-
1
-
-
0037304408
-
Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins
-
Anantharaman V, Aravind L, Koonin EV. 2003. Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins. Curr Opin Chem Biol. 7:12-20.
-
(2003)
Curr Opin Chem Biol
, vol.7
, pp. 12-20
-
-
Anantharaman, V.1
Aravind, L.2
Koonin, E.V.3
-
2
-
-
0034667684
-
Plasticity, evolvability, and modularity in RNA
-
Ancel LW, Fontana W. 2000. Plasticity, evolvability, and modularity in RNA. J Exp Zool (Mol Dev Evol). 288:242-283.
-
(2000)
J Exp Zool (Mol Dev Evol)
, vol.288
, pp. 242-283
-
-
Ancel, L.W.1
Fontana, W.2
-
3
-
-
4644335054
-
A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain
-
Aravind L, Iyer LM, Leipe DD, Koonin EV. 2004. A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain. Genome Biol. 5:R30.
-
(2004)
Genome Biol
, vol.5
-
-
Aravind, L.1
Iyer, L.M.2
Leipe, D.D.3
Koonin, E.V.4
-
4
-
-
0034069495
-
Gene Ontology: Tool for the unification of biology
-
Ashburner M, Ball CA, Blake JA, et al. (20 co-authors). 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
-
5
-
-
0031582719
-
Major "anastrophes in the origin and early evolution of biological energy conversion
-
Baltscheffsky H. 1997. Major "Anastrophes in the origin and early evolution of biological energy conversion. J Theor Biol. 187: 495-501.
-
(1997)
J Theor Biol
, vol.187
, pp. 495-501
-
-
Baltscheffsky, H.1
-
6
-
-
0742305866
-
Network biology: Understanding the cell?s functional organization
-
Barabási A-L, Oltvai ZN. 2004. Network biology: understanding the cell?s functional organization. Nat Rev. 5:101-113.
-
(2004)
Nat Rev
, vol.5
, pp. 101-113
-
-
Barabási, A.-L.1
Oltvai, Z.N.2
-
7
-
-
3042728487
-
New strategy for the representation and the integration of biomolecular knowledge at a cellular scale
-
Barriot R, Poix J, Croppi A, Barré A, Goffard N, Sherman D, Dutour I, de Daruvar A. 2004. New strategy for the representation and the integration of biomolecular knowledge at a cellular scale. Nucleic Acids Res. 32:3581-3589.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 3581-3589
-
-
Barriot, R.1
Poix, J.2
Croppi, A.3
Barré, A.4
Goffard, N.5
Sherman, D.6
Dutour, I.7
De Daruvar, A.8
-
9
-
-
12344269924
-
GO:TermFinder\open source software for accessing Gene Ontology information and finding significantly enriched gene ontology terms associated with a list of genes
-
Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G. 2004. GO:TermFinder\open source software for accessing Gene Ontology information and finding significantly enriched gene ontology terms associated with a list of genes. Bio-informatics. 20:3710-3715.
-
(2004)
Bio-informatics
, vol.20
, pp. 3710-3715
-
-
Boyle, E.I.1
Weng, S.2
Gollub, J.3
Jin, H.4
Botstein, D.5
Cherry, J.M.6
Sherlock, G.7
-
10
-
-
0036182064
-
Evolved RNA secondary structure and the rooting of the universal tree of life
-
Caetano-Anollés G. 2002. Evolved RNA secondary structure and the rooting of the universal tree of life. J Mol Evol. 54:333-345.
-
(2002)
J Mol Evol
, vol.54
, pp. 333-345
-
-
Caetano-Anollés, G.1
-
11
-
-
0038486929
-
An evolutionarily structured universe of protein architecture
-
Caetano-Anollés G, 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
-
12
-
-
19944393249
-
Universal sharing patterns in proteomes and evolution of protein fold architecture and life
-
Caetano-Anollés G, Caetano-Anollés D. 2005. Universal sharing patterns in proteomes and evolution of protein fold architecture and life. J Mol Evol. 60:484-498.
-
(2005)
J Mol Evol
, vol.60
, pp. 484-498
-
-
Caetano-Anollés, G.1
Caetano-Anollés, D.2
-
13
-
-
34547170043
-
The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture
-
Caetano-Anollés G, Kim HS, Mittenthal JE. 2007. The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture. Proc Natl Acad Sci USA. 104:9358-9363.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 9358-9363
-
-
Caetano-Anollés, G.1
Kim, H.S.2
Mittenthal, J.E.3
-
14
-
-
59849127275
-
The origin, evolution and structure of the protein world
-
Caetano-Anollés G, Wang M, Caetano-Anollés D, Mittenthal JE. 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
-
15
-
-
56949085134
-
The origin and evolution of modern metabolism
-
Caetano-Anollés G, Yafremava LS, Gee H, Caetano-Anollés D, Kim HS, Mittenthal JE. 2009. The origin and evolution of modern metabolism. Intl J Biochem Cell Biol. 41:285-297.
-
(2009)
Intl J Biochem Cell Biol
, vol.41
, pp. 285-297
-
-
Caetano-Anollés, G.1
Yafremava, L.S.2
Gee, H.3
Caetano-Anollés, D.4
Kim, H.S.5
Mittenthal, J.E.6
-
16
-
-
77952263209
-
Modularity and dissipation in evolution of macromolecular structures, functions, and networks
-
Caetano-Anollés G, editor Hoboken (NJ): Wiley-Blackwell
-
Caetano-Anollés G, Yafremava LS, Mittenthal JE. 2010. Modularity and dissipation in evolution of macromolecular structures, functions, and networks. In: Caetano-Anollés G, editor. Evolutionary genomics and systems biology. Hoboken (NJ): Wiley-Blackwell. p. 431-450.
-
(2010)
Evolutionary Genomics and Systems Biology
, pp. 431-450
-
-
Caetano-Anollés, G.1
Yafremava, L.S.2
Mittenthal, J.E.3
-
17
-
-
34248396432
-
Global extent of horizontal gene transfer
-
Choi I-G, Kim S-H. 2007. Global extent of horizontal gene transfer. Proc Natl Acad Sci USA. 104:4489-4494.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 4489-4494
-
-
Choi, I.-G.1
Kim, S.-H.2
-
18
-
-
47149117454
-
Evolution of genes and genomes on the Drosophila phylogeny
-
Clark AG, Eisen MB, Smith DR, et al. (412 co-authors). 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450:203-218.
-
(2007)
Nature
, vol.450
, pp. 203-218
-
-
Clark, A.G.1
Eisen, M.B.2
Smith, D.R.3
-
19
-
-
48249151749
-
Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution
-
Dagan T, Artzy-Randrup Y, Martin W. 2008. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad Sci USA. 105:10039-10044.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 10039-10044
-
-
Dagan, T.1
Artzy-Randrup, Y.2
Martin, W.3
-
20
-
-
33947725697
-
The extant core bacterial proteome is an archive of the origin of life
-
Danchin A, Fang G, Noria S. 2007. The extant core bacterial proteome is an archive of the origin of life. Proteomics. 7:875-889.
-
(2007)
Proteomics
, vol.7
, pp. 875-889
-
-
Danchin, A.1
Fang, G.2
Noria, S.3
-
21
-
-
77953734706
-
The role of information in evolutionary genomics of bacteria
-
Caetano-Anollés G, editor Hoboken (NJ): Wiley-Blackwell
-
Danchin A, Sekowska A. 2010. The role of information in evolutionary genomics of bacteria. In: Caetano-Anollés G, editor. Evolutionary genomics and systems biology. Hoboken (NJ): Wiley-Blackwell. p. 81-94.
-
(2010)
Evolutionary Genomics and Systems Biology
, pp. 81-94
-
-
Danchin, A.1
Sekowska, A.2
-
23
-
-
17744394753
-
Phylogenomics and the reconstruction of the tree of life
-
Delsuc F, Brinkmann H, Philippe H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 6:361-375.
-
(2005)
Nat Rev Genet
, vol.6
, pp. 361-375
-
-
Delsuc, F.1
Brinkmann, H.2
Philippe, H.3
-
24
-
-
0033603539
-
Phylogenetic classification and the universal tree
-
Doolittle WF. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2129.
-
(1999)
Science
, vol.284
, pp. 2124-2129
-
-
Doolittle, W.F.1
-
25
-
-
20444500847
-
Evolutionary aspects of whole-genome biology
-
Doolittle RF. 2005. Evolutionary aspects of whole-genome biology. Curr Opin Struct Biol. 15:248-253.
-
(2005)
Curr Opin Struct Biol
, vol.15
, pp. 248-253
-
-
Doolittle, R.F.1
-
26
-
-
33845230241
-
Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry
-
Dupont CL, Yang S, Palenik B, Bourne PE. 2006. Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry. Proc Natl Acad Sci USA. 103:17822-17827.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 17822-17827
-
-
Dupont, C.L.1
Yang, S.2
Palenik, B.3
Bourne, P.E.4
-
27
-
-
0033511841
-
Paralogy and the centre of origin concept
-
Ebach MC. 1999. Paralogy and the centre of origin concept. Cladistics 15:387-391.
-
(1999)
Cladistics
, vol.15
, pp. 387-391
-
-
Ebach, M.C.1
-
28
-
-
70349556093
-
Peptide-dominated membranes preceding the genetic takeover by RNA: Latest thinking on a classic controversy
-
Egel R. 2009. Peptide-dominated membranes preceding the genetic takeover by RNA: latest thinking on a classic controversy. BioEssays 31:1100-1109.
-
(2009)
BioEssays
, vol.31
, pp. 1100-1109
-
-
Egel, R.1
-
29
-
-
4143093598
-
A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes
-
Esser C, Ahmadinejad N, Wiegand C, et al. (15 co-authors). 2004. A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol. 21:1643-1660.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 1643-1660
-
-
Esser, C.1
Ahmadinejad, N.2
Wiegand, C.3
-
30
-
-
0000122573
-
PHYLIP (Phylogeny inference package)
-
Felsenstein J. 1989. PHYLIP (Phylogeny inference package). Cladistics. 5:164-166.
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
33
-
-
0033670249
-
Horizontal gene transfer in bacterial and archaeal complete genomes
-
Garcia-Vallvé S, Romeu A, Palau J. 2000. Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res. 10:1719-1725.
-
(2000)
Genome Res
, vol.10
, pp. 1719-1725
-
-
Garcia-Vallvé, S.1
Romeu, A.2
Palau, J.3
-
35
-
-
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
-
36
-
-
0035798406
-
Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
-
Gough J, Karplus K, Hughey R, Chothia C. 2001. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol. 313:903-919.
-
(2001)
J Mol Biol
, vol.313
, pp. 903-919
-
-
Gough, J.1
Karplus, K.2
Hughey, R.3
Chothia, C.4
-
37
-
-
0033428970
-
Helicase motifs: The engine that powers DNA unwinding
-
Hall MC, Matson SW. 1999. Helicase motifs: the engine that powers DNA unwinding. Mol Microbiol. 34:867-877.
-
(1999)
Mol Microbiol
, vol.34
, pp. 867-877
-
-
Hall, M.C.1
Matson, S.W.2
-
38
-
-
0346801873
-
The Gene Ontology (GO) database and informatics resource
-
Harris MA, Clark J, Ireland A, et al. (59 co-authors). 2004. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32:D258-D261.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Harris, M.A.1
Clark, J.2
Ireland, A.3
-
41
-
-
0000470352
-
Primary homology assessment, characters and character states
-
Hawkins JA, Hughes CE, Scotland RW. 1997. Primary homology assessment, characters and character states. Cladistics 13:275-283.
-
(1997)
Cladistics
, vol.13
, pp. 275-283
-
-
Hawkins, J.A.1
Hughes, C.E.2
Scotland, R.W.3
-
42
-
-
0027055554
-
Signal, noise, and reliability in molecular phylogenetic analyses
-
Hillis DM, Huelsenbeck JP. 1992. Signal, noise, and reliability in molecular phylogenetic analyses. J Hered. 83:189-195.
-
(1992)
J Hered
, vol.83
, pp. 189-195
-
-
Hillis, D.M.1
Huelsenbeck, J.P.2
-
43
-
-
0642344263
-
Duplication is more common among laterally transferred genes than among indigenous genes
-
Hooper SD, Berg OG. 2003. Duplication is more common among laterally transferred genes than among indigenous genes. Genome Biol. 4:R48.
-
(2003)
Genome Biol
, vol.4
-
-
Hooper, S.D.1
Berg, O.G.2
-
44
-
-
33750443637
-
A-Hydroxy and a-amino acids under possible Hadean, volcanic origin-of-life conditions
-
Huber C, Wächtershäuser G. 2007. a-Hydroxy and a-amino acids under possible Hadean, volcanic origin-of-life conditions. Science 314:630-632.
-
(2007)
Science
, vol.314
, pp. 630-632
-
-
Huber, C.1
Wächtershäuser, G.2
-
45
-
-
33644623020
-
The evolution of information in the major transitions
-
Jablonka E, Lamb MJ. 2006. The evolution of information in the major transitions. J Theor Biol. 239:236-246.
-
(2006)
J Theor Biol
, vol.239
, pp. 236-246
-
-
Jablonka, E.1
Lamb, M.J.2
-
46
-
-
0033616714
-
Horizontal gene transfer among genomes: The complexity hypothesis
-
Jain R, Rivera MC, Lake JA. 1999. Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA. 96:3801-3806.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 3801-3806
-
-
Jain, R.1
Rivera, M.C.2
Lake, J.A.3
-
47
-
-
0038148710
-
Conformational diversity and protein evolution\a 60-year-old hypothesis revisited
-
James LC, Tawfik DS. 2003. Conformational diversity and protein evolution\a 60-year-old hypothesis revisited. Trends Biochem Sci. 28:361-368.
-
(2003)
Trends Biochem Sci
, vol.28
, pp. 361-368
-
-
James, L.C.1
Tawfik, D.S.2
-
49
-
-
0017272554
-
Enzyme recruitment in evolution of new function
-
Jensen RA. 1976. Enzyme recruitment in evolution of new function. Annu Rev Microbiol. 30:409-425.
-
(1976)
Annu Rev Microbiol
, vol.30
, pp. 409-425
-
-
Jensen, R.A.1
-
50
-
-
70349966236
-
Evolutionary formation of new protein folds is linked to metallic cofactor recruitment
-
Ji H-F, Chen L, Jiang Y-Y, Zhang H-Y. 2009. Evolutionary formation of new protein folds is linked to metallic cofactor recruitment. BioEssays 31:975-980.
-
(2009)
BioEssays
, vol.31
, pp. 975-980
-
-
Ji, H.-F.1
Chen, L.2
Jiang, Y.-Y.3
Zhang, H.-Y.4
-
51
-
-
48949094822
-
Organic cofactors participated more frequently than transition metals in redox reactions of primitive proteins
-
Ji H-F, Chen L, Zhang H-Y. 2007. Organic cofactors participated more frequently than transition metals in redox reactions of primitive proteins. BioEssays 30:766-771.
-
(2007)
BioEssays
, vol.30
, pp. 766-771
-
-
Ji, H.-F.1
Chen, L.2
Zhang, H.-Y.3
-
52
-
-
35148837586
-
Distribution patterns of small-molecule ligands in the protein universe and impliations for origin of life and drug discovery
-
Ji H-F, Kong D-X, Shen L, Chen LL, Ma B-G, Zhang H-Y. 2007. Distribution patterns of small-molecule ligands in the protein universe and impliations for origin of life and drug discovery. Genome Biol. 8:R176.
-
(2007)
Genome Biol
, vol.8
-
-
Ji, H.-F.1
Kong, D.-X.2
Shen, L.3
Chen, L.L.4
Ma, B.-G.5
Zhang, H.-Y.6
-
53
-
-
33847126268
-
Protein architecture chronology deduced from structures of amino acid synthases
-
Ji H-F, Zhang H-Y. 2007. Protein architecture chronology deduced from structures of amino acid synthases. J Biomol Struct Dyn. 24:321-323.
-
(2007)
J Biomol Struct Dyn
, vol.24
, pp. 321-323
-
-
Ji, H.-F.1
Zhang, H.-Y.2
-
54
-
-
0037062978
-
The antiquity of RNA-based evolution
-
Joyce GF. 2002. The antiquity of RNA-based evolution. Nature 418:214-221.
-
(2002)
Nature
, vol.418
, pp. 214-221
-
-
Joyce, G.F.1
-
55
-
-
0021277007
-
Evolution of catalytic proteins or on the origin of enzyme species by means of natural selection
-
Kacser H, Beeby R. 1984. Evolution of catalytic proteins or on the origin of enzyme species by means of natural selection. J Mol Evol. 20:38-51.
-
(1984)
J Mol Evol
, vol.20
, pp. 38-51
-
-
Kacser, H.1
Beeby, R.2
-
56
-
-
33748313110
-
MANET: Tracing evolution of protein architecture in metabolic networks
-
Kim HS, Mittenthal J, Caetano-Anollés G. 2006. MANET: tracing evolution of protein architecture in metabolic networks. BMC Bioinformatics. 7:351.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 351
-
-
Kim, H.S.1
Mittenthal, J.2
Caetano-Anollés, G.3
-
57
-
-
55249117540
-
An approach of orthology detection from homologous sequences under minimum evolution
-
Kim KM, Sung S, Caetano-Anollés G, Han JY, Kim H. 2008. An approach of orthology detection from homologous sequences under minimum evolution. Nucleic Acids Res. 36:e110.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Kim, K.M.1
Sung, S.2
Caetano-Anollés, G.3
Han, J.Y.4
Kim, H.5
-
58
-
-
0000941526
-
Quantitative phyletics and the evolution of anurans
-
Kluge AG, Farris JS. 1969. Quantitative phyletics and the evolution of anurans. Syst Zool. 30:1-32.
-
(1969)
Syst Zool
, vol.30
, pp. 1-32
-
-
Kluge, A.G.1
Farris, J.S.2
-
59
-
-
0027480463
-
A superfamily of ATPase with diverse functions containing either classical or deviant ATP-binding motif
-
Koonin EV. 1993. A superfamily of ATPase with diverse functions containing either classical or deviant ATP-binding motif. J Mol Biol. 229:1165-1174.
-
(1993)
J Mol Biol
, vol.229
, pp. 1165-1174
-
-
Koonin, E.V.1
-
60
-
-
0034625235
-
The impact of comparative genomics on our understanding of evolution
-
Koonin EV, Aravind L, Kondrashov AS. 2000. The impact of comparative genomics on our understanding of evolution. Cell 101:573-576.
-
(2000)
Cell
, vol.101
, pp. 573-576
-
-
Koonin, E.V.1
Aravind, L.2
Kondrashov, A.S.3
-
61
-
-
0033941641
-
Protein fold recognition using sequence profiles and its application in structural genomics
-
Koonin EV, Wolf YI, Aravind L. 2000. Protein fold recognition using sequence profiles and its application in structural genomics. Adv Protein Chem. 54:245-275.
-
(2000)
Adv Protein Chem
, vol.54
, pp. 245-275
-
-
Koonin, E.V.1
Wolf, Y.I.2
Aravind, L.3
-
62
-
-
0037022396
-
Redundancy, antiredundancy, and the robustness of genomes
-
Krakauer DC, Plotkin JB. 2002. Redundancy, antiredundancy, and the robustness of genomes. Proc Natl Acad Sci USA. 99:1405-1409.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 1405-1409
-
-
Krakauer, D.C.1
Plotkin, J.B.2
-
64
-
-
0029905462
-
The origin and early evolution of life: Prebiotic chemistry, the pre-RNA world, and time
-
DOI 10.1016/S0092-8674(00)81263-5
-
Lazcano A, Miller SL. 1996. The origin and early evolution of life: prebiotic chemistry, the pre-RNA world, and time. Cell 85:793-798. (Pubitemid 26192133)
-
(1996)
Cell
, vol.85
, Issue.6
, pp. 793-798
-
-
Lazcano, A.1
Miller, S.L.2
-
65
-
-
0036295212
-
Classification and evolution of P-loop GTPases and Related ATPases
-
Leipe DD, Wolf YI, Koonin EV, Aravind L. 2002. Classification and evolution of P-loop GTPases and Related ATPases. J Mol Biol. 317:41-72.
-
(2002)
J Mol Biol
, vol.317
, pp. 41-72
-
-
Leipe, D.D.1
Wolf, Y.I.2
Koonin, E.V.3
Aravind, L.4
-
66
-
-
33847616971
-
Growth of novel protein structural data
-
Levitt M. 2007. Growth of novel protein structural data. Proc Natl Acad Sci USA. 104:3183-3188.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 3183-3188
-
-
Levitt, M.1
-
67
-
-
61349193830
-
Self-sustained replication of an RNA enzyme
-
Lincoln TA, Joyce GF. 2009. Self-sustained replication of an RNA enzyme. Science 323:1229-1232.
-
(2009)
Science
, vol.323
, pp. 1229-1232
-
-
Lincoln, T.A.1
Joyce, G.F.2
-
68
-
-
77349104670
-
Compensatory gene amplification restores fitness after inter-species gene replacements
-
Lind PA, Tobin C, Berg OG, Kurland CG, Andersson DI. 2010. Compensatory gene amplification restores fitness after inter-species gene replacements. Mol Microbiol. 75:1078-1089.
-
(2010)
Mol Microbiol.
, vol.75
, pp. 1078-1089
-
-
Lind, P.A.1
Tobin, C.2
Berg, O.G.3
Kurland, C.G.4
Andersson, D.I.5
-
69
-
-
0033523854
-
A combined algorithm for genome-wide prediction of protein function
-
Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D. 1999. A combined algorithm for genome-wide prediction of protein function. Nature 402:83-86.
-
(1999)
Nature
, vol.402
, pp. 83-86
-
-
Marcotte, E.M.1
Pellegrini, M.2
Thompson, M.J.3
Yeates, T.O.4
Eisenberg, D.5
-
70
-
-
0028961335
-
SCOP: A structural classification of protein database for the investigation of sequences and structures
-
Murzin AG, Brenner SE, Hubbard T, Chothia C. 1995. SCOP: a structural classification of protein 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
-
71
-
-
0031764044
-
Indigo: A World-Wide-Web review of genomes and gene functions
-
Nitschke P, Guerdoux-Jamet P, Chiapello H, Faroux G, Henaut C, Henaut A, Danchin A. 1998. Indigo: a World-Wide-Web review of genomes and gene functions. FEMS Microbiol Rev. 22:207-227.
-
(1998)
FEMS Microbiol Rev
, vol.22
, pp. 207-227
-
-
Nitschke, P.1
Guerdoux-Jamet, P.2
Chiapello, H.3
Faroux, G.4
Henaut, C.5
Henaut, A.6
Danchin, A.7
-
73
-
-
0035843908
-
Genes lost and genes found: Evolution of bacterial pathogenesis and symbiosis
-
Ochman H, Moran NA. 2001. Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292:1096-1098.
-
(2001)
Science
, vol.292
, pp. 1096-1098
-
-
Ochman, H.1
Moran, N.A.2
-
75
-
-
0033739570
-
Self-organizing biochemical cycles
-
Orgel LE. 2000. Self-organizing biochemical cycles. Proc Natl Acad Sci USA. 97:12503-12507.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 12503-12507
-
-
Orgel, L.E.1
-
76
-
-
0033055062
-
The use of gene clusters to infer functional coupling
-
Overbeek R, Fonstein M, D?Souza M, Pusch GD, Maltsev N. 1999. The use of gene clusters to infer functional coupling. Proc Natl Acad Sci USA. 96:2896-2901.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 2896-2901
-
-
Overbeek, R.1
Fonstein, M.2
Dsouza, M.3
Pusch, G.D.4
Maltsev, N.5
-
77
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
-
Pellegrini M, Marcotte ED, Thompson MJ, Eisenberg D, Yeates TO. 1999. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA. 96:4285-4288.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 4285-4288
-
-
Pellegrini, M.1
Marcotte, E.D.2
Thompson, M.J.3
Eisenberg, D.4
Yeates, T.O.5
-
78
-
-
22744439567
-
The evolution of connectivity in metabolic networks
-
Pfeiffer T, Soyer OS, Bonhoeffer S. 2005. The evolution of connectivity in metabolic networks. PLoS Biol. 3:1269-1275.
-
(2005)
PLoS Biol
, vol.3
, pp. 1269-1275
-
-
Pfeiffer, T.1
Soyer, O.S.2
Bonhoeffer, S.3
-
79
-
-
0035425040
-
Intein spread and extinction in evolution
-
Pietrokovski S. 2001. Intein spread and extinction in evolution. Trends Genet. 17:465-472.
-
(2001)
Trends Genet
, vol.17
, pp. 465-472
-
-
Pietrokovski, S.1
-
80
-
-
66149108671
-
Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions
-
Powner MW, Gerland B, Sutherland JD. 2009. Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459:171-172.
-
(2009)
Nature
, vol.459
, pp. 171-172
-
-
Powner, M.W.1
Gerland, B.2
Sutherland, J.D.3
-
83
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction network
-
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction network. Genome Res. 13:2498-2504.
-
(2003)
Genome Res
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
84
-
-
0036678862
-
Waddington?s canalization revisited: Developmental stability and evolution
-
Siegal ML, Bergman A. 2002. Waddington?s canalization revisited: developmental stability and evolution. Proc Natl Acad Sci USA. 99:10528-10532.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 10528-10532
-
-
Siegal, M.L.1
Bergman, A.2
-
86
-
-
41849150727
-
Evolutionary patterns in the sequences and structure of transfer RNA: Early origins of Archaea and Viruses
-
Sun F-J, Caetano-Anollés G. 2008. Evolutionary patterns in the sequences and structure of transfer RNA: early origins of Archaea and Viruses. PLoS Comput Biol. 4:e1000018.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Sun, F.-J.1
Caetano-Anollés, G.2
-
87
-
-
72449132771
-
The evolutionary history of the structure of 5S ribosomal RNA
-
Sun F-J, Caetano-Anollés G. 2009. The evolutionary history of the structure of 5S ribosomal RNA. J Mol Evol. 69:430-443.
-
(2009)
J Mol Evol
, vol.69
, pp. 430-443
-
-
Sun, F.-J.1
Caetano-Anollés, G.2
-
88
-
-
84885535303
-
Phylogenetic utility of RNA structure: Evolution?s arrow and emergence of early biochemistry and diversified life
-
Caetano-Anollés G, editor Hoboken (NJ): Wiley-Blackwell
-
Sun F-J, Harish A, Caetano-Anollés G. 2010. Phylogenetic utility of RNA structure: evolution?s arrow and emergence of early biochemistry and diversified life. In: Caetano-Anollés G, editor. Evolutionary genomics and systems biology. Hoboken (NJ): Wiley-Blackwell. p. 329-360.
-
(2010)
Evolutionary Genomics and Systems Biology
, pp. 329-360
-
-
Sun, F.-J.1
Harish, A.2
Caetano-Anollés, G.3
-
90
-
-
0028987952
-
The major evolutionary transitions
-
Szathmáry E, Smith JM. 1995. The major evolutionary transitions. Nature 374:227-232.
-
(1995)
Nature
, vol.374
, pp. 227-232
-
-
Szathmáry, E.1
Smith, J.M.2
-
91
-
-
0042902833
-
The COG database: An updated version includes eukaryotes
-
Tatusov RL, Fedorova ND, Jackson JD, et al. (17 co-authors). 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 41
-
-
Tatusov, R.L.1
Fedorova, N.D.2
Jackson, J.D.3
-
92
-
-
0032859140
-
Evolution of protein function, from a structural perspective
-
Todd AE, Orengo CA, Thornton JM. 1999. Evolution of protein function, from a structural perspective. Curr Opin Chem Biol. 3:548-556.
-
(1999)
Curr Opin Chem Biol.
, vol.3
, pp. 548-556
-
-
Todd, A.E.1
Orengo, C.A.2
Thornton, J.M.3
-
94
-
-
34249713769
-
On the chemistry and evolution of the pioneer organism
-
Wächtershäuser G. 2007. On the chemistry and evolution of the pioneer organism. Chem Biodivers. 4:584-602.
-
(2007)
Chem Biodivers
, vol.4
, pp. 584-602
-
-
Wächtershäuser, G.1
-
95
-
-
33748311638
-
A phylogenomic reconstruction of the protein world based on a genomic census of protein fold architecture
-
Wang M, Boca SM, Kalelkar R, Mittenthal JE, Caetano-Anollés G. 2006. A phylogenomic reconstruction of the protein world based on a genomic census of protein fold architecture. Complexity 12:27-40.
-
(2006)
Complexity
, vol.12
, pp. 27-40
-
-
Wang, M.1
Boca, S.M.2
Kalelkar, R.3
Mittenthal, J.E.4
Caetano-Anollés, G.5
-
96
-
-
33750951499
-
Global phylogeny determined by the combination of protein domains in proteomes
-
Wang M, Caetano-Anollés G. 2006. Global phylogeny determined by the combination of protein domains in proteomes. Mol Biol Evol. 23:2444-2454.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 2444-2454
-
-
Wang, M.1
Caetano-Anollés, G.2
-
97
-
-
58149196295
-
The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world
-
Wang M, 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
-
98
-
-
35948990789
-
Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world
-
Wang M, Yafremava LS, Caetano-Anollés D, Mittenthal JE, Caetano-Anollés G. 2007. Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world. Genome Res. 17:1572-1585.
-
(2007)
Genome Res
, vol.17
, pp. 1572-1585
-
-
Wang, M.1
Yafremava, L.S.2
Caetano-Anollés, D.3
Mittenthal, J.E.4
Caetano-Anollés, G.5
-
99
-
-
33846044585
-
The Superfamily database in 2007: Families and functions
-
Wilson D, Madera M, Vogel C, Chothia C, Gough J. 2007. The Superfamily database in 2007: families and functions. Nucleic Acids Res. 35:D308-D313.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Wilson, D.1
Madera, M.2
Vogel, C.3
Chothia, C.4
Gough, J.5
-
101
-
-
77949513721
-
The evolutionary history of protein domains viewed by species phylogeny
-
Yang S, Bourne PE. 2009. The evolutionary history of protein domains viewed by species phylogeny. PLoS One 4:e8378.
-
(2009)
PLoS One
, vol.4
-
-
Yang, S.1
Bourne, P.E.2
-
103
-
-
0015980083
-
On earlier states of the biochemical system
-
Ycas M. 1974. On earlier states of the biochemical system. J Theor Biol. 44:145-160.
-
(1974)
J Theor Biol
, vol.44
, pp. 145-160
-
-
Ycas, M.1
-
104
-
-
0032811061
-
Gradual development of protein-like global structures through functional selection
-
Yomo T, Saito S, Sasai M. 1999. Gradual development of protein-like global structures through functional selection. Nat Struct Biol. 6:743-746.
-
(1999)
Nat Struct Biol
, vol.6
, pp. 743-746
-
-
Yomo, T.1
Saito, S.2
Sasai, M.3
|