-
1
-
-
33745256005
-
Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative
-
Anisimova M, Gascuel O. 2006. Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst Biol. 55: 539-552.
-
(2006)
Syst Biol.
, vol.55
, pp. 539-552
-
-
Anisimova, M.1
Gascuel, O.2
-
2
-
-
80052014395
-
Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes
-
Anisimova M, Gil M, Dufayard J-F, Dessimoz C, Gascuel O. 2011. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol. 60:685-699.
-
(2011)
Syst Biol.
, vol.60
, pp. 685-699
-
-
Anisimova, M.1
Gil, M.2
Dufayard, J.-F.3
Dessimoz, C.4
Gascuel, O.5
-
3
-
-
0037162885
-
Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes
-
Aparicio S, Chapman J, Stupka E, et al. (41 co-authors). 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297:1301-1310.
-
(2002)
Science
, vol.297
, pp. 1301-1310
-
-
Aparicio, S.1
Chapman, J.2
Stupka, E.3
-
4
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The gene ontology consortium
-
Ashburner M, Ball CA, Blake JA, et al. (20 co-authors). 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 25:25-29.
-
(2000)
Nat Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
-
6
-
-
0037270595
-
Maximum likelihood methods for detecting adaptive evolution after gene duplication
-
Bielawski JP, Yang Z. 2003. Maximum likelihood methods for detecting adaptive evolution after gene duplication. J Struct Funct Genomics. 3: 201-212.
-
(2003)
J Struct Funct Genomics.
, vol.3
, pp. 201-212
-
-
Bielawski, J.P.1
Yang, Z.2
-
7
-
-
0001159614
-
Role of the lateral line in fish behaviour
-
Pitcher TJ, editor. London: Chapman and Hall
-
Bleckmann H. 1993. Role of the lateral line in fish behaviour. In: Pitcher TJ, editor. Behaviour of teleost fishes. London: Chapman and Hall. p. 201-246.
-
(1993)
Behaviour of Teleost Fishes
, pp. 201-246
-
-
Bleckmann, H.1
-
8
-
-
0000357923
-
Central nervous physiology of the lateral line, with special reference to cartilaginous fishes
-
Coombs S, Gorner P, Munz H, editors. New York: Springer
-
Bleckmann H, Bullock TH. 1989. Central nervous physiology of the lateral line, with special reference to cartilaginous fishes. In: Coombs S, Gorner P, Munz H, editors. The mechanosensory lateral line. Neurobiology and evolution. New York: Springer. p. 387-408.
-
(1989)
The Mechanosensory Lateral Line. Neurobiology and Evolution
, pp. 387-408
-
-
Bleckmann, H.1
Bullock, T.H.2
-
10
-
-
57049135670
-
The evolution of teleost pigmentation and the fish-specific genome duplication
-
Braasch I, Volff J-N, Schartl M. 2008. The evolution of teleost pigmentation and the fish-specific genome duplication. J Fish Biol. 73: 1891-1918.
-
(2008)
J Fish Biol.
, vol.73
, pp. 1891-1918
-
-
Braasch, I.1
Volff, J.-N.2
Schartl, M.3
-
11
-
-
33748183184
-
Gene loss and evolutionary rates following whole-genome duplication in teleost fishes
-
Brunet FG, Crollius HR, Paris M, Aury J-M, Gibert P, Jaillon O, Laudet V, Robinson-Rechavi M. 2006. Gene loss and evolutionary rates following whole-genome duplication in teleost fishes. Mol Biol Evol. 23: 1808-1816.
-
(2006)
Mol Biol Evol.
, vol.23
, pp. 1808-1816
-
-
Brunet, F.G.1
Crollius, H.R.2
Paris, M.3
Aury, J.-M.4
Gibert, P.5
Jaillon, O.6
Laudet, V.7
Robinson-Rechavi, M.8
-
12
-
-
4043076435
-
A comparison of lateral line morphology of blue cod and torrentfish: Two sandperches of the family Pinguipedidae
-
Carton AG, Montgomery JC. 2004. A comparison of lateral line morphology of blue cod and torrentfish: two sandperches of the family Pinguipedidae. Environ Biol Fishes. 70:123-131.
-
(2004)
Environ Biol Fishes.
, vol.70
, pp. 123-131
-
-
Carton, A.G.1
Montgomery, J.C.2
-
13
-
-
0034043778
-
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
-
Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17: 540-552.
-
(2000)
Mol Biol Evol.
, vol.17
, pp. 540-552
-
-
Castresana, J.1
-
14
-
-
2442707716
-
Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes
-
Christoffels A, Koh EGL, Chia J-ming, Brenner S, Aparicio S, Venkatesh B. 2004. Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. Mol Biol Evol. 21:1146-1151.
-
(2004)
Mol Biol Evol.
, vol.21
, pp. 1146-1151
-
-
Christoffels, A.1
Koh, E.G.L.2
Chia, J.-M.3
Brenner, S.4
Aparicio, S.5
Venkatesh, B.6
-
15
-
-
28944450051
-
The "fish-specific" Hox cluster duplication is coincident with the origin of teleosts
-
Crow KD, Stadler PF, Lynch VJ, Amemiya C, Wagner GP. 2006. The "fish-specific" Hox cluster duplication is coincident with the origin of teleosts. Mol Biol Evol. 23:121-136.
-
(2006)
Mol Biol Evol.
, vol.23
, pp. 121-136
-
-
Crow, K.D.1
Stadler, P.F.2
Lynch, V.J.3
Amemiya, C.4
Wagner, G.P.5
-
16
-
-
0037058994
-
Molecular basis of cell migration in the fish lateral line: Role of the chemokine receptor CXCR4 and of its ligand, SDF1
-
David NB, Sapede D, Saint-Etienne L, Thisse C, Thisse B, Dambly-Chaudiere C, Rosa FM, Ghysen A. 2002. Molecular basis of cell migration in the fish lateral line: role of the chemokine receptor CXCR4 and of its ligand, SDF1. Proc Natl Acad Sci U S A. 99: 16297-16302.
-
(2002)
Proc Natl Acad Sci U S A.
, vol.99
, pp. 16297-16302
-
-
David, N.B.1
Sapede, D.2
Saint-Etienne, L.3
Thisse, C.4
Thisse, B.5
Dambly-Chaudiere, C.6
Rosa, F.M.7
Ghysen, A.8
-
18
-
-
75449126520
-
The functioning and significance of the lateral line organs
-
Dijkgraaf S. 1963. The functioning and significance of the lateral line organs. Biol Rev. 38:51-105.
-
(1963)
Biol Rev.
, vol.38
, pp. 51-105
-
-
Dijkgraaf, S.1
-
19
-
-
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. 32:1792-1797.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
20
-
-
0032893932
-
Preservation of duplicate genes by complementary, degenerative mutations
-
Force A, Lynch M, Pickett FB, Amores A, Yan Y, Postlethwait J. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531.
-
(1999)
Genetics
, vol.151
, pp. 1531
-
-
Force, A.1
Lynch, M.2
Pickett, F.B.3
Amores, A.4
Yan, Y.5
Postlethwait, J.6
-
21
-
-
18144429071
-
Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B
-
Frost SDW, Liu Y, Pond SLK, Chappey C, Wrin T, PetropoulosCJ, Little SJ, Richman DD. 2005. Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B. J Virol. 79: 6523-6527.
-
(2005)
J Virol.
, vol.79
, pp. 6523-6527
-
-
Frost, S.D.W.1
Liu, Y.2
Pond, S.L.K.3
Chappey, C.4
Wrin, T.5
Petropoulos, C.J.6
Little, S.J.7
Richman, D.D.8
-
24
-
-
74549125386
-
SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building
-
Gouy M, Guindon S, Gascuel O. 2010. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol. 27:221-224.
-
(2010)
Mol Biol Evol.
, vol.27
, pp. 221-224
-
-
Gouy, M.1
Guindon, S.2
Gascuel, O.3
-
26
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
-
Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 59:307-321.
-
(2010)
Syst Biol.
, vol.59
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.-F.2
Lefort, V.3
Anisimova, M.4
Hordijk, W.5
Gascuel, O.6
-
27
-
-
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 Biol. 52: 696-704.
-
(2003)
Syst Biol.
, vol.52
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
28
-
-
0346801873
-
The Gene Ontology (GO) database and informatics resource
-
Harris MA, Clark J, Ireland A, et al. (60 co-authors). 2004. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32:D258-D261.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Harris, M.A.1
Clark, J.2
Ireland, A.3
-
29
-
-
0022376704
-
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
-
Hasegawa M, Kishino H, Yano T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 22: 160-174.
-
(1985)
J Mol Evol.
, vol.22
, pp. 160-174
-
-
Hasegawa, M.1
Kishino, H.2
Yano, T.3
-
31
-
-
0002295194
-
Hydrodynamic imaging of the surroundings by the lateral line of the blind cave fish Anoptichthys jordani
-
Coombs S, Gorner P, Munz H, editors. New York: Springer
-
Hassan ES. 1989. Hydrodynamic imaging of the surroundings by the lateral line of the blind cave fish Anoptichthys jordani. In: Coombs S, Gorner P, Munz H, editors. The mechanosensory lateral line. Neurobiology and evolution. New York: Springer. p. 217-228.
-
(1989)
The Mechanosensory Lateral Line. Neurobiology and Evolution
, pp. 217-228
-
-
Hassan, E.S.1
-
32
-
-
77957736749
-
The evolution of vertebrate tetraspanins: Gene loss, retention, and massive positive selection after whole genome duplications
-
Huang S, Tian H, Chen Z, Yu T, Xu A. 2010. The evolution of vertebrate tetraspanins: gene loss, retention, and massive positive selection after whole genome duplications. BMC Evol Biol. 10:306.
-
(2010)
BMC Evol Biol.
, vol.10
, pp. 306
-
-
Huang, S.1
Tian, H.2
Chen, Z.3
Yu, T.4
Xu, A.5
-
34
-
-
79551634894
-
PHAST and RPHAST: Phylogenetic analysis with space/time models
-
Hubisz MJ, Pollard KS, Siepel A. 2011. PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform. 12:41-51.
-
(2011)
Brief Bioinform.
, vol.12
, pp. 41-51
-
-
Hubisz, M.J.1
Pollard, K.S.2
Siepel, A.3
-
35
-
-
0028342845
-
The evolution of functionally novel proteins after gene duplication
-
Hughes AL. 1994. The evolution of functionally novel proteins after gene duplication. Proc Biol Sci. 256:119-124.
-
(1994)
Proc Biol Sci.
, vol.256
, pp. 119-124
-
-
Hughes, A.L.1
-
36
-
-
33747828645
-
Protein evolution: Causes of trends in amino-acid gain and loss
-
Hurst LD, Feil EJ, Rocha EPC. 2006. Protein evolution: causes of trends in amino-acid gain and loss. Nature 442:E11-E12.
-
(2006)
Nature
, vol.442
-
-
Hurst, L.D.1
Feil, E.J.2
Rocha, E.P.C.3
-
37
-
-
75549087305
-
The evolution of gene duplications: Classifying and distinguishing between models
-
Innan H, Kondrashov F. 2010. The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet. 11: 97-108.
-
(2010)
Nat Rev Genet.
, vol.11
, pp. 97-108
-
-
Innan, H.1
Kondrashov, F.2
-
38
-
-
7244259101
-
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
-
Jaillon O, Aury J-M, Brunet F, et al. (61 co-authors). 2004. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431:946-957.
-
(2004)
Nature
, vol.431
, pp. 946-957
-
-
Jaillon, O.1
Aury, J.-M.2
Brunet, F.3
-
39
-
-
0033082758
-
Use of the lateral line for feeding in two Lake Baikal sculpins
-
Janssen J, Sideleva V, Biga H. 1999. Use of the lateral line for feeding in two Lake Baikal sculpins. J Fish Biol. 54:404-416.
-
(1999)
J Fish Biol.
, vol.54
, pp. 404-416
-
-
Janssen, J.1
Sideleva, V.2
Biga, H.3
-
40
-
-
34249994907
-
The medaka draft genome and insights into vertebrate genome evolution
-
Kasahara M, Naruse K, Sasaki S, et al. (38 co-authors). 2007. The medaka draft genome and insights into vertebrate genome evolution. Nature 447:714-719.
-
(2007)
Nature
, vol.447
, pp. 714-719
-
-
Kasahara, M.1
Naruse, K.2
Sasaki, S.3
-
41
-
-
34748893838
-
PyCogent: A toolkit for making sense from sequence
-
Knight R, Maxwell P, Birmingham A, et al. (21 co-authors). 2007. PyCogent: a toolkit for making sense from sequence. Genome Biol. 8:R171.
-
(2007)
Genome Biol.
, vol.8
-
-
Knight, R.1
Maxwell, P.2
Birmingham, A.3
-
42
-
-
69649109364
-
Circos: An information aesthetic for comparative genomics
-
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ,Marra MA. 2009. Circos: an information aesthetic for comparative genomics. Genome Res. 19:1639-1645.
-
(2009)
Genome Res.
, vol.19
, pp. 1639-1645
-
-
Krzywinski, M.1
Schein, J.2
Birol, I.3
Connors, J.4
Gascoyne, R.5
Horsman, D.6
Jones, S.J.7
Marra, M.A.8
-
43
-
-
77952682719
-
Differential modes of selection on the rhodopsin gene in coastal Baltic and North Sea populations of the sand goby, Pomatoschistus minutus
-
Larmuseau MHD, Vancampenhout K, Raeymaekers JAM, Van Houdt JKJ, Volckaert FAM. 2010. Differential modes of selection on the rhodopsin gene in coastal Baltic and North Sea populations of the sand goby, Pomatoschistus minutus. Mol Ecol. 19:2256-2268.
-
(2010)
Mol Ecol.
, vol.19
, pp. 2256-2268
-
-
Larmuseau, M.H.D.1
Vancampenhout, K.2
Raeymaekers, J.A.M.3
Van Houdt, J.K.J.4
Volckaert, F.A.M.5
-
44
-
-
0036340007
-
Postembryonic development of the posterior lateral line in zebrafish
-
Ledent V. 2002. Postembryonic development of the posterior lateral line in zebrafish. Development 129:597-604.
-
(2002)
Development
, vol.129
, pp. 597-604
-
-
Ledent, V.1
-
45
-
-
65449144302
-
Signaling pathways regulating zebrafish lateral line development
-
Ma EY, Raible DW. 2009. Signaling pathways regulating zebrafish lateral line development. Curr Biol. 19:R381-R386.
-
(2009)
Curr Biol.
, vol.19
-
-
Ma, E.Y.1
Raible, D.W.2
-
46
-
-
26244444380
-
From 2R to 3R: Evidence for a fish-specific genome duplication (FSGD)
-
Meyer A, Van de Peer Y. 2005. From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). BioEssays 27:937-945.
-
(2005)
BioEssays
, vol.27
, pp. 937-945
-
-
Meyer, A.1
Van De Peer, Y.2
-
47
-
-
0030695817
-
The lateral line canmediate rheotaxis in fish
-
Montgomery JC, Baker CF, Carton AG. 1997. The lateral line canmediate rheotaxis in fish. Nature 389:960-963.
-
(1997)
Nature
, vol.389
, pp. 960-963
-
-
Montgomery, J.C.1
Baker, C.F.2
Carton, A.G.3
-
48
-
-
0034758828
-
The mechanosensory lateral line system of the hypogean form of Astyanax fasciatus
-
Montgomery JC, Coombs S, Baker CF. 2001. The mechanosensory lateral line system of the hypogean form of Astyanax fasciatus. Environ Biol Fishes. 62:87-96.
-
(2001)
Environ Biol Fishes.
, vol.62
, pp. 87-96
-
-
Montgomery, J.C.1
Coombs, S.2
Baker, C.F.3
-
49
-
-
0023491804
-
Sensory tuning of lateral line receptors in Antarctic fish to the movements of planktonic prey
-
Montgomery JC, MacDonald JA. 1987. Sensory tuning of lateral line receptors in Antarctic fish to the movements of planktonic prey. Science 235:195-196.
-
(1987)
Science
, vol.235
, pp. 195-196
-
-
Montgomery, J.C.1
MacDonald, J.A.2
-
50
-
-
77951972053
-
Genomicus: A database and a browser to study gene synteny in modern and ancestral genomes
-
Muffato M, Louis A, Poisnel C-E, Crollius HR. 2010. Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. Bioinformatics 26:1119-1121.
-
(2010)
Bioinformatics
, vol.26
, pp. 1119-1121
-
-
Muffato, M.1
Louis, A.2
Poisnel, C.-E.3
Crollius, H.R.4
-
51
-
-
0028024626
-
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
-
Muse SV, Gaut BS. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol. 11:715-724.
-
(1994)
Mol Biol Evol.
, vol.11
, pp. 715-724
-
-
Muse, S.V.1
Gaut, B.S.2
-
53
-
-
0036804625
-
Mapping mutations on phylogenies
-
Nielsen R. 2002. Mapping mutations on phylogenies. Syst Biol. 51: 729-739.
-
(2002)
Syst Biol.
, vol.51
, pp. 729-739
-
-
Nielsen, R.1
-
54
-
-
0001830475
-
The phylogenetic distribution and innervation of craniate mechanoreceptive lateral lines
-
Coombs S, Gorner P, Munz H, editors. New York: Springer
-
Northcutt RG. 1989. The phylogenetic distribution and innervation of craniate mechanoreceptive lateral lines. In: Coombs S, Gorner P, Munz H, editors. The mechanosensory lateral line. Neurobiology and evolution. New York: Springer. p. 17-78.
-
(1989)
The Mechanosensory Lateral Line. Neurobiology and Evolution
, pp. 17-78
-
-
Northcutt, R.G.1
-
55
-
-
1842287947
-
Animal behaviour: Swimming against the current
-
Northcutt RG. 1997. Animal behaviour: swimming against the current. Nature 389:915-916.
-
(1997)
Nature
, vol.389
, pp. 915-916
-
-
Northcutt, R.G.1
-
58
-
-
57149084079
-
Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes
-
Penn O, Stern A, Rubinstein ND, Dutheil J, Bacharach E, Galtier N, Pupko T. 2008. Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes. PLoS Comput Biol. 4: e1000214.
-
(2008)
PLoS Comput Biol.
, vol.4
-
-
Penn, O.1
Stern, A.2
Rubinstein, N.D.3
Dutheil, J.4
Bacharach, E.5
Galtier, N.6
Pupko, T.7
-
59
-
-
2342570962
-
Evolution of posterior lateral line development in fish and amphibians
-
Pichon F, Ghysen A. 2004. Evolution of posterior lateral line development in fish and amphibians. Evol Dev. 6:187-193.
-
(2004)
Evol Dev.
, vol.6
, pp. 187-193
-
-
Pichon, F.1
Ghysen, A.2
-
63
-
-
0034526131
-
Zebrafish comparative genomics and the origins of vertebrate chromosomes
-
Postlethwait JH, Woods IG, Ngo-Hazelett P, Yan Y-L, Kelly PD, Chu F, Huang H, Hill-Force A, Talbot WS. 2000. Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res. 10:1890-1902.
-
(2000)
Genome Res.
, vol.10
, pp. 1890-1902
-
-
Postlethwait, J.H.1
Woods, I.G.2
Ngo-Hazelett, P.3
Yan, Y.-L.4
Kelly, P.D.5
Chu, F.6
Huang, H.7
Hill-Force, A.8
Talbot, W.S.9
-
64
-
-
84858383488
-
Improving the performance of positive selection inference by filtering unreliable alignment regions
-
Privman E, Penn O, Pupko T. 2011. Improving the performance of positive selection inference by filtering unreliable alignment regions. Mol Biol Evol. 29:1-5.
-
(2011)
Mol Biol Evol.
, vol.29
, pp. 1-5
-
-
Privman, E.1
Penn, O.2
Pupko, T.3
-
65
-
-
58649118651
-
Rapidly evolving fish genomes and teleost diversity
-
Ravi V, Venkatesh B. 2008. Rapidly evolving fish genomes and teleost diversity. Curr Opin Genetics Dev. 18:544-550.
-
(2008)
Curr Opin Genetics Dev.
, vol.18
, pp. 544-550
-
-
Ravi, V.1
Venkatesh, B.2
-
66
-
-
0035064946
-
Evolutionary rates of duplicate genes in fish and mammals
-
Robinson-Rechavi M, Laudet V. 2001. Evolutionary rates of duplicate genes in fish and mammals. Mol Biol Evol. 18:681-683.
-
(2001)
Mol Biol Evol.
, vol.18
, pp. 681-683
-
-
Robinson-Rechavi, M.1
Laudet, V.2
-
67
-
-
77954065271
-
I-TASSER: A unified platform for automated protein structure and function prediction
-
Roy A, Kucukural A, Zhang Y. 2010. I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc. 5: 725-738.
-
(2010)
Nat Protoc.
, vol.5
, pp. 725-738
-
-
Roy, A.1
Kucukural, A.2
Zhang, Y.3
-
68
-
-
0028079327
-
Behavioral and electrophysiological evidences that the lateral line is involved in the inter-sexual vibrational communication of the hime salmon (landlocked red salmon, Oncorhynchus nerka)
-
Satou M, Takeuchi HA, Nishii J, Tanabe M, Kitamura S, Okumoto N, Iwata M. 1994. Behavioral and electrophysiological evidences that the lateral line is involved in the inter-sexual vibrational communication of the hime salmon (landlocked red salmon, Oncorhynchus nerka). J Comp Physiol A. 174:539-549.
-
(1994)
J Comp Physiol A.
, vol.174
, pp. 539-549
-
-
Satou, M.1
Takeuchi, H.A.2
Nishii, J.3
Tanabe, M.4
Kitamura, S.5
Okumoto, N.6
Iwata, M.7
-
69
-
-
62649155906
-
Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway
-
Sato Y, Hashiguchi Y, Nishida M. 2009a. Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway. BMC Syst Biol. 3:23.
-
(2009)
BMC Syst Biol.
, vol.3
, pp. 23
-
-
Sato, Y.1
Hashiguchi, Y.2
Nishida, M.3
-
70
-
-
67649807765
-
Temporal pattern of loss/persistence of duplicate genes involved in signal transduction and metabolic pathways after teleost-specific genome duplication
-
Sato Y, Hashiguchi Y, Nishida M. 2009b. Temporal pattern of loss/persistence of duplicate genes involved in signal transduction and metabolic pathways after teleost-specific genome duplication. BMC Evol Biol. 9:127.
-
(2009)
BMC Evol Biol.
, vol.9
, pp. 127
-
-
Sato, Y.1
Hashiguchi, Y.2
Nishida, M.3
-
71
-
-
53349119883
-
Speciation through sensory drive in cichlid fish
-
Seehausen O, Terai Y, Magalhaes IS, et al. (13 co-authors). 2008. Speciation through sensory drive in cichlid fish. Nature 455:620-626.
-
(2008)
Nature
, vol.455
, pp. 620-626
-
-
Seehausen, O.1
Terai, Y.2
Magalhaes, I.S.3
-
72
-
-
33645230553
-
Many genes in fish have species-specific asymmetric rates of molecular evolution
-
Steinke D, Salzburger W, Braasch I, Meyer A. 2006. Many genes in fish have species-specific asymmetric rates of molecular evolution. BMC Genomics 7:20.
-
(2006)
BMC Genomics
, vol.7
, pp. 20
-
-
Steinke, D.1
Salzburger, W.2
Braasch, I.3
Meyer, A.4
-
73
-
-
34547489084
-
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
-
Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 56:564-577.
-
(2007)
Syst Biol.
, vol.56
, pp. 564-577
-
-
Talavera, G.1
Castresana, J.2
-
74
-
-
0002671410
-
Some probabilistic and statisical problems on the analysis of DNA sequences
-
Tavare S. 1986. Some probabilistic and statisical problems on the analysis of DNA sequences. Lect Math Life Sci. 17:57-86.
-
(1986)
Lect Math Life Sci.
, vol.17
, pp. 57-86
-
-
Tavare, S.1
-
75
-
-
79959353390
-
Intraspecific divergence in the lateral line system in the nine-spined stickleback (Pungitius pungitius)
-
Trokovic N, Herczeg G, Scott McCairns RJ, Izza Ab Ghani N, Merila J. 2011. Intraspecific divergence in the lateral line system in the nine-spined stickleback (Pungitius pungitius). J Evol Biol. 24: 1546-1558.
-
(2011)
J Evol Biol.
, vol.24
, pp. 1546-1558
-
-
Trokovic, N.1
Herczeg, G.2
Scott McCairns, R.J.3
Izza Ab Ghani, N.4
Merila, J.5
-
76
-
-
1242274629
-
Major events in the genome evolution of vertebrates: Paranome age and size differ considerably between ray-finned fishes and land vertebrates
-
Vandepoele K, De VosW, Taylor JS, Meyer A, Van de Peer Y. 2004. Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates. Proc Natl Acad Sci U S A. 101:1638-1643.
-
(2004)
Proc Natl Acad Sci U S A.
, vol.101
, pp. 1638-1643
-
-
Vandepoele, K.1
De Vos, W.2
Taylor, J.S.3
Meyer, A.4
Van De Peer, Y.5
-
77
-
-
0025360879
-
Themorphology of the lateral line system in 3 species of Pacific cottoid fishes occupying disparate habitats
-
Vischer H. 1990. Themorphology of the lateral line system in 3 species of Pacific cottoid fishes occupying disparate habitats. Cellular Mol Life Sci. 46:244-250.
-
(1990)
Cellular Mol Life Sci.
, vol.46
, pp. 244-250
-
-
Vischer, H.1
-
78
-
-
54549112080
-
Development of diverse lateral line patterns on the teleost caudal fin
-
Wada H, Hamaguchi S, Sakaizumi M. 2008. Development of diverse lateral line patterns on the teleost caudal fin. Dev Dynamics. 237: 2889-2902.
-
(2008)
Dev Dynamics.
, vol.237
, pp. 2889-2902
-
-
Wada, H.1
Hamaguchi, S.2
Sakaizumi, M.3
-
79
-
-
76149093199
-
Lateral line diversity among ecologically divergent threespine stickleback populations
-
Wark AR, Peichel CL. 2010. Lateral line diversity among ecologically divergent threespine stickleback populations. J Exp Biol. 213: 108-117.
-
(2010)
J Exp Biol.
, vol.213
, pp. 108-117
-
-
Wark, A.R.1
Peichel, C.L.2
-
80
-
-
0024513053
-
Gross morphology and evolution of the mechanoreceptive lateral-line system in teleost fishes
-
Webb JF. 1989. Gross morphology and evolution of the mechanoreceptive lateral-line system in teleost fishes. Brain Behav Evol. 33: 34-53.
-
(1989)
Brain Behav Evol.
, vol.33
, pp. 34-53
-
-
Webb, J.F.1
-
81
-
-
24344440632
-
The zebrafish gene map defines ancestral vertebrate chromosomes
-
Woods IG, Wilson C, Friedlander B, Chang P, Reyes DK, Nix R, Kelly PD, Chu F, Postlethwait JH, Talbot WS. 2005. The zebrafish gene map defines ancestral vertebrate chromosomes. Genome Res. 15: 1307-1314.
-
(2005)
Genome Res.
, vol.15
, pp. 1307-1314
-
-
Woods, I.G.1
Wilson, C.2
Friedlander, B.3
Chang, P.4
Reyes, D.K.5
Nix, R.6
Kelly, P.D.7
Chu, F.8
Postlethwait, J.H.9
Talbot, W.S.10
-
82
-
-
0028214103
-
Estimating the pattern of nucleotide substitution
-
Yang Z. 1994. Estimating the pattern of nucleotide substitution. J Mol Evol. 39:105-111.
-
(1994)
J Mol Evol.
, vol.39
, pp. 105-111
-
-
Yang, Z.1
-
83
-
-
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
-
84
-
-
0036270185
-
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
-
Yang Z, Nielsen R. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol. 19:908.
-
(2002)
Mol Biol Evol.
, vol.19
, pp. 908
-
-
Yang, Z.1
Nielsen, R.2
-
85
-
-
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
-
86
-
-
0037202369
-
Molecular evolution of color vision in vertebrates
-
Yokoyama S. 2002. Molecular evolution of color vision in vertebrates. Gene 300:69-78.
-
(2002)
Gene
, vol.300
, pp. 69-78
-
-
Yokoyama, S.1
-
87
-
-
3042637218
-
Frequent false detection of positive selection by the likelihood method with branch-site models
-
Zhang J. 2004. Frequent false detection of positive selection by the likelihood method with branch-site models. Mol Biol Evol. 21: 1332.
-
(2004)
Mol Biol Evol.
, vol.21
, pp. 1332
-
-
Zhang, J.1
-
88
-
-
27844439855
-
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
-
Zhang J, Nielsen R, Yang Z. 2005. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol. 22:2472-2479.
-
(2005)
Mol Biol Evol.
, vol.22
, pp. 2472-2479
-
-
Zhang, J.1
Nielsen, R.2
Yang, Z.3
-
89
-
-
39449115394
-
I-TASSER server for protein 3D structure prediction
-
Zhang Y. 2008. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9:40.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 40
-
-
Zhang, Y.1
|