-
1
-
-
80053164707
-
Arbovirus high fidelity variant loses fitness in mosquitoes and mice
-
Coffey LL, Beeharry Y, Borderia AV, Blanc H, Vignuzzi M (2011) Arbovirus high fidelity variant loses fitness in mosquitoes and mice. Proc Natl Acad Sci U S A 108(38):16038-16043. doi: 10.1073/pnas.1111650108
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, Issue.38
, pp. 16038-16043
-
-
Coffey, L.L.1
Beeharry, Y.2
Borderia, A.V.3
Blanc, H.4
Vignuzzi, M.5
-
2
-
-
0036147047
-
Rates of molecular evolution in RNA viruses: A quantitative phylogenetic analysis
-
Jenkins GM, Rambaut A, Pybus OG, Holmes EC (2002) Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J Mol Evol 54(2):156-165. doi: 10.1007?s00239-001-0064-3
-
(2002)
J Mol Evol
, vol.54
, Issue.2
, pp. 156-165
-
-
Jenkins, G.M.1
Rambaut, A.2
Pybus, O.G.3
Holmes, E.C.4
-
3
-
-
0037377762
-
Molecular clocks and the puzzle of RNA virus origins
-
Holmes EC (2003) Molecular clocks and the puzzle of RNA virus origins. J Virol 77(7):3893-3897
-
(2003)
J Virol
, vol.77
, Issue.7
, pp. 3893-3897
-
-
Holmes, E.C.1
-
4
-
-
77949470329
-
Identification of microRNAs expressed in two mosquito vectors, Aedes albopictus and Culex quinquefasciatus
-
Skalsky RL, Vanlandingham DL, Scholle F, Higgs S, Cullen BR (2010) Identification of microRNAs expressed in two mosquito vectors, Aedes albopictus and Culex quinquefasciatus . BMC Genomics 11:119. doi: 10.1186/1471-2164-11-119
-
(2010)
BMC Genomics
, vol.11
-
-
Skalsky, R.L.1
Vanlandingham, D.L.2
Scholle, F.3
Higgs, S.4
Cullen, B.R.5
-
5
-
-
77950447605
-
Transcriptome response to pollutants and insecticides in the dengue vector Aedes aegypti using next-generation sequencing technology
-
David JP, Coissac E, Melodelima C, Poupardin R, Riaz MA, Chandor-Proust A, Reynaud S (2010) Transcriptome response to pollutants and insecticides in the dengue vector Aedes aegypti using next-generation sequencing technology. BMC Genomics 11:216. doi: 10.1186/1471-2164-11-216
-
(2010)
BMC Genomics
, vol.11
-
-
David, J.P.1
Coissac, E.2
Melodelima, C.3
Poupardin, R.4
Riaz, M.A.5
Chandor-Proust, A.6
Reynaud, S.7
-
6
-
-
84875980690
-
Host cell transcriptome profile during wild-type and attenuated dengue virus infection
-
Sessions OM, Tan Y, Goh KC, Liu Y, Tan P, Rozen S, Ooi EE (2013) Host cell transcriptome profile during wild-type and attenuated dengue virus infection. PLoS Negl Trop Dis 7(3):e2107. doi: 10.1371/journal.pntd.0002107
-
(2013)
Plos Negl Trop Dis
, vol.7
, Issue.3
-
-
Sessions, O.M.1
Tan, Y.2
Goh, K.C.3
Liu, Y.4
Tan, P.5
Rozen, S.6
Ooi, E.E.7
-
7
-
-
84857846563
-
Virus identification in unknown tropical febrile illness cases using deep sequencing
-
Yozwiak NL, Skewes-Cox P, Stenglein MD, Balmaseda A, Harris E, DeRisi JL (2012) Virus identification in unknown tropical febrile illness cases using deep sequencing. PLoS Negl Trop Dis 6(2):e1485. doi: 10.1371/journal. pntd.0001485
-
(2012)
Plos Negl Trop Dis
, vol.6
, Issue.2
-
-
Yozwiak, N.L.1
Skewes-Cox, P.2
Stenglein, M.D.3
Balmaseda, A.4
Harris, E.5
Derisi, J.L.6
-
8
-
-
82955203174
-
RNA virus population diversity: Implications for inter-species transmission
-
Borderia AV, Stapleford KA, Vignuzzi M (2011) RNA virus population diversity: implications for inter-species transmission. Curr Opin Virol 1(6):643-648. doi: 10.1016/j.coviro.2011.09.012
-
(2011)
Curr Opin Virol
, vol.1
, Issue.6
, pp. 643-648
-
-
Borderia, A.V.1
Stapleford, K.A.2
Vignuzzi, M.3
-
9
-
-
84871227763
-
LoFreq: A sequencequality 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 sequencequality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res 40(22):11189-11201. doi: 10.1093/nar/gks918
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.22
, 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
-
10
-
-
0030747157
-
RNA virus mutations and fitness for survival
-
Domingo E, Holland JJ (1997) RNA virus mutations and fitness for survival. Annu Rev Microbiol 51:151-178. doi: 10.1146/annurev.micro.51.1.151
-
(1997)
Annu Rev Microbiol
, vol.51
, pp. 151-178
-
-
Domingo, E.1
Holland, J.J.2
-
11
-
-
77956543002
-
Rhinovirus genome evolution during experimental human infection
-
Cordey S, Junier T, Gerlach D, Gobbini F, Farinelli L, Zdobnov EM, Winther B, Tapparel C, Kaiser L (2010) Rhinovirus genome evolution during experimental human infection. PLoS One 5(5):e10588. doi: 10.1371/journal.pone.0010588
-
(2010)
Plos One
, vol.5
, Issue.5
-
-
Cordey, S.1
Junier, T.2
Gerlach, D.3
Gobbini, F.4
Farinelli, L.5
Zdobnov, E.M.6
Winther, B.7
Tapparel, C.8
Kaiser, L.9
-
12
-
-
77954055072
-
Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing
-
Eckerle LD, Becker MM, Halpin RA, Li K, Venter E, Lu X, Scherbakova S, Graham RL, Baric RS, Stockwell TB, Spiro DJ, Denison MR (2010) Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing. PLoS Pathog 6(5):e1000896. doi: 10.1371/journal.ppat.1000896
-
(2010)
Plos Pathog
, vol.6
, Issue.5
-
-
Eckerle, L.D.1
Becker, M.M.2
Halpin, R.A.3
Li, K.4
Venter, E.5
Lu, X.6
Scherbakova, S.7
Graham, R.L.8
Baric, R.S.9
Stockwell, T.B.10
Spiro, D.J.11
Denison, M.R.12
-
13
-
-
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(3):e1002529. doi: 10.1371/journal.ppat.1002529
-
(2012)
Plos Pathog
, vol.8
, Issue.3
-
-
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..
-
14
-
-
80053081987
-
Genetic heterogeneity of hepatitis C virus in association with antiviral therapy determined by ultra-deep sequencing
-
Nasu A, Marusawa H, Ueda Y, Nishijima N, Takahashi K, Osaki Y, Yamashita Y, Inokuma T, Tamada T, Fujiwara T, Sato F, Shimizu K, Chiba T (2011) Genetic heterogeneity of hepatitis C virus in association with antiviral therapy determined by ultra-deep sequencing. PLoS One 6(9):e24907. doi: 10.1371/journal.pone.0024907
-
(2011)
Plos One
, vol.6
, Issue.9
-
-
Nasu, A.1
Marusawa, H.2
Ueda, Y.3
Nishijima, N.4
Takahashi, K.5
Osaki, Y.6
Yamashita, Y.7
Inokuma, T.8
Tamada, T.9
Fujiwara, T.10
Sato, F.11
Shimizu, K.12
Chiba, T.13
-
15
-
-
78650545749
-
Massively parallel sequencing for monitoring genetic consistency and quality control of live viral vaccines
-
Neverov A, Chumakov K (2010) Massively parallel sequencing for monitoring genetic consistency and quality control of live viral vaccines. Proc Natl Acad Sci U S A 107(46):20063-20068. doi: 10.1073/pnas.1012537107
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, Issue.46
, pp. 20063-20068
-
-
Neverov, A.1
Chumakov, K.2
-
16
-
-
84865073496
-
Genome-wide patterns of intrahuman dengue virus diversity reveal associations with viral phylogenetic clade and interhost diversity
-
Parameswaran P, Charlebois P, Tellez Y, Nunez A, Ryan EM, Malboeuf CM, Levin JZ, Lennon NJ, Balmaseda A, Harris E, Henn MR (2012) Genome-wide patterns of intrahuman dengue virus diversity reveal associations with viral phylogenetic clade and interhost diversity. J Virol 86(16):8546-8558. doi: 10.1128?JVI.00736-12
-
(2012)
J Virol
, vol.86
, Issue.16
, pp. 8546-8558
-
-
Parameswaran, P.1
Charlebois, P.2
Tellez, Y.3
Nunez, A.4
Ryan, E.M.5
Malboeuf, C.M.6
Levin, J.Z.7
Lennon, N.J.8
Balmaseda, A.9
Harris, E.10
Henn, M.R.11
-
17
-
-
79551712478
-
Beyond the consensus: Dissecting withinhost viral population diversity of foot-andmouth disease virus by using next-generation genome sequencing
-
Wright CF, Morelli MJ, Thebaud G, Knowles NJ, Herzyk P, Paton DJ, Haydon DT, King DP (2011) Beyond the consensus: dissecting withinhost viral population diversity of foot-andmouth disease virus by using next-generation genome sequencing. J Virol 85(5):2266-2275. doi: 10.1128/JVI.01396-10
-
(2011)
J Virol
, vol.85
, Issue.5
, pp. 2266-2275
-
-
Wright, C.F.1
Morelli, M.J.2
Thebaud, G.3
Knowles, N.J.4
Herzyk, P.5
Paton, D.J.6
Haydon, D.T.7
King, D.P.8
-
18
-
-
84878809082
-
Feasibility of using 454 pyrosequencing for studying quasispecies of the whole dengue viral genome
-
Chin-inmanu K, Suttitheptumrong A, Sangsrakru D, Tangphatsornruang S, Tragoonrung S, Malasit P, Tungpradabkul S, Suriyaphol P (2012) Feasibility of using 454 pyrosequencing for studying quasispecies of the whole dengue viral genome. BMC Genomics 13(Suppl 7):S7. doi: doi:10.1186/1471-2164-13-S7-S7
-
(2012)
BMC Genomics
, vol.13
-
-
Chin-Inmanu, K.1
Suttitheptumrong, A.2
Sangsrakru, D.3
Tangphatsornruang, S.4
Tragoonrung, S.5
Malasit, P.6
Tungpradabkul, S.7
Suriyaphol, P.8
-
19
-
-
84872327586
-
Tracking the evolution of dengue virus strains D2S10 and D2S20 by 454 pyrosequencing
-
Makhluf H, Buck MD, King K, Perry ST, Henn MR, Shresta S (2013) Tracking the evolution of dengue virus strains D2S10 and D2S20 by 454 pyrosequencing. PLoS One 8(1):e54220. doi: 10.1371/journal.pone.0054220
-
(2013)
Plos One
, vol.8
, Issue.1
-
-
Makhluf, H.1
Buck, M.D.2
King, K.3
Perry, S.T.4
Henn, M.R.5
Shresta, S.6
-
20
-
-
78649429437
-
The early whole-blood transcriptional signature of dengue virus and features associated with progression to dengue shock syndrome in Vietnamese children and young adults
-
Hoang LT, Lynn DJ, Henn M, Birren BW, Lennon NJ, Le PT, Duong KT, Nguyen TT, Mai LN, Farrar JJ, Hibberd ML, Simmons CP (2010) The early whole-blood transcriptional signature of dengue virus and features associated with progression to dengue shock syndrome in Vietnamese children and young adults. J Virol 84(24):12982-12994. doi: 10.1128/JVI.01224-10
-
(2010)
J Virol
, vol.84
, Issue.24
, pp. 12982-12994
-
-
Hoang, L.T.1
Lynn, D.J.2
Henn, M.3
Birren, B.W.4
Lennon, N.J.5
Le, P.T.6
Duong, K.T.7
Nguyen, T.T.8
Mai, L.N.9
Farrar, J.J.10
Hibberd, M.L.11
Simmons, C.P.12
-
21
-
-
84861108474
-
Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data
-
Macalalad AR, Zody MC, Charlebois P, Lennon NJ, Newman RM, Malboeuf CM, Ryan EM, Boutwell CL, Power KA, Brackney DE, Pesko KN, Levin JZ, Ebel GD, Allen TM, Birren BW, Henn MR (2012) Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data. PLoS Comput Biol 8(3):e1002417. doi: 10.1371/journal.pcbi.1002417
-
(2012)
Plos Comput Biol
, vol.8
, Issue.3
-
-
Macalalad, A.R.1
Zody, M.C.2
Charlebois, P.3
Lennon, N.J.4
Newman, R.M.5
Malboeuf, C.M.6
Ryan, E.M.7
Boutwell, C.L.8
Power, K.A.9
Brackney, D.E.10
Pesko, K.N.11
Levin, J.Z.12
Ebel, G.D.13
Allen, T.M.14
Birren, B.W.15
Henn, M.R.16
-
22
-
-
84866113768
-
De novo assembly of highly diverse viral populations
-
Yang X, Charlebois P, Gnerre S, Coole MG, Lennon NJ, Levin JZ, Qu J, Ryan EM, Zody MC, Henn MR (2012) De novo assembly of highly diverse viral populations. BMC Genomics 13:475. doi: 10.1186/1471-2164-13-475
-
(2012)
BMC Genomics
, vol.13
, pp. 475
-
-
Yang, X.1
Charlebois, P.2
Gnerre, S.3
Coole, M.G.4
Lennon, N.J.5
Levin, J.Z.6
Qu, J.7
Ryan, E.M.8
Zody, M.C.9
Henn, M.R.10
-
23
-
-
80455129691
-
SNVer: A statistical tool for variant calling in analysis of pooled or individual nextgeneration sequencing data
-
Wei Z, Wang W, Hu P, Lyon GJ, Hakonarson H (2011) SNVer: a statistical tool for variant calling in analysis of pooled or individual nextgeneration sequencing data. Nucleic Acids Res 39(19):e132. doi: 10.1093/nar/gkr599
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.19
-
-
Wei, Z.1
Wang, W.2
Hu, P.3
Lyon, G.J.4
Hakonarson, H.5
-
24
-
-
70350641005
-
Genome evolution and adaptation in a long-term experiment with Escherichia coli
-
Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461(7268):1243-1247. doi: 10.1038?nature08480
-
(2009)
Nature
, vol.461
, Issue.7268
, pp. 1243-1247
-
-
Barrick, J.E.1
Yu, D.S.2
Yoon, S.H.3
Jeong, H.4
Oh, T.K.5
Schneider, D.6
Lenski, R.E.7
Kim, J.F.8
-
25
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754-1760. doi: 10.1093/bioinformatics/btp324
-
(2009)
Bioinformatics
, vol.25
, Issue.14
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
26
-
-
84942887758
-
SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler
-
Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1(1):18. doi: 10.1186/2047-217X-1-18
-
(2012)
Gigascience
, vol.1
, Issue.1
, pp. 18
-
-
Luo, R.1
Liu, B.2
Xie, Y.3
Li, Z.4
Huang, W.5
Yuan, J.6
He, G.7
Chen, Y.8
Pan, Q.9
Liu, Y.10
Tang, J.11
Wu, G.12
Zhang, H.13
Shi, Y.14
Liu, Y.15
Yu, C.16
Wang, B.17
Lu, Y.18
Han, C.19
Cheung, D.W.20
Yiu, S.M.21
Peng, S.22
Xiaoqian, Z.23
Liu, G.24
Liao, X.25
Li, Y.26
Yang, H.27
Wang, J.28
Lam, T.W.29
Wang, J.30
more..
-
27
-
-
77954523593
-
Iterative Correction of Reference Nucleotides (ICORN) using second generation sequencing technology
-
Otto TD, Sanders M, Berriman M, Newbold C (2010) Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics 26(14):1704-1707. doi: 10.1093/bioinformatics?btq269
-
(2010)
Bioinformatics
, vol.26
, Issue.14
, pp. 1704-1707
-
-
Otto, T.D.1
Sanders, M.2
Berriman, M.3
Newbold, C.4
-
28
-
-
68549104404
-
The sequence alignment/Map format and SAMtools
-
Genome Project Data Processing S
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S (2009) The sequence alignment/Map format and SAMtools. Bioinformatics 25(16):2078-2079. doi: 10.1093/bioinformatics/btp352
-
(2009)
Bioinformatics
, vol.25
, Issue.16
, 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
-
29
-
-
77956295988
-
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
-
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20(9):1297-1303. doi: 10.1101/gr.107524.110
-
(2010)
Genome Res
, vol.20
, Issue.9
, pp. 1297-1303
-
-
McKenna, A.1
Hanna, M.2
Banks, E.3
Sivachenko, A.4
Cibulskis, K.5
Kernytsky, A.6
Garimella, K.7
Altshuler, D.8
Gabriel, S.9
Daly, M.10
Depristo, M.A.11
-
30
-
-
84869876659
-
The effect of strand bias in Illumina short-read sequencing data
-
Guo Y, Li J, Li CI, Long J, Samuels DC, Shyr Y (2012) The effect of strand bias in Illumina short-read sequencing data. BMC Genomics 13:666. doi: 10.1186/1471-2164-13-666
-
(2012)
BMC Genomics
, vol.13
-
-
Guo, Y.1
Li, J.2
Li, C.I.3
Long, J.4
Samuels, D.C.5
Shyr, Y.6
|