A citation-based method for searching scientific literature

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, Xingfan Huang, Muhammad S Shamim, Jaeweon Shin, Douglass Turner, Ziyi Ye, Arina D Omer, James T Robinson, Tamar Schlick, Bradley E Bernstein, Rafael Casellas, Eric S Lander, Erez Lieberman Aiden. Cell 2017
Times Cited: 667







List of co-cited articles
1427 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


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
73

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
64

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
626
59

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
58

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
433
55

Formation of Chromosomal Domains by Loop Extrusion.
Geoffrey Fudenberg, Maxim Imakaev, Carolyn Lu, Anton Goloborodko, Nezar Abdennur, Leonid A Mirny. Cell Rep 2016
721
49

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
47

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
766
45

The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension.
Judith H I Haarhuis, Robin H van der Weide, Vincent A Blomen, J Omar Yáñez-Cuna, Mario Amendola, Marjon S van Ruiten, Peter H L Krijger, Hans Teunissen, René H Medema, Bas van Steensel,[...]. Cell 2017
311
34

Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins.
Gordana Wutz, Csilla Várnai, Kota Nagasaka, David A Cisneros, Roman R Stocsits, Wen Tang, Stefan Schoenfelder, Gregor Jessberger, Matthias Muhar, M Julius Hossain,[...]. EMBO J 2017
271
33

Organizational principles of 3D genome architecture.
M Jordan Rowley, Victor G Corces. Nat Rev Genet 2018
323
33

DNA loop extrusion by human cohesin.
Iain F Davidson, Benedikt Bauer, Daniela Goetz, Wen Tang, Gordana Wutz, Jan-Michael Peters. Science 2019
203
32

Human cohesin compacts DNA by loop extrusion.
Yoori Kim, Zhubing Shi, Hongshan Zhang, Ilya J Finkelstein, Hongtao Yu. Science 2019
186
30

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
942
29

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
308
27

Chromatin organization by an interplay of loop extrusion and compartmental segregation.
Johannes Nuebler, Geoffrey Fudenberg, Maxim Imakaev, Nezar Abdennur, Leonid A Mirny. Proc Natl Acad Sci U S A 2018
221
24

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
96
23

Capturing chromosome conformation.
Job Dekker, Karsten Rippe, Martijn Dekker, Nancy Kleckner. Science 2002
22

Evolutionarily Conserved Principles Predict 3D Chromatin Organization.
M Jordan Rowley, Michael H Nichols, Xiaowen Lyu, Masami Ando-Kuri, I Sarahi M Rivera, Karen Hermetz, Ping Wang, Yijun Ruan, Victor G Corces. Mol Cell 2017
225
22

A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture.
Johanna Gassler, Hugo B Brandão, Maxim Imakaev, Ilya M Flyamer, Sabrina Ladstätter, Wendy A Bickmore, Jan-Michael Peters, Leonid A Mirny, Kikuë Tachibana. EMBO J 2017
147
21

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
21

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus.
Sofia A Quinodoz, Noah Ollikainen, Barbara Tabak, Ali Palla, Jan Marten Schmidt, Elizabeth Detmar, Mason M Lai, Alexander A Shishkin, Prashant Bhat, Yodai Takei,[...]. Cell 2018
286
20

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
729
20

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
440
20

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
20

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
19

Multiscale 3D Genome Rewiring during Mouse Neural Development.
Boyan Bonev, Netta Mendelson Cohen, Quentin Szabo, Lauriane Fritsch, Giorgio L Papadopoulos, Yaniv Lubling, Xiaole Xu, Xiaodan Lv, Jean-Philippe Hugnot, Amos Tanay,[...]. Cell 2017
467
19

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure.
Takashi Nagano, Yaniv Lubling, Tim J Stevens, Stefan Schoenfelder, Eitan Yaffe, Wendy Dean, Ernest D Laue, Amos Tanay, Peter Fraser. Nature 2013
783
18

Ultrastructural Details of Mammalian Chromosome Architecture.
Nils Krietenstein, Sameer Abraham, Sergey V Venev, Nezar Abdennur, Johan Gibcus, Tsung-Han S Hsieh, Krishna Mohan Parsi, Liyan Yang, René Maehr, Leonid A Mirny,[...]. Mol Cell 2020
90
20

CTCF Binding Polarity Determines Chromatin Looping.
Elzo de Wit, Erica S M Vos, Sjoerd J B Holwerda, Christian Valdes-Quezada, Marjon J A M Verstegen, Hans Teunissen, Erik Splinter, Patrick J Wijchers, Peter H L Krijger, Wouter de Laat. Mol Cell 2015
295
18

Condensin-driven remodelling of X chromosome topology during dosage compensation.
Emily Crane, Qian Bian, Rachel Patton McCord, Bryan R Lajoie, Bayly S Wheeler, Edward J Ralston, Satoru Uzawa, Job Dekker, Barbara J Meyer. Nature 2015
359
17

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin.
Adam G Larson, Daniel Elnatan, Madeline M Keenen, Michael J Trnka, Jonathan B Johnston, Alma L Burlingame, David A Agard, Sy Redding, Geeta J Narlikar. Nature 2017
679
17

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function.
Ya Guo, Quan Xu, Daniele Canzio, Jia Shou, Jinhuan Li, David U Gorkin, Inkyung Jung, Haiyang Wu, Yanan Zhai, Yuanxiao Tang,[...]. Cell 2015
491
17

3D structures of individual mammalian genomes studied by single-cell Hi-C.
Tim J Stevens, David Lando, Srinjan Basu, Liam P Atkinson, Yang Cao, Steven F Lee, Martin Leeb, Kai J Wohlfahrt, Wayne Boucher, Aoife O'Shaughnessy-Kirwan,[...]. Nature 2017
365
17

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition.
Ilya M Flyamer, Johanna Gassler, Maxim Imakaev, Hugo B Brandão, Sergey V Ulianov, Nezar Abdennur, Sergey V Razin, Leonid A Mirny, Kikuë Tachibana-Konwalski. Nature 2017
334
17

Complex multi-enhancer contacts captured by genome architecture mapping.
Robert A Beagrie, Antonio Scialdone, Markus Schueler, Dorothee C A Kraemer, Mita Chotalia, Sheila Q Xie, Mariano Barbieri, Inês de Santiago, Liron-Mark Lavitas, Miguel R Branco,[...]. Nature 2017
279
17

Long-range enhancer-promoter contacts in gene expression control.
Stefan Schoenfelder, Peter Fraser. Nat Rev Genet 2019
242
17

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
85
20

Chromatin architecture reorganization during stem cell differentiation.
Jesse R Dixon, Inkyung Jung, Siddarth Selvaraj, Yin Shen, Jessica E Antosiewicz-Bourget, Ah Young Lee, Zhen Ye, Audrey Kim, Nisha Rajagopal, Wei Xie,[...]. Nature 2015
779
17

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
17

Architectural protein subclasses shape 3D organization of genomes during lineage commitment.
Jennifer E Phillips-Cremins, Michael E G Sauria, Amartya Sanyal, Tatiana I Gerasimova, Bryan R Lajoie, Joshua S K Bell, Chin-Tong Ong, Tracy A Hookway, Changying Guo, Yuhua Sun,[...]. Cell 2013
720
16

The Energetics and Physiological Impact of Cohesin Extrusion.
Laura Vian, Aleksandra Pękowska, Suhas S P Rao, Kyong-Rim Kieffer-Kwon, Seolkyoung Jung, Laura Baranello, Su-Chen Huang, Laila El Khattabi, Marei Dose, Nathanael Pruett,[...]. Cell 2018
169
16

Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription.
Clemens B Hug, Alexis G Grimaldi, Kai Kruse, Juan M Vaquerizas. Cell 2017
216
16

Visualizing DNA folding and RNA in embryos at single-cell resolution.
Leslie J Mateo, Sedona E Murphy, Antonina Hafner, Isaac S Cinquini, Carly A Walker, Alistair N Boettiger. Nature 2019
127
16

Cell-cycle dynamics of chromosomal organization at single-cell resolution.
Takashi Nagano, Yaniv Lubling, Csilla Várnai, Carmel Dudley, Wing Leung, Yael Baran, Netta Mendelson Cohen, Steven Wingett, Peter Fraser, Amos Tanay. Nature 2017
300
16

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
167
16

Organization and function of the 3D genome.
Boyan Bonev, Giacomo Cavalli. Nat Rev Genet 2016
388
16

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
334
16

Phase separation drives heterochromatin domain formation.
Amy R Strom, Alexander V Emelyanov, Mustafa Mir, Dmitry V Fyodorov, Xavier Darzacq, Gary H Karpen. Nature 2017
729
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
341
16


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.