-
2
-
-
0031736121
-
Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles
-
Aravind, L., R. L. Tatusov, Y. I. Wolf, D. R. Walker, and E. V. Koonin. 1998. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet. 14:442-444.
-
(1998)
Trends Genet.
, vol.14
, pp. 442-444
-
-
Aravind, L.1
Tatusov, R.L.2
Wolf, Y.I.3
Walker, D.R.4
Koonin, E.V.5
-
3
-
-
0036137155
-
Eubacterial phylogeny based on translational apparatus proteins
-
Brochier, C., E. Bapteste, D. Moreira, and H. Philippe. 2002. Eubacterial phylogeny based on translational apparatus proteins. Trends Genet. 18:1-5.
-
(2002)
Trends Genet.
, vol.18
, pp. 1-5
-
-
Brochier, C.1
Bapteste, E.2
Moreira, D.3
Philippe, H.4
-
4
-
-
0034565944
-
The evolutionary history of ribosomal protein RpS14: Horizontal gene transfer at the heart of the ribosome
-
Brochier, C., H. Philippe, and D. Moreira. 2000. The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome. Trends Genet. 16:529-533.
-
(2000)
Trends Genet.
, vol.16
, pp. 529-533
-
-
Brochier, C.1
Philippe, H.2
Moreira, D.3
-
5
-
-
0037373563
-
The modern molecular clock
-
Bromham, L., and D. Penny. 2003. The modern molecular clock. Nat. Rev. Genet. 4:216-224.
-
(2003)
Nat. Rev. Genet.
, vol.4
, pp. 216-224
-
-
Bromham, L.1
Penny, D.2
-
6
-
-
0037306453
-
Ancient horizontal gene transfer
-
Brown, J. R. 2003. Ancient horizontal gene transfer. Nat. Rev. Genet. 4:121-132.
-
(2003)
Nat. Rev. Genet.
, vol.4
, pp. 121-132
-
-
Brown, J.R.1
-
7
-
-
0036210883
-
Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores
-
Clarke, G. D., R. G. Beiko, M. A. Ragan, and R. L. Charlebois. 2002. Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J. Bacteriol. 184:2072-2080.
-
(2002)
J. Bacteriol.
, vol.184
, pp. 2072-2080
-
-
Clarke, G.D.1
Beiko, R.G.2
Ragan, M.A.3
Charlebois, R.L.4
-
8
-
-
0034100202
-
Understanding the overdispersed molecular clock
-
Cutler, D. J. 2000. Understanding the overdispersed molecular clock. Genetics 154:1403-1417.
-
(2000)
Genetics
, vol.154
, pp. 1403-1417
-
-
Cutler, D.J.1
-
9
-
-
0042027842
-
Phylogenetics and the cohesion of bacterial genomes
-
Daubin, V., N. A. Moran, and H. Ochntan. 2003. Phylogenetics and the cohesion of bacterial genomes. Science 301:829-832.
-
(2003)
Science
, vol.301
, pp. 829-832
-
-
Daubin, V.1
Moran, N.A.2
Ochntan, H.3
-
10
-
-
0031769997
-
Evolutionary anomalies among the aminoacyl-tRNA synthetases
-
Doolittle, R. F., and J. Handy. 1998. Evolutionary anomalies among the aminoacyl-tRNA synthetases. Curr. Opin. Genet. Dev. 8:630-636.
-
(1998)
Curr. Opin. Genet. Dev.
, vol.8
, pp. 630-636
-
-
Doolittle, R.F.1
Handy, J.2
-
12
-
-
0033603539
-
Phylogenetic classification and the universal tree
-
Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2129.
-
(1999)
Science
, vol.284
, pp. 2124-2129
-
-
Doolittle, W.F.1
-
13
-
-
0035546129
-
The neutral theory in the genomic era
-
Fay, J. C., and C. I. Wu. 2001. The neutral theory in the genomic era. Curr. Opin. Genet. Dev. 11:642-646.
-
(2001)
Curr. Opin. Genet. Dev.
, vol.11
, pp. 642-646
-
-
Fay, J.C.1
Wu, C.I.2
-
15
-
-
0029901637
-
Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods
-
Felsenstein, J. 1996. Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol. 266:418-427.
-
(1996)
Methods Enzymol.
, vol.266
, pp. 418-427
-
-
Felsenstein, J.1
-
16
-
-
0014800108
-
Distinguishing homologous from analogous proteins
-
Fitch, W. M. 1970. Distinguishing homologous from analogous proteins. Syst. Zool. 19:99-106.
-
(1970)
Syst. Zool.
, vol.19
, pp. 99-106
-
-
Fitch, W.M.1
-
17
-
-
0036139471
-
Eukaryotic genes in Mycobacterium tuberculosis could have a role in pathogenesis and immunomodulation
-
Gamieldien, J., A. Ptitsyn, and W. Hide. 2002. Eukaryotic genes in Mycobacterium tuberculosis could have a role in pathogenesis and immunomodulation. Trends Genet. 18:5-8.
-
(2002)
Trends Genet.
, vol.18
, pp. 5-8
-
-
Gamieldien, J.1
Ptitsyn, A.2
Hide, W.3
-
19
-
-
0021715830
-
The molecular clock may be an episodic clock
-
Gillespie, J. H. 1984. The molecular clock may be an episodic clock. Proc. Natl. Acad. Sci. USA 81:8009-8013.
-
(1984)
Proc. Natl. Acad. Sci. USA
, vol.81
, pp. 8009-8013
-
-
Gillespie, J.H.1
-
21
-
-
0033858110
-
From complete genomes to measures of substitution rate variability within and between proteins
-
Grishin, N. V., Y. I. Wolf, and E. V. Koonin. 2000. From complete genomes to measures of substitution rate variability within and between proteins. Genome Res. 10:991-1000.
-
(2000)
Genome Res.
, vol.10
, pp. 991-1000
-
-
Grishin, N.V.1
Wolf, Y.I.2
Koonin, E.V.3
-
22
-
-
0033859839
-
Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: Influence of excluding poorly alignable sites from analysis
-
Hansmann, S., and W. Martin. 2000. Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis. Int. J. Syst. Evol. Microbiol. 50:1655-1663.
-
(2000)
Int. J. Syst. Evol. Microbiol.
, vol.50
, pp. 1655-1663
-
-
Hansmann, S.1
Martin, W.2
-
23
-
-
0028304908
-
On global sequence alignment
-
Huang, X. 1994. On global sequence alignment. Comput. Appl. Biosci. 10:227-235.
-
(1994)
Comput. Appl. Biosci.
, vol.10
, pp. 227-235
-
-
Huang, X.1
-
24
-
-
2942576138
-
Evolution of bacterial RNA polymerase: Implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer
-
Iyer, L. M., E. V. Koonin, and L. Aravind. 2004. Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. Gene 335:73-88.
-
(2004)
Gene
, vol.335
, pp. 73-88
-
-
Iyer, L.M.1
Koonin, E.V.2
Aravind, L.3
-
25
-
-
0033616714
-
Horizontal gene transfer among genomes: The complexity hypothesis
-
Jain, R., M. C. Rivera, and J. A. Lake. 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
-
27
-
-
0242606207
-
Horizontal gene transfer: The path to maturity
-
Koonin, E. V. 2003. Horizontal gene transfer: the path to maturity. Mol. Microbiol. 50:725-727.
-
(2003)
Mol. Microbiol.
, vol.50
, pp. 725-727
-
-
Koonin, E.V.1
-
28
-
-
16444381885
-
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
-
Koonin, E. V., N. D. Fedorova, J. D. Jackson, A. R. Jacobs, D. M. Krylov, K. S. Makarova, R. Mazumder, S. L. Mekhedov, A. N. Nikolskaya, B. S. Rao, I. B. Rogozin, S. Smirnov, A. V. Sorokin, A. V. Sverdlov, S. Vasudevan, Y. I. Wolf, J. J. Yin, and D. A. Natale. 2004. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol. 5:R7.
-
(2004)
Genome Biol.
, vol.5
-
-
Koonin, E.V.1
Fedorova, N.D.2
Jackson, J.D.3
Jacobs, A.R.4
Krylov, D.M.5
Makarova, K.S.6
Mazumder, R.7
Mekhedov, S.L.8
Nikolskaya, A.N.9
Rao, B.S.10
Rogozin, I.B.11
Smirnov, S.12
Sorokin, A.V.13
Sverdlov, A.V.14
Vasudevan, S.15
Wolf, Y.I.16
Yin, J.J.17
Natale, D.A.18
-
30
-
-
0034780910
-
Horizontal gene transfer in prokaryotes: Quantification and classification
-
Koonin, E. V., K. S. Makarova, and L. Aravind. 2001. Horizontal gene transfer in prokaryotes: quantification and classification. Annu. Rev. Microbiol. 55:709-742.
-
(2001)
Annu. Rev. Microbiol.
, vol.55
, pp. 709-742
-
-
Koonin, E.V.1
Makarova, K.S.2
Aravind, L.3
-
31
-
-
0034992826
-
The closest BLAST hit is often not the nearest neighbor
-
Koski, L. B., and G. B. Golding. 2001. The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol. 52:540-542.
-
(2001)
J. Mol. Evol.
, vol.52
, pp. 540-542
-
-
Koski, L.B.1
Golding, G.B.2
-
32
-
-
0242490943
-
Lateral gene transfer: When will adolescence end?
-
Lawrence, J. G., and H. Hendrickson. 2003. Lateral gene transfer: when will adolescence end? Mol. Microbiol. 50:739-749.
-
(2003)
Mol. Microbiol.
, vol.50
, pp. 739-749
-
-
Lawrence, J.G.1
Hendrickson, H.2
-
33
-
-
1342271382
-
From gene trees to organismal phylogeny in prokaryotes: The case of the gamma-proteobacteria
-
Lerat, E., V. Daubin, and N. A. Moran. 2003. From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-proteobacteria. PLoS Biol. 1:E19.
-
(2003)
PLoS Biol.
, vol.1
-
-
Lerat, E.1
Daubin, V.2
Moran, N.A.3
-
34
-
-
0035225012
-
Two C or not two C: Recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins
-
RESEARCH 0033
-
Makarova, K. S., V. A. Ponomarev, and E. V. Koonin. 2001. Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins. Genome Biol. 2:RESEARCH 0033.
-
(2001)
Genome Biol.
, vol.2
-
-
Makarova, K.S.1
Ponomarev, V.A.2
Koonin, E.V.3
-
35
-
-
0023984847
-
Optimal alignments in linear space
-
Myers, E. W., and W. Miller. 1988. Optimal alignments in linear space. Comput. Appl. Biosci. 4:11-17.
-
(1988)
Comput. Appl. Biosci.
, vol.4
, pp. 11-17
-
-
Myers, E.W.1
Miller, W.2
-
36
-
-
0033609333
-
Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima
-
Nelson, K. E., R. A. Clayton, S. R. Gill, M. L. Gwinn, R. J. Dodson, D. H. Haft, E. K. Hickey, J. D. Peterson, W. C. Nelson, K. A. Ketchum, L. McDonald, T. R. Utterback, J. A. Malek, K. D. Linher, M. M. Garrett, A. M. Stewart, M. D. Cotton, M. S. Pratt, C. A. Phillips, D. Richardson, J. Heidelberg, G. G. Sutton, R. D. Fleischmann, J. A. Eisen, C. M. Fraser, et al. 1999. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399:323-329.
-
(1999)
Nature
, vol.399
, pp. 323-329
-
-
Nelson, K.E.1
Clayton, R.A.2
Gill, S.R.3
Gwinn, M.L.4
Dodson, R.J.5
Haft, D.H.6
Hickey, E.K.7
Peterson, J.D.8
Nelson, W.C.9
Ketchum, K.A.10
McDonald, L.11
Utterback, T.R.12
Malek, J.A.13
Linher, K.D.14
Garrett, M.M.15
Stewart, A.M.16
Cotton, M.D.17
Pratt, M.S.18
Phillips, C.A.19
Richardson, D.20
Heidelberg, J.21
Sutton, G.G.22
Fleischmann, R.D.23
Eisen, J.A.24
Fraser, C.M.25
more..
-
37
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame, C., D. G. Higgins, and J. Heringa. 2000. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302:205-217.
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
38
-
-
0034682335
-
Lateral gene transfer and the nature of bacterial innovation
-
Ochman, H., J. G. Lawrence, and E. A. Groisman. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304.
-
(2000)
Nature
, vol.405
, pp. 299-304
-
-
Ochman, H.1
Lawrence, J.G.2
Groisman, E.A.3
-
39
-
-
0001654122
-
Development of neutral and nearly neutral theories
-
Ohta, T., and J. H. Gillespie. 1996. Development of neutral and nearly neutral theories. Theor. Popul. Biol. 49:128-142.
-
(1996)
Theor. Popul. Biol.
, vol.49
, pp. 128-142
-
-
Ohta, T.1
Gillespie, J.H.2
-
40
-
-
0033057517
-
Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer
-
Pouting, C. P., L. Aravind, J. Schultz, P. Bork, and E. V. Koonin. 1999. Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer. J. Mol. Biol. 289:729-745.
-
(1999)
J. Mol. Biol.
, vol.289
, pp. 729-745
-
-
Pouting, C.P.1
Aravind, L.2
Schultz, J.3
Bork, P.4
Koonin, E.V.5
-
41
-
-
0035943134
-
On surrogate methods for detecting lateral gene transfer
-
Ragan, M. A. 2001. On surrogate methods for detecting lateral gene transfer. FEMS Microbiol. Lett. 201:187-191.
-
(2001)
FEMS Microbiol. Lett.
, vol.201
, pp. 187-191
-
-
Ragan, M.A.1
-
42
-
-
0036205377
-
TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
-
Schmidt, H. A., K. Strimmer, M. Vingron, and A. von Haeseler. 2002. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.
-
(2002)
Bioinformatics
, vol.18
, pp. 502-504
-
-
Schmidt, H.A.1
Strimmer, K.2
Vingron, M.3
Von Haeseler, A.4
-
44
-
-
0036889686
-
Orthology, paralogy and proposed classification for paralog subtypes
-
Sonnhammer, E. L., and E. V. Koonin. 2002. Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet. 18:619-620.
-
(2002)
Trends Genet.
, vol.18
, pp. 619-620
-
-
Sonnhammer, E.L.1
Koonin, E.V.2
-
45
-
-
0036017383
-
Rates of ribosomal RNA evolution are uniquely accelerated in eukaryotes
-
Syvanen, M. 2002. Rates of ribosomal RNA evolution are uniquely accelerated in eukaryotes. J. Mol. Evol. 55:85-91.
-
(2002)
J. Mol. Evol.
, vol.55
, pp. 85-91
-
-
Syvanen, M.1
-
46
-
-
0042902833
-
The COG database: An updated version includes eukaryotes
-
Tatusov, R. L., N. D. Fedorova, J. D. Jackson, A. R. Jacobs, B. Kiryutin, E. V. Koonin, D. M. Krylov, R. Mazumder, S. L. Mekhedov, A. N. Nikolskaya, B. S. Rao, S. Smirnov, A. V. Sverdlov, S. Vasudevan, Y. I. Wolf, J. J. Yin, and D. A. Natale. 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
Jacobs, A.R.4
Kiryutin, B.5
Koonin, E.V.6
Krylov, D.M.7
Mazumder, R.8
Mekhedov, S.L.9
Nikolskaya, A.N.10
Rao, B.S.11
Smirnov, S.12
Sverdlov, A.V.13
Vasudevan, S.14
Wolf, Y.I.15
Yin, J.J.16
Natale, D.A.17
-
47
-
-
0030660581
-
A genomic perspective on protein families
-
Tatusov, R. L., E. V. Koonin, and D. J. Lipman. 1997. A genomic perspective on protein families. Science 278:631-637.
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
48
-
-
0035162592
-
The COG database: New developments in phylogenetic classification of proteins from complete genomes
-
Tatusov, R. L., D. A. Natale, I. V. Garkavtsev, T. A. Tatusova, U. T. Shankavaram, B. S. Rao, B. Kiryutin, M. Y. Galperin, N. D. Fedorova, and E. V. Koonin. 2001. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29:22-28.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 22-28
-
-
Tatusov, R.L.1
Natale, D.A.2
Garkavtsev, I.V.3
Tatusova, T.A.4
Shankavaram, U.T.5
Rao, B.S.6
Kiryutin, B.7
Galperin, M.Y.8
Fedorova, N.D.9
Koonin, E.V.10
-
49
-
-
0034053846
-
Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process
-
Woese, C. R., G. J. Olsen, M. Ibba, and D. Soll. 2000. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol. Mol. Biol. Rev. 64:202-236.
-
(2000)
Microbiol. Mol. Biol. Rev.
, vol.64
, pp. 202-236
-
-
Woese, C.R.1
Olsen, G.J.2
Ibba, M.3
Soll, D.4
-
50
-
-
0032830481
-
Evolution of aminoacyl-tRNA synthetases-analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events
-
Wolf Y. I., L. Aravind, N. V. Grishin, and E. V. Koonin. 1999. Evolution of aminoacyl-tRNA synthetases-analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 9:689-710.
-
(1999)
Genome Res.
, vol.9
, pp. 689-710
-
-
Wolf, Y.I.1
Aravind, L.2
Grishin, N.V.3
Koonin, E.V.4
-
51
-
-
0036719929
-
Genome trees and the tree of life
-
Wolf, Y. I., I. B. Rogozin, N. V. Grishin, and E. V. Koonin. 2002. Genome trees and the tree of life. Trends Genet. 18:472-479.
-
(2002)
Trends Genet.
, vol.18
, pp. 472-479
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Grishin, N.V.3
Koonin, E.V.4
-
52
-
-
0348044549
-
Genome trees constructed using five different approaches suggest new major bacterial clades
-
Wolf, Y. I., I. B. Rogozin, N. V. Grishin, R. L. Tatusov, and E. V. Koonin. 2001. Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol. Biol. 1:8.
-
(2001)
BMC Evol. Biol.
, vol.1
, pp. 8
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Grishin, N.V.3
Tatusov, R.L.4
Koonin, E.V.5
-
53
-
-
0345874732
-
Coelomata and not ecdysozoa: Evidence from genome-wide phylogenetic analysis
-
Wolf, Y. I., I. B. Rogozin, and E. V. Koonin. 2004. Coelomata and not ecdysozoa: evidence from genome-wide phylogenetic analysis. Genome Res. 14:29-36.
-
(2004)
Genome Res.
, vol.14
, pp. 29-36
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Koonin, E.V.3
-
54
-
-
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
-
56
-
-
0002331493
-
Molecular evolution
-
M. Kasha and B. Pullman (ed.). Academic Press, New York, N.Y.
-
Zuckerkandl, E., and L. Pauling. 1962. Molecular evolution, p. 189-225. In M. Kasha and B. Pullman (ed.), Horizons in biochemistry. Academic Press, New York, N.Y.
-
(1962)
Horizons in Biochemistry
, pp. 189-225
-
-
Zuckerkandl, E.1
Pauling, L.2
-
57
-
-
0013776758
-
Molecules as documents of evolutionary history
-
Zuckerkandl, E., and L. Pauling. 1965. Molecules as documents of evolutionary history. J. Theor. Biol. 8:357-366.
-
(1965)
J. Theor. Biol.
, vol.8
, pp. 357-366
-
-
Zuckerkandl, E.1
Pauling, L.2
|