major rearrangements, rewriting -> first draft from RAN, needs fleshing out, new...
[synmut.git] / synmut.bbl
1 \begin{thebibliography}{}
2
3 \bibitem[Barat {\em et~al.}(1991)Barat, Grice, and
4 Daelix]{barat_interaction_1991}
5 Barat, C., Grice, S. F. J.~L., and Daelix, J.-L. (1991).
6 \newblock Interaction of {HIV-1} reverse transcriptase with a synthetic form of
7 its replication primer, {tRNALys},3.
8 \newblock {\em Nucleic Acids Research\/}, {\bf 19}(4), 751--757.
9
10 \bibitem[Batorsky {\em et~al.}(2011)Batorsky, Kearney, Palmer, Maldarelli,
11 Rouzine, and Coffin]{batorsky_estimate_2011}
12 Batorsky, R., Kearney, M.~F., Palmer, S.~E., Maldarelli, F., Rouzine, I.~M.,
13 and Coffin, J.~M. (2011).
14 \newblock Estimate of effective recombination rate and average selection
15 coefficient for {HIV} in chronic infection.
16 \newblock {\em Proceedings of the National Academy of Sciences of the United
17 States of America\/}, {\bf 108}(14), 5661--6.
18
19 \bibitem[Boltz {\em et~al.}(2012)Boltz, Ambrose, Kearney, Shao, {KewalRamani},
20 Maldarelli, Mellors, and Coffin]{boltz_ultrasensitive_2012}
21 Boltz, V.~F., Ambrose, Z., Kearney, M.~F., Shao, W., {KewalRamani}, V.~N.,
22 Maldarelli, F., Mellors, J.~W., and Coffin, J.~M. (2012).
23 \newblock Ultrasensitive allele-specific {PCR} reveals rare preexisting
24 drug-resistant variants and a large replicating virus population in macaques
25 infected with a simian immunodeficiency virus containing human
26 immunodeficiency virus reverse transcriptase.
27 \newblock {\em Journal of Virology\/}, {\bf 86}(23), 12525--12530.
28
29 \bibitem[Brenner {\em et~al.}(2007)Brenner, Roger, Routy, Moisi, Ntemgwa,
30 Matte, Baril, Thomas, Rouleau, Bruneau, Leblanc, Legault, Tremblay, Charest,
31 and Wainberg]{brenner_high_2007}
32 Brenner, B.~G., Roger, M., Routy, J.-P., Moisi, D., Ntemgwa, M., Matte, C.,
33 Baril, J.-G., Thomas, R., Rouleau, D., Bruneau, J., Leblanc, R., Legault, M.,
34 Tremblay, C., Charest, H., and Wainberg, M.~A. (2007).
35 \newblock High rates of forward transmission events after acute/early hiv-1
36 infection.
37 \newblock {\em Journal of Infectious Diseases\/}, {\bf 195}(7), 951--959.
38
39 \bibitem[Bronson and Anderson(1994)Bronson and
40 Anderson]{bronson_nucleotide_1994}
41 Bronson, E.~C. and Anderson, J.~N. (1994).
42 \newblock Nucleotide composition as a driving force in the evolution of
43 retroviruses.
44 \newblock {\em Journal of Molecular Evolution\/}, {\bf 38}(5), 506--532.
45
46 \bibitem[Bunnik {\em et~al.}(2008)Bunnik, Pisas, Van~Nuenen, and
47 Schuitemaker]{bunnik_autologous_2008}
48 Bunnik, E., Pisas, L., Van~Nuenen, A., and Schuitemaker, H. (2008).
49 \newblock Autologous neutralizing humoral immunity and evolution of the viral
50 envelope in the course of subtype b human immunodeficiency virus type 1
51 infection.
52 \newblock {\em Journal of virology\/}, {\bf 82}(16), 7932.
53
54 \bibitem[Coleman {\em et~al.}(2008)Coleman, Papamichail, Skiena, Futcher,
55 Wimmer, and Mueller]{coleman_virus_2008}
56 Coleman, J.~R., Papamichail, D., Skiena, S., Futcher, B., Wimmer, E., and
57 Mueller, S. (2008).
58 \newblock Virus attenuation by genome-scale changes in codon pair bias.
59 \newblock {\em Science\/}, {\bf 320}(5884), 1784--1787.
60
61 \bibitem[Desai and Fisher(2007)Desai and Fisher]{desai_beneficial_2007}
62 Desai, M.~M. and Fisher, D.~S. (2007).
63 \newblock Beneficial mutation selection balance and the effect of linkage on
64 positive selection.
65 \newblock {\em Genetics\/}, {\bf 176}(3), 1759--98.
66
67 \bibitem[Ewens(2004)Ewens]{ewens_mathematical_2004}
68 Ewens, W.~J. (2004).
69 \newblock {\em Mathematical Population Genetics: I. Theoretical
70 Introduction\/}.
71 \newblock Springer.
72
73 \bibitem[Fernandes {\em et~al.}(2012)Fernandes, Jayaraman, and
74 Frankel]{fernandes_hiv-1_2012}
75 Fernandes, J., Jayaraman, B., and Frankel, A. (2012).
76 \newblock The {HIV-1} rev response element: An {RNA} scaffold that directs the
77 cooperative assembly of a homo-oligomeric ribonucleoprotein complex.
78 \newblock {\em {RNA} Biology\/}, {\bf 9}(1), 4--9.
79
80 \bibitem[Forsdyke(1995)Forsdyke]{forsdyke_reciprocal_1995}
81 Forsdyke, D. (1995).
82 \newblock Reciprocal relationship between stem-loop potential and substitution
83 density in retroviral quasispecies under positive darwinian selection.
84 \newblock {\em Journal of Molecular Evolution\/}, {\bf 41}(6).
85
86 \bibitem[Jenkins and Holmes(2003)Jenkins and Holmes]{jenkins_extent_2003}
87 Jenkins, G.~M. and Holmes, E.~C. (2003).
88 \newblock The extent of codon usage bias in human {RNA} viruses and its
89 evolutionary origin.
90 \newblock {\em Virus Research\/}, {\bf 92}(1), 1--7.
91
92 \bibitem[Li {\em et~al.}(2012)Li, Kao, Gao, Sandig, Limmer, Pavon-Eternod,
93 Jones, Landry, Pan, Weitzman, and David]{li_codon-usage-based_2012}
94 Li, M., Kao, E., Gao, X., Sandig, H., Limmer, K., Pavon-Eternod, M., Jones,
95 T.~E., Landry, S., Pan, T., Weitzman, M.~D., and David, M. (2012).
96 \newblock Codon-usage-based inhibition of {HIV} protein synthesis by human
97 schlafen 11.
98 \newblock {\em Nature\/}.
99
100 \bibitem[Liu {\em et~al.}(2006)Liu, {McNevin}, Cao, Zhao, Genowati, Wong,
101 {McLaughlin}, {McSweyn}, Diem, Stevens, {\em et~al.}]{liu_selection_2006}
102 Liu, Y., {McNevin}, J., Cao, J., Zhao, H., Genowati, I., Wong, K.,
103 {McLaughlin}, S., {McSweyn}, M., Diem, K., Stevens, C., {\em et~al.} (2006).
104 \newblock Selection on the human immunodeficiency virus type 1 proteome
105 following primary infection.
106 \newblock {\em Journal of virology\/}, {\bf 80}(19), 9519.
107
108 \bibitem[Moore {\em et~al.}(2009)Moore, Ranchobe, Lambson, Gray, Cave,
109 Abrahams, Bandawe, Mlisana, Abdool~Karim, Williamson, Morris, the {CAPRISA}
110 002~study, and the {NIAID} Center~for {HIV/AIDS} Vaccine
111 Immunology~{(CHAVI)}]{moore_limited_2009}
112 Moore, P.~L., Ranchobe, N., Lambson, B.~E., Gray, E.~S., Cave, E., Abrahams,
113 M.-R., Bandawe, G., Mlisana, K., Abdool~Karim, S.~S., Williamson, C., Morris,
114 L., the {CAPRISA} 002~study, and the {NIAID} Center~for {HIV/AIDS} Vaccine
115 Immunology~{(CHAVI)} (2009).
116 \newblock Limited neutralizing antibody specificities drive neutralization
117 escape in early hiv-1 subtype c infection.
118 \newblock {\em PLoS Pathog\/}, {\bf 5}(9), e1000598.
119
120 \bibitem[Neher and Leitner(2010)Neher and Leitner]{neher_recombination_2010}
121 Neher, R. and Leitner, T. (2010).
122 \newblock Recombination rate and selection strength in {HIV} intra-patient
123 evolution.
124 \newblock {\em {PLoS} Comput Biol\/}, {\bf 6}(1), e1000660.
125
126 \bibitem[Neher and Shraiman(2011)Neher and Shraiman]{neher_genetic_2011}
127 Neher, R.~A. and Shraiman, B. (2011).
128 \newblock Genetic draft and quasi-neutrality in large facultatively sexual
129 populations.
130 \newblock {\em Genetics\/}, {\bf 188}(4), 975--996.
131
132 \bibitem[Ngumbela {\em et~al.}(2008)Ngumbela, Ryan, Sivamurthy, Brockman,
133 Gandhi, Bhardwaj, and Kavanagh]{ngumbela_quantitative_2008}
134 Ngumbela, K.~C., Ryan, K.~P., Sivamurthy, R., Brockman, M.~A., Gandhi, R.~T.,
135 Bhardwaj, N., and Kavanagh, D.~G. (2008).
136 \newblock Quantitative effect of suboptimal codon usage on translational
137 efficiency of {mRNA} encoding {HIV-1} gag in intact t cells.
138 \newblock {\em {PLoS} {ONE}\/}, {\bf 3}(6), e2356.
139
140 \bibitem[Paillart {\em et~al.}(2002)Paillart, Skripkin, Ehresmann, Ehresmann,
141 and Marquet]{paillart_vitro_2002}
142 Paillart, J.-C., Skripkin, E., Ehresmann, B., Ehresmann, C., and Marquet, R.
143 (2002).
144 \newblock In vitro evidence for a long range pseudoknot in the
145 5′-untranslated and matrix coding regions of {HIV-1} genomic {RNA}.
146 \newblock {\em Journal of Biological Chemistry\/}, {\bf 277}(8), 5995--6004.
147
148 \bibitem[Pantaleo and Fauci(1996)Pantaleo and
149 Fauci]{pantaleo_immunopathogenesis_1996}
150 Pantaleo, G. and Fauci, A.~S. (1996).
151 \newblock Immunopathogenesis of hiv infection1.
152 \newblock {\em Annual Review of Microbiology\/}, {\bf 50}(1), 825--854.
153 \newblock {PMID:} 8905100.
154
155 \bibitem[Perelson {\em et~al.}(1996)Perelson, Neumann, Markowitz, Leonard, and
156 Ho]{perelson_hiv-1_1996}
157 Perelson, a.~S., Neumann, a.~U., Markowitz, M., Leonard, J.~M., and Ho, D.~D.
158 (1996).
159 \newblock Hiv-1 dynamics in vivo: virion clearance rate, infected cell
160 life-span, and viral generation time.
161 \newblock {\em Science {(New York, N.Y.)}\/}, {\bf 271}(5255), 1582--6.
162
163 \bibitem[Richman {\em et~al.}(2003)Richman, Wrin, Little, and
164 Petropoulos]{richman_rapid_2003}
165 Richman, D.~D., Wrin, T., Little, S.~J., and Petropoulos, C.~J. (2003).
166 \newblock Rapid evolution of the neutralizing antibody response to {HIV} type 1
167 infection.
168 \newblock {\em Proceedings of the National Academy of Sciences\/}, {\bf
169 100}(7), 4144--4149.
170
171 \bibitem[Sanjuan and Borderia(2011)Sanjuan and
172 Borderia]{sanjuan_interplay_2011}
173 Sanjuan, R. and Borderia, A.~V. (2011).
174 \newblock Interplay between rna structure and protein evolution in hiv-1.
175 \newblock {\em Molecular Biology and Evolution\/}, {\bf 28}(4), 1333--1338.
176
177 \bibitem[Shankarappa {\em et~al.}(1999)Shankarappa, Margolick, Gange, Rodrigo,
178 Upchurch, Farzadegan, Gupta, Rinaldo, Learn, He, {\em
179 et~al.}]{shankarappa_consistent_1999}
180 Shankarappa, R., Margolick, J., Gange, S., Rodrigo, A., Upchurch, D.,
181 Farzadegan, H., Gupta, P., Rinaldo, C., Learn, G., He, X., {\em et~al.}
182 (1999).
183 \newblock Consistent viral evolutionary changes associated with the progression
184 of human immunodeficiency virus type 1 infection.
185 \newblock {\em Journal of Virology\/}, {\bf 73}(12), 10489.
186
187 \bibitem[Strelkowa and Laessig(2012)Strelkowa and
188 Laessig]{strelkowa_clonal_2012}
189 Strelkowa, N. and Laessig, M. (2012).
190 \newblock Clonal interference in the evolution of influenza.
191 \newblock {\em Genetics\/}.
192
193 \bibitem[Watts {\em et~al.}(2009)Watts, Dang, Gorelick, Leonard, Jr, Swanstrom,
194 Burch, and Weeks]{watts_architecture_2009}
195 Watts, J.~M., Dang, K.~K., Gorelick, R.~J., Leonard, C.~W., Jr, J. W.~B.,
196 Swanstrom, R., Burch, C.~L., and Weeks, K.~M. (2009).
197 \newblock Architecture and secondary structure of an entire {HIV-1} {RNA}
198 genome.
199 \newblock {\em Nature\/}, {\bf 460}(7256), 711--716.
200
201 \bibitem[Zanini and Neher(2012)Zanini and Neher]{zanini_ffpopsim:_2012}
202 Zanini, F. and Neher, R.~A. (2012).
203 \newblock {FFPopSim:} an efficient forward simulation package for the evolution
204 of large populations.
205 \newblock {\em Bioinformatics\/}.
206
207 \end{thebibliography}