-
1
-
-
38549153238
-
Data growth and its impact on the SCOP database: new developments
-
Andreeva, A., Howorth, D., Chandonia, J. M., Brenner, S. E., Hubbard, T. J., Chothia, C., and Murzin, A. G. (2008). Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res. 36, D419-D425.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Andreeva, A.1
Howorth, D.2
Chandonia, J.M.3
Brenner, S.E.4
Hubbard, T.J.5
Chothia, C.6
Murzin, A.G.7
-
2
-
-
80052262050
-
Finding the balance between the mathematical and biological optima in multiple sequence alignment
-
Anisimova, M., Cannarozzi, G. M., and Liberles, D. A. (2010). Finding the balance between the mathematical and biological optima in multiple sequence alignment. Trends Evol. Biol. 2, e7.
-
(2010)
Trends Evol. Biol.
, vol.2
-
-
Anisimova, M.1
Cannarozzi, G.M.2
Liberles, D.A.3
-
3
-
-
0034069495
-
Gene Ontology: tool for the unification of biology
-
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E, Ringwald, M., Rubin, G. M., and Sherlock, G. (2000). Gene Ontology: tool for the unification of biology. Nat. Genet. 25, 25-29.
-
(2000)
Nat. Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
4
-
-
0038486929
-
An evolutionarily structured universe of protein architecture
-
Caetano-Anollés, G., and Caetano-Anollés, D. (2003). An evolutionarily structured universe of protein architecture. Genome Res. 13, 1563-1571.
-
(2003)
Genome Res
, vol.13
, pp. 1563-1571
-
-
Caetano-Anollés, G.1
Caetano-Anollés, D.2
-
5
-
-
84862687324
-
The phylogenomic roots of modern biochemistry: origins of proteins, cofactors and protein biosynthesis
-
Caetano-Anollés, G., Kim, K. M., and Caetano-Anollés, D. (2012). The phylogenomic roots of modern biochemistry: origins of proteins, cofactors and protein biosynthesis. J. Mol. Evol. 74, 1-34.
-
(2012)
J. Mol. Evol.
, vol.74
, pp. 1-34
-
-
Caetano-Anollés, G.1
Kim, K.M.2
Caetano-Anollés, D.3
-
6
-
-
59849127275
-
The origin, evolution and structure of the protein world
-
Caetano-Anollés, G., Wang, M., Caetano-Anollés, D., and Mittenthal, J. E. (2009). The origin, evolution and structure of the protein world. Biochem. J. 417, 621-637.
-
(2009)
Biochem. J.
, vol.417
, pp. 621-637
-
-
Caetano-Anollés, G.1
Wang, M.2
Caetano-Anollés, D.3
Mittenthal, J.E.4
-
7
-
-
77952263209
-
Modularity and dissipation in the evolution of molecular function, structures and networks
-
ed. G. Caetano-Anollés (Hoboken, NJ: Wiley-Blackwell)
-
Caetano-Anollés, G., Yafremava, L., and Mittenthal, J. M. (2010). "Modularity and dissipation in the evolution of molecular function, structures and networks," in Evolutionary Bioinformatics and Systems Biology, ed. G. Caetano-Anollés (Hoboken, NJ: Wiley-Blackwell), 431-450.
-
(2010)
Evolutionary Bioinformatics and Systems Biology
, pp. 431-450
-
-
Caetano-Anollés, G.1
Yafremava, L.2
Mittenthal, J.M.3
-
8
-
-
33646172143
-
Structural classification of small, disulfide-rich protein domains
-
Cheek, S., Krishna, S. S., and Grishin, N. V. (2006). Structural classification of small, disulfide-rich protein domains. J. Mol. Biol. 356, 215-237.
-
(2006)
J. Mol. Biol.
, vol.356
, pp. 215-237
-
-
Cheek, S.1
Krishna, S.S.2
Grishin, N.V.3
-
9
-
-
34248396432
-
Global extent of horizontal gene transfer
-
Choi, I. G., and Kim, S. H. (2007). Global extent of horizontal gene transfer. Proc. Natl. Acad. Sci. U.S.A. 104, 4489-4494.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 4489-4494
-
-
Choi, I.G.1
Kim, S.H.2
-
10
-
-
62749097935
-
Genomic and structural aspects of protein evolution
-
Chothia, C., and Gough, J. (2009). Genomic and structural aspects of protein evolution. Biochem. J. 419, 15-28.
-
(2009)
Biochem. J.
, vol.419
, pp. 15-28
-
-
Chothia, C.1
Gough, J.2
-
11
-
-
41049083552
-
Why should we care about molecular coevolution?
-
Cordoñer, F. M., and Fares, M. A. (2008). Why should we care about molecular coevolution? Evol. Bioinformatics 4, 29-38.
-
(2008)
Evol. Bioinformatics
, vol.4
, pp. 29-38
-
-
Cordoñer, F.M.1
Fares, M.A.2
-
12
-
-
17444363410
-
Parsimony and the problem of inap-plicables in sequence data
-
in Parsimony, Phylogeny and Genomics, ed. V. A. Albert (Oxford: Oxford University Press)
-
De Laet, J. (2005). "Parsimony and the problem of inap-plicables in sequence data," in Parsimony, Phylogeny and Genomics, ed. V. A. Albert (Oxford: Oxford University Press), 81-116.
-
(2005)
, pp. 81-116
-
-
De Laet, J.1
-
13
-
-
38949097787
-
Domain tree-based analysis of protein architecture evolution
-
Forslund, K., Henricson, A., Hollich, V., and Sonnhammer, E. L. (2008). Domain tree-based analysis of protein architecture evolution. Mol. Biol. Evol. 25, 254-264.
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 254-264
-
-
Forslund, K.1
Henricson, A.2
Hollich, V.3
Sonnhammer, E.L.4
-
14
-
-
84862105854
-
Genome sizes and the Benford distribution
-
doi: 10.1371/journal.pone.0036624
-
Friar, J. L., Goldman, T., and Pérez-Mercader, J. (2012). Genome sizes and the Benford distribution. PLoS ONE 7, e36624. doi: 10.1371/journal.pone.0036624
-
(2012)
PLoS ONE
, vol.7
-
-
Friar, J.L.1
Goldman, T.2
Pérez-Mercader, J.3
-
15
-
-
17444385984
-
Tracing the evolution of a large protein complex in the eukaryotes. NADH:uniquinone oxidoreductase (Complex I)
-
Gabaldon, T., Rainey, D., and Huynen, M. A. (2005). Tracing the evolution of a large protein complex in the eukaryotes, NADH:uniquinone oxidoreductase (Complex I). J. Mol. Biol. 348, 857-870.
-
(2005)
J. Mol. Biol.
, vol.348
, pp. 857-870
-
-
Gabaldon, T.1
Rainey, D.2
Huynen, M.A.3
-
16
-
-
0032387685
-
Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census
-
Gerstein, M. (1998). Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census. Proteins 33, 518-534.
-
(1998)
Proteins
, vol.33
, pp. 518-534
-
-
Gerstein, M.1
-
17
-
-
17544367678
-
Convergent evolution of domain architectures (is rare)
-
Gough, J. (2005). Convergent evolution of domain architectures (is rare). Bioinformatics 21, 1464-1471.
-
(2005)
Bioinformatics
, vol.21
, pp. 1464-1471
-
-
Gough, J.1
-
18
-
-
84858040413
-
Ribosomal history reveals origins of modern protein synthesis
-
doi: 10.1371/journal.pone.0032776
-
Harish, A., and Caetano-Anollés, G. (2012). Ribosomal history reveals origins of modern protein synthesis. PLoS ONE 7, e32776. doi: 10.1371/journal.pone.0032776
-
(2012)
PLoS ONE
, vol.7
-
-
Harish, A.1
Caetano-Anollés, G.2
-
19
-
-
0030484686
-
Patterns of phylogenetic tree balance with variable or evolving speciation rates
-
Heard, S. B. (1996). Patterns of phylogenetic tree balance with variable or evolving speciation rates. Evolution 50, 2141-2148.
-
(1996)
Evolution
, vol.50
, pp. 2141-2148
-
-
Heard, S.B.1
-
20
-
-
79957884361
-
Scaling properties of protein family phylogenies
-
doi: 10.1186/1471-2148-11-155
-
Herrada, A., Eguiluz, V. M., Hernandez-Garcia, E., and Duarte, C. M. (2011). Scaling properties of protein family phylogenies. BMC Evol. Biol. 11, 155. doi: 10.1186/1471-2148-11-155
-
(2011)
BMC Evol. Biol
, vol.11
, pp. 155
-
-
Herrada, A.1
Eguiluz, V.M.2
Hernandez-Garcia, E.3
Duarte, C.M.4
-
21
-
-
0033824470
-
DaliLite workbench for protein structure comparison
-
Holm, L., and Park, J. (2000). DaliLite workbench for protein structure comparison. Bioinformatics 16, 566-567.
-
(2000)
Bioinformatics
, vol.16
, pp. 566-567
-
-
Holm, L.1
Park, J.2
-
22
-
-
84888206365
-
Protein structure alignment
-
Holm, L., and Sander, C. (1993). Protein structure alignment. J. Mol. Biol. 208, 1-22.
-
(1993)
J. Mol. Biol.
, vol.208
, pp. 1-22
-
-
Holm, L.1
Sander, C.2
-
23
-
-
0033139150
-
Effect of non-independent substitution on phylogenetic accuracy
-
Huelsenbeck, J. P., and Nielsen, R. (1999). Effect of non-independent substitution on phylogenetic accuracy. Syst. Biol. 48, 317-328.
-
(1999)
Syst. Biol.
, vol.48
, pp. 317-328
-
-
Huelsenbeck, J.P.1
Nielsen, R.2
-
24
-
-
77953753370
-
Emergence and evolution of modern molecular functions inferred from phylogenomic analysis of ontological data
-
Kim, K. M., and Caetano-Anollés, G. (2010). Emergence and evolution of modern molecular functions inferred from phylogenomic analysis of ontological data. Mol. Biol. Evol. 27, 1710-1733.
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 1710-1733
-
-
Kim, K.M.1
Caetano-Anollés, G.2
-
25
-
-
84862830777
-
The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms
-
doi: 10.1186/1471-2148-12-13
-
Kim, K. M., and Caetano-Anollés, G. (2012). The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms. BMC Evol. Biol. 12, 13. doi: 10.1186/1471-2148-12-13
-
(2012)
BMC Evol. Biol
, vol.12
, pp. 13
-
-
Kim, K.M.1
Caetano-Anollés, G.2
-
27
-
-
84963036271
-
Quantitative phyletics and the evolution of anurans
-
Kluge, A. G., and Farris, J. S. (1969). Quantitative phyletics and the evolution of anurans. Syst. Zool. 18, 1-32.
-
(1969)
Syst. Zool.
, vol.18
, pp. 1-32
-
-
Kluge, A.G.1
Farris, J.S.2
-
28
-
-
0035367071
-
Protein structure similarities
-
Koehl, P. (2001). Protein structure similarities. Curr. Opin. Struct. Biol. 11, 348-353.
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 348-353
-
-
Koehl, P.1
-
29
-
-
13444279981
-
Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures
-
Kolodny, R., Koehl, P., and Levitt, M. (2005). Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. J. Mol. Biol. 346, 1173-1188.
-
(2005)
J. Mol. Biol.
, vol.346
, pp. 1173-1188
-
-
Kolodny, R.1
Koehl, P.2
Levitt, M.3
-
30
-
-
33744807172
-
The building blocks and motifs of RNA architecture
-
Leontis, N. B., Lescoute, A., and Westhof, E. (2006). The building blocks and motifs of RNA architecture. Curr. Opin. Struct. Biol. 16, 279-287.
-
(2006)
Curr. Opin. Struct. Biol.
, vol.16
, pp. 279-287
-
-
Leontis, N.B.1
Lescoute, A.2
Westhof, E.3
-
31
-
-
67650497792
-
Nature of the protein universe
-
Levitt, M. (2009). Nature of the protein universe. Proc. Natl. Acad. Sci. U.S.A. 106, 11079-11084.
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 11079-11084
-
-
Levitt, M.1
-
32
-
-
12044251313
-
Missing data versus missing characters in phylogenetic analysis
-
Maddison, W. P. (1993). Missing data versus missing characters in phylogenetic analysis. Syst. Biol. 42, 576-581.
-
(1993)
Syst. Biol.
, vol.42
, pp. 576-581
-
-
Maddison, W.P.1
-
33
-
-
65249164850
-
A database of domain definitions for proteins with complex interdomain geometry
-
doi: 10.1371/journal.pone.0005084
-
Majumdar, I., Kinch, L. N., and Grishin, N. V. (2009). A database of domain definitions for proteins with complex interdomain geometry. PLoS ONE 4, e5084. doi: 10.1371/journal.pone.0005084
-
(2009)
PLoS ONE
, vol.4
-
-
Majumdar, I.1
Kinch, L.N.2
Grishin, N.V.3
-
34
-
-
84872567399
-
Biphasic patterns of diversification and the emergence of modules
-
doi: 10.3389/fgene.2012.00147
-
Mittenthal, J. E., Caetano-Anollés, D., and Caetano-Anolles, G. (2012). Biphasic patterns of diversification and the emergence of modules. Front. Genet. 3, 147. doi: 10.3389/fgene.2012.00147
-
(2012)
Front. Genet
, vol.3
, pp. 147
-
-
Mittenthal, J.E.1
Caetano-Anollés, D.2
Caetano-Anolles, G.3
-
35
-
-
0002638760
-
Inferring evolutionary process from the phylogenetic tree shape
-
Mooers, A. O., and Heard, S. B. (1998). Inferring evolutionary process from the phylogenetic tree shape. Q. Rev. Biol. 72, 31-74.
-
(1998)
Q. Rev. Biol.
, vol.72
, pp. 31-74
-
-
Mooers, A.O.1
Heard, S.B.2
-
36
-
-
84855873427
-
The dynamics and evolutionary potential of domain loss and emergence
-
Moore, A. D., and Bornberg-Bauer, E. (2012). The dynamics and evolutionary potential of domain loss and emergence. Mol. Biol. Evol. 29, 787-796.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 787-796
-
-
Moore, A.D.1
Bornberg-Bauer, E.2
-
37
-
-
67449131437
-
Why would phylogeneticists ignore computerized sequence alignment
-
Morrison, D. A. (2009). Why would phylogeneticists ignore computerized sequence alignment? Syst. Biol. 58, 150-158.
-
(2009)
Syst Biol
, vol.58
, pp. 150-158
-
-
Morrison, D.A.1
-
38
-
-
0028961335
-
SCOP: a structural classification of proteins database for the investigation of sequences and structures
-
Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
39
-
-
84865305042
-
Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya
-
doi: 10.1186/1471-2148-12-156
-
Nasir, A., Kim, K. M., and Caetano-Anollés, G. (2012). Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya. BMC Evol. Biol. 12, 156. doi: 10.1186/1471-2148-12-156
-
(2012)
BMC Evol. Biol
, vol.12
, pp. 156
-
-
Nasir, A.1
Kim, K.M.2
Caetano-Anollés, G.3
-
40
-
-
84055190820
-
Annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms
-
Nasir, A., Naeem, A., Khan, M. J., Lopez Nicora, H. D., and Caetano-Anollés, G. (2011). Annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms. Genes 2, 869-911.
-
(2011)
Genes
, vol.2
, pp. 869-911
-
-
Nasir, A.1
Naeem, A.2
Khan, M.J.3
Lopez Nicora, H.D.4
Caetano-Anollés, G.5
-
41
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
Shindyalov, I. N., and Bourne, P. E. (1998). Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 1, 739-747.
-
(1998)
Protein Eng
, vol.1
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
42
-
-
0036416151
-
Testing the hypothesis of common ancestry
-
Sober, E., and Steel, M. (2002). Testing the hypothesis of common ancestry. J. Theor. Biol. 218, 395-408.
-
(2002)
J. Theor. Biol.
, vol.218
, pp. 395-408
-
-
Sober, E.1
Steel, M.2
-
43
-
-
38649093627
-
The origin and evolution of tRNA inferred from phylogenetic analysis of structure
-
Sun, F. J., and Caetano-Anollés, G. (2008). The origin and evolution of tRNA inferred from phylogenetic analysis of structure. J. Mol. Evol. 66, 21-35.
-
(2008)
J. Mol. Evol.
, vol.66
, pp. 21-35
-
-
Sun, F.J.1
Caetano-Anollés, G.2
-
44
-
-
77952276437
-
The ancient history of the structure of ribonuclease P and the early origins of Archaea
-
10.1186/1471-2105-11-153
-
Sun, F. J., and Caetano-Anollés, G. (2010). The ancient history of the structure of ribonuclease P and the early origins of Archaea. BMC Bioinformatics 11, 153. 10.1186/1471-2105-11-153
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 153
-
-
Sun, F.J.1
Caetano-Anollés, G.2
-
45
-
-
34347383961
-
Evolutionary transitions in protein fold space
-
Taylor, W. R. (2007). Evolutionary transitions in protein fold space. Curr. Opin. Struct. Biol. 17, 354-361.
-
(2007)
Curr. Opin. Struct. Biol.
, vol.17
, pp. 354-361
-
-
Taylor, W.R.1
-
46
-
-
72049102605
-
Speciation as an active force in promoting genetic evolution
-
Venditti, C., and Pagel, M. (2010). Speciation as an active force in promoting genetic evolution. Trends Ecol. Evol. 25, 14-20.
-
(2010)
Trends Ecol. Evol.
, vol.25
, pp. 14-20
-
-
Venditti, C.1
Pagel, M.2
-
47
-
-
58149196295
-
The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world
-
Wang, M., and Caetano-Anollés, G. (2009). The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world. Structure 17, 66-78.
-
(2009)
Structure
, vol.17
, pp. 66-78
-
-
Wang, M.1
Caetano-Anollés, G.2
-
48
-
-
78650476811
-
A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation
-
Wang, M., Jiang, Y. -Y., Kim, K. M., Qu, G., Ji, H. -F., Mittenthal, J. E., Zhang, H. -Y., and Caetano-Anollés, G. (2011). A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation. Mol. Biol. Evol. 28, 567-582.
-
(2011)
Mol. Biol. Evol.
, vol.28
, pp. 567-582
-
-
Wang, M.1
Jiang, Y.-Y.2
Kim, K.M.3
Qu, G.4
Ji, H.-F.5
Mittenthal, J.E.6
Zhang, H.-Y.7
Caetano-Anollés, G.8
-
49
-
-
77949513721
-
The evolutionary history of protein domains viewed by species phylogeny
-
doi: 10.1371/journal.pone.0008378
-
Yang, S., and Bourne, P. E. (2009). The evolutionary history of protein domains viewed by species phylogeny. PLoS ONE 4, e8378. doi: 10.1371/journal.pone.0008378
-
(2009)
PLoS ONE
, vol.4
-
-
Yang, S.1
Bourne, P.E.2
-
50
-
-
0036699481
-
Increased taxon sampling greatly reduces phylogenetic error
-
Zwickl, D. J., and Hillis, D. M. (2002). Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51, 588-598.
-
(2002)
Syst. Biol.
, vol.51
, pp. 588-598
-
-
Zwickl, D.J.1
Hillis, D.M.2
|