Merge branch 'master' of inn.eb.local:/ebio/ag-neher/home/fzanini/phd/papers/synmut
[synmut.git] / bib.bib
1
2 @article{batorsky_estimate_2011,
3 title = {Estimate of effective recombination rate and average selection coefficient for {HIV} in chronic infection.},
4 volume = {108},
5 url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3078368&tool=pmcentrez&rendertype=abstract},
6 doi = {10.1073/pnas.1102036108},
7 number = {14},
8 journal = {Proceedings of the National Academy of Sciences of the United States of America},
9 author = {Batorsky, Rebecca and Kearney, Mary F and Palmer, Sarah E and Maldarelli, Frank and Rouzine, Igor M and Coffin, John M},
10 month = apr,
11 year = {2011},
12 pages = {5661--6},
13 },
14
15 @article{bunnik_autologous_2008,
16 title = {Autologous neutralizing humoral immunity and evolution of the viral envelope in the course of subtype B human immunodeficiency virus type 1 infection},
17 volume = {82},
18 issn = {3120566829},
19 url = {http://jvi.asm.org/cgi/content/abstract/82/16/7932},
20 doi = {10.1128/JVI.00757-08},
21 number = {16},
22 journal = {Journal of virology},
23 author = {Bunnik, {E.M.} and Pisas, Linaida and Van Nuenen, {A.C.} and Schuitemaker, Hanneke},
24 year = {2008},
25 pages = {7932},
26 },
27
28 @article{liu_selection_2006,
29 title = {Selection on the human immunodeficiency virus type 1 proteome following primary infection},
30 volume = {80},
31 url = {http://jvi.asm.org/cgi/content/abstract/80/19/9519},
32 doi = {10.1128/JVI.00575-06},
33 number = {19},
34 journal = {Journal of virology},
35 author = {Liu, Yi and {McNevin}, J. and Cao, Jianhong and Zhao, Hong and Genowati, Indira and Wong, Kim and {McLaughlin}, S. and {McSweyn}, {M.D.} and Diem, Kurt and Stevens, {C.E.} and others},
36 year = {2006},
37 pages = {9519},
38 },
39
40 @article{wilkinson_high-throughput_2008,
41 title = {High-Throughput {SHAPE} Analysis Reveals Structures in {HIV-1} Genomic {RNA} Strongly Conserved across Distinct Biological States},
42 volume = {6},
43 url = {http://dx.doi.org/10.1371/journal.pbio.0060096},
44 doi = {10.1371/journal.pbio.0060096},
45 number = {4},
46 urldate = {2012-07-03},
47 journal = {{PLoS} Biol},
48 author = {Wilkinson, Kevin A and Gorelick, Robert J and Vasa, Suzy M and Guex, Nicolas and Rein, Alan and Mathews, David H and Giddings, Morgan C and Weeks, Kevin M},
49 month = apr,
50 year = {2008},
51 pages = {e96},
52 },
53
54 @article{neher_recombination_2010,
55 title = {Recombination rate and selection strength in {HIV} intra-patient evolution},
56 volume = {6},
57 url = {http://dx.plos.org/10.1371/journal.pcbi.1000660},
58 doi = {10.1371/journal.pcbi.1000660},
59 number = {1},
60 journal = {{PLoS} Comput Biol},
61 author = {Neher, {R.A.} and Leitner, Thomas},
62 month = jan,
63 year = {2010},
64 pages = {e1000660},
65 },
66
67 @article{neher_genetic_2011,
68 title = {Genetic Draft and Quasi-Neutrality in Large Facultatively Sexual Populations},
69 volume = {188},
70 url = {http://www.genetics.org/content/188/4/975.short},
71 number = {4},
72 journal = {Genetics},
73 author = {Neher, Richard A and Shraiman, Boris},
74 year = {2011},
75 pages = {975--996},
76 },
77
78 @article{perelson_hiv-1_1996,
79 title = {HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time.},
80 volume = {271},
81 url = {http://www.ncbi.nlm.nih.gov/pubmed/8599114},
82 number = {5255},
83 journal = {Science {(New York, N.Y.)}},
84 author = {Perelson, a S and Neumann, a U and Markowitz, M and Leonard, J M and Ho, D D},
85 month = mar,
86 year = {1996},
87 pages = {1582--6},
88 },
89
90 @article{shankarappa_consistent_1999,
91 title = {Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection},
92 volume = {73},
93 url = {http://jvi.asm.org/cgi/content/abstract/73/12/10489},
94 number = {12},
95 journal = {Journal of Virology},
96 author = {Shankarappa, R. and Margolick, {J.B.} and Gange, {S.J.} and Rodrigo, {A.G.} and Upchurch, David and Farzadegan, Homayoon and Gupta, Phalguni and Rinaldo, {C.R.} and Learn, {G.H.} and He, X. and others},
97 year = {1999},
98 pages = {10489},
99 },
100
101 @article{watts_architecture_2009,
102 title = {Architecture and secondary structure of an entire {HIV-1} {RNA} genome},
103 volume = {460},
104 copyright = {© 2009 Nature Publishing Group},
105 issn = {0028-0836},
106 url = {http://www.nature.com/nature/journal/v460/n7256/full/nature08237.html},
107 doi = {10.1038/nature08237},
108 language = {en},
109 number = {7256},
110 urldate = {2012-07-01},
111 journal = {Nature},
112 author = {Watts, Joseph M. and Dang, Kristen K. and Gorelick, Robert J. and Leonard, Christopher W. and Jr, Julian W. Bess and Swanstrom, Ronald and Burch, Christina L. and Weeks, Kevin M.},
113 month = aug,
114 year = {2009},
115 pages = {711--716},
116 },
117
118 @article{forsdyke_reciprocal_1995,
119 title = {Reciprocal relationship between stem-loop potential and substitution density in retroviral
120 quasispecies under positive {Darwinian} selection},
121 volume = {41},
122 issn = {0022-2844, 1432-1432},
123 url = {http://www.springerlink.com/content/n7621n18505m418m/},
124 doi = {10.1007/BF00173184},
125 number = {6},
126 urldate = {2012-07-06},
127 journal = {Journal of Molecular Evolution},
128 author = {Forsdyke, {D.R.}},
129 month = dec,
130 year = {1995},
131 },
132
133 @article{sanjuan_interplay_2011,
134 title = {Interplay between {RNA} Structure and Protein Evolution in {HIV-1}},
135 volume = {28},
136 issn = {0737-4038, 1537-1719},
137 url = {http://mbe.oxfordjournals.org/content/28/4/1333},
138 doi = {10.1093/molbev/msq329},
139 language = {en},
140 number = {4},
141 urldate = {2012-08-14},
142 journal = {Molecular Biology and Evolution},
143 author = {Sanjuan, Rafael and Borderia, Antonio V.},
144 month = apr,
145 year = {2011},
146 pages = {1333--1338},
147 },
148
149 @article{fernandes_hiv-1_2012,
150 title = {The {HIV-1} rev response element: An {RNA} scaffold that directs the cooperative assembly of a homo-oligomeric ribonucleoprotein complex},
151 volume = {9},
152 issn = {1547-6286},
153 shorttitle = {The {HIV-1} rev response element},
154 url = {http://www.landesbioscience.com/journals/rnabiology/article/18178/?nocache=886329209},
155 doi = {10.4161/rna.9.1.18178},
156 number = {1},
157 urldate = {2012-09-03},
158 journal = {{RNA} Biology},
159 author = {Fernandes, Jason and Jayaraman, Bhargavi and Frankel, Alan},
160 month = jan,
161 year = {2012},
162 pages = {4--9},
163 },
164
165 @article{coleman_virus_2008,
166 title = {Virus Attenuation by Genome-Scale Changes in Codon Pair Bias},
167 volume = {320},
168 issn = {0036-8075, 1095-9203},
169 url = {http://www.sciencemag.org/content/320/5884/1784},
170 doi = {10.1126/science.1155761},
171 language = {en},
172 number = {5884},
173 urldate = {2012-10-08},
174 journal = {Science},
175 author = {Coleman, J. Robert and Papamichail, Dimitris and Skiena, Steven and Futcher, Bruce and Wimmer, Eckard and Mueller, Steffen},
176 month = jun,
177 year = {2008},
178 pages = {1784--1787},
179 },
180
181 @article{ngumbela_quantitative_2008,
182 title = {Quantitative Effect of Suboptimal Codon Usage on Translational Efficiency of {mRNA} Encoding {HIV-1} gag in Intact {T} Cells},
183 volume = {3},
184 url = {http://dx.plos.org/10.1371/journal.pone.0002356},
185 doi = {10.1371/journal.pone.0002356},
186 number = {6},
187 urldate = {2012-10-08},
188 journal = {{PLoS} {ONE}},
189 author = {Ngumbela, Kholiswa C. and Ryan, Kieran P. and Sivamurthy, Rohini and Brockman, Mark A. and Gandhi, Rajesh T. and Bhardwaj, Nina and Kavanagh, Daniel G.},
190 month = jun,
191 year = {2008},
192 pages = {e2356},
193 },
194
195 @article{plotkin_codon_2003,
196 title = {Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza {A} virus},
197 volume = {100},
198 issn = {0027-8424, 1091-6490},
199 url = {http://www.pnas.org/content/100/12/7152},
200 doi = {10.1073/pnas.1132114100},
201 language = {en},
202 number = {12},
203 urldate = {2012-10-17},
204 journal = {Proceedings of the National Academy of Sciences},
205 author = {Plotkin, Joshua B. and Dushoff, Jonathan},
206 month = jun,
207 year = {2003},
208 pages = {7152--7157},
209 },
210
211 @article{jenkins_extent_2003,
212 title = {The extent of codon usage bias in human {RNA} viruses and its evolutionary origin},
213 volume = {92},
214 issn = {0168-1702},
215 url = {http://www.sciencedirect.com/science/article/pii/S016817020200309X},
216 doi = {10.1016/S0168-1702(02)00309-X},
217 number = {1},
218 urldate = {2012-10-19},
219 journal = {Virus Research},
220 author = {Jenkins, Gareth M and Holmes, Edward C},
221 month = mar,
222 year = {2003},
223 keywords = {Base composition, codon usage bias, Dinucleotide, Mutation pressure, Translational selection},
224 pages = {1--7},
225 },
226
227 @article{bronson_nucleotide_1994,
228 title = {Nucleotide composition as a driving force in the evolution of retroviruses},
229 volume = {38},
230 issn = {0022-2844, 1432-1432},
231 url = {http://www.springerlink.com/content/c7m6653t2751w071/},
232 doi = {10.1007/BF00178851},
233 number = {5},
234 urldate = {2012-10-22},
235 journal = {Journal of Molecular Evolution},
236 author = {Bronson, Edward C. and Anderson, John N.},
237 month = may,
238 year = {1994},
239 pages = {506--532},
240 },
241
242 @article{li_codon-usage-based_2012,
243 title = {Codon-usage-based inhibition of {HIV} protein synthesis by human schlafen 11},
244 copyright = {© 2012 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
245 issn = {0028-0836},
246 url = {http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11433.html?WT.ec_id=NATURE-20120927},
247 doi = {10.1038/nature11433},
248 language = {en},
249 urldate = {2012-11-05},
250 journal = {Nature},
251 author = {Li, Manqing and Kao, Elaine and Gao, Xia and Sandig, Hilary and Limmer, Kirsten and Pavon-Eternod, Mariana and Jones, Thomas E. and Landry, Sebastien and Pan, Tao and Weitzman, Matthew D. and David, Michael},
252 year = {2012},
253 },
254
255 @article{boltz_ultrasensitive_2012,
256 title = {Ultrasensitive Allele-Specific {PCR} Reveals Rare Preexisting Drug-Resistant Variants and a Large Replicating Virus Population in Macaques Infected with a Simian Immunodeficiency Virus Containing Human Immunodeficiency Virus Reverse Transcriptase},
257 volume = {86},
258 issn = {0022-{538X}, 1098-5514},
259 url = {http://jvi.asm.org/content/86/23/12525},
260 doi = {10.1128/JVI.01963-12},
261 language = {en},
262 number = {23},
263 urldate = {2012-11-08},
264 journal = {Journal of Virology},
265 author = {Boltz, Valerie F. and Ambrose, Zandrea and Kearney, Mary F. and Shao, Wei and {KewalRamani}, Vineet N. and Maldarelli, Frank and Mellors, John W. and Coffin, John M.},
266 month = dec,
267 year = {2012},
268 pages = {12525--12530},
269 },
270 @article{Chen:2004p22606,
271 author = {Lamei Chen and Alla Perlina and Christopher J Lee},
272 journal = {J Virol},
273 title = {Positive selection detection in 40,000 human immunodeficiency virus ({HIV}) type 1 sequences automatically identifies drug resistance and positive fitness mutations in HIV protease and reverse transcriptase},
274 abstract = {Drug resistance is a major problem in the treatment of AIDS, due to the very high mutation rate of human immunodeficiency virus (HIV) and subsequent rapid development of resistance to new drugs. Identification of mutations associated with drug resistance is critical for both individualized treatment selection and new drug design. We have performed an automated mutation analysis of HIV Type 1 (HIV-1) protease and reverse transcriptase (RT) from approximately 40,000 AIDS patient plasma samples sequenced by Specialty Laboratories Inc. from 1999 to mid-2002. This data set provides a nearly complete mutagenesis of HIV protease and enables the calculation of statistically significant K(a)/K(s) values for each individual amino acid mutation in protease and RT. Positive selection (i.e., a K(a)/K(s) ratio of >1, indicating increased reproductive fitness) detected 19 of 23 known drug-resistant mutation positions in protease and 20 of 34 such positions in RT. We also discovered 163 new amino acid mutations in HIV protease and RT that are strong candidates for drug resistance or fitness. Our results match available independent data on protease mutations associated with specific drug treatments and mutations with positive reproductive fitness, with high statistical significance (the P values for the observed matches to occur by random chance are 10(-5.2) and 10(-16.6), respectively). Our mutation analysis provides a valuable resource for AIDS research and will be available to academic researchers upon publication at http://www.bioinformatics.ucla.edu/HIV. Our data indicate that positive selection mapping is an analysis that can yield powerful insights from high-throughput sequencing of rapidly mutating pathogens.},
275 affiliation = {Molecular Biology Institute, Center for Genomics and Proteomics, Dept. of Chemistry {\&} Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1570, USA.},
276 number = {7},
277 pages = {3722--32},
278 volume = {78},
279 year = {2004},
280 month = {Apr},
281 language = {eng},
282 keywords = {Automation, HIV Protease, Amino Acid Sequence, Structure-Activity Relationship, HIV Infections, Databases: Genetic, Drug Resistance: Viral, Mutation: Missense, Humans, DNA Mutational Analysis, Anti-HIV Agents, Phenotype, Selection (Genetics), Base Sequence, Lod Score, HIV-1, HIV Reverse Transcriptase},
283 date-added = {2009-04-23 20:07:20 +0200},
284 date-modified = {2009-04-23 20:07:24 +0200},
285 pmid = {15016892},
286 URL = {http://jvi.asm.org/cgi/content/full/78/7/3722?view=long&pmid=15016892},
287 local-url = {file://localhost/Users/richard/Papers/2004/Chen/Chen_J%20Virol_2004.pdf},
288 uri = {papers://C4A19094-F88E-460C-9862-A50496958974/Paper/p22606},
289 read = {Yes},
290 rating = {0}
291 }
292 @article{Rouzine:2005p17398,
293 author = {I M Rouzine and J M Coffin},
294 journal = {Genetics},
295 title = {Evolution of human immunodeficiency virus under selection and weak recombination},
296 abstract = {To predict emergence of drug resistance in patients undergoing antiretroviral therapy, we study accumulation of preexisting beneficial alleles in a haploid population of N genomes. The factors included in the model are selection with the coefficient s and recombination with the small rate per genome r (r << s sqrt of k, where k is the average number of less-fit loci per genome). Mutation events are neglected. To describe evolution at a large number of linked loci, we generalize the analytic method we developed recently for an asexual population. We show that the distribution of genomes over the deleterious allele number moves in time as a "solitary wave" that is quasi-deterministic in the middle (on the average) but has stochastic edges. We arrive at a single-locus expression for the average accumulation rate, in which the effects of linkage, recombination, and random drift are all accounted for by the effective selection coefficient s lnNr/lnNs(2)k/r. At large N, the effective selection coefficient approaches the single-locus value s. Below the critical size N(c) approximately 1/r, a population eventually becomes a clone, recombination cannot produce new sequences, and virus evolution stops. Taking into account finite mutation rate predicts a small, finite rate of evolution at N < N(c). We verify the accuracy of the results analytically and by Monte Carlo simulation. On the basis of our findings, we predict that partial depletion of the HIV population by combined anti-retroviral therapy can suppress emergence of drug-resistant strains.},
297 affiliation = {School of Medicine, Tufts University, Boston, Massachusetts 02111, USA. irouzine@tufts.edu},
298 number = {1},
299 pages = {7--18},
300 volume = {170},
301 year = {2005},
302 month = {May},
303 language = {eng},
304 keywords = {Models: Genetic, Mutation, Humans, Selection (Genetics), HIV, Population, Evolution: Molecular, Recombination: Genetic, Monte Carlo Method, Data Interpretation: Statistical, Computer Simulation},
305 date-added = {2008-09-02 18:50:47 +0200},
306 date-modified = {2008-09-02 18:50:51 +0200},
307 doi = {10.1534/genetics.104.029926},
308 pii = {genetics.104.029926},
309 pmid = {15744057},
310 local-url = {file://localhost/Users/richard/Papers/2005/Rouzine/Rouzine_Genetics_2005.pdf},
311 uri = {papers://C4A19094-F88E-460C-9862-A50496958974/Paper/p17398},
312 read = {Yes},
313 rating = {0}
314 }
315
316 @article{nijhuis_stochastic_1998,
317 title = {Stochastic processes strongly influence {HIV-1} evolution during suboptimal protease-inhibitor therapy},
318 volume = {95},
319 issn = {0027-8424, 1091-6490},
320 url = {http://www.pnas.org/content/95/24/14441},
321 doi = {10.1073/pnas.95.24.14441},
322 abstract = {It has long been assumed that {HIV-1} evolution is best described by deterministic evolutionary models because of the large population size. Recently, however, it was suggested that the effective population size (Ne) may be rather small, thereby allowing chance to influence evolution, a situation best described by a stochastic evolutionary model. To gain experimental evidence supporting one of the evolutionary models, we investigated whether the development of resistance to the protease inhibitor ritonavir affected the evolution of the env gene. Sequential serum samples from five patients treated with ritonavir were used for analysis of the protease gene and the V3 domain of the env gene. Multiple reverse {transcription–PCR} products were cloned, sequenced, and used to construct phylogenetic trees and to calculate the genetic variation and Ne. Genotypic resistance to ritonavir developed in all five patients, but each patient displayed a unique combination of mutations, indicating a stochastic element in the development of ritonavir resistance. Furthermore, development of resistance induced clear bottleneck effects in the env gene. The mean intrasample genetic variation, which ranged from 1.2\% to 5.7\% before treatment, decreased significantly (P {\textless} 0.025) during treatment. In agreement with these findings, Ne was estimated to be very small (500–15,000) compared with the total {HIV-1} {RNA} copy number. This study combines three independent observations, strong population bottlenecking, small Ne, and selection of different combinations of protease-resistance mutations, all of which indicate that {HIV-1} evolution is best described by a stochastic evolutionary model.},
323 language = {en},
324 number = {24},
325 urldate = {2013-01-04},
326 journal = {Proceedings of the National Academy of Sciences},
327 author = {Nijhuis, Monique and Boucher, Charles A. B. and Schipper, Pauline and Leitner, Thomas and Schuurman, Rob and Albert, Jan},
328 month = nov,
329 year = {1998},
330 pages = {14441--14446},
331 file = {Full Text PDF:/Users/richard/Library/Application Support/Firefox/Profiles/076bam2d.default/zotero/storage/4FT4XGAE/Nijhuis et al. - 1998 - Stochastic processes strongly influence HIV-1 evol.pdf:application/pdf;Snapshot:/Users/richard/Library/Application Support/Firefox/Profiles/076bam2d.default/zotero/storage/N8AR7JZX/14441.html:text/html}
332 }
333 @article{plotkin_synonymous_2011,
334 title = {Synonymous but not the same: the causes and consequences of codon bias},
335 volume = {12},
336 issn = {1471-0056},
337 shorttitle = {Synonymous but not the same},
338 url = {http://www.nature.com/nrg/journal/v12/n1/abs/nrg2899.html},
339 doi = {10.1038/nrg2899},
340 abstract = {Despite their name, synonymous mutations have significant consequences for cellular processes in all taxa. As a result, an understanding of codon bias is central to fields as diverse as molecular evolution and biotechnology. Although recent advances in sequencing and synthetic biology have helped to resolve longstanding questions about codon bias, they have also uncovered striking patterns that suggest new hypotheses about protein synthesis. Ongoing work to quantify the dynamics of initiation and elongation is as important for understanding natural synonymous variation as it is for designing transgenes in applied contexts.},
341 language = {en},
342 number = {1},
343 urldate = {2013-01-04},
344 journal = {Nature Reviews Genetics},
345 author = {Plotkin, Joshua B. and Kudla, Grzegorz},
346 month = jan,
347 year = {2011},
348 pages = {32--42},
349 file = {Full Text PDF:/Users/richard/Library/Application Support/Firefox/Profiles/076bam2d.default/zotero/storage/GQMNXPHJ/Plotkin and Kudla - 2011 - Synonymous but not the same the causes and conseq.pdf:application/pdf}
350 }
351 @article{Bhatt:2011p43255,
352 author = {S Bhatt and E. C Holmes and O. G Pybus},
353 journal = {Molecular Biology and Evolution},
354 title = {The Genomic Rate of Molecular Adaptation of the Human Influenza A Virus},
355 number = {9},
356 pages = {2443--2451},
357 volume = {28},
358 year = {2011},
359 month = {Sep},
360 date-added = {2011-08-29 16:05:32 +0200},
361 date-modified = {2011-08-29 16:05:32 +0200},
362 doi = {10.1093/molbev/msr044},
363 URL = {http://mbe.oxfordjournals.org/cgi/content/abstract/28/9/2443?etoc},
364 local-url = {file://localhost/Users/richard/Papers/2011/Bhatt/Bhatt_Molecular%20Biology%20and%20Evolution_2011.pdf},
365 uri = {papers://C4A19094-F88E-460C-9862-A50496958974/Paper/p43255},
366 rating = {0}
367 }
368 @article{Hurst:2002p32608,
369 author = {Laurence D Hurst},
370 journal = {Trends Genet},
371 title = {The {Ka/Ks} ratio: diagnosing the form of sequence evolution},
372 affiliation = {Department of Biology and Biochemistry, University of Bath, Bath, UK BA2 7AY. bssldh@bath.ac.uk},
373 number = {9},
374 pages = {486},
375 volume = {18},
376 year = {2002},
377 month = {Sep},
378 language = {eng},
379 keywords = {Humans, Selection: Genetic, Animals, Genetic Variation, Evolution: Molecular, Sequence Alignment},
380 date-added = {2010-02-09 02:35:04 +0100},
381 date-modified = {2010-02-09 02:35:09 +0100},
382 pii = {S0168952502027221},
383 pmid = {12175810},
384 URL = {http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=inwardhub&_urlversion=4&_method=citationSearch&_piikey=S0168952502027221&_version=1&md5=994712d847438f6994ce2a092b0f78a2},
385 local-url = {file://localhost/Users/richard/Papers/2002/Hurst/Hurst_Trends%20Genet_2002.pdf},
386 uri = {papers://C4A19094-F88E-460C-9862-A50496958974/Paper/p32608},
387 rating = {0}
388 }
389
390 @article{rambaut_causes_2004,
391 title = {The causes and consequences of {HIV} evolution},
392 volume = {5},
393 issn = {1471-0056},
394 url = {http://www.nature.com/nrg/journal/v5/n1/full/nrg1246.html},
395 doi = {10.1038/nrg1246},
396 abstract = {Understanding the evolution of the human immunodeficiency virus ({HIV)} is crucial for reconstructing its origin, deciphering its interaction with the immune system and developing effective control strategies. Although it is clear that {HIV-1} and {HIV-2} originated in African primates, dating their transmission to humans is problematic, especially because of frequent recombination. Our ability to predict the spread of drug-resistance and immune-escape mutations depends on understanding how {HIV} evolution differs within and among hosts and on the role played by positive selection. For this purpose, extensive sampling of {HIV} genetic diversity is required, and is essential for informing the design of {HIV} vaccines.},
397 language = {en},
398 number = {1},
399 urldate = {2013-01-04},
400 journal = {Nature Reviews Genetics},
401 author = {Rambaut, Andrew and Posada, David and Crandall, Keith A. and Holmes, Edward C.},
402 month = jan,
403 year = {2004},
404 pages = {52--61},
405 file = {Full Text PDF:/Users/richard/Library/Application Support/Firefox/Profiles/076bam2d.default/zotero/storage/JPSPZUU9/Rambaut et al. - 2004 - The causes and consequences of HIV evolution.pdf:application/pdf}
406 }
407
408 @article{kwong_hiv-1_2002,
409 title = {{HIV-1} evades antibody-mediated neutralization through conformational masking of receptor-binding sites},
410 volume = {420},
411 url = {http://www.nature.com/nature/journal/v420/n6916/abs/nature01188.html},
412 doi = {10.1038/nature01188},
413 number = {6916},
414 urldate = {2012-11-22},
415 journal = {Nature},
416 author = {Kwong, Peter D. and Doyle, Michael L. and Casper, David J. and Cicala, Claudia and Leavitt, Stephanie A. and Majeed, Shahzad and Steenbeke, Tavis D. and Venturi, Miro and Chaiken, Irwin and Fung, Michael and Katinger, Hermann and Parren, Paul W. I. H. and Robinson, James and Ryk, Donald Van and Wang, Liping and Burton, Dennis R. and Freire, Ernesto and Wyatt, Richard and Sodroski, Joseph and Hendrickson, Wayne A. and Arthos, James},
417 month = dec,
418 year = {2002},
419 pages = {678},
420 },
421
422 @article{pantaleo_immunopathogenesis_1996,
423 title = {Immunopathogenesis of {HIV} Infection},
424 volume = {50},
425 url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.micro.50.1.825},
426 doi = {10.1146/annurev.micro.50.1.825},
427 number = {1},
428 urldate = {2012-11-28},
429 journal = {Annual Review of Microbiology},
430 author = {Pantaleo, G. and Fauci, A. S.},
431 year = {1996},
432 note = {{PMID:} 8905100},
433 pages = {825--854},
434 },
435
436 @article{barat_interaction_1991,
437 title = {Interaction of {HIV-1} reverse transcriptase with a synthetic form of its replication primer, {tRNALys},3},
438 volume = {19},
439 issn = {0305-1048, 1362-4962},
440 url = {http://nar.oxfordjournals.org/content/19/4/751},
441 doi = {10.1093/nar/19.4.751},
442 language = {en},
443 number = {4},
444 urldate = {2012-11-28},
445 journal = {Nucleic Acids Research},
446 author = {Barat, Corinne and Grice, Stuart F. J. Le and Daelix, Jean-Luc},
447 month = feb,
448 year = {1991},
449 pages = {751--757},
450 },
451
452 @article{barat_hiv-1_1989,
453 title = {{HIV-1} reverse transcriptase specifically interacts with the anticodon domain of its cognate primer {tRNA.}},
454 volume = {8},
455 issn = {0261-4189},
456 url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC401457/},
457 number = {11},
458 urldate = {2012-11-28},
459 journal = {The {EMBO} Journal},
460 author = {Barat, C and Lullien, V and Schatz, O and Keith, G and Nugeyre, M T and Grüninger-Leitch, F and Barré-Sinoussi, F and {LeGrice}, S F and Darlix, J L},
461 month = nov,
462 year = {1989},
463 note = {{PMID:} 2479543
464 {PMCID:} {PMC401457}},
465 pages = {3279--3285},
466 },
467
468 @article{paillart_vitro_2002,
469 title = {In Vitro Evidence for a Long Range Pseudoknot in the 5-Untranslated and Matrix Coding Regions of {HIV-1} Genomic {RNA}},
470 volume = {277},
471 issn = {0021-9258, 1083-{351X}},
472 url = {http://www.jbc.org/content/277/8/5995},
473 doi = {10.1074/jbc.M108972200},
474 language = {en},
475 number = {8},
476 urldate = {2012-11-28},
477 journal = {Journal of Biological Chemistry},
478 author = {Paillart, Jean-Christophe and Skripkin, Eugene and Ehresmann, Bernard and Ehresmann, Chantal and Marquet, Roland},
479 month = feb,
480 year = {2002},
481 pages = {5995--6004},
482 },
483
484 @book{ewens_mathematical_2004,
485 title = {Mathematical Population Genetics: {I.}~Theoretical Introduction},
486 isbn = {9780387201917},
487 shorttitle = {Mathematical Population Genetics},
488 language = {en},
489 publisher = {Springer},
490 author = {Ewens, Warren J.},
491 month = jan,
492 year = {2004},
493 },
494
495 @article{zanini_ffpopsim:_2012,
496 title = {{FFPopSim:} An efficient forward simulation package for the evolution of large populations},
497 issn = {1367-4803, 1460-2059},
498 shorttitle = {{FFPopSim}},
499 url = {http://bioinformatics.oxfordjournals.org/content/early/2012/10/24/bioinformatics.bts633},
500 doi = {10.1093/bioinformatics/bts633},
501 language = {en},
502 urldate = {2012-12-01},
503 journal = {Bioinformatics},
504 author = {Zanini, Fabio and Neher, Richard A.},
505 month = oct,
506 year = {2012},
507 },
508
509 @article{desai_beneficial_2007,
510 title = {Beneficial mutation selection balance and the effect of linkage on positive selection.},
511 volume = {176},
512 doi = {10.1534/genetics.106.067678},
513 number = {3},
514 journal = {Genetics},
515 author = {Desai, Michael M and Fisher, Daniel S},
516 month = jul,
517 year = {2007},
518 pages = {1759--98},
519 },
520
521 @article{richman_rapid_2003,
522 title = {Rapid evolution of the neutralizing antibody response to {HIV} type 1 infection},
523 volume = {100},
524 issn = {0027-8424, 1091-6490},
525 url = {http://www.pnas.org/content/100/7/4144},
526 doi = {10.1073/pnas.0630530100},
527 number = {7},
528 urldate = {2012-11-22},
529 journal = {Proceedings of the National Academy of Sciences},
530 author = {Richman, Douglas D. and Wrin, Terri and Little, Susan J. and Petropoulos, Christos J.},
531 month = apr,
532 year = {2003},
533 pages = {4144--4149},
534 },
535
536 @article{moore_limited_2009,
537 title = {Limited Neutralizing Antibody Specificities Drive Neutralization Escape in Early {HIV-1} Subtype {C} Infection},
538 volume = {5},
539 url = {http://dx.doi.org/10.1371/journal.ppat.1000598},
540 doi = {10.1371/journal.ppat.1000598},
541 number = {9},
542 urldate = {2012-08-17},
543 journal = {PLoS Pathog},
544 author = {Moore, Penny L. and Ranchobe, Nthabeleng and Lambson, Bronwen E. and Gray, Elin S. and Cave, Eleanor and Abrahams, Melissa-Rose and Bandawe, Gama and Mlisana, Koleka and Abdool Karim, Salim S. and Williamson, Carolyn and Morris, Lynn and the {CAPRISA} 002 study and the {NIAID} Center for {HIV/AIDS} Vaccine Immunology {(CHAVI)}},
545 month = sep,
546 year = {2009},
547 pages = {e1000598},
548 },
549
550 @article{brenner_high_2007,
551 title = {High Rates of Forward Transmission Events after Acute/Early {HIV-1} Infection},
552 volume = {195},
553 issn = {0022-1899, 1537-6613},
554 url = {http://jid.oxfordjournals.org/content/195/7/951},
555 doi = {10.1086/512088},
556 language = {en},
557 number = {7},
558 urldate = {2012-12-02},
559 journal = {Journal of Infectious Diseases},
560 author = {Brenner, Bluma G. and Roger, Michel and Routy, Jean-Pierre and Moisi, Daniela and Ntemgwa, Michel and Matte, Claudine and Baril, Jean-Guy and Thomas, Rejean and Rouleau, Danielle and Bruneau, Julie and Leblanc, Roger and Legault, Mario and Tremblay, Cecile and Charest, Hugues and Wainberg, Mark A.},
561 month = apr,
562 year = {2007},
563 pages = {951--959},
564 },
565
566 @article{strelkowa_clonal_2012,
567 title = {Clonal Interference in the Evolution of Influenza},
568 issn = {0016-6731, 1943-2631},
569 url = {http://www.genetics.org/content/early/2012/07/20/genetics.112.143396},
570 doi = {10.1534/genetics.112.143396},
571 language = {en},
572 urldate = {2012-08-01},
573 journal = {Genetics},
574 author = {Strelkowa, Natalja and Laessig, Michael},
575 month = jul,
576 year = {2012},
577 },
578
579 @article{mansky_lower_1995,
580 title = {Lower In Vivo Mutation Rate of Human Immunodeficiency Virus Type 1 than That Predicted from the Fidelity of Purified Reverse Transcriptase},
581 volume = {69},
582 url = {file:///home/fabio/university/evolution/references/J. Virol.-1995-Mansky-5087-94.pdf},
583 number = {8},
584 journal = {Journal of virology},
585 author = {Mansky, L M and Temin, H M},
586 year = {1995},
587 pages = {5087--5094},
588 },
589
590 @article{mcmichael_immune_2009,
591 title = {The immune response during acute {HIV-1} infection: clues for vaccine development},
592 volume = {10},
593 url = {http://www.nature.com/doifinder/10.1038/nri2674},
594 doi = {10.1038/nri2674},
595 number = {1},
596 journal = {Nature Reviews Immunology},
597 author = {{McMichael}, Andrew J. and Borrow, Persephone and Tomaras, Georgia D. and Goonetilleke, Nilu and Haynes, Barton F.},
598 month = dec,
599 year = {2009},
600 pages = {11--23},
601 },
602
603 @article{williamson_adaptation_2003,
604 title = {Adaptation in the env gene of {HIV-1} and evolutionary theories of disease progression.},
605 volume = {20},
606 url = {http://www.ncbi.nlm.nih.gov/pubmed/12777505},
607 doi = {10.1093/molbev/msg144},
608 number = {8},
609 journal = {Molecular biology and evolution},
610 author = {Williamson, Scott},
611 year = {2003},
612 pages = {1318--25},
613 },
614
615 @article{smith_hitch-hiking_1974,
616 title = {The hitch-hiking effect of a favourable gene},
617 volume = {23},
618 number = {1},
619 journal = {Genetical research},
620 author = {Smith, J M and Haigh, J},
621 month = feb,
622 year = {1974},
623 note = {{PMID:} 4407212},
624 pages = {23--35}
625 },
626
627 @article{josefsson_majority_2011,
628 title = {Majority of {CD4+} T cells from peripheral blood of {HIV-1} infected individuals contain only one {HIV} {DNA} molecule},
629 volume = {108},
630 issn = {0027-8424, 1091-6490},
631 url = {http://www.pnas.org/content/108/27/11199},
632 doi = {10.1073/pnas.1107729108},
633 language = {en},
634 number = {27},
635 urldate = {2012-12-06},
636 journal = {Proceedings of the National Academy of Sciences},
637 author = {Josefsson, Lina and King, Martin S. and Makitalo, Barbro and Br\"annstr\"om, Johan and Shao, Wei and Maldarelli, Frank and Kearney, Mary F. and Hu, Wei-Shau and Chen, Jianbo and Gaines, Hans and Mellors, John W. and Albert, Jan and Coffin, John M. and Palmer, Sarah E.},
638 month = jul,
639 year = {2011},
640 pages = {11199--11204},
641 },
642
643 @article{bar_early_2012,
644 title = {Early Low-Titer Neutralizing Antibodies Impede {HIV-1} Replication and Select for Virus Escape},
645 volume = {8},
646 url = {http://dx.doi.org/10.1371/journal.ppat.1002721},
647 doi = {10.1371/journal.ppat.1002721},
648 number = {5},
649 urldate = {2012-12-06},
650 journal = {{PLoS} Pathog},
651 author = {Bar, Katharine J. and Tsao, Chun-yen and Iyer, Shilpa S. and Decker, Julie M. and Yang, Yongping and Bonsignori, Mattia and Chen, Xi and Hwang, Kwan-Ki and Montefiori, David C. and Liao, Hua-Xin and Hraber, Peter and Fischer, William and Li, Hui and Wang, Shuyi and Sterrett, Sarah and Keele, Brandon F. and Ganusov, Vitaly V. and Perelson, Alan S. and Korber, Bette T. and Georgiev, Ivelin and {McLellan}, Jason S. and Pavlicek, Jeffrey W. and Gao, Feng and Haynes, Barton F. and Hahn, Beatrice H. and Kwong, Peter D. and Shaw, George M.},
652 month = may,
653 year = {2012},
654 pages = {e1002721}
655 },
656
657 @article{gillespie_genetic_2000,
658 title = {Genetic drift in an infinite population. The pseudohitchhiking model.},
659 volume = {155},
660 url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1461093&tool=pmcentrez&rendertype=abstract},
661 number = {2},
662 journal = {Genetics},
663 author = {Gillespie, J H},
664 month = jul,
665 year = {2000},
666 pages = {909--19},
667 },
668
669 @article{yang_statistical_2000,
670 title = {Statistical methods for detecting molecular adaptation},
671 volume = {15},
672 issn = {0169-5347},
673 url = {http://www.sciencedirect.com/science/article/pii/S0169534700019947},
674 doi = {10.1016/S0169-5347(00)01994-7},
675 number = {12},
676 urldate = {2012-12-14},
677 journal = {Trends in Ecology \& Evolution},
678 author = {Yang, Ziheng and Bielawski, Joseph P.},
679 month = dec,
680 year = {2000},
681 pages = {496--503},
682 },
683
684 @article{neher_rate_2010,
685 title = {Rate of adaptation in large sexual populations},
686 volume = {184},
687 url = {http://www.genetics.org/cgi/content/abstract/184/2/467},
688 doi = {10.1534/genetics.109.109009},
689 number = {2},
690 journal = {Genetics},
691 author = {Neher, {R.A.} and Shraiman, {B.I.} and Fisher, {D.S.}},
692 year = {2010},
693 pages = {467},
694 },
695
696 @book{LANL2012,
697 title = {HIV Sequence Compendium 2012},
698 author = {Kuiken, Carla and Leitner, Thomas and Hahn, Beatrice and Mullins, James and Wolinsky, Steven and Foley, Brian and Apetrei, Cristian and Mizrachi, Ilene and Rambaut, Andrew and Korber, Bette},
699 year = {2012},
700 publisher = {Theoretical Biology and Biophysics Group T-6, Mail Stop K710 Los Alamos National Laboratory Los Alamos, New Mexico 87545 U.S.A.},
701 },
702
703 @article{edgar_muscle:_2004,
704 title = {{MUSCLE:} multiple sequence alignment with high accuracy and high throughput},
705 volume = {32},
706 issn = {0305-1048, 1362-4962},
707 shorttitle = {{MUSCLE}},
708 url = {http://nar.oxfordjournals.org/content/32/5/1792},
709 doi = {10.1093/nar/gkh340},
710 language = {en},
711 number = {5},
712 urldate = {2012-12-20},
713 journal = {Nucleic Acids Research},
714 author = {Edgar, Robert C.},
715 month = mar,
716 year = {2004},
717 pages = {1792--1797},
718 },
719
720 @article{mueller_live_2010,
721 title = {Live attenuated influenza virus vaccines by computer-aided rational design},
722 volume = {28},
723 copyright = {© 2010 Nature Publishing Group},
724 issn = {1087-0156},
725 url = {http://www.nature.com/nbt/journal/v28/n7/abs/nbt.1636.html},
726 doi = {10.1038/nbt.1636},
727 language = {en},
728 number = {7},
729 urldate = {2012-10-08},
730 journal = {Nature Biotechnology},
731 author = {Mueller, Steffen and Coleman, J. Robert and Papamichail, Dimitris and Ward, Charles B. and Nimnual, Anjaruwee and Futcher, Bruce and Skiena, Steven and Wimmer, Eckard},
732 year = {2010},
733 pages = {723--726},
734 }
735