-
1
-
-
0042208362
-
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites
-
Anisimova M, Nielsen R, Yang Z (2003) Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164:1229-1236
-
(2003)
Genetics
, vol.164
, pp. 1229-1236
-
-
Anisimova, M.1
Nielsen, R.2
Yang, Z.3
-
2
-
-
11944256168
-
Molecular evolution of hepatitis delta virus antigen gene: Recombination or positive selection?
-
Anisimova A, Yang Z (2004) Molecular evolution of hepatitis delta virus antigen gene: Recombination or positive selection? J Mol Evol 59:815-826
-
(2004)
J Mol Evol
, vol.59
, pp. 815-826
-
-
Anisimova, A.1
Yang, Z.2
-
3
-
-
0026655022
-
Safety, immunogenicity, and efficacy in infancy of oligosaccharide conjugate Haemophilus influenzae Type B vaccine in a United States population - possible implications for optimal use
-
Black SB, Shinefield HR, Fireman B, Hiatt R (1992) Safety, immunogenicity, and efficacy in infancy of oligosaccharide conjugate Haemophilus influenzae Type B vaccine in a United States population - possible implications for optimal use. J Infect Dis 165:S139-S143
-
(1992)
J Infect Dis
, vol.165
-
-
Black, S.B.1
Shinefield, H.R.2
Fireman, B.3
Hiatt, R.4
-
4
-
-
0033915313
-
Variability of outer membrane protein P1 and its evaluation as a vaccine candidate against experimental otitis media due to nontypeable Haemophilus influenzae: An unambiguous, multifaceted approach
-
Bolduc GR, Bouchet V, Jiang RZ, Geisselsoder J, Truong-Bolduc QC, Rice PA, Pelton SI, Goldstein R (2000) Variability of outer membrane protein P1 and its evaluation as a vaccine candidate against experimental otitis media due to nontypeable Haemophilus influenzae: an unambiguous, multifaceted approach. Infect Immun 68:4505-4517
-
(2000)
Infect Immun
, vol.68
, pp. 4505-4517
-
-
Bolduc, G.R.1
Bouchet, V.2
Jiang, R.Z.3
Geisselsoder, J.4
Truong-Bolduc, Q.C.5
Rice, P.A.6
Pelton, S.I.7
Goldstein, R.8
-
6
-
-
0029117860
-
Immunogenicity of synthetic peptides of Haemophilus influenzae Type B outer-membrane protein P1
-
Chong PL, Yang YP, Persaud D, Haer M, Tripet B, Tam E, Sia C, Klein M (1995) Immunogenicity of synthetic peptides of Haemophilus influenzae Type B outer-membrane protein P1. Infect Immun 63:3751-3758
-
(1995)
Infect Immun
, vol.63
, pp. 3751-3758
-
-
Chong, P.L.1
Yang, Y.P.2
Persaud, D.3
Haer, M.4
Tripet, B.5
Tam, E.6
Sia, C.7
Klein, M.8
-
8
-
-
0033106244
-
Evaluation and improvement of multiple sequence methods for protein secondary structure prediction
-
Cuff JA, Barton GJ (1999) Evaluation and improvement of multiple sequence methods for protein secondary structure prediction. Prot Struct Funct Genet 34:508-519
-
(1999)
Prot Struct Funct Genet
, vol.34
, pp. 508-519
-
-
Cuff, J.A.1
Barton, G.J.2
-
9
-
-
0032420333
-
JPred: A consensus secondary structure prediction server
-
Cuff JA, Clamp ME, Siddiqui AS, Finlay M, Barton GJ (1998) JPred: a consensus secondary structure prediction server. Bioinformatics 14:892-893
-
(1998)
Bioinformatics
, vol.14
, pp. 892-893
-
-
Cuff, J.A.1
Clamp, M.E.2
Siddiqui, A.S.3
Finlay, M.4
Barton, G.J.5
-
10
-
-
4444304990
-
Intranasal immunisation of mice with liposomes containing recombinant meningococcal OpaB and OpaJ proteins
-
de Jonge MI, Hamstra HJ, Jiskoot W, Roholl P, Williams NA, Dankert J, van Alphen L, van der Ley P (2004) Intranasal immunisation of mice with liposomes containing recombinant meningococcal OpaB and OpaJ proteins. Vaccine 22:4021-4028
-
(2004)
Vaccine
, vol.22
, pp. 4021-4028
-
-
de Jonge, M.I.1
Hamstra, H.J.2
Jiskoot, W.3
Roholl, P.4
Williams, N.A.5
Dankert, J.6
van Alphen, L.7
van der Ley, P.8
-
11
-
-
0032954440
-
Structural and evolutionary inference from molecular variation in Neisseria porins
-
Derrick JP, Urwin R, Suker J, Feavers IM, Maiden MCJ (1999) Structural and evolutionary inference from molecular variation in Neisseria porins. Infect Immun 67:2406-2413
-
(1999)
Infect Immun
, vol.67
, pp. 2406-2413
-
-
Derrick, J.P.1
Urwin, R.2
Suker, J.3
Feavers, I.M.4
Maiden, M.C.J.5
-
12
-
-
24944576100
-
Characterization of a novel porin protein from Moraxella catarrhalis and identification of an immunodominant surface loop
-
Easton DM, Smith A, Gallego SG, Foxwell AR, Cripps AW, Kyd JM (2005) Characterization of a novel porin protein from Moraxella catarrhalis and identification of an immunodominant surface loop. J Bacteriol 187:6528-6535
-
(2005)
J Bacteriol
, vol.187
, pp. 6528-6535
-
-
Easton, D.M.1
Smith, A.2
Gallego, S.G.3
Foxwell, A.R.4
Cripps, A.W.5
Kyd, J.M.6
-
13
-
-
21544435705
-
Characterization of native outer membrane vesicles from lpxL mutant strains of Neisseria meningitidis for use in parenteral vaccination
-
Fisseha M, Chen P, Brandt B, Kijek T, Moran E, Zollinger W (2005) Characterization of native outer membrane vesicles from lpxL mutant strains of Neisseria meningitidis for use in parenteral vaccination. Infect Immun 73:4070-4080
-
(2005)
Infect Immun
, vol.73
, pp. 4070-4080
-
-
Fisseha, M.1
Chen, P.2
Brandt, B.3
Kijek, T.4
Moran, E.5
Zollinger, W.6
-
14
-
-
16444378767
-
Evidence of positive Darwinian selection in Omp85, a highly conserved bacterial outer membrane protein essential for cell viability
-
Fitzpatrick DA, McInerney JO (2005) Evidence of positive Darwinian selection in Omp85, a highly conserved bacterial outer membrane protein essential for cell viability. J Mol Evol 60:268-273
-
(2005)
J Mol Evol
, vol.60
, pp. 268-273
-
-
Fitzpatrick, D.A.1
McInerney, J.O.2
-
15
-
-
0028168856
-
Codon-based model of nucleotide substitution for protein-coding DNA sequences
-
Goldman N, Yang ZH (1994) Codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11:725-736
-
(1994)
Mol Biol Evol
, vol.11
, pp. 725-736
-
-
Goldman, N.1
Yang, Z.H.2
-
16
-
-
0023507234
-
Cloning and expression in Escherichia coli of the Gene encoding the heat-modifiable major outer-membrane protein of Haemophilus influenzae Type B
-
Gonzales FR, Leachman S, Norgard MV, Radolf JD, Mccracken GH, Evans C, Hansen EJ (1987) Cloning and expression in Escherichia coli of the Gene encoding the heat-modifiable major outer-membrane protein of Haemophilus influenzae Type B. Infect Immun 55:2993-3000
-
(1987)
Infect Immun
, vol.55
, pp. 2993-3000
-
-
Gonzales, F.R.1
Leachman, S.2
Norgard, M.V.3
Radolf, J.D.4
Mccracken, G.H.5
Evans, C.6
Hansen, E.J.7
-
17
-
-
0036667695
-
Host-symbiont conflicts: Positive selection on an outer membrane protein of parasitic but not mutualistic Rickettsiaceae
-
Jiggins FM, Hurst GDD, Yang ZH (2002) Host-symbiont conflicts: Positive selection on an outer membrane protein of parasitic but not mutualistic Rickettsiaceae. Mol Biol Evol 19:1341-1349
-
(2002)
Mol Biol Evol
, vol.19
, pp. 1341-1349
-
-
Jiggins, F.M.1
Hurst, G.D.D.2
Yang, Z.H.3
-
18
-
-
17744395033
-
Datamonkey: Rapid detection of selective pressure on individual sites of codon alignments
-
Kosakovsky Pond SL, Frost SDW (2005) Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21:2531-2533
-
(2005)
Bioinformatics
, vol.21
, pp. 2531-2533
-
-
Kosakovsky Pond, S.L.1
Frost, S.D.W.2
-
19
-
-
0035910270
-
Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
-
Krogh A, Larsson B, von Heijne G, Sonnhammer ELL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305:567-580
-
(2001)
J Mol Biol
, vol.305
, pp. 567-580
-
-
Krogh, A.1
Larsson, B.2
von Heijne, G.3
Sonnhammer, E.L.L.4
-
20
-
-
0041922339
-
HMM-based method to predict the transmembrane regions of beta-barrel membrane proteins
-
Liu Q, Zhu YS, Wang BH, Li YH (2003) HMM-based method to predict the transmembrane regions of beta-barrel membrane proteins. Comput Biol Chem 27:69-76
-
(2003)
Comput Biol Chem
, vol.27
, pp. 69-76
-
-
Liu, Q.1
Zhu, Y.S.2
Wang, B.H.3
Li, Y.H.4
-
21
-
-
17444412589
-
Detecting amino acid sites under positive selection and purifying selection
-
Massingham T, Goldman N (2005) Detecting amino acid sites under positive selection and purifying selection. Genetics 169:1753-1762
-
(2005)
Genetics
, vol.169
, pp. 1753-1762
-
-
Massingham, T.1
Goldman, N.2
-
22
-
-
12444303202
-
Characterization of encapsulated and noncapsulated Haemophilus influenzae and determination of phylogenetic relationships by multilocus sequence typing
-
Meats E, Feil EJ, Stringer S, Cody AJ, Goldstein R, Kroll JS, Popovic T, Spratt BG (2003) Characterization of encapsulated and noncapsulated Haemophilus influenzae and determination of phylogenetic relationships by multilocus sequence typing. J Clin Microbiol 41:1623-1636
-
(2003)
J Clin Microbiol
, vol.41
, pp. 1623-1636
-
-
Meats, E.1
Feil, E.J.2
Stringer, S.3
Cody, A.J.4
Goldstein, R.5
Kroll, J.S.6
Popovic, T.7
Spratt, B.G.8
-
23
-
-
0023751426
-
Purification, cloning, and sequence of outer-membrane protein P1 of Hemophilus influenzae Type B
-
Munson R, Grass S (1988) Purification, cloning, and sequence of outer-membrane protein P1 of Hemophilus influenzae Type B. Infect Immun 56:2235-2242
-
(1988)
Infect Immun
, vol.56
, pp. 2235-2242
-
-
Munson, R.1
Grass, S.2
-
24
-
-
0026762863
-
Outer-membrane proteins P1 and P2 of Haemophilus influenzae Type B - Structure and identification of surface-exposed epitopes
-
Munson R, Brodeur B, Chong P, Grass S, Martin D, Proulx C (1992) Outer-membrane proteins P1 and P2 of Haemophilus influenzae Type B - Structure and identification of surface-exposed epitopes. J Infect Dis 165:S86-S89
-
(1992)
J Infect Dis
, vol.165
-
-
Munson, R.1
Brodeur, B.2
Chong, P.3
Grass, S.4
Martin, D.5
Proulx, C.6
-
25
-
-
0027194901
-
Identification of surface-exposed B-cell epitopes recognized by Haemophilus influenzae Type B P1-specific monoclonal antibodies
-
Panezutti H, James O, Hansen EJ, Choi Y, Harkness RE, Klein MH, Chong P (1993) Identification of surface-exposed B-cell epitopes recognized by Haemophilus influenzae Type B P1-specific monoclonal antibodies. Infect Immun 61:1867-1872
-
(1993)
Infect Immun
, vol.61
, pp. 1867-1872
-
-
Panezutti, H.1
James, O.2
Hansen, E.J.3
Choi, Y.4
Harkness, R.E.5
Klein, M.H.6
Chong, P.7
-
26
-
-
0030053370
-
ProMod and Swiss model: Internet-based tools for automated comparative protein modeling
-
Peitsch MC (1996) ProMod and Swiss model: Internet-based tools for automated comparative protein modeling. Biochem Soc Trans 24:274-279
-
(1996)
Biochem Soc Trans
, vol.24
, pp. 274-279
-
-
Peitsch, M.C.1
-
27
-
-
0031773680
-
Modeltest: Testing the model of DNA substitution
-
Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818
-
(1998)
Bioinformatics
, vol.14
, pp. 817-818
-
-
Posada, D.1
Crandall, K.A.2
-
28
-
-
0026058059
-
Identification of a surface-exposed immunodominant epitope on outer-membrane protein P1 of Haemophilus influenzae Type B
-
Proulx C, Munson RS, Grass S, Hamel J, Martin D, Brodeur BR (1991) Identification of a surface-exposed immunodominant epitope on outer-membrane protein P1 of Haemophilus influenzae Type B. Infect Immun 59:963-970
-
(1991)
Infect Immun
, vol.59
, pp. 963-970
-
-
Proulx, C.1
Munson, R.S.2
Grass, S.3
Hamel, J.4
Martin, D.5
Brodeur, B.R.6
-
29
-
-
0026872909
-
Epitope analysis of an immunodominant domain on the P1 protein of Haemophilus influenzae Type B using synthetic peptides and antiidiotypic antibodies
-
Proulx C, Hamel J, Chong P, Martin D, Brodeur BR (1992) Epitope analysis of an immunodominant domain on the P1 protein of Haemophilus influenzae Type B using synthetic peptides and antiidiotypic antibodies. Microbial Pathogenesis 12:433-442
-
(1992)
Microbial Pathogenesis
, vol.12
, pp. 433-442
-
-
Proulx, C.1
Hamel, J.2
Chong, P.3
Martin, D.4
Brodeur, B.R.5
-
30
-
-
0038433313
-
Construction of recombinant S-layer proteins (rSbsA) and their expression in bacterial ghosts - a delivery system for the nontypeable Haemophilus influenzae antigen Omp26
-
Riedmann EM, Kyd JM, Smith AM, Gomez-Gallego S, Jalava K, Cripps AW, Lubitz W (2003) Construction of recombinant S-layer proteins (rSbsA) and their expression in bacterial ghosts - a delivery system for the nontypeable Haemophilus influenzae antigen Omp26. FEMS Immunol Med Microbiol 37:185-192
-
(2003)
FEMS Immunol Med Microbiol
, vol.37
, pp. 185-192
-
-
Riedmann, E.M.1
Kyd, J.M.2
Smith, A.M.3
Gomez-Gallego, S.4
Jalava, K.5
Cripps, A.W.6
Lubitz, W.7
-
31
-
-
0347513220
-
DnaSP, DNA polymorphism analyses by the coalescent and other methods
-
Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497
-
(2003)
Bioinformatics
, vol.19
, pp. 2496-2497
-
-
Rozas, J.1
Sanchez-DelBarrio, J.C.2
Messeguer, X.3
Rozas, R.4
-
33
-
-
0019201629
-
Bactericidal antibody and susceptibility to otitis media caused by non-typable strains of Haemophilus influenzae
-
Shurin PA, Pelton SI, Tager IB, Kasper DL (1980) Bactericidal antibody and susceptibility to otitis media caused by non-typable strains of Haemophilus influenzae. J Pediatr 97:364-369
-
(1980)
J Pediatr
, vol.97
, pp. 364-369
-
-
Shurin, P.A.1
Pelton, S.I.2
Tager, I.B.3
Kasper, D.L.4
-
34
-
-
0028906959
-
Sequence evolution of the PorB gene of Neisseria gonorrhoeae and Neisseria meningitidis - evidence of positive Darwinian selection
-
Smith NH, Smith JM, Spratt BG (1995) Sequence evolution of the PorB gene of Neisseria gonorrhoeae and Neisseria meningitidis - evidence of positive Darwinian selection. Mol Biol Evol 12:363-370
-
(1995)
Mol Biol Evol
, vol.12
, pp. 363-370
-
-
Smith, N.H.1
Smith, J.M.2
Spratt, B.G.3
-
35
-
-
0032849322
-
A method for detecting positive selection at single amino acid sites
-
Suzuki Y, Gojobori T (1999) A method for detecting positive selection at single amino acid sites. Mol Biol Evol 16:1315-1328
-
(1999)
Mol Biol Evol
, vol.16
, pp. 1315-1328
-
-
Suzuki, Y.1
Gojobori, T.2
-
36
-
-
34247895139
-
-
Swofford DL (2003) PAUP*. Phylogenetic analysis using parsimony *and other methods, Version 4. Sinauer Associates, Sunderland, MA
-
Swofford DL (2003) PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, MA
-
-
-
-
37
-
-
0031574072
-
The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
-
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 4876-4882
-
-
Thompson, J.D.1
Gibson, T.J.2
Plewniak, F.3
Jeanmougin, F.4
Higgins, D.G.5
-
38
-
-
0036791109
-
Phylogenetic evidence for frequent positive selection and recombination in the meningococcal surface antigen PorB
-
Urwin R, Holmes EC, Fox AJ, Derrick JP, Maiden MCJ (2002) Phylogenetic evidence for frequent positive selection and recombination in the meningococcal surface antigen PorB. Mol Biol Evol 19:1686-1694
-
(2002)
Mol Biol Evol
, vol.19
, pp. 1686-1694
-
-
Urwin, R.1
Holmes, E.C.2
Fox, A.J.3
Derrick, J.P.4
Maiden, M.C.J.5
-
39
-
-
4644237146
-
Distribution of surface protein variants among hyperinvasive meningococci: Implication for vaccine design
-
Urwin R, Russell JE, Thompson EAL, Holmes EC, Feavers IM, Maiden MCJ (2004) Distribution of surface protein variants among hyperinvasive meningococci: implication for vaccine design. Infect Immun 72:5955-5962
-
(2004)
Infect Immun
, vol.72
, pp. 5955-5962
-
-
Urwin, R.1
Russell, J.E.2
Thompson, E.A.L.3
Holmes, E.C.4
Feavers, I.M.5
Maiden, M.C.J.6
-
41
-
-
0041884768
-
Widespread adaptive evolution in the human immunodeficiency virus type 1 genome
-
Yang W, Bielawski JP, Yang ZH (2003) Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. J Mol Evol 57:212-221
-
(2003)
J Mol Evol
, vol.57
, pp. 212-221
-
-
Yang, W.1
Bielawski, J.P.2
Yang, Z.H.3
-
42
-
-
0030683599
-
PAML: A program package for phylogenetic analysis by maximum likelihood
-
Yang ZH (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comp Appl Biosci 13:555-556
-
(1997)
Comp Appl Biosci
, vol.13
, pp. 555-556
-
-
Yang, Z.H.1
-
43
-
-
0036134765
-
Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes
-
Yang ZH, Swanson WJ (2002) Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol Biol Evol 19:49-57
-
(2002)
Mol Biol Evol
, vol.19
, pp. 49-57
-
-
Yang, Z.H.1
Swanson, W.J.2
-
44
-
-
0034097381
-
Codon-substitution models for heterogeneous selection pressure at amino acid sites
-
Yang ZH, Nielsen R, Goldman N, Pedersen AMK (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449
-
(2000)
Genetics
, vol.155
, pp. 431-449
-
-
Yang, Z.H.1
Nielsen, R.2
Goldman, N.3
Pedersen, A.M.K.4
-
45
-
-
16344378246
-
Bayes empirical Bayes inference of amino acid sites under positive selection
-
Yang ZH, Wong WSW, Nielsen R (2005) Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol 22:1107-1118
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1107-1118
-
-
Yang, Z.H.1
Wong, W.S.W.2
Nielsen, R.3
-
46
-
-
0026634051
-
Loracarbef (Ly163892) versus amoxicillin clavulanate in the treatment of acute bacterial exacerbations of chronic bronchitis
-
Zeckel ML, Jacobson KD, Guerra FJ, Therasse DG, Farlow D (1992) Loracarbef (Ly163892) versus amoxicillin clavulanate in the treatment of acute bacterial exacerbations of chronic bronchitis. Clin Ther 14:214-229
-
(1992)
Clin Ther
, vol.14
, pp. 214-229
-
-
Zeckel, M.L.1
Jacobson, K.D.2
Guerra, F.J.3
Therasse, D.G.4
Farlow, D.5
|