A citation-based method for searching scientific literature

Denes Hnisz, Abraham S Weintraub, Daniel S Day, Anne-Laure Valton, Rasmus O Bak, Charles H Li, Johanna Goldmann, Bryan R Lajoie, Zi Peng Fan, Alla A Sigova, Jessica Reddy, Diego Borges-Rivera, Tong Ihn Lee, Rudolf Jaenisch, Matthew H Porteus, Job Dekker, Richard A Young. Science 2016
Times Cited: 493







List of co-cited articles
1094 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
53

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
47

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
46

Insulator dysfunction and oncogene activation in IDH mutant gliomas.
William A Flavahan, Yotam Drier, Brian B Liau, Shawn M Gillespie, Andrew S Venteicher, Anat O Stemmer-Rachamimov, Mario L Suvà, Bradley E Bernstein. Nature 2016
634
37

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
36

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
31

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
679
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
721
25

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
23

Formation of Chromosomal Domains by Loop Extrusion.
Geoffrey Fudenberg, Maxim Imakaev, Carolyn Lu, Anton Goloborodko, Nezar Abdennur, Leonid A Mirny. Cell Rep 2016
766
23

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma.
Paul A Northcott, Catherine Lee, Thomas Zichner, Adrian M Stütz, Serap Erkek, Daisuke Kawauchi, David J H Shih, Volker Hovestadt, Marc Zapatka, Dominik Sturm,[...]. Nature 2014
341
22

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
22

Formation of new chromatin domains determines pathogenicity of genomic duplications.
Martin Franke, Daniel M Ibrahim, Guillaume Andrey, Wibke Schwarzer, Verena Heinrich, Robert Schöpflin, Katerina Kraft, Rieke Kempfer, Ivana Jerković, Wing-Lee Chan,[...]. Nature 2016
322
20

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
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
20

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
19

Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking.
Joachim Weischenfeldt, Taronish Dubash, Alexandros P Drainas, Balca R Mardin, Yuanyuan Chen, Adrian M Stütz, Sebastian M Waszak, Graziella Bosco, Ann Rita Halvorsen, Benjamin Raeder,[...]. Nat Genet 2017
191
19

Organizational principles of 3D genome architecture.
M Jordan Rowley, Victor G Corces. Nat Rev Genet 2018
377
19

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
18

A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia.
Stefan Gröschel, Mathijs A Sanders, Remco Hoogenboezem, Elzo de Wit, Britta A M Bouwman, Claudia Erpelinck, Vincent H J van der Velden, Marije Havermans, Roberto Avellino, Kirsten van Lom,[...]. Cell 2014
374
18

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
17

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
17

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
16


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
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

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
15

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription.
Zhonghui Tang, Oscar Junhong Luo, Xingwang Li, Meizhen Zheng, Jacqueline Jufen Zhu, Przemyslaw Szalaj, Pawel Trzaskoma, Adriana Magalska, Jakub Wlodarczyk, Blazej Ruszczycki,[...]. Cell 2015
508
14

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
433
14

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
14

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations.
Phillippa C Taberlay, Joanna Achinger-Kawecka, Aaron T L Lun, Fabian A Buske, Kenneth Sabir, Cathryn M Gould, Elena Zotenko, Saul A Bert, Katherine A Giles, Denis C Bauer,[...]. Genome Res 2016
150
13

Organization and function of the 3D genome.
Boyan Bonev, Giacomo Cavalli. Nat Rev Genet 2016
405
13

Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture.
Matteo Vietri Rudan, Christopher Barrington, Stephen Henderson, Christina Ernst, Duncan T Odom, Amos Tanay, Suzana Hadjur. Cell Rep 2015
389
13

HiChIP: efficient and sensitive analysis of protein-directed genome architecture.
Maxwell R Mumbach, Adam J Rubin, Ryan A Flynn, Chao Dai, Paul A Khavari, William J Greenleaf, Howard Y Chang. Nat Methods 2016
434
13


A NOTCH1-driven MYC enhancer promotes T cell development, transformation and acute lymphoblastic leukemia.
Daniel Herranz, Alberto Ambesi-Impiombato, Teresa Palomero, Stephanie A Schnell, Laura Belver, Agnieszka A Wendorff, Luyao Xu, Mireia Castillo-Martin, David Llobet-Navás, Carlos Cordon-Cardo,[...]. Nat Med 2014
252
13

DNA loop extrusion by human cohesin.
Iain F Davidson, Benedikt Bauer, Daniela Goetz, Wen Tang, Gordana Wutz, Jan-Michael Peters. Science 2019
236
13

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
13

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
13

On the existence and functionality of topologically associating domains.
Jonathan A Beagan, Jennifer E Phillips-Cremins. Nat Genet 2020
87
13

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
12

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
12

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
387
12

TAD disruption as oncogenic driver.
Anne-Laure Valton, Job Dekker. Curr Opin Genet Dev 2016
108
12

CTCF/cohesin-binding sites are frequently mutated in cancer.
Riku Katainen, Kashyap Dave, Esa Pitkänen, Kimmo Palin, Teemu Kivioja, Niko Välimäki, Alexandra E Gylfe, Heikki Ristolainen, Ulrika A Hänninen, Tatiana Cajuso,[...]. Nat Genet 2015
244
12

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments.
Neva C Durand, Muhammad S Shamim, Ido Machol, Suhas S P Rao, Miriam H Huntley, Eric S Lander, Erez Lieberman Aiden. Cell Syst 2016
704
12

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
809
12

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
239
12

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
12

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
11


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.