A citation-based method for searching scientific literature

Weiyu Zhang, Fuquan Chen, Ruiqing Chen, Dan Xie, Jiao Yang, Xin Zhao, Renpeng Guo, Yongwang Zhang, Yang Shen, Jonathan Göke, Lin Liu, Xinyi Lu. Nucleic Acids Res 2019
Times Cited: 24







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



Times Cited
  Times     Co-cited
Similarity


Embryonic stem cell potency fluctuates with endogenous retrovirus activity.
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
546
95

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
244
66

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
205
58

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
158
54

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
91
50

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
156
45

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
127
41


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
413
41

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
61
37

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
47
33

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
31
33

DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs.
Mohammad M Karimi, Preeti Goyal, Irina A Maksakova, Misha Bilenky, Danny Leung, Jie Xin Tang, Yoichi Shinkai, Dixie L Mager, Steven Jones, Martin Hirst,[...]. Cell Stem Cell 2011
276
33

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
246
33

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
113
33

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
119
33

Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition.
Yun Huang, Jong Kyoung Kim, Dang Vinh Do, Caroline Lee, Christopher A Penfold, Jan J Zylicz, John C Marioni, Jamie A Hackett, M Azim Surani. Elife 2017
45
29

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
29

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
30
25

Systematic identification of factors for provirus silencing in embryonic stem cells.
Bin Xia Yang, Chadi A El Farran, Hong Chao Guo, Tao Yu, Hai Tong Fang, Hao Fei Wang, Sharon Schlesinger, Yu Fen Samantha Seah, Germaine Yen Lin Goh, Suat Peng Neo,[...]. Cell 2015
97
25

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
96
25

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
92
25

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
155
25

Precise temporal regulation of Dux is important for embryo development.
Mingyue Guo, Yanping Zhang, Jianfeng Zhou, Yan Bi, Junqin Xu, Ce Xu, Xiaochen Kou, Yanhong Zhao, Yanhe Li, Zhifen Tu,[...]. Cell Res 2019
25
25

DUX-miR-344-ZMYM2-Mediated Activation of MERVL LTRs Induces a Totipotent 2C-like State.
Fan Yang, Xin Huang, Ruge Zang, Jiayu Chen, Miguel Fidalgo, Carlos Sanchez-Priego, Jihong Yang, Alexander Caichen, Fanglin Ma, Todd Macfarlan,[...]. Cell Stem Cell 2020
21
28

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
447
25

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
147
25

SETDB1-Mediated Cell Fate Transition between 2C-Like and Pluripotent States.
Kaixin Wu, He Liu, Yaofeng Wang, Jiangping He, Shuyang Xu, Yaping Chen, Junqi Kuang, Jiadong Liu, Lin Guo, Dongwei Li,[...]. Cell Rep 2020
20
30

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
56
20

Transient bursts of Zscan4 expression are accompanied by the rapid derepression of heterochromatin in mouse embryonic stem cells.
Tomohiko Akiyama, Li Xin, Mayumi Oda, Alexei A Sharov, Misa Amano, Yulan Piao, J Scotty Cadet, Dawood B Dudekula, Yong Qian, Weidong Wang,[...]. DNA Res 2015
47
20

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
450
20

Dynamics of the epigenetic landscape during the maternal-to-zygotic transition.
Melanie A Eckersley-Maslin, Celia Alda-Catalinas, Wolf Reik. Nat Rev Mol Cell Biol 2018
112
20

MuERV-L is one of the earliest transcribed genes in mouse one-cell embryos.
Daisuke Kigami, Naojiro Minami, Hanae Takayama, Hiroshi Imai. Biol Reprod 2003
122
20

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
279
20

Cooperative Binding of Transcription Factors Orchestrates Reprogramming.
Constantinos Chronis, Petko Fiziev, Bernadett Papp, Stefan Butz, Giancarlo Bonora, Shan Sabri, Jason Ernst, Kathrin Plath. Cell 2017
222
20

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
154
20

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
20

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
278
20

Maternal factor NELFA drives a 2C-like state in mouse embryonic stem cells.
Zhenhua Hu, Dennis Eng Kiat Tan, Gloryn Chia, Haihan Tan, Hwei Fen Leong, Benjamin Jieming Chen, Mei Sheng Lau, Kelly Yu Sing Tan, Xuezhi Bi, Dongxiao Yang,[...]. Nat Cell Biol 2020
18
27

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
177
20

Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.
Qiaolin Deng, Daniel Ramsköld, Björn Reinius, Rickard Sandberg. Science 2014
598
16

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
564
16


Resetting Epigenetic Memory by Reprogramming of Histone Modifications in Mammals.
Hui Zheng, Bo Huang, Bingjie Zhang, Yunlong Xiang, Zhenhai Du, Qianhua Xu, Yuanyuan Li, Qiujun Wang, Jing Ma, Xu Peng,[...]. Mol Cell 2016
157
16

3D Chromatin Structures of Mature Gametes and Structural Reprogramming during Mammalian Embryogenesis.
Yuwen Ke, Yanan Xu, Xuepeng Chen, Songjie Feng, Zhenbo Liu, Yaoyu Sun, Xuelong Yao, Fangzhen Li, Wei Zhu, Lei Gao,[...]. Cell 2017
186
16

Stella safeguards the oocyte methylome by preventing de novo methylation mediated by DNMT1.
Yingfeng Li, Zhuqiang Zhang, Jiayu Chen, Wenqiang Liu, Weiyi Lai, Baodong Liu, Xiang Li, Liping Liu, Shaohua Xu, Qiang Dong,[...]. Nature 2018
82
16

The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes.
Tian-Peng Gu, Fan Guo, Hui Yang, Hai-Ping Wu, Gui-Fang Xu, Wei Liu, Zhi-Guo Xie, Linyu Shi, Xinyi He, Seung-gi Jin,[...]. Nature 2011
705
16

Histone chaperone CAF-1 mediates repressive histone modifications to protect preimplantation mouse embryos from endogenous retrotransposons.
Yuki Hatanaka, Kimiko Inoue, Mami Oikawa, Satoshi Kamimura, Narumi Ogonuki, Eiichi N Kodama, Yasuyuki Ohkawa, Yu-ichi Tsukada, Atsuo Ogura. Proc Natl Acad Sci U S A 2015
45
16

RNAi and expression of retrotransposons MuERV-L and IAP in preimplantation mouse embryos.
Petr Svoboda, Paula Stein, Martin Anger, Emily Bernstein, Gregory J Hannon, Richard M Schultz. Dev Biol 2004
136
16

Allelic reprogramming of the histone modification H3K4me3 in early mammalian development.
Bingjie Zhang, Hui Zheng, Bo Huang, Wenzhi Li, Yunlong Xiang, Xu Peng, Jia Ming, Xiaotong Wu, Yu Zhang, Qianhua Xu,[...]. Nature 2016
271
16


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.