-
1
-
-
79951694175
-
Analyzing and minimizing PCR amplification bias in illumina sequencing libraries
-
Aird, D., Ross, M.G., Chen, W.S., Danielsson, M., Fennell, T., Russ, C., Jaffe, D.B., Nusbaum, C. and Gnirke, A. (2010) Analyzing and minimizing PCR amplification bias in illumina sequencing libraries. Genome Biol., 12, R18.
-
(2010)
Genome Biol.
, vol.12
, pp. R18
-
-
Aird, D.1
Ross, M.G.2
Chen, W.S.3
Danielsson, M.4
Fennell, T.5
Russ, C.6
Jaffe, D.B.7
Nusbaum, C.8
Gnirke, A.9
-
2
-
-
84857271408
-
Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries
-
Dabney, J. and Meyer, M. (2012) Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. Biotechniques, 52, 87-94.
-
(2012)
Biotechniques
, vol.52
, pp. 87-94
-
-
Dabney, J.1
Meyer, M.2
-
3
-
-
84878234942
-
Characterizing and measuring bias in sequence data
-
Ross, M.G., Russ, C., Costello, M., Hollinger, A., Lennon, N.J., Hegarty, R., Nusbaum, C. and Jaffe, D.B. (2013) Characterizing and measuring bias in sequence data. Genome Biol., 14, R51.
-
(2013)
Genome Biol.
, vol.14
, pp. R51
-
-
Ross, M.G.1
Russ, C.2
Costello, M.3
Hollinger, A.4
Lennon, N.J.5
Hegarty, R.6
Nusbaum, C.7
Jaffe, D.B.8
-
4
-
-
0142092731
-
Random variation and concentration effects in PCR
-
Jagers, P. and Klebaner, F. (2003) Random variation and concentration effects in PCR. J. Theor. Biol., 224, 299-304.
-
(2003)
J. Theor. Biol.
, vol.224
, pp. 299-304
-
-
Jagers, P.1
Klebaner, F.2
-
5
-
-
0029826566
-
Efficiency of DNA replication in the polymerase chain reaction
-
Stolovitzky, G. and Cecchi, G. (1996) Efficiency of DNA replication in the polymerase chain reaction. Proc. Natl. Acad. Sci. U.S.A., 93, 12947-12952.
-
(1996)
Proc. Natl. Acad. Sci. U.S.A.
, vol.93
, pp. 12947-12952
-
-
Stolovitzky, G.1
Cecchi, G.2
-
7
-
-
17044401808
-
Confidence intervals for nonhomogeneous branching processes and polymerase chain reactions
-
Piau, D. (2005) Confidence intervals for nonhomogeneous branching processes and polymerase chain reactions. Ann. Probability, 33, 674-702.
-
(2005)
Ann. Probability
, vol.33
, pp. 674-702
-
-
Piau, D.1
-
8
-
-
3142666986
-
Modelling the PCR amplification process by a size-dependent branching process and estimation of the efficiency
-
Lalam, N., Jacob, C. and Jagers, P. (2004) Modelling the PCR amplification process by a size-dependent branching process and estimation of the efficiency. Adv. Appl. Probability, 36, 602-615.
-
(2004)
Adv. Appl. Probability
, vol.36
, pp. 602-615
-
-
Lalam, N.1
Jacob, C.2
Jagers, P.3
-
9
-
-
0029935969
-
Theoretical uncertainty of measurements using quantitative polymerase chain reaction
-
Peccoud, J. and Jacob, C. (1996) Theoretical uncertainty of measurements using quantitative polymerase chain reaction. Biophys. J., 71, 101-108.
-
(1996)
Biophys. J.
, vol.71
, pp. 101-108
-
-
Peccoud, J.1
Jacob, C.2
-
10
-
-
0025230558
-
DNA damage promotes jumping between templates during enzymatic amplification
-
Pääbo, S., Irwin, D. and Wilson, A. (1990) DNA damage promotes jumping between templates during enzymatic amplification. J. Biol. Chem., 265, 4718-4721.
-
(1990)
J. Biol. Chem.
, vol.265
, pp. 4718-4721
-
-
Pääbo, S.1
Irwin, D.2
Wilson, A.3
-
11
-
-
0029059015
-
Template-switching during DNA synthesis by thermus aquaticus DNA polymerase i
-
Odelberg, S., Weiss, R., Hata, A. and White, R. (1995) Template-switching during DNA synthesis by thermus aquaticus DNA polymerase i. Nucleic Acids Res., 23, 2049-2057.
-
(1995)
Nucleic Acids Res.
, vol.23
, pp. 2049-2057
-
-
Odelberg, S.1
Weiss, R.2
Hata, A.3
White, R.4
-
12
-
-
79952006773
-
Chimeric 16S rRNA sequence formation and detection in sanger and 454-pyrosequenced PCR amplicons
-
Haas, B.J., Gevers, D., Earl, A.M., Feldgarden, M., Ward, D.V., Giannoukos, G., Ciulla, D., Tabbaa, D., Highlander, S.K., Sodergren, E. 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
Giannoukos, G.6
Ciulla, D.7
Tabbaa, D.8
Highlander, S.K.9
Sodergren, E.10
-
13
-
-
77956304094
-
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions
-
Reeder, J. and Knight, R. (2010) Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat. Methods, 7, 668-669.
-
(2010)
Nat. Methods
, vol.7
, pp. 668-669
-
-
Reeder, J.1
Knight, R.2
-
14
-
-
79251565226
-
Removing noise from pyrosequenced amplicons
-
Quince, C., Lanzen, A., Davenport, R.J. and Turnbaugh, P.J. (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
-
15
-
-
69549112742
-
Accurate determination of microbial diversity from 454 pyrosequencing data
-
Quince, C., Lanzn, A., Curtis, T.P., Davenport, R.J., Hall, N., Head, I.M., Read, L.F. and Sloan, W.T. (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
Lanzn, A.2
Curtis, T.P.3
Davenport, R.J.4
Hall, N.5
Head, I.M.6
Read, L.F.7
Sloan, W.T.8
-
16
-
-
79959353421
-
Detection and quantification of rare mutations with massively parallel sequencing
-
Kinde, I., Wu, J., Papadopoulos, N., Kinzler, K.W. and Vogelstein, B. (2011) Detection and quantification of rare mutations with massively parallel sequencing. Proc. Natl. Acad. Sci. U.S.A., 108, 9530-9535.
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 9530-9535
-
-
Kinde, I.1
Wu, J.2
Papadopoulos, N.3
Kinzler, K.W.4
Vogelstein, B.5
-
17
-
-
79959327151
-
Counting individual DNA molecules by the stochastic attachment of diverse labels
-
Fu, G.K., Hu, J., Wang, P. and Fodor, S.P.A. (2011) Counting individual DNA molecules by the stochastic attachment of diverse labels. Proc. Natl. Acad. Sci. U.S.A., 108, 9026-9031.
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 9026-9031
-
-
Fu, G.K.1
Hu, J.2
Wang, P.3
Fodor, S.P.A.4
-
18
-
-
79960226263
-
A method for counting PCR template molecules with application to next-generation sequencing
-
Casbon, J.A., Osborne, R.J., Brenner, S. and Lichtenstein, C.P. (2011) A method for counting PCR template molecules with application to next-generation sequencing. Nucleic Acids Res., 39, e81.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. e81
-
-
Casbon, J.A.1
Osborne, R.J.2
Brenner, S.3
Lichtenstein, C.P.4
-
19
-
-
84856484968
-
Counting absolute numbers of molecules using unique molecular identifiers
-
Kivioja, T., Vähärautio, A., Karlsson, K., Bonke, M., Enge, M., Linnarsson, S. and Taipale, J. (2012) Counting absolute numbers of molecules using unique molecular identifiers. Nat. Methods, 9, 72-74.
-
(2012)
Nat. Methods
, vol.9
, pp. 72-74
-
-
Kivioja, T.1
Vähärautio, A.2
Karlsson, K.3
Bonke, M.4
Enge, M.5
Linnarsson, S.6
Taipale, J.7
-
20
-
-
84856398949
-
Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes
-
Shiroguchi, K., Jia, T.Z., Sims, P.A. and Xie, X. (2012) Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes. Proc. Natl. Acad. Sci. U.S.A., 109, 1347-1352.
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. 1347-1352
-
-
Shiroguchi, K.1
Jia, T.Z.2
Sims, P.A.3
Xie, X.4
-
21
-
-
31844453813
-
Structure-independent and quantitative ligation of single-stranded DNA
-
Li, T.W. and Weeks, K.M. (2006) Structure-independent and quantitative ligation of single-stranded DNA. Anal. Biochem., 349, 242-246.
-
(2006)
Anal. Biochem.
, vol.349
, pp. 242-246
-
-
Li, T.W.1
Weeks, K.M.2
-
22
-
-
84897676120
-
MergeRPEAR: A fast and accurate illumina Paired-End reAd mergeR
-
Zhang, J., Kobert, K., Flouri, T. and Stamatakis, A. (2013) mergeRPEAR: a fast and accurate illumina Paired-End reAd mergeR. Bioinformatics, 30, 614-620.
-
(2013)
Bioinformatics
, vol.30
, pp. 614-620
-
-
Zhang, J.1
Kobert, K.2
Flouri, T.3
Stamatakis, A.4
-
23
-
-
52649157765
-
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
-
Dohm, J.C., Lottaz, C., Borodina, T. and Himmelbauer, H. (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res., 36, e105.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. e105
-
-
Dohm, J.C.1
Lottaz, C.2
Borodina, T.3
Himmelbauer, H.4
-
24
-
-
0026207466
-
DNA polymerase fidelity and the polymerase chain reaction
-
Eckert, K. and Kunkel, T. (1991) DNA polymerase fidelity and the polymerase chain reaction. PCR Methods Appl., 1, 17-24.
-
(1991)
PCR Methods Appl.
, vol.1
, pp. 17-24
-
-
Eckert, K.1
Kunkel, T.2
-
25
-
-
0024282746
-
Fidelity of DNA synthesis by the thermus aquaticus DNA polymerase
-
Tindall, K. and Kunkel, T. (1988) Fidelity of DNA synthesis by the thermus aquaticus DNA polymerase. Biochemistry, 27, 6008-6013.
-
(1988)
Biochemistry
, vol.27
, pp. 6008-6013
-
-
Tindall, K.1
Kunkel, T.2
-
26
-
-
0024368667
-
Fidelity of DNA polymerases in DNA amplification
-
Keohavong, P. and Thilly, W. (1989) Fidelity of DNA polymerases in DNA amplification. Proc. Natl. Acad. Sci. U.S.A., 86, 9253-9257.
-
(1989)
Proc. Natl. Acad. Sci. U.S.A.
, vol.86
, pp. 9253-9257
-
-
Keohavong, P.1
Thilly, W.2
-
27
-
-
79953766940
-
Tumour evolution inferred by single-cell sequencing
-
Navin, N., Kendall, J., Troge, J., Andrews, P., Rodgers, L., McIndoo, J., Cook, K., Stepansky, A., Levy, D., Esposito, D. et al. (2011) Tumour evolution inferred by single-cell sequencing. Nature, 472, 90-94.
-
(2011)
Nature
, vol.472
, pp. 90-94
-
-
Navin, N.1
Kendall, J.2
Troge, J.3
Andrews, P.4
Rodgers, L.5
McIndoo, J.6
Cook, K.7
Stepansky, A.8
Levy, D.9
Esposito, D.10
-
28
-
-
84864880991
-
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
-
Ramsköld, D., Luo, S., Wang, Y.C., Li, R., Deng, Q., Faridani, O.R., Daniels, G.A., Khrebtukova, I., Loring, J.F., Laurent, L.C. et al. (2012) Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat. Biotechn., 30, 777-782.
-
(2012)
Nat. Biotechn.
, vol.30
, pp. 777-782
-
-
Ramsköld, D.1
Luo, S.2
Wang, Y.C.3
Li, R.4
Deng, Q.5
Faridani, O.R.6
Daniels, G.A.7
Khrebtukova, I.8
Loring, J.F.9
Laurent, L.C.10
-
29
-
-
84887109584
-
Accounting for technical noise in single-cell RNA-seq experiments
-
Brennecke, P., Anders, S., Kim, J.K., Koodziejczyk, A.A., Zhang, X., Proserpio, V., Baying, B., Benes, V., Teichmann, S.A., Marioni, J.C. et al. (2013) Accounting for technical noise in single-cell RNA-seq experiments. Nature Methods, 10, 1093-1095.
-
(2013)
Nature Methods
, vol.10
, pp. 1093-1095
-
-
Brennecke, P.1
Anders, S.2
Kim, J.K.3
Koodziejczyk, A.A.4
Zhang, X.5
Proserpio, V.6
Baying, B.7
Benes, V.8
Teichmann, S.A.9
Marioni, J.C.10
-
30
-
-
84901831004
-
Validation of noise models for single-cell transcriptomics
-
Grn, D., Kester, L. and vanOudenaarden, A. (2014) Validation of noise models for single-cell transcriptomics. Nature Methods, 11, 637-640.
-
(2014)
Nature Methods
, vol.11
, pp. 637-640
-
-
Grn, D.1
Kester, L.2
VanOudenaarden, A.3
-
31
-
-
18344396798
-
Comprehensive human genome amplification using multiple displacement amplification
-
Dean, F.B., Hosono, S., Fang, L., Wu, X., Faruqi, A.F., Bray-Ward, P., Sun, Z., Zong, Q., Du, Y., Du, J. et al. (2002) Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl. Acad. Sci. U.S.A., 99, 5261-5266.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 5261-5266
-
-
Dean, F.B.1
Hosono, S.2
Fang, L.3
Wu, X.4
Faruqi, A.F.5
Bray-Ward, P.6
Sun, Z.7
Zong, Q.8
Du, Y.9
Du, J.10
-
32
-
-
0030560897
-
Antisense RNA amplification: A linear amplification method for analyzing the mRNA population from single living cells
-
Phillips, J. and Eberwine, J. (1996) Antisense RNA amplification: a linear amplification method for analyzing the mRNA population from single living cells. Methods Enzymol., 10, 283-288.
-
(1996)
Methods Enzymol.
, vol.10
, pp. 283-288
-
-
Phillips, J.1
Eberwine, J.2
-
33
-
-
84871461434
-
Genome-wide detection of single-nucleotide and copy-number variations of a single human cell
-
Zong, C., Lu, S., Chapman, A.R. and Xie, X.S. (2012) Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science, 338, 1622-1626.
-
(2012)
Science
, vol.338
, pp. 1622-1626
-
-
Zong, C.1
Lu, S.2
Chapman, A.R.3
Xie, X.S.4
|