A citation-based method for searching scientific literature

Todd S Macfarlan, Wesley D Gifford, Shawn Driscoll, Karen Lettieri, Helen M Rowe, Dario Bonanomi, Amy Firth, Oded Singer, Didier Trono, Samuel L Pfaff. Nature 2012
Times Cited: 529







List of co-cited articles
1187 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons.
Peter G Hendrickson, Jessie A Doráis, Edward J Grow, Jennifer L Whiddon, Jong-Won Lim, Candice L Wike, Bradley D Weaver, Christian Pflueger, Benjamin R Emery, Aaron L Wilcox,[...]. Nat Genet 2017
227
37

DUX-family transcription factors regulate zygotic genome activation in placental mammals.
Alberto De Iaco, Evarist Planet, Andrea Coluccio, Sonia Verp, Julien Duc, Didier Trono. Nat Genet 2017
194
33

Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly.
Takashi Ishiuchi, Rocio Enriquez-Gasca, Eiji Mizutani, Ana Bošković, Celine Ziegler-Birling, Diego Rodriguez-Terrones, Teruhiko Wakayama, Juan M Vaquerizas, Maria-Elena Torres-Padilla. Nat Struct Mol Biol 2015
151
29

MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs.
Mélanie A Eckersley-Maslin, Valentine Svensson, Christel Krueger, Thomas M Stubbs, Pascal Giehr, Felix Krueger, Ricardo J Miragaia, Charalampos Kyriakopoulos, Rebecca V Berrens, Inês Milagre,[...]. Cell Rep 2016
86
26

A molecular roadmap for the emergence of early-embryonic-like cells in culture.
Diego Rodriguez-Terrones, Xavier Gaume, Takashi Ishiuchi, Amélie Weiss, Arnaud Kopp, Kai Kruse, Audrey Penning, Juan M Vaquerizas, Laurent Brino, Maria-Elena Torres-Padilla. Nat Genet 2018
52
44

A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity.
Michelle Percharde, Chih-Jen Lin, Yafei Yin, Juan Guan, Gabriel A Peixoto, Aydan Bulut-Karslioglu, Steffen Biechele, Bo Huang, Xiaohua Shen, Miguel Ramalho-Santos. Cell 2018
147
22

Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos.
Anne E Peaston, Alexei V Evsikov, Joel H Graber, Wilhelmine N de Vries, Andrea E Holbrook, Davor Solter, Barbara B Knowles. Dev Cell 2004
404
21

Derivation of Pluripotent Stem Cells with In Vivo Embryonic and Extraembryonic Potency.
Yang Yang, Bei Liu, Jun Xu, Jinlin Wang, Jun Wu, Cheng Shi, Yaxing Xu, Jiebin Dong, Chengyan Wang, Weifeng Lai,[...]. Cell 2017
186
20

The ground state of embryonic stem cell self-renewal.
Qi-Long Ying, Jason Wray, Jennifer Nichols, Laura Batlle-Morera, Bradley Doble, James Woodgett, Philip Cohen, Austin Smith. Nature 2008
19

Conservation and innovation in the DUX4-family gene network.
Jennifer L Whiddon, Ashlee T Langford, Chao-Jen Wong, Jun Wen Zhong, Stephen J Tapscott. Nat Genet 2017
119
19

Zscan4 regulates telomere elongation and genomic stability in ES cells.
Michal Zalzman, Geppino Falco, Lioudmila V Sharova, Akira Nishiyama, Marshall Thomas, Sung-Lim Lee, Carole A Stagg, Hien G Hoang, Hsih-Te Yang, Fred E Indig,[...]. Nature 2010
240
19

Zscan4: a novel gene expressed exclusively in late 2-cell embryos and embryonic stem cells.
Geppino Falco, Sung-Lim Lee, Ilaria Stanghellini, Uwem C Bassey, Toshio Hamatani, Minoru S H Ko. Dev Biol 2007
151
18

Dppa2 and Dppa4 directly regulate the Dux-driven zygotic transcriptional program.
Mélanie Eckersley-Maslin, Celia Alda-Catalinas, Marloes Blotenburg, Elisa Kreibich, Christel Krueger, Wolf Reik. Genes Dev 2019
56
32


Establishment of mouse expanded potential stem cells.
Jian Yang, David J Ryan, Wei Wang, Jason Cheuk-Ho Tsang, Guocheng Lan, Hideki Masaki, Xuefei Gao, Liliana Antunes, Yong Yu, Zhexin Zhu,[...]. Nature 2017
99
17

Regulatory activities of transposable elements: from conflicts to benefits.
Edward B Chuong, Nels C Elde, Cédric Feschotte. Nat Rev Genet 2017
447
16

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells.
Edward J Grow, Ryan A Flynn, Shawn L Chavez, Nicholas L Bayless, Mark Wossidlo, Daniel J Wesche, Lance Martin, Carol B Ware, Catherine A Blish, Howard Y Chang,[...]. Nature 2015
267
16

Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells.
Yong Jin Choi, Chao-Po Lin, Davide Risso, Sean Chen, Thomas Aquinas Kim, Meng How Tan, Jin Billy Li, Yalei Wu, Caifu Chen, Zhenyu Xuan,[...]. Science 2017
82
18

LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo.
Joanna W Jachowicz, Xinyang Bing, Julien Pontabry, Ana Bošković, Oliver J Rando, Maria-Elena Torres-Padilla. Nat Genet 2017
101
15

Transposable elements have rewired the core regulatory network of human embryonic stem cells.
Galih Kunarso, Na-Yu Chia, Justin Jeyakani, Catalina Hwang, Xinyi Lu, Yun-Shen Chan, Huck-Hui Ng, Guillaume Bourque. Nat Genet 2010
459
15



DPPA2 and DPPA4 are necessary to establish a 2C-like state in mouse embryonic stem cells.
Alberto De Iaco, Alexandre Coudray, Julien Duc, Didier Trono. EMBO Rep 2019
43
32

KAP1 controls endogenous retroviruses in embryonic stem cells.
Helen M Rowe, Johan Jakobsson, Daniel Mesnard, Jacques Rougemont, Séverine Reynard, Tugce Aktas, Pierre V Maillard, Hillary Layard-Liesching, Sonia Verp, Julien Marquis,[...]. Nature 2010
437
14

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
14

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
14

The regulated retrotransposon transcriptome of mammalian cells.
Geoffrey J Faulkner, Yasumasa Kimura, Carsten O Daub, Shivangi Wani, Charles Plessy, Katharine M Irvine, Kate Schroder, Nicole Cloonan, Anita L Steptoe, Timo Lassmann,[...]. Nat Genet 2009
510
13

Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes.
Weiyu Zhang, Fuquan Chen, Ruiqing Chen, Dan Xie, Jiao Yang, Xin Zhao, Renpeng Guo, Yongwang Zhang, Yang Shen, Jonathan Göke,[...]. Nucleic Acids Res 2019
20
65

Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells.
Jichang Wang, Gangcai Xie, Manvendra Singh, Avazeh T Ghanbarian, Tamás Raskó, Attila Szvetnik, Huiqiang Cai, Daniel Besser, Alessandro Prigione, Nina V Fuchs,[...]. Nature 2014
219
13

The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity.
Xinyi Lu, Friedrich Sachs, LeeAnn Ramsay, Pierre-Étienne Jacques, Jonathan Göke, Guillaume Bourque, Huck-Hui Ng. Nat Struct Mol Biol 2014
189
13

Dynamic transcription of distinct classes of endogenous retroviral elements marks specific populations of early human embryonic cells.
Jonathan Göke, Xinyi Lu, Yun-Shen Chan, Huck-Hui Ng, Lam-Ha Ly, Friedrich Sachs, Iwona Szczerbinska. Cell Stem Cell 2015
143
13

Endogenous retroviruses function as species-specific enhancer elements in the placenta.
Edward B Chuong, M A Karim Rumi, Michael J Soares, Julie C Baker. Nat Genet 2013
194
12

Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A.
Todd S Macfarlan, Wesley D Gifford, Saurabh Agarwal, Shawn Driscoll, Karen Lettieri, Jianxun Wang, Shane E Andrews, Laura Franco, Michael G Rosenfeld, Bing Ren,[...]. Genes Dev 2011
148
12


Higher chromatin mobility supports totipotency and precedes pluripotency in vivo.
Ana Bošković, André Eid, Julien Pontabry, Takashi Ishiuchi, Coralie Spiegelhalter, Edupuganti V S Raghu Ram, Eran Meshorer, Maria-Elena Torres-Padilla. Genes Dev 2014
94
12

Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells.
Irina A Maksakova, Peter J Thompson, Preeti Goyal, Steven Jm Jones, Prim B Singh, Mohammad M Karimi, Matthew C Lorincz. Epigenetics Chromatin 2013
89
13

Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development.
Chenfei Wang, Xiaoyu Liu, Yawei Gao, Lei Yang, Chong Li, Wenqiang Liu, Chuan Chen, Xiaochen Kou, Yanhong Zhao, Jiayu Chen,[...]. Nat Cell Biol 2018
107
12

Myc and Dnmt1 impede the pluripotent to totipotent state transition in embryonic stem cells.
Xudong Fu, Xiaoji Wu, Mohamed Nadhir Djekidel, Yi Zhang. Nat Cell Biol 2019
26
42

The transcriptional and epigenomic foundations of ground state pluripotency.
Hendrik Marks, Tüzer Kalkan, Roberta Menafra, Sergey Denissov, Kenneth Jones, Helmut Hofemeister, Jennifer Nichols, Andrea Kranz, A Francis Stewart, Austin Smith,[...]. Cell 2012
561
11

Totipotent embryonic stem cells arise in ground-state culture conditions.
Sophie M Morgani, Maurice A Canham, Jennifer Nichols, Alexei A Sharov, Rosa Portero Migueles, Minoru S H Ko, Joshua M Brickman. Cell Rep 2013
134
11

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET.
Toshiyuki Matsui, Danny Leung, Hiroki Miyashita, Irina A Maksakova, Hitoshi Miyachi, Hiroshi Kimura, Makoto Tachibana, Matthew C Lorincz, Yoichi Shinkai. Nature 2010
440
11

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
11

Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.
Qiaolin Deng, Daniel Ramsköld, Björn Reinius, Rickard Sandberg. Science 2014
582
11

Regulatory evolution of innate immunity through co-option of endogenous retroviruses.
Edward B Chuong, Nels C Elde, Cédric Feschotte. Science 2016
349
11

Establishment of porcine and human expanded potential stem cells.
Xuefei Gao, Monika Nowak-Imialek, Xi Chen, Dongsheng Chen, Doris Herrmann, Degong Ruan, Andy Chun Hang Chen, Melanie A Eckersley-Maslin, Shakil Ahmad, Yin Lau Lee,[...]. Nat Cell Biol 2019
100
11

Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance.
Alexandre Fort, Kosuke Hashimoto, Daisuke Yamada, Md Salimullah, Chaman A Keya, Alka Saxena, Alessandro Bonetti, Irina Voineagu, Nicolas Bertin, Anton Kratz,[...]. Nat Genet 2014
172
11

New cell lines from mouse epiblast share defining features with human embryonic stem cells.
Paul J Tesar, Josh G Chenoweth, Frances A Brook, Timothy J Davies, Edward P Evans, David L Mack, Richard L Gardner, Ronald D G McKay. Nature 2007
10

DPPA2/4 and SUMO E3 ligase PIAS4 opposingly regulate zygotic transcriptional program.
Yao-Long Yan, Chao Zhang, Jing Hao, Xue-Lian Wang, Jia Ming, Li Mi, Jie Na, Xinli Hu, Yangming Wang. PLoS Biol 2019
28
35

The landscape of accessible chromatin in mammalian preimplantation embryos.
Jingyi Wu, Bo Huang, He Chen, Qiangzong Yin, Yang Liu, Yunlong Xiang, Bingjie Zhang, Bofeng Liu, Qiujun Wang, Weikun Xia,[...]. Nature 2016
269
10

Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos.
Xiaoyu Liu, Chenfei Wang, Wenqiang Liu, Jingyi Li, Chong Li, Xiaochen Kou, Jiayu Chen, Yanhong Zhao, Haibo Gao, Hong Wang,[...]. Nature 2016
269
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.