-
1
-
-
46249130709
-
The beginning of the end for microarrays?
-
10.1038/nmeth0708-585, 18587314
-
Shendure J. The beginning of the end for microarrays?. Nat Methods 2008, 5:585-587. 10.1038/nmeth0708-585, 18587314.
-
(2008)
Nat Methods
, vol.5
, pp. 585-587
-
-
Shendure, J.1
-
2
-
-
74049148179
-
3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer
-
10.1186/1471-2164-10-531, 2781828, 19917133
-
Asmann Y, Klee E, Thompson EA, Perez E, Middha S, Oberg A, Therneau T, Smith D, Poland G, Wieben E, Kocher JP. 3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer. BMC Genomics 2009, 10:531. 10.1186/1471-2164-10-531, 2781828, 19917133.
-
(2009)
BMC Genomics
, vol.10
, pp. 531
-
-
Asmann, Y.1
Klee, E.2
Thompson, E.A.3
Perez, E.4
Middha, S.5
Oberg, A.6
Therneau, T.7
Smith, D.8
Poland, G.9
Wieben, E.10
Kocher, J.P.11
-
3
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
10.1038/nmeth.1226, 18516045
-
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5:621-628. 10.1038/nmeth.1226, 18516045.
-
(2008)
Nat Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
4
-
-
77950460661
-
Understanding mechanisms underlying human gene expression variation with RNA sequencing
-
10.1038/nature08872, 3089435, 20220758
-
Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras J, Stephens M, Gilad Y, Pritchard JK. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 2010, 464:768-772. 10.1038/nature08872, 3089435, 20220758.
-
(2010)
Nature
, vol.464
, pp. 768-772
-
-
Pickrell, J.K.1
Marioni, J.C.2
Pai, A.A.3
Degner, J.F.4
Engelhardt, B.E.5
Nkadori, E.6
Veyrieras, J.7
Stephens, M.8
Gilad, Y.9
Pritchard, J.K.10
-
5
-
-
47649124124
-
A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome
-
10.1126/science.1160342, 18599741
-
Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O'Keefe S, Haas S, Vingron M, Lehrach H, Yaspo ML. A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome. Science 2008, 321:956-960. 10.1126/science.1160342, 18599741.
-
(2008)
Science
, vol.321
, pp. 956-960
-
-
Sultan, M.1
Schulz, M.H.2
Richard, H.3
Magen, A.4
Klingenhoff, A.5
Scherf, M.6
Seifert, M.7
Borodina, T.8
Soldatov, A.9
Parkhomchuk, D.10
Schmidt, D.11
O'Keefe, S.12
Haas, S.13
Vingron, M.14
Lehrach, H.15
Yaspo, M.L.16
-
6
-
-
57749195712
-
RNA-Seq: a revolutionary tool for transcriptomics
-
10.1038/nrg2484, 2949280, 19015660
-
Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10:57-63. 10.1038/nrg2484, 2949280, 19015660.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
7
-
-
70349910898
-
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
-
10.1093/bioinformatics/btp579, 2788925, 19808877
-
Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, Gilad Y, Pritchard JK. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics 2009, 25:3207-3212. 10.1093/bioinformatics/btp579, 2788925, 19808877.
-
(2009)
Bioinformatics
, vol.25
, pp. 3207-3212
-
-
Degner, J.F.1
Marioni, J.C.2
Pai, A.A.3
Pickrell, J.K.4
Nkadori, E.5
Gilad, Y.6
Pritchard, J.K.7
-
8
-
-
70350088369
-
Quantitative miRNA expression analysis: Comparing microarrays with next-generation sequencing
-
10.1261/rna.1699809, 2764476, 19745027
-
Willenbrock H, Salomon J, Søkilde R, Barken KB, Hansen TN, Nielsen FC, Møller S, Litman T. Quantitative miRNA expression analysis: Comparing microarrays with next-generation sequencing. RNA 2009, 15:2028-2034. 10.1261/rna.1699809, 2764476, 19745027.
-
(2009)
RNA
, vol.15
, pp. 2028-2034
-
-
Willenbrock, H.1
Salomon, J.2
Søkilde, R.3
Barken, K.B.4
Hansen, T.N.5
Nielsen, F.C.6
Møller, S.7
Litman, T.8
-
9
-
-
77954139210
-
Incorporating sequence quality data into alignment improves DNA read mapping
-
10.1093/nar/gkq010, 2853142, 20110255
-
Frith MC, Wan R, Horton P. Incorporating sequence quality data into alignment improves DNA read mapping. Nucleic Acids Res 2010, 38:e100. 10.1093/nar/gkq010, 2853142, 20110255.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Frith, M.C.1
Wan, R.2
Horton, P.3
-
10
-
-
65649126066
-
Transcript length bias in RNA-seq data confounds systems biology
-
10.1186/1745-6150-4-14, 2678084, 19371405
-
Oshlack A, Wakefield M. Transcript length bias in RNA-seq data confounds systems biology. Biol Direct 2009, 4:14. 10.1186/1745-6150-4-14, 2678084, 19371405.
-
(2009)
Biol Direct
, vol.4
, pp. 14
-
-
Oshlack, A.1
Wakefield, M.2
-
11
-
-
69849093232
-
Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity
-
10.1093/nar/gkp492, 2731892, 19531739
-
Philippe N, Boureux A, Bréhélin L, Tarhio J, Commes T, Rivals E. Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity. Nucleic Acids Res 2009, 37:e104. 10.1093/nar/gkp492, 2731892, 19531739.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Philippe, N.1
Boureux, A.2
Bréhélin, L.3
Tarhio, J.4
Commes, T.5
Rivals, E.6
-
12
-
-
77955504378
-
Statistical Design and Analysis of RNA Sequencing Data Genetics
-
Auer P, Doerge RW. Statistical Design and Analysis of RNA Sequencing Data Genetics. 2010, 185:405-416.
-
(2010)
, vol.185
, pp. 405-416
-
-
Auer, P.1
Doerge, R.W.2
-
13
-
-
0004245434
-
The Design of Experiments
-
Hafner, New York
-
Fisher RA. The Design of Experiments. 1960, Hafner, New York.
-
(1960)
-
-
Fisher, R.A.1
-
14
-
-
77949481052
-
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
-
Bullard J, Purdom E, Hansen K, Dudoit S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinf 2010, 11:94.
-
(2010)
BMC Bioinf
, vol.11
, pp. 94
-
-
Bullard, J.1
Purdom, E.2
Hansen, K.3
Dudoit, S.4
-
15
-
-
50649089207
-
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
-
10.1101/gr.079558.108, 2527709, 18550803
-
Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008, 18:1509-1517. 10.1101/gr.079558.108, 2527709, 18550803.
-
(2008)
Genome Res
, vol.18
, pp. 1509-1517
-
-
Marioni, J.C.1
Mason, C.E.2
Mane, S.M.3
Stephens, M.4
Gilad, Y.5
-
16
-
-
67649292737
-
Unlocking the secrets of the genome
-
10.1038/459927a, 2843545, 19536255, modENCODE Consortium
-
Celniker SE, Dillon LAL, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Stein L, White KP, Waqterston RH, . modENCODE Consortium Unlocking the secrets of the genome. Nature 2009, 459:927-930. 10.1038/459927a, 2843545, 19536255, modENCODE Consortium.
-
(2009)
Nature
, vol.459
, pp. 927-930
-
-
Celniker, S.E.1
Dillon, L.A.L.2
Gerstein, M.B.3
Gunsalus, K.C.4
Henikoff, S.5
Karpen, G.H.6
Stein, L.7
White, K.P.8
Waqterston, R.H.9
-
17
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
10.1038/nbt.1621, 20436464
-
Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 2010, 28:511-5. 10.1038/nbt.1621, 20436464.
-
(2010)
Nature Biotechnology
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.M.4
Kwan, G.5
van Baren, M.J.6
Salzberg, S.L.7
Wold, B.8
Pachter, L.9
-
18
-
-
75949093653
-
Identifiability of isoform deconvolution from junction arrays and RNA-Seq
-
10.1093/bioinformatics/btp544, 19762346
-
Hiller D, Jiang H, Xu W, Wong WH. Identifiability of isoform deconvolution from junction arrays and RNA-Seq. Bioinformatics 2009, 25:3056-3059. 10.1093/bioinformatics/btp544, 19762346.
-
(2009)
Bioinformatics
, vol.25
, pp. 3056-3059
-
-
Hiller, D.1
Jiang, H.2
Xu, W.3
Wong, W.H.4
-
19
-
-
49649116149
-
FlyBase: a database for the Drosophila research community
-
10.1007/978-1-59745-583-1_3, 18641940, FlyBase Consortium
-
Drysdale R, . FlyBase Consortium FlyBase: a database for the Drosophila research community. Methods Mol Biol 2008, 420:45-59. 10.1007/978-1-59745-583-1_3, 18641940, FlyBase Consortium.
-
(2008)
Methods Mol Biol
, vol.420
, pp. 45-59
-
-
Drysdale, R.1
-
20
-
-
65449136284
-
TopHat: discovering splice junctions with RNA-Seq
-
10.1093/bioinformatics/btp120, 2672628, 19289445
-
Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111. 10.1093/bioinformatics/btp120, 2672628, 19289445.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
21
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
10.1186/gb-2009-10-3-r25, 2690996, 19261174
-
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
22
-
-
35948940895
-
Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans
-
10.1371/journal.pbio.0050310, 2062478, 17988176
-
Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, Hahn MW, Nista PM, Jones CD, Kern AD, Dewey CN, Pachter L, Myers E, Langley CH. Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans. PLoS Biol 2007, 5:e310. 10.1371/journal.pbio.0050310, 2062478, 17988176.
-
(2007)
PLoS Biol
, vol.5
-
-
Begun, D.J.1
Holloway, A.K.2
Stevens, K.3
Hillier, L.W.4
Poh, Y.P.5
Hahn, M.W.6
Nista, P.M.7
Jones, C.D.8
Kern, A.D.9
Dewey, C.N.10
Pachter, L.11
Myers, E.12
Langley, C.H.13
-
23
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
10.1093/bioinformatics/btp352, 2723002, 19505943, 1000 Genome Project Data Processing Subgroup
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, . 1000 Genome Project Data Processing Subgroup The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25:2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943, 1000 Genome Project Data Processing Subgroup.
-
(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
-
24
-
-
0023676027
-
Misleading Statistics: errors in textbooks, software and manuals
-
Bland JM, Altman DG. Misleading Statistics: errors in textbooks, software and manuals. International Journal of Epidemiology 1988, 17:201-203.
-
(1988)
International Journal of Epidemiology
, vol.17
, pp. 201-203
-
-
Bland, J.M.1
Altman, D.G.2
-
25
-
-
0003877646
-
Statistical methods for rates and proportions
-
John Wiley, New York, 2
-
Fleiss JL. Statistical methods for rates and proportions. 1981, 38-46. John Wiley, New York, 2.
-
(1981)
, pp. 38-46
-
-
Fleiss, J.L.1
-
26
-
-
84908219488
-
Statistical methods for assessing agreement between two methods of clinical measurement
-
Bland JM, Altman DG. Statistical methods for assessing agreement between two methods of clinical measurement. Lancet 1986, 307-310.
-
(1986)
Lancet
, pp. 307-310
-
-
Bland, J.M.1
Altman, D.G.2
-
27
-
-
0036376993
-
Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments
-
Dudoit S, Yang YH, Callow MJ, Speed TP. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica 2002, 12:111-139.
-
(2002)
Statistica Sinica
, vol.12
, pp. 111-139
-
-
Dudoit, S.1
Yang, Y.H.2
Callow, M.J.3
Speed, T.P.4
-
28
-
-
38649099066
-
Statistical Analysis of Relative Labeled Mass Spectrometry Data from Complex Samples Using ANOVA
-
10.1021/pr700734f, 2528956, 18173221
-
Oberg AL, Mahoney DW, Eckel-Passow JE, Malone CJ, Wolfinger RD, Hill EG, Cooper LT, Onuma OK, Spiro C, Therneau TM, Bergen HR. Statistical Analysis of Relative Labeled Mass Spectrometry Data from Complex Samples Using ANOVA. J Proteome Res 2008, 7:225-233. 10.1021/pr700734f, 2528956, 18173221.
-
(2008)
J Proteome Res
, vol.7
, pp. 225-233
-
-
Oberg, A.L.1
Mahoney, D.W.2
Eckel-Passow, J.E.3
Malone, C.J.4
Wolfinger, R.D.5
Hill, E.G.6
Cooper, L.T.7
Onuma, O.K.8
Spiro, C.9
Therneau, T.M.10
Bergen, H.R.11
-
29
-
-
77953176036
-
A scaling normalization method for differential expression analysis of RNA-seq data
-
10.1186/gb-2010-11-3-r25, 2864565, 20196867
-
Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology 2010, 11:R25. 10.1186/gb-2010-11-3-r25, 2864565, 20196867.
-
(2010)
Genome Biology
, vol.11
-
-
Robinson, M.D.1
Oshlack, A.2
-
30
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
10.1093/bioinformatics/19.2.185, 12538238
-
Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:185-193. 10.1093/bioinformatics/19.2.185, 12538238.
-
(2003)
Bioinformatics
, vol.19
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
31
-
-
70349260261
-
Evaluation of a new high-dimensional miRNA profiling platform
-
Cunningham JM, Oberg AL, Borralho PM, Kren BT, French AJ, Wang L, Bot BM, Morlan BW, Silverstein KAT, Staggs R, Zeng Y, Lamblin AF, Hilker CA, Fan J-B, Steer CJ, Thibodeau SN. Evaluation of a new high-dimensional miRNA profiling platform. BMC Genomics 2009, 2:57.
-
(2009)
BMC Genomics
, vol.2
, pp. 57
-
-
Cunningham, J.M.1
Oberg, A.L.2
Borralho, P.M.3
Kren, B.T.4
French, A.J.5
Wang, L.6
Bot, B.M.7
Morlan, B.W.8
Silverstein, K.A.T.9
Staggs, R.10
Zeng, Y.11
Lamblin, A.F.12
Hilker, C.A.13
Fan, J.-B.14
Steer, C.J.15
Thibodeau, S.N.16
-
32
-
-
0001223199
-
On the error of counting with a haemacytometer
-
Student
-
Student On the error of counting with a haemacytometer. Biometrika 1907, 5:351-360. Student.
-
(1907)
Biometrika
, vol.5
, pp. 351-360
-
-
-
33
-
-
77958471357
-
Differential expression analysis for sequence count data
-
10.1186/gb-2010-11-10-r106, 20979621
-
Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biology 2010, 11:R106. 10.1186/gb-2010-11-10-r106, 20979621.
-
(2010)
Genome Biology
, vol.11
-
-
Anders, S.1
Huber, W.2
-
34
-
-
41149085992
-
-
9,2, pp. 321-332, and Bioinformatics (2007), vol. 23 n° 21, pages 2881-2887), Robinson and Smyth, Biostatistics
-
Robinson and Smyth, Biostatistics 2008, 9,2, pp. 321-332, and Bioinformatics (2007), vol. 23 n° 21, pages 2881-2887), Robinson and Smyth, Biostatistics.
-
(2008)
-
-
-
35
-
-
63949083912
-
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes
-
10.1038/nmeth.1311, 2664327, 19287394
-
Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods 2009, 6:291-295. 10.1038/nmeth.1311, 2664327, 19287394.
-
(2009)
Nat Methods
, vol.6
, pp. 291-295
-
-
Kozarewa, I.1
Ning, Z.2
Quail, M.A.3
Sanders, M.J.4
Berriman, M.5
Turner, D.J.6
-
36
-
-
0029937426
-
DNA condensation
-
10.1016/S0959-440X(96)80052-2, 8804837
-
Bloomfield VA. DNA condensation. Curr Opin Struct Biol 1996, 6:334-341. 10.1016/S0959-440X(96)80052-2, 8804837.
-
(1996)
Curr Opin Struct Biol
, vol.6
, pp. 334-341
-
-
Bloomfield, V.A.1
-
37
-
-
79960639076
-
Assay of Random RNA Oligomerization in Buffers with High Concentrations of Divalent Metal Ions
-
[Accessed April 28, 2010]
-
Vlassov A. Assay of Random RNA Oligomerization in Buffers with High Concentrations of Divalent Metal Ions. ChemInform 2005, 36. [Accessed April 28, 2010].
-
(2005)
ChemInform
, vol.36
-
-
Vlassov, A.1
-
38
-
-
0027488624
-
Isolation of new ribozymes from a large pool of random sequences
-
10.1126/science.7690155, 7690155
-
Bartel DP, Szostak JW. Isolation of new ribozymes from a large pool of random sequences. Science 1993, 261:1411-1418. 10.1126/science.7690155, 7690155.
-
(1993)
Science
, vol.261
, pp. 1411-1418
-
-
Bartel, D.P.1
Szostak, J.W.2
-
39
-
-
0003493777
-
Statistical Methods for Research Workers
-
London, Oliver and Boyd
-
Fisher RA. Statistical Methods for Research Workers. 1932, London, Oliver and Boyd.
-
(1932)
-
-
Fisher, R.A.1
-
40
-
-
66749171697
-
Statistical design of quantitative mass spectrometry-based proteomic experiments
-
10.1021/pr8010099, 19222236
-
Oberg AL, Vitek O. Statistical design of quantitative mass spectrometry-based proteomic experiments. J Proteome Res 2009, 8(5):2144-56. 10.1021/pr8010099, 19222236.
-
(2009)
J Proteome Res
, vol.8
, Issue.5
, pp. 2144-2156
-
-
Oberg, A.L.1
Vitek, O.2
-
41
-
-
0000884487
-
Experimental design for gene expression microarrays
-
10.1093/biostatistics/2.2.183, 12933549
-
Kerr MK, Churchill GA. Experimental design for gene expression microarrays. Biostatistics 2001, 2(2):183-201. 10.1093/biostatistics/2.2.183, 12933549.
-
(2001)
Biostatistics
, vol.2
, Issue.2
, pp. 183-201
-
-
Kerr, M.K.1
Churchill, G.A.2
-
42
-
-
0036855402
-
Comparison of microarray designs for class comparison and class discovery
-
10.1093/bioinformatics/18.11.1438, 12424114
-
Dobbin K, Simon R. Comparison of microarray designs for class comparison and class discovery. Bioinformatics 2002, 18:1438-1445. 10.1093/bioinformatics/18.11.1438, 12424114.
-
(2002)
Bioinformatics
, vol.18
, pp. 1438-1445
-
-
Dobbin, K.1
Simon, R.2
-
43
-
-
2942608807
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Design and Analysis of DNA Microarray Investigations
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Springer-Verlag
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Simon RM, Korn EL, McShane LM, Radmacher MD, Wright GW, Zhao Y. Design and Analysis of DNA Microarray Investigations. 2003, Springer-Verlag.
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(2003)
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Simon, R.M.1
Korn, E.L.2
McShane, L.M.3
Radmacher, M.D.4
Wright, G.W.5
Zhao, Y.6
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