-
1
-
-
18744382506
-
ProtTest: Selection of best-fit models of protein evolution
-
Abascal, F., Zardoya, R., and Posada, D. (2005). ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21, 2104-2105.
-
(2005)
Bioinformatics
, vol.21
, pp. 2104-2105
-
-
Abascal, F.1
Zardoya, R.2
Posada, D.3
-
2
-
-
84879704517
-
Experimental evidence for the thermophilicity of ancestral life
-
Akanuma, S., Nakajima, Y., Yokobori, S., Kimura, M., Nemoto, N., Mase, T., Miyazono, K., Tanokura, M., and Yamagishi, A. (2013). Experimental evidence for the thermophilicity of ancestral life. Proc. Natl. Acad. Sci. USA 110, 11067-11072.
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 11067-11072
-
-
Akanuma, S.1
Nakajima, Y.2
Yokobori, S.3
Kimura, M.4
Nemoto, N.5
Mase, T.6
Miyazono, K.7
Tanokura, M.8
Yamagishi, A.9
-
3
-
-
65249107239
-
Simultaneous Bayesian gene tree reconstruction and reconciliation analysis
-
Akerborg, O., Sennblad, B., Arvestad, L., and Lagergren, J. (2009). Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc. Natl. Acad. Sci. USA 106, 5714-5719.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 5714-5719
-
-
Akerborg, O.1
Sennblad, B.2
Arvestad, L.3
Lagergren, J.4
-
4
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
5
-
-
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., and 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
-
6
-
-
0028289475
-
Molecular determinants of human red/green color discrimination
-
Asenjo, A.B., Rim, J., and Oprian, D.D. (1994). Molecular determinants of human red/green color discrimination. Neuron 12, 1131-1138.
-
(1994)
Neuron
, vol.12
, pp. 1131-1138
-
-
Asenjo, A.B.1
Rim, J.2
Oprian, D.D.3
-
7
-
-
84882392687
-
The evolutionary origins of detoxifying enzymes: The mammalian serum paraoxonases (PONs) relate to bacterial homoserine lactonases
-
Bar-Rogovsky, H., Hugenmatter, A., and Tawfik, D.S. (2013). The evolutionary origins of detoxifying enzymes: the mammalian serum paraoxonases (PONs) relate to bacterial homoserine lactonases. J. Biol. Chem. 288, 23914-23927.
-
(2013)
J. Biol. Chem.
, vol.288
, pp. 23914-23927
-
-
Bar-Rogovsky, H.1
Hugenmatter, A.2
Tawfik, D.S.3
-
8
-
-
10644230266
-
A genomic timescale of prokaryote evolution: Insights into the origin of methanogenesis, phototrophy, and the colonization of land
-
Battistuzzi, F.U., Feijao, A., and Hedges, S.B. (2004). A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol. Biol. 4, 44.
-
(2004)
BMC Evol. Biol.
, vol.4
, pp. 44
-
-
Battistuzzi, F.U.1
Feijao, A.2
Hedges, S.B.3
-
9
-
-
84906244271
-
A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0
-
Bazinet, A.L., Zwickl, D.J., and Cummings, M.P. (2014). A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0. Syst. Biol. 63, 812-818.
-
(2014)
Syst. Biol.
, vol.63
, pp. 812-818
-
-
Bazinet, A.L.1
Zwickl, D.J.2
Cummings, M.P.3
-
10
-
-
34548028860
-
The very early stages of biological evolution and the nature of the last common ancestor of the three major cell domains
-
Becerra, A., Delaye, L., Islas, S., and Lazcano, A. (2007). The very early stages of biological evolution and the nature of the last common ancestor of the three major cell domains. Annu. Rev. Ecol. Evol. Syst. 38, 361-379.
-
(2007)
Annu. Rev. Ecol. Evol. Syst.
, vol.38
, pp. 361-379
-
-
Becerra, A.1
Delaye, L.2
Islas, S.3
Lazcano, A.4
-
11
-
-
47249122561
-
A site- and time-heterogeneous model of amino acid replacement
-
Blanquart, S. and Lartillot, N. (2008). A site- and time-heterogeneous model of amino acid replacement. Mol. Biol. Evol. 25, 842-858.
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 842-858
-
-
Blanquart, S.1
Lartillot, N.2
-
12
-
-
35248857403
-
Efficient likelihood computations with nonreversible models of evolution
-
Boussau, B. and Gouy, M. (2006). Efficient likelihood computations with nonreversible models of evolution. Syst. Biol. 55, 756-768.
-
(2006)
Syst. Biol.
, vol.55
, pp. 756-768
-
-
Boussau, B.1
Gouy, M.2
-
13
-
-
57749185463
-
Parallel adaptations to high temperatures in the Archaean eon
-
Boussau, B., Blanquart, S., Necsulea, A., Lartillot, N., and Gouy, M. (2008). Parallel adaptations to high temperatures in the Archaean eon. Nature 456, 942-945.
-
(2008)
Nature
, vol.456
, pp. 942-945
-
-
Boussau, B.1
Blanquart, S.2
Necsulea, A.3
Lartillot, N.4
Gouy, M.5
-
14
-
-
33645691679
-
Evolution of hormone-receptor complexity by molecular exploitation
-
Bridgham, J.T., Carroll, S.M., and Thornton, J.W. (2006). Evolution of hormone-receptor complexity by molecular exploitation. Science 312, 97-101.
-
(2006)
Science
, vol.312
, pp. 97-101
-
-
Bridgham, J.T.1
Carroll, S.M.2
Thornton, J.W.3
-
15
-
-
38949122865
-
A thermophilic last universal ancestor inferred from its estimated amino acid composition
-
D.A. Liberles, ed. (Oxford, UK: Oxford University Press)
-
Brooks, D.J. and Gaucher, E.A. (2007). A thermophilic last universal ancestor inferred from its estimated amino acid composition. In: Ancestral Sequence Reconstruction, D.A. Liberles, ed. (Oxford, UK: Oxford University Press), pp. 200-207.
-
(2007)
Ancestral Sequence Reconstruction
, pp. 200-207
-
-
Brooks, D.J.1
Gaucher, E.A.2
-
16
-
-
84908587486
-
New insights about enzyme evolution from large scale studies of sequence and structure relationships
-
Brown, S.D. and Babbitt, P.C. (2014). New insights about enzyme evolution from large scale studies of sequence and structure relationships. J. Biol. Chem. 289, 30221-30228.
-
(2014)
J. Biol. Chem.
, vol.289
, pp. 30221-30228
-
-
Brown, S.D.1
Babbitt, P.C.2
-
17
-
-
8744259751
-
Reconstruction of ancestral protein sequences and its applications
-
Cai, W., Pei, J., and Grishin, N.V. (2004). Reconstruction of ancestral protein sequences and its applications. BMC Evol. Biol. 4, 33.
-
(2004)
BMC Evol. Biol.
, Issue.4
, pp. 33
-
-
Cai, W.1
Pei, J.2
Grishin, N.V.3
-
18
-
-
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
-
19
-
-
0029671221
-
Angiotensin II-forming activity in a reconstructed ancestral chymase
-
Chandrasekharan, U.M., Sanker, S., Glynias, M.J., Karnik, S.S., and Husain, A. (1996). Angiotensin II-forming activity in a reconstructed ancestral chymase. Science 271, 502-505.
-
(1996)
Science
, vol.271
, pp. 502-505
-
-
Chandrasekharan, U.M.1
Sanker, S.2
Glynias, M.J.3
Karnik, S.S.4
Husain, A.5
-
20
-
-
29144484019
-
Maximum likelihood of evolutionary trees: Hardness and approximation
-
Chor, B. and Tuller, T. (2005). Maximum likelihood of evolutionary trees: hardness and approximation. Bioinformatics 21(Suppl 1), i97-106.
-
(2005)
Bioinformatics
, vol.21
, pp. i97-106
-
-
Chor, B.1
Tuller, T.2
-
21
-
-
0033442555
-
Some limitations of ancestral characterstate reconstruction when testing evolutionary hypotheses
-
Cunningham, C.W. (1999). Some limitations of ancestral characterstate reconstruction when testing evolutionary hypotheses. Syst. Biol. 48, 665-674.
-
(1999)
Syst. Biol.
, vol.48
, pp. 665-674
-
-
Cunningham, C.W.1
-
22
-
-
0000228203
-
A model of evolutionary change in proteins
-
M. Dayhoff, ed. (Washington, DC, USA: National Biomedical Research Foundation)
-
Dayhoff, M.O., Schwartz, R.M., and Orcutt, B.C. (1978). A model of evolutionary change in proteins. In: Atlas of Protein Sequence and Structure, M. Dayhoff, ed. (Washington, DC, USA: National Biomedical Research Foundation), pp. 345-352.
-
(1978)
Atlas of Protein Sequence and Structure
, pp. 345-352
-
-
Dayhoff, M.O.1
Schwartz, R.M.2
Orcutt, B.C.3
-
23
-
-
84950144948
-
A Bayesian supertree model for genome-wide species tree reconstruction
-
Pii:syu082
-
De Oliveira Martins, L., Mallo, D., and Posada, D. (2014). A Bayesian supertree model for genome-wide species tree reconstruction. Syst. Biol. pii:syu082.
-
(2014)
Syst. Biol
-
-
De Oliveira Martins, L.1
Mallo, D.2
Posada, D.3
-
24
-
-
0002629270
-
Maximum likelihood from incomplete data via the em algorithm
-
Dempster, A.P., Laird, N.M., and Rubin, D.B. (1977). Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc. Ser. B. (Stat. Method.) 39, 1-38.
-
(1977)
J. R. Stat. Soc. Ser. B. (Stat. Method.)
, vol.39
, pp. 1-38
-
-
Dempster, A.P.1
Laird, N.M.2
Rubin, D.B.3
-
25
-
-
0034027594
-
The nature of the universal ancestor and the evolution of the proteome
-
Doolittle, W.F. (2000). The nature of the universal ancestor and the evolution of the proteome. Curr. Opin. Struct. Biol. 10, 355-358.
-
(2000)
Curr. Opin. Struct. Biol.
, vol.10
, pp. 355-358
-
-
Doolittle, W.F.1
-
26
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar, R.C. (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
-
27
-
-
84870687980
-
Evolution of minimal specificity and promiscuity in steroid hormone receptors
-
Eick, G.N., Colucci, J.K., Harms, M.J., Ortlund, E.A., and Thornton, J.W. (2012). Evolution of minimal specificity and promiscuity in steroid hormone receptors. PLoS Genet. 8, e1003072.
-
(2012)
PLoS Genet.
, vol.8
, pp. e1003072
-
-
Eick, G.N.1
Colucci, J.K.2
Harms, M.J.3
Ortlund, E.A.4
Thornton, J.W.5
-
28
-
-
0032434101
-
Problems with parsimony in sequences of biased base composition
-
Eyre-Walker, A. (1998). Problems with parsimony in sequences of biased base composition. J. Mol. Evol. 47, 686-690.
-
(1998)
J. Mol. Evol.
, vol.47
, pp. 686-690
-
-
Eyre-Walker, A.1
-
29
-
-
84906322381
-
Evolutionary relationship of two ancient protein superfolds
-
Farias-Rico, J.A., Schmidt, S., and Hocker, B. (2014). Evolutionary relationship of two ancient protein superfolds. Nat. Chem. Biol. 10, 710-715.
-
(2014)
Nat. Chem. Biol.
, vol.10
, pp. 710-715
-
-
Farias-Rico, J.A.1
Schmidt, S.2
Hocker, B.3
-
30
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368-376.
-
(1981)
J. Mol. Evol.
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
31
-
-
74549160887
-
Retracing evolution of red fluorescence in GFP-like proteins from Faviina corals
-
Field, S.F. and Matz, M.V. (2010). Retracing evolution of red fluorescence in GFP-like proteins from Faviina corals. Mol. Biol. Evol. 27, 225-233.
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 225-233
-
-
Field, S.F.1
Matz, M.V.2
-
32
-
-
84856022796
-
Evolution of increased complexity in a molecular machine
-
Finnigan, G.C., Hanson-Smith, V., Stevens, T.H., and Thornton, J.W. (2012). Evolution of increased complexity in a molecular machine. Nature 481, 360-364.
-
(2012)
Nature
, vol.481
, pp. 360-364
-
-
Finnigan, G.C.1
Hanson-Smith, V.2
Stevens, T.H.3
Thornton, J.W.4
-
33
-
-
84959747425
-
Toward defining the course of evolution: Minimum change for a specific tree topology
-
Fitch, W.M. (1971). Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Biol. 20, 406-416.
-
(1971)
Syst. Biol.
, vol.20
, pp. 406-416
-
-
Fitch, W.M.1
-
34
-
-
0028010308
-
Using phylogenies to test hypotheses of adaptation: A critique of some current proposals
-
Frumhoff, P.C. and Reeve, H.K. (1994). Using phylogenies to test hypotheses of adaptation: a critique of some current proposals. Evolution 48, 172-180.
-
(1994)
Evolution
, vol.48
, pp. 172-180
-
-
Frumhoff, P.C.1
Reeve, H.K.2
-
35
-
-
0030900384
-
Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes
-
Galtier, N. and Lobry, J.R. (1997). Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J. Mol. Evol. 44, 632-636.
-
(1997)
J. Mol. Evol.
, vol.44
, pp. 632-636
-
-
Galtier, N.1
Lobry, J.R.2
-
37
-
-
0141828152
-
Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins
-
Gaucher, E.A., Thomson, J.M., Burgan, M.F., and Benner, S.A. (2003). Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 425, 285-288.
-
(2003)
Nature
, vol.425
, pp. 285-288
-
-
Gaucher, E.A.1
Thomson, J.M.2
Burgan, M.F.3
Benner, S.A.4
-
38
-
-
38949093003
-
Palaeotemperature trend for Precambrian life inferred from resurrected proteins
-
Gaucher, E.A., Govindarajan, S., and Ganesh, O.K. (2008). Palaeotemperature trend for Precambrian life inferred from resurrected proteins. Nature 451, 704-707.
-
(2008)
Nature
, vol.451
, pp. 704-707
-
-
Gaucher, E.A.1
Govindarajan, S.2
Ganesh, O.K.3
-
39
-
-
65249143885
-
Enzyme (re)design: Lessons from natural evolution and computation
-
Gerlt, J.A. and Babbitt, P.C. (2009). Enzyme (re)design: lessons from natural evolution and computation. Curr. Opin. Chem. Biol. 13, 10-18.
-
(2009)
Curr. Opin. Chem. Biol.
, vol.13
, pp. 10-18
-
-
Gerlt, J.A.1
Babbitt, P.C.2
-
40
-
-
0000365320
-
Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences
-
Goodman, M., Czelusniak, J., Moore, G.W., Romero-Herrera, A.E., and Matsuda, G. (1979). Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool. 28, 132-163.
-
(1979)
Syst. Zool.
, vol.28
, pp. 132-163
-
-
Goodman, M.1
Czelusniak, J.2
Moore, G.W.3
Romero-Herrera, A.E.4
Matsuda, G.5
-
41
-
-
0030498194
-
Ancestral inference from samples of DNA sequences with recombination
-
Griffiths, R.C. and Marjoram, P. (1996). Ancestral inference from samples of DNA sequences with recombination. J. Comput. Biol. 3, 479-502.
-
(1996)
J. Comput. Biol.
, vol.3
, pp. 479-502
-
-
Griffiths, R.C.1
Marjoram, P.2
-
42
-
-
0032715527
-
Important amino acid properties for enhanced thermostability from mesophilic to thermophilic proteins
-
Gromiha, M.M., Oobatake, M., and Sarai, A. (1999). Important amino acid properties for enhanced thermostability from mesophilic to thermophilic proteins. Biophys. Chem. 82, 51-67.
-
(1999)
Biophys. Chem.
, vol.82
, pp. 51-67
-
-
Gromiha, M.M.1
Oobatake, M.2
Sarai, A.3
-
43
-
-
84922378481
-
Toward more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees
-
Groussin, M., Hobbs, J.K., Szollosi, G.J., Gribaldo, S., Arcus, V.L., and Gouy, M. (2015). Toward more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees. Mol. Biol. Evol. 32, 13-22.
-
(2015)
Mol. Biol. Evol.
, vol.32
, pp. 13-22
-
-
Groussin, M.1
Hobbs, J.K.2
Szollosi, G.J.3
Gribaldo, S.4
Arcus, V.L.5
Gouy, M.6
-
44
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
Guindon, S. and 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
-
45
-
-
23144433822
-
PHYML Online - A web server for fast maximum likelihood-based phylogenetic inference
-
Guindon, S., Lethiec, F., Duroux, P., and Gascuel, O. (2005). PHYML Online-a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res. 33, W557-W559.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. W557-W559
-
-
Guindon, S.1
Lethiec, F.2
Duroux, P.3
Gascuel, O.4
-
46
-
-
77955975654
-
Robustness of ancestral sequence reconstruction to phylogenetic uncertainty
-
Hanson-Smith, V., Kolaczkowski, B., and Thornton, J.W. (2010). Robustness of ancestral sequence reconstruction to phylogenetic uncertainty. Mol. Biol. Evol. 27, 1988-1999.
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 1988-1999
-
-
Hanson-Smith, V.1
Kolaczkowski, B.2
Thornton, J.W.3
-
47
-
-
77955584075
-
Analyzing protein structure and function using ancestral gene reconstruction
-
Harms, M.J. and Thornton, J.W. (2010). Analyzing protein structure and function using ancestral gene reconstruction. Curr. Opin. Struct. Biol. 20, 360-366.
-
(2010)
Curr. Opin. Struct. Biol.
, vol.20
, pp. 360-366
-
-
Harms, M.J.1
Thornton, J.W.2
-
48
-
-
84879943516
-
Biophysical mechanisms for large-effect mutations in the evolution of steroid hormone receptors
-
Harms, M.J., Eick, G.N., Goswami, D., Colucci, J.K., Griffin, P.R., Ortlund, E.A., and Thornton, J.W. (2013). Biophysical mechanisms for large-effect mutations in the evolution of steroid hormone receptors. Proc. Natl. Acad. Sci. USA 110, 11475-11480.
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 11475-11480
-
-
Harms, M.J.1
Eick, G.N.2
Goswami, D.3
Colucci, J.K.4
Griffin, P.R.5
Ortlund, E.A.6
Thornton, J.W.7
-
49
-
-
84855870416
-
On the origin and evolution of thermophily: Reconstruction of functional precambrian enzymes from ancestors of Bacillus
-
Hobbs, J.K., Shepherd, C., Saul, D.J., Demetras, N.J., Haaning, S., Monk, C.R., Daniel, R.M., and Arcus, V.L. (2012). On the origin and evolution of thermophily: reconstruction of functional precambrian enzymes from ancestors of Bacillus. Mol. Biol. Evol. 29, 825-835.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 825-835
-
-
Hobbs, J.K.1
Shepherd, C.2
Saul, D.J.3
Demetras, N.J.4
Haaning, S.5
Monk, C.R.6
Daniel, R.M.7
Arcus, V.L.8
-
50
-
-
0035527347
-
Empirical and hierarchical Bayesian estimation of ancestral states
-
Huelsenbeck, J.P. and Bollback, J.P. (2001). Empirical and hierarchical Bayesian estimation of ancestral states. Syst. Biol. 50, 351-366.
-
(2001)
Syst. Biol.
, vol.50
, pp. 351-366
-
-
Huelsenbeck, J.P.1
Bollback, J.P.2
-
51
-
-
0035861456
-
Bayesian inference of phylogeny and its impact on evolutionary biology
-
Huelsenbeck, J.P., Ronquist, F., Nielsen, R., and Bollback, J.P. (2001). Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294, 2310-2314.
-
(2001)
Science
, vol.294
, pp. 2310-2314
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
Nielsen, R.3
Bollback, J.P.4
-
52
-
-
84883487142
-
Conservation of protein structure over four billion years
-
Ingles-Prieto, A., Ibarra-Molero, B., Delgado-Delgado, A., Perez- Jimenez, R., Fernandez, J.M., Gaucher, E.A., Sanchez- Ruiz, J.M., and Gavira, J.A. (2013). Conservation of protein structure over four billion years. Structure 21, 1690-1697.
-
(2013)
Structure
, vol.21
, pp. 1690-1697
-
-
Ingles-Prieto, A.1
Ibarra-Molero, B.2
Delgado-Delgado, A.3
Perez-Jimenez, R.4
Fernandez, J.M.5
Gaucher, E.A.6
Sanchez-Ruiz, J.M.7
Gavira, J.A.8
-
53
-
-
0028895702
-
Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily
-
Jermann, T.M., Opitz, J.G., Stackhouse, J., and Benner, S.A. (1995). Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily. Nature 374, 57-59.
-
(1995)
Nature
, vol.374
, pp. 57-59
-
-
Jermann, T.M.1
Opitz, J.G.2
Stackhouse, J.3
Benner, S.A.4
-
54
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones, D.T., Taylor, W.R., and Thornton, J.M. (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.T.1
Taylor, W.R.2
Thornton, J.M.3
-
55
-
-
84866465344
-
ANGES: Reconstructing ANcestral GEnomeS maps
-
Jones, B.R., Rajaraman, A., Tannier, E., and Chauve, C. (2012). ANGES: reconstructing ANcestral GEnomeS maps. Bioinformatics 28, 2388-2390.
-
(2012)
Bioinformatics
, vol.28
, pp. 2388-2390
-
-
Jones, B.R.1
Rajaraman, A.2
Tannier, E.3
Chauve, C.4
-
56
-
-
0000732090
-
Evolution of protein molecules
-
H.N. Munro, ed. (New York, USA: Academic Press)
-
Jukes, T.H. and Cantor, C.R. (1969). Evolution of protein molecules. In: Mammalian protein metabolism, H.N. Munro, ed. (New York, USA: Academic Press), pp. 21-132.
-
(1969)
Mammalian Protein Metabolism
, pp. 21-132
-
-
Jukes, T.H.1
Cantor, C.R.2
-
57
-
-
77953623874
-
Enzyme promiscuity: A mechanistic and evolutionary perspective
-
Khersonsky, O. and Tawfik, D.S. (2010). Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu. Rev. Biochem. 79, 471-505.
-
(2010)
Annu. Rev. Biochem.
, vol.79
, pp. 471-505
-
-
Khersonsky, O.1
Tawfik, D.S.2
-
58
-
-
0001464973
-
Estimation of evolutionary distances between homologous nucleotide sequences
-
Kimura, M. (1981). Estimation of evolutionary distances between homologous nucleotide sequences. Proc. Natl. Acad. Sci. USA 78, 454-458.
-
(1981)
Proc. Natl. Acad. Sci. USA
, vol.78
, pp. 454-458
-
-
Kimura, M.1
-
59
-
-
0029881442
-
Probabilistic reconstruction of ancestral protein sequences
-
Koshi, J.M. and Goldstein, R.A. (1996). Probabilistic reconstruction of ancestral protein sequences. J. Mol. Evol. 42, 313-320.
-
(1996)
J. Mol. Evol.
, vol.42
, pp. 313-320
-
-
Koshi, J.M.1
Goldstein, R.A.2
-
60
-
-
0032976397
-
Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees
-
Larget, B. and Simon, D.L. (1999). Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16, 750-759.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 750-759
-
-
Larget, B.1
Simon, D.L.2
-
61
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., et al. (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
McWilliam, H.6
Valentin, F.7
Wallace, I.M.8
Wilm, A.9
Lopez, R.10
-
62
-
-
69949126557
-
PhyloBayes 3: A Bayesian software package for phylogenetic reconstruction and molecular dating
-
Lartillot, N., Lepage, T., and Blanquart, S. (2009). PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25, 2286-2288.
-
(2009)
Bioinformatics
, vol.25
, pp. 2286-2288
-
-
Lartillot, N.1
Lepage, T.2
Blanquart, S.3
-
63
-
-
33745634395
-
Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li, W. and Godzik, A. (2006). Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658-1659.
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
65
-
-
84934441394
-
-
Bioinformatics, J.M. Keith, ed. (Totowa, NJ, USA: Springer)
-
Lio, P. and Bishop, M. (2008). Modeling sequence evolution. In: Bioinformatics, J.M. Keith, ed. (Totowa, NJ, USA: Springer), pp. 255-285.
-
(2008)
Modeling Sequence Evolution
, pp. 255-285
-
-
Lio, P.1
Bishop, M.2
-
66
-
-
46249095233
-
Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis
-
Loytynoja, A. and Goldman, N. (2008). Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320, 1632-1635.
-
(2008)
Science
, vol.320
, pp. 1632-1635
-
-
Loytynoja, A.1
Goldman, N.2
-
67
-
-
0031504952
-
Gene trees in species trees
-
Maddison, W.P. (1997). Gene trees in species trees. Syst. Biol. 46, 523-536.
-
(1997)
Syst. Biol.
, vol.46
, pp. 523-536
-
-
Maddison, W.P.1
-
69
-
-
5744249209
-
Equation of state calculations by fast computing machines
-
Metropolis, N., Rosenbluth, A.W., Rosenbluth, M.N., Teller, A.H., and Teller, E. (1953). Equation of state calculations by fast computing machines. J. Chem. Phys. 21, 1087-1092.
-
(1953)
J. Chem. Phys.
, vol.21
, pp. 1087-1092
-
-
Metropolis, N.1
Rosenbluth, A.W.2
Rosenbluth, M.N.3
Teller, A.H.4
Teller, E.5
-
70
-
-
84931034856
-
ASTRAL-II: Coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
-
Mirarab, S. and Warnow, T. (2015). ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics 31, i44-52.
-
(2015)
Bioinformatics
, vol.31
, pp. i44-52
-
-
Mirarab, S.1
Warnow, T.2
-
71
-
-
84907019380
-
ASTRAL: Genome-scale coalescentbased species tree estimation
-
Mirarab, S., Reaz, R., Bayzid, M.S., Zimmermann, T., Swenson, M.S., and Warnow, T. (2014). ASTRAL: genome-scale coalescentbased species tree estimation. Bioinformatics 30, i541-548.
-
(2014)
Bioinformatics
, vol.30
, pp. i541-548
-
-
Mirarab, S.1
Reaz, R.2
Bayzid, M.S.3
Zimmermann, T.4
Swenson, M.S.5
Warnow, T.6
-
72
-
-
84878935759
-
Evolution of mammalian diving capacity traced by myoglobin net surface charge
-
Mirceta, S., Signore, A.V., Burns, J.M., Cossins, A.R., Campbell, K.L., and Berenbrink, M. (2013). Evolution of mammalian diving capacity traced by myoglobin net surface charge. Science 340, 1234192.
-
(2013)
Science
, vol.340
, pp. 1234192
-
-
Mirceta, S.1
Signore, A.V.2
Burns, J.M.3
Cossins, A.R.4
Campbell, K.L.5
Berenbrink, M.6
-
73
-
-
0035931935
-
The habitat and nature of early life
-
Nisbet, E.G. and Sleep, N.H. (2001). The habitat and nature of early life. Nature 409, 1083-1091.
-
(2001)
Nature
, vol.409
, pp. 1083-1091
-
-
Nisbet, E.G.1
Sleep, N.H.2
-
74
-
-
39149141072
-
AWTY (are we there yet?): A system for graphical exploration of MCMC convergence in Bayesian phylogenetics
-
Nylander, J.A., Wilgenbusch, J.C., Warren, D.L., and Swofford, D.L. (2008). AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24, 581-583.
-
(2008)
Bioinformatics
, vol.24
, pp. 581-583
-
-
Nylander, J.A.1
Wilgenbusch, J.C.2
Warren, D.L.3
Swofford, D.L.4
-
75
-
-
34548040966
-
Crystal structure of an ancient protein: Evolution by conformational epistasis
-
Ortlund, E.A., Bridgham, J.T., Redinbo, M.R., and Thornton, J.W. (2007). Crystal structure of an ancient protein: evolution by conformational epistasis. Science 317, 1544-1548.
-
(2007)
Science
, vol.317
, pp. 1544-1548
-
-
Ortlund, E.A.1
Bridgham, J.T.2
Redinbo, M.R.3
Thornton, J.W.4
-
76
-
-
0002725360
-
Chemical paleogenetics: Molecular "restoration studies" of extinct forms of life
-
Pauling, L. and Zuckerkandl, E. (1963). Chemical paleogenetics: molecular "restoration studies" of extinct forms of life. Acta. Chem. Scand. 17, 9-16.
-
(1963)
Acta. Chem. Scand.
, vol.17
, pp. 9-16
-
-
Pauling, L.1
Zuckerkandl, E.2
-
77
-
-
79955640296
-
Single-molecule paleoenzymology probes the chemistry of resurrected enzymes
-
Perez-Jimenez, R., Inglés-Prieto, A., Zhao, Z.M., Sanchez-Romero, I., Alegre-Cebollada, J., Kosuri, P., Garcia-Manyes, S., Kappock, T.J., Tanokura, M., Holmgren, A., et al. (2011). Single-molecule paleoenzymology probes the chemistry of resurrected enzymes. Nat. Struct. Mol. Biol. 18, 592-596.
-
(2011)
Nat. Struct. Mol. Biol.
, vol.18
, pp. 592-596
-
-
Perez-Jimenez, R.1
Inglés-Prieto, A.2
Zhao, Z.M.3
Sanchez-Romero, I.4
Alegre-Cebollada, J.5
Kosuri, P.6
Garcia-Manyes, S.7
Kappock, T.J.8
Tanokura, M.9
Holmgren, A.10
-
78
-
-
84919477203
-
Evolution of oligomeric state through allosteric pathways that mimic ligand binding
-
Perica, T., Kondo, Y., Tiwari, S.P., McLaughlin, S.H., Kemplen, K.R., Zhang, X., Steward, A., Reuter, N., Clarke, J., and Teichmann, S.A. (2014). Evolution of oligomeric state through allosteric pathways that mimic ligand binding. Science 346, 1254346.
-
(2014)
Science
, vol.346
, pp. 1254346
-
-
Perica, T.1
Kondo, Y.2
Tiwari, S.P.3
McLaughlin, S.H.4
Kemplen, K.R.5
Zhang, X.6
Steward, A.7
Reuter, N.8
Clarke, J.9
Teichmann, S.A.10
-
79
-
-
0034117082
-
A fast algorithm for joint reconstruction of ancestral amino acid sequences
-
Pupko, T., Peer, I., Shamir, R., and Graur, D. (2000). A fast algorithm for joint reconstruction of ancestral amino acid sequences. Mol. Biol. Evol. 17, 890-896.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 890-896
-
-
Pupko, T.1
Peer, I.2
Shamir, R.3
Graur, D.4
-
80
-
-
84893809813
-
-
Ancestral sequence reconstruction D.A. Liberles, ed. (Oxford, UK: Oxford University Press)
-
Pupko, T., Doron-Faigenboim, A., Liberles, D.A., and Cannarozzi, G.M. (2007). Probabilistic models and their impact on the accuracy of reconstructed ancestral protein sequences. In: Ancestral sequence reconstruction, D.A. Liberles, ed. (Oxford, UK: Oxford University Press).
-
(2007)
Probabilistic models and their impact on the accuracy of reconstructed ancestral protein sequences
-
-
Pupko, T.1
Doron-Faigenboim, A.2
Liberles, D.A.3
Cannarozzi, G.M.4
-
81
-
-
0034983479
-
Quartet-based phylogenetic inference: Improvements and limits
-
Ranwez, V. and Gascuel, O. (2001). Quartet-based phylogenetic inference: improvements and limits. Mol. Biol. Evol. 18, 1103-1116.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 1103-1116
-
-
Ranwez, V.1
Gascuel, O.2
-
82
-
-
84892153217
-
Evidence for the existence of elaborate enzyme complexes in the Paleoarchean era
-
Reisinger, B., Sperl, J., Holinski, A., Schmid, V., Rajendran, C., Carstensen, L., Schlee, S., Blanquart, S., Merkl, R., and Sterner, R. (2014). Evidence for the existence of elaborate enzyme complexes in the Paleoarchean era. J. Am. Chem. Soc. 136, 122-129.
-
(2014)
J. Am. Chem. Soc.
, vol.136
, pp. 122-129
-
-
Reisinger, B.1
Sperl, J.2
Holinski, A.3
Schmid, V.4
Rajendran, C.5
Carstensen, L.6
Schlee, S.7
Blanquart, S.8
Merkl, R.9
Sterner, R.10
-
83
-
-
77952303485
-
Computational and experimental evidence for the evolution of a (aa)8-barrel protein from an ancestral quarter-barrel stabilised by disulfide bonds
-
Richter, M., Bosnali, M., Carstensen, L., Seitz, T., Durchschlag, H., Blanquart, S., Merkl, R., and Sterner, R. (2010). Computational and experimental evidence for the evolution of a (aa)8-barrel protein from an ancestral quarter-barrel stabilised by disulfide bonds. J. Mol. Biol. 398, 763-773.
-
(2010)
J. Mol. Biol.
, vol.398
, pp. 763-773
-
-
Richter, M.1
Bosnali, M.2
Carstensen, L.3
Seitz, T.4
Durchschlag, H.5
Blanquart, S.6
Merkl, R.7
Sterner, R.8
-
84
-
-
84874602326
-
Hyperstability and substrate promiscuity in laboratory resurrections of Precambrian a-lactamases
-
Risso, V.A., Gavira, J.A., Mejia-Carmona, D.F., Gaucher, E.A., and Sanchez-Ruiz, J.M. (2013). Hyperstability and substrate promiscuity in laboratory resurrections of Precambrian a-lactamases. J. Am. Chem. Soc. 135, 2899-2902.
-
(2013)
J. Am. Chem. Soc.
, vol.135
, pp. 2899-2902
-
-
Risso, V.A.1
Gavira, J.A.2
Mejia-Carmona, D.F.3
Gaucher, E.A.4
Sanchez-Ruiz, J.M.5
-
85
-
-
85027940591
-
Thermostable and promiscuous Precambrian proteins
-
Risso, V.A., Gavira, J.A., and Sanchez-Ruiz, J.M. (2014). Thermostable and promiscuous Precambrian proteins. Environ. Microbiol. 16, 1485-1489.
-
(2014)
Environ. Microbiol.
, vol.16
, pp. 1485-1489
-
-
Risso, V.A.1
Gavira, J.A.2
Sanchez-Ruiz, J.M.3
-
86
-
-
84988239865
-
Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history
-
Risso, V.A., Manssour-Triedo, F., Delgado-Delgado, A., Arco, R., Barroso- delJesus, A., Ingles-Prieto, A., Godoy-Ruiz, R., Gavira, J.A., Gaucher, E.A., Ibarra-Molero, B., et al. (2015). Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Mol. Biol. Evol. 32, 440-455.
-
(2015)
Mol. Biol. Evol.
, vol.32
, pp. 440-455
-
-
Risso, V.A.1
Manssour-Triedo, F.2
Delgado-Delgado, A.3
Arco, R.4
Barroso-Deljesus, A.5
Ingles-Prieto, A.6
Godoy-Ruiz, R.7
Gavira, J.A.8
Gaucher, E.A.9
Ibarra-Molero, B.10
-
87
-
-
33750466236
-
A palaeotemperature curve for the Precambrian oceans based on silicon isotopes in cherts
-
Robert, F. and Chaussidon, M. (2006). A palaeotemperature curve for the Precambrian oceans based on silicon isotopes in cherts. Nature 443, 969-972.
-
(2006)
Nature
, vol.443
, pp. 969-972
-
-
Robert, F.1
Chaussidon, M.2
-
88
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
Ronquist, F. and Huelsenbeck, J.P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574.
-
(2003)
Bioinformatics
, vol.19
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
-
89
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou, N. and Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
-
(1987)
Mol. Biol. Evol.
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
90
-
-
0016424695
-
Minimal mutation trees of sequences
-
Sankoff, D. (1975). Minimal mutation trees of sequences. SIAM J. Appl. Math. 28, 35-42.
-
(1975)
SIAM J. Appl. Math.
, vol.28
, pp. 35-42
-
-
Sankoff, D.1
-
91
-
-
0029731915
-
The reconstruction of ancestral character states
-
Schultz, T.R., Cocroft, R.B., and Churchill, G.A. (1996). The reconstruction of ancestral character states. Evolution 50, 504-511.
-
(1996)
Evolution
, vol.50
, pp. 504-511
-
-
Schultz, T.R.1
Cocroft, R.B.2
Churchill, G.A.3
-
92
-
-
84925250621
-
Joint amalgamation of most parsimonious reconciled gene trees
-
Scornavacca, C., Jacox, E., and Szollosi, G.J. (2015). Joint amalgamation of most parsimonious reconciled gene trees. Bioinformatics 31, 841-848.
-
(2015)
Bioinformatics
, vol.31
, pp. 841-848
-
-
Scornavacca, C.1
Jacox, E.2
Szollosi, G.J.3
-
93
-
-
0036139287
-
CONSEL: For assessing the confidence of phylogenetic tree selection
-
Shimodaira, H. and Hasegawa, M. (2001). CONSEL: For assessing the confidence of phylogenetic tree selection. Bioinformatics 17, 1246-1247.
-
(2001)
Bioinformatics
, vol.17
, pp. 1246-1247
-
-
Shimodaira, H.1
Hasegawa, M.2
-
94
-
-
0025237024
-
The ribonuclease from an extinct bovid ruminant
-
Stackhouse, J., Presnell, S.R., McGeehan, G.M., Nambiar, K.P., and Benner, S.A. (1990). The ribonuclease from an extinct bovid ruminant. FEBS Lett. 262, 104-106.
-
(1990)
FEBS Lett.
, vol.262
, pp. 104-106
-
-
Stackhouse, J.1
Presnell, S.R.2
McGeehan, G.M.3
Nambiar, K.P.4
Benner, S.A.5
-
95
-
-
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, 2688-2690.
-
(2006)
Bioinformatics
, vol.22
, pp. 2688-2690
-
-
Stamatakis, A.1
-
96
-
-
0029836454
-
Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies
-
Strimmer, K. and Von Haeseler, A. (1996). Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13, 964-969.
-
(1996)
Mol. Biol. Evol.
, vol.13
, pp. 964-969
-
-
Strimmer, K.1
Von Haeseler, A.2
-
97
-
-
0242487523
-
Estimation of rates-across-sites distributions in phylogenetic substitution models
-
Susko, E., Field, C., Blouin, C., and Roger, A.J. (2003). Estimation of rates-across-sites distributions in phylogenetic substitution models. Syst. Biol. 52, 594-603.
-
(2003)
Syst. Biol.
, vol.52
, pp. 594-603
-
-
Susko, E.1
Field, C.2
Blouin, C.3
Roger, A.J.4
-
99
-
-
0001336205
-
Phylogenetic inference
-
D.M. Hillis, C. Moritz, and B.K. Mable, eds. (Sunderland, MA, USA: Sinauer and Associates)
-
Swofford, D.L., Olsen, G.J., Waddell, P.J., and Hillis, D.M. (1996). Phylogenetic inference. In: Molecular Systematics, D.M. Hillis, C. Moritz, and B.K. Mable, eds. (Sunderland, MA, USA: Sinauer and Associates), pp. 407-514.
-
(1996)
Molecular Systematics
, pp. 407-514
-
-
Swofford, D.L.1
Olsen, G.J.2
Waddell, P.J.3
Hillis, D.M.4
-
100
-
-
84860135294
-
-
Evolutionary Genomics A. Anismimova, ed. (New York, USA: Springer)
-
Szollosi, G.J. and Daubin, V. (2012). Modeling gene family evolution and reconciling phylogenetic discord. In: Evolutionary Genomics, A. Anismimova, ed. (New York, USA: Springer), pp. 29-51.
-
(2012)
Modeling gene family evolution and reconciling phylogenetic discord
, pp. 29-51
-
-
Szollosi, G.J.1
Daubin, V.2
-
101
-
-
84876253028
-
Lateral gene transfer from the dead
-
Szollosi, G.J., Tannier, E., Lartillot, N., and Daubin, V. (2013). Lateral gene transfer from the dead. Syst. Biol. 62, 386-397.
-
(2013)
Syst. Biol.
, vol.62
, pp. 386-397
-
-
Szollosi, G.J.1
Tannier, E.2
Lartillot, N.3
Daubin, V.4
-
102
-
-
84928749156
-
The inference of gene trees with species trees
-
Szollosi, G.J., Tannier, E., Daubin, V., and Boussau, B. (2015). The inference of gene trees with species trees. Syst. Biol. 64, e42-62.
-
(2015)
Syst. Biol.
, vol.64
, pp. e42-62
-
-
Szollosi, G.J.1
Tannier, E.2
Daubin, V.3
Boussau, B.4
-
103
-
-
79957613599
-
MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
-
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731-2739.
-
(2011)
Mol. Biol. Evol.
, vol.28
, pp. 2731-2739
-
-
Tamura, K.1
Peterson, D.2
Peterson, N.3
Stecher, G.4
Nei, M.5
Kumar, S.6
-
104
-
-
0002671410
-
Some probabilistic and statistical problems in the analysis of DNA sequences
-
Tavaré, S. (1986). Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures Math. Life Sci. 17, 57-86.
-
(1986)
Lectures Math. Life Sci.
, vol.17
, pp. 57-86
-
-
Tavaré, S.1
-
105
-
-
1942531303
-
Resurrecting ancient genes: Experimental analysis of extinct molecules
-
Thornton, J.W. (2004). Resurrecting ancient genes: experimental analysis of extinct molecules. Nat. Rev. Genet. 5, 366-375.
-
(2004)
Nat. Rev. Genet.
, vol.5
, pp. 366-375
-
-
Thornton, J.W.1
-
106
-
-
74949120671
-
Reconstructing ancestral gene content by coevolution
-
Tuller, T., Birin, H., Gophna, U., Kupiec, M., and Ruppin, E. (2010). Reconstructing ancestral gene content by coevolution. Genome Res. 20, 122-132.
-
(2010)
Genome Res.
, vol.20
, pp. 122-132
-
-
Tuller, T.1
Birin, H.2
Gophna, U.3
Kupiec, M.4
Ruppin, E.5
-
107
-
-
19244366496
-
Evolution of coral pigments recreated
-
Ugalde, J.A., Chang, B.S., and Matz, M.V. (2004). Evolution of coral pigments recreated. Science 305, 1433.
-
(2004)
Science
, vol.305
, pp. 1433
-
-
Ugalde, J.A.1
Chang, B.S.2
Matz, M.V.3
-
108
-
-
84871697209
-
Reconstruction of ancestral metabolic enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplication
-
Voordeckers, K., Brown, C.A., Vanneste, K., van der Zande, E., Voet, A., Maere, S., and Verstrepen, K.J. (2012). Reconstruction of ancestral metabolic enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplication. PLoS Biol. 10, e1001446.
-
(2012)
PLoS Biol.
, vol.10
, pp. e1001446
-
-
Voordeckers, K.1
Brown, C.A.2
Vanneste, K.3
Van Der Zande, E.4
Voet, A.5
Maere, S.6
Verstrepen, K.J.7
-
109
-
-
0020646715
-
Possible limits on the composition of the Archaean ocean
-
Walker, J.C.G. (1983). Possible limits on the composition of the Archaean ocean. Nature 302, 518-520.
-
(1983)
Nature
, vol.302
, pp. 518-520
-
-
Walker, J.C.G.1
-
110
-
-
84934434878
-
-
Bioinformatics J.M. Keith, ed. (Totowa, NJ, USA: Springer)
-
Whelan, S. (2008). Inferring trees. In: Bioinformatics, J.M. Keith, ed. (Totowa, NJ, USA: Springer), pp. 287-309.
-
(2008)
Inferring trees
, pp. 287-309
-
-
Whelan, S.1
-
111
-
-
0035031966
-
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
-
Whelan, S. and 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
-
112
-
-
33745605535
-
Assessing the accuracy of ancestral protein reconstruction methods
-
Williams, P.D., Pollock, D.D., Blackburne, B.P., and Goldstein, R.A. (2006). Assessing the accuracy of ancestral protein reconstruction methods. PLoS Comp. Biol. 2, e69.
-
(2006)
PLoS Comp. Biol.
, vol.2
, pp. e69
-
-
Williams, P.D.1
Pollock, D.D.2
Blackburne, B.P.3
Goldstein, R.A.4
-
113
-
-
0032499698
-
The universal ancestor
-
Woese, C. (1998). The universal ancestor. Proc. Natl. Acad. Sci. USA 95, 6854-6859.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 6854-6859
-
-
Woese, C.1
-
114
-
-
0028064845
-
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
-
Yang, Z. (1994). Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39, 306-314.
-
(1994)
J. Mol. Evol.
, vol.39
, pp. 306-314
-
-
Yang, Z.1
-
115
-
-
0030683599
-
PAML: A program package for phylogenetic analysis by maximum likelihood
-
Yang, Z. (1997). PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555-556.
-
(1997)
Comput. Appl. Biosci.
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
116
-
-
0033979433
-
Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
-
Yang, Z. and Nielsen, R. (2000). Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17, 32-43.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 32-43
-
-
Yang, Z.1
Nielsen, R.2
-
117
-
-
0028820333
-
A new method of inference of ancestral nucleotide and amino acid sequences
-
Yang, Z., Kumar, S., and Nei, M. (1995). A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141, 1641-1650.
-
(1995)
Genetics
, vol.141
, pp. 1641-1650
-
-
Yang, Z.1
Kumar, S.2
Nei, M.3
-
118
-
-
0034097381
-
Codon-substitution models for heterogeneous selection pressure at amino acid sites
-
Yang, Z., Nielsen, R., Goldman, N., and Pedersen, A.M. (2000). Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155, 431-449.
-
(2000)
Genetics
, vol.155
, pp. 431-449
-
-
Yang, Z.1
Nielsen, R.2
Goldman, N.3
Pedersen, A.M.4
-
119
-
-
84865076321
-
REGEN: Ancestral Genome Reconstruction for Bacteria
-
Yang, K., Heath, L.S., and Setubal, J.C. (2012). REGEN: Ancestral Genome Reconstruction for Bacteria. Genes (Basel) 3, 423-443.
-
(2012)
Genes (Basel)
, vol.3
, pp. 423-443
-
-
Yang, K.1
Heath, L.S.2
Setubal, J.C.3
-
120
-
-
0034857787
-
The molecular genetics and evolution of red and green color vision in vertebrates
-
Yokoyama, S. and Radlwimmer, F.B. (2001). The molecular genetics and evolution of red and green color vision in vertebrates. Genetics 158, 1697-1710.
-
(2001)
Genetics
, vol.158
, pp. 1697-1710
-
-
Yokoyama, S.1
Radlwimmer, F.B.2
-
121
-
-
55749097435
-
Molecular basis of spectral tuning in the red- and green-sensitive (M/LWS) pigments in vertebrates
-
Yokoyama, S., Yang, H., and Starmer, W.T. (2008). Molecular basis of spectral tuning in the red- and green-sensitive (M/LWS) pigments in vertebrates. Genetics 179, 2037-2043.
-
(2008)
Genetics
, vol.179
, pp. 2037-2043
-
-
Yokoyama, S.1
Yang, H.2
Starmer, W.T.3
-
122
-
-
33846519263
-
Protein and DNA sequence determinants of thermophilic adaptation
-
Zeldovich, K.B., Berezovsky, I.N., and Shakhnovich, E.I. (2007). Protein and DNA sequence determinants of thermophilic adaptation. PLoS Comp. Biol. 3, e5.
-
(2007)
PLoS Comp. Biol.
, vol.3
, pp. e5
-
-
Zeldovich, K.B.1
Berezovsky, I.N.2
Shakhnovich, E.I.3
-
123
-
-
84922379085
-
Evolution of conformational dynamics determines the conversion of a promiscuous generalist into a specialist enzyme
-
Zou, T., Risso, V.A., Gavira, J.A., Sanchez-Ruiz, J.M., and Ozkan, S.B. (2015). Evolution of conformational dynamics determines the conversion of a promiscuous generalist into a specialist enzyme. Mol. Biol. Evol. 32, 132-143.
-
(2015)
Mol. Biol. Evol.
, vol.32
, pp. 132-143
-
-
Zou, T.1
Risso, V.A.2
Gavira, J.A.3
Sanchez-Ruiz, J.M.4
Ozkan, S.B.5
|