-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
-
2
-
-
0034897709
-
Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution
-
Anisimova M, Bielawski JP, Yang Z (2001). Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol Biol Evol 18: 1585-1592.
-
(2001)
Mol Biol Evol
, vol.18
, pp. 1585-1592
-
-
Anisimova, M.1
Bielawski, J.P.2
Yang, Z.3
-
3
-
-
30344482922
-
The population biology of mitochondrial DNA and its phylogenetic implications
-
Ballard JWO, Rand DM (2005). The population biology of mitochondrial DNA and its phylogenetic implications. Annu Rev Ecol Evol Syst 36: 621-642.
-
(2005)
Annu Rev Ecol Evol Syst
, vol.36
, pp. 621-642
-
-
Ballard, J.W.O.1
Rand, D.M.2
-
4
-
-
0029610067
-
Uniparental inheritance of mitochondrial and chloroplast genes: Mechanisms and evolution
-
Birky Jr CW (1995). Uniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolution. Proc Natl Acad Sci USA 92: 11331-11338.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 11331-11338
-
-
Birky Jr, C.W.1
-
5
-
-
0035399727
-
Natural selection and the evolution of mtDNA-encoded peptides: Evidence for intergenomic co-adaptation
-
Blier PU, Dufresne F, Burton RS (2001). Natural selection and the evolution of mtDNA-encoded peptides: evidence for intergenomic co-adaptation. Trends Genet 17: 400-406.
-
(2001)
Trends Genet
, vol.17
, pp. 400-406
-
-
Blier, P.U.1
Dufresne, F.2
Burton, R.S.3
-
6
-
-
3042840997
-
Computational inference of scenarios for α-proteo-bacterial genome evolution
-
Boussau B, Karlberg EO, Frank AC, Legault B, Andersson SGE (2004). Computational inference of scenarios for α-proteo-bacterial genome evolution. Proc Natl Acad Sci USA 101: 9722-9727.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 9722-9727
-
-
Boussau, B.1
Karlberg, E.O.2
Frank, A.C.3
Legault, B.4
Andersson, S.G.E.5
-
7
-
-
0000316105
-
Hybrid breakdown between two haplodiploid species: The role of nuclear and cytoplasmic genes
-
Breeuwer JAJ, Werren JH (1995). Hybrid breakdown between two haplodiploid species: the role of nuclear and cytoplasmic genes. Evolution 49: 705-717.
-
(1995)
Evolution
, vol.49
, pp. 705-717
-
-
Breeuwer, J.A.J.1
Werren, J.H.2
-
8
-
-
33751577950
-
Two Dobzhansky-Muller genes interact to cause hybrid lethality in Drosophila
-
Brideau NJ, Flores HA, Wang J, Maheshwari S, Wang X, Barbash DA (2006). Two Dobzhansky-Muller genes interact to cause hybrid lethality in Drosophila. Science 314: 1292-1295.
-
(2006)
Science
, vol.314
, pp. 1292-1295
-
-
Brideau, N.J.1
Flores, H.A.2
Wang, J.3
Maheshwari, S.4
Wang, X.5
Barbash, D.A.6
-
9
-
-
33646362551
-
Systematic identification of human mitochondrial disease genes through integrative genomics
-
Calvo S, Jain M, Xie X, Sheth SA, Chang B, Goldberger OA et al. (2006). Systematic identification of human mitochondrial disease genes through integrative genomics. Nat Genet 38: 576-582.
-
(2006)
Nat Genet
, vol.38
, pp. 576-582
-
-
Calvo, S.1
Jain, M.2
Xie, X.3
Sheth, S.A.4
Chang, B.5
Goldberger, O.A.6
-
10
-
-
0027145271
-
Phylo-geny of the Nasonia species complex (Hymenoptera: Pter-omalidae) inferred from an rDNA internal transcribed spacer (ITS2)
-
Campbell BC, Steffen-Campbell JD, Werren JH (1993). Phylo-geny of the Nasonia species complex (Hymenoptera: Pter-omalidae) inferred from an rDNA internal transcribed spacer (ITS2). Insect Mol Biol 2: 225-237.
-
(1993)
Insect Mol Biol
, vol.2
, pp. 225-237
-
-
Campbell, B.C.1
Steffen-Campbell, J.D.2
Werren, J.H.3
-
11
-
-
33749993739
-
The MitoDrome database annotates and compares the OXPHOS nuclear genes of Drosophila melano-gaster, Drosophila pseudoobscura and Anopheles gambiae
-
D'Elia D, Catalano D, Licciulli F, Turi A, Tripoli G, Porcelli D et al. (2006). The MitoDrome database annotates and compares the OXPHOS nuclear genes of Drosophila melano-gaster, Drosophila pseudoobscura and Anopheles gambiae. Mitochondrion 6: 252-257.
-
(2006)
Mitochondrion
, vol.6
, pp. 252-257
-
-
D'Elia, D.1
Catalano, D.2
Licciulli, F.3
Turi, A.4
Tripoli, G.5
Porcelli, D.6
-
12
-
-
0000228203
-
A model of evolutionary change in proteins
-
Dayhoff M ed, National Biomedical Research Foundation: Washington, DC. pp
-
Dayhoff M, Schwartz R, Orcutt B (1978). A model of evolutionary change in proteins. In: Dayhoff M (ed). Atlas of Protein Sequence and Structure, Vol. 5. National Biomedical Research Foundation: Washington, DC. pp 345-352.
-
(1978)
Atlas of Protein Sequence and Structure
, vol.5
, pp. 345-352
-
-
Dayhoff, M.1
Schwartz, R.2
Orcutt, B.3
-
14
-
-
33748201194
-
Disruption of mitochondrial function in interpopulation hybrids of Tigriopus californicus
-
Ellison CK, Burton RS (2006). Disruption of mitochondrial function in interpopulation hybrids of Tigriopus californicus. Evolution 60: 1382-1391.
-
(2006)
Evolution
, vol.60
, pp. 1382-1391
-
-
Ellison, C.K.1
Burton, R.S.2
-
15
-
-
40449103705
-
Interpopulation hybrid breakdown maps to the mitochondrial genome
-
Ellison CK, Burton RS (2008). Interpopulation hybrid breakdown maps to the mitochondrial genome. Evolution 62: 631-638.
-
(2008)
Evolution
, vol.62
, pp. 631-638
-
-
Ellison, C.K.1
Burton, R.S.2
-
16
-
-
54049123388
-
Hybrid breakdown and mitochondrial dysfunction in hybrids of Nasonia parasitoid wasps
-
Ellison CK, Niehuis O, Gadau J (2008). Hybrid breakdown and mitochondrial dysfunction in hybrids of Nasonia parasitoid wasps. J Evol Biol 21: 1844-1851.
-
(2008)
J Evol Biol
, vol.21
, pp. 1844-1851
-
-
Ellison, C.K.1
Niehuis, O.2
Gadau, J.3
-
17
-
-
0028168856
-
A codon-based model of nucleotide substitution for protein-coding DNA sequences
-
Goldman N, Yang Z (1994). A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11: 725-736.
-
(1994)
Mol Biol Evol
, vol.11
, pp. 725-736
-
-
Goldman, N.1
Yang, Z.2
-
19
-
-
67649755680
-
Mitochondrial and plastid evolution in eukaryotes: An outsiders' perspective
-
Gross J, Bhattacharya D (2009). Mitochondrial and plastid evolution in eukaryotes: an outsiders' perspective. Nature Rev Genet 10: 495-505.
-
(2009)
Nature Rev Genet
, vol.10
, pp. 495-505
-
-
Gross, J.1
Bhattacharya, D.2
-
20
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
Guindon S, Gascuel O (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biology 52: 696-704.
-
(2003)
Syst Biology
, vol.52
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
21
-
-
77149178736
-
-
Hall TA (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41: 95-98.
-
Hall TA (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41: 95-98.
-
-
-
-
22
-
-
0035830860
-
Principles for the buffering of genetic variation
-
Hartman JL, Garvik B, Hartwell L (2001). Principles for the buffering of genetic variation. Science 291: 1001-1004.
-
(2001)
Science
, vol.291
, pp. 1001-1004
-
-
Hartman, J.L.1
Garvik, B.2
Hartwell, L.3
-
24
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones D, Taylor W, Thornton J (1992). The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8: 275-282.
-
(1992)
Comput Appl Biosci
, vol.8
, pp. 275-282
-
-
Jones, D.1
Taylor, W.2
Thornton, J.3
-
25
-
-
0030750574
-
Expanding the functional human mitochondrial DNA database by establishment of primate xenomitochondrial cybrids
-
Kenyon L, Moraes CT (1997). Expanding the functional human mitochondrial DNA database by establishment of primate xenomitochondrial cybrids. Proc Natl Acad Sci USA 94: 9131-9135.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 9131-9135
-
-
Kenyon, L.1
Moraes, C.T.2
-
26
-
-
0024448458
-
Human cells lacking mtDNA: Repopulation with exogenous mitochondria by complementation
-
King MP, Attardi G (1989). Human cells lacking mtDNA: repopulation with exogenous mitochondria by complementation. Science 246: 500-503.
-
(1989)
Science
, vol.246
, pp. 500-503
-
-
King, M.P.1
Attardi, G.2
-
27
-
-
49849088157
-
Near intron positions are reliable phylogenetic markers: An application to holometabolous insects
-
Krauss V, Thümmler C, Georgi F, Lehmann J, Stadler PF, Eisenhardt C (2008). Near intron positions are reliable phylogenetic markers: an application to holometabolous insects. Mol Biol Evol 25: 821-830.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 821-830
-
-
Krauss, V.1
Thümmler, C.2
Georgi, F.3
Lehmann, J.4
Stadler, P.F.5
Eisenhardt, C.6
-
28
-
-
0012306021
-
Apollo: A sequence annotation editor
-
research0082.1-0082.14
-
Lewis SE, Searle SMJ, Harris N, Gibson M, Iyer V, Ricter J et al. (2002). Apollo: a sequence annotation editor. Genome Biol 3, research0082.1-0082.14.
-
(2002)
Genome Biol
, vol.3
-
-
Lewis, S.E.1
Searle, S.M.J.2
Harris, N.3
Gibson, M.4
Iyer, V.5
Ricter, J.6
-
29
-
-
0038420036
-
Functional respiratory chain analyses in murid xenomito-chondrial cybrids expose coevolutionary constraints of cytochrome b and nuclear subunits of complex III
-
McKenzie M, Chiotis M, Pinkert CA, Trounce IA (2003). Functional respiratory chain analyses in murid xenomito-chondrial cybrids expose coevolutionary constraints of cytochrome b and nuclear subunits of complex III. Mol Biol Evol 20: 1117-1124.
-
(2003)
Mol Biol Evol
, vol.20
, pp. 1117-1124
-
-
McKenzie, M.1
Chiotis, M.2
Pinkert, C.A.3
Trounce, I.A.4
-
30
-
-
50249117097
-
The spectrum of mitochondrial mutation differs across species
-
Montooth KL, Rand DM (2008). The spectrum of mitochondrial mutation differs across species. PLoS Biol 6: e213.
-
(2008)
PLoS Biol
, vol.6
-
-
Montooth, K.L.1
Rand, D.M.2
-
31
-
-
0002101476
-
Isolating mechanisms, speciation, and temperature
-
Muller HJ (1942). Isolating mechanisms, speciation, and temperature. Biol Symp 6: 71-125.
-
(1942)
Biol Symp
, vol.6
, pp. 71-125
-
-
Muller, H.J.1
-
32
-
-
77649312033
-
-
Niehuis O, Gibson JD, Rosenberg MS, Pannebakker BA, Koevoets T, Judson AK et al. (2010). Recombination and its impact on the genome of the haplodiploid parasitoid wasp Nasonia. PLoS ONE (doi:10.1371/journal.pone. 0008597).
-
Niehuis O, Gibson JD, Rosenberg MS, Pannebakker BA, Koevoets T, Judson AK et al. (2010). Recombination and its impact on the genome of the haplodiploid parasitoid wasp Nasonia. PLoS ONE (doi:10.1371/journal.pone. 0008597).
-
-
-
-
34
-
-
52449104857
-
Rapidly evolving mitochondrial genome and directional selection in mitochondrial genes in the parasitic wasp Nasonia (Hymenoptera: Pteromalidae)
-
Oliveira DCSG, Raychoudhury R, Lavrov DV, Werren JH (2008). Rapidly evolving mitochondrial genome and directional selection in mitochondrial genes in the parasitic wasp Nasonia (Hymenoptera: Pteromalidae). Mol Biol Evol 25: 2167-2180.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 2167-2180
-
-
Oliveira, D.C.S.G.1
Raychoudhury, R.2
Lavrov, D.V.3
Werren, J.H.4
-
35
-
-
39049149474
-
The nuclear OXPHOS genes in Insecta: A common evolutionary origin, a common cis-regulatory motif, a common destiny for gene duplicates
-
Porcelli D, Barsanti P, Pesole G, Caggese C (2007). The nuclear OXPHOS genes in Insecta: a common evolutionary origin, a common cis-regulatory motif, a common destiny for gene duplicates. BMC Evol Biol 7: 215.
-
(2007)
BMC Evol Biol
, vol.7
, pp. 215
-
-
Porcelli, D.1
Barsanti, P.2
Pesole, G.3
Caggese, C.4
-
36
-
-
8144226823
-
Cytonuclear coevolution: The genomics of cooperation
-
Rand DM, Haney RA, Fry AJ (2004). Cytonuclear coevolution: the genomics of cooperation. Trends Ecol Evol 19: 645-653.
-
(2004)
Trends Ecol Evol
, vol.19
, pp. 645-653
-
-
Rand, D.M.1
Haney, R.A.2
Fry, A.J.3
-
37
-
-
0242416051
-
Cytonuclear co-adaptation in Drosophila: Disruption of cytochrome coxidase activity in backcross genotypes
-
Sackton TB, Haney RA, Rand DM (2003). Cytonuclear co-adaptation in Drosophila: disruption of cytochrome coxidase activity in backcross genotypes. Evolution 57: 2315-2325.
-
(2003)
Evolution
, vol.57
, pp. 2315-2325
-
-
Sackton, T.B.1
Haney, R.A.2
Rand, D.M.3
-
38
-
-
33750526053
-
Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects
-
Savard J, Tautz D, Richards S, Weinstock GM, Gibbs RA, Werren JH et al. (2006). Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects. Genome Res 16: 1334-1338.
-
(2006)
Genome Res
, vol.16
, pp. 1334-1338
-
-
Savard, J.1
Tautz, D.2
Richards, S.3
Weinstock, G.M.4
Gibbs, R.A.5
Werren, J.H.6
-
39
-
-
22244437614
-
Pysicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity
-
Stone EA, Sidow A (2005). Pysicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity. Genome Res 15: 978-986.
-
(2005)
Genome Res
, vol.15
, pp. 978-986
-
-
Stone, E.A.1
Sidow, A.2
-
40
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson JD, Higgins DG, Gibson TJ (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
41
-
-
74549184089
-
-
Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK et al. (2010). Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science 327: 343.
-
Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK et al. (2010). Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science 327: 343.
-
-
-
-
42
-
-
0035031966
-
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
-
Whelan S, Goldman N (2001). A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18: 691-699.
-
(2001)
Mol Biol Evol
, vol.18
, pp. 691-699
-
-
Whelan, S.1
Goldman, N.2
-
43
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
Yang Z (2007). PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
44
-
-
16344378246
-
Bayes empirical Bayes inference of amino acid sites under positive selection
-
Yang Z, Wong WSW, Nielsen R (2005). Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol 22: 1107-1118.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1107-1118
-
-
Yang, Z.1
Wong, W.S.W.2
Nielsen, R.3
-
45
-
-
0026784796
-
Direct evidence for extensive paternal mitochondrial DNA inheritance in the marine mussel Mytilus
-
Zouros E, Freeman KR, Ball AO, Pogson GH (1992). Direct evidence for extensive paternal mitochondrial DNA inheritance in the marine mussel Mytilus. Nature 359: 412-414.
-
(1992)
Nature
, vol.359
, pp. 412-414
-
-
Zouros, E.1
Freeman, K.R.2
Ball, A.O.3
Pogson, G.H.4
|