expression Heterogeneity.
Joseph Rodriguez, Gang Ren, Christopher R Day, Keji Zhao, Carson C Chow, Daniel R Larson. Cell 2019
77
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
15

Single-molecule dynamics of enhanceosome assembly in embryonic stem cells.
Jiji Chen, Zhengjian Zhang, Li Li, Bi-Chang Chen, Andrey Revyakin, Bassam Hajj, Wesley Legant, Maxime Dahan, Timothée Lionnet, Eric Betzig,[...]. Cell 2014
354
15

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
138
15

Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization.
Elizabeth H Finn, Gianluca Pegoraro, Hugo B Brandão, Anne-Laure Valton, Marlies E Oomen, Job Dekker, Leonid Mirny, Tom Misteli. Cell 2019
194
15

Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells.
Bogdan Bintu, Leslie J Mateo, Jun-Han Su, Nicholas A Sinnott-Armstrong, Mirae Parker, Seon Kinrot, Kei Yamaya, Alistair N Boettiger, Xiaowei Zhuang. Science 2018
374
15

Three-dimensional folding and functional organization principles of the Drosophila genome.
Tom Sexton, Eitan Yaffe, Ephraim Kenigsberg, Frédéric Bantignies, Benjamin Leblanc, Michael Hoichman, Hugues Parrinello, Amos Tanay, Giacomo Cavalli. Cell 2012
15

Reactivation of developmentally silenced globin genes by forced chromatin looping.
Wulan Deng, Jeremy W Rupon, Ivan Krivega, Laura Breda, Irene Motta, Kristen S Jahn, Andreas Reik, Philip D Gregory, Stefano Rivella, Ann Dean,[...]. Cell 2014
267
15


Stochastic gene expression in a single cell.
Michael B Elowitz, Arnold J Levine, Eric D Siggia, Peter S Swain. Science 2002
15

Temporal control of gene expression by the pioneer factor Zelda through transient interactions in hubs.
Jeremy Dufourt, Antonio Trullo, Jennifer Hunter, Carola Fernandez, Jorge Lazaro, Matthieu Dejean, Lucas Morales, Saida Nait-Amer, Katharine N Schulz, Melissa M Harrison,[...]. Nat Commun 2018
63
22

Real-time observation of transcription initiation and elongation on an endogenous yeast gene.
Daniel R Larson, Daniel Zenklusen, Bin Wu, Jeffrey A Chao, Robert H Singer. Science 2011
394
14

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes.
Adrian L Sanborn, Suhas S P Rao, Su-Chen Huang, Neva C Durand, Miriam H Huntley, Andrew I Jewett, Ivan D Bochkov, Dharmaraj Chinnappan, Ashok Cutkosky, Jian Li,[...]. Proc Natl Acad Sci U S A 2015
837
14

A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting.
Katjana Tantale, Florian Mueller, Alja Kozulic-Pirher, Annick Lesne, Jean-Marc Victor, Marie-Cécile Robert, Serena Capozi, Racha Chouaib, Volker Bäcker, Julio Mateos-Langerak,[...]. Nat Commun 2016
137
14

RNA polymerase II clustering through carboxy-terminal domain phase separation.
Marc Boehning, Claire Dugast-Darzacq, Marija Rankovic, Anders S Hansen, Taekyung Yu, Herve Marie-Nelly, David T McSwiggen, Goran Kokic, Gina M Dailey, Patrick Cramer,[...]. Nat Struct Mol Biol 2018
258
13

Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements.
Bo Gu, Tomek Swigut, Andrew Spencley, Matthew R Bauer, Mingyu Chung, Tobias Meyer, Joanna Wysocka. Science 2018
160
13


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.