-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul S, Madden T, Scḧaffer A, Zhang J, Zhang Z, Miller W, Lip-man D. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.1
Madden, T.2
Scḧaffer, A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lip-Man, D.7
-
2
-
-
10044247612
-
Lecture notes on optimal transport problems
-
Berlin (Germany): Springer Verlag
-
Ambrosio L. 2003. Lecture notes on optimal transport problems. In: Mathematical aspects of evolving interfaces. Berlin (Germany): Springer Verlag. p. 1-52.
-
(2003)
Mathematical Aspects of Evolving Interfaces
, pp. 1-52
-
-
Ambrosio, L.1
-
3
-
-
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(3):1229-1236.
-
(2003)
Genetics
, vol.164
, Issue.3
, pp. 1229-1236
-
-
Anisimova, M.1
Nielsen, R.2
Yang, Z.3
-
4
-
-
33646244720
-
Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome
-
Arbiza L, Dopazo J, Dopazo H. 2006. Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome. PLoS Comput Biol. 2(4):e38.
-
(2006)
PLoS Comput Biol
, vol.2
, Issue.4
-
-
Arbiza, L.1
Dopazo, J.2
Dopazo, H.3
-
5
-
-
37849052232
-
The influenza virus resource at the national center for biotechnology information
-
Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L, Tatusova T, Ostell J, Lipman D. 2007. The influenza virus resource at the national center for biotechnology information. J Virol. 82(2):596-601.
-
(2007)
J Virol
, vol.82
, Issue.2
, pp. 596-601
-
-
Bao, Y.1
Bolotov, P.2
Dernovoy, D.3
Kiryutin, B.4
Zaslavsky, L.5
Tatusova, T.6
Ostell, J.7
Lipman, D.8
-
6
-
-
31144465926
-
Hearing silence: Non-neutral evolution at synonymous sites in mammals
-
Chamary JV, Parmley JL, Hurst LD. 2006. Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet. 7(2):98-108.
-
(2006)
Nat Rev Genet
, vol.7
, Issue.2
, pp. 98-108
-
-
Chamary, J.V.1
Parmley, J.L.2
Hurst, L.D.3
-
7
-
-
0842326022
-
Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes
-
Choisy M, Woelk CH, Guegan JF, Robertson DL. 2004. Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes. J Virol. 78:1962-1970.
-
(2004)
J Virol
, vol.78
, pp. 1962-1970
-
-
Choisy, M.1
Woelk, C.H.2
Guegan, J.F.3
Robertson, D.L.4
-
8
-
-
0020981606
-
Evidence that natural selection acts on silent mutation
-
Conrad M, Friedlander C, Goodman M. 1983. Evidence that natural selection acts on silent mutation. Biosystems 16(2):101-111.
-
(1983)
Biosystems
, vol.16
, Issue.2
, pp. 101-111
-
-
Conrad, M.1
Friedlander, C.2
Goodman, M.3
-
9
-
-
0028104077
-
Selection on silent sites in the rodent H3 histone gene family
-
DeBry RW, Marzluff WF. 1994. Selection on silent sites in the rodent H3 histone gene family. Genetics 138(1):191-202.
-
(1994)
Genetics
, vol.138
, Issue.1
, pp. 191-202
-
-
Debry, R.W.1
Marzluff, W.F.2
-
10
-
-
0001334115
-
The CHC adaptive search algorithm
-
Rawlins GJE, editor San Francisco (CA): Morgan Kaufman
-
Eshelman LJ. 1991. The CHC adaptive search algorithm. In: Rawlins GJE, editor. Foundations of genetic algorithms. Vol.I. San Francisco (CA): Morgan Kaufman. p. 265-283.
-
(1991)
Foundations of Genetic Algorithms
, vol.1
, pp. 265-283
-
-
Eshelman, L.J.1
-
11
-
-
0000159540
-
A method for minimising the impact of distributional assumptions in econometric models for duration data
-
Heckman J, Singer B. 1984. A method for minimising the impact of distributional assumptions in econometric models for duration data. Econometrica 52(2):271-320.
-
(1984)
Econometrica
, vol.52
, Issue.2
, pp. 271-320
-
-
Heckman, J.1
Singer, B.2
-
12
-
-
33646586721
-
A Dirichlet process model for detecting positive selection in protein-coding DNA sequences
-
Huelsenbeck JP, Jain S, Frost SWD, Pond SLK. 2006. A Dirichlet process model for detecting positive selection in protein-coding DNA sequences. Proc Natl Acad Sci USA. 103(16):6263-6268.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, Issue.16
, pp. 6263-6268
-
-
Huelsenbeck, J.P.1
Jain, S.2
Frost, S.W.D.3
Pond, S.L.K.4
-
13
-
-
0035252561
-
Evidence for purifying selection acting on silent sites in BRCA1
-
Hurst L, Pal C. 2001. Evidence for purifying selection acting on silent sites in BRCA1. Trends Genet. 17:62-65.
-
(2001)
Trends Genet
, vol.17
, pp. 62-65
-
-
Hurst, L.1
Pal, C.2
-
14
-
-
31344478786
-
On the translocation of masses
-
Kantorovich L. 2006. On the translocation of masses. J Math Sci. 133(4):1381-1382.
-
(2006)
J Math Sci
, vol.133
, Issue.4
, pp. 1381-1382
-
-
Kantorovich, L.1
-
16
-
-
14544275616
-
A genetic algorithm approach to detecting lineage-specific variation in selection pressure
-
Kosakovsky Pond SL, Frost SDW. 2005a. A genetic algorithm approach to detecting lineage-specific variation in selection pressure. Mol Biol Evol. 22(3):478-485.
-
(2005)
Mol Biol Evol
, vol.22
, Issue.3
, pp. 478-485
-
-
Kosakovsky Pond, S.L.1
Frost, S.D.W.2
-
17
-
-
17744395033
-
Datamonkey: Rapid detection of selective pressure on individual sites of codon alignments
-
Kosakovsky Pond SL, Frost SDW. 2005b. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioin-formatics 21(10):2531-2533.
-
(2005)
Bioin-formatics
, vol.21
, Issue.10
, pp. 2531-2533
-
-
Kosakovsky Pond, S.L.1
Frost, S.D.W.2
-
18
-
-
17744396121
-
Not so different after all: A comparison of methods for detecting amino acid sites under selection
-
Kosakovsky Pond SL, Frost SDW. 2005c. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol. 22(5):1208-1222.
-
(2005)
Mol Biol Evol
, vol.22
, Issue.5
, pp. 1208-1222
-
-
Kosakovsky Pond, S.L.1
Frost, S.D.W.2
-
19
-
-
33745611774
-
Adaptation to different human populations by HIV-1 revealed by codon-based analyses
-
Kosakovsky Pond SL, Frost SDW, Grossman Z, Gravenor MB, Richman DD, Leigh Brown AJ. 2006. Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLoS Comput Biol. 2(6):e62.
-
(2006)
PLoS Comput Biol
, vol.2
, Issue.6
-
-
Kosakovsky Pond, S.L.1
Frost, S.D.W.2
Grossman, Z.3
Gravenor, M.B.4
Richman, D.D.5
Leigh Brown, A.J.6
-
21
-
-
33845874638
-
Evolutionary model selection with a genetic algorithm: A case study using stem RNA
-
Kosakovsky Pond SL, Mannino FV, Gravenor MB, Muse SV, Frost SDW. 2007. Evolutionary model selection with a genetic algorithm: a case study using stem RNA. Mol Biol Evol. 24(1):159-170.
-
(2007)
Mol Biol Evol
, vol.24
, Issue.1
, pp. 159-170
-
-
Kosakovsky Pond, S.L.1
Mannino, F.V.2
Gravenor, M.B.3
Muse, S.V.4
Frost, S.D.W.5
-
22
-
-
27844569825
-
Site-to-site variation of synonymous substitution rates
-
Kosakovsky Pond SL, Muse SV. 2005. Site-to-site variation of synonymous substitution rates. Mol Biol Evol. 22(12):2375-2385.
-
(2005)
Mol Biol Evol
, vol.22
, Issue.12
, pp. 2375-2385
-
-
Kosakovsky Pond, S.L.1
Muse, S.V.2
-
23
-
-
33748770095
-
Automated phylogenetic detection of recombination using a genetic algorithm
-
Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD. 2006. Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol. 23(10):1891-1901.
-
(2006)
Mol Biol Evol
, vol.23
, Issue.10
, pp. 1891-1901
-
-
Kosakovsky Pond, S.L.1
Posada, D.2
Gravenor, M.B.3
Woelk, C.H.4
Frost, S.D.5
-
24
-
-
0028900746
-
Positive selection is a general phenomenon in the evolution of abalone sperm lysin
-
Lee YH, Ota T, Vacquier VD. 1995. Positive selection is a general phenomenon in the evolution of abalone sperm lysin. Mol Biol Evol. 12(2):231-238.
-
(1995)
Mol Biol Evol
, vol.12
, Issue.2
, pp. 231-238
-
-
Lee, Y.H.1
Ota, T.2
Vacquier, V.D.3
-
25
-
-
0028024626
-
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates with application to the chloroplast genome
-
Muse SV, Gaut BS. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates with application to the chloroplast genome. Mol Biol Evol. 11:715-724.
-
(1994)
Mol Biol Evol
, vol.11
, pp. 715-724
-
-
Muse, S.V.1
Gaut, B.S.2
-
26
-
-
20444430245
-
A scan for positively selected genes in the genomes of humans and chimpanzees
-
Nielsen R, Bustamante C, Clark AG, et al. 2005. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol. 3(6):e170.
-
(2005)
PLoS Biol
, vol.3
, Issue.6
-
-
Nielsen, R.1
Bustamante, C.2
Clark, A.G.3
-
27
-
-
0031972161
-
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
-
Nielsen R, Yang ZH. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936.
-
(1998)
Genetics
, vol.148
, pp. 929-936
-
-
Nielsen, R.1
Yang, Z.H.2
-
28
-
-
18844407852
-
Codon volatility does not reflect selective pressure on the HIV-1 genome
-
Pillai SK, Kosakovsky Pond SL, Woelk CH, Richman DD, Smith DM. 2005. Codon volatility does not reflect selective pressure on the HIV-1 genome. Virology 336(2):137-143.
-
(2005)
Virology
, vol.336
, Issue.2
, pp. 137-143
-
-
Pillai, S.K.1
Kosakovsky Pond, S.L.2
Woelk, C.H.3
Richman, D.D.4
Smith, D.M.5
-
29
-
-
84950788916
-
A noniterative sampling/importance resampling alternative to the data augmentation algorithm for creating a few imputations when fractions of missing information are modest: The SIR algorithm
-
Rubin D. 1987. A noniterative sampling/importance resampling alternative to the data augmentation algorithm for creating a few imputations when fractions of missing information are modest: the SIR algorithm. J Am Stat Assoc. 82(398):543-546.
-
(1987)
J Am Stat Assoc
, vol.82
, Issue.398
, pp. 543-546
-
-
Rubin, D.1
-
30
-
-
0032319998
-
A metric for distributions with applications to image databases
-
1998 Jan 4; New Delhi, India. Bombay (India): Narosa Publishing House
-
Rubner Y, Tomasi C, Guibas LJ. 1998. A metric for distributions with applications to image databases. Sixth International Conference on Computer Vision; 1998 Jan 4; New Delhi, India. Bombay (India): Narosa Publishing House. p. 59-66.
-
(1998)
Sixth International Conference on Computer Vision
, pp. 59-66
-
-
Rubner, Y.1
Tomasi, C.2
Guibas, L.J.3
-
31
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4(4):406-425.
-
(1987)
Mol Biol Evol
, vol.4
, Issue.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
32
-
-
19344362934
-
Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G
-
Sawyer SL, Emerman M, Malik HS. 2004. Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G. PLoS Biol. 2(9):E275.
-
(2004)
PLoS Biol
, vol.2
, Issue.9
-
-
Sawyer, S.L.1
Emerman, M.2
Malik, H.S.3
-
33
-
-
33749827106
-
Robust inference of positive selection from recombining coding sequences
-
Scheffler K, Martin DP, Seoighe C. 2006. Robust inference of positive selection from recombining coding sequences. Bioinformatics 22(20):2493-2499.
-
(2006)
Bioinformatics
, vol.22
, Issue.20
, pp. 2493-2499
-
-
Scheffler, K.1
Martin, D.P.2
Seoighe, C.3
-
35
-
-
0032710838
-
Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection
-
Shankarappa R, Margolick J, Gange S, et al. (12 co-authors) 1999. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J Virol. 73(12):10489-10502.
-
(1999)
J Virol
, vol.73
, Issue.12
, pp. 10489-10502
-
-
Shankarappa, R.1
Margolick, J.2
Gange, S.3
-
37
-
-
0037986694
-
Potential impact of recombination on sitewise approaches for detecting positive natural selection
-
Shriner D, Nickle DC, Jensen MA, Mullins JI. 2003. Potential impact of recombination on sitewise approaches for detecting positive natural selection. Genet Res. 81(2): 115-121.
-
(2003)
Genet Res
, vol.81
, Issue.2
, pp. 115-121
-
-
Shriner, D.1
Nickle, D.C.2
Jensen, M.A.3
Mullins, J.I.4
-
38
-
-
84873894047
-
Hepatitis C virus: Types, subtypes, and beyond
-
Lau JYN, editor Methods in molecular medicine. Totowa (NJ): Humana Press Inc
-
Smith D, Simmonds P. 1998. Hepatitis C virus: types, subtypes, and beyond. In: Lau JYN, editor. Hepatitis C protocols. Vol.19. Methods in molecular medicine. Totowa (NJ): Humana Press Inc. p. 133-146.
-
(1998)
Hepatitis C Protocols
, vol.19
, pp. 133-146
-
-
Smith, D.1
Simmonds, P.2
-
39
-
-
0344585286
-
Adaptive evolution of genes and gene families
-
Swanson WJ. 2003. Adaptive evolution of genes and gene families. Curr Opin Genet Dev. 13(6):617-622.
-
(2003)
Curr Opin Genet Dev
, vol.13
, Issue.6
, pp. 617-622
-
-
Swanson, W.J.1
-
40
-
-
0037230001
-
Pervasive adaptive evolution in mammalian fertilization proteins
-
Swanson WJ, Nielsen R, Yang Q. 2003. Pervasive adaptive evolution in mammalian fertilization proteins. Mol Biol Evol. 20(1):18-20.
-
(2003)
Mol Biol Evol
, vol.20
, Issue.1
, pp. 18-20
-
-
Swanson, W.J.1
Nielsen, R.2
Yang, Q.3
-
41
-
-
0027157960
-
Estimation of the number of nucleotide substitutions in the control region of mitochondrial-DNA in humans and chimpanzees
-
Tamura K, Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial-DNA in humans and chimpanzees. Mol Biol Evol. 10:512-526.
-
(1993)
Mol Biol Evol
, vol.10
, pp. 512-526
-
-
Tamura, K.1
Nei, M.2
-
42
-
-
5444272324
-
Detailed mapping of RNA secondary structures in core and NS5B-encoding region sequences of hepatitis C virus by RNase cleavage and novel bioinformatic prediction methods
-
Tuplin A, Evans DJ, Simmonds P. 2004. Detailed mapping of RNA secondary structures in core and NS5B-encoding region sequences of hepatitis C virus by RNase cleavage and novel bioinformatic prediction methods. J Gen Virol. 85(Pt 10):3037-3047.
-
(2004)
J Gen Virol
, vol.85
, Issue.PART 10
, pp. 3037-3047
-
-
Tuplin, A.1
Evans, D.J.2
Simmonds, P.3
-
43
-
-
0036269759
-
Thermody-namic and phylogenetic prediction of RNA secondary structures in the coding region of hepatitis C virus
-
Tuplin A, Wood J, Evans D, Patel A, Simmonds P. 2002. Thermody-namic and phylogenetic prediction of RNA secondary structures in the coding region of hepatitis C virus. RNA 82(6):824-841.
-
(2002)
RNA
, vol.82
, Issue.6
, pp. 824-841
-
-
Tuplin, A.1
Wood, J.2
Evans, D.3
Patel, A.4
Simmonds, P.5
-
44
-
-
0034097381
-
Codon-substitution models for heterogeneous selection pressure at amino acid sites
-
Yang Z, Nielsen R, Goldman N, Pedersen AMK. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155(1):431-449.
-
(2000)
Genetics
, vol.155
, Issue.1
, pp. 431-449
-
-
Yang, Z.1
Nielsen, R.2
Goldman, N.3
Pedersen, A.M.K.4
-
45
-
-
0036134765
-
Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes
-
Yang Z, 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.1
Swanson, W.J.2
-
46
-
-
16344378246
-
Bayes Empirical Bayes inference of amino acid sites under positive selection
-
Yang Z, Wong WSW, Nielsen R. 2005. Bayes Empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol. 22(4):1107-1118.
-
(2005)
Mol Biol Evol
, vol.22
, Issue.4
, pp. 1107-1118
-
-
Yang, Z.1
Wong, W.S.W.2
Nielsen, R.3
|