-
1
-
-
0000586792
-
Convergence assessment for reversible jump MCMC simulations
-
(J. Bernardo, J. Berger, A. Dawid, and A. Smith, eds.). Oxford Univ. Press, New York
-
Brooks, S., and P. Guidici. 1999. Convergence assessment for reversible jump MCMC simulations. Pages 733-742 in Bayesian Statistics 6 (J. Bernardo, J. Berger, A. Dawid, and A. Smith, eds.). Oxford Univ. Press, New York.
-
(1999)
Bayesian Statistics
, vol.6
, pp. 733-742
-
-
Brooks, S.1
Guidici, P.2
-
2
-
-
0000506629
-
Bayesian model choice via Markov chain Monte Carlo methods
-
Carlin, B., and S. Chib. 1995. Bayesian model choice via Markov chain Monte Carlo methods. J. R. Stat. Soc. Ser. B 57:473-484.
-
(1995)
J. R. Stat. Soc. Ser. B
, vol.57
, pp. 473-484
-
-
Carlin, B.1
Chib, S.2
-
3
-
-
0002436375
-
Molecular biology of HIV
-
(K. Crandall, ed.). Johns Hopkins Univ. Press, Baltimore
-
Coffin, J. 1999. Molecular biology of HIV. Pages 3-40 in The Evolution of HIV (K. Crandall, ed.). Johns Hopkins Univ. Press, Baltimore.
-
(1999)
The Evolution of HIV
, pp. 3-40
-
-
Coffin, J.1
-
4
-
-
0029795283
-
Human immunodeficiency virus type 1 subtypes defined by env show high frequency of recombinant gag genes
-
Cornelissen, M., G. Kampinga, F. Zorgdrager, and J. Goudsmit. 1996. Human immunodeficiency virus type 1 subtypes defined by env show high frequency of recombinant gag genes. J. Virol. 70:8209-8212.
-
(1996)
J. Virol.
, vol.70
, pp. 8209-8212
-
-
Cornelissen, M.1
Kampinga, G.2
Zorgdrager, F.3
Goudsmit, J.4
-
5
-
-
0000091731
-
Statistical approaches to detecting recombination
-
(K. Crandall, ed.). Johns Hopkins Univ. Press, Baltimore
-
Crandall, K., and A. Templeton. 1999. Statistical approaches to detecting recombination. Pages 153-176 in The evolution of HIV (K. Crandall, ed.). Johns Hopkins Univ. Press, Baltimore.
-
(1999)
The Evolution of HIV
, pp. 153-176
-
-
Crandall, K.1
Templeton, A.2
-
6
-
-
0003732783
-
-
Technical Report 716. Department of Statistics, Carnegie Mellon Univ., Pittsburgh, Pennsylvania
-
Dimatteo, I., C. Genovese, and R. Kass. 2000. Bayesian Curve Fitting with Free-knot Splines. Technical Report 716. Department of Statistics, Carnegie Mellon Univ., Pittsburgh, Pennsylvania.
-
(2000)
Bayesian Curve Fitting with Free-knot Splines
-
-
DiMatteo, I.1
Genovese, C.2
Kass, R.3
-
7
-
-
0036144957
-
Bootstrap confidence levels for HIV-1 recombination
-
Dorman, K., A. Kaplan, and J. Sinsheimer. 2002. Bootstrap confidence levels for HIV-1 recombination. J. Mol. Evol. 54:200-209.
-
(2002)
J. Mol. Evol.
, vol.54
, pp. 200-209
-
-
Dorman, K.1
Kaplan, A.2
Sinsheimer, J.3
-
8
-
-
77956889087
-
Reversible jump Markov chain Monte Carlo computation and Bayesian model determination
-
Green, P. 1995. Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82:711-732.
-
(1995)
Biometrika
, vol.82
, pp. 711-732
-
-
Green, P.1
-
9
-
-
0022376704
-
Dating the human-ape splitting by a molecular clock of mitochondrial DNA
-
Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
-
(1985)
J. Mol. Evol.
, vol.22
, pp. 160-174
-
-
Hasegawa, M.1
Kishino, H.2
Yano, T.3
-
10
-
-
0027471670
-
A heuristic method to reconstruct the history of sequences subject to recombination
-
Hein, J. 1993. A heuristic method to reconstruct the history of sequences subject to recombination. J. Mol. Evol. 36:396-405.
-
(1993)
J. Mol. Evol.
, vol.36
, pp. 396-405
-
-
Hein, J.1
-
11
-
-
0025095253
-
Genetic consequences of packaging two RNA genomes in one retroviral particle: Pseudodiploidy and high rate of genetic recombination
-
Hu, W., and H. Temin. 1990. Genetic consequences of packaging two RNA genomes in one retroviral particle: Pseudodiploidy and high rate of genetic recombination. Proc. Nat. Acad. Sci. USA 87:1556-1560.
-
(1990)
Proc. Nat. Acad. Sci. USA
, vol.87
, pp. 1556-1560
-
-
Hu, W.1
Temin, H.2
-
14
-
-
0028874043
-
Retroviral recombination can lead to linkage of reverse transcriptase mutations that confer increased zidovudine resistance
-
Kellam, P., and B. Larder. 1995. Retroviral recombination can lead to linkage of reverse transcriptase mutations that confer increased zidovudine resistance. J. Virol. 69:669-674.
-
(1995)
J. Virol.
, vol.69
, pp. 669-674
-
-
Kellam, P.1
Larder, B.2
-
15
-
-
0001720445
-
Numbering positions in HIV relative to HXB2
-
(B. Korber, C. Kuiken, B. Foley, B. Hahn, F. McCutchan, J. Mellors, and J. Sodroski, eds.). Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
-
Korber, B., B. Foley, C. Kuiken, S. Pillai, and J. Sodroski. 1998. Numbering positions in HIV relative to HXB2. Pages 102-111 in Human Retroviruses and AIDS 1998 (B. Korber, C. Kuiken, B. Foley, B. Hahn, F. McCutchan, J. Mellors, and J. Sodroski, eds.). Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico.
-
(1998)
Human Retroviruses and AIDS 1998
, pp. 102-111
-
-
Korber, B.1
Foley, B.2
Kuiken, C.3
Pillai, S.4
Sodroski, J.5
-
16
-
-
0030763038
-
The rapid spread of recombinants during a natural in vitro infection with two human immunodeficiency virus type 1 strains
-
Kuwata, T., Y. Miyazaki, T. Igarashi, J. Takehisa, and M. Hayami. 1997. The rapid spread of recombinants during a natural in vitro infection with two human immunodeficiency virus type 1 strains. J. Virol. 71:7088-7091.
-
(1997)
J. Virol.
, vol.71
, pp. 7088-7091
-
-
Kuwata, T.1
Miyazaki, Y.2
Igarashi, T.3
Takehisa, J.4
Hayami, M.5
-
17
-
-
0032976397
-
Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees
-
Larget, B., and D. Simon. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16:750-759.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 750-759
-
-
Larget, B.1
Simon, D.2
-
18
-
-
1542532208
-
Phylogenetic tree construction using Markov chain Monte Carlo
-
Li, S., D. Pearl, and H. Doss. 2000. Phylogenetic tree construction using Markov chain Monte Carlo. J. Am. Stat. Assoc. 95:493-508.
-
(2000)
J. Am. Stat. Assoc.
, vol.95
, pp. 493-508
-
-
Li, S.1
Pearl, D.2
Doss, H.3
-
19
-
-
0023740248
-
Rates and dates of divergence between AIDS virus nucleotide sequences
-
Li, W., M. Tanimura, and P. Sharp. 1988. Rates and dates of divergence between AIDS virus nucleotide sequences. Mol. Biol. Evol. 5:313-330.
-
(1988)
Mol. Biol. Evol.
, vol.5
, pp. 313-330
-
-
Li, W.1
Tanimura, M.2
Sharp, P.3
-
20
-
-
2142812683
-
HIV-1 genetic subtype A/B recombinant strain causing an explosive epidemic in injecting drug users in Kaliningrad
-
Liitsola, K., I. Tashkinova, T. Laukkanen, G. Korovina, T. Smolskaja, O. Momot, N. Mashkilleyson, S. Chaplinskas, H. Brummer-Korvenkontio, J. Vanhatalo, P. Leinikki, and M. Salminen. 1998. HIV-1 genetic subtype A/B recombinant strain causing an explosive epidemic in injecting drug users in Kaliningrad. AIDS 12:1907-1919.
-
(1998)
AIDS
, vol.12
, pp. 1907-1919
-
-
Liitsola, K.1
Tashkinova, I.2
Laukkanen, T.3
Korovina, G.4
Smolskaja, T.5
Momot, O.6
Mashkilleyson, N.7
Chaplinskas, S.8
Brummer-Korvenkontio, H.9
Vanhatalo, J.10
Leinikki, P.11
Salminen, M.12
-
21
-
-
0026708873
-
Analysing the mosaic structure of genes
-
Maynard Smith, J. 1992. Analysing the mosaic structure of genes. J. Mol. Evol. 34:126-129.
-
(1992)
J. Mol. Evol.
, vol.34
, pp. 126-129
-
-
Maynard Smith, J.1
-
23
-
-
0033965571
-
Estimation of population parameters and recombination rates from single nucleotide polymorphisms
-
Nielsen, R. 2000. Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics 154:931-942.
-
(2000)
Genetics
, vol.154
, pp. 931-942
-
-
Nielsen, R.1
-
24
-
-
0035923699
-
Evaluation of methods for detecting recombination from DNA sequences: Computer simulations
-
Posada, D., and K. Crandall. 2001. Evaluation of methods for detecting recombination from DNA sequences: Computer simulations. Proc. Nat. Acad. Sci. USA 98:13757-13762.
-
(2001)
Proc. Nat. Acad. Sci. USA
, vol.98
, pp. 13757-13762
-
-
Posada, D.1
Crandall, K.2
-
25
-
-
0026664651
-
On the historical origins of HIV-1 (MN) and (RF)
-
Reitz, M., H. Guo, J. Oleske, J. Hoxie, M. Popovic, E. Read-Connole, P. Markham, H. Streicher, and R. Gallo. 1992. On the historical origins of HIV-1 (MN) and (RF). AIDS Res. Hum. Retroviruses 8:1539-1541.
-
(1992)
AIDS Res. Hum. Retroviruses
, vol.8
, pp. 1539-1541
-
-
Reitz, M.1
Guo, H.2
Oleske, J.3
Hoxie, J.4
Popovic, M.5
Read-Connole, E.6
Markham, P.7
Streicher, H.8
Gallo, R.9
-
26
-
-
0001325020
-
HIV-1 nomenclature proposal: A reference guide to HIV-1 classification
-
(B. Korber, C. Kuiken, B. Foley, B. Hahn, F. McCutchan, J. Mellors, and J. Sodroski, eds.). Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
-
Robertson, D., J. Anderson, J. Bradac, J. Carr, B. Foley, R. Funkhouser, F. Gao, B. Hahn, M. Kallish, C. Kuiken, G. Learn, T. Leitner, F. Mccutchan, S. Osmanov, M. Peeters, D. Pieniazek, M. Salminen, P. Sharp, S. Wollinksy, and B. Korber. 1999. HIV-1 nomenclature proposal: A reference guide to HIV-1 classification. Pages 492-505 in Human Retroviruses and AIDS 1999 (B. Korber, C. Kuiken, B. Foley, B. Hahn, F. McCutchan, J. Mellors, and J. Sodroski, eds.). Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico.
-
(1999)
Human Retroviruses and AIDS 1999
, pp. 492-505
-
-
Robertson, D.1
Anderson, J.2
Bradac, J.3
Carr, J.4
Foley, B.5
Funkhouser, R.6
Gao, F.7
Hahn, B.8
Kallish, M.9
Kuiken, C.10
Learn, G.11
Leitner, T.12
McCutchan, F.13
Osmanov, S.14
Peeters, M.15
Pieniazek, D.16
Salminen, M.17
Sharp, P.18
Wollinksy, S.19
Korber, B.20
more..
-
28
-
-
0028939919
-
Recombination in HIV-1
-
Robertson, D., P. Sharp, F. McCutchan, and B. Hahn. 1995b. Recombination in HIV-1. Nature 374:124-126.
-
(1995)
Nature
, vol.374
, pp. 124-126
-
-
Robertson, D.1
Sharp, P.2
McCutchan, F.3
Hahn, B.4
-
29
-
-
0002667169
-
Coalescent approaches to HIV population genetics
-
(K. Crandall, ed.). Johns Hopkins Univ. Press, Baltimore
-
Rodrigo, A., and J. Felsenstein. 1999. Coalescent approaches to HIV population genetics. Pages 233-274 in The evolution of HIV (K. Crandall, ed.). Johns Hopkins Univ. Press, Baltimore.
-
(1999)
The Evolution of HIV
, pp. 233-274
-
-
Rodrigo, A.1
Felsenstein, J.2
-
30
-
-
0028793170
-
Identification of breakpoints in intergenotype recombinants of HIV type 1 by bootscanning
-
Salminen, M., J. Carr, D. Burke, and F. McCutchan. 1995. Identification of breakpoints in intergenotype recombinants of HIV type 1 by bootscanning. AIDS Res. Hum. Retroviruses 11:1423-1425.
-
(1995)
AIDS Res. Hum. Retroviruses
, vol.11
, pp. 1423-1425
-
-
Salminen, M.1
Carr, J.2
Burke, D.3
McCutchan, F.4
-
31
-
-
0003230677
-
Scanning the database for recombinant HIV-1 genomes
-
(G. Myers, B. Korber, B. Hahn, K.-T. Jeang, J. Mellors, F. McCutchan, L. Henderson, and G. Pavlakis, eds.). Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
-
Siepel, A., and B. Korber. 1995. Scanning the database for recombinant HIV-1 genomes. Pages III-35-60 in Human Retroviruses and AIDS 1995 Compendium (G. Myers, B. Korber, B. Hahn, K.-T. Jeang, J. Mellors, F. McCutchan, L. Henderson, and G. Pavlakis, eds.). Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico.
-
(1995)
Human Retroviruses and AIDS 1995 Compendium
, pp. III35-III60
-
-
Siepel, A.1
Korber, B.2
-
32
-
-
0031713226
-
Neutralization of HIV-1 subtypes: Implications for vaccine formulations
-
Smith, T., E. van Rensburg, and S. Engelbrecht. 1998. Neutralization of HIV-1 subtypes: Implications for vaccine formulations. J. Med. Virol. 56:264-268.
-
(1998)
J. Med. Virol.
, vol.56
, pp. 264-268
-
-
Smith, T.1
Van Rensburg, E.2
Engelbrecht, S.3
-
33
-
-
0022459886
-
Identification and characterization of conserved and variable regions in the envelope gene of HTLV-III/LAV, the retrovirus of AIDS
-
Starcich, B., B. Hahn, G. Shaw, P. McNeely, S. Modrow, H. Wolf, E. Parks, W. Parks, S. Josephs, F. Wong-Staal, and R. Gallo. 1986. Identification and characterization of conserved and variable regions in the envelope gene of HTLV-III/LAV, the retrovirus of AIDS. Cell 45:637-648.
-
(1986)
Cell
, vol.45
, pp. 637-648
-
-
Starcich, B.1
Hahn, B.2
Shaw, G.3
McNeely, P.4
Modrow, S.5
Wolf, H.6
Parks, E.7
Parks, W.8
Josephs, S.9
Wong-Staal, F.10
Gallo, R.11
-
35
-
-
0034983646
-
Bayesian selection of continuous-time Markov chain evolutionary models
-
Suchard, M., R. Weiss, and J. Sinsheimer. 2001. Bayesian selection of continuous-time Markov chain evolutionary models. Mol. Biol. Evol. 18:1001-1013.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 1001-1013
-
-
Suchard, M.1
Weiss, R.2
Sinsheimer, J.3
-
36
-
-
0025959787
-
Sex and recombination in retroviruses
-
Temin, H. 1991. Sex and recombination in retroviruses. Trends Genet. 7:71-74.
-
(1991)
Trends Genet.
, vol.7
, pp. 71-74
-
-
Temin, H.1
-
37
-
-
12944281693
-
The HIV epidemic in the Amazon basin is driven by prototypic and recombinant HIV-1 subtypes B and F
-
Vicente, A., K. Otsuki, N. Silva, M. Castilho, F. Barros, D. Pieniazek, D. Hu, M. Rayfield, G. Bretas, and A. Tanuri. 2000. The HIV epidemic in the Amazon basin is driven by prototypic and recombinant HIV-1 subtypes B and F. J. Acquired Immune Defic. Syndr. 23:327-331.
-
(2000)
J. Acquired Immune Defic. Syndr.
, vol.23
, pp. 327-331
-
-
Vicente, A.1
Otsuki, K.2
Silva, N.3
Castilho, M.4
Barros, F.5
Pieniazek, D.6
Hu, D.7
Rayfield, M.8
Bretas, G.9
Tanuri, A.10
-
38
-
-
0011245956
-
Sufficiency and influence
-
(J. Berger, B. Betro, E. Moreno, L. Pericchi, F. Ruggeri, G. Salinetti, and L. Wasserman, eds.). Institute of Mathematical Statistics, Hayward, California
-
Weiss, R. 1996. Sufficiency and influence. Pages 211-229 in Bayesian Robustness (J. Berger, B. Betro, E. Moreno, L. Pericchi, F. Ruggeri, G. Salinetti, and L. Wasserman, eds.). Institute of Mathematical Statistics, Hayward, California.
-
(1996)
Bayesian Robustness
, pp. 211-229
-
-
Weiss, R.1
-
39
-
-
0033618086
-
On Bayesian calculations for mixture likelihoods and priors
-
Weiss, R., M. Cho, and M. Yanuzzi. 1999. On Bayesian calculations for mixture likelihoods and priors. Stat. Med. 18:1555-1570.
-
(1999)
Stat. Med.
, vol.18
, pp. 1555-1570
-
-
Weiss, R.1
Cho, M.2
Yanuzzi, M.3
-
40
-
-
0029067458
-
Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites
-
Yang, Z. 1995a. Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites. J. Mol. Evol. 40:689-697.
-
(1995)
J. Mol. Evol.
, vol.40
, pp. 689-697
-
-
Yang, Z.1
-
41
-
-
0028813337
-
A space-time process model for the evolution of DNA sequences
-
Yang, Z. 1995b. A space-time process model for the evolution of DNA sequences. Genetics 139:993-1005.
-
(1995)
Genetics
, vol.139
, pp. 993-1005
-
-
Yang, Z.1
-
42
-
-
0031452514
-
HIV-1 acquires resistance to two classes of antiviral drugs through homologous recombination
-
Yusa, K., M. Kavlick, P. Kosalaraksas, and H. Mitsuya. 1997. HIV-1 acquires resistance to two classes of antiviral drugs through homologous recombination. Antiviral Res. 36:179-189.
-
(1997)
Antiviral Res.
, vol.36
, pp. 179-189
-
-
Yusa, K.1
Kavlick, M.2
Kosalaraksas, P.3
Mitsuya, H.4
|