A citation-based method for searching scientific literature

Matteo Vietri Rudan, Christopher Barrington, Stephen Henderson, Christina Ernst, Duncan T Odom, Amos Tanay, Suzana Hadjur. Cell Rep 2015
Times Cited: 389







List of co-cited articles
1385 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
79

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
77

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
56

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
49

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
46

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
43

Formation of Chromosomal Domains by Loop Extrusion.
Geoffrey Fudenberg, Maxim Imakaev, Carolyn Lu, Anton Goloborodko, Nezar Abdennur, Leonid A Mirny. Cell Rep 2016
766
40

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
39

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
38

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
38

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
31

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
31

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
28

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
28

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
27

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
25

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
23

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
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
239
22

Activation of proto-oncogenes by disruption of chromosome neighborhoods.
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,[...]. Science 2016
493
21

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
20

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
20

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
19

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

Functional and topological characteristics of mammalian regulatory domains.
Orsolya Symmons, Veli Vural Uslu, Taro Tsujimura, Sandra Ruf, Sonya Nassari, Wibke Schwarzer, Laurence Ettwiller, François Spitz. Genome Res 2014
234
18

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
18

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

Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription.
Clemens B Hug, Alexis G Grimaldi, Kai Kruse, Juan M Vaquerizas. Cell 2017
229
18

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
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
740
17

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
159
17

Organizational principles of 3D genome architecture.
M Jordan Rowley, Victor G Corces. Nat Rev Genet 2018
377
17

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
16

Topologically associating domains are stable units of replication-timing regulation.
Benjamin D Pope, Tyrone Ryba, Vishnu Dileep, Feng Yue, Weisheng Wu, Olgert Denas, Daniel L Vera, Yanli Wang, R Scott Hansen, Theresa K Canfield,[...]. Nature 2014
472
16

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
733
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
126
16

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

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome.
Anthony D Schmitt, Ming Hu, Inkyung Jung, Zheng Xu, Yunjiang Qiu, Catherine L Tan, Yun Li, Shin Lin, Yiing Lin, Cathy L Barr,[...]. Cell Rep 2016
363
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
339
15

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
386
15

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

DNA loop extrusion by human cohesin.
Iain F Davidson, Benedikt Bauer, Daniela Goetz, Wen Tang, Gordana Wutz, Jan-Michael Peters. Science 2019
236
15

Human cohesin compacts DNA by loop extrusion.
Yoori Kim, Zhubing Shi, Hongshan Zhang, Ilya J Finkelstein, Hongtao Yu. Science 2019
212
15


Iterative correction of Hi-C data reveals hallmarks of chromosome organization.
Maxim Imakaev, Geoffrey Fudenberg, Rachel Patton McCord, Natalia Naumova, Anton Goloborodko, Bryan R Lajoie, Job Dekker, Leonid A Mirny. Nat Methods 2012
623
14

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
817
14

Functional dissection of the Sox9-Kcnj2 locus identifies nonessential and instructive roles of TAD architecture.
Alexandra Despang, Robert Schöpflin, Martin Franke, Salaheddine Ali, Ivana Jerković, Christina Paliou, Wing-Lee Chan, Bernd Timmermann, Lars Wittler, Martin Vingron,[...]. Nat Genet 2019
100
14


Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages.
Dominic Schmidt, Petra C Schwalie, Michael D Wilson, Benoit Ballester, Angela Gonçalves, Claudia Kutter, Gordon D Brown, Aileen Marshall, Paul Flicek, Duncan T Odom. Cell 2012
349
14


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.