-
1
-
-
58149507192
-
Effects of retroviruses on host genome function
-
Jern P, Coffin JM (2008) Effects of retroviruses on host genome function. Annu Rev Genet 42:709-732.
-
(2008)
Annu Rev Genet
, vol.42
, pp. 709-732
-
-
Jern, P.1
Coffin, J.M.2
-
2
-
-
84861188188
-
Studies of endogenous retroviruses reveal a continuing evolutionary saga
-
Stoye JP (2012) Studies of endogenous retroviruses reveal a continuing evolutionary saga. Nat Rev Microbiol 10(6):395-406.
-
(2012)
Nat Rev Microbiol
, vol.10
, Issue.6
, pp. 395-406
-
-
Stoye, J.P.1
-
3
-
-
84871209027
-
Retroviridae
-
eds King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (Elsevier Academic, San Diego)
-
Stoye JP, et al. (2012) Retroviridae. Virus Taxonomy: Classification and Nomenclature of Viruses: Ninth Report of the International Committee on Taxonomy of Viruses, eds King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (Elsevier Academic, San Diego), pp 477-495.
-
(2012)
Virus Taxonomy: Classification and Nomenclature of Viruses: Ninth Report of the International Committee on Taxonomy of Viruses
, pp. 477-495
-
-
Stoye, J.P.1
-
4
-
-
27344432183
-
Use of endogenous retroviral sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy
-
Jern P, Sperber GO, Blomberg J (2005) Use of endogenous retroviral sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy. Retrovirology 2:50.
-
(2005)
Retrovirology
, vol.2
, pp. 50
-
-
Jern, P.1
Sperber, G.O.2
Blomberg, J.3
-
5
-
-
84858429240
-
Endogenous viruses: Insights into viral evolution and impact on host biology
-
Feschotte C, Gilbert C (2012) Endogenous viruses: Insights into viral evolution and impact on host biology. Nat Rev Genet 13(4):283-296.
-
(2012)
Nat Rev Genet
, vol.13
, Issue.4
, pp. 283-296
-
-
Feschotte, C.1
Gilbert, C.2
-
6
-
-
0001602245
-
Retroviral pathogenesis
-
eds Coffin JM, Hughes SH, Varmus HE (Cold Spring Harbor Lab Press, Cold Spring Harbor, NY)
-
Rosenberg N, Jolicoeur P (1997) Retroviral pathogenesis. Retroviruses, eds Coffin JM, Hughes SH, Varmus HE (Cold Spring Harbor Lab Press, Cold Spring Harbor, NY), pp 475-586.
-
(1997)
Retroviruses
, pp. 475-586
-
-
Rosenberg, N.1
Jolicoeur, P.2
-
7
-
-
0033049550
-
Interclass transmission and phyletic host tracking in murine leukemia virus-related retroviruses
-
Martin J, Herniou E, Cook J, O'Neill RW, Tristem M (1999) Interclass transmission and phyletic host tracking in murine leukemia virus-related retroviruses. J Virol 73(3):2442-2449.
-
(1999)
J Virol
, vol.73
, Issue.3
, pp. 2442-2449
-
-
Martin, J.1
Herniou, E.2
Cook, J.3
O'Neill, R.W.4
Tristem, M.5
-
8
-
-
0034004490
-
The nucleotide sequence of koala (Phascolarctos cinereus) retrovirus: A novel type C endogenous virus related to Gibbon ape leukemia virus
-
Hanger JJ, Bromham LD, McKee JJ, O'Brien TM, Robinson WF (2000) The nucleotide sequence of koala (Phascolarctos cinereus) retrovirus: A novel type C endogenous virus related to Gibbon ape leukemia virus. J Virol 74(9):4264-4272.
-
(2000)
J Virol
, vol.74
, Issue.9
, pp. 4264-4272
-
-
Hanger, J.J.1
Bromham, L.D.2
McKee, J.J.3
O'Brien, T.M.4
Robinson, W.F.5
-
9
-
-
84869003221
-
Analyses of pig genomes provide insight into porcine demography and evolution
-
Groenen MAM, et al. (2012) Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491(7424):393-398.
-
(2012)
Nature
, vol.491
, Issue.7424
, pp. 393-398
-
-
Groenen, M.A.M.1
-
10
-
-
84855858621
-
Characterization, mapping, and distribution of the two XMRV parental proviruses
-
Cingöz O, et al. (2012) Characterization, mapping, and distribution of the two XMRV parental proviruses. J Virol 86(1):328-338.
-
(2012)
J Virol
, vol.86
, Issue.1
, pp. 328-338
-
-
Cingöz, O.1
-
11
-
-
33646721361
-
Transspecies transmission of the endogenous koala retrovirus
-
Fiebig U, Hartmann MG, Bannert N, Kurth R, Denner J (2006) Transspecies transmission of the endogenous koala retrovirus. J Virol 80(11):5651-5654.
-
(2006)
J Virol
, vol.80
, Issue.11
, pp. 5651-5654
-
-
Fiebig, U.1
Hartmann, M.G.2
Bannert, N.3
Kurth, R.4
Denner, J.5
-
12
-
-
0030722726
-
Two sets of humantropic pig retrovirus
-
Le Tissier P, Stoye JP, Takeuchi Y, Patience C, Weiss RA (1997) Two sets of humantropic pig retrovirus. Nature 389(6652):681-682.
-
(1997)
Nature
, vol.389
, Issue.6652
, pp. 681-682
-
-
Le Tissier, P.1
Stoye, J.P.2
Takeuchi, Y.3
Patience, C.4
Weiss, R.A.5
-
13
-
-
0031054438
-
Infection of human cells by an endogenous retrovirus of pigs
-
Patience C, Takeuchi Y, Weiss RA (1997) Infection of human cells by an endogenous retrovirus of pigs. Nat Med 3(3):282-286.
-
(1997)
Nat Med
, vol.3
, Issue.3
, pp. 282-286
-
-
Patience, C.1
Takeuchi, Y.2
Weiss, R.A.3
-
14
-
-
34548590461
-
Automated recognition of retroviral sequences in genomic data - RetroTector
-
Sperber GO, Airola T, Jern P, Blomberg J (2007) Automated recognition of retroviral sequences in genomic data - RetroTector. Nucleic Acids Res 35(15):4964-4976.
-
(2007)
Nucleic Acids Res
, vol.35
, Issue.15
, pp. 4964-4976
-
-
Sperber, G.O.1
Airola, T.2
Jern, P.3
Blomberg, J.4
-
15
-
-
40849097775
-
Rates of evolutionary change in viruses: Patterns and determinants
-
Duffy S, Shackelton LA, Holmes EC (2008) Rates of evolutionary change in viruses: Patterns and determinants. Nat Rev Genet 9(4):267-276.
-
(2008)
Nat Rev Genet
, vol.9
, Issue.4
, pp. 267-276
-
-
Duffy, S.1
Shackelton, L.A.2
Holmes, E.C.3
-
16
-
-
84879977879
-
An exogenous retrovirus isolated from koalas with malignant neoplasias in a US zoo
-
Xu W, et al. (2013) An exogenous retrovirus isolated from koalas with malignant neoplasias in a US zoo. Proc Natl Acad Sci USA 110(28):11547-11552.
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, Issue.28
, pp. 11547-11552
-
-
Xu, W.1
-
17
-
-
33745972414
-
Retroviral invasion of the koala genome
-
Tarlinton RE, Meers J, Young PR (2006) Retroviral invasion of the koala genome. Nature 442(7098):79-81.
-
(2006)
Nature
, vol.442
, Issue.7098
, pp. 79-81
-
-
Tarlinton, R.E.1
Meers, J.2
Young, P.R.3
-
18
-
-
84879324277
-
One hundred twenty years of koala retrovirus evolution determined from museum skins
-
Ávila-Arcos MC, et al. (2013) One hundred twenty years of koala retrovirus evolution determined from museum skins. Mol Biol Evol 30(2):299-304.
-
(2013)
Mol Biol Evol
, vol.30
, Issue.2
, pp. 299-304
-
-
Ávila-Arcos, M.C.1
-
19
-
-
0032766857
-
Multiple comparisons of log-likelihoods with applications to phylogenetic inference
-
Shimodaira H, Hasegawa M (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16(8):1114-1116.
-
(1999)
Mol Biol Evol
, vol.16
, Issue.8
, pp. 1114-1116
-
-
Shimodaira, H.1
Hasegawa, M.2
-
20
-
-
84883170936
-
The extraordinary evolutionary history of the reticuloendotheliosis viruses
-
Niewiadomska AM, Gifford RJ (2013) The extraordinary evolutionary history of the reticuloendotheliosis viruses. PLoS Biol 11(8):e1001642.
-
(2013)
PLoS Biol
, vol.11
, Issue.8
-
-
Niewiadomska, A.M.1
Gifford, R.J.2
-
21
-
-
84865124450
-
Identification of diverse groups of endogenous gammaretroviruses in mega- and microbats
-
Cui J, et al. (2012) Identification of diverse groups of endogenous gammaretroviruses in mega- and microbats. J Gen Virol 93(Pt 9):2037-2045.
-
(2012)
J Gen Virol
, vol.93
, Issue.PART 9
, pp. 2037-2045
-
-
Cui, J.1
-
22
-
-
84858792076
-
Behavioral, ecological, and evolutionary aspects of meateating by Sumatran orangutans (Pongo abelii)
-
Hardus ME, et al. (2012) Behavioral, ecological, and evolutionary aspects of meateating by Sumatran orangutans (Pongo abelii). Int J Primatol 33(2):287-304.
-
(2012)
Int J Primatol
, vol.33
, Issue.2
, pp. 287-304
-
-
Hardus, M.E.1
-
23
-
-
77949733453
-
Vertebrate DNA in fecal samples from bonobos and gorillas: Evidence for meat consumption or artefact?
-
Hofreiter M, Kreuz E, Eriksson J, Schubert G, Hohmann G (2010) Vertebrate DNA in fecal samples from bonobos and gorillas: Evidence for meat consumption or artefact? PLoS ONE 5(2):e9419.
-
(2010)
PLoS ONE
, vol.5
, Issue.2
-
-
Hofreiter, M.1
Kreuz, E.2
Eriksson, J.3
Schubert, G.4
Hohmann, G.5
-
24
-
-
30344481292
-
Superfamily Muroidea
-
eds Wilson DE, Reeder DM (Johns Hopkins Univ Press, Baltimore), 3rd Ed
-
Musser G, Carleton M (2005) Superfamily Muroidea. Mammal Species of the World: A Taxonomic and Geographic Reference, eds Wilson DE, Reeder DM (Johns Hopkins Univ Press, Baltimore), 3rd Ed, Vol 2, pp 894-1531.
-
(2005)
Mammal Species of the World: A Taxonomic and Geographic Reference
, vol.2
, pp. 894-1531
-
-
Musser, G.1
Carleton, M.2
-
25
-
-
80355129314
-
Multiple geographic origins of commensalism and complex dispersal history of Black Rats
-
Aplin KP, et al. (2011) Multiple geographic origins of commensalism and complex dispersal history of Black Rats. PLoS ONE 6(11):e26357.
-
(2011)
PLoS ONE
, vol.6
, Issue.11
-
-
Aplin, K.P.1
-
26
-
-
72849122986
-
Molecular characterization of a novel gammaretrovirus in killer whales (Orcinus orca)
-
Lamere SA, et al. (2009) Molecular characterization of a novel gammaretrovirus in killer whales (Orcinus orca). J Virol 83(24):12956-12967.
-
(2009)
J Virol
, vol.83
, Issue.24
, pp. 12956-12967
-
-
Lamere, S.A.1
-
27
-
-
84877597071
-
Ancient invasion of an extinct gammaretrovirus in cetaceans
-
Wang L, et al. (2013) Ancient invasion of an extinct gammaretrovirus in cetaceans. Virology 441(1):66-69.
-
(2013)
Virology
, vol.441
, Issue.1
, pp. 66-69
-
-
Wang, L.1
-
28
-
-
0343117821
-
Isolation from the Asian mouse Mus caroli of an endogenous type C virus related to infectious primate type C viruses
-
Lieber MM, et al. (1975) Isolation from the Asian mouse Mus caroli of an endogenous type C virus related to infectious primate type C viruses. Proc Natl Acad Sci USA 72(6):2315-2319.
-
(1975)
Proc Natl Acad Sci USA
, vol.72
, Issue.6
, pp. 2315-2319
-
-
Lieber, M.M.1
-
29
-
-
84898673851
-
On the concept and elucidation of endogenous retroviruses
-
Weiss RA (2013) On the concept and elucidation of endogenous retroviruses. Philos Trans R Soc Lond B Biol Sci 368(1626):20120494.
-
(2013)
Philos Trans R Soc Lond B Biol Sci
, vol.368
, Issue.1626
, pp. 20120494
-
-
Weiss, R.A.1
-
30
-
-
84883304227
-
The avian XPR1 gammaretrovirus receptor is under positive selection and is disabled in bird species in contact with virus-infected wild mice
-
Martin C, Buckler-White A, Wollenberg K, Kozak CA (2013) The avian XPR1 gammaretrovirus receptor is under positive selection and is disabled in bird species in contact with virus-infected wild mice. J Virol 87(18):10094-10104.
-
(2013)
J Virol
, vol.87
, Issue.18
, pp. 10094-10104
-
-
Martin, C.1
Buckler-White, A.2
Wollenberg, K.3
Kozak, C.A.4
-
31
-
-
77956477507
-
The evolution of HIV-1 and the origin of AIDS
-
Sharp PM, Hahn BH (2010) The evolution of HIV-1 and the origin of AIDS. Philos Trans R Soc Lond B Biol Sci 365(1552):2487-2494.
-
(2010)
Philos Trans R Soc Lond B Biol Sci
, vol.365
, Issue.1552
, pp. 2487-2494
-
-
Sharp, P.M.1
Hahn, B.H.2
-
32
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792-1797.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.5
, pp. 1792-1797
-
-
Edgar, R.C.1
-
33
-
-
67650757433
-
trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses
-
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T (2009) trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25(15):1972-1973.
-
(2009)
Bioinformatics
, vol.25
, Issue.15
, pp. 1972-1973
-
-
Capella-Gutiérrez, S.1
Silla-Martínez, J.M.2
Gabaldón, T.3
-
34
-
-
80052006478
-
Missing data in phylogenetic analysis: Reconciling results from simulations and empirical data
-
Wiens JJ, Morrill MC (2011) Missing data in phylogenetic analysis: Reconciling results from simulations and empirical data. Syst Biol 60(5):719-731.
-
(2011)
Syst Biol
, vol.60
, Issue.5
, pp. 719-731
-
-
Wiens, J.J.1
Morrill, M.C.2
-
35
-
-
84858080561
-
Misleading results of likelihood-based phylogenetic analyses in the presence of missing data
-
Simmons MP (2012) Misleading results of likelihood-based phylogenetic analyses in the presence of missing data. Cladistics 28(2):208-222.
-
(2012)
Cladistics
, vol.28
, Issue.2
, pp. 208-222
-
-
Simmons, M.P.1
-
36
-
-
33845296602
-
Identification of an infectious progenitor for the multiplecopy HERV-K human endogenous retroelements
-
Dewannieux M, et al. (2006) Identification of an infectious progenitor for the multiplecopy HERV-K human endogenous retroelements. Genome Res 16(12):1548-1556.
-
(2006)
Genome Res
, vol.16
, Issue.12
, pp. 1548-1556
-
-
Dewannieux, M.1
-
37
-
-
18144390153
-
Sequence variability, gene structure, and expression of full-length human endogenous retrovirus H
-
Jern P, Sperber GO, Ahlsén G, Blomberg J (2005) Sequence variability, gene structure, and expression of full-length human endogenous retrovirus H. J Virol 79(10):6325-6337.
-
(2005)
J Virol
, vol.79
, Issue.10
, pp. 6325-6337
-
-
Jern, P.1
Sperber, G.O.2
Ahlsén, G.3
Blomberg, J.4
-
38
-
-
70349326734
-
Macroevolution of complex retroviruses
-
Katzourakis A, Gifford RJ, Tristem M, Gilbert MT, Pybus OG (2009) Macroevolution of complex retroviruses. Science 325(5947):1512.
-
(2009)
Science
, vol.325
, Issue.5947
, pp. 1512
-
-
Katzourakis, A.1
Gifford, R.J.2
Tristem, M.3
Gilbert, M.T.4
Pybus, O.G.5
-
39
-
-
58749086368
-
Identification of a RELIK orthologue in the European hare (Lepus europaeus) reveals a minimum age of 12 million years for the lagomorph lentiviruses
-
Keckesova Z, Ylinen LM, Towers GJ, Gifford RJ, Katzourakis A (2009) Identification of a RELIK orthologue in the European hare (Lepus europaeus) reveals a minimum age of 12 million years for the lagomorph lentiviruses. Virology 384(1):7-11.
-
(2009)
Virology
, vol.384
, Issue.1
, pp. 7-11
-
-
Keckesova, Z.1
Ylinen, L.M.2
Towers, G.J.3
Gifford, R.J.4
Katzourakis, A.5
-
40
-
-
35948967657
-
Role of APOBEC3 in genetic diversity among endogenous murine leukemia viruses
-
Jern P, Stoye JP, Coffin JM (2007) Role of APOBEC3 in genetic diversity among endogenous murine leukemia viruses. PLoS Genet 3(10):2014-2022.
-
(2007)
PLoS Genet
, vol.3
, Issue.10
, pp. 2014-2022
-
-
Jern, P.1
Stoye, J.P.2
Coffin, J.M.3
-
41
-
-
84884836922
-
Novel parallelization schemes for large-scale likelihood-based phylogenetic inference
-
IEEE Computer Society, New York
-
Stamatakis A, Aberer J (2013) Novel parallelization schemes for large-scale likelihood-based phylogenetic inference. 2013 IEEE International Parallel & Distributed Processing Symposium (IPDPS), May 20-24, Boston (IEEE Computer Society, New York), pp 1195-1204.
-
(2013)
2013 IEEE International Parallel & Distributed Processing Symposium (IPDPS), May 20-24, Boston
, pp. 1195-1204
-
-
Stamatakis, A.1
Aberer, J.2
-
42
-
-
33750403801
-
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis A (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21):2688-2690.
-
(2006)
Bioinformatics
, vol.22
, Issue.21
, pp. 2688-2690
-
-
Stamatakis, A.1
-
43
-
-
79951952562
-
BIO:Phylo-phyloinformatic analysis using perl
-
Vos RA, Caravas J, Hartmann K, Jensen MA, Miller C (2011) BIO:Phylo-phyloinformatic analysis using perl. BMC Bioinformatics 12:63.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 63
-
-
Vos, R.A.1
Caravas, J.2
Hartmann, K.3
Jensen, M.A.4
Miller, C.5
-
44
-
-
77949718257
-
FastTree 2 - Approximately maximum-likelihood trees for large alignments
-
Price MN, Dehal PS, Arkin AP (2010) FastTree 2 - approximately maximum-likelihood trees for large alignments. PLoS ONE 5(3):e9490.
-
(2010)
PLoS ONE
, vol.5
, Issue.3
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
45
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19(12):1572-1574.
-
(2003)
Bioinformatics
, vol.19
, Issue.12
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
-
46
-
-
84865382153
-
More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs
-
Crawford NG, et al. (2012) More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Biol Lett 8(5):783-786.
-
(2012)
Biol Lett
, vol.8
, Issue.5
, pp. 783-786
-
-
Crawford, N.G.1
-
47
-
-
80055070300
-
Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification
-
Meredith RW, et al. (2011) Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science 334(6055):521-524.
-
(2011)
Science
, vol.334
, Issue.6055
, pp. 521-524
-
-
Meredith, R.W.1
-
48
-
-
77952854165
-
Genome-wide synteny through highly sensitive sequence alignment: Satsuma
-
Grabherr MG, et al. (2010) Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics 26(9):1145-1151.
-
(2010)
Bioinformatics
, vol.26
, Issue.9
, pp. 1145-1151
-
-
Grabherr, M.G.1
|