-
1
-
-
84894634227
-
The effects of female sex, viral genotype, and IL28B genotype on spontaneous clearance of acute hepatitis C virus infection
-
Grebely J, Page K, Sacks-Davis R, van der Loeff MS, Rice TM, Bruneau J, Morris MD, Hajarizadeh B, Amin J, Cox AL, Kim AY, McGovern BH, Schinkel J, George J, Shoukry NH, Lauer GM, Maher L, Lloyd AR, Hellard M, Dore GJ, Prins M, InC3 Study Group. 2014. The effects of female sex, viral genotype, and IL28B genotype on spontaneous clearance of acute hepatitis C virus infection. Hepatology 59:109-120. http://dx.doi.org/10.1002/hep.26639.
-
(2014)
Hepatology
, vol.59
, pp. 109-120
-
-
Grebely, J.1
Page, K.2
Sacks-Davis, R.3
van der Loeff, M.S.4
Rice, T.M.5
Bruneau, J.6
Morris, M.D.7
Hajarizadeh, B.8
Amin, J.9
Cox, A.L.10
Kim, A.Y.11
McGovern, B.H.12
Schinkel, J.13
George, J.14
Shoukry, N.H.15
Lauer, G.M.16
Maher, L.17
Lloyd, A.R.18
Hellard, M.19
Dore, G.J.20
Prins, M.21
more..
-
2
-
-
0036829816
-
Natural history of chronic hepatitis C
-
Seeff LB. 2002. Natural history of chronic hepatitis C. Hepatology 36:S35-46. http://dx.doi.org/10.1053/jhep.2002.36806.
-
(2002)
Hepatology
, vol.36
, pp. S35-S46
-
-
Seeff, L.B.1
-
3
-
-
80053439798
-
Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection
-
Bull RA, Luciani F, McElroy K, Gaudieri S, Pham ST, Chopra A, Cameron B, Maher L, Dore GJ, White PA, Lloyd AR. 2011. Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection. PLoS Pathog 7:e1002243. http://dx.doi.org/10.1371/journal.ppat.1002243.
-
(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
Cameron, B.7
Maher, L.8
Dore, G.J.9
White, P.A.10
Lloyd, A.R.11
-
4
-
-
84866144158
-
Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing
-
Li H, Stoddard MB, Wang S, Blair LM, Giorgi EE, Parrish EH, Learn GH, Hraber P, Goepfert PA, Saag MS, Denny TN, Haynes BF, Hahn BH, Ribeiro RM, Perelson AS, Korber BT, Bhattacharya T, Shaw GM. 2012. Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing. PLoS Pathog 8:e1002880. http://dx.doi.org/10.1371/journal.ppat.1002880.
-
(2012)
PLoS Pathog
, vol.8
-
-
Li, H.1
Stoddard, M.B.2
Wang, S.3
Blair, L.M.4
Giorgi, E.E.5
Parrish, E.H.6
Learn, G.H.7
Hraber, P.8
Goepfert, P.A.9
Saag, M.S.10
Denny, T.N.11
Haynes, B.F.12
Hahn, B.H.13
Ribeiro, R.M.14
Perelson, A.S.15
Korber, B.T.16
Bhattacharya, T.17
Shaw, G.M.18
-
5
-
-
21344442507
-
Cellular immune selection with hepatitis C virus persistence in humans
-
Cox AL, Mosbruger T, Mao Q, Liu Z, Wang XH, Yang HC, Sidney J, Sette A, Pardoll D, Thomas DL, Ray SC. 2005. Cellular immune selection with hepatitis C virus persistence in humans. J Exp Med 201:1741-1752. http://dx.doi.org/10.1084/jem.20050121.
-
(2005)
J Exp Med
, vol.201
, pp. 1741-1752
-
-
Cox, A.L.1
Mosbruger, T.2
Mao, Q.3
Liu, Z.4
Wang, X.H.5
Yang, H.C.6
Sidney, J.7
Sette, A.8
Pardoll, D.9
Thomas, D.L.10
Ray, S.C.11
-
6
-
-
21344442371
-
Comprehensive analyses of CD8+ T cell responses during longitudinal study of acute human hepatitis C
-
Cox AL, Mosbruger T, Lauer GM, Pardoll D, Thomas DL, Ray SC. 2005. Comprehensive analyses of CD8+ T cell responses during longitudinal study of acute human hepatitis C. Hepatology 42:104-112. http://dx.doi.org/10.1002/hep.20749.
-
(2005)
Hepatology
, vol.42
, pp. 104-112
-
-
Cox, A.L.1
Mosbruger, T.2
Lauer, G.M.3
Pardoll, D.4
Thomas, D.L.5
Ray, S.C.6
-
7
-
-
17644444485
-
Analysis of successful immune responses in persons infected with hepatitis C virus
-
Lechner F, Wong DK, Dunbar PR, Chapman R, Chung RT, Dohrenwend P, Robbins G, Phillips R, Klenerman P, Walker BD. 2000. Analysis of successful immune responses in persons infected with hepatitis C virus. J Exp Med 191:1499-1512. http://dx.doi.org/10.1084/jem.191.9.1499.
-
(2000)
J Exp Med
, vol.191
, pp. 1499-1512
-
-
Lechner, F.1
Wong, D.K.2
Dunbar, P.R.3
Chapman, R.4
Chung, R.T.5
Dohrenwend, P.6
Robbins, G.7
Phillips, R.8
Klenerman, P.9
Walker, B.D.10
-
8
-
-
33745876557
-
Outcome of acute hepatitis C is related to virus-specific CD4 function and maturation of antiviral memory CD8 responses
-
Urbani S, Amadei B, Fisicaro P, Tola D, Orlandini A, Sacchelli L, Mori C, Missale G, Ferrari C. 2006. Outcome of acute hepatitis C is related to virus-specific CD4 function and maturation of antiviral memory CD8 responses. Hepatology 44:126-139. http://dx.doi.org/10.1002/hep.21242.
-
(2006)
Hepatology
, vol.44
, pp. 126-139
-
-
Urbani, S.1
Amadei, B.2
Fisicaro, P.3
Tola, D.4
Orlandini, A.5
Sacchelli, L.6
Mori, C.7
Missale, G.8
Ferrari, C.9
-
9
-
-
0035914925
-
Determinants of viral clearance and persistence during acute hepatitis C virus infection
-
Thimme R, Oldach D, Chang KM, Steiger C, Ray SC, Chisari FV. 2001. Determinants of viral clearance and persistence during acute hepatitis C virus infection. J Exp Med 194:1395-1406. http://dx.doi.org/10.1084/jem.194.10.1395.
-
(2001)
J Exp Med
, vol.194
, pp. 1395-1406
-
-
Thimme, R.1
Oldach, D.2
Chang, K.M.3
Steiger, C.4
Ray, S.C.5
Chisari, F.V.6
-
10
-
-
34247612265
-
Flying under the radar: the immunobiology of hepatitis C
-
Dustin LB, Rice CM. 2007. Flying under the radar: the immunobiology of hepatitis C. Annu Rev Immunol 25:71-99. http://dx.doi.org/10.1146/annurev.immunol.25.022106.141602.
-
(2007)
Annu Rev Immunol
, vol.25
, pp. 71-99
-
-
Dustin, L.B.1
Rice, C.M.2
-
11
-
-
0034646996
-
The outcome of acute hepatitis C predicted by the evolution of the viral quasispecies
-
Farci P, Shimoda A, Coiana A, Diaz G, Peddis G, Melpolder JC, Strazzera A, Chien DY, Munoz SJ, Balestrieri A, Purcell RH, Alter HJ. 2000. The outcome of acute hepatitis C predicted by the evolution of the viral quasispecies. Science 288:339-344. http://dx.doi.org/10.1126/science.288.5464.339.
-
(2000)
Science
, vol.288
, pp. 339-344
-
-
Farci, P.1
Shimoda, A.2
Coiana, A.3
Diaz, G.4
Peddis, G.5
Melpolder, J.C.6
Strazzera, A.7
Chien, D.Y.8
Munoz, S.J.9
Balestrieri, A.10
Purcell, R.H.11
Alter, H.J.12
-
12
-
-
22344447485
-
Divergent and convergent evolution after a common-source outbreak of hepatitis C virus
-
Ray SC, Fanning L, Wang XH, Netski DM, Kenny-Walsh E, Thomas DL. 2005. Divergent and convergent evolution after a common-source outbreak of hepatitis C virus. J Exp Med 201:1753-1759. http://dx.doi.org/10.1084/jem.20050122.
-
(2005)
J Exp Med
, vol.201
, pp. 1753-1759
-
-
Ray, S.C.1
Fanning, L.2
Wang, X.H.3
Netski, D.M.4
Kenny-Walsh, E.5
Thomas, D.L.6
-
14
-
-
35448965263
-
Viral sequence evolution in acute hepatitis C virus infection
-
Kuntzen T, Timm J, Berical A, Lewis-Ximenez LL, Jones A, Nolan B, Schulze Zur Wiesch J, Li B, Schneidewind A, Kim AY, Chung RT, Lauer GM, Allen TM. 2007. Viral sequence evolution in acute hepatitis C virus infection. J Virol 81:11658-11668. http://dx.doi.org/10.1128/JVI.00995-07.
-
(2007)
J Virol
, vol.81
, pp. 11658-11668
-
-
Kuntzen, T.1
Timm, J.2
Berical, A.3
Lewis-Ximenez, L.L.4
Jones, A.5
Nolan, B.6
Schulze Zur Wiesch, J.7
Li, B.8
Schneidewind, A.9
Kim, A.Y.10
Chung, R.T.11
Lauer, G.M.12
Allen, T.M.13
-
15
-
-
79951560262
-
Constrained pattern of viral evolution in acute and early HCVinfection limits viral plasticity
-
Pfafferott K, Gaudieri S, Ulsenheimer A, James I, Heeg M, Nolan D, John M, Rauch A, Mallal S, Lucas A, Klenerman P, Diepolder HM, Lucas M. 2011. Constrained pattern of viral evolution in acute and early HCVinfection limits viral plasticity. PLoS One 6:e16797. http://dx.doi.org/10.1371/journal.pone.0016797.
-
(2011)
PLoS One
, vol.6
-
-
Pfafferott, K.1
Gaudieri, S.2
Ulsenheimer, A.3
James, I.4
Heeg, M.5
Nolan, D.6
John, M.7
Rauch, A.8
Mallal, S.9
Lucas, A.10
Klenerman, P.11
Diepolder, H.M.12
Lucas, M.13
-
16
-
-
79151474495
-
Effect of immune pressure on hepatitis C virus evolution: insights from a single-source outbreak
-
Merani S, Petrovic D, James I, Chopra A, Cooper D, Freitas E, Rauch A, di Iulio J, John M, Lucas M, Fitzmaurice K, McKiernan S, Norris S, Kelleher D, Klenerman P, Gaudieri S. 2011. Effect of immune pressure on hepatitis C virus evolution: insights from a single-source outbreak. Hepatology 53:396-405. http://dx.doi.org/10.1002/hep.24076.
-
(2011)
Hepatology
, vol.53
, pp. 396-405
-
-
Merani, S.1
Petrovic, D.2
James, I.3
Chopra, A.4
Cooper, D.5
Freitas, E.6
Rauch, A.7
di Iulio, J.8
John, M.9
Lucas, M.10
Fitzmaurice, K.11
McKiernan, S.12
Norris, S.13
Kelleher, D.14
Klenerman, P.15
Gaudieri, S.16
-
17
-
-
80655142505
-
+ T cells in early viral evolution
-
+ T cells in early viral evolution. J Virol 85:11833-11845. http://dx.doi.org/10.1128/JVI.02654-10.
-
(2011)
J Virol
, vol.85
, pp. 11833-11845
-
-
Callendret, B.1
Bukh, J.2
Eccleston, H.B.3
Heksch, R.4
Hasselschwert, D.L.5
Purcell, R.H.6
Hughes, A.L.7
Walker, C.M.8
-
18
-
-
23944467250
-
Adaptive immune responses in acute and chronic hepatitis C virus infection
-
Bowen D, Walker C. 2005. Adaptive immune responses in acute and chronic hepatitis C virus infection. Nature 436:946-952. http://dx.doi.org/10.1038/nature04079.
-
(2005)
Nature
, vol.436
, pp. 946-952
-
-
Bowen, D.1
Walker, C.2
-
19
-
-
26044434059
-
Positive selection of cytotoxic T lymphocyte escape variants during acute hepatitis C virus infection
-
Guglietta S, Garbuglia AR, Pacciani V, Scotta C, Perrone MP, Laurenti L, Spada E, Mele A, Capobianchi MR, Taliani G, Folgori A, Vitelli A, Ruggeri L, Nicosia A, Piccolella E, Del Porto P. 2005. Positive selection of cytotoxic T lymphocyte escape variants during acute hepatitis C virus infection. Eur J Immunol 35:2627-2637. http://dx.doi.org/10.1002/eji.200526067.
-
(2005)
Eur J Immunol
, vol.35
, pp. 2627-2637
-
-
Guglietta, S.1
Garbuglia, A.R.2
Pacciani, V.3
Scotta, C.4
Perrone, M.P.5
Laurenti, L.6
Spada, E.7
Mele, A.8
Capobianchi, M.R.9
Taliani, G.10
Folgori, A.11
Vitelli, A.12
Ruggeri, L.13
Nicosia, A.14
Piccolella, E.15
Del Porto, P.16
-
20
-
-
22344440368
-
Immune evasion versus recovery after acute hepatitis C virus infection from a shared source
-
Tester I, Smyk-Pearson S, Wang P, Wertheimer A, Yao E, Lewinsohn DM, Tavis JE, Rosen HR. 2005. Immune evasion versus recovery after acute hepatitis C virus infection from a shared source. J Exp Med 201: 1725-1731. http://dx.doi.org/10.1084/jem.20042284.
-
(2005)
J Exp Med
, vol.201
, pp. 1725-1731
-
-
Tester, I.1
Smyk-Pearson, S.2
Wang, P.3
Wertheimer, A.4
Yao, E.5
Lewinsohn, D.M.6
Tavis, J.E.7
Rosen, H.R.8
-
21
-
-
67449147145
-
The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection
-
Goonetilleke N, Liu MK, Salazar-Gonzalez JF, Ferrari G, Giorgi E, Ganusov VV, Keele BF, Learn GH, Turnbull EL, Salazar MG, Weinhold KJ, Moore S, Letvin N, Haynes BF, Cohen MS, Hraber P, Bhattacharya T, Borrow P, Perelson AS, Hahn BH, Shaw GM, Korber BT, McMichael AJ. 2009. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J Exp Med 206: 1253-1272. http://dx.doi.org/10.1084/jem.20090365.
-
(2009)
J Exp Med
, vol.206
, pp. 1253-1272
-
-
Goonetilleke, N.1
Liu, M.K.2
Salazar-Gonzalez, J.F.3
Ferrari, G.4
Giorgi, E.5
Ganusov, V.V.6
Keele, B.F.7
Learn, G.H.8
Turnbull, E.L.9
Salazar, M.G.10
Weinhold, K.J.11
Moore, S.12
Letvin, N.13
Haynes, B.F.14
Cohen, M.S.15
Hraber, P.16
Bhattacharya, T.17
Borrow, P.18
Perelson, A.S.19
Hahn, B.H.20
Shaw, G.M.21
Korber, B.T.22
McMichael, A.J.23
more..
-
22
-
-
84908876253
-
A human vaccine strategy based on chimpanzee adenoviral and MVA vectors that primes, boosts, and sustains functional HCVspecific T cell memory
-
Swadling L, Capone S, Antrobus RD, Brown A, Richardson R, Newell EW, Halliday J, Kelly C, Bowen D, Fergusson J, Kurioka A, Ammendola V, Del Sorbo M, Grazioli F, Esposito ML, Siani L, Traboni C, Hill A, Colloca S, Davis M, Nicosia A, Cortese R, Folgori A, Klenerman P, Barnes E. 2014. A human vaccine strategy based on chimpanzee adenoviral and MVA vectors that primes, boosts, and sustains functional HCVspecific T cell memory. Sci Transl Med 6:261ra153. http://dx.doi.org/10.1126/scitranslmed.3009185.
-
(2014)
Sci Transl Med
, vol.6
-
-
Swadling, L.1
Capone, S.2
Antrobus, R.D.3
Brown, A.4
Richardson, R.5
Newell, E.W.6
Halliday, J.7
Kelly, C.8
Bowen, D.9
Fergusson, J.10
Kurioka, A.11
Ammendola, V.12
Del Sorbo, M.13
Grazioli, F.14
Esposito, M.L.15
Siani, L.16
Traboni, C.17
Hill, A.18
Colloca, S.19
Davis, M.20
Nicosia, A.21
Cortese, R.22
Folgori, A.23
Klenerman, P.24
Barnes, E.25
more..
-
23
-
-
84855388574
-
Novel adenovirus-based vaccines induce broad and sustained T cell responses to HCV in man
-
Barnes E, Folgori A, Capone S, Swadling L, Aston S, Kurioka A, Meyer J, Huddart R, Smith K, Townsend R, Brown A, Antrobus R, Ammendola V, Naddeo M, O'Hara G, Willberg C, Harrison A, Grazioli F, Esposito ML, Siani L, Traboni C, Oo Y, Adams D, Hill A, Colloca S, Nicosia A, Cortese R, Klenerman P. 2012. Novel adenovirus-based vaccines induce broad and sustained T cell responses to HCV in man. Sci Transl Med 4:115ra1. http://dx.doi.org/10.1126/scitranslmed.3003155.
-
(2012)
Sci Transl Med
, vol.4
-
-
Barnes, E.1
Folgori, A.2
Capone, S.3
Swadling, L.4
Aston, S.5
Kurioka, A.6
Meyer, J.7
Huddart, R.8
Smith, K.9
Townsend, R.10
Brown, A.11
Antrobus, R.12
Ammendola, V.13
Naddeo, M.14
O'Hara, G.15
Willberg, C.16
Harrison, A.17
Grazioli, F.18
Esposito, M.L.19
Siani, L.20
Traboni, C.21
Oo, Y.22
Adams, D.23
Hill, A.24
Colloca, S.25
Nicosia, A.26
Cortese, R.27
Klenerman, P.28
more..
-
24
-
-
84903648326
-
A bioinformatics pipeline for the analyses of viral escape dynamics and host immune responses during an infection
-
264519
-
Leung P, Bull R, Lloyd A, Luciani F. 2014. A bioinformatics pipeline for the analyses of viral escape dynamics and host immune responses during an infection. Biomed Res Int 2014:264519. http://dx.doi.org/10.1155/2014/264519.
-
(2014)
Biomed Res Int
, vol.2014
-
-
Leung, P.1
Bull, R.2
Lloyd, A.3
Luciani, F.4
-
25
-
-
77958072659
-
Incidence of primary hepatitis C infection and risk factors for transmission in an Australian prisoner cohort
-
Teutsch S, Luciani F, Scheuer N, McCredie L, Hosseiny P, Rawlinson W, Kaldor J, Dore GJ, Dolan K, Ffrench R, Lloyd A, Haber P, Levy M. 2010. Incidence of primary hepatitis C infection and risk factors for transmission in an Australian prisoner cohort. BMC Public Health 10:633. http://dx.doi.org/10.1186/1471-2458-10-633.
-
(2010)
BMC Public Health
, vol.10
, pp. 633
-
-
Teutsch, S.1
Luciani, F.2
Scheuer, N.3
McCredie, L.4
Hosseiny, P.5
Rawlinson, W.6
Kaldor, J.7
Dore, G.J.8
Dolan, K.9
Ffrench, R.10
Lloyd, A.11
Haber, P.12
Levy, M.13
-
26
-
-
38949120134
-
Testing strategy to identify cases of acute hepatitisCvirus (HCV) infection and to project HCV incidence rates
-
Page-Shafer K, Pappalardo BL, Tobler LH, Phelps BH, Edlin BR, Moss AR, Wright TL, Wright DJ, O'Brien TR, Caglioti S, Busch MP. 2008. Testing strategy to identify cases of acute hepatitisCvirus (HCV) infection and to project HCV incidence rates. J Clin Microbiol 46:499-506. http://dx.doi.org/10.1128/JCM.01229-07.
-
(2008)
J Clin Microbiol
, vol.46
, pp. 499-506
-
-
Page-Shafer, K.1
Pappalardo, B.L.2
Tobler, L.H.3
Phelps, B.H.4
Edlin, B.R.5
Moss, A.R.6
Wright, T.L.7
Wright, D.J.8
O'Brien, T.R.9
Caglioti, S.10
Busch, M.P.11
-
27
-
-
33750735455
-
Evidence of viral adaptation to HLA class I-restricted immune pressure in chronic hepatitis C virus infection
-
Gaudieri S, Rauch A, Park LP, Freitas E, Herrmann S, Jeffrey G, Cheng W, Pfafferott K, Naidoo K, Chapman R, Battegay M, Weber R, Telenti A, Furrer H, James I, Lucas M, Mallal SA. 2006. Evidence of viral adaptation to HLA class I-restricted immune pressure in chronic hepatitis C virus infection. J Virol 80:11094-11104. http://dx.doi.org/10.1128/JVI.00912-06.
-
(2006)
J Virol
, vol.80
, pp. 11094-11104
-
-
Gaudieri, S.1
Rauch, A.2
Park, L.P.3
Freitas, E.4
Herrmann, S.5
Jeffrey, G.6
Cheng, W.7
Pfafferott, K.8
Naidoo, K.9
Chapman, R.10
Battegay, M.11
Weber, R.12
Telenti, A.13
Furrer, H.14
James, I.15
Lucas, M.16
Mallal, S.A.17
-
28
-
-
77949587649
-
Fast and accurate long-read alignment with Burrows-Wheeler transform
-
Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26:589-595. http://dx.doi.org/10.1093/bioinformatics/btp698.
-
(2010)
Bioinformatics
, vol.26
, pp. 589-595
-
-
Li, H.1
Durbin, R.2
-
29
-
-
84875578097
-
Using Tablet for visual exploration of secondgeneration sequencing data
-
Milne I, Stephen G, Bayer M, Cock PJ, Pritchard L, Cardle L, Shaw PD, Marshall D. 2013. Using Tablet for visual exploration of secondgeneration sequencing data. Brief Bioinform 14:193-202. http://dx.doi.org/10.1093/bib/bbs012.
-
(2013)
Brief Bioinform
, vol.14
, pp. 193-202
-
-
Milne, I.1
Stephen, G.2
Bayer, M.3
Cock, P.J.4
Pritchard, L.5
Cardle, L.6
Shaw, P.D.7
Marshall, D.8
-
30
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078-2079. http://dx.doi.org/10.1093/bioinformatics/btp352.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
31
-
-
84871227763
-
LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets
-
Wilm A, Aw PP, Bertrand D, Yeo GH, Ong SH, Wong CH, Khor CC, Petric R, Hibberd ML, Nagarajan N. 2012. LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res 40:11189-11201. http://dx.doi.org/10.1093/nar/gks918.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 11189-11201
-
-
Wilm, A.1
Aw, P.P.2
Bertrand, D.3
Yeo, G.H.4
Ong, S.H.5
Wong, C.H.6
Khor, C.C.7
Petric, R.8
Hibberd, M.L.9
Nagarajan, N.10
-
32
-
-
84880370368
-
Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias
-
McElroy K, Zagordi O, Bull R, Luciani F, Beerenwinkel N. 2013. Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias. BMC Genomics 14:501. http://dx.doi.org/10.1186/1471-2164-14-501.
-
(2013)
BMC Genomics
, vol.14
, pp. 501
-
-
McElroy, K.1
Zagordi, O.2
Bull, R.3
Luciani, F.4
Beerenwinkel, N.5
-
33
-
-
78649901946
-
Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies
-
Zagordi O, Klein R, Daumer M, Beerenwinkel N. 2010. Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies. Nucleic Acids Res 38:7400-7409. http://dx.doi.org/10.1093/nar/gkq655.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 7400-7409
-
-
Zagordi, O.1
Klein, R.2
Daumer, M.3
Beerenwinkel, N.4
-
34
-
-
77958143449
-
Estimating time since infection in early homogeneous HIV-1 samples using a poisson model
-
Giorgi EE, Funkhouser B, Athreya G, Perelson AS, Korber BT, Bhattacharya T. 2010. Estimating time since infection in early homogeneous HIV-1 samples using a poisson model. BMC Bioinformatics 11:532. http://dx.doi.org/10.1186/1471-2105-11-532.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 532
-
-
Giorgi, E.E.1
Funkhouser, B.2
Athreya, G.3
Perelson, A.S.4
Korber, B.T.5
Bhattacharya, T.6
-
35
-
-
34547781750
-
MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0
-
Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599. http://dx.doi.org/10.1093/molbev/msm092.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1596-1599
-
-
Tamura, K.1
Dudley, J.2
Nei, M.3
Kumar, S.4
-
36
-
-
9644301241
-
Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests
-
Posada D, Buckley TR. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst Biol 53:793-808. http://dx.doi.org/10.1080/10635150490522304.
-
(2004)
Syst Biol
, vol.53
, pp. 793-808
-
-
Posada, D.1
Buckley, T.R.2
-
37
-
-
65049088939
-
Automation of the ELISpot assay for high-throughput detection of antigen-specific T-cell responses
-
Almeida CA, Roberts SG, Laird R, McKinnon E, Ahmed I, Pfafferott K, Turley J, Keane NM, Lucas A, Rushton B, Chopra A, Mallal S, John M. 2009. Automation of the ELISpot assay for high-throughput detection of antigen-specific T-cell responses. J Immunol Methods 344:1-5. http://dx.doi.org/10.1016/j.jim.2009.02.007.
-
(2009)
J Immunol Methods
, vol.344
, pp. 1-5
-
-
Almeida, C.A.1
Roberts, S.G.2
Laird, R.3
McKinnon, E.4
Ahmed, I.5
Pfafferott, K.6
Turley, J.7
Keane, N.M.8
Lucas, A.9
Rushton, B.10
Chopra, A.11
Mallal, S.12
John, M.13
-
38
-
-
33645768069
-
Inefficient cytotoxic T lymphocyte-mediated killing of HIV-1-infected cells in vivo
-
Asquith B, Edwards CT, Lipsitch M, McLean AR. 2006. Inefficient cytotoxic T lymphocyte-mediated killing of HIV-1-infected cells in vivo. PLoS Biol 4:e90. http://dx.doi.org/10.1371/journal.pbio.0040090.
-
(2006)
PLoS Biol
, vol.4
-
-
Asquith, B.1
Edwards, C.T.2
Lipsitch, M.3
McLean, A.R.4
-
39
-
-
84863304598
-
-
R Foundation for Statistical Computing, Vienna, Austria
-
R Core Development Team. 2012. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
-
(2012)
R: a language and environment for statistical computing
-
-
-
40
-
-
77955377373
-
CodonTest: modeling amino acid substitution preferences in coding sequences
-
Delport W, Scheffler K, Botha G, Gravenor MB, Muse SV, Kosakovsky Pond SL. 2010. CodonTest: modeling amino acid substitution preferences in coding sequences. PLoS Comput Biol 6:e1000885. http://dx.doi.org/10.1371/journal.pcbi.1000885.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Delport, W.1
Scheffler, K.2
Botha, G.3
Gravenor, M.B.4
Muse, S.V.5
Kosakovsky Pond, S.L.6
-
41
-
-
0042424602
-
Statistical significance for genomewide studies
-
Storey JD, Tibshirani R. 2003. Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100:9440-9445. http://dx.doi.org/10.1073/pnas.1530509100.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 9440-9445
-
-
Storey, J.D.1
Tibshirani, R.2
-
42
-
-
84861214061
-
Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection
-
Henn MR, Boutwell CL, Charlebois P, Lennon NJ, Power KA, Macalalad AR, Berlin AM, Malboeuf CM, Ryan EM, Gnerre S, Zody MC, Erlich RL, Green LM, Berical A, Wang Y, Casali M, Streeck H, Bloom AK, Dudek T, Tully D, Newman R, Axten KL, Gladden AD, Battis L, Kemper M, Zeng Q, Shea TP, Gujja S, Zedlack C, Gasser O, Brander C, Hess C, Gunthard HF, Brumme ZL, Brumme CJ, Bazner S, Rychert J, Tinsley JP, Mayer KH, Rosenberg E, Pereyra F, Levin JZ, Young SK, Jessen H, Altfeld M, Birren BW, Walker BD, Allen TM. 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. http://dx.doi.org/10.1371/journal.ppat.1002529.
-
(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
Berlin, A.M.7
Malboeuf, C.M.8
Ryan, E.M.9
Gnerre, S.10
Zody, M.C.11
Erlich, R.L.12
Green, L.M.13
Berical, A.14
Wang, Y.15
Casali, M.16
Streeck, H.17
Bloom, A.K.18
Dudek, T.19
Tully, D.20
Newman, R.21
Axten, K.L.22
Gladden, A.D.23
Battis, L.24
Kemper, M.25
Zeng, Q.26
Shea, T.P.27
Gujja, S.28
Zedlack, C.29
Gasser, O.30
Brander, C.31
Hess, C.32
Gunthard, H.F.33
Brumme, Z.L.34
Brumme, C.J.35
Bazner, S.36
Rychert, J.37
Tinsley, J.P.38
Mayer, K.H.39
Rosenberg, E.40
Pereyra, F.41
Levin, J.Z.42
Young, S.K.43
Jessen, H.44
Altfeld, M.45
Birren, B.W.46
Walker, B.D.47
Allen, T.M.48
more..
-
43
-
-
84873830139
-
Vertical T cell immunodominance and epitope entropy determine HIV-1 escape
-
Liu MK, Hawkins N, Ritchie AJ, Ganusov VV, Whale V, Brackenridge S, Li H, Pavlicek JW, Cai F, Rose-Abrahams M, Treurnicht F, Hraber P, Riou C, Gray C, Ferrari G, Tanner R, Ping LH, Anderson JA, Swanstrom R, Cohen M, Karim SS, Haynes B, Borrow P, Perelson AS, Shaw GM, Hahn BH, Williamson C, Korber BT, Gao F, Self S, McMichael A, Goonetilleke N. 2013. Vertical T cell immunodominance and epitope entropy determine HIV-1 escape. J Clin Invest 123:380-393. http://dx.doi.org/10.1172/JCI65330.
-
(2013)
J Clin Invest
, vol.123
, pp. 380-393
-
-
Liu, M.K.1
Hawkins, N.2
Ritchie, A.J.3
Ganusov, V.V.4
Whale, V.5
Brackenridge, S.6
Li, H.7
Pavlicek, J.W.8
Cai, F.9
Rose-Abrahams, M.10
Treurnicht, F.11
Hraber, P.12
Riou, C.13
Gray, C.14
Ferrari, G.15
Tanner, R.16
Ping, L.H.17
Anderson, J.A.18
Swanstrom, R.19
Cohen, M.20
Karim, S.S.21
Haynes, B.22
Borrow, P.23
Perelson, A.S.24
Shaw, G.M.25
Hahn, B.H.26
Williamson, C.27
Korber, B.T.28
Gao, F.29
Self, S.30
McMichael, A.31
Goonetilleke, N.32
more..
-
44
-
-
80055017715
-
Fitness costs and diversity of the cytotoxic T lymphocyte (CTL) response determine the rate of CTL escape during acute and chronic phases of HIV infection
-
Ganusov VV, Goonetilleke N, Liu MK, Ferrari G, Shaw GM, McMichael AJ, Borrow P, Korber BT, Perelson AS. 2011. Fitness costs and diversity of the cytotoxic T lymphocyte (CTL) response determine the rate of CTL escape during acute and chronic phases of HIV infection. J Virol 85: 10518-10528. http://dx.doi.org/10.1128/JVI.00655-11.
-
(2011)
J Virol
, vol.85
, pp. 10518-10528
-
-
Ganusov, V.V.1
Goonetilleke, N.2
Liu, M.K.3
Ferrari, G.4
Shaw, G.M.5
McMichael, A.J.6
Borrow, P.7
Korber, B.T.8
Perelson, A.S.9
-
45
-
-
80655125485
-
Compensatory mutations restore the replication defects caused by cytotoxic T lymphocyte escape mutations in hepatitis C virus polymerase
-
Oniangue-Ndza C, Kuntzen T, Kemper M, Berical A, Wang YE, Neumann-Haefelin C, Foote PK, Hills-Evans K, Reyor LL, Kane K, Gladden AD, Bloom AK, Power KA, Thimme R, Lauer GM, Henn MR, Kim AY, Allen TM. 2011. Compensatory mutations restore the replication defects caused by cytotoxic T lymphocyte escape mutations in hepatitis C virus polymerase. J Virol 85:11883-11890. http://dx.doi.org/10.1128/JVI.00779-11.
-
(2011)
J Virol
, vol.85
, pp. 11883-11890
-
-
Oniangue-Ndza, C.1
Kuntzen, T.2
Kemper, M.3
Berical, A.4
Wang, Y.E.5
Neumann-Haefelin, C.6
Foote, P.K.7
Hills-Evans, K.8
Reyor, L.L.9
Kane, K.10
Gladden, A.D.11
Bloom, A.K.12
Power, K.A.13
Thimme, R.14
Lauer, G.M.15
Henn, M.R.16
Kim, A.Y.17
Allen, T.M.18
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