-
1
-
-
0021109593
-
A Markov analysis of DNA sequences
-
Almagor, H. 1983. A Markov analysis of DNA sequences. J. Theor. Biol. 104: 633-645.
-
(1983)
J. Theor. Biol.
, vol.104
, pp. 633-645
-
-
Almagor, H.1
-
2
-
-
0026552754
-
DNA mismatch correction by very short patch repair may have altered the abundance of oligonucleotides in the E. coli genome
-
Bhagwat, A.S. and McClelland, M. 1992. DNA mismatch correction by very short patch repair may have altered the abundance of oligonucleotides in the E. coli genome. Nucleic Acids Res. 20: 1663-1668.
-
(1992)
Nucleic Acids Res.
, vol.20
, pp. 1663-1668
-
-
Bhagwat, A.S.1
McClelland, M.2
-
3
-
-
0026502711
-
Over- And under-representation of short oligonucleotides in DNA sequences
-
Burge, C., Campbell, A.M., and Karlin, S. 1992. Over- and under-representation of short oligonucleotides in DNA sequences. Proc. Natl. Acad. Sci. 89: 1358-1362.
-
(1992)
Proc. Natl. Acad. Sci.
, vol.89
, pp. 1358-1362
-
-
Burge, C.1
Campbell, A.M.2
Karlin, S.3
-
4
-
-
0028028028
-
Computational DNA sequence analysis
-
Cardon, L.R. and Karlin, S. 1994. Computational DNA sequence analysis. Annu. Rev. Microbiol. 48: 619-654.
-
(1994)
Annu. Rev. Microbiol.
, vol.48
, pp. 619-654
-
-
Cardon, L.R.1
Karlin, S.2
-
5
-
-
0033603539
-
Phylogenetic classification and the universal tree
-
Doolittle, W.F. 1999. Phylogenetic classification and the universal tree. Science 284: 2124-2128.
-
(1999)
Science
, vol.284
, pp. 2124-2128
-
-
Doolittle, W.F.1
-
6
-
-
0033783996
-
Assessing evolutionary relationships among microbes from whole-genome analysis
-
Eisen, J.A. 2000a. Assessing evolutionary relationships among microbes from whole-genome analysis. Curr. Opin. Microbiol. 3: 475-480.
-
(2000)
Curr. Opin. Microbiol.
, vol.3
, pp. 475-480
-
-
Eisen, J.A.1
-
7
-
-
0033669672
-
Horizontal gene transfer among microbial genomes: New insights from complete genome analysis
-
Eisen, J.A. 2000b. Horizontal gene transfer among microbial genomes: New insights from complete genome analysis. Curr. Opin. Genet. Dev. 10: 606-611.
-
(2000)
Curr. Opin. Genet. Dev.
, vol.10
, pp. 606-611
-
-
Eisen, J.A.1
-
8
-
-
0035793056
-
Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences
-
Feil, E.J., Holmes, E.C., Bessen, D.E., Chan, M.-S., Day, N.P.J., Enright, M.C., Goldstein, R., Hood, D.W., Kalia, A., Moore, C.E., et al. 2001. Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences. Proc. Natl. Acad. Sci. 98: 182-187.
-
(2001)
Proc. Natl. Acad. Sci.
, vol.98
, pp. 182-187
-
-
Feil, E.J.1
Holmes, E.C.2
Bessen, D.E.3
Chan, M.-S.4
Day, N.P.J.5
Enright, M.C.6
Goldstein, R.7
Hood, D.W.8
Kalia, A.9
Moore, C.E.10
-
10
-
-
0033231209
-
Whole-genome based phylogenetic analysis of free-living microorganisms
-
Fitz-Gibbon, S.T. and House, C.H. 1999. Whole-genome based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res. 27: 4218-4222.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 4218-4222
-
-
Fitz-Gibbon, S.T.1
House, C.H.2
-
11
-
-
0030740993
-
Avoidance of palindromic words in bacterial and archaeal genome: A close connection with restriction enzymes
-
Gelfand, M.S. and Koonin, E.V. 1997. Avoidance of palindromic words in bacterial and archaeal genome: A close connection with restriction enzymes. Nucleic Acids Res. 25: 2430-2439.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 2430-2439
-
-
Gelfand, M.S.1
Koonin, E.V.2
-
12
-
-
0019519371
-
Codon catalog usage is a genome strategy modulated for gene expressivity
-
Grantham, R., Gautier, C., Guoy, M., Jacobzone, M., and Mercier, R. 1981. Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Res. 9: R43-R74.
-
(1981)
Nucleic Acids Res.
, vol.9
-
-
Grantham, R.1
Gautier, C.2
Guoy, M.3
Jacobzone, M.4
Mercier, R.5
-
13
-
-
0020363515
-
Preferential codon usage in prokaryotic genes: The optimal codon-anti-codon interaction energy and the selective codon usage in efficiently expressed genes
-
Grosjean, H. and Freirs, W. 1982. Preferential codon usage in prokaryotic genes: The optimal codon-anti-codon interaction energy and the selective codon usage in efficiently expressed genes. Gene 18: 199-209.
-
(1982)
Gene
, vol.18
, pp. 199-209
-
-
Grosjean, H.1
Freirs, W.2
-
14
-
-
17144462135
-
DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae
-
Heidelberg, J.F., Eisen, J.A., Nelson, W.C., Clayton, R.A., Gwinn, M.L., Dodson, R.J., Haft, D.H., Hickey, E.K., Peterson, J.D., Umayam, L., et al. 2000. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406: 477-483.
-
(2000)
Nature
, vol.406
, pp. 477-483
-
-
Heidelberg, J.F.1
Eisen, J.A.2
Nelson, W.C.3
Clayton, R.A.4
Gwinn, M.L.5
Dodson, R.J.6
Haft, D.H.7
Hickey, E.K.8
Peterson, J.D.9
Umayam, L.10
-
15
-
-
0343586537
-
Uneven distribution of GATC motifs in the Escherichia coli chromosome, its plasmids and its phages
-
Henaut, A., Rouxel, T., Gleizes, A., Moszer, I., and Danchin, A. 1996. Uneven distribution of GATC motifs in the Escherichia coli chromosome, its plasmids and its phages. J. Mol. Biol. 257: 574-585.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 574-585
-
-
Henaut, A.1
Rouxel, T.2
Gleizes, A.3
Moszer, I.4
Danchin, A.5
-
16
-
-
0033053213
-
The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitides
-
Holmes, E.C., Urwin, R., and Maiden, M.C.J. 1999. The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitides. Mol. Biol. Evol. 16: 741-749.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 741-749
-
-
Holmes, E.C.1
Urwin, R.2
Maiden, M.C.J.3
-
17
-
-
1842332701
-
Compositional biases of bacterial genomes and evolutionary implications
-
Karlin S., Mrazek, J., and Campbell, A.M. 1997. Compositional biases of bacterial genomes and evolutionary implications. J. Bacteriol. 179: 3899-3913.
-
(1997)
J. Bacteriol.
, vol.179
, pp. 3899-3913
-
-
Karlin, S.1
Mrazek, J.2
Campbell, A.M.3
-
18
-
-
0032426005
-
Comparative DNA analysis across diverse genomes
-
Karlin, S., Campbell, A.M., and Mrazek, J. 1998. Comparative DNA analysis across diverse genomes. Annu. Rev. Genet. 32: 185-225.
-
(1998)
Annu. Rev. Genet.
, vol.32
, pp. 185-225
-
-
Karlin, S.1
Campbell, A.M.2
Mrazek, J.3
-
19
-
-
0034625235
-
The impact of comparative genomics on our understanding of evolution
-
Koonin, E.V., Aravind, L., and Kondrashov, A.S. 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
-
20
-
-
0034284411
-
Functional analysis of putative restriction-modification system genes in the Helicobacter pylori J99 genome
-
Kong, H., Lin, L.-F., Porter, N., Stickel, S., Byrd, D., Posfai, J., and Roberts, R.J. 2000. Functional analysis of putative restriction-modification system genes in the Helicobacter pylori J99 genome. Nucleic Acids Res. 28: 3216-3223.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 3216-3223
-
-
Kong, H.1
Lin, L.-F.2
Porter, N.3
Stickel, S.4
Byrd, D.5
Posfai, J.6
Roberts, R.J.7
-
21
-
-
0030994798
-
Amelioration of bacterial genomes: Rates of change and exchange
-
Lawrence, J.G. and Ochman, H. 1997. Amelioration of bacterial genomes: Rates of change and exchange. J. Mol. Evol. 44: 383-397.
-
(1997)
J. Mol. Evol.
, vol.44
, pp. 383-397
-
-
Lawrence, J.G.1
Ochman, H.2
-
22
-
-
0029795578
-
Over- and underrepresentation of short DNA words in herpesvirus genomes
-
Leung, M.Y., Marsh, G.M., and Speed, T.P. 1996. Over- and underrepresentation of short DNA words in herpesvirus genomes. J. Comp. Biol. 3: 345-360.
-
(1996)
J. Comp. Biol.
, vol.3
, pp. 345-360
-
-
Leung, M.Y.1
Marsh, G.M.2
Speed, T.P.3
-
23
-
-
0035956977
-
Comparative genomics of the restriction-modification systems in Helicobacter pylori
-
Lin, L.-F., Posfai, J., Roberts, R. J., and Kong, H. 2001. Comparative genomics of the restriction-modification systems in Helicobacter pylori. Proc. Natl. Acad. Sci. 98: 2740-2745.
-
(2001)
Proc. Natl. Acad. Sci.
, vol.98
, pp. 2740-2745
-
-
Lin, L.-F.1
Posfai, J.2
Roberts, R.J.3
Kong, H.4
-
24
-
-
0035175274
-
The RDP-II (ribosomal database project)
-
Maiden, B.L., Cole, J.R., Lilburn, T.G., Parker Jr., C.T., Saxman, P.R., Farris, R.J., Garrity, G.M., Olsen, G.J., Schmidt, T.M., and Tiedie, J.M. 2001. The RDP-II (ribosomal database project). Nucleic Acids Res. 29: 173-174.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 173-174
-
-
Maiden, B.L.1
Cole, J.R.2
Lilburn, T.G.3
Parker C.T., Jr.4
Saxman, P.R.5
Farris, R.J.6
Garrity, G.M.7
Olsen, G.J.8
Schmidt, T.M.9
Tiedie, J.M.10
-
25
-
-
0031897789
-
Detecting recombination from gene trees
-
Maynard Smith, J. and Smith, N.H. 1998. Detecting recombination from gene trees. Mol. Biol. Evol. 15: 590-599.
-
(1998)
Mol. Biol. Evol.
, vol.15
, pp. 590-599
-
-
Maynard Smith, J.1
Smith, N.H.2
-
26
-
-
0013596021
-
The guanine and cytosine content of genomic DNA and bacterial-evolution
-
Muto, A. and Osawa, S. 1987. The guanine and cytosine content of genomic DNA and bacterial-evolution. Proc. Natl. Acad. Sci. 84: 166-169.
-
(1987)
Proc. Natl. Acad. Sci.
, vol.84
, pp. 166-169
-
-
Muto, A.1
Osawa, S.2
-
27
-
-
0033609333
-
Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritime
-
Nelson, K.E., Clayton, R.A., Gill, S.R., Gwinn, M.L., Dodson, R.J., Haft, D.H., Hickey, E.K., Peterson, J.D., Nelson, W.C., Ketchum, K.A., et al. 1999. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritime. 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
-
28
-
-
0028055018
-
The winds of (evolutionary) change: Breathing new life into microbiology
-
Olsen, G.J., Woese, C.R., and Overbeek, R. 1994. The winds of (evolutionary) change: Breathing new life into microbiology. J. Bacteriol. 176: 1-6.
-
(1994)
J. Bacteriol.
, vol.176
, pp. 1-6
-
-
Olsen, G.J.1
Woese, C.R.2
Overbeek, R.3
-
29
-
-
0030982247
-
A molecular view of microbial diversity and the biosphere
-
Pace, N.R. 1997. A molecular view of microbial diversity and the biosphere. Science 276: 734-740.
-
(1997)
Science
, vol.276
, pp. 734-740
-
-
Pace, N.R.1
-
30
-
-
0030203863
-
TREEVIEW: An application to display phylogenetic trees on personal computers
-
Page, R.D.M. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Comp. Appl. Biosci. 12: 357-458.
-
(1996)
Comp. Appl. Biosci.
, vol.12
, pp. 357-458
-
-
Page, R.D.M.1
-
31
-
-
0034628526
-
The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences
-
Parkhill, J., Wren, B.W., Mungall, K., Ketley, J.M., Churcher, C., Basham, D., Chillingworth, T., Davies, R.M., Feltwell, T., Holroyd, S., et al. 2000. The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature 403: 665-668.
-
(2000)
Nature
, vol.403
, pp. 665-668
-
-
Parkhill, J.1
Wren, B.W.2
Mungall, K.3
Ketley, J.M.4
Churcher, C.5
Basham, D.6
Chillingworth, T.7
Davies, R.M.8
Feltwell, T.9
Holroyd, S.10
-
32
-
-
0002393841
-
The use of tree comparison metrics
-
Penny, D. and Hendy, M.D. 1985. The use of tree comparison metrics. Systematic Zoology 34: 75-82.
-
(1985)
Systematic Zoology
, vol.34
, pp. 75-82
-
-
Penny, D.1
Hendy, M.D.2
-
33
-
-
0035945586
-
Genome sequence of enterohaemorrhagic Escherichia coli O157:H7
-
Perna, N.T., Plunkett III, G., Burland, V., Mau, B., Glasner, J.D., Rose, D.J., Mayhew, G.F., Evans, P.S., Gregor, J., Kirkpatrick, H.A., et al. 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409: 529-533.
-
(2001)
Nature
, vol.409
, pp. 529-533
-
-
Perna, N.T.1
Plunkett G. III2
Burland, V.3
Mau, B.4
Glasner, J.D.5
Rose, D.J.6
Mayhew, G.F.7
Evans, P.S.8
Gregor, J.9
Kirkpatrick, H.A.10
-
34
-
-
0002576679
-
Identification of horizontally acquired genetic elements in Helicobacter pylori and other prokaryotes using oligonucleotide difference analysis
-
Pride, D.T. and Blaser, MJ. 2002. Identification of horizontally acquired genetic elements in Helicobacter pylori and other prokaryotes using oligonucleotide difference analysis. Genome Letters 1: 2-15.
-
(2002)
Genome Letters
, vol.1
, pp. 2-15
-
-
Pride, D.T.1
Blaser, M.J.2
-
35
-
-
0032526323
-
Oligonucleotide bias in Bacillus subtilis: General trends and taxonomic comparisons
-
Rocha, E.P.C., Viari, A., and Danchin, A. 1998. Oligonucleotide bias in Bacillus subtilis: General trends and taxonomic comparisons. Nucleic Acids Res. 26: 2971-2980.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 2971-2980
-
-
Rocha, E.P.C.1
Viari, A.2
Danchin, A.3
-
36
-
-
0026680446
-
Gene order comparisons for phylogenetic inference: Evolution of the mitochondrial genome
-
Sankoff, D., Leduc, G., Antoine, N., Paquin, B., Lang, B.F., and Cedergren, R. 1992. Gene order comparisons for phylogenetic inference: Evolution of the mitochondrial genome. Proc. Natl. Acad. Sci. 89: 6575-6579.
-
(1992)
Proc. Natl. Acad. Sci.
, vol.89
, pp. 6575-6579
-
-
Sankoff, D.1
Leduc, G.2
Antoine, N.3
Paquin, B.4
Lang, B.F.5
Cedergren, R.6
-
37
-
-
0029365207
-
Exceptional motifs in different Markov chain models for a statistical analysis of DNA sequences
-
Schbath, S., Prum, B., and de Turckheim, E. 1995. Exceptional motifs in different Markov chain models for a statistical analysis of DNA sequences. J. Comp. Biol. 2: 417-437.
-
(1995)
J. Comp. Biol.
, vol.2
, pp. 417-437
-
-
Schbath, S.1
Prum, B.2
de Turckheim, E.3
-
38
-
-
0027715731
-
Codon usage: Mutational bias, translational selection, or both?
-
Sharp, P.M., Stenico, M., Peden, J.F., and Lloyd, A.T. 1993. Codon usage: Mutational bias, translational selection, or both? Biochem. Soc. Trans. 21: 835-841.
-
(1993)
Biochem. Soc. Trans.
, vol.21
, pp. 835-841
-
-
Sharp, P.M.1
Stenico, M.2
Peden, J.F.3
Lloyd, A.T.4
-
39
-
-
0032900532
-
Genome phylogeny based on gene content
-
Snel, B., Bork, P., and Huynen, M.A. 1999. Genome phylogeny based on gene content. Nature Genetics 21: 108-110.
-
(1999)
Nature Genetics
, vol.21
, pp. 108-110
-
-
Snel, B.1
Bork, P.2
Huynen, M.A.3
-
40
-
-
0023991945
-
Directional mutation pressure and neutral molecular evolution
-
Suoeka, N. 1988. Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. 85: 2653-2657.
-
(1988)
Proc. Natl. Acad. Sci.
, vol.85
, pp. 2653-2657
-
-
Suoeka, N.1
-
41
-
-
0004248459
-
Paup 4.0b2. Phylogenetic analysis using parsimony (* and other methods)
-
Version 4. Sinauer Associates, Sunderland, Massachusetts
-
Swofford, D.L. 1998. Paup 4.0b2. Phylogenetic analysis using parsimony (* and other methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
-
(1998)
-
-
Swofford, D.L.1
-
42
-
-
0035162592
-
The Cog Database: New developments in phylogenetic classification of proteins from complete genomes
-
Tatusov, R.L., Natale, D.A., Garkavtsev, I.V., Shankavaram, U.T., Rao, B.S., Kiryutin, B., Galperin, M.Y., Fedorova, N.D., and Koonin, E.V. 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
Shankavaram, U.T.4
Rao, B.S.5
Kiryutin, B.6
Galperin, M.Y.7
Fedorova, N.D.8
Koonin, E.V.9
-
43
-
-
0030835739
-
The complete genome sequence of the gastric pathogen Helicobacter pylori
-
Tomb, J.-F., White, O., Kervalage, A.R., Clayton, R.A., Sutton, G.G., Fleischman, R.D., Ketchum, K.A., Klenk, H.P., Gill, S., Dougherty, B.A., et al. 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388: 539-547.
-
(1997)
Nature
, vol.388
, pp. 539-547
-
-
Tomb, J.-F.1
White, O.2
Kervalage, A.R.3
Clayton, R.A.4
Sutton, G.G.5
Fleischman, R.D.6
Ketchum, K.A.7
Klenk, H.P.8
Gill, S.9
Dougherty, B.A.10
-
44
-
-
0001271789
-
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
-
Woese, C.R. and Fox, G.E. 1977. Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proc. Natl. Acad. Sci. 74:5088-5090.
-
(1977)
Proc. Natl. Acad. Sci.
, vol.74
, pp. 5088-5090
-
-
Woese, C.R.1
Fox, G.E.2
-
45
-
-
0025300402
-
Towards a natural system of organisms: Proposal for the domains archaea, bacteria, and eukarya
-
Woese, C.R., Kandler, O., and Wheelis, M.L. 1990. Towards a natural system of organisms: Proposal for the domains archaea, bacteria, and eukarya. Proc. Natl. Acad. Sci. 87: 4576-4579.
-
(1990)
Proc. Natl. Acad. Sci.
, vol.87
, pp. 4576-4579
-
-
Woese, C.R.1
Kandler, O.2
Wheelis, M.L.3
-
46
-
-
0034662923
-
Identification of type II restriction and modification systems in Helicobacter pylori reveals their substantial diversity among strains
-
Xu, Q., Morgan, R.D., Roberts, R.J., and Blaser, M.J. 2000. Identification of type II restriction and modification systems in Helicobacter pylori reveals their substantial diversity among strains. Proc. Natl. Acad. Sci. 97: 9671-9676.
-
(2000)
Proc. Natl. Acad. Sci.
, vol.97
, pp. 9671-9676
-
-
Xu, Q.1
Morgan, R.D.2
Roberts, R.J.3
Blaser, M.J.4
|