A citation-based method for searching scientific literature

Siyuan Kong, Yubo Zhang. Cell Biol Toxicol 2019
Times Cited: 29







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



Times Cited
  Times     Co-cited
Similarity


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
41

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
27

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
27

Definition of clinical gene tests.
Duojiao Wu, Yunfeng Cheng, Xiangdong Wang. Cell Biol Toxicol 2019
13
46

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
569
20

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
920
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
858
13

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
919
13

Analysis methods for studying the 3D architecture of the genome.
Ferhat Ay, William S Noble. Genome Biol 2015
90
13

A three-dimensional model of the yeast genome.
Zhijun Duan, Mirela Andronescu, Kevin Schutz, Sean McIlwain, Yoo Jung Kim, Choli Lee, Jay Shendure, Stanley Fields, C Anthony Blau, William S Noble. Nature 2010
642
13

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells.
Horng D Ou, Sébastien Phan, Thomas J Deerinck, Andrea Thor, Mark H Ellisman, Clodagh C O'Shea. Science 2017
423
13

Organization and function of the 3D genome.
Boyan Bonev, Giacomo Cavalli. Nat Rev Genet 2016
450
13


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
13

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
699
13

Capturing chromosome conformation.
Job Dekker, Karsten Rippe, Martijn Dekker, Nancy Kleckner. Science 2002
13

Principles of genome folding into topologically associating domains.
Quentin Szabo, Frédéric Bantignies, Giacomo Cavalli. Sci Adv 2019
225
13


Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
13

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
880
13

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
13

Massively multiplex single-cell Hi-C.
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
289
13

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
890
13

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
337
13

An artificial intelligent single cell is part of the cell dream world.
Yiming Zeng, Xiaoyang Chen, Hongzhi Gao, Xiangdong Wang. Cell Biol Toxicol 2018
18
16

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
375
10

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes.
Wenxiu Ma, Ferhat Ay, Choli Lee, Gunhan Gulsoy, Xinxian Deng, Savannah Cook, Jennifer Hesson, Christopher Cavanaugh, Carol B Ware, Anton Krumm,[...]. Nat Methods 2015
136
10

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
551
10

A decade of 3C technologies: insights into nuclear organization.
Elzo de Wit, Wouter de Laat. Genes Dev 2012
490
10

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
317
10

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
10

HiCUP: pipeline for mapping and processing Hi-C data.
Steven Wingett, Philip Ewels, Mayra Furlan-Magaril, Takashi Nagano, Stefan Schoenfelder, Peter Fraser, Simon Andrews. F1000Res 2015
262
10

Allelic reprogramming of 3D chromatin architecture during early mammalian development.
Zhenhai Du, Hui Zheng, Bo Huang, Rui Ma, Jingyi Wu, Xianglin Zhang, Jing He, Yunlong Xiang, Qiujun Wang, Yuanyuan Li,[...]. Nature 2017
254
10

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts.
Ferhat Ay, Timothy L Bailey, William Stafford Noble. Genome Res 2014
252
10

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
461
10

Proteomic and genomic profiling of pancreatic cancer.
Daniel Ansari, William Torén, Qimin Zhou, Dingyuan Hu, Roland Andersson. Cell Biol Toxicol 2019
37
10

Applying switchable Cas9 variants to in vivo gene editing for therapeutic applications.
Emily M Mills, Victoria L Barlow, Louis Y P Luk, Yu-Hsuan Tsai. Cell Biol Toxicol 2020
7
42

Battling CRISPR-Cas9 off-target genome editing.
Daisy Li, Hong Zhou, Xiao Zeng. Cell Biol Toxicol 2019
21
14

Condensin- and Replication-Mediated Bacterial Chromosome Folding and Origin Condensation Revealed by Hi-C and Super-resolution Imaging.
Martial Marbouty, Antoine Le Gall, Diego I Cattoni, Axel Cournac, Alan Koh, Jean-Bernard Fiche, Julien Mozziconacci, Heath Murray, Romain Koszul, Marcelo Nollmann. Mol Cell 2015
167
10

High-resolution mapping of the spatial organization of a bacterial chromosome.
Tung B K Le, Maxim V Imakaev, Leonid A Mirny, Michael T Laub. Science 2013
354
10

Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins.
Virginia S Lioy, Axel Cournac, Martial Marbouty, Stéphane Duigou, Julien Mozziconacci, Olivier Espéli, Frédéric Boccard, Romain Koszul. Cell 2018
148
10

Regulation of chromatin by histone modifications.
Andrew J Bannister, Tony Kouzarides. Cell Res 2011
10

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.
Jonathan Cairns, Paula Freire-Pritchett, Steven W Wingett, Csilla Várnai, Andrew Dimond, Vincent Plagnol, Daniel Zerbino, Stefan Schoenfelder, Biola-Maria Javierre, Cameron Osborne,[...]. Genome Biol 2016
198
10


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
370
10

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
755
10

Hi-C: a comprehensive technique to capture the conformation of genomes.
Jon-Matthew Belton, Rachel Patton McCord, Johan Harmen Gibcus, Natalia Naumova, Ye Zhan, Job Dekker. Methods 2012
452
10

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
382
10

3D Chromatin Architecture of Large Plant Genomes Determined by Local A/B Compartments.
Pengfei Dong, Xiaoyu Tu, Po-Yu Chu, Peitao Lü, Ning Zhu, Donald Grierson, Baijuan Du, Pinghua Li, Silin Zhong. Mol Plant 2017
139
10

Hi-C: a method to study the three-dimensional architecture of genomes.
Nynke L van Berkum, Erez Lieberman-Aiden, Louise Williams, Maxim Imakaev, Andreas Gnirke, Leonid A Mirny, Job Dekker, Eric S Lander. J Vis Exp 2010
238
10


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.