-
1
-
-
4944263648
-
A robust measure of HIV-1 population turnover within chronically infected individuals
-
DOI 10.1093/molbev/msh196
-
ACHAZ G., PALMER S., KEARNEY M., MALDARELLI F., MELLORS J.W., COFFIN J.M., ET AL. (2004). A robust measure of HIV-1 population turnover within chronically infected individuals. Mol. Biol. Evol. 21, 1902-1912. (Pubitemid 39331637)
-
(2004)
Molecular Biology and Evolution
, vol.21
, Issue.10
, pp. 1902-1912
-
-
Achaz, G.1
Palmer, S.2
Kearney, M.3
Maldarelli, F.4
Mellors, J.W.5
Coffin, J.M.6
Wakeley, J.7
-
2
-
-
77952309592
-
Epidemic dynamics revealed in dengue evolution
-
BENNETT S.N., DRUMMOND A.J., KAPAN D.D., SUCHARD M.A., MUNOZ-JORDAN J.L., PYBUS O.G., ET AL. (2010). Epidemic dynamics revealed in dengue evolution. Mol. Biol. Evol. 27, 811-818.
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 811-818
-
-
Bennett, S.N.1
Drummond, A.J.2
Kapan, D.D.3
Suchard, M.A.4
Munoz-Jordan, J.L.5
Pybus, O.G.6
-
3
-
-
80053439798
-
Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection
-
BULL R.A., LUCIANI F., MCELROY K., GAUDIERI S., PHAM S.T., CHOPRA A., ET AL. (2011). Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection. PLoS Pathog. 7, e1002243.
-
(2011)
PLoS Pathog.
, vol.7
-
-
Bull, R.A.1
Luciani, F.2
McElroy, K.3
Gaudieri, S.4
Pham, S.T.5
Chopra, A.6
-
5
-
-
80055078962
-
Deep molecular characterization of HIV-1 dynamics under suppressive HAART
-
BUZONM.J., CODONER F.M., FROST S.D., POU C., PUERTAS M.C., MASSANELLA M., ET AL. (2011). Deep molecular characterization of HIV-1 dynamics under suppressive HAART. PLoS Pathog. 7, e1002314.
-
(2011)
PLoS Pathog.
, vol.7
-
-
Buzonm, J.1
Codoner, F.M.2
Frost, S.D.3
Pou, C.4
Puertas, M.C.5
Massanella, M.6
-
6
-
-
33644911496
-
Recombination estimation under complex evolutionary models with the coalescent compositelikelihood method
-
CARVAJAL-RODRIGUEZ A., CRANDALL K.A., POSADA D. (2006). Recombination estimation under complex evolutionary models with the coalescent compositelikelihood method. Mol. Biol. Evol. 23, 817-827.
-
(2006)
Mol. Biol. Evol.
, vol.23
, pp. 817-827
-
-
Carvajal-Rodriguez, A.1
Crandall, K.A.2
Posada, D.3
-
7
-
-
82455188363
-
Molecular phylodynamics and protein modeling of infectious salmon anemia virus (ISAV
-
CASTRO-NALLAR E., CORTEZ-SANMARTIN M., MASCAYANO C., MOLINA C., CRANDALL K.A. (2011). Molecular phylodynamics and protein modeling of infectious salmon anemia virus (ISAV). BMC. Evol. Biol. 11, 349.
-
(2011)
BMC. Evol. Biol.
, vol.11
, pp. 349
-
-
Castro-Nallar, E.1
Cortez-Sanmartin, M.2
Mascayano, C.3
Molina, C.4
Crandall, K.A.5
-
8
-
-
84858609379
-
Characterization of drug resistance mutations in naive and ART-treated patients infected with HIV-1 in Yaounde, Cameroon
-
CECCARELLI L., SALPINI R., MOUDOUROU S., CENTO V., SANTORO M.M., FOKAM J., ET AL. (2012). Characterization of drug resistance mutations in naive and ART-treated patients infected with HIV-1 in Yaounde, Cameroon. J. Med. Virol. 84, 721-727.
-
(2012)
J. Med. Virol.
, vol.84
, pp. 721-727
-
-
Ceccarelli, L.1
Salpini, R.2
Moudourou, S.3
Cento, V.4
Santoro, M.M.5
Fokam, J.6
-
9
-
-
79956305415
-
Reconstruction of the evolutionary dynamics of the hepatitis C virus 1b epidemic in Turkey
-
CICCOZZIM., CICCAGLIONE A.R., LO PRESTI A., YALCINKAYA T., TASKAN Z.P., EQUESTRE M., ET AL. (2011). Reconstruction of the evolutionary dynamics of the hepatitis C virus 1b epidemic in Turkey. Infect. Genet. Evol. 11, 863-868.
-
(2011)
Infect. Genet. Evol.
, vol.11
, pp. 863-868
-
-
Ciccozzi, M.1
Ciccaglione, A.R.2
Presti A, L.O.3
Yalcinkaya, T.4
Taskan, Z.P.5
Equestre, M.6
-
10
-
-
33845901234
-
Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak
-
DOI 10.1038/444836a, PII 444836A
-
DE OLIVEIRA T., PYBUS O.G., RAMBAUT A., SALEMI M., CASSOL S., CICCOZZIM., ET AL. (2006). Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak. Nature. 444, 836-837. (Pubitemid 46024988)
-
(2006)
Nature
, vol.444
, Issue.7121
, pp. 836-837
-
-
De Oliveira, T.1
Pybus, O.G.2
Rambaut, A.3
Salemi, M.4
Cassol, S.5
Ciccozzi, M.6
Rezza, G.7
Gattinara, G.C.8
D'Arrigo, R.9
Amicosante, M.10
Perrin, L.11
Colizzi, V.12
Perno, C.F.13
-
11
-
-
0042512083
-
Measurably evolving populations
-
DOI 10.1016/S0169-5347(03)00216-7
-
DRUMMOND A.J., PYBUS O.G., RAMBAUT A., FORSBERG R., RODRIGO A.G. (2003). Measurably evolving populations. Trends. Ecol. Evol. 18, 481-488. (Pubitemid 37007509)
-
(2003)
Trends in Ecology and Evolution
, vol.18
, Issue.9
, pp. 481-488
-
-
Drummond, A.J.1
Pybus, O.G.2
Rambaut, A.3
Forsberg, R.4
Rodrigo, A.G.5
-
12
-
-
17744381574
-
Bayesian coalescent inference of past population dynamics from molecular sequences
-
DOI 10.1093/molbev/msi103
-
DRUMMOND A.J., RAMBAUT A., SHAPIRO B., PYBUS O.G. (2005). Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol 22, 1185-1192. (Pubitemid 40577756)
-
(2005)
Molecular Biology and Evolution
, vol.22
, Issue.5
, pp. 1185-1192
-
-
Drummond, A.J.1
Rambaut, A.2
Shapiro, B.3
Pybus, O.G.4
-
16
-
-
33244495782
-
Accuracy of coalescent likelihood estimates: Do we need more sites, more sequences, or more loci?
-
DOI 10.1093/molbev/msj079
-
FELSENSTEIN J. (2006). Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci? Mol. Biol. Evol. 23, 691-700. (Pubitemid 43278281)
-
(2006)
Molecular Biology and Evolution
, vol.23
, Issue.3
, pp. 691-700
-
-
Felsenstein, J.1
-
17
-
-
0014211361
-
Construction of phylogenetic trees
-
FITCH W.M., MARGOLIASH E. (1967). Construction of phylogenetic trees. Science. 155, 279-284.
-
(1967)
Science
, vol.155
, pp. 279-284
-
-
Fitch, W.M.1
Margoliash, E.2
-
19
-
-
36749031231
-
The emergence of HIV/AIDS in the Americas and beyond
-
DOI 10.1073/pnas.0705329104
-
GILBERT M.T., RAMBAUT A., WLASIUK G., SPIRA T.J., PITCHENIK A.E., WOROBEYM. (2007). The emergence of HIV/AIDS in the Americas and beyond. Proc. Natl. Acad. Sci USA. 104, 18566-18570. (Pubitemid 350210737)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.47
, pp. 18566-18570
-
-
Gilbert, M.T.P.1
Rambaut, A.2
Wlasiuk, G.3
Spira, T.J.4
Pitchenik, A.E.5
Worobey, M.6
-
20
-
-
70249113753
-
Spatial phylodynamics of HIV-1 epidemic emergence in east Africa
-
GRAY R.R., TATEM A.J., LAMERS S., HOU W., LAEYENDECKER O., SERWADDA D., ET AL. (2009). Spatial phylodynamics of HIV-1 epidemic emergence in east Africa. Aids. 23, F9-F17.
-
(2009)
Aids
, vol.23
-
-
Gray, R.R.1
Tatem, A.J.2
Lamers, S.3
Hou, W.4
Laeyendecker, O.5
Serwadda, D.6
-
21
-
-
77953136732
-
Evolutionary characterization of the West Nile Virus complete genome
-
GRAY R.R., VERAS N.M., SANTOS L.A., SALEMIM. (2010). Evolutionary characterization of the West Nile Virus complete genome. Mol. Phylogenet. Evol. 56, 195-200.
-
(2010)
Mol. Phylogenet. Evol.
, vol.56
, pp. 195-200
-
-
Gray, R.R.1
Veras, N.M.2
Santos, L.A.3
Salemi, M.4
-
22
-
-
79955998952
-
The mode and tempo of hepatitis C virus evolution within and among hosts
-
GRAY R.R., PARKER J., LEMEY P., SALEMIM., KATZOURAKIS A., PYBUS O.G. (2011a). The mode and tempo of hepatitis C virus evolution within and among hosts. BMC Evol. Biol. 11, 131.
-
(2011)
BMC Evol. Biol.
, vol.11
, pp. 131
-
-
Gray, R.R.1
Parker, J.2
Lemey Salemi P, M.3
Katzourakis, A.4
Pybus, O.G.5
-
23
-
-
84862153320
-
Measuring the temporal structure in serially-sampled phylogenies
-
GRAY R.R., PYBUS O.G., SALEMI M. (2011b). Measuring the temporal structure in serially-sampled phylogenies. Methods Ecol. Evol. 2, 437-445.
-
(2011)
Methods Ecol. Evol.
, vol.2
, pp. 437-445
-
-
Gray, R.R.1
Pybus, O.G.2
Salemi, M.3
-
24
-
-
78650915121
-
Multiple independent lineages of HIV-1 persist in breast milk and plasma
-
GRAY R.R., SALEMIM., LOWE A., NAKAMURA K.J., DECKER W.D., SINKALA M., ET AL. (2011c). Multiple independent lineages of HIV-1 persist in breast milk and plasma. Aids. 25, 143-152.
-
(2011)
Aids
, vol.25
, pp. 143-152
-
-
Gray, R.R.1
Salemi, M.2
Lowe, A.3
Nakamura, K.J.4
Decker, W.D.5
Sinkala, M.6
-
25
-
-
79955416536
-
Testing spatiotemporal hypothesis of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wide data within a bayesian framework
-
GRAY R.R., TATEM A.J., JOHNSON J.A., ALEKSEYENKO A.V., PYBUS O.G., SUCHARD M.A., ET AL. (2011d). Testing spatiotemporal hypothesis of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wide data within a bayesian framework. Mol. Biol. Evol. 28, 1593-1603.
-
(2011)
Mol. Biol. Evol.
, vol.28
, pp. 1593-1603
-
-
Gray, R.R.1
Tatem, A.J.2
Johnson, J.A.3
Alekseyenko, A.V.4
Pybus, O.G.5
Suchard, M.A.6
-
26
-
-
84862119350
-
A new evolutionary model for Hepatitis C virus chronic infection
-
In press
-
GRAY R.R., SALEMI M., KLENERMAN P., PYBUS O.G. (2012). A new evolutionary model for Hepatitis C virus chronic infection. PLoS Pathog. In press.
-
(2012)
PLoS Pathog
-
-
Gray, R.R.1
Salemi, M.2
Klenerman, P.3
Pybus, O.G.4
-
27
-
-
0346373759
-
Unifying the epidemiological and evolutionary dynamics of pathogens
-
DOI 10.1126/science.1090727
-
GRENFELL B.T., PYBUS O.G., GOG J.R., WOOD J.L., DALY J.M., MUMFORD J.A., ET AL. 2004). Unifying the epidemiological and evolutionary dynamics of pathogens. Science. 303, 327-332. (Pubitemid 38095764)
-
(2004)
Science
, vol.303
, Issue.5656
, pp. 327-332
-
-
Grenfell, B.T.1
Pybus, O.G.2
Gog, J.R.3
Wood, J.L.N.4
Daly, J.M.5
Mumford, J.A.6
Holmes, E.C.7
-
29
-
-
75649084906
-
Evolution of MRSA during hospital transmission and intercontinental spread
-
HARRIS S.R., FEIL E.J., HOLDEN M.T., QUAIL M.A., NICKERSON E.K., CHANTRATITA N., ET AL. (2010). Evolution of MRSA during hospital transmission and intercontinental spread. Science. 327, 469-474.
-
(2010)
Science
, vol.327
, pp. 469-474
-
-
Harris, S.R.1
Feil, E.J.2
Holden, M.T.3
Quail, M.A.4
Nickerson, E.K.5
Chantratita, N.6
-
30
-
-
84861214061
-
Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection
-
HENN M.R., BOUTWELL C.L., CHARLEBOIS P., LENNON N.J., POWER K.A., MACALALAD A.R., ET AL. (2012). Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection. PLoS Pathog. 8, e1002529.
-
(2012)
PLoS Pathog.
, vol.8
-
-
Henn, M.R.1
Boutwell, C.L.2
Charlebois, P.3
Lennon, N.J.4
Power, K.A.5
MacAlalad, A.R.6
-
31
-
-
79960419997
-
Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes
-
HERBECK J.T., ROLLAND M., LIU Y., MCLAUGHLIN S., MCNEVIN J., ZHAO H., ET AL. (2011). Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes. J. Virol. 85, 7523-7534.
-
(2011)
J. Virol.
, vol.85
, pp. 7523-7534
-
-
Herbeck, J.T.1
Rolland, M.2
Liu, Y.3
McLaughlin, S.4
McNevin, J.5
Zhao, H.6
-
32
-
-
77951432232
-
Intrahost evolutionary dynamics of canine influenza virus in naive and partially immune dogs
-
HOELZER K., MURCIA P.R., BAILLIE G.J., WOOD J.L., METZGER S.M., OSTERRIEDER N., ET AL. (2010). Intrahost evolutionary dynamics of canine influenza virus in naive and partially immune dogs. J. Virol. 84, 5329-5335.
-
(2010)
J. Virol.
, vol.84
, pp. 5329-5335
-
-
Hoelzer, K.1
Murcia, P.R.2
Baillie, G.J.3
Wood, J.L.4
Metzger, S.M.5
Osterrieder, N.6
-
33
-
-
70350476886
-
Discovering the phylodynamics of RNA viruses
-
HOLMES E.C., GRENFELL B.T. (2009). Discovering the phylodynamics of RNA viruses. PLoS Comput. Biol. 5, e1000505.
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Holmes, E.C.1
Grenfell, B.T.2
-
34
-
-
15444367844
-
Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups
-
DOI 10.1073/pnas.0407534102
-
HUE S., PILLAY D., CLEWLEY J.P., PYBUS O.G. (2005). Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups. Proc. Natl. Acad. Sci USA. 102, 4425-4429. (Pubitemid 40397128)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.12
, pp. 4425-4429
-
-
Hue, S.1
Pillay, D.2
Clewley, J.P.3
Pybus, O.G.4
-
35
-
-
34547894542
-
Sequential broadening of CTL responses in early HIV-1 infection is associated with viral escape
-
KARLSSON A.C., IVERSEN A.K., CHAPMAN J.M., DE OLIVIERA T., SPOTTS G., MCMICHAEL A.J., ET AL. (2007). Sequential broadening of CTL responses in early HIV-1 infection is associated with viral escape. PLoS One. 2, e225.
-
(2007)
PLoS One
, vol.2
-
-
Karlsson, A.C.1
Iversen, A.K.2
Chapman, J.M.3
De Oliviera, T.4
Spotts, G.5
McMichael, A.J.6
-
36
-
-
70450191608
-
Origin and phylodynamics of rabbit hemorrhagic disease virus
-
KERR P.J., KITCHEN A., HOLMES E.C. (2009). Origin and phylodynamics of rabbit hemorrhagic disease virus. J. Virol. 83, 12129-12138.
-
(2009)
J. Virol.
, vol.83
, pp. 12129-12138
-
-
Kerr, P.J.1
Kitchen, A.2
Holmes, E.C.3
-
37
-
-
0014553632
-
The rate of molecular evolution considered from the standpoint of population genetics
-
KIMURAM. (1969). The rate of molecular evolution considered from the standpoint of population genetics. Proc. Natl. Acad. Sci. USA. 63, 1181-1188.
-
(1969)
Proc. Natl. Acad. Sci. USA
, vol.63
, pp. 1181-1188
-
-
Kimura, M.1
-
38
-
-
0019296687
-
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
-
DOI 10.1007/BF01731581
-
KIMURAM. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120. (Pubitemid 11166431)
-
(1980)
Journal of Molecular Evolution
, vol.16
, Issue.2
, pp. 111-120
-
-
Kimura, M.1
-
40
-
-
33845879635
-
Epochal evolution shapes the phylodynamics of interpandemic influenza a (H3N2) in humans
-
DOI 10.1126/science.1132745
-
KOELLE K., COBEY S., GRENFELL B., PASCUAL M. (2006). Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans. Science. 314, 1898-1903. (Pubitemid 46026107)
-
(2006)
Science
, vol.314
, Issue.5807
, pp. 1898-1903
-
-
Koelle, K.1
Cobey, S.2
Grenfell, B.3
Pascual, M.4
-
41
-
-
33645108873
-
LAMARC 2.0: Maximum likelihood and Bayesian estimation of population parameters
-
KUHNER M.K. (2006). LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics. 22, 768-770.
-
(2006)
Bioinformatics
, vol.22
, pp. 768-770
-
-
Kuhner, M.K.1
-
42
-
-
82655162070
-
Phylogenetic and epidemic modeling of rapidly evolving infectious diseases
-
KUHNERT D., WU C.H., DRUMMOND A.J. (2011). Phylogenetic and epidemic modeling of rapidly evolving infectious diseases. Infect. Genet. Evol. 11, 1825-1841.
-
(2011)
Infect. Genet. Evol.
, vol.11
, pp. 1825-1841
-
-
Kuhnert, D.1
H, W.U.C.2
Drummond, A.J.3
-
43
-
-
78650222420
-
HIV-1 phylogenetic analysis shows HIV-1 transits through the meninges to brain and peripheral tissues
-
LAMERS S.L., GRAY R.R., SALEMIM., HUYSENTRUYT L.C., MCGRATHM.S. (2011). HIV-1 phylogenetic analysis shows HIV-1 transits through the meninges to brain and peripheral tissues. Infect. Genet. Evol. 11, 31-37.
-
(2011)
Infect. Genet. Evol.
, vol.11
, pp. 31-37
-
-
Lamers, S.L.1
Gray, R.R.2
Salemi, M.3
Huysentruyt, L.C.4
McGrath, M.S.5
-
44
-
-
58149175798
-
Dynamic correlation between intrahost HIV-1 quasispecies evolution and disease progression
-
LEE H.Y., PERELSON A.S., PARK S.C., LEITNER T. (2008). Dynamic correlation between intrahost HIV-1 quasispecies evolution and disease progression. PLoS Comput. Biol. 4, e1000240.
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Lee, H.Y.1
Perelson, A.S.2
Park, S.C.3
Leitner, T.4
-
46
-
-
33847246314
-
Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics
-
LEMEY P., KOSAKOVSKY POND S.L., DRUMMOND A.J., PYBUS O.G., SHAPIRO B., BARROSO H., ET AL. (2007). Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. PLoS Comput. Biol. 3, e29.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Lemey, P.1
Kosakovsky Pond, S.L.2
Drummond, A.J.3
Pybus, O.G.4
Shapiro, B.5
Barroso, H.6
-
49
-
-
84873403934
-
Reconstructing the initial global spread of a human influenza pandemic: A Bayesian spatial-temporal model for the global spread of H1N1pdm
-
LEMEY P., SUCHARD M., RAMBAUT A. (2009b). Reconstructing the initial global spread of a human influenza pandemic: a Bayesian spatial-temporal model for the global spread of H1N1pdm. PLoS Curr. 1, RRN1031.
-
(2009)
PLoS Curr.
, vol.1
-
-
Lemey, P.1
Suchard, M.2
Rambaut, A.3
-
50
-
-
41549160713
-
Episodic sexual transmission of HIV revealed by molecular phylodynamics
-
LEWIS F., HUGHES G.J., RAMBAUT A., POZNIAK A., LEIGH BROWN A.J. (2008). Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Med. 5, e50.
-
(2008)
PLoS Med.
, vol.5
-
-
Lewis, F.1
Hughes, G.J.2
Rambaut, A.3
Pozniak, A.4
Leigh Brown, A.J.5
-
51
-
-
80051634063
-
Phylodynamics and molecular evolution of influenza A virus nucleoprotein genes in Taiwan between 1979 and 2009
-
LIN J.H., CHIU S.C., CHENG J.C., CHANG H.W., HSIAO K.L., LIN Y.C., ET AL. (2011). Phylodynamics and molecular evolution of influenza A virus nucleoprotein genes in Taiwan between 1979 and 2009. PLoS One. 6, e23454.
-
(2011)
PLoS One
, vol.6
-
-
Lin, J.H.1
Chiu, S.C.2
Cheng, J.C.3
Chang, H.W.4
Hsiao, K.L.5
Lin, Y.C.6
-
52
-
-
68049117371
-
Reduction of the HIV-1 reservoir in resting CD4+ Tlymphocytes by high dosage intravenous immunoglobulin treatment: A proof-of-concept study
-
LINDKVIST A., EDEN A., NORSTROMM.M., GONZALEZ V.D., NILSSON S., SVENNERHOLM B., ET AL. (2009). Reduction of the HIV-1 reservoir in resting CD4+ Tlymphocytes by high dosage intravenous immunoglobulin treatment: a proof-of-concept study. AIDS Res Ther. 6, 15.
-
(2009)
AIDS Res Ther.
, vol.6
, pp. 15
-
-
Lindkvist, A.1
Eden, A.2
Norstrom, M.M.3
Gonzalez, V.D.4
Nilsson, S.5
Svennerholm, B.6
-
53
-
-
74049120411
-
The global spread of hepatitis C virus 1a and 1b: A phylodynamic and phylogeographic analysis
-
MAGIORKINIS G., MAGIORKINIS E., PARASKEVIS D., HO S.Y., SHAPIRO B., PYBUS O.G., ET AL. (2009). The global spread of hepatitis C virus 1a and 1b: a phylodynamic and phylogeographic analysis. PLoS Med. 6, e1000198.
-
(2009)
PLoS Med.
, vol.6
-
-
Magiorkinis, G.1
Magiorkinis, E.2
Paraskevis, D.3
Y, H.O.S.4
Shapiro, B.5
Pybus, O.G.6
-
54
-
-
80054087236
-
Analysing recombination in nucleotide sequences
-
MARTIN D.P., LEMEY P., POSADA D. (2011). Analysing recombination in nucleotide sequences. Mol. Ecol. Resour. 11, 943-955.
-
(2011)
Mol. Ecol. Resour.
, vol.11
, pp. 943-955
-
-
Martin, D.P.1
Lemey, P.2
Posada, D.3
-
55
-
-
79956150523
-
Genomescale evolution and phylodynamics of equine H3N8 influenza A virus
-
MURCIA P.R., WOOD J.L., HOLMES E.C. (2011). Genomescale evolution and phylodynamics of equine H3N8 influenza A virus. J. Virol. 85, 5312-5322.
-
(2011)
J. Virol.
, vol.85
, pp. 5312-5322
-
-
Murcia, P.R.1
Wood, J.L.2
Holmes, E.C.3
-
56
-
-
80053133499
-
Evidence for several waves of global transmission in the seventh cholera pandemic
-
MUTREJA A., KIM D.W., THOMSON N.R., CONNOR T.R., LEE J.H., KARIUKI S., ET AL. (2011). Evidence for several waves of global transmission in the seventh cholera pandemic. Nature. 477, 462-465.
-
(2011)
Nature
, vol.477
, pp. 462-465
-
-
Mutreja, A.1
Kim, D.W.2
Thomson, N.R.3
Connor, T.R.4
Lee, J.H.5
Kariuki, S.6
-
57
-
-
77954065669
-
A timescale for evolution, population expansion, and spatial spread of an emerging clone of methicillin-resistant Staphylococcus aureus
-
NUBEL U., DORDEL J., KURT K., STROMMENGER B., WESTH H., SHUKLA S.K., ET AL. (2010). A timescale for evolution, population expansion, and spatial spread of an emerging clone of methicillin-resistant Staphylococcus aureus. PLoS Pathog. 6, e1000855.
-
(2010)
PLoS Pathog.
, vol.6
-
-
Nubel, U.1
Dordel, J.2
Kurt, K.3
Strommenger, B.4
Westh, H.5
Shukla, S.K.6
-
59
-
-
19944428265
-
Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis
-
DOI 10.1128/JCM.43.1.406-413.2005
-
PALMER S., KEARNEY M., MALDARELLI F., HALVAS E.K., BIXBY C.J., BAZMI H., ET AL. (2005). Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis. J. Clin. Microbiol. 43, 406-413. (Pubitemid 40096331)
-
(2005)
Journal of Clinical Microbiology
, vol.43
, Issue.1
, pp. 406-413
-
-
Palmer, S.1
Kearney, M.2
Maldarelli, F.3
Halvas, E.K.4
Bixby, C.J.5
Bazmi, H.6
Rock, D.7
Falloon, J.8
Davey Jr., R.T.9
Dewar, R.L.10
Metcalf, J.A.11
Hammer, S.12
Mellors, J.W.13
Coffin, J.M.14
-
60
-
-
84859866095
-
Global phylogeography and evolution of the chelonid fibropapilloma- associated herpesvirus
-
PATRICIO A.R., HERBST L.H., DUARTE A., VELEZ-ZUAZO X., SANTOS LOUREIRO N., PEREIRA N., ET AL. (2012). Global Phylogeography and Evolution of the Chelonid Fibropapilloma-associated Herpesvirus. J. Gen. Virol.
-
(2012)
J. Gen. Virol
-
-
Patricio, A.R.1
Herbst, L.H.2
Duarte, A.3
Velez-Zuazo, X.4
Santos Loureiro, N.5
Pereira, N.6
-
61
-
-
0034814736
-
Unveiling the molecular clock in the presence of recombination
-
POSADA D. (2001). Unveiling the molecular clock in the presence of recombination. Mol. Biol. Evol. 18, 1976-1978. (Pubitemid 32916649)
-
(2001)
Molecular Biology and Evolution
, vol.18
, Issue.10
, pp. 1976-1978
-
-
Posada, D.1
-
63
-
-
0036183042
-
The effect of recombination on the accuracy of phylogeny estimation
-
POSADA D., CRANDALL K.A. (2002). The effect of recombination on the accuracy of phylogeny estimation. J. Mol. Evol. 54, 396-402. (Pubitemid 34165424)
-
(2002)
Journal of Molecular Evolution
, vol.54
, Issue.3
, pp. 396-402
-
-
Posada, D.1
Crandall, K.A.2
-
64
-
-
0036948655
-
Recombination in evolutionary genomics
-
DOI 10.1146/annurev.genet.36.040202.111115
-
POSADA D., CRANDALL K.A., HOLMES E.C. (2002). Recombination in evolutionary genomics. Annu. Rev. Genet. 36, 75-97. (Pubitemid 36109184)
-
(2002)
Annual Review of Genetics
, vol.36
, pp. 75-97
-
-
Posada, D.1
Crandall, K.A.2
Holmes, E.C.3
-
65
-
-
79957564900
-
A novel methodology for large-scale phylogeny partition
-
PROSPERI M.C., CICCOZZI M., FANTI I., SALADINI F., PECORARI M., BORGHI V., ET AL. (2011). A novel methodology for large-scale phylogeny partition. Nat. Commun. 2, 321.
-
(2011)
Nat. Commun.
, vol.2
, pp. 321
-
-
Prosperi, M.C.1
Ciccozzi, M.2
Fanti, I.3
Saladini, F.4
Pecorari, M.5
Borghi, V.6
-
66
-
-
0033911330
-
An integrated framework for the inference of viral population history from reconstructed genealogies
-
PYBUS O.G., RAMBAUT A., HARVEY P.H. (2000). An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics. 155, 1429-1437. (Pubitemid 30463449)
-
(2000)
Genetics
, vol.155
, Issue.3
, pp. 1429-1437
-
-
Pybus, O.G.1
Rambaut, A.2
Harvey, P.H.3
-
67
-
-
53649099618
-
Parasites as predators: Unifying natural enemy ecology
-
RAFFEL T.R., MARTIN L.B., ROHR J.R. (2008). Parasites as predators: unifying natural enemy ecology. Trends. Ecol. Evol. 23, 610-618.
-
(2008)
Trends. Ecol. Evol.
, vol.23
, pp. 610-618
-
-
Raffel, T.R.1
Martin, L.B.2
Rohr, J.R.3
-
68
-
-
79960848222
-
Temporal variations in the hepatitis C virus intrahost population during chronic infection
-
RAMACHANDRAN S., CAMPO D.S., DIMITROVA Z.E., XIA G.L., PURDYM.A., KHUDYAKOV Y.E. (2011). Temporal variations in the hepatitis C virus intrahost population during chronic infection. J. Virol. 85, 6369-6380.
-
(2011)
J. Virol.
, vol.85
, pp. 6369-6380
-
-
Ramachandran, S.1
Campo, D.S.2
Dimitrova, Z.E.3
Xia, G.L.4
Purdy, M.A.5
Khudyakov, Y.E.6
-
69
-
-
0347989161
-
The causes and consequences of HIV evolution
-
DOI 10.1038/nrg1246
-
RAMBAUT A., POSADA D., CRANDALL K.A., HOLMES E.C. (2004). The causes and consequences of HIV evolution. Nat. Rev. Genet. 5, 52-61. (Pubitemid 38055336)
-
(2004)
Nature Reviews Genetics
, vol.5
, Issue.1
, pp. 52-61
-
-
Rambaut, A.1
Posada, D.2
Crandall, K.A.3
Holmes, E.C.4
-
70
-
-
0036133193
-
Hepatitis C virus evolutionary patterns studied through analysis of full-genome sequences
-
SALEMI M., VANDAMME A.M. (2002). Hepatitis C virus evolutionary patterns studied through analysis of full-genome sequences. J. Mol. Evol. 54, 62-70. (Pubitemid 33132005)
-
(2002)
Journal of Molecular Evolution
, vol.54
, Issue.1
, pp. 62-70
-
-
Salemi, M.1
Vandamme, A.-M.2
-
71
-
-
0347003547
-
Severe acute respiratory syndrome coronavirus sequence characteristics and evolutionary rate estimate from maximum likelihood analysis
-
DOI 10.1128/JVI.78.3.1602-1603.2004
-
SALEMIM., FITCHW.M., CICCOZZIM., RUIZ-ALVAREZM.J., REZZA G., LEWIS M.J. (2004). Severe acute respiratory syndrome coronavirus sequence characteristics and evolutionary rate estimate from maximum likelihood analysis. J. Virol. 78, 1602-1603. (Pubitemid 38095870)
-
(2004)
Journal of Virology
, vol.78
, Issue.3
, pp. 1602-1603
-
-
Salemi, M.1
Fitch, W.M.2
Ciccozzi, M.3
Ruiz-Alvarez, M.J.4
Rezza, G.5
Lewis, M.J.6
-
72
-
-
21244449912
-
Different epidemic potentials of the HIV-1B and C subtypes
-
DOI 10.1007/s00239-004-0206-5
-
SALEMI M., DE OLIVEIRA T., SOARES M.A., PYBUS O., DUMANS A.T., VANDAMME A.M., ET AL. (2005a). Different epidemic potentials of the HIV-1B and C subtypes. J. Mol. Evol. 60, 598-605. (Pubitemid 40896559)
-
(2005)
Journal of Molecular Evolution
, vol.60
, Issue.5
, pp. 598-605
-
-
Salemi, M.1
De Oliveira, T.2
Soares, M.A.3
Pybus, O.4
Dumans, A.T.5
Vandamme, A.-M.6
Tanuri, A.7
Cassol, S.8
Fitch, W.M.9
-
73
-
-
23844484143
-
Phylodynamic analysis of human immunodeficiency virus type 1 in distinct brain compartments provides a model for the neuropathogenesis of AIDS
-
DOI 10.1128/JVI.79.17.11343-11352.2005
-
SALEMI M., LAMERS S.L., YU S., DE OLIVEIRA T., FITCH W.M., MCGRATHM.S. (2005b). Phylodynamic analysis of human immunodeficiency virus type 1 in distinct brain compartments provides a model for the neuropathogenesis of AIDS. J. Virol. 79, 11343-11352. (Pubitemid 41170676)
-
(2005)
Journal of Virology
, vol.79
, Issue.17
, pp. 11343-11352
-
-
Salemi, M.1
Lamers, S.L.2
Yu, S.3
De Oliveira, T.4
Fitch, W.M.5
McGrath, M.S.6
-
74
-
-
41649086532
-
Phylodynamics of HIV-1 in lymphoid and non-lymphoid tissues reveals a central role for the thymus in emergence of CXCR4-using quasispecies
-
SALEMI M., BURKHARDT B.R., GRAY R.R., GHAFFARI G., SLEASMAN J.W., GOODENOW M.M. (2007). Phylodynamics of HIV-1 in lymphoid and non-lymphoid tissues reveals a central role for the thymus in emergence of CXCR4-using quasispecies. PLoS One. 2, e950.
-
(2007)
PLoS One
, vol.2
-
-
Salemi, M.1
Burkhardt, B.R.2
Gray, R.R.3
Ghaffari, G.4
Sleasman, J.W.5
Goodenow, M.M.6
-
75
-
-
45849139771
-
The HIV type 1 epidemic in Bulgaria involves multiple subtypes and is sustained by continuous viral inflow from West and East European countries
-
DOI 10.1089/aid.2007.0181
-
SALEMIM., GOODENOWM.M., MONTIERI S., DE OLIVEIRA T., SANTORO M.M., BESHKOV D., ET AL. (2008). The HIV type 1 epidemic in Bulgaria involves multiple subtypes and is sustained by continuous viral inflow from West and East European countries. AIDS Res. Hum. Retroviruses. 24, 771-779. (Pubitemid 351876981)
-
(2008)
AIDS Research and Human Retroviruses
, vol.24
, Issue.6
, pp. 771-779
-
-
Salemi, M.1
Goodenow, M.M.2
Montieri, S.3
De Oliveira, T.4
Santoro, M.M.5
Beshkov, D.6
Alexiev, I.7
Elenkov, I.8
Elenkov, I.9
Yakimova, T.10
Varleva, T.11
Rezza, G.12
Ciccozzi, M.13
-
77
-
-
77949518476
-
Distinct patterns of HIV-1 evolution within metastatic tissues in patients with non-Hodgkins lymphoma
-
SALEMI M., LAMERS S.L., HUYSENTRUYT L.C., GALLIGAN D., GRAY R.R., MORRIS A., ET AL. (2009). Distinct patterns of HIV-1 evolution within metastatic tissues in patients with non-Hodgkins lymphoma. PLoS One. 4, e8153.
-
(2009)
PLoS One
, vol.4
-
-
Salemi, M.1
Lamers, S.L.2
Huysentruyt, L.C.3
Galligan, D.4
Gray, R.R.5
Morris, A.6
-
79
-
-
0032710838
-
Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection
-
SHANKARAPPA R., MARGOLICK J.B., GANGE S.J., RODRIGO A.G., UPCHURCH D., FARZADEGAN H., ET AL. (1999). Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J. Virol. 73, 10489-10502.
-
(1999)
J. Virol.
, vol.73
, pp. 10489-10502
-
-
Shankarappa, R.1
Margolick, J.B.2
Gange, S.J.3
Rodrigo, A.G.4
Upchurch, D.5
Farzadegan, H.6
-
80
-
-
4644245699
-
Pervasive genomic recombination of HIV-1 in vivo
-
DOI 10.1534/genetics.103.023382
-
SHRINER D., RODRIGO A.G., NICKLE D.C., MULLINS J.I. (2004). Pervasive genomic recombination of HIV-1 in vivo. Genetics. 167, 1573-1583. (Pubitemid 39265897)
-
(2004)
Genetics
, vol.167
, Issue.4
, pp. 1573-1583
-
-
Shriner, D.1
Rodrigo, A.G.2
Nickle, D.C.3
Mullins, J.I.4
-
81
-
-
0024341852
-
A cladistic measure of gene flow inferred from the phylogenies of alleles
-
SLATKINM., MADDISONW.P. (1989). A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics. 123, 603-613. (Pubitemid 19274683)
-
(1989)
Genetics
, vol.123
, Issue.3
, pp. 603-613
-
-
Slatkin, M.1
Maddison, W.P.2
-
82
-
-
67649538978
-
Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic
-
SMITH G.J., VIJAYKRISHNA D., BAHL J., LYCETT S.J., WOROBEYM., PYBUS O.G., ET AL. (2009). Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature. 459, 1122-1125.
-
(2009)
Nature
, vol.459
, pp. 1122-1125
-
-
Smith, G.J.1
Vijaykrishna, D.2
Bahl, J.3
Lycett, S.J.4
Worobey, M.5
Pybus, O.G.6
-
84
-
-
0035211479
-
Exploring the demographic history of DNA sequences using the generalized skyline plot
-
STRIMMER K., PYBUS O.G. (2001). Exploring the demographic history of DNA sequences using the generalized skyline plot. Mol. Biol. Evol. 18, 2298-2305. (Pubitemid 33134359)
-
(2001)
Molecular Biology and Evolution
, vol.18
, Issue.12
, pp. 2298-2305
-
-
Strimmer, K.1
Pybus, O.G.2
-
86
-
-
78449237743
-
Phylodynamics and human-mediated dispersal of a zoonotic virus
-
TALBI C., LEMEY P., SUCHARD M.A., ABDELATIF E., ELHARRAK M., NOURLIL J., ET AL. (2010). Phylodynamics and human-mediated dispersal of a zoonotic virus. PLoS Pathog. 6, e1001166.
-
(2010)
PLoS Pathog.
, vol.6
-
-
Talbi, C.1
Lemey, P.2
Suchard, M.A.3
Abdelatif, E.4
Elharrak, M.5
Nourlil, J.6
-
89
-
-
0037214757
-
An index of substitution saturation and its application
-
DOI 10.1016/S1055-7903(02)00326-3, PII S1055790302003263
-
XIA X., XIE Z., SALEMIM., CHEN L., WANG Y. (2003). An index of substitution saturation and its application. Mol. Phylogenet. Evol. 26, 1-7. (Pubitemid 36029247)
-
(2003)
Molecular Phylogenetics and Evolution
, vol.26
, Issue.1
, pp. 1-7
-
-
Xia, X.1
Xie, Z.2
Salemi, M.3
Chen, L.4
Wang, Y.5
-
90
-
-
79953116795
-
Phylogeography and epidemiological history of West Nile virus genotype 1a in Europe and the Mediterranean basin
-
ZEHENDER G., EBRANATI E., BERNINI F., LO PRESTI A., REZZA G., DELOGUM., ET AL. (2011). Phylogeography and epidemiological history of West Nile virus genotype 1a in Europe and the Mediterranean basin. Infect. Genet. Evol. 11, 646-653.
-
(2011)
Infect. Genet. Evol.
, vol.11
, pp. 646-653
-
-
Zehender, G.1
Ebranati, E.2
Bernini, F.3
Presti A, L.O.4
Rezza, G.5
Delogu, M.6
-
91
-
-
0002331493
-
Molecular disease, evolution, and genetic heterogeneity
-
M. Kasha and Pullman B. New York, Academic Press
-
ZUCKERKANDL E., PAULING L. (1962). Molecular disease, evolution, and genetic heterogeneity. Horizonz in Biochemistry. M. Kasha and Pullman B. New York, Academic Press: 189-225.
-
(1962)
Horizonz in Biochemistry
, pp. 189-225
-
-
Zuckerkandl, E.1
Pauling, L.2
-
92
-
-
0001895697
-
Evolutionary divergence and convergence in proteins
-
V. Bryson and Vogel H. J. New York, Academic Press
-
ZUCKERKANDL E., PAULING L. (1965). Evolutionary divergence and convergence in proteins. Evolving Genes and Proteins. V. Bryson and Vogel H. J. New York, Academic Press: 97-166.
-
(1965)
Evolving Genes and Proteins
, pp. 97-166
-
-
Zuckerkandl, E.1
Pauling, L.2
|