A citation-based method for searching scientific literature

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, Erez Lieberman Aiden. Cell 2014
Times Cited: 2768







List of co-cited articles
971 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
51

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
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
26

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
591
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

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
562
19

Capturing chromosome conformation.
Job Dekker, Karsten Rippe, Martijn Dekker, Nancy Kleckner. Science 2002
18


Formation of Chromosomal Domains by Loop Extrusion.
Geoffrey Fudenberg, Maxim Imakaev, Carolyn Lu, Anton Goloborodko, Nezar Abdennur, Leonid A Mirny. Cell Rep 2016
693
17

Organizational principles of 3D genome architecture.
M Jordan Rowley, Victor G Corces. Nat Rev Genet 2018
307
16

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
602
16

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
744
16

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
756
15

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
641
15

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
15

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
373
14

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
156
14

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
290
14

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
418
14

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom.
Neva C Durand, James T Robinson, Muhammad S Shamim, Ido Machol, Jill P Mesirov, Eric S Lander, Erez Lieberman Aiden. Cell Syst 2016
392
14

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
13

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
13

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
267
13

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
319
13

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
12

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
920
12

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
12

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
763
11

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
441
11

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
11

Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
11


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
265
11

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
203
11

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
214
11

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming.
Ralph Stadhouders, Enrique Vidal, François Serra, Bruno Di Stefano, François Le Dily, Javier Quilez, Antonio Gomez, Samuel Collombet, Clara Berenguer, Yasmina Cuartero,[...]. Nat Genet 2018
136
10

Comparison of computational methods for Hi-C data analysis.
Mattia Forcato, Chiara Nicoletti, Koustav Pal, Carmen Maria Livi, Francesco Ferrari, Silvio Bicciato. Nat Methods 2017
131
10

Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C).
Marieke Simonis, Petra Klous, Erik Splinter, Yuri Moshkin, Rob Willemsen, Elzo de Wit, Bas van Steensel, Wouter de Laat. Nat Genet 2006
862
10

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
348
10

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
155
10

High-resolution TADs reveal DNA sequences underlying genome organization in flies.
Fidel Ramírez, Vivek Bhardwaj, Laura Arrigoni, Kin Chung Lam, Björn A Grüning, José Villaveces, Bianca Habermann, Asifa Akhtar, Thomas Manke. Nat Commun 2018
197
10

Human cohesin compacts DNA by loop extrusion.
Yoori Kim, Zhubing Shi, Hongshan Zhang, Ilya J Finkelstein, Hongtao Yu. Science 2019
167
9

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
9

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
270
9

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
324
9

Phase separation drives heterochromatin domain formation.
Amy R Strom, Alexander V Emelyanov, Mustafa Mir, Dmitry V Fyodorov, Xavier Darzacq, Gary H Karpen. Nature 2017
691
9

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
289
9

Principles of genome folding into topologically associating domains.
Quentin Szabo, Frédéric Bantignies, Giacomo Cavalli. Sci Adv 2019
148
9


Three-dimensional genome structures of single diploid human cells.
Longzhi Tan, Dong Xing, Chi-Han Chang, Heng Li, X Sunney Xie. Science 2018
133
9


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.