A citation-based method for searching scientific literature

Vijay Ramani, Xinxian Deng, Ruolan Qiu, Kevin L Gunderson, Frank J Steemers, Christine M Disteche, William S Noble, Zhijun Duan, Jay Shendure. Nat Methods 2017
Times Cited: 260







List of co-cited articles
1312 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


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
831
63

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

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
50

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
401
47

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
45

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
368
41

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
327
41

Three-dimensional genome structures of single diploid human cells.
Longzhi Tan, Dong Xing, Chi-Han Chang, Heng Li, X Sunney Xie. Science 2018
166
39

Capturing chromosome conformation.
Job Dekker, Karsten Rippe, Martijn Dekker, Nancy Kleckner. Science 2002
33

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
32

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
353
30

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
317
29

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
305
27

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
451
26

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
190
23

Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.
Darren A Cusanovich, Riza Daza, Andrew Adey, Hannah A Pliner, Lena Christiansen, Kevin L Gunderson, Frank J Steemers, Cole Trapnell, Jay Shendure. Science 2015
543
23

Spatial organization of chromatin domains and compartments in single chromosomes.
Siyuan Wang, Jun-Han Su, Brian J Beliveau, Bogdan Bintu, Jeffrey R Moffitt, Chao-ting Wu, Xiaowei Zhuang. Science 2016
286
23

Single-cell chromatin accessibility reveals principles of regulatory variation.
Jason D Buenrostro, Beijing Wu, Ulrike M Litzenburger, Dave Ruff, Michael L Gonzales, Michael P Snyder, Howard Y Chang, William J Greenleaf. Nature 2015
912
22

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
892
21

Simultaneous profiling of 3D genome structure and DNA methylation in single human cells.
Dong-Sung Lee, Chongyuan Luo, Jingtian Zhou, Sahaana Chandran, Angeline Rivkin, Anna Bartlett, Joseph R Nery, Conor Fitzpatrick, Carolyn O'Connor, Jesse R Dixon,[...]. Nat Methods 2019
71
29

Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements.
Josée Dostie, Todd A Richmond, Ramy A Arnaout, Rebecca R Selzer, William L Lee, Tracey A Honan, Eric D Rubio, Anton Krumm, Justin Lamb, Chad Nusbaum,[...]. Genome Res 2006
732
20

An oestrogen-receptor-alpha-bound human chromatin interactome.
Melissa J Fullwood, Mei Hui Liu, You Fu Pan, Jun Liu, Han Xu, Yusoff Bin Mohamed, Yuriy L Orlov, Stoyan Velkov, Andrea Ho, Poh Huay Mei,[...]. Nature 2009
19

Formation of Chromosomal Domains by Loop Extrusion.
Geoffrey Fudenberg, Maxim Imakaev, Carolyn Lu, Anton Goloborodko, Nezar Abdennur, Leonid A Mirny. Cell Rep 2016
795
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

Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq.
Rongxin Fang, Miao Yu, Guoqiang Li, Sora Chee, Tristin Liu, Anthony D Schmitt, Bing Ren. Cell Res 2016
150
18

CUT&Tag for efficient epigenomic profiling of small samples and single cells.
Hatice S Kaya-Okur, Steven J Wu, Christine A Codomo, Erica S Pledger, Terri D Bryson, Jorja G Henikoff, Kami Ahmad, Steven Henikoff. Nat Commun 2019
380
18

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.
Evan Z Macosko, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, Allison R Bialas, Nolan Kamitaki, Emily M Martersteck,[...]. Cell 2015
17

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
748
16

Joint profiling of DNA methylation and chromatin architecture in single cells.
Guoqiang Li, Yaping Liu, Yanxiao Zhang, Naoki Kubo, Miao Yu, Rongxin Fang, Manolis Kellis, Bing Ren. Nat Methods 2019
67
23

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
814
15

Comprehensive single-cell transcriptional profiling of a multicellular organism.
Junyue Cao, Jonathan S Packer, Vijay Ramani, Darren A Cusanovich, Chau Huynh, Riza Daza, Xiaojie Qiu, Choli Lee, Scott N Furlan, Frank J Steemers,[...]. Science 2017
530
15

Joint profiling of chromatin accessibility and gene expression in thousands of single cells.
Junyue Cao, Darren A Cusanovich, Vijay Ramani, Delasa Aghamirzaie, Hannah A Pliner, Andrew J Hill, Riza M Daza, Jose L McFaline-Figueroa, Jonathan S Packer, Lena Christiansen,[...]. Science 2018
303
15

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
521
15

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
706
15

Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin.
Jun-Han Su, Pu Zheng, Seon S Kinrot, Bogdan Bintu, Xiaowei Zhuang. Cell 2020
94
15

Multiplex chromatin interactions with single-molecule precision.
Meizhen Zheng, Simon Zhongyuan Tian, Daniel Capurso, Minji Kim, Rahul Maurya, Byoungkoo Lee, Emaly Piecuch, Liang Gong, Jacqueline Jufen Zhu, Zhihui Li,[...]. Nature 2019
88
15

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes.
Brian J Beliveau, Eric F Joyce, Nicholas Apostolopoulos, Feyza Yilmaz, Chamith Y Fonseka, Ruth B McCole, Yiming Chang, Jin Billy Li, Tharanga Niroshini Senaratne, Benjamin R Williams,[...]. Proc Natl Acad Sci U S A 2012
225
14

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment.
Jim R Hughes, Nigel Roberts, Simon McGowan, Deborah Hay, Eleni Giannoulatou, Magnus Lynch, Marco De Gobbi, Stephen Taylor, Richard Gibbons, Douglas R Higgs. Nat Genet 2014
284
14

The 4D nucleome project.
Job Dekker, Andrew S Belmont, Mitchell Guttman, Victor O Leshyk, John T Lis, Stavros Lomvardas, Leonid A Mirny, Clodagh C O'Shea, Peter J Park, Bing Ren,[...]. Nature 2017
275
14

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state.
Assaf Rotem, Oren Ram, Noam Shoresh, Ralph A Sperling, Alon Goren, David A Weitz, Bradley E Bernstein. Nat Biotechnol 2015
464
14

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
154
14

Organization and function of the 3D genome.
Boyan Bonev, Giacomo Cavalli. Nat Rev Genet 2016
414
14

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C.
Tsung-Han S Hsieh, Assaf Weiner, Bryan Lajoie, Job Dekker, Nir Friedman, Oliver J Rando. Cell 2015
300
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

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C.
Borbala Mifsud, Filipe Tavares-Cadete, Alice N Young, Robert Sugar, Stefan Schoenfelder, Lauren Ferreira, Steven W Wingett, Simon Andrews, William Grey, Philip A Ewels,[...]. Nat Genet 2015
532
13

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling.
Reza Kalhor, Harianto Tjong, Nimanthi Jayathilaka, Frank Alber, Lin Chen. Nat Biotechnol 2011
373
13

Organizational principles of 3D genome architecture.
M Jordan Rowley, Victor G Corces. Nat Rev Genet 2018
395
13

Methods for mapping 3D chromosome architecture.
Rieke Kempfer, Ana Pombo. Nat Rev Genet 2020
148
13

Comprehensive Integration of Single-Cell Data.
Tim Stuart, Andrew Butler, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M Mauck, Yuhan Hao, Marlon Stoeckius, Peter Smibert, Rahul Satija. Cell 2019
13

Chromosome territories.
Thomas Cremer, Marion Cremer. Cold Spring Harb Perspect Biol 2010
667
12


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.