A citation-based method for searching scientific literature

Han Luo, Xinxin Li, Haitao Fu, Cheng Peng. BMC Genomics 2020
Times Cited: 2







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



Times Cited
  Times     Co-cited
Similarity


A statistical approach for inferring the 3D structure of the genome.
Nelle Varoquaux, Ferhat Ay, William Stafford Noble, Jean-Philippe Vert. Bioinformatics 2014
128
100

Three-dimensional genome structures of single diploid human cells.
Longzhi Tan, Dong Xing, Chi-Han Chang, Heng Li, X Sunney Xie. Science 2018
204
100

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
437
100


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
100

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
100

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
261
100

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
100

Protein:protein interactions and the pairing of boundary elements in vivo.
Jason Blanton, Miklos Gaszner, Paul Schedl. Genes Dev 2003
144
50

Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C.
Ferhat Ay, Thanh H Vu, Michael J Zeitz, Nelle Varoquaux, Jan E Carette, Jean-Philippe Vert, Andrew R Hoffman, William S Noble. BMC Genomics 2015
35
50

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
556
50

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.
Job Dekker, Marc A Marti-Renom, Leonid A Mirny. Nat Rev Genet 2013
674
50

Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome.
Wei Xie, Cathy L Barr, Audrey Kim, Feng Yue, Ah Young Lee, James Eubanks, Emma L Dempster, Bing Ren. Cell 2012
359
50

Widespread monoallelic expression on human autosomes.
Alexander Gimelbrant, John N Hutchinson, Benjamin R Thompson, Andrew Chess. Science 2007
416
50

Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages.
Evelien M Bunnik, Kate B Cook, Nelle Varoquaux, Gayani Batugedara, Jacques Prudhomme, Anthony Cort, Lirong Shi, Chiara Andolina, Leila S Ross, Declan Brady,[...]. Nat Commun 2018
49
50

Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell.
Takashi Nagano, Yaniv Lubling, Eitan Yaffe, Steven W Wingett, Wendy Dean, Amos Tanay, Peter Fraser. Nat Protoc 2015
96
50

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
876
50

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements.
Maxwell R Mumbach, Ansuman T Satpathy, Evan A Boyle, Chao Dai, Benjamin G Gowen, Seung Woo Cho, Michelle L Nguyen, Adam J Rubin, Jeffrey M Granja, Katelynn R Kazane,[...]. Nat Genet 2017
256
50

Extensive variation in chromatin states across humans.
Maya Kasowski, Sofia Kyriazopoulou-Panagiotopoulou, Fabian Grubert, Judith B Zaugg, Anshul Kundaje, Yuling Liu, Alan P Boyle, Qiangfeng Cliff Zhang, Fouad Zakharia, Damek V Spacek,[...]. Science 2013
255
50

Maternal H3K27me3 controls DNA methylation-independent imprinting.
Azusa Inoue, Lan Jiang, Falong Lu, Tsukasa Suzuki, Yi Zhang. Nature 2017
221
50


Homologue pairing in flies and mammals: gene regulation when two are involved.
Manasi S Apte, Victoria H Meller. Genet Res Int 2012
29
50


Mapping human epigenomes.
Chloe M Rivera, Bing Ren. Cell 2013
333
50

Structural organization of the inactive X chromosome in the mouse.
Luca Giorgetti, Bryan R Lajoie, Ava C Carter, Mikael Attia, Ye Zhan, Jin Xu, Chong Jian Chen, Noam Kaplan, Howard Y Chang, Edith Heard,[...]. Nature 2016
230
50

Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture.
Emily M Darrow, Miriam H Huntley, Olga Dudchenko, Elena K Stamenova, Neva C Durand, Zhuo Sun, Su-Chen Huang, Adrian L Sanborn, Ido Machol, Muhammad Shamim,[...]. Proc Natl Acad Sci U S A 2016
148
50

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
377
50

Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.
Qiaolin Deng, Daniel Ramsköld, Björn Reinius, Rickard Sandberg. Science 2014
696
50

Identification of genetic variants that affect histone modifications in human cells.
Graham McVicker, Bryce van de Geijn, Jacob F Degner, Carolyn E Cain, Nicholas E Banovich, Anil Raj, Noah Lewellen, Marsha Myrthil, Yoav Gilad, Jonathan K Pritchard. Science 2013
303
50

AlleleSeq: analysis of allele-specific expression and binding in a network framework.
Joel Rozowsky, Alexej Abyzov, Jing Wang, Pedro Alves, Debasish Raha, Arif Harmanci, Jing Leng, Robert Bjornson, Yong Kong, Naoki Kitabayashi,[...]. Mol Syst Biol 2011
194
50

Bipartite structure of the inactive mouse X chromosome.
Xinxian Deng, Wenxiu Ma, Vijay Ramani, Andrew Hill, Fan Yang, Ferhat Ay, Joel B Berletch, Carl Anthony Blau, Jay Shendure, Zhijun Duan,[...]. Genome Biol 2015
146
50

The three-dimensional genome organization of Drosophila melanogaster through data integration.
Qingjiao Li, Harianto Tjong, Xiao Li, Ke Gong, Xianghong Jasmine Zhou, Irene Chiolo, Frank Alber. Genome Biol 2017
52
50

A second generation human haplotype map of over 3.1 million SNPs.
Kelly A Frazer, Dennis G Ballinger, David R Cox, David A Hinds, Laura L Stuve, Richard A Gibbs, John W Belmont, Andrew Boudreau, Paul Hardenbol, Suzanne M Leal,[...]. Nature 2007
50

An integrated map of genetic variation from 1,092 human genomes.
Goncalo R Abecasis, Adam Auton, Lisa D Brooks, Mark A DePristo, Richard M Durbin, Robert E Handsaker, Hyun Min Kang, Gabor T Marth, Gil A McVean. Nature 2012
50

The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos.
Jelena Erceg, Jumana AlHaj Abed, Anton Goloborodko, Bryan R Lajoie, Geoffrey Fudenberg, Nezar Abdennur, Maxim Imakaev, Ruth B McCole, Son C Nguyen, Wren Saylor,[...]. Nat Commun 2019
21
50

The whole-genome landscape of medulloblastoma subtypes.
Paul A Northcott, Ivo Buchhalter, A Sorana Morrissy, Volker Hovestadt, Joachim Weischenfeldt, Tobias Ehrenberger, Susanne Gröbner, Maia Segura-Wang, Thomas Zichner, Vasilisa A Rudneva,[...]. Nature 2017
542
50

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
50

Organizational principles of 3D genome architecture.
M Jordan Rowley, Victor G Corces. Nat Rev Genet 2018
461
50

Chromosomes. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation.
Anand Minajigi, John Froberg, Chunyao Wei, Hongjae Sunwoo, Barry Kesner, David Colognori, Derek Lessing, Bernhard Payer, Myriam Boukhali, Wilhelm Haas,[...]. Science 2015
310
50

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
898
50

A map of human genome variation from population-scale sequencing.
Gonçalo R Abecasis, David Altshuler, Adam Auton, Lisa D Brooks, Richard M Durbin, Richard A Gibbs, Matt E Hurles, Gil A McVean. Nature 2010
50

An integrated map of structural variation in 2,504 human genomes.
Peter H Sudmant, Tobias Rausch, Eugene J Gardner, Robert E Handsaker, Alexej Abyzov, John Huddleston, Yan Zhang, Kai Ye, Goo Jun, Markus Hsi-Yang Fritz,[...]. Nature 2015
50

A global reference for human genetic variation.
Adam Auton, Lisa D Brooks, Richard M Durbin, Erik P Garrison, Hyun Min Kang, Jan O Korbel, Jonathan L Marchini, Shane McCarthy, Gil A McVean, Gonçalo R Abecasis. Nature 2015
50

Highly structured homolog pairing reflects functional organization of the Drosophila genome.
Jumana AlHaj Abed, Jelena Erceg, Anton Goloborodko, Son C Nguyen, Ruth B McCole, Wren Saylor, Geoffrey Fudenberg, Bryan R Lajoie, Job Dekker, Leonid A Mirny,[...]. Nat Commun 2019
27
50

Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome.
G Bonora, X Deng, H Fang, V Ramani, R Qiu, J B Berletch, G N Filippova, Z Duan, J Shendure, W S Noble,[...]. Nat Commun 2018
35
50

Allele-specific control of replication timing and genome organization during development.
Juan Carlos Rivera-Mulia, Andrew Dimond, Daniel Vera, Claudia Trevilla-Garcia, Takayo Sasaki, Jared Zimmerman, Catherine Dupont, Joost Gribnau, Peter Fraser, David M Gilbert. Genome Res 2018
35
50

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
50

Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription.
Helena Kilpinen, Sebastian M Waszak, Andreas R Gschwind, Sunil K Raghav, Robert M Witwicki, Andrea Orioli, Eugenia Migliavacca, Michaël Wiederkehr, Maria Gutierrez-Arcelus, Nikolaos I Panousis,[...]. Science 2013
261
50

Understanding Spatial Genome Organization: Methods and Insights.
Vijay Ramani, Jay Shendure, Zhijun Duan. Genomics Proteomics Bioinformatics 2016
33
50

The dynamic three-dimensional organization of the diploid yeast genome.
Seungsoo Kim, Ivan Liachko, Donna G Brickner, Kate Cook, William S Noble, Jason H Brickner, Jay Shendure, Maitreya J Dunham. Elife 2017
37
50


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.