-
1
-
-
84855295457
-
Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
-
Kircher M, Sawyer S, Meyer M, (2011) Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Research 40: e3-e3.
-
(2011)
Nucleic Acids Research
, vol.40
-
-
Kircher, M.1
Sawyer, S.2
Meyer, M.3
-
2
-
-
80052520350
-
Barcoding bias in high-throughput multiplex sequencing of miRNA
-
Alon S, Vigneault F, Eminaga S, Christodoulou DC, Seidman JG, et al. (2011) Barcoding bias in high-throughput multiplex sequencing of miRNA. Genome Research 21: 1506-1511.
-
(2011)
Genome Research
, vol.21
, pp. 1506-1511
-
-
Alon, S.1
Vigneault, F.2
Eminaga, S.3
Christodoulou, D.C.4
Seidman, J.G.5
-
3
-
-
53249132629
-
Identification of genetic variants using bar-coded multiplexed sequencing
-
Craig DW, Pearson JV, Szelinger S, Sekar A, Redman M, et al. (2008) Identification of genetic variants using bar-coded multiplexed sequencing. Nature Methods 5: 887-93.
-
(2008)
Nature Methods
, vol.5
, pp. 887-893
-
-
Craig, D.W.1
Pearson, J.V.2
Szelinger, S.3
Sekar, A.4
Redman, M.5
-
4
-
-
0034760329
-
A clone-array pooled strategy for sequencing large genomes
-
Cai WW, Chen R, Gibbs RA, Bradley A, (2001) A clone-array pooled strategy for sequencing large genomes. Genome Research 11: 1619-1623.
-
(2001)
Genome Research
, vol.11
, pp. 1619-1623
-
-
Cai, W.W.1
Chen, R.2
Gibbs, R.A.3
Bradley, A.4
-
5
-
-
84957005432
-
Pooled genomic indexing (PGI): mathematical analysis and experiment design. In: Proceedings of Workshop on Algorithms in Bioinformatics
-
Csuros M, Milosavljevic A, (2002) Pooled genomic indexing (PGI): mathematical analysis and experiment design. In: Proceedings of Workshop on Algorithms in Bioinformatics. LNCS 2452: 10-28.
-
(2002)
LNCS
, vol.2452
, pp. 10-28
-
-
Csuros, M.1
Milosavljevic, A.2
-
6
-
-
3242718140
-
Clone-array pooled shotgun mapping and sequencing: design and analysis of experiments
-
Csuros M, Li B, Milosavljevic A, (2003) Clone-array pooled shotgun mapping and sequencing: design and analysis of experiments. Genome Inform 14: 186-195.
-
(2003)
Genome Inform
, vol.14
, pp. 186-195
-
-
Csuros, M.1
Li, B.2
Milosavljevic, A.3
-
7
-
-
20044367103
-
Pooled genomic indexing of Rhesus macaque
-
Milosavljevic A, Harris R, Sodergren E, Jackson A, Kalafus K, et al. (2005) Pooled genomic indexing of Rhesus macaque. Genome Research 15: 292-301.
-
(2005)
Genome Research
, vol.15
, pp. 292-301
-
-
Milosavljevic, A.1
Harris, R.2
Sodergren, E.3
Jackson, A.4
Kalafus, K.5
-
8
-
-
67650034261
-
Overlapping pools for high-throughput targeted resequencing
-
Prabhu S, Pe'er I, (2009) Overlapping pools for high-throughput targeted resequencing. Genome Research 19: 1254-1261.
-
(2009)
Genome Research
, vol.19
, pp. 1254-1261
-
-
Prabhu, S.1
Pe'er, I.2
-
9
-
-
67650047735
-
DNA sudoku - harnessing highthroughput sequencing for multiplexed specimen analysis
-
Erlich Y, Chang K, Gordon A, Ronen R, Navon O, et al. (2009) DNA sudoku - harnessing highthroughput sequencing for multiplexed specimen analysis. Genome Research 19: 1243-1253.
-
(2009)
Genome Research
, vol.19
, pp. 1243-1253
-
-
Erlich, Y.1
Chang, K.2
Gordon, A.3
Ronen, R.4
Navon, O.5
-
10
-
-
84975780137
-
Optimal pooling for genome resequencing with ultra-high-throughput short-read technologies
-
Hajirasouliha I, Hormozdiari F, Sahinalp SC, Birol I, (2008) Optimal pooling for genome resequencing with ultra-high-throughput short-read technologies. Bioinformatics 24: i32-i40.
-
(2008)
Bioinformatics
, vol.24
-
-
Hajirasouliha, I.1
Hormozdiari, F.2
Sahinalp, S.C.3
Birol, I.4
-
11
-
-
78049366216
-
Identification of rare alleles and their carriers using compressed se(que)nsing
-
Shental N, Amir A, Zuk O, (2010) Identification of rare alleles and their carriers using compressed se(que)nsing. Nucleic Acids Research 38: e179-e179.
-
(2010)
Nucleic Acids Research
, vol.38
-
-
Shental, N.1
Amir, A.2
Zuk, O.3
-
12
-
-
77649284211
-
Compressed genotyping
-
Erlich Y, Gordon A, Brand M, Hannon GJ, Mitra PP, (2010) Compressed genotyping. IEEE Transactions on Information Theory 56: 706-723.
-
(2010)
IEEE Transactions on Information Theory
, vol.56
, pp. 706-723
-
-
Erlich, Y.1
Gordon, A.2
Brand, M.3
Hannon, G.J.4
Mitra, P.P.5
-
13
-
-
0141630427
-
Locating sequence on FPC maps and selecting a minimal tiling path
-
Engler FW, Hatfield J, Nelson W, Soderlund CA, (2003) Locating sequence on FPC maps and selecting a minimal tiling path. Genome Research 13: 2152-2163.
-
(2003)
Genome Research
, vol.13
, pp. 2152-2163
-
-
Engler, F.W.1
Hatfield, J.2
Nelson, W.3
Soderlund, C.A.4
-
14
-
-
56649109633
-
Computing the minimal tiling path from a physical map by integer linear programming. In: Proceedings of the Workshop on Algorithms in Bioinformatics
-
Bozdag S, Close TJ, Lonardi S, (2008) Computing the minimal tiling path from a physical map by integer linear programming. In: Proceedings of the Workshop on Algorithms in Bioinformatics. WABI 2008: 148-161.
-
(2008)
WABI
, vol.2008
, pp. 148-161
-
-
Bozdag, S.1
Close, T.J.2
Lonardi, S.3
-
15
-
-
33645151681
-
A new pooling strategy for high-throughput screening: the shifted transversal design
-
Thierry-Mieg N, (2006) A new pooling strategy for high-throughput screening: the shifted transversal design. BMC Bioinformatics 7: 28.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 28
-
-
Thierry-Mieg, N.1
-
16
-
-
0035366295
-
Five-color-based highinformation- content fingerprinting of bacterial artificial chromosome clones using type IIS restriction endonucleases
-
Ding Y, Johnson MD, Chen WQ, Wong D, Chen YJ, et al. (2001) Five-color-based highinformation- content fingerprinting of bacterial artificial chromosome clones using type IIS restriction endonucleases. Genomics 74: 142-154.
-
(2001)
Genomics
, vol.74
, pp. 142-154
-
-
Ding, Y.1
Johnson, M.D.2
Chen, W.Q.3
Wong, D.4
Chen, Y.J.5
-
17
-
-
12444325815
-
High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis
-
Luo MC, Thomas C, You FM, Hsiao J, Ouyang S, et al. (2003) High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 82: 378-389.
-
(2003)
Genomics
, vol.82
, pp. 378-389
-
-
Luo, M.C.1
Thomas, C.2
You, F.M.3
Hsiao, J.4
Ouyang, S.5
-
18
-
-
0033674122
-
Contigs built with fingerprints, markers, and FPC v4.7
-
Soderlund C, Humphray S, Dunham A, French L, (2000) Contigs built with fingerprints, markers, and FPC v4.7. Genome Research 10: 1772-1787.
-
(2000)
Genome Research
, vol.10
, pp. 1772-1787
-
-
Soderlund, C.1
Humphray, S.2
Dunham, A.3
French, L.4
-
19
-
-
47649107470
-
A compartmentalized approach to the assembly of physical maps. In: Proceedings of IEEE International Symposium on Bioinformatics & Bioengineering
-
Bozdag S, Close T, Lonardi S, (2007) A compartmentalized approach to the assembly of physical maps. In: Proceedings of IEEE International Symposium on Bioinformatics & Bioengineering. BIBE 2007: 218-225.
-
(2007)
BIBE
, vol.2007
, pp. 218-225
-
-
Bozdag, S.1
Close, T.2
Lonardi, S.3
-
20
-
-
84890566932
-
Combinatorial Group Testing and Applications. (Series on Applied Mathematics)
-
Du DZ, Hwang FK, (1993) Combinatorial Group Testing and Applications. (Series on Applied Mathematics). World Scientific Publishing Company.
-
(1993)
World Scientific Publishing Company
-
-
Du, D.Z.1
Hwang, F.K.2
-
21
-
-
33745309316
-
New construction for transversal design
-
Du DZ, Hwang F, Wu W, Znati T, (2006) New construction for transversal design. Journal of Computational Biology 13: 990-995.
-
(2006)
Journal of Computational Biology
, vol.13
, pp. 990-995
-
-
Du, D.Z.1
Hwang, F.2
Wu, W.3
Znati, T.4
-
22
-
-
34547624524
-
Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping
-
Vermeirssen V, Deplancke B, Barrasa MI, Reece-Hoyes JS, Arda HE, et al. (2007) Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping. Nat Meth 4: 659-664.
-
(2007)
Nat Meth
, vol.4
, pp. 659-664
-
-
Vermeirssen, V.1
Deplancke, B.2
Barrasa, M.I.3
Reece-Hoyes, J.S.4
Arda, H.E.5
-
23
-
-
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: 1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
24
-
-
43149115851
-
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino D, Birney E, (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 8: 821-9.
-
(2008)
Genome Research
, vol.8
, pp. 821-829
-
-
Zerbino, D.1
Birney, E.2
-
25
-
-
75649124547
-
De novo assembly of human genomes with massively parallel short read sequencing
-
Li R, Zhu H, Ruan J, Qian W, Fang X, et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Research 20: 265-272.
-
(2010)
Genome Research
, vol.20
, pp. 265-272
-
-
Li, R.1
Zhu, H.2
Ruan, J.3
Qian, W.4
Fang, X.5
-
26
-
-
66449136667
-
ABySS: A parallel assembler for short read sequence data
-
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, et al. (2009) ABySS: A parallel assembler for short read sequence data. Genome Research 19: 1117-1123.
-
(2009)
Genome Research
, vol.19
, pp. 1117-1123
-
-
Simpson, J.T.1
Wong, K.2
Jackman, S.D.3
Schein, J.E.4
Jones, S.J.5
-
27
-
-
73449108400
-
Development and implementation of high-throughput SNP genotyping in barley
-
Close T, Bhat P, Lonardi S, Wu Y, Rostoks N, et al. (2009) Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10: 582.
-
(2009)
BMC Genomics
, vol.10
, pp. 582
-
-
Close, T.1
Bhat, P.2
Lonardi, S.3
Wu, Y.4
Rostoks, N.5
-
28
-
-
85167516304
-
An improved consensus linkage map of barley based on flow-sorted chromosomes and single nucleotide polymorphism markers
-
Muñoz-Amatriaín M, Moscou MJ, Bhat PR, Svensson JT, Bartoš J, et al. (2011) An improved consensus linkage map of barley based on flow-sorted chromosomes and single nucleotide polymorphism markers. The Plant Genome 4: 1-12.
-
(2011)
The Plant Genome
, vol.4
, pp. 1-12
-
-
Muñoz-Amatriaín, M.1
Moscou, M.J.2
Bhat, P.R.3
Svensson, J.T.4
Bartoš, J.5
-
29
-
-
84867395711
-
A genome sequence resource for barley
-
Alpert M, Wanamaker S, Duma D, Fenton RD, Ma Y, et al. (2011) A genome sequence resource for barley. Barley Genetics Newsletter 41: 10-11.
-
(2011)
Barley Genetics Newsletter
, vol.41
, pp. 10-11
-
-
Alpert, M.1
Wanamaker, S.2
Duma, D.3
Fenton, R.D.4
Ma, Y.5
-
30
-
-
12844272411
-
A detailed look at 7 million years of genome evolution in a 439 kb continuous sequence at the barley Hv-eIF4E locus: recombination, rearrangements and repeats
-
Wicker T, Zimmermann W, Perovic D, Paterson A, Ganal M, et al. (2005) A detailed look at 7 million years of genome evolution in a 439 kb continuous sequence at the barley Hv-eIF4E locus: recombination, rearrangements and repeats. The Plant J 41: 184-194.
-
(2005)
The Plant J
, vol.41
, pp. 184-194
-
-
Wicker, T.1
Zimmermann, W.2
Perovic, D.3
Paterson, A.4
Ganal, M.5
-
31
-
-
0033711956
-
A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes
-
Yu Y, Tomkins JP, Waugh R, Frisch DA, Kudrna D, et al. (2000) A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes. Theoretical and Applied Genetics 101: 1093-1099.
-
(2000)
Theoretical and Applied Genetics
, vol.101
, pp. 1093-1099
-
-
Yu, Y.1
Tomkins, J.P.2
Waugh, R.3
Frisch, D.A.4
Kudrna, D.5
-
32
-
-
33846668211
-
An improved method to identify BAC clones using pooled overgos
-
Madishetty K, Condamine P, Svensson JT, Rodriguez E, Close TJ, (2007) An improved method to identify BAC clones using pooled overgos. Nucleic Acids Research 35: e5.
-
(2007)
Nucleic Acids Research
, vol.35
-
-
Madishetty, K.1
Condamine, P.2
Svensson, J.T.3
Rodriguez, E.4
Close, T.J.5
-
34
-
-
77957758142
-
Reptile: representative tiling for short read error correction
-
Yang X, Dorman KS, Aluru S, (2010) Reptile: representative tiling for short read error correction. Bioinformatics 26: 2526-2533.
-
(2010)
Bioinformatics
, vol.26
, pp. 2526-2533
-
-
Yang, X.1
Dorman, K.S.2
Aluru, S.3
-
35
-
-
83855165105
-
Repetitive DNA and next-generation sequencing: computational challenges and solutions
-
Treangen TJ, Salzberg SL, (2011) Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nature Reviews Genetics 13: 36-46.
-
(2011)
Nature Reviews Genetics
, vol.13
, pp. 36-46
-
-
Treangen, T.J.1
Salzberg, S.L.2
-
36
-
-
0028987725
-
Pairwise end sequencing: a unified approach to genomic mapping and sequencing
-
Roach J, Boysen C, Wang K, Hood L, (1995) Pairwise end sequencing: a unified approach to genomic mapping and sequencing. Genomics 26: 345-353.
-
(1995)
Genomics
, vol.26
, pp. 345-353
-
-
Roach, J.1
Boysen, C.2
Wang, K.3
Hood, L.4
-
37
-
-
0030950735
-
Human whole-genome shotgun sequencing
-
Weber J, Myers E, (1997) Human whole-genome shotgun sequencing. Genome Research 7: 401-409.
-
(1997)
Genome Research
, vol.7
, pp. 401-409
-
-
Weber, J.1
Myers, E.2
-
38
-
-
0035432364
-
Strategies for the systematic sequencing of complex genomes
-
Green E, (2001) Strategies for the systematic sequencing of complex genomes. Nature Reviews Genetics 2: 573-583.
-
(2001)
Nature Reviews Genetics
, vol.2
, pp. 573-583
-
-
Green, E.1
-
39
-
-
84857893016
-
GAGE: A critical evaluation of genome assemblies and assembly algorithms
-
Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, et al. (2012) GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Research 22: 557-567.
-
(2012)
Genome Research
, vol.22
, pp. 557-567
-
-
Salzberg, S.L.1
Phillippy, A.M.2
Zimin, A.3
Puiu, D.4
Magoc, T.5
-
40
-
-
83055181941
-
Assemblathon 1: A competitive assessment of de novo short read assembly methods
-
Earl D, Bradnam K, St John J, Darling A, Lin D, et al. (2011) Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Research 21: 2224-2241.
-
(2011)
Genome Research
, vol.21
, pp. 2224-2241
-
-
Earl, D.1
Bradnam, K.2
St John, J.3
Darling, A.4
Lin, D.5
-
41
-
-
79955105933
-
Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes
-
Haiminen N, Feltus FA, Parida L, (2011) Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes. BMC Genomics 12: 194.
-
(2011)
BMC Genomics
, vol.12
, pp. 194
-
-
Haiminen, N.1
Feltus, F.A.2
Parida, L.3
|