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Google Scholar Profile | Selected Research | Review Articles

All Publications:

2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | prior

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* : equal contribution

 

 

2017

 

 

 

Kapusta A, Suh A, Feschotte C (2017) Dynamics of genome size evolution in birds and mammals (in revision). Preprint at BioRxiv

 

85

 

Chuong EB, Elde NC, Feschotte C (2017) Regulatory activities of transposable elements: from conflicts to benefits. Nature Reviews Genetics (in press)

 

84

 

Hamilton EP*, Kapusta A*, Huvos PE, Bidwell SL, Zafar N, Tang H, Hadjithomas M, Krishnakumar V, Badger JH, Caler EV, Russ C, Zeng Q, Fan L, Levin JZ, Shea T, Young SK, Hegarty R, Daza R, Gujja S, Wortman JR, Birren BW, Nusbaum C, Thomas J, Carey CM, Pritham EJ, Feschotte C, Noto T, Mochizuki K, Papazyan R, Taverna SD, Dear PH, Cassidy-Hanley DM, Xiong J, Miao W, Orias E, Coyne RS (2017) Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome. eLIFE (in press)

 

2016

 

 

83

 

Chuong EB, Elde NC*, Feschotte C* (2016) Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Science 351:1083-1087

 

82

 

Rius N, Guillén Y, Delprat A, Kapusta A, Feschotte C, Ruiz A (2016) Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes. BMC Genomics 17:344-358

 

2015

 

 

81

Zhuo X. & Feschotte C. (2015) Cross-species transmission and differential fate of an endogenous retrovirus in three mammal lineages. PLOS Pathogens 11: e1005279 [Nov 12]

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80

 

Henssen A.G., Henaff E., Jiang E., Eisenberg A.R., Carson J.R., Villasante C.M., Ray M., Still E., Burns M., Gandara J., Feschotte C., Mason C.E., Kentsis A. (2015) Genomic transposition induced by human PGBD5. eLIFE 4: e10565 [Sep 25]

 

79

 

Nath A, Kury P, Sciascia do Olival G, Dolei A, Karlsson H, Groc K, Scheinder M, Kriesel J, Tourraine JL, Mallet F, Marche PN, Arnaud P, Feschotte C & Perron H (2015) Meeting report: First international workshop on human endogenous retroviruses and diseases, HERVs & disease 2015. Mobile DNA 6:20 [Oct 15]

 

78

 

Hoen et al. (2015) A call for benchmarking transposable element annotation methods. Mobile DNA 6:13 [Aug 4]

 

77

 

Cheng S., Feschotte C. & Mueller R.L. (2015) DNA transposons have colonized the genome of the giant virus Pandoravirus salinus. BMC Biology 13:38 [Jun 12]

 

76

 

Malfavon-Borja R. & Feschotte C. (2015) Fighting fire with fire: endogenous retrovirus envelopes as restriction factors. Journal of Virology 89: 4047-4050 [Feb 4]

 

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75

 

Lynch VJ, Nnamani M, Kapusta A, Brayer KJ, Plaza SL, Mazur EC, Emera D, Sheikh SZ, Grützner F, Bauersachs S, Graf A, Young SL, Lieb JD, DeMayo FJ, Feschotte C & Wagner GP (2015) Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy. Cell Reports 10: 551-561  [Jan 29]

 

Disc

74

 

Feschotte C (2015) Transposable Elements. Discoveries in Modern Science: Exploration, Invention, Technology. Ed. James Trefill. Macmillan (in press)

 

PNAS

73

 

Guillén Y, Rius N, Delprat A, Williford A, Muyas F, Puig M, Casillas S. Ràmia ., Egea R, Negre B, Mir G, Camps J. Moncunill V. Ruiz-Ruano FJ, Cabrero J, de Lima LG, Dias GB, Ruiz JC, Kapusta A, Garcia-Mas J, Gut M, Gut IG, Torrents D, Camacho JP, Kuhn G.C., Feschotte C, Clark AG, Betrán E, Barbadilla A, Ruiz A (2015) Genomics of ecological adaptation in cactophilic Drosophila. Genome Biology and Evolution 7: 349-66 [Dec 31]

 

2014

 

 

72

 

Kapusta A & Feschotte C (2014) Volatile evolution of long noncoding RNAs: mechanisms and biological implications. Trends in Genetics 30:439-452 [sep 1] [Feature Review] [cover]

 

PNAS

71

 

Ha H, Song J, Wang S, Kapusta A, Feschotte C, Chen KC & Xing J (2014) A comprehensive analysis of piRNAs from adult human testis and their relationship with genes and mobile elements. BMC Genomics 15: 545-561 [Jul 1]

 

70

 

 

Han M-J, Xu H-E, Zhang H-H, Feschotte C. & Zhang Z. (2014) Spy: a new superfamily of eukaryotic DNA transposons without target site duplications. Genome Biology and Evolution 6: 1748-1757 [Jun 24]

 

 

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69

Zhang HH, Feschotte C, Han MJ, Zhang Z (2014) Recurrent horizontal transfer of Chapaev transposons in diverse invertebrate and vertebrate animals. Genome Biology and Evolution 6: 1375-1386 [May 27]

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MBE

68

 

Campos-Sanchez R, Kapusta A, Feschotte C, Chiaromonte F & Makova KD (2014) Genomic Landscape of human, bat and ex vivo DNA transposon integrations. Molecular Biology and Evolution31: 1816-1832 [Apr 22]

 

2013

 

 

PNAS

67

Castoe TA et al. (2013) The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. PNAS 110: 20645-20650 [Dec 17]

66

 

Chuong EB & Feschotte C (2013) Transposons up the dosage. Science 342: 812-813 [ Nov 15]

 

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65

Feschotte C & McCormick JF (2013) Evolutionary history and impact of human DNA transposons. In: Encyclopedia of Life Sciences, Wiley and Sons. [Oct 18]

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64

 

Zhuo X, Rho M & Feschotte C (2013) Genome-wide characterization of endogenous retroviruses in the bat Myotis lucifugus reveals recent and diverse infections. Journal of Virology 87: 8493-8501 [May 29]

[spotlight] [cover]

 

 

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63

Kapusta A, Kronenberg Z*, Lynch VJ*,  Zhuo X, Ramsay L, Bourque G, Yandell M & Feschotte C (2013) Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genetics 9(4): e1003470 [Apr 25]

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PNAS

62

 

Gilbert C, Waters R, Feschotte C & Schaack S (2013) Horizontal transfer of OC1 transposons in the Tasmanian devil. BMC Genomics 14: 134 [Feb 27]

 

PNAS

61

 

Li X*, Mitra R*, Kapusta A, Mayhew D, Mitra RD, Feschotte C & Craig NL (2013) Functional characterization of piggyBat from the bat Myotis lucifugus unveils an active mammalian DNA transposon. PNAS 110: 234-239 [Dec 17]

[supplementary material]

 

60

 

Li X, Ewis H, Hice RH, Malani N, Parker N, Zhou L, Feschotte C Bushman FD, Atkinson PW & Craig NL (2013) A resurrected mammalian hAT transposable element and a closely related insect element are highly active in human cell culture. PNAS 110: E478-487 [Oct 22]

 

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2012

 

 

MGE

59

 

Llorens C, Bernet GP, Ramasamy S, Feschotte C & Moya A (2012) On the transposon origins of mammalian SCAND3 and ZRBA2, two zinc-finger genes carrying an integrase/transposase domain. Mobile Genetic Elements 2: 205-210 [Dec 2]

 

 

58

Arkhipova I., Batzer MA, Brosius J, Feschotte C, Moran JV, Schmitz J & Jurka J  (2012) Genomic impact of eukaryotic transposable elements.  Mobile DNA 3: 19-27 [meeting report]

 

PDF

 

57

Feschotte C. (2012) Review of "Mobile DNA - finding treasure in junk" by Haig H. Kazazian Mobile DNA 3:16 [book review]

 

PDF

 

56

Feschotte C & Gilbert C (2012) Endogenous viruses: insight into viral evolution and impact on host biology. Nature Reviews Genetics 13: 283-296 [March 16]

 

PDF

 

55

Sun C, Shepard DB, Chong RA, Lopez-Arriaza J, Hall K, Castoe TA, Feschotte C, Pollock DD, Mueller R. (2012) LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. Genome Biology and Evolution 4:168-183 [Dec 26]

 

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MBE

54

 

Gilbert C, Hernandez SS, Flores-Benabib J, Smith EN & Feschotte C (2012) Rampant horizontal transfer of SPIN transposons in squamate reptiles. Molecular Biology and Evolution 29:503-515 [July 18]

[supplementary material]

MBE

53

 

Kejnovsky E, Hawkins JS & Feschotte C (2012) Plant transposable elements: biology and evolution. Pp. 17-34. In: Plant Genome Diversity Vol. 1 (Wendel J.F., Greilhuber J., Leitch I.J., Dolezel J. eds.) Springer

 

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2011

 

 

 

 

 

 

52

Castoe TA, de Koning JAP., Hall KT. Yokoyama KD, Gu W, Smith EN, Feschotte C, Uetz P, Ray DA, Dobry J, Bogden R, Mackessy SP, Bronikowski AM, Warren WC, Secor SM, & Pollock DD (2011) Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes. Genome Biology 12: 406 [8 pages]

 

51

Castoe TA, Hall KA, Guibotsy Mboulas ML, Gu W, de Koning AP, Fox SE, Poole AW, Vemulapalli V, Daza JM, Mockler T, Smith EN, Feschotte C & Pollock DD. (2011) Discovery of highly divergent repeat landscapes in snake genomes using high throughput sequencing.   Genome Biology and Evolution 3: 641-653 [May 13]

[supplementary material]

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2010

 

 

 

 

 

50

 

Gilbert C, Schaack S & Feschotte C (2010) Mobile elements jump between parasites and vertebrate hosts. Medecine Sciences (Paris) 26: 1025-1027 [Dec 26] [in French]

 

PDF

49

 

Arensburger P. et al. (2010) Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics. Science 330: 86-88 [1 Oct 2010]

 

PDF

48

 

Chaconas G, Craig NL, Curcio MJ, Deininger PL, Feschotte C, Levin H, Rice PA & Voytas DF (2010) Meeting Report for Mobile DNA 2010. Mobile DNA 1:20

 

PDF

47

Gilbert C & Feschotte C (2010) Genomic fossils calibrate the long-term evolution of Hepadnaviruses PLoS Biology 8: e1000495 [28 Sep 2010]

[supplementary material]

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46

 

Schaack S*, Gilbert C* & Feschotte C (2010) Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends in Ecology & Evolution 25: 537-546 [28 June 2010]

* These authors contributed equally to this work

[supplementary table]

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45

Gilbert C*, Schaack S*, Pace JK II, Brindley PD & Feschotte C (2010) A role for host-parasite interactions in the horizontal transfer of transposons across phyla. Nature 464: 1347-1350 [29 April 2010]

* These authors contributed equally to this work

[Editor's summary] [supplementary material]

F1000
PDF
44
Singh A, Keswani U, Levine D, Feschotte C & Stojanovic N (2010) An algorithm for the reconstruction of consensus sequences of ancient segmental duplications and transposon copies in eukaryotic genomes. International Journal of Bioinformatics Research & Applications 6:147-162 PDF

43

Feschotte C (2010) Bornavirus enters the genome. Nature 463: 39-40

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2009

 

 

 

 

42

Feschotte C & Pritham EJ (2009) A cornucopia of Helitrons shapes the maize genome. PNAS 106:19747-19748

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41

Yang G, Holligan-Nagel D, Feschotte C, Hancock NH, Wessler SR (2009) Tuned for transposition: molecular determinants underlying the hyperactivity of a Stowaway MITE. Science 325:1391-1394

[supplementary material] [commentary by Gonzales & Petrov]

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40

Feschotte C, Keswani U*, Ranganathan N*, Guibotsy ML & Levine D (2009) Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes. Genome Biology and Evolution 1 :205-220

* These authors contributed equally to this work

[supplementary material] [download and manual] [sourceforge]

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39

Venner S, Feschotte C & Biemont C (2009) Dynamics of transposable elements: toward a community ecology of the genome. Trends in Genetics 25:317-323

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38

Pace JK, II, Sen SK, Batzer MA & Feschotte C (2009) Repair-mediated duplication by capture of proximal chromosomal DNA has shaped vertebrate genome evolution. PLoS Genetics 5(5):e1000469. Epub 2009 May 8

[supplementary material]

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37

Gilbert C, Maxfield D. Goodman SM & Feschotte C (2009) Parallel germline infiltration of a lentivirus in two Malagasy lemurs. PLoS Genetics 5(3):e1000425. Epub 2009 Mar 20

[supplementary material]

PDF

36

Gilbert C, Pace JK, II, & Feschotte C (2009) Horizontal SPINning of transposons. Communicative and Integrative Biology 2: 1-3

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2008

 

 

 

 

35

Pace JK, II, Gilbert C, Clark MS & Feschotte C (2008) Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods. PNAS 105:17023-17028

[supplementary material] [commentary by Lisch] [highlight] F1000

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34

Feschotte C (2008) Transposable elements and the evolution of regulatory networks. Nature Reviews Genetics 9:397-405

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Ray DA*, Feschotte C*, Smith JD, Pagan HJT, Pritham EJ, Arensburger P, Atkinson PW & Craig NL (2008) Multiple waves of recent DNA transposon activity in the bat Myotis lucifugus. Genome Research 18:717-728

* These authors contributed equally to this work

[supplementary material] [cover image]

PDF

32

Feschotte C. (2008) Evolutionary history and impact of human DNA transposons. In: Handbook of Human Molecular Evolution (D. Cooper, ed.), Wiley and Sons.

Also published online in Encyclopedia of Life Sciences on March 14 2008.

PDF

MBE

31

 

Casola C*, Hucks DV* & Feschotte C (2008) Convergent domestication of pogo-like transposases into centromere-binding proteins in mammals and fission yeast. Molecular Biology and Evolution 25: 29-41

* These authors contributed equally to this work [supplementary material]

PDF

2007

 

 

30

 

Lin R, Ding L, Casola C, Ripoll DR, Feschotte C & Wang H. (2007) Transposase-derived transcription factors regulate light signaling in Arabidopsis. Science 318:1302-1305

[supplementary material] F1000

PDF
AnnRev
29
Feschotte C. & Pritham EJ (2007) DNA transposons and the evolution of eukaryotic genomes. Annual Review of Genetics 41: 331-368 PDF
28

Singh A, Feschotte C & Stojanovic N (2007) Micro-repetitive structure of genomic sequences and the identification of ancient repeat elements. Proceedings IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007)pp. 165-171

 

 
MBE
27
Casola C, Lawing AM, Betran E & Feschotte C (2007) PIF-like transposons are common in Drosophila and have been repeatedly domesticated to generate new host genes. Molecular Biology and Evolution 24: 1872-1888 [supplementary material] PDF
26
Singh A, Feschotte C & Stojanovic N (2007) A study of the repetitive structure and distribution of short motifs in human genomic sequences. International Journal of Bioinformatics Research & Applications 3:523-535 PDF
25

Pace JK, II & Feschotte C (2007) The evolutionary history of human DNA transposons: evidence for intense activity in the primate lineage. Genome Research 17:422-432

[supplemental data]F1000

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24

Pritham EJ* & Feschotte C* (2007) Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus. PNAS 104:1895-1900

] [supporting information]

* The authors contributed equally to this work

23

Bai Y, Casola C, Feschotte C and Betrán E. (2007) Constant rate of origination and convergent acquisition of functional retrogenes in Drosophila. Genome Biology 8: R11

22
Feschotte C & Pritham EJ  (2007) Computational Analysis and Paleogenomics of Interspersed Repeats in Eukaryotes. in Computational Genomics: Current Methods Ed: N. Stojanovic. Horizon Scientific Press Pp. 31-53.  
21
Pritham EJ, Putliwala T & Feschotte C (2007) Mavericks, a new class of giant transposable elements widespread in eukaryotes and related to DNA viruses. Gene (Special Issue) 390:3-17 [Aug 23, 2006; Epub ahead of print]

2006

 

 

 

 
pnas
20
Feschotte C (2006) The piggyBac transposon holds promises for human gene therapy. PNAS 103: 14981-14982
gb
19
Feschotte C & Pritham EJ (2006) Mobile DNA: genomes under the influence. Genome Biology 7:320-324
Cordaux R, Udit S, Batzer MA & Feschotte C (2006) Birth of a chimeric primate gene by capture of the transposase gene from a mobile element. PNAS 103:8101-8106

[Supporting Information] [cover image] [highlight] [commentary by Jordan]

 
 
17
Ranganathan N, Feschotte C & Levine D (2006) Cluster- and Grid-based classification of transposable elements in eukaryotic genomes. Proc. Sixth IEEE Int. Symp. Cluster Computing and the Grid (CCGRID '06)

2005

 

 

 

 
16
Feschotte C & Pritham EJ (2005) Non-mammalian c-integrases are encoded by giant transposable elements Trends in Genetics 21:551-552 [Supplementary Table] [Supplementary Figure]
MBE
15

Pritham EJ, Feschotte C & Wessler SR (2005) Unexpected diversity and differential success of DNA transposons in four species of Entamoeba protozoans. Molecular Biology and Evolution 22:1751-1763 [Supplemental Data]

14
Feschotte C, Osterlund MT, Peeler R & Wessler SR (2005) DNA binding specificity of rice mariner-like transposases and interactions with Stowaway MITEs. Nucleic Acids Research 33:2153-2165

2004

 

 

 

 
MBE
13

Feschotte C (2004) Merlin, a new superfamily of DNA transposons identified in diverse animal genomes and related to bacterial IS1016 insertion sequences. Molecular Biology and Evolution 21:1769-1780 [Supplemental Data]

Pre-lab

 

 

 

 
12
Jiang N, Feschotte C, Zhang X & Wessler SR (2004) Using rice to understand the origin and amplification of MITEs. Current Opinion in Plant Biology 7:115-119
11
Zhang X, Jiang N, Feschotte C & Wessler SR (2004) PIF- and Pong-like transposable elements: distribution, evolution and relationships with Tourist-like MITEs. Genetics 166:971-986
genetics
10
Pritham EJ, Zhang YH, Feschotte C & Kesseli RV (2003) An Ac-like transposable element family with trancriptionally active Y-linked copies in the white campion, Silene latifolia. Genetics 165: 799-807
genetics
9
Feschotte C, Swamy L & Wessler SR (2003) Genome-wide analysis of mariner-like transposable elements reveals complex relationships with Stowaway MITEs. Genetics 163: 747-758
8
Feschotte C, Jiang N & Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nature Reviews Genetics 3: 329-341
7
Feschotte C, Zhang X & Wessler SR (2002) Miniature inverted-repeat transposable elements (MITEs) and their relationship with established DNA transposons. in Mobile DNA II (Craig N, Craigie R, Gellert M & Lambowitz A, eds.) American Society of Microbiology Press. Washington D.C
pnas
6
Feschotte C & Wessler SR (2002) Mariner-like transposases are widespread and diverse in flowering plants. Proc. Natl. Acad. Sci. USA 99: 280-285. [Supplementary Table 1] [Supplementary Table 2]
pnas
5

Zhang X, Feschotte C, Zhang Q, Jiang N, Eggleston WB & Wessler SR (2001) P instability factor: An active maize transposon system associated with the amplification of Tourist-like MITEs and a new superfamily of transposases. Proc. Natl. Acad. Sci. USA 98:12572-12577. [commentary by J. Jurka & V. Kapitonov]

pnas
4
Feschotte C & Wessler SR (2001) Treasures in the attic: Rolling circle transposons discovered in eukaryotic genomes. Proc. Natl. Acad. Sci. USA 98: 8923-8924
3
Feschotte C, Fourrier N, Desmons I, Mouches C (2001) Birth of a retroposon: The Twin SINE family from the vector mosquito Culex pipiens may have originated from a dimeric tRNA precursor. Molecular Biology and Evolution 18:74-84
2
Feschotte C & Mouches C (2000) Recent amplification of miniature inverted-repeat transposable elements in the vector mosquito Culex pipiens: characterization of the Mimo family. Gene 250:109-116
1
Feschotte C & Mouches C (2000) Evidence that a family of miniature inverted-repeat transposable elements (MITEs) from the Arabidopsis thaliana genome has arisen from a pogo-like DNA transposon. Molecular Biology and Evolution 17:730-737