-
1
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
-
(2005)
Nature
, vol.437
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
Attiya, S.4
Bader, J.S.5
-
2
-
-
65949108590
-
Metagenomic pyrosequencing and microbial identification
-
Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic J, (2009) Metagenomic pyrosequencing and microbial identification. Clin Chem 55: 856-866.
-
(2009)
Clin Chem
, vol.55
, pp. 856-866
-
-
Petrosino, J.F.1
Highlander, S.2
Luna, R.A.3
Gibbs, R.A.4
Versalovic, J.5
-
3
-
-
84865179264
-
High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity
-
Loman NJ, Constantinidou C, Chan JZ, Halachev M, Sergeant M, et al. (2012) High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol 10: 599-606.
-
(2012)
Nat Rev Microbiol
, vol.10
, pp. 599-606
-
-
Loman, N.J.1
Constantinidou, C.2
Chan, J.Z.3
Halachev, M.4
Sergeant, M.5
-
4
-
-
34948842866
-
Accuracy and quality of massively parallel DNA pyrosequencing
-
Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM, (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8: R143.
-
(2007)
Genome Biol
, vol.8
-
-
Huse, S.M.1
Huber, J.A.2
Morrison, H.G.3
Sogin, M.L.4
Welch, D.M.5
-
5
-
-
79956044149
-
Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing
-
Gilles A, Meglecz E, Pech N, Ferreira S, Malausa T, et al. (2011) Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 12: 245.
-
(2011)
BMC Genomics
, vol.12
, pp. 245
-
-
Gilles, A.1
Meglecz, E.2
Pech, N.3
Ferreira, S.4
Malausa, T.5
-
6
-
-
84055200527
-
Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID
-
Jabara CB, Jones CD, Roach J, Anderson JA, Swanstrom R, (2011) Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. Proc Natl Acad Sci U S A 108: 20166-20171.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 20166-20171
-
-
Jabara, C.B.1
Jones, C.D.2
Roach, J.3
Anderson, J.A.4
Swanstrom, R.5
-
7
-
-
84865979581
-
Detection of ultra-rare mutations by next-generation sequencing
-
Schmitt MW, Kennedy SR, Salk JJ, Fox EJ, Hiatt JB, et al. (2012) Detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci U S A.
-
(2012)
Proc Natl Acad Sci U S A
-
-
Schmitt, M.W.1
Kennedy, S.R.2
Salk, J.J.3
Fox, E.J.4
Hiatt, J.B.5
-
8
-
-
43149107930
-
Quality scores and SNP detection in sequencing-by-synthesis systems
-
Brockman W, Alvarez P, Young S, Garber M, Giannoukos G, et al. (2008) Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res 18: 763-770.
-
(2008)
Genome Res
, vol.18
, pp. 763-770
-
-
Brockman, W.1
Alvarez, P.2
Young, S.3
Garber, M.4
Giannoukos, G.5
-
9
-
-
69549112742
-
Accurate determination of microbial diversity from 454 pyrosequencing data
-
Quince C, Lanzen A, Curtis TP, Davenport RJ, Hall N, et al. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 6: 639-641.
-
(2009)
Nat Methods
, vol.6
, pp. 639-641
-
-
Quince, C.1
Lanzen, A.2
Curtis, T.P.3
Davenport, R.J.4
Hall, N.5
-
10
-
-
79251565226
-
Removing noise from pyrosequenced amplicons
-
Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ, (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12: 38.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 38
-
-
Quince, C.1
Lanzen, A.2
Davenport, R.J.3
Turnbaugh, P.J.4
-
11
-
-
44949250815
-
Viral population estimation using pyrosequencing
-
Eriksson N, Pachter L, Mitsuya Y, Rhee SY, Wang C, et al. (2008) Viral population estimation using pyrosequencing. PLoS Comput Biol 4: e1000074.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Eriksson, N.1
Pachter, L.2
Mitsuya, Y.3
Rhee, S.Y.4
Wang, C.5
-
12
-
-
78651228163
-
The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time-an ultra-deep approach
-
Archer J, Rambaut A, Taillon BE, Harrigan PR, Lewis M, et al. (2010) The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time-an ultra-deep approach. PLoS Comput Biol 6: e1001022.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Archer, J.1
Rambaut, A.2
Taillon, B.E.3
Harrigan, P.R.4
Lewis, M.5
-
13
-
-
81755185962
-
Ultra-deep sequencing for the analysis of viral populations
-
Beerenwinkel N, Zagordi O, (2011) Ultra-deep sequencing for the analysis of viral populations. Curr Opin Virol 1: 413-418.
-
(2011)
Curr Opin Virol
, vol.1
, pp. 413-418
-
-
Beerenwinkel, N.1
Zagordi, O.2
-
14
-
-
78650798688
-
Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing
-
Prosperi MC, Prosperi L, Bruselles A, Abbate I, Rozera G, et al. (2011) Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing. BMC Bioinformatics 12: 5.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 5
-
-
Prosperi, M.C.1
Prosperi, L.2
Bruselles, A.3
Abbate, I.4
Rozera, G.5
-
15
-
-
79957814500
-
Correcting errors in short reads by multiple alignments
-
Salmela L, Schroder J, (2011) Correcting errors in short reads by multiple alignments. Bioinformatics 27: 1455-1461.
-
(2011)
Bioinformatics
, vol.27
, pp. 1455-1461
-
-
Salmela, L.1
Schroder, J.2
-
16
-
-
79955125679
-
ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data
-
Zagordi O, Bhattacharya A, Eriksson N, Beerenwinkel N, (2011) ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. BMC Bioinformatics 12: 119.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 119
-
-
Zagordi, O.1
Bhattacharya, A.2
Eriksson, N.3
Beerenwinkel, N.4
-
17
-
-
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, et al. (2012) Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data. PLoS Comput Biol 8: e1002417.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Macalalad, A.R.1
Zody, M.C.2
Charlebois, P.3
Lennon, N.J.4
Newman, R.M.5
-
18
-
-
84855173088
-
QuRe: software for viral quasispecies reconstruction from next-generation sequencing data
-
Prosperi MC, Salemi M, (2012) QuRe: software for viral quasispecies reconstruction from next-generation sequencing data. Bioinformatics 28: 132-133.
-
(2012)
Bioinformatics
, vol.28
, pp. 132-133
-
-
Prosperi, M.C.1
Salemi, M.2
-
19
-
-
34547643929
-
Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance
-
Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW, (2007) Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res 17: 1195-1201.
-
(2007)
Genome Res
, vol.17
, pp. 1195-1201
-
-
Wang, C.1
Mitsuya, Y.2
Gharizadeh, B.3
Ronaghi, M.4
Shafer, R.W.5
-
20
-
-
77952158672
-
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins
-
Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, et al. (2010) Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A 107: 7503-7508.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 7503-7508
-
-
Turnbaugh, P.J.1
Quince, C.2
Faith, J.J.3
McHardy, A.C.4
Yatsunenko, T.5
-
21
-
-
77952709675
-
Hepatitis C virus transmission bottlenecks analyzed by deep sequencing
-
Wang GP, Sherrill-Mix SA, Chang KM, Quince C, Bushman FD, (2010) Hepatitis C virus transmission bottlenecks analyzed by deep sequencing. J Virol 84: 6218-6228.
-
(2010)
J Virol
, vol.84
, pp. 6218-6228
-
-
Wang, G.P.1
Sherrill-Mix, S.A.2
Chang, K.M.3
Quince, C.4
Bushman, F.D.5
-
22
-
-
38749091304
-
Pyrobayes: an improved base caller for SNP discovery in pyrosequences
-
Quinlan AR, Stewart DA, Stromberg MP, Marth GT, (2008) Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nature methods 5: 179-181.
-
(2008)
Nature Methods
, vol.5
, pp. 179-181
-
-
Quinlan, A.R.1
Stewart, D.A.2
Stromberg, M.P.3
Marth, G.T.4
-
23
-
-
79960419997
-
Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes
-
Herbeck JT, Rolland M, Liu Y, McLaughlin S, McNevin J, et al. (2011) Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes. Journal of virology 85: 7523-7534.
-
(2011)
Journal of Virology
, vol.85
, pp. 7523-7534
-
-
Herbeck, J.T.1
Rolland, M.2
Liu, Y.3
McLaughlin, S.4
McNevin, J.5
-
24
-
-
77956543003
-
Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim
-
Balzer S, Malde K, Lanzen A, Sharma A, Jonassen I, (2010) Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim. Bioinformatics 26: i420-425.
-
(2010)
Bioinformatics
, vol.26
-
-
Balzer, S.1
Malde, K.2
Lanzen, A.3
Sharma, A.4
Jonassen, I.5
-
26
-
-
79952006773
-
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
-
Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, et al. (2011) Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21: 494-504.
-
(2011)
Genome Res
, vol.21
, pp. 494-504
-
-
Haas, B.J.1
Gevers, D.2
Earl, A.M.3
Feldgarden, M.4
Ward, D.V.5
-
27
-
-
0035162494
-
Evolutionary and immunological implications of contemporary HIV-1 variation
-
Korber B, Gaschen B, Yusim K, Thakallapally R, Kesmir C, et al. (2001) Evolutionary and immunological implications of contemporary HIV-1 variation. Br Med Bull 58: 19-42.
-
(2001)
Br Med Bull
, vol.58
, pp. 19-42
-
-
Korber, B.1
Gaschen, B.2
Yusim, K.3
Thakallapally, R.4
Kesmir, C.5
-
28
-
-
77956820495
-
Nature, position, and frequency of mutations made in a single cycle of HIV-1 replication
-
Abram ME, Ferris AL, Shao W, Alvord WG, Hughes SH, (2010) Nature, position, and frequency of mutations made in a single cycle of HIV-1 replication. J Virol 84: 9864-9878.
-
(2010)
J Virol
, vol.84
, pp. 9864-9878
-
-
Abram, M.E.1
Ferris, A.L.2
Shao, W.3
Alvord, W.G.4
Hughes, S.H.5
-
29
-
-
0032710838
-
Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection
-
Shankarappa R, Margolick JB, Gange SJ, Rodrigo AG, Upchurch D, 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
|