-
1
-
-
79952706183
-
The struggle for life of the genome's selfish architects
-
doi:10.1186/1745-6150-6-19
-
Hua-Van A, Le Rouzic A, Boutin TS, Filée J, Capy P, (2011) The struggle for life of the genome's selfish architects. Biol Direct 6: 19. doi:10.1186/1745-6150-6-19. PubMed: 21414203.
-
(2011)
Biol Direct
, vol.6
, pp. 19
-
-
Hua-Van, A.1
Le Rouzic, A.2
Boutin, T.S.3
Filée, J.4
Capy, P.5
-
2
-
-
0032992818
-
Multiple Ty-mediated chromosomal translocations lead to karyotype changes in a wine strain of Saccharomyces cerevisiae
-
doi:10.1007/s004380050028
-
Rachidi N, Barre P, Blondin B, (1999) Multiple Ty-mediated chromosomal translocations lead to karyotype changes in a wine strain of Saccharomyces cerevisiae. Mol Gen Genet 261: 841-850. doi:10.1007/s004380050028. PubMed: 10394922.
-
(1999)
Mol Gen Genet
, vol.261
, pp. 841-850
-
-
Rachidi, N.1
Barre, P.2
Blondin, B.3
-
3
-
-
59349083791
-
Methylation and deamination of CpGs generate p53-binding sites on a genomic scale
-
doi:10.1016/j.tig.2008.11.005
-
Zemojtel T, Kielbasa SM, Arndt PF, Chung HR, Vingron M, (2009) Methylation and deamination of CpGs generate p53-binding sites on a genomic scale. Trends Genet 25: 63-66. doi:10.1016/j.tig.2008.11.005. PubMed: 19101055.
-
(2009)
Trends Genet
, vol.25
, pp. 63-66
-
-
Zemojtel, T.1
Kielbasa, S.M.2
Arndt, P.F.3
Chung, H.R.4
Vingron, M.5
-
4
-
-
80052854314
-
Families of transposable elements, population structure and the origin of species
-
doi:10.1186/1745-6150-6-44
-
Jurka J, Bao W, Kojima KK, (2011) Families of transposable elements, population structure and the origin of species. Biol Direct 6: 44. doi:10.1186/1745-6150-6-44. PubMed: 21929767.
-
(2011)
Biol Direct
, vol.6
, pp. 44
-
-
Jurka, J.1
Bao, W.2
Kojima, K.K.3
-
5
-
-
4043067987
-
RNAi-dependent and RNAi-independent mechanisms contribute to the silencing of RIPed sequences in Neurospora crassa
-
doi:10.1093/nar/gkh764
-
Chicas A, Cogoni C, Macino G, (2004) RNAi-dependent and RNAi-independent mechanisms contribute to the silencing of RIPed sequences in Neurospora crassa. Nucleic Acids Res 32: 4237-4243. doi:10.1093/nar/gkh764. PubMed: 15302921.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 4237-4243
-
-
Chicas, A.1
Cogoni, C.2
Macino, G.3
-
6
-
-
4143050271
-
RIP: the evolutionary cost of genome defense
-
doi:10.1016/j.tig.2004.07.007
-
Galagan JE, Selker EU, (2004) RIP: the evolutionary cost of genome defense. Trends Genet 20: 417-423. doi:10.1016/j.tig.2004.07.007. PubMed: 15313550.
-
(2004)
Trends Genet
, vol.20
, pp. 417-423
-
-
Galagan, J.E.1
Selker, E.U.2
-
7
-
-
78349241121
-
Sex-induced silencing defends the genome of Cryptococcus neoformans via RNAi
-
doi:10.1101/gad.1970910
-
Wang X, Hsueh YP, Li W, Floyd A, Skalsky R, et al. (2010) Sex-induced silencing defends the genome of Cryptococcus neoformans via RNAi. Genes Dev 24: 2566-2582. doi:10.1101/gad.1970910. PubMed: 21078820.
-
(2010)
Genes Dev
, vol.24
, pp. 2566-2582
-
-
Wang, X.1
Hsueh, Y.P.2
Li, W.3
Floyd, A.4
Skalsky, R.5
-
8
-
-
0343963241
-
Methylation of the foreign transposon Restless in vegetative mycelia of Neurospora crassa
-
doi:10.1007/s002940050519
-
Windhofer F, Catcheside DE, Kempken F, (2000) Methylation of the foreign transposon Restless in vegetative mycelia of Neurospora crassa. Curr Genet 37: 194-199. doi:10.1007/s002940050519. PubMed: 10794177.
-
(2000)
Curr Genet
, vol.37
, pp. 194-199
-
-
Windhofer, F.1
Catcheside, D.E.2
Kempken, F.3
-
9
-
-
79959340303
-
Obligate biotrophy features unraveled by the genomic analysis of rust fungi
-
doi:10.1073/pnas.1019315108
-
Duplessis S, Cuomo CA, Lin YC, Aerts A, Tisserant E, et al. (2011) Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proc Natl Acad Sci U S A 108: 9166-9171. doi:10.1073/pnas.1019315108. PubMed: 21536894.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 9166-9171
-
-
Duplessis, S.1
Cuomo, C.A.2
Lin, Y.C.3
Aerts, A.4
Tisserant, E.5
-
10
-
-
34848876954
-
Helitrons on a roll: eukaryotic rolling-circle transposons
-
doi:10.1016/j.tig.2007.08.004
-
Kapitonov VV, Jurka J, (2007) Helitrons on a roll: eukaryotic rolling-circle transposons. Trends Genet 23: 521-529. doi:10.1016/j.tig.2007.08.004. PubMed: 17850916.
-
(2007)
Trends Genet
, vol.23
, pp. 521-529
-
-
Kapitonov, V.V.1
Jurka, J.2
-
11
-
-
33846939973
-
Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses
-
doi:10.1016/j.gene.2006.08.008
-
Pritham EJ, Putliwala T, Feschotte C, (2007) Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses. Gene 390: 3-17. doi:10.1016/j.gene.2006.08.008. PubMed: 17034960.
-
(2007)
Gene
, vol.390
, pp. 3-17
-
-
Pritham, E.J.1
Putliwala, T.2
Feschotte, C.3
-
12
-
-
36249023071
-
A unified classification system for eukaryotic transposable elements
-
doi:10.1038/nrg2165
-
Wicker T, Sabot F, Hua-Van A, [!(surname)!], Capy P, et al. (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8: 973-982. doi:10.1038/nrg2165. PubMed: 17984973.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 973-982
-
-
Wicker, T.1
Sabot, F.2
Hua-Van, A.3
Capy, P.4
-
13
-
-
30544451181
-
The VIPER elements of trypanosomes constitute a novel group of tyrosine recombinase-enconding retrotransposons
-
doi:10.1016/j.molbiopara.2005.10.002
-
Lorenzi HA, Robledo G, Levin MJ, (2006) The VIPER elements of trypanosomes constitute a novel group of tyrosine recombinase-enconding retrotransposons. Mol Biochem Parasitol 145: 184-194. doi:10.1016/j.molbiopara.2005.10.002. PubMed: 16297462.
-
(2006)
Mol Biochem Parasitol
, vol.145
, pp. 184-194
-
-
Lorenzi, H.A.1
Robledo, G.2
Levin, M.J.3
-
14
-
-
83655183283
-
Eukaryote DIRS1-like retrotransposons: an overview
-
doi:10.1186/1471-2164-12-621
-
Piednoël M, Gonçalves IR, Higuet D, Bonnivard E, (2011) Eukaryote DIRS1-like retrotransposons: an overview. BMC Genomics 12: 621. doi:10.1186/1471-2164-12-621. PubMed: 22185659.
-
(2011)
BMC Genomics
, vol.12
, pp. 621
-
-
Piednoël, M.1
Gonçalves, I.R.2
Higuet, D.3
Bonnivard, E.4
-
15
-
-
1842609646
-
A new group of tyrosine recombinase-encoding retrotransposons
-
doi:10.1093/molbev/msh072
-
Goodwin TJ, Poulter RT, (2004) A new group of tyrosine recombinase-encoding retrotransposons. Mol Biol Evol 21: 746-759. doi:10.1093/molbev/msh072. PubMed: 14963102.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 746-759
-
-
Goodwin, T.J.1
Poulter, R.T.2
-
16
-
-
0030451271
-
Prt1, an unusual retrotransposon-like sequence in the fungus Phycomyces blakesleeanus
-
doi:10.1007/PL00008599
-
Ruiz-Pérez VL, Murillo FJ, Torres-Martínez S, (1996) Prt1, an unusual retrotransposon-like sequence in the fungus Phycomyces blakesleeanus. Mol Gen Genet 253: 324-333. doi:10.1007/PL00008599. PubMed: 9003319.
-
(1996)
Mol Gen Genet
, vol.253
, pp. 324-333
-
-
Ruiz-Pérez, V.L.1
Murillo, F.J.2
Torres-Martínez, S.3
-
19
-
-
23844525077
-
Repbase Update, a database of eukaryotic repetitive elements
-
doi:10.1159/000084979
-
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, et al. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110: 462-467. doi:10.1159/000084979. PubMed: 16093699.
-
(2005)
Cytogenet Genome Res
, vol.110
, pp. 462-467
-
-
Jurka, J.1
Kapitonov, V.V.2
Pavlicek, A.3
Klonowski, P.4
Kohany, O.5
-
20
-
-
84859742466
-
Unipro UGENE: a unified bioinformatics toolkit
-
doi:10.1093/bioinformatics/bts091
-
Okonechnikov K, Golosova O, Fursov M, (2012) Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28: 1166-1167. doi:10.1093/bioinformatics/bts091. PubMed: 22368248.
-
(2012)
Bioinformatics
, vol.28
, pp. 1166-1167
-
-
Okonechnikov, K.1
Golosova, O.2
Fursov, M.3
-
21
-
-
0036513591
-
EMBOSS opens up sequence analysis. European Molecular Biology Open Software Suite
-
doi:10.1093/bib/3.1.87
-
Olson SA, (2002) EMBOSS opens up sequence analysis. European Molecular Biology Open Software Suite. Brief Bioinform 3: 87-91. doi:10.1093/bib/3.1.87. PubMed: 12002227.
-
(2002)
Brief Bioinform
, vol.3
, pp. 87-91
-
-
Olson, S.A.1
-
22
-
-
77952988108
-
A new generation of homology search tools based on probabilistic inference
-
Eddy SR, (2009) A new generation of homology search tools based on probabilistic inference. Genome INFORM 23: 205-211. PubMed: 20180275.
-
(2009)
Genome INFORM
, vol.23
, pp. 205-211
-
-
Eddy, S.R.1
-
23
-
-
84858077472
-
The Pfam protein families database
-
doi:10.1093/nar/gkr717
-
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, et al. (2012) The Pfam protein families database. Nucleic Acids Res 40: D290-D301. doi:10.1093/nar/gkr717. PubMed: 22127870.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Punta, M.1
Coggill, P.C.2
Eberhardt, R.Y.3
Mistry, J.4
Tate, J.5
-
24
-
-
78651285748
-
CDD: a Conserved Domain Database for the functional annotation of proteins
-
doi:10.1093/nar/gkq1189
-
Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, et al. (2011) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39: D225-D229. doi:10.1093/nar/gkq1189. PubMed: 21109532.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Marchler-Bauer, A.1
Lu, S.2
Anderson, J.B.3
Chitsaz, F.4
Derbyshire, M.K.5
-
25
-
-
0037433034
-
PCMA: fast and accurate multiple sequence alignment based on profile consistency
-
doi:10.1093/bioinformatics/btg008
-
Pei J, Sadreyev R, Grishin NV, (2003) PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics 19: 427-428. doi:10.1093/bioinformatics/btg008. PubMed: 12584134.
-
(2003)
Bioinformatics
, vol.19
, pp. 427-428
-
-
Pei, J.1
Sadreyev, R.2
Grishin, N.V.3
-
26
-
-
2142738304
-
WebLogo: a sequence logo generator
-
doi:10.1101/gr.849004
-
Crooks GE, Hon G, Chandonia JM, Brenner SE, (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188-1190. doi:10.1101/gr.849004. PubMed: 15173120.
-
(2004)
Genome Res
, vol.14
, pp. 1188-1190
-
-
Crooks, G.E.1
Hon, G.2
Chandonia, J.M.3
Brenner, S.E.4
-
27
-
-
10044222704
-
CLANS: a Java application for visualizing protein families based on pairwise similarity
-
doi:10.1093/bioinformatics/bth444
-
Frickey T, Lupas A, (2004) CLANS: a Java application for visualizing protein families based on pairwise similarity. Bioinformatics 20: 3702-3704. doi:10.1093/bioinformatics/bth444. PubMed: 15284097.
-
(2004)
Bioinformatics
, vol.20
, pp. 3702-3704
-
-
Frickey, T.1
Lupas, A.2
-
28
-
-
84875619226
-
MAFFT Multiple Sequence Alignment Software
-
Katoh K, Standley DM, (2013) MAFFT Multiple Sequence Alignment Software, version 7 Improvements in Performance and Usability. Mol Biol Evol.
-
(2013)
Mol Biol Evol
-
-
Katoh, K.1
Standley, D.M.2
-
29
-
-
67650757433
-
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
-
doi:10.1093/bioinformatics/btp348
-
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T, (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25: 1972-1973. doi:10.1093/bioinformatics/btp348. PubMed: 19505945.
-
(2009)
Bioinformatics
, vol.25
, pp. 1972-1973
-
-
Capella-Gutiérrez, S.1
Silla-Martínez, J.M.2
Gabaldón, T.3
-
30
-
-
79954529507
-
ProtTest 3: fast selection of best-fit models of protein evolution
-
doi:10.1093/bioinformatics/btr088
-
Darriba D, Taboada GL, Doallo R, Posada D, (2011) ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27: 1164-1165. doi:10.1093/bioinformatics/btr088. PubMed: 21335321.
-
(2011)
Bioinformatics
, vol.27
, pp. 1164-1165
-
-
Darriba, D.1
Taboada, G.L.2
Doallo, R.3
Posada, D.4
-
31
-
-
68049139485
-
Estimating maximum likelihood phylogenies with PhyML
-
doi:10.1007/978-1-59745-251-9_6
-
Guindon S, Delsuc F, Dufayard JF, Gascuel O, (2009) Estimating maximum likelihood phylogenies with PhyML. Methods Mol Biol 537: 113-137. doi:10.1007/978-1-59745-251-9_6. PubMed: 19378142.
-
(2009)
Methods Mol Biol
, vol.537
, pp. 113-137
-
-
Guindon, S.1
Delsuc, F.2
Dufayard, J.F.3
Gascuel, O.4
-
32
-
-
33745256005
-
Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative
-
doi:10.1080/10635150600755453
-
Anisimova M, Gascuel O, (2006) Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst Biol 55: 539-552. doi:10.1080/10635150600755453. PubMed: 16785212.
-
(2006)
Syst Biol
, vol.55
, pp. 539-552
-
-
Anisimova, M.1
Gascuel, O.2
-
33
-
-
33845873289
-
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
-
doi:10.1093/bioinformatics/btl529
-
Letunic I, Bork P, (2007) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23: 127-128. doi:10.1093/bioinformatics/btl529. PubMed: 17050570.
-
(2007)
Bioinformatics
, vol.23
, pp. 127-128
-
-
Letunic, I.1
Bork, P.2
-
34
-
-
71749099862
-
phyloXML: XML for evolutionary biology and comparative genomics
-
doi:10.1186/1471-2105-10-356
-
Han MV, Zmasek CM, (2009) phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics 10: 356. doi:10.1186/1471-2105-10-356. PubMed: 19860910.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 356
-
-
Han, M.V.1
Zmasek, C.M.2
-
35
-
-
23844460512
-
Ribonuclease H evolution in retrotransposable elements
-
doi:10.1159/000084971
-
Malik HS, (2005) Ribonuclease H evolution in retrotransposable elements. Cytogenet Genome Res 110: 392-401. doi:10.1159/000084971. PubMed: 16093691.
-
(2005)
Cytogenet Genome Res
, vol.110
, pp. 392-401
-
-
Malik, H.S.1
-
36
-
-
72249109366
-
Phylogenomic analyses predict sistergroup relationship of nucleariids and fungi and paraphily of zygomycetes with significant support
-
doi:10.1186/1471-2148-9-272
-
Liu Y, Steenkamp ET, Brinkmann H, Forget L, Philippe H, et al. (2009) Phylogenomic analyses predict sistergroup relationship of nucleariids and fungi and paraphily of zygomycetes with significant support. BMC Evol Biol 9: 272. doi:10.1186/1471-2148-9-272. PubMed: 19939264.
-
(2009)
BMC Evol Biol
, vol.9
, pp. 272
-
-
Liu, Y.1
Steenkamp, E.T.2
Brinkmann, H.3
Forget, L.4
Philippe, H.5
-
37
-
-
84855864009
-
Taxonomy of fungi causing mucormycosis and entomophthoramycosis (Zygomycosis) and nomenclature of the disease: molecular mycologic perspectives
-
doi:10.1093/cid/cir864
-
Kwon-Chung KJ, (2012) Taxonomy of fungi causing mucormycosis and entomophthoramycosis (Zygomycosis) and nomenclature of the disease: molecular mycologic perspectives. Clin Infect Dis 54 (Suppl 1):: S8-S15. doi:10.1093/cid/cir864. PubMed: 22247451.
-
(2012)
Clin Infect Dis
, vol.54
, Issue.SUPPL. 1
-
-
Kwon-Chung, K.J.1
-
38
-
-
84855291327
-
LTR retrotransposons in fungi
-
doi:10.1371/journal.pone.0029425
-
Muszewska A, Hoffman-Sommer M, Grynberg M, (2011) LTR retrotransposons in fungi. PLOS ONE 6: e29425. doi:10.1371/journal.pone.0029425. PubMed: 22242120.
-
(2011)
PLOS ONE
, vol.6
-
-
Muszewska, A.1
Hoffman-Sommer, M.2
Grynberg, M.3
-
39
-
-
79955649699
-
The Gypsy Database (GyDB) of mobile genetic elements
-
Lloréns C, Futami R, Covelli L, Dominguez-Escriba L, Viu JM, et al. (2011) The Gypsy Database (GyDB) of mobile genetic elements, Release 2.0. Nucleic Acids Res 39: D70-74.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 70-74
-
-
Lloréns, C.1
Futami, R.2
Covelli, L.3
Dominguez-Escriba, L.4
Viu, J.M.5
-
40
-
-
34547396004
-
The frailty of adaptive hypotheses for the origins of organismal complexity
-
doi:10.1073/pnas.0702207104
-
Lynch M, (2007) The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci U S A 104 (Suppl 1):: 8597-8604. doi:10.1073/pnas.0702207104. PubMed: 17494740.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, Issue.SUPPL. 1
, pp. 8597-8604
-
-
Lynch, M.1
-
41
-
-
0345306751
-
The origins of genome complexity
-
doi:10.1126/science.1089370
-
Lynch M, Conery JS, (2003) The origins of genome complexity. Science 302: 1401-1404. doi:10.1126/science.1089370. PubMed: 14631042.
-
(2003)
Science
, vol.302
, pp. 1401-1404
-
-
Lynch, M.1
Conery, J.S.2
|