A citation-based method for searching scientific literature

Edward B Chuong, Nels C Elde, Cédric Feschotte. Nat Rev Genet 2017
Times Cited: 474







List of co-cited articles
1282 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


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
24

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
24

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
23

Regulatory evolution of innate immunity through co-option of endogenous retroviruses.
Edward B Chuong, Nels C Elde, Cédric Feschotte. Science 2016
359
23

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
232
20


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
20


Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
17

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
197
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
80
18

Host-transposon interactions: conflict, cooperation, and cooption.
Rachel L Cosby, Ni-Chen Chang, Cédric Feschotte. Genes Dev 2019
67
19

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
466
13

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
517
13

KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks.
Michaël Imbeault, Pierre-Yves Helleboid, Didier Trono. Nature 2017
188
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
202
13

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
350
12

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
24
50

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
12

Repbase Update, a database of repetitive elements in eukaryotic genomes.
Weidong Bao, Kenji K Kojima, Oleksiy Kohany. Mob DNA 2015
970
11

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

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
11

The Dfam database of repetitive DNA families.
Robert Hubley, Robert D Finn, Jody Clements, Sean R Eddy, Thomas A Jones, Weidong Bao, Arian F A Smit, Travis J Wheeler. Nucleic Acids Res 2016
227
11

Landscape of somatic retrotransposition in human cancers.
Eunjung Lee, Rebecca Iskow, Lixing Yang, Omer Gokcumen, Psalm Haseley, Lovelace J Luquette, Jens G Lohr, Christopher C Harris, Li Ding, Richard K Wilson,[...]. Science 2012
454
10

The impact of transposable elements on mammalian development.
Jose L Garcia-Perez, Thomas J Widmann, Ian R Adams. Development 2016
76
13


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
225
10

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
10

The majority of primate-specific regulatory sequences are derived from transposable elements.
Pierre-Étienne Jacques, Justin Jeyakani, Guillaume Bourque. PLoS Genet 2013
171
10


Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
10

Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells.
Christopher D Todd, Özgen Deniz, Darren Taylor, Miguel R Branco. Elife 2019
37
24

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
9

LINE-mediated retrotransposition of marked Alu sequences.
Marie Dewannieux, Cécile Esnault, Thierry Heidmann. Nat Genet 2003
682
9

Roles for retrotransposon insertions in human disease.
Dustin C Hancks, Haig H Kazazian. Mob DNA 2016
267
9

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
9

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
9

Measuring and interpreting transposable element expression.
Sophie Lanciano, Gael Cristofari. Nat Rev Genet 2020
41
21

Transposable elements in human genetic disease.
Lindsay M Payer, Kathleen H Burns. Nat Rev Genet 2019
62
14

Author Correction: Regulation of transposable elements by DNA modifications.
Özgen Deniz, Jennifer M Frost, Miguel R Branco. Nat Rev Genet 2019
64
14

The impact of retrotransposons on human genome evolution.
Richard Cordaux, Mark A Batzer. Nat Rev Genet 2009
943
9

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
Mihaela Pertea, Geo M Pertea, Corina M Antonescu, Tsung-Cheng Chang, Joshua T Mendell, Steven L Salzberg. Nat Biotechnol 2015
8

A family of transposable elements co-opted into developmental enhancers in the mouse neocortex.
James H Notwell, Tisha Chung, Whitney Heavner, Gill Bejerano. Nat Commun 2015
48
16

Which transposable elements are active in the human genome?
Ryan E Mills, E Andrew Bennett, Rebecca C Iskow, Scott E Devine. Trends Genet 2007
279
8

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
331
8

deepTools2: a next generation web server for deep-sequencing data analysis.
Fidel Ramírez, Devon P Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S Richter, Steffen Heyne, Friederike Dündar, Thomas Manke. Nucleic Acids Res 2016
8

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
198
8

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
8

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
8

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
47
17


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.