A citation-based method for searching scientific literature

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
Times Cited: 679







List of co-cited articles
1163 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


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
62

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
62

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
721
61

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
52

Formation of Chromosomal Domains by Loop Extrusion.
Geoffrey Fudenberg, Maxim Imakaev, Carolyn Lu, Anton Goloborodko, Nezar Abdennur, Leonid A Mirny. Cell Rep 2016
766
43

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
468
42

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
41

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
796
37

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
300
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
998
30

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
502
24

DNA loop extrusion by human cohesin.
Iain F Davidson, Benedikt Bauer, Daniela Goetz, Wen Tang, Gordana Wutz, Jan-Michael Peters. Science 2019
236
24

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
512
24

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
311
24

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
339
22

Human cohesin compacts DNA by loop extrusion.
Yoori Kim, Zhubing Shi, Hongshan Zhang, Ilya J Finkelstein, Hongtao Yu. Science 2019
212
22

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
333
22

Organizational principles of 3D genome architecture.
M Jordan Rowley, Victor G Corces. Nat Rev Genet 2018
377
21

Capturing chromosome conformation.
Job Dekker, Karsten Rippe, Martijn Dekker, Nancy Kleckner. Science 2002
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
118
19

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
246
18

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
18

CTCF and cohesin regulate chromatin loop stability with distinct dynamics.
Anders S Hansen, Iryna Pustova, Claudia Cattoglio, Robert Tjian, Xavier Darzacq. Elife 2017
243
17

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
818
17

Long-range enhancer-promoter contacts in gene expression control.
Stefan Schoenfelder, Peter Fraser. Nat Rev Genet 2019
295
17

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.
Nicolas Servant, Nelle Varoquaux, Bryan R Lajoie, Eric Viara, Chong-Jian Chen, Jean-Philippe Vert, Edith Heard, Job Dekker, Emmanuel Barillot. Genome Biol 2015
696
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

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
356
16

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
16

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
16


CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation.
Varun Narendra, Pedro P Rocha, Disi An, Ramya Raviram, Jane A Skok, Esteban O Mazzoni, Danny Reinberg. Science 2015
323
16

Preformed chromatin topology assists transcriptional robustness of Shh during limb development.
Christina Paliou, Philine Guckelberger, Robert Schöpflin, Verena Heinrich, Andrea Esposito, Andrea M Chiariello, Simona Bianco, Carlo Annunziatella, Johannes Helmuth, Stefan Haas,[...]. Proc Natl Acad Sci U S A 2019
58
25

Real-time imaging of DNA loop extrusion by condensin.
Mahipal Ganji, Indra A Shaltiel, Shveta Bisht, Eugene Kim, Ana Kalichava, Christian H Haering, Cees Dekker. Science 2018
295
15

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells.
Jessica Zuin, Jesse R Dixon, Michael I J A van der Reijden, Zhen Ye, Petros Kolovos, Rutger W W Brouwer, Mariëtte P C van de Corput, Harmen J G van de Werken, Tobias A Knoch, Wilfred F J van IJcken,[...]. Proc Natl Acad Sci U S A 2014
485
15

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
371
15

The structural basis for cohesin-CTCF-anchored loops.
Yan Li, Judith H I Haarhuis, Ángela Sedeño Cacciatore, Roel Oldenkamp, Marjon S van Ruiten, Laureen Willems, Hans Teunissen, Kyle W Muir, Elzo de Wit, Benjamin D Rowland,[...]. Nature 2020
87
17

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
488
15

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
126
15

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
310
14

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
179
14

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
300
14

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states.
Alistair N Boettiger, Bogdan Bintu, Jeffrey R Moffitt, Siyuan Wang, Brian J Beliveau, Geoffrey Fudenberg, Maxim Imakaev, Leonid A Mirny, Chao-ting Wu, Xiaowei Zhuang. Nature 2016
422
14

Heterochromatin drives compartmentalization of inverted and conventional nuclei.
Martin Falk, Yana Feodorova, Natalia Naumova, Maxim Imakaev, Bryan R Lajoie, Heinrich Leonhardt, Boris Joffe, Job Dekker, Geoffrey Fudenberg, Irina Solovei,[...]. Nature 2019
199
14

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
101
14


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
372
14

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
740
13


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
734
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.