A citation-based method for searching scientific literature

Guillaume Bourque, Kathleen H Burns, Mary Gehring, Vera Gorbunova, Andrei Seluanov, Molly Hammell, Michaël Imbeault, Zsuzsanna Izsvák, Henry L Levin, Todd S Macfarlan, Dixie L Mager, Cédric Feschotte. Genome Biol 2018
Times Cited: 303







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



Times Cited
  Times     Co-cited
Similarity


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
28

Regulatory activities of transposable elements: from conflicts to benefits.
Edward B Chuong, Nels C Elde, Cédric Feschotte. Nat Rev Genet 2017
549
22

Repbase Update, a database of repetitive elements in eukaryotic genomes.
Weidong Bao, Kenji K Kojima, Oleksiy Kohany. Mob DNA 2015
15

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
15

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
14

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
14

Regulatory evolution of innate immunity through co-option of endogenous retroviruses.
Edward B Chuong, Nels C Elde, Cédric Feschotte. Science 2016
391
13

DNA transposons and the evolution of eukaryotic genomes.
Cédric Feschotte, Ellen J Pritham. Annu Rev Genet 2007
659
12




Host-transposon interactions: conflict, cooperation, and cooption.
Rachel L Cosby, Ni-Chen Chang, Cédric Feschotte. Genes Dev 2019
88
11

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
10

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
488
10

Integration site selection by retroviruses and transposable elements in eukaryotes.
Tania Sultana, Alessia Zamborlini, Gael Cristofari, Pascale Lesage. Nat Rev Genet 2017
99
10

The origin and behavior of mutable loci in maize.
B McCLINTOCK. Proc Natl Acad Sci U S A 1950
735
9

The impact of retrotransposons on human genome evolution.
Richard Cordaux, Mark A Batzer. Nat Rev Genet 2009
972
9

Transposable elements and the epigenetic regulation of the genome.
R Keith Slotkin, Robert Martienssen. Nat Rev Genet 2007
9

Roles for retrotransposon insertions in human disease.
Dustin C Hancks, Haig H Kazazian. Mob DNA 2016
293
9

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
219
9

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
339
9

Retrotransposons as regulators of gene expression.
Reyad A Elbarbary, Bronwyn A Lucas, Lynne E Maquat. Science 2016
192
9

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
9

Transposable elements in human genetic disease.
Lindsay M Payer, Kathleen H Burns. Nat Rev Genet 2019
84
10

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
349
8


Transposable Element Domestication As an Adaptation to Evolutionary Conflicts.
Diwash Jangam, Cédric Feschotte, Esther Betrán. Trends Genet 2017
101
8

A Field Guide to Eukaryotic Transposable Elements.
Jonathan N Wells, Cédric Feschotte. Annu Rev Genet 2020
43
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
369
7


Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
7


Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution.
Sarah Schaack, Clément Gilbert, Cédric Feschotte. Trends Ecol Evol 2010
267
7


The impact of transposable elements on mammalian development.
Jose L Garcia-Perez, Thomas J Widmann, Ian R Adams. Development 2016
81
8

Restricting retrotransposons: a review.
John L Goodier. Mob DNA 2016
201
7

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
97
7

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
588
7

The B73 maize genome: complexity, diversity, and dynamics.
Patrick S Schnable, Doreen Ware, Robert S Fulton, Joshua C Stein, Fusheng Wei, Shiran Pasternak, Chengzhi Liang, Jianwei Zhang, Lucinda Fulton, Tina A Graves,[...]. Science 2009
7

Transposable elements in cancer.
Kathleen H Burns. Nat Rev Cancer 2017
188
7


Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
7


Dynamic interactions between transposable elements and their hosts.
Henry L Levin, John V Moran. Nat Rev Genet 2011
348
6

Coevolution between transposable elements and recombination.
Tyler V Kent, Jasmina Uzunović, Stephen I Wright. Philos Trans R Soc Lond B Biol Sci 2017
97
6

Repetitive elements may comprise over two-thirds of the human genome.
A P Jason de Koning, Wanjun Gu, Todd A Castoe, Mark A Batzer, David D Pollock. PLoS Genet 2011
617
6

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
298
6

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
186
6

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
6

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
431
6


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.