-
1
-
-
0027364941
-
Evolutionarily mobile modules in proteins
-
Doolittle R.F., Bork P. Evolutionarily mobile modules in proteins. Sci Am 1993, 269:50-56.
-
(1993)
Sci Am
, vol.269
, pp. 50-56
-
-
Doolittle, R.F.1
Bork, P.2
-
2
-
-
67650497792
-
Nature of the protein universe
-
Levitt M. Nature of the protein universe. Proc Natl Acad Sci USA 2009, 106:11079-11084.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 11079-11084
-
-
Levitt, M.1
-
3
-
-
25444525409
-
Comparative mapping of sequence-based and structure-based protein domains
-
Zhang Y., Chandonia J.M., Ding C., Holbrook S.R. Comparative mapping of sequence-based and structure-based protein domains. BMC Bioinformatics 2005, 6:77.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 77
-
-
Zhang, Y.1
Chandonia, J.M.2
Ding, C.3
Holbrook, S.R.4
-
4
-
-
50849114838
-
Arrangements in the modular evolution of proteins
-
Moore A.D., Björklund A.K., Ekman D., Bornberg-Bauer E., Elofsson A. Arrangements in the modular evolution of proteins. Trends Biochem Sci 2008, 33:444-451.
-
(2008)
Trends Biochem Sci
, vol.33
, pp. 444-451
-
-
Moore, A.D.1
Björklund, A.K.2
Ekman, D.3
Bornberg-Bauer, E.4
Elofsson, A.5
-
7
-
-
0035816218
-
Domain combinations in archaeal, eubacterial and eukaryotic proteomes
-
Apic G., Gough J., Teichmann S.A. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol 2001, 310:311-325.
-
(2001)
J Mol Biol
, vol.310
, pp. 311-325
-
-
Apic, G.1
Gough, J.2
Teichmann, S.A.3
-
8
-
-
0036340797
-
Randomness, structural uniqueness, modularity and neutral evolution in sequence space of model proteins
-
Bornberg-Bauer E. Randomness, structural uniqueness, modularity and neutral evolution in sequence space of model proteins. Zeitschrift für Physikalische Chemie 2002, 216:139.
-
(2002)
Zeitschrift für Physikalische Chemie
, vol.216
, pp. 139
-
-
Bornberg-Bauer, E.1
-
10
-
-
62749097935
-
Genomic and structural aspects of protein evolution
-
Chothia C., Gough J. Genomic and structural aspects of protein evolution. Biochem J 2009, 419:15-28.
-
(2009)
Biochem J
, vol.419
, pp. 15-28
-
-
Chothia, C.1
Gough, J.2
-
11
-
-
0842268045
-
Supra-domains: evolutionary units larger than single protein domains
-
Vogel C., Berzuini C., Bashton M., Gough J., Teichmann S.A. Supra-domains: evolutionary units larger than single protein domains. J Mol Biol 2004, 336:809-823.
-
(2004)
J Mol Biol
, vol.336
, pp. 809-823
-
-
Vogel, C.1
Berzuini, C.2
Bashton, M.3
Gough, J.4
Teichmann, S.A.5
-
12
-
-
84861434537
-
Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution
-
Kersting A.R., Bornberg-Bauer E., Moore A.D., Grath S. Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution. Genome Biol Evol 2012, 4:316-329.
-
(2012)
Genome Biol Evol
, vol.4
, pp. 316-329
-
-
Kersting, A.R.1
Bornberg-Bauer, E.2
Moore, A.D.3
Grath, S.4
-
13
-
-
84876281976
-
Bornberg-Bauer E: Quantification and functional analysis of modular protein evolution in a dense phylogenetic tree
-
BBA Proteins 2013, in press
-
Moore AD, Grath S, Schüler A, Huylmans AK, Bornberg-Bauer E: Quantification and functional analysis of modular protein evolution in a dense phylogenetic tree. BBA Proteins 2013, in press.
-
-
-
Moore, A.D.1
Grath, S.2
Schüler, A.3
Huylmans, A.K.4
-
14
-
-
17544367678
-
Convergent evolution of domain architectures (is rare)
-
Gough J. Convergent evolution of domain architectures (is rare). Method Biochem Anal 2005, 21:1464-1471.
-
(2005)
Method Biochem Anal
, vol.21
, pp. 1464-1471
-
-
Gough, J.1
-
15
-
-
38949097787
-
Domain tree-based analysis of protein architecture evolution
-
Forslund K., Henricson A., Hollich V., Sonnhammer E.L.L. Domain tree-based analysis of protein architecture evolution. Mol Biol Evol 2008, 25:254-264.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 254-264
-
-
Forslund, K.1
Henricson, A.2
Hollich, V.3
Sonnhammer, E.L.L.4
-
16
-
-
84870662087
-
This déjá vu feeling-analysis of multidomain protein evolution in eukaryotic genomes
-
Zmasek C.M., Godzik A. This déjá vu feeling-analysis of multidomain protein evolution in eukaryotic genomes. PLoS Comput Biol 2012, 8:e1002701.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Zmasek, C.M.1
Godzik, A.2
-
17
-
-
84873192706
-
Repeated evolution of identical domain architecture in metazoan netrin domain-containing proteins
-
Leclère L., Rentzsch F. Repeated evolution of identical domain architecture in metazoan netrin domain-containing proteins. Genome Biol Evol 2012, 4:883-899.
-
(2012)
Genome Biol Evol
, vol.4
, pp. 883-899
-
-
Leclère, L.1
Rentzsch, F.2
-
18
-
-
33646268799
-
Domain deletions and substitutions in the modular protein evolution
-
Weiner J., Beaussart F., Bornberg-Bauer E. Domain deletions and substitutions in the modular protein evolution. FEBS J 2006, 273:2037-2047.
-
(2006)
FEBS J
, vol.273
, pp. 2037-2047
-
-
Weiner, J.1
Beaussart, F.2
Bornberg-Bauer, E.3
-
21
-
-
77956170943
-
Nebulin: a study of protein repeat evolution
-
Björklund A.K., Light S., Sagit R., Elofsson A. Nebulin: a study of protein repeat evolution. J Mol Biol 2010, 402:38-51.
-
(2010)
J Mol Biol
, vol.402
, pp. 38-51
-
-
Björklund, A.K.1
Light, S.2
Sagit, R.3
Elofsson, A.4
-
22
-
-
77955842416
-
Increased sequence conservation of domain repeats in prokaryotic proteins
-
Reshef D., Itzhaki Z., Schueler-Furman O. Increased sequence conservation of domain repeats in prokaryotic proteins. Trends Genet 2010, 26:383-387.
-
(2010)
Trends Genet
, vol.26
, pp. 383-387
-
-
Reshef, D.1
Itzhaki, Z.2
Schueler-Furman, O.3
-
23
-
-
77951848200
-
WD-repeat instability and diversification of the Podospora anserina hnwd non-self recognition gene family
-
Chevanne D., Saupe S.J., Clav C., Paoletti M. WD-repeat instability and diversification of the Podospora anserina hnwd non-self recognition gene family. BMC Evol Biol 2010, 10:134.
-
(2010)
BMC Evol Biol
, vol.10
, pp. 134
-
-
Chevanne, D.1
Saupe, S.J.2
Clav, C.3
Paoletti, M.4
-
24
-
-
25144494777
-
Intragenic tandem repeats generate functional variability
-
Verstrepen K.J., Jansen A., Lewitter F., Fink G.R. Intragenic tandem repeats generate functional variability. Nat Genet 2005, 37:986-990.
-
(2005)
Nat Genet
, vol.37
, pp. 986-990
-
-
Verstrepen, K.J.1
Jansen, A.2
Lewitter, F.3
Fink, G.R.4
-
25
-
-
66649105285
-
Evolution of pathogenicity and sexual reproduction in eight candida genomes
-
Butler G., Rasmussen M.D., Lin M.F., Santos M.A.S., Sakthikumar S., Munro C.A., Rheinbay E., Grabherr M., Forche A., Reedy J.L., Agrafioti I., Arnaud M.B., Bates S., Brown A.J.P., Brunke S., Costanzo M.C., Fitzpatrick D.A., de Groot P.W.J., Harris D., Hoyer L.L., Hube B., Klis F.M., Kodira C., Lennard N., Logue M.E., Martin R., Neiman A.M., Nikolaou E., Quail M.A., Quinn J., Santos M.C., Schmitzberger F.F., Sherlock G., Shah P., Silverstein K.A.T., Skrzypek M.S., Soll D., Staggs R., Stansfield I., Stumpf M.P.H., Sudbery P.E., Srikantha T., Zeng Q., Berman J., Berriman M., Heitman J., Gow N.A.R., Lorenz M.C., Birren B.W., Kellis M., Cuomo C.A. Evolution of pathogenicity and sexual reproduction in eight candida genomes. Nature 2009, 459:657-662.
-
(2009)
Nature
, vol.459
, pp. 657-662
-
-
Butler, G.1
Rasmussen, M.D.2
Lin, M.F.3
Santos, M.A.S.4
Sakthikumar, S.5
Munro, C.A.6
Rheinbay, E.7
Grabherr, M.8
Forche, A.9
Reedy, J.L.10
Agrafioti, I.11
Arnaud, M.B.12
Bates, S.13
Brown, A.J.P.14
Brunke, S.15
Costanzo, M.C.16
Fitzpatrick, D.A.17
de Groot, P.W.J.18
Harris, D.19
Hoyer, L.L.20
Hube, B.21
Klis, F.M.22
Kodira, C.23
Lennard, N.24
Logue, M.E.25
Martin, R.26
Neiman, A.M.27
Nikolaou, E.28
Quail, M.A.29
Quinn, J.30
Santos, M.C.31
Schmitzberger, F.F.32
Sherlock, G.33
Shah, P.34
Silverstein, K.A.T.35
Skrzypek, M.S.36
Soll, D.37
Staggs, R.38
Stansfield, I.39
Stumpf, M.P.H.40
Sudbery, P.E.41
Srikantha, T.42
Zeng, Q.43
Berman, J.44
Berriman, M.45
Heitman, J.46
Gow, N.A.R.47
Lorenz, M.C.48
Birren, B.W.49
Kellis, M.50
Cuomo, C.A.51
more..
-
26
-
-
0242323637
-
Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination
-
Apic G., Huber W., Teichmann S.A. Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination. J Struct Funct Genomics 2003, 4:67-78.
-
(2003)
J Struct Funct Genomics
, vol.4
, pp. 67-78
-
-
Apic, G.1
Huber, W.2
Teichmann, S.A.3
-
27
-
-
84855873427
-
The dynamics and evolutionary potential of domain loss and emergence
-
Moore A.D., Bornberg-Bauer E. The dynamics and evolutionary potential of domain loss and emergence. Mol Biol Evol 2012, 29:787-796.
-
(2012)
Mol Biol Evol
, vol.29
, pp. 787-796
-
-
Moore, A.D.1
Bornberg-Bauer, E.2
-
28
-
-
0018692402
-
The spandrels of san marco and the panglossian paradigm: a critique of the adaptationist programme
-
Gould S.J., Lewontin R.C. The spandrels of san marco and the panglossian paradigm: a critique of the adaptationist programme. Proc R Soc Lond B Biol Sci 1979, 205:581-598.
-
(1979)
Proc R Soc Lond B Biol Sci
, vol.205
, pp. 581-598
-
-
Gould, S.J.1
Lewontin, R.C.2
-
29
-
-
84862907907
-
Evolution at the subgene level: domain rearrangements in the Drosophila phylogeny
-
Wu Y., Rasmussen M., Kellis M. Evolution at the subgene level: domain rearrangements in the Drosophila phylogeny. Mol Biol Evol 2012, 29:689-705.
-
(2012)
Mol Biol Evol
, vol.29
, pp. 689-705
-
-
Wu, Y.1
Rasmussen, M.2
Kellis, M.3
-
30
-
-
77954539775
-
The role of internal duplication in the evolution of multi-domain proteins
-
Nacher J., Hayashida M., Akutsu T. The role of internal duplication in the evolution of multi-domain proteins. Biosystems 2010, 101:127-135.
-
(2010)
Biosystems
, vol.101
, pp. 127-135
-
-
Nacher, J.1
Hayashida, M.2
Akutsu, T.3
-
31
-
-
58149196295
-
The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world
-
Wang M., Caetano-Anolls G. The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world. Structure 2009, 17:66-78.
-
(2009)
Structure
, vol.17
, pp. 66-78
-
-
Wang, M.1
Caetano-Anolls, G.2
-
32
-
-
84873957913
-
Albá MM: Emergence of novel domains in proteins
-
BMC Evol Biol 2013, in press
-
Toll-Riera M, Albá MM: Emergence of novel domains in proteins. BMC Evol Biol 2013, in press.
-
-
-
Toll-Riera, M.1
-
33
-
-
84155175837
-
Quantifying the mechanisms of domain gain in animal proteins
-
Buljan M., Frankish A., Bateman A. Quantifying the mechanisms of domain gain in animal proteins. Genome Biol 2010, 11:R74.
-
(2010)
Genome Biol
, vol.11
-
-
Buljan, M.1
Frankish, A.2
Bateman, A.3
-
34
-
-
0020769933
-
The primitive code and repeats of base oligomers as the primordial protein-encoding sequence
-
Ohno S., Epplen J.T. The primitive code and repeats of base oligomers as the primordial protein-encoding sequence. Proc Natl Acad Sci USA 1983, 80:3391-3395.
-
(1983)
Proc Natl Acad Sci USA
, vol.80
, pp. 3391-3395
-
-
Ohno, S.1
Epplen, J.T.2
-
35
-
-
0042819915
-
Intrinsically unstructured proteins evolve by repeat expansion
-
Tompa P. Intrinsically unstructured proteins evolve by repeat expansion. Bioessays 2003, 25:847-855.
-
(2003)
Bioessays
, vol.25
, pp. 847-855
-
-
Tompa, P.1
-
36
-
-
84857224836
-
Role of low-complexity sequences in the formation of novel protein coding sequences
-
Toll-Riera M., Rado-Trilla N., Martys F., Albà M.M. Role of low-complexity sequences in the formation of novel protein coding sequences. Mol Biol Evol 2012, 29:883-886.
-
(2012)
Mol Biol Evol
, vol.29
, pp. 883-886
-
-
Toll-Riera, M.1
Rado-Trilla, N.2
Martys, F.3
Albà, M.M.4
-
37
-
-
84871231239
-
Dissecting the role of low-complexity regions in the evolution of vertebrate proteins
-
Rado-Trilla N., Albà M.M. Dissecting the role of low-complexity regions in the evolution of vertebrate proteins. BMC Evol Biol 2012, 12:155.
-
(2012)
BMC Evol Biol
, vol.12
, pp. 155
-
-
Rado-Trilla, N.1
Albà, M.M.2
-
38
-
-
80052969570
-
The evolutionary origin of orphan genes
-
Tautz D., Domazet-Loso T. The evolutionary origin of orphan genes. Nat Rev Genet 2011, 12:692-702.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 692-702
-
-
Tautz, D.1
Domazet-Loso, T.2
-
39
-
-
69449089723
-
More than just orphans: are taxonomically-restricted genes important in evolution?
-
Khalturin K., Hemmrich G., Fraune S., Augustin R., Bosch T.C.G. More than just orphans: are taxonomically-restricted genes important in evolution?. Trends Genet 2009, 25:404-413.
-
(2009)
Trends Genet
, vol.25
, pp. 404-413
-
-
Khalturin, K.1
Hemmrich, G.2
Fraune, S.3
Augustin, R.4
Bosch, T.C.G.5
-
40
-
-
79951566081
-
Evolutionary origins of brassicaceae specific genes in Arabidopsis thaliana
-
Donoghue M.T., Keshavaiah C., Swamidatta S.H., Spillane C. Evolutionary origins of brassicaceae specific genes in Arabidopsis thaliana. BMC Evol Biol 2011, 11:47.
-
(2011)
BMC Evol Biol
, vol.11
, pp. 47
-
-
Donoghue, M.T.1
Keshavaiah, C.2
Swamidatta, S.H.3
Spillane, C.4
-
41
-
-
70349645640
-
Recent de novo origin of human protein-coding genes
-
Knowles D.G., McLysaght A. Recent de novo origin of human protein-coding genes. Genome Res 2009, 19:1752-1759.
-
(2009)
Genome Res
, vol.19
, pp. 1752-1759
-
-
Knowles, D.G.1
McLysaght, A.2
-
42
-
-
81755187310
-
De novo origin of human protein-coding genes
-
Wu D.D., Irwin D.M., Zhang Y.P. De novo origin of human protein-coding genes. PLoS Genet 2011, 7:e1002379.
-
(2011)
PLoS Genet
, vol.7
-
-
Wu, D.D.1
Irwin, D.M.2
Zhang, Y.P.3
-
43
-
-
60149097110
-
Origin of primate orphan genes: a comparative genomics approach
-
Toll-Riera M., Bosch N., Bellora N., Castelo R., Armengol L., Estivill X., Albà M.M. Origin of primate orphan genes: a comparative genomics approach. Mol Biol Evol 2009, 26:603-612.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 603-612
-
-
Toll-Riera, M.1
Bosch, N.2
Bellora, N.3
Castelo, R.4
Armengol, L.5
Estivill, X.6
Albà, M.M.7
-
44
-
-
84876523559
-
Bornberg-Bauer E: Mechanisms and dynamics of orphan gene emergence in insect genomes
-
Genome Biol Evol 2013, in press
-
Wissler L, Gadau J, Simola DF, Helmkampf M, Bornberg-Bauer E: Mechanisms and dynamics of orphan gene emergence in insect genomes. Genome Biol Evol 2013, in press.
-
-
-
Wissler, L.1
Gadau, J.2
Simola, D.F.3
Helmkampf, M.4
-
45
-
-
79958071293
-
Metagenomics and the protein universe
-
Godzik A. Metagenomics and the protein universe. Curr Opin Struct Biol 2011, 21:398-403.
-
(2011)
Curr Opin Struct Biol
, vol.21
, pp. 398-403
-
-
Godzik, A.1
-
46
-
-
34247488321
-
On homology searches by protein blast and the characterization of the age of genes
-
Albà M.M., Castresana J. On homology searches by protein blast and the characterization of the age of genes. BMC Evol Biol 2007, 7:53.
-
(2007)
BMC Evol Biol
, vol.7
, pp. 53
-
-
Albà, M.M.1
Castresana, J.2
-
47
-
-
33646559207
-
On the formation of novel genes by duplication in the Caenorhabditis elegans genome
-
Katju V., Lynch M. On the formation of novel genes by duplication in the Caenorhabditis elegans genome. Mol Biol Evol 2006, 23:1056-1067.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 1056-1067
-
-
Katju, V.1
Lynch, M.2
-
48
-
-
75949115003
-
Detection of new protein domains using co-occurrence: application to Plasmodium falciparum
-
Terrapon N., Gascuel O., Marechal E., Breehelin L. Detection of new protein domains using co-occurrence: application to Plasmodium falciparum. Bioinformatics 2009, 25:3077-3083.
-
(2009)
Bioinformatics
, vol.25
, pp. 3077-3083
-
-
Terrapon, N.1
Gascuel, O.2
Marechal, E.3
Breehelin, L.4
-
49
-
-
16344391964
-
Rapid motif-based prediction of circular permutations in multi-domain proteins
-
Weiner J., Thomas G., Bornberg-Bauer E. Rapid motif-based prediction of circular permutations in multi-domain proteins. Bioinformatics (Oxford, England) 2005, 21:932-937.
-
(2005)
Bioinformatics (Oxford, England)
, vol.21
, pp. 932-937
-
-
Weiner, J.1
Thomas, G.2
Bornberg-Bauer, E.3
-
50
-
-
33745585334
-
Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression
-
Levine M.L., Jones C.D., Kern A.D., Lindfors H.A., Begun D.J. Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. Proc Natl Acad Sci USA 2006, 103:9935.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 9935
-
-
Levine, M.L.1
Jones, C.D.2
Kern, A.D.3
Lindfors, H.A.4
Begun, D.J.5
-
51
-
-
77950801106
-
A human-specific de novo protein-coding gene associated with human brain functions
-
Li C.Y., Zhang Y., Wang Z., Zhang Y., Cao C., Zhang P.W., Lu S.J., Li X.M., Yu Q., Zheng X., Du Q., Uhl G.R., Liu Q.R., Wei L. A human-specific de novo protein-coding gene associated with human brain functions. PLoS Comput Biol 2010, 6:e1000734.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Li, C.Y.1
Zhang, Y.2
Wang, Z.3
Zhang, Y.4
Cao, C.5
Zhang, P.W.6
Lu, S.J.7
Li, X.M.8
Yu, Q.9
Zheng, X.10
Du, Q.11
Uhl, G.R.12
Liu, Q.R.13
Wei, L.14
-
52
-
-
84863988094
-
Proto-genes and de novo gene birth
-
Carvunis A.R., Rolland T., Wapinski I., Calderwood M.A., Yildirim M.A., Simonis N., Charloteaux B., Hidalgo C.A., Barbette J., Santhanam B., Brar G.A., Weissman J.S., Regev A., Thierry-Mieg N., Cusick M.E., Vidal M. Proto-genes and de novo gene birth. Nature 2012, 487:370-374.
-
(2012)
Nature
, vol.487
, pp. 370-374
-
-
Carvunis, A.R.1
Rolland, T.2
Wapinski, I.3
Calderwood, M.A.4
Yildirim, M.A.5
Simonis, N.6
Charloteaux, B.7
Hidalgo, C.A.8
Barbette, J.9
Santhanam, B.10
Brar, G.A.11
Weissman, J.S.12
Regev, A.13
Thierry-Mieg, N.14
Cusick, M.E.15
Vidal, M.16
-
53
-
-
84894896330
-
Pervasive antisense transcription is evolutionarily conserved in budding yeast
-
Goodman A.J., Daugharthy E.R., Kim J. Pervasive antisense transcription is evolutionarily conserved in budding yeast. Mol Biol Evol 2012.
-
(2012)
Mol Biol Evol
-
-
Goodman, A.J.1
Daugharthy, E.R.2
Kim, J.3
-
54
-
-
84869060468
-
Evolution of viral proteins originated de novo by overprinting
-
Sabath N., Wagner A., Karlin D. Evolution of viral proteins originated de novo by overprinting. Mol Biol Evol 2012, 29:3767-3780.
-
(2012)
Mol Biol Evol
, vol.29
, pp. 3767-3780
-
-
Sabath, N.1
Wagner, A.2
Karlin, D.3
-
55
-
-
74549184089
-
Functional and evolutionary insights from the genomes of three parasitoid Nasonia species
-
Werren J.H., Richards S., Desjardins C.A., Niehuis O., Gadau J., Colbourne J.K., Beukeboom L.W., Desplan C., Elsik C.G., Grimmelikhuijzen C.J.P., Kitts P., Lynch J.A., Murphy T., Oliveira D.C.S.G., Smith C.D., van de Zande L., Worley K.C., Zdobnov E.M., Aerts M., Albert S., Anaya V.H., Anzola J.M., Barchuk A.R., Behura S.K., Bera A.N., Berenbaum M.R., Bertossa R.C., Bitondi M.M.G., Bordenstein S.R., Bork P., Bornberg-Bauer E., Brunain M., Cazzamali G., Chaboub L., Chacko J., Chavez D., Childers C.P., Choi J.H., Clark M.E., Claudianos C., Clinton R.A., Cree A.G., Cristino A.S., Dang P.M., Darby A.C., de Graaf D.C., Devreese B., Dinh H.H., Edwards R., Elango N., Elhaik E., Ermolaeva O., Evans J.D., Foret S., Fowler G.R., Gerlach D., Gibson J.D., Gilbert D.G., Graur D., Gründer S., Hagen D.E., Han Y., Hauser F., Hultmark D., Hunter H.C., Hurst G.D.D., Jhangian S.N., Jiang H., Johnson R.M., Jones A.K., Junier T., Kadowaki T., Kamping A., Kapustin Y., Kechavarzi B., Kim J., Kim J., Kiryutin B., Koevoets T., Kovar C.L., Kriventseva E.V., Kucharski R., Lee H., Lee S.L., Lees K., Lewis L.R., Loehlin D.W., Logsdon J.M., Lopez J.A., Lozado R.J., Maglott D., Maleszka R., Mayampurath A., Mazur D.J., McClure M.A., Moore A.D., Morgan M.B., Muller J., Munoz-Torres M.C., Muzny D.M., Nazareth L.V., Neupert S., Nguyen N.B., Nunes F.M.F., Oakeshott J.G., Okwuonu G.O., Pannebakker B.A., Pejaver V.R., Peng Z., Pratt S.C., Predel R., Pu L.L., Ranson H., Raychoudhury R., Rechtsteiner A., Reese J.T., Reid J.G., Riddle M., Robertson H.M., Romero-Severson J., Rosenberg M., Sackton T.B., Sattelle D.B., Schlüns H., Schmitt T., Schneider M., Schüler A., Schurko A.M., Shuker D.M., Simes Z.L.P., Sinha S., Smith Z., Solovyev V., Souvorov A., Springauf A., Stafflinger E., Stage D.E., Stanke M., Tanaka Y., Telschow A., Trent C., Vattathil S., Verhulst E.C., Viljakainen L., Wanner K.W., Waterhouse R.M., Whitfield J.B., Wilkes T.E., Williamson M., Willis J.H., Wolschin F., Wyder S., Yamada T., Yi S.V., Zecher C.N., Zhang L., Gibbs R.A. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science 2010, 327:343-348.
-
(2010)
Science
, vol.327
, pp. 343-348
-
-
Werren, J.H.1
Richards, S.2
Desjardins, C.A.3
Niehuis, O.4
Gadau, J.5
Colbourne, J.K.6
Beukeboom, L.W.7
Desplan, C.8
Elsik, C.G.9
Grimmelikhuijzen, C.J.P.10
Kitts, P.11
Lynch, J.A.12
Murphy, T.13
Oliveira, D.C.S.G.14
Smith, C.D.15
van de Zande, L.16
Worley, K.C.17
Zdobnov, E.M.18
Aerts, M.19
Albert, S.20
Anaya, V.H.21
Anzola, J.M.22
Barchuk, A.R.23
Behura, S.K.24
Bera, A.N.25
Berenbaum, M.R.26
Bertossa, R.C.27
Bitondi, M.M.G.28
Bordenstein, S.R.29
Bork, P.30
Bornberg-Bauer, E.31
Brunain, M.32
Cazzamali, G.33
Chaboub, L.34
Chacko, J.35
Chavez, D.36
Childers, C.P.37
Choi, J.H.38
Clark, M.E.39
Claudianos, C.40
Clinton, R.A.41
Cree, A.G.42
Cristino, A.S.43
Dang, P.M.44
Darby, A.C.45
de Graaf, D.C.46
Devreese, B.47
Dinh, H.H.48
Edwards, R.49
Elango, N.50
Elhaik, E.51
Ermolaeva, O.52
Evans, J.D.53
Foret, S.54
Fowler, G.R.55
Gerlach, D.56
Gibson, J.D.57
Gilbert, D.G.58
Graur, D.59
Gründer, S.60
Hagen, D.E.61
Han, Y.62
Hauser, F.63
Hultmark, D.64
Hunter, H.C.65
Hurst, G.D.D.66
Jhangian, S.N.67
Jiang, H.68
Johnson, R.M.69
Jones, A.K.70
Junier, T.71
Kadowaki, T.72
Kamping, A.73
Kapustin, Y.74
Kechavarzi, B.75
Kim, J.76
Kim, J.77
Kiryutin, B.78
Koevoets, T.79
Kovar, C.L.80
Kriventseva, E.V.81
Kucharski, R.82
Lee, H.83
Lee, S.L.84
Lees, K.85
Lewis, L.R.86
Loehlin, D.W.87
Logsdon, J.M.88
Lopez, J.A.89
Lozado, R.J.90
Maglott, D.91
Maleszka, R.92
Mayampurath, A.93
Mazur, D.J.94
McClure, M.A.95
Moore, A.D.96
Morgan, M.B.97
Muller, J.98
Munoz-Torres, M.C.99
more..
-
56
-
-
79960471404
-
Are viruses a source of new protein folds for organisms?-virosphere structure space and evolution
-
Abroi A., Gough J. Are viruses a source of new protein folds for organisms?-virosphere structure space and evolution. Bioessays 2011, 33:626-635.
-
(2011)
Bioessays
, vol.33
, pp. 626-635
-
-
Abroi, A.1
Gough, J.2
-
57
-
-
56449118064
-
Retrocopy contributions to the evolution of the human genome
-
Baertsch R., Diekhans M., James W., Haussler D., Brosius J. Retrocopy contributions to the evolution of the human genome. BMC Genomics 2008, 9:466.
-
(2008)
BMC Genomics
, vol.9
, pp. 466
-
-
Baertsch, R.1
Diekhans, M.2
James, W.3
Haussler, D.4
Brosius, J.5
-
58
-
-
0036838856
-
Construction and characterization of protein libraries composed of secondary structure modules
-
Matsuura T., Ernst A., Plückthun A. Construction and characterization of protein libraries composed of secondary structure modules. Protein Sci Publ Protein Soc 2002, 11:2631-2643.
-
(2002)
Protein Sci Publ Protein Soc
, vol.11
, pp. 2631-2643
-
-
Matsuura, T.1
Ernst, A.2
Plückthun, A.3
-
59
-
-
84861434946
-
The interface of protein structure, protein biophysic, and molecular evolution
-
Liberles D., Teichmann S., Bahar I., Bastolla U., Bloom J., Bornberg-Bauer E., Colwell L., de Koning A., Dokholyan N., Echave J., Elofsson A., Gerloff D., Goldstein R., Grahnen J., Holder M., Lakner C., Lartillot N., Lovell S., Naylor G., Perica T., Pollock D., Pupko T., Regan L., Roger A., Rubinstein N., Shakhnovich E., Sjlander K., Sunyaev S., Teufel A., Thorne J., Thornton, Weinreich D., Wheelan S. The interface of protein structure, protein biophysic, and molecular evolution. Protein Sci 2012, 21:769-785.
-
(2012)
Protein Sci
, vol.21
, pp. 769-785
-
-
Liberles, D.1
Teichmann, S.2
Bahar, I.3
Bastolla, U.4
Bloom, J.5
Bornberg-Bauer, E.6
Colwell, L.7
de Koning, A.8
Dokholyan, N.9
Echave, J.10
Elofsson, A.11
Gerloff, D.12
Goldstein, R.13
Grahnen, J.14
Holder, M.15
Lakner, C.16
Lartillot, N.17
Lovell, S.18
Naylor, G.19
Perica, T.20
Pollock, D.21
Pupko, T.22
Regan, L.23
Roger, A.24
Rubinstein, N.25
Shakhnovich, E.26
Sjlander, K.27
Sunyaev, S.28
Teufel, A.29
Thorne, J.30
Thornton31
Weinreich, D.32
Wheelan, S.33
more..
-
60
-
-
34247224735
-
The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?
-
Zheng D., Gerstein M.B. The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?. Trends Genet 2007, 23:219-224.
-
(2007)
Trends Genet
, vol.23
, pp. 219-224
-
-
Zheng, D.1
Gerstein, M.B.2
-
61
-
-
84857384562
-
Putatively noncoding transcripts show extensive association with ribosomes
-
Wilson B.A., Masel J. Putatively noncoding transcripts show extensive association with ribosomes. Genome Biol Evol 2011, 3:1245-1252.
-
(2011)
Genome Biol Evol
, vol.3
, pp. 1245-1252
-
-
Wilson, B.A.1
Masel, J.2
-
62
-
-
70349270547
-
Emergence of a new gene from an intergenic region
-
Heinen T.J., Staubach F., Häming D., Tautz D. Emergence of a new gene from an intergenic region. Curr Biol 2009, 19:1527-1531.
-
(2009)
Curr Biol
, vol.19
, pp. 1527-1531
-
-
Heinen, T.J.1
Staubach, F.2
Häming, D.3
Tautz, D.4
-
63
-
-
84655169215
-
Wnt gene loss in flatworms
-
Riddiford N., Olson P. Wnt gene loss in flatworms. Dev Genes Evol 2011, 221:187-197.
-
(2011)
Dev Genes Evol
, vol.221
, pp. 187-197
-
-
Riddiford, N.1
Olson, P.2
-
64
-
-
12144288568
-
Myosin gene mutation correlates with anatomical changes in the human lineage
-
Stedman H.H., Kozyak B., Nelson A., Thesier D., Su L., Low D., Bridges C., Shrager J., Minugh-Purvis N., Mitchell M. Myosin gene mutation correlates with anatomical changes in the human lineage. Nature 2004, 428:415-418.
-
(2004)
Nature
, vol.428
, pp. 415-418
-
-
Stedman, H.H.1
Kozyak, B.2
Nelson, A.3
Thesier, D.4
Su, L.5
Low, D.6
Bridges, C.7
Shrager, J.8
Minugh-Purvis, N.9
Mitchell, M.10
-
65
-
-
79951662075
-
Evolution of domain promiscuity in eukaryotic genomes-a perspective from the inferred ancestral domain architectures
-
Cohen-Gihon I., Fong J.H., Sharan R., Nussinov R., Przytycka T.M., Panchenko A.R. Evolution of domain promiscuity in eukaryotic genomes-a perspective from the inferred ancestral domain architectures. Mol Biosyst 2011, 7:784-792.
-
(2011)
Mol Biosyst
, vol.7
, pp. 784-792
-
-
Cohen-Gihon, I.1
Fong, J.H.2
Sharan, R.3
Nussinov, R.4
Przytycka, T.M.5
Panchenko, A.R.6
-
66
-
-
33751204154
-
Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level
-
Pal L.R., Guda C. Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level. BMC Evol Biol 2006, 6:91.
-
(2006)
BMC Evol Biol
, vol.6
, pp. 91
-
-
Pal, L.R.1
Guda, C.2
-
67
-
-
39549096663
-
Evolutionary history and functional implications of protein domains and their combinations in eukaryotes
-
C N.J.
-
Masumi I., C N.J., Kei-ichi K., Goto, Susumo, Minoru K. Evolutionary history and functional implications of protein domains and their combinations in eukaryotes. Genome Biol 2007, 8:R121.
-
(2007)
Genome Biol
, vol.8
-
-
Masumi, I.1
Kei-ichi, K.2
Goto3
Susumo4
Minoru, K.5
-
68
-
-
40449102414
-
Metabolism of halophilic archaea
-
Falb M., Müller K., Königsmaier L., Oberwinkler T., Horn P., von Gronau S., Gonzalez O., Pfeiffer F., Bornberg-Bauer E., Oesterhelt D. Metabolism of halophilic archaea. Extremophiles 2008, 12:177-196.
-
(2008)
Extremophiles
, vol.12
, pp. 177-196
-
-
Falb, M.1
Müller, K.2
Königsmaier, L.3
Oberwinkler, T.4
Horn, P.5
von Gronau, S.6
Gonzalez, O.7
Pfeiffer, F.8
Bornberg-Bauer, E.9
Oesterhelt, D.10
-
69
-
-
84855870527
-
Chimeric genes as a source of rapid evolution in Drosophila melanogaster
-
Rogers R.L., Hartl D.L. Chimeric genes as a source of rapid evolution in Drosophila melanogaster. Mol Biol Evol 2012, 29:517-529.
-
(2012)
Mol Biol Evol
, vol.29
, pp. 517-529
-
-
Rogers, R.L.1
Hartl, D.L.2
-
70
-
-
77951159012
-
Rapid diversification of cell signaling phenotypes by modular domain recombination
-
Peisajovich S.G., Garbarino J.E., Wei P., Lim W.A. Rapid diversification of cell signaling phenotypes by modular domain recombination. Science (New York, NY) 2010, 328:368-372.
-
(2010)
Science (New York, NY)
, vol.328
, pp. 368-372
-
-
Peisajovich, S.G.1
Garbarino, J.E.2
Wei, P.3
Lim, W.A.4
-
71
-
-
2442631981
-
Convergent evolution of gene networks by single-gene duplications in higher eukaryotes
-
Amoutzias G.D., Robertson D.L., Oliver S.G., Bornberg-Bauer E. Convergent evolution of gene networks by single-gene duplications in higher eukaryotes. EMBO Rep 2004, 5:274-279.
-
(2004)
EMBO Rep
, vol.5
, pp. 274-279
-
-
Amoutzias, G.D.1
Robertson, D.L.2
Oliver, S.G.3
Bornberg-Bauer, E.4
-
72
-
-
77949912922
-
On the origin of MADS-domain transcription factors
-
Gramzow L., Ritz M.S., Theissen G. On the origin of MADS-domain transcription factors. Trends Genet 2010, 26:149-153.
-
(2010)
Trends Genet
, vol.26
, pp. 149-153
-
-
Gramzow, L.1
Ritz, M.S.2
Theissen, G.3
-
73
-
-
75549086174
-
Eukaryotic protein domains as functional units of cellular evolution
-
Jin J., Xie X., Chen C., Park J.G., Stark C., James D.A., Olhovsky M., Linding R., Mao Y., Pawson T. Eukaryotic protein domains as functional units of cellular evolution. Sci Signal 2009, 2:ra76.
-
(2009)
Sci Signal
, vol.2
-
-
Jin, J.1
Xie, X.2
Chen, C.3
Park, J.G.4
Stark, C.5
James, D.A.6
Olhovsky, M.7
Linding, R.8
Mao, Y.9
Pawson, T.10
-
74
-
-
77957915336
-
Identity and divergence of protein domain architectures after the yeast whole-genome duplication event
-
Grassi L., Fusco D., Sellerio A., Corá D., Bassetti B., Caselle M., Lagomarsino M. Identity and divergence of protein domain architectures after the yeast whole-genome duplication event. Mol Biosyst 2010, 6:2305-2315.
-
(2010)
Mol Biosyst
, vol.6
, pp. 2305-2315
-
-
Grassi, L.1
Fusco, D.2
Sellerio, A.3
Corá, D.4
Bassetti, B.5
Caselle, M.6
Lagomarsino, M.7
-
75
-
-
84864088733
-
Widespread polymorphism in the positions of stop codons in Drosophila melanogaster
-
Lee Y., Reinhardt J. Widespread polymorphism in the positions of stop codons in Drosophila melanogaster. Genome Biol Evol 2012, 4:533-549.
-
(2012)
Genome Biol Evol
, vol.4
, pp. 533-549
-
-
Lee, Y.1
Reinhardt, J.2
-
77
-
-
77958156358
-
How do proteins gain new domains?
-
Marsh j.A., Teichmann S.A. How do proteins gain new domains?. Genome Biol 2010, 11:126.
-
(2010)
Genome Biol
, vol.11
, pp. 126
-
-
Marsh, J.1
Teichmann, S.A.2
-
78
-
-
14844342815
-
The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins
-
Dosztányi Z., Csizmók V., Tompa P., Simon I. The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J Mol Biol 2005, 347:827-839.
-
(2005)
J Mol Biol
, vol.347
, pp. 827-839
-
-
Dosztányi, Z.1
Csizmók, V.2
Tompa, P.3
Simon, I.4
|