A citation-based method for searching scientific literature

Edward B Chuong, Nels C Elde, Cédric Feschotte. Science 2016
Times Cited: 367







List of co-cited articles
1363 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Regulatory activities of transposable elements: from conflicts to benefits.
Edward B Chuong, Nels C Elde, Cédric Feschotte. Nat Rev Genet 2017
494
33

Widespread contribution of transposable elements to the innovation of gene regulatory networks.
Vasavi Sundaram, Yong Cheng, Zhihai Ma, Daofeng Li, Xiaoyun Xing, Peter Edge, Michael P Snyder, Ting Wang. Genome Res 2014
202
28

Initial sequencing and analysis of the human genome.
E S Lander, L M Linton, B Birren, C Nusbaum, M C Zody, J Baldwin, K Devon, K Dewar, M Doyle, W FitzHugh,[...]. Nature 2001
27

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
470
20

The majority of primate-specific regulatory sequences are derived from transposable elements.
Pierre-Étienne Jacques, Justin Jeyakani, Guillaume Bourque. PLoS Genet 2013
171
19

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
205
19

Inhibiting DNA Methylation Causes an Interferon Response in Cancer via dsRNA Including Endogenous Retroviruses.
Katherine B Chiappinelli, Pamela L Strissel, Alexis Desrichard, Huili Li, Christine Henke, Benjamin Akman, Alexander Hein, Neal S Rote, Leslie M Cope, Alexandra Snyder,[...]. Cell 2015
745
18

Ten things you should know about transposable elements.
Guillaume Bourque, Kathleen H Burns, Mary Gehring, Vera Gorbunova, Andrei Seluanov, Molly Hammell, Michaël Imbeault, Zsuzsanna Izsvák, Henry L Levin, Todd S Macfarlan,[...]. Genome Biol 2018
246
18

Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis.
S Mi, X Lee, X Li, G M Veldman, H Finnerty, L Racie, E LaVallie, X Y Tang, P Edouard, S Howes,[...]. Nature 2000
985
17

Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53.
Ting Wang, Jue Zeng, Craig B Lowe, Robert G Sellers, Sofie R Salama, Min Yang, Shawn M Burgess, Rainer K Brachmann, David Haussler. Proc Natl Acad Sci U S A 2007
243
17

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
17

DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts.
David Roulois, Helen Loo Yau, Rajat Singhania, Yadong Wang, Arnavaz Danesh, Shu Yi Shen, Han Han, Gangning Liang, Peter A Jones, Trevor J Pugh,[...]. Cell 2015
600
17

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
17

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
228
16

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals.
Vincent J Lynch, Robert D Leclerc, Gemma May, Günter P Wagner. Nat Genet 2011
236
16

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
520
16


Transposable elements drive widespread expression of oncogenes in human cancers.
Hyo Sik Jang, Nakul M Shah, Alan Y Du, Zea Z Dailey, Erica C Pehrsson, Paula M Godoy, David Zhang, Daofeng Li, Xiaoyun Xing, Sungsu Kim,[...]. Nat Genet 2019
84
19

Evolution of the mammalian transcription factor binding repertoire via transposable elements.
Guillaume Bourque, Bernard Leong, Vinsensius B Vega, Xi Chen, Yen Ling Lee, Kandhadayar G Srinivasan, Joon-Lin Chew, Yijun Ruan, Chia-Lin Wei, Huck Hui Ng,[...]. Genome Res 2008
322
15

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
454
15

KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks.
Michaël Imbeault, Pierre-Yves Helleboid, Didier Trono. Nature 2017
191
15

Transposable elements are the primary source of novelty in primate gene regulation.
Marco Trizzino, YoSon Park, Marcia Holsbach-Beltrame, Katherine Aracena, Katelyn Mika, Minal Caliskan, George H Perry, Vincent J Lynch, Christopher D Brown. Genome Res 2017
85
17

A unified classification system for eukaryotic transposable elements.
Thomas Wicker, François Sabot, Aurélie Hua-Van, Jeffrey L Bennetzen, Pierre Capy, Boulos Chalhoub, Andrew Flavell, Philippe Leroy, Michele Morgante, Olivier Panaud,[...]. Nat Rev Genet 2007
14

The impact of retrotransposons on human genome evolution.
Richard Cordaux, Mark A Batzer. Nat Rev Genet 2009
950
14

Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages.
Dominic Schmidt, Petra C Schwalie, Michael D Wilson, Benoit Ballester, Angela Gonçalves, Claudia Kutter, Gordon D Brown, Aileen Marshall, Paul Flicek, Duncan T Odom. Cell 2012
336
14

Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells.
Yanxiao Zhang, Ting Li, Sebastian Preissl, Maria Luisa Amaral, Jonathan D Grinstein, Elie N Farah, Eugin Destici, Yunjiang Qiu, Rong Hu, Ah Young Lee,[...]. Nat Genet 2019
78
17

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
286
14

Roles for retrotransposon insertions in human disease.
Dustin C Hancks, Haig H Kazazian. Mob DNA 2016
275
13

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
556
13

The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
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
201
12

Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses.
Jumpei Ito, Ryota Sugimoto, Hirofumi Nakaoka, Shiro Yamada, Tetsuaki Kimura, Takahide Hayano, Ituro Inoue. PLoS Genet 2017
48
25

Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs.
Julien Pontis, Evarist Planet, Sandra Offner, Priscilla Turelli, Julien Duc, Alexandre Coudray, Thorold W Theunissen, Rudolf Jaenisch, Didier Trono. Cell Stem Cell 2019
64
18

Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs.
Aurélie Kapusta, Zev Kronenberg, Vincent J Lynch, Xiaoyu Zhuo, LeeAnn Ramsay, Guillaume Bourque, Mark Yandell, Cédric Feschotte. PLoS Genet 2013
358
12

Transposable elements and the epigenetic regulation of the genome.
R Keith Slotkin, Robert Martienssen. Nat Rev Genet 2007
11

Hot L1s account for the bulk of retrotransposition in the human population.
Brook Brouha, Joshua Schustak, Richard M Badge, Sheila Lutz-Prigge, Alexander H Farley, John V Moran, Haig H Kazazian. Proc Natl Acad Sci U S A 2003
659
11

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons.
Frank M J Jacobs, David Greenberg, Ngan Nguyen, Maximilian Haeussler, Adam D Ewing, Sol Katzman, Benedict Paten, Sofie R Salama, David Haussler. Nature 2014
234
11

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
151
11

Endogenous retroviral promoter exaptation in human cancer.
Artem Babaian, Dixie L Mager. Mob DNA 2016
80
13


Interplay of TRIM28 and DNA methylation in controlling human endogenous retroelements.
Priscilla Turelli, Nathaly Castro-Diaz, Flavia Marzetta, Adamandia Kapopoulou, Charlène Raclot, Julien Duc, Vannary Tieng, Simon Quenneville, Didier Trono. Genome Res 2014
104
10


ERVmap analysis reveals genome-wide transcription of human endogenous retroviruses.
Maria Tokuyama, Yong Kong, Eric Song, Teshika Jayewickreme, Insoo Kang, Akiko Iwasaki. Proc Natl Acad Sci U S A 2018
62
16


Transposable elements generate regulatory novelty in a tissue-specific fashion.
Marco Trizzino, Aurélie Kapusta, Christopher D Brown. BMC Genomics 2018
35
28

Initial sequencing and comparative analysis of the mouse genome.
Robert H Waterston, Kerstin Lindblad-Toh, Ewan Birney, Jane Rogers, Josep F Abril, Pankaj Agarwal, Richa Agarwala, Rachel Ainscough, Marina Alexandersson, Peter An,[...]. Nature 2002
10

Author Correction: Regulation of transposable elements by DNA modifications.
Özgen Deniz, Jennifer M Frost, Miguel R Branco. Nat Rev Genet 2019
68
14

Diseases of the nERVous system: retrotransposon activity in neurodegenerative disease.
Oliver H Tam, Lyle W Ostrow, Molly Gale Hammell. Mob DNA 2019
41
24

Transposable elements: an abundant and natural source of regulatory sequences for host genes.
Rita Rebollo, Mark T Romanish, Dixie L Mager. Annu Rev Genet 2012
298
10

Transposable elements as a potent source of diverse cis-regulatory sequences in mammalian genomes.
Vasavi Sundaram, Joanna Wysocka. Philos Trans R Soc Lond B Biol Sci 2020
25
40


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.