-
1
-
-
55549097836
-
Mapping short DNA sequencing reads and calling variants using mapping quality scores
-
Li, H., Ruan, J., and Durbin, R. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res., 18 (11), 1851-1858.
-
(2008)
Genome Res.
, vol.18
, Issue.11
, pp. 1851-1858
-
-
Li, H.1
Ruan, J.2
Durbin, R.3
-
2
-
-
78651377251
-
The UCSC genome browser: what every molecular biologist should know
-
19.9.1-19.9.28
-
Mangan, M.E., Williams, J.M., Kuhn, R.M., and Lathe, W.C. (2009) The UCSC genome browser: what every molecular biologist should know. Curr. Protoc. Mol. Biol., 88, 19.9.1-19.9.28.
-
(2009)
Curr. Protoc. Mol. Biol.
, vol.88
-
-
Mangan, M.E.1
Williams, J.M.2
Kuhn, R.M.3
Lathe, W.C.4
-
3
-
-
70349884341
-
RNA-mate: a recursive mapping strategy for highthroughput RNA-sequencing data
-
Cloonan, N., Xu, Q., Faulkner, G.J., Taylor, D.F., Tang, D.T.P., Kolle, G., and Grimmond, S.M. (2009) RNA-mate: a recursive mapping strategy for highthroughput RNA-sequencing data. Bioinformatics, 25 (19), 2615-2616.
-
(2009)
Bioinformatics
, vol.25
, Issue.19
, pp. 2615-2616
-
-
Cloonan, N.1
Xu, Q.2
Faulkner, G.J.3
Taylor, D.F.4
Tang, D.T.P.5
Kolle, G.6
Grimmond, S.M.7
-
4
-
-
39149083734
-
A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE
-
Faulkner, G.J., Forrest, A.R.R., Chalk, A.M., Schroder, K., Hayashizaki, Y., Carninci, P., Hume, D.A., andGrimmond, S.M. (2008)A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics, 91 (3), 281-288.
-
(2008)
Genomics
, vol.91
, Issue.3
, pp. 281-288
-
-
Faulkner, G.J.1
Forrest, A.R.R.2
Chalk, A.M.3
Schroder, K.4
Hayashizaki, Y.5
Carninci, P.6
Hume, D.A.7
Grimmond, S.M.8
-
5
-
-
50949105626
-
A general definition and nomenclature for alternative splicing events
-
Sammeth, M., Foissac, S., and Guigo, R. (2008) A general definition and nomenclature for alternative splicing events. PLoS Comput. Biol., 4 (8), e1000147.
-
(2008)
PLoS Comput. Biol.
, vol.4
, Issue.8
-
-
Sammeth, M.1
Foissac, S.2
Guigo, R.3
-
6
-
-
64549119707
-
Statistical inferences for isoform expression in RNASeq
-
Jiang, H. andWong,W.H. (2009) Statistical inferences for isoform expression in RNASeq. Bioinformatics, 25 (8), 1026-1032.
-
(2009)
Bioinformatics
, vol.25
, Issue.8
, pp. 1026-1032
-
-
Jiang, H.1
Wong, W.H.2
-
7
-
-
70449516738
-
Transcript quantification with RNA-Seq data
-
Bohnert, R., Behr, J., and Ratsch, G. (2009) Transcript quantification with RNA-Seq data. BMC Bioinformatics, 10 (Suppl. 13)
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.SUPPL. 13
-
-
Bohnert, R.1
Behr, J.2
Ratsch, G.3
-
8
-
-
33748645500
-
GENCODE: producing a reference annotation for ENCODE
-
Harrow, J., Denoeud, F., Frankish, A., Reymond, A., Chen, C., Chrast, J., Lagarde, J., Gilbert, J.G.R., Storey, R., Swarbreck, D., Rossier, C., Ucla, C., Hubbard, T., Antonarakis, S.E., and Guigo, R. (2006) GENCODE: producing a reference annotation for ENCODE. Genome Biol., 7 (Suppl. 1), S4.1-S4.9.
-
(2006)
Genome Biol.
, vol.7
, Issue.SUPPL. 1
-
-
Harrow, J.1
Denoeud, F.2
Frankish, A.3
Reymond, A.4
Chen, C.5
Chrast, J.6
Lagarde, J.7
Gilbert, J.G.R.8
Storey, R.9
Swarbreck, D.10
Rossier, C.11
Ucla, C.12
Hubbard, T.13
Antonarakis, S.E.14
Guigo, R.15
-
9
-
-
56649100471
-
Exact transcriptome reconstruction from short sequence reads
-
Lacroix, V., Sammeth, M., Guigo, R., and Bergeron, A. (2008) Exact transcriptome reconstruction from short sequence reads. Lect. Notes Comput. Sci., 5268, 50-63.
-
(2008)
Lect. Notes Comput. Sci.
, vol.5268
, pp. 50-63
-
-
Lacroix, V.1
Sammeth, M.2
Guigo, R.3
Bergeron, A.4
-
10
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
Birney, E.,et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447 (7146), 799-816.
-
(2007)
Nature
, vol.447
, Issue.7146
, pp. 799-816
-
-
Birney, E.1
-
11
-
-
70350653808
-
Transcriptome analysis by strand-specific sequencing of complementary DNA
-
Parkhomchuk, D., Borodina, T., Amstislavskiy, V., Banaru, M., Hallen, L., Krobitsch, S., Lehrach, H., and Soldatov, A. (2009) Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res., 37 (18), e123.
-
(2009)
Nucleic Acids Res.
, vol.37
, Issue.18
-
-
Parkhomchuk, D.1
Borodina, T.2
Amstislavskiy, V.3
Banaru, M.4
Hallen, L.5
Krobitsch, S.6
Lehrach, H.7
Soldatov, A.8
-
12
-
-
77949582444
-
-
U.C. Berkeley Division of Biostatistics Working Paper Series
-
Bullard, J., Purdom, E., Hansen, K., Durinck, S., and Dudoit, S. (2009) Statistical Inference in mRNA-Seq: Exploratory Data Analysis and Differential Expression. Technical report, U.C. Berkeley Division of Biostatistics Working Paper Series.
-
(2009)
Statistical Inference in mRNA-Seq: Exploratory Data Analysis and Differential Expression. Technical report
-
-
Bullard, J.1
Purdom, E.2
Hansen, K.3
Durinck, S.4
Dudoit, S.5
-
13
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L., and Wold, B. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods, 5 (7), 621-628.
-
(2008)
Nat. Methods
, vol.5
, Issue.7
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
14
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
Wang, E.T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S.F., Schroth, G.P., and Burge, C.B. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature, 456 (7221), 470-476.
-
(2008)
Nature
, vol.456
, Issue.7221
, pp. 470-476
-
-
Wang, E.T.1
Sandberg, R.2
Luo, S.3
Khrebtukova, I.4
Zhang, L.5
Mayr, C.6
Kingsmore, S.F.7
Schroth, G.P.8
Burge, C.B.9
-
15
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25 (14), 1754-1760.
-
(2009)
Bioinformatics
, vol.25
, Issue.14
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
16
-
-
57049122389
-
A large genome center?s improvements to the Illumina sequencing system
-
Quail, M.A., Kozarewa, I., Smith, F., Scally, A., Stephens, P.J., Durbin, R., Swerdlow, H., and Turner, D.J. (2008) A large genome center?s improvements to the Illumina sequencing system. Nat. Methods, 5 (12), 1005-1010.
-
(2008)
Nat. Methods
, vol.5
, Issue.12
, pp. 1005-1010
-
-
Quail, M.A.1
Kozarewa, I.2
Smith, F.3
Scally, A.4
Stephens, P.J.5
Durbin, R.6
Swerdlow, H.7
Turner, D.J.8
-
17
-
-
65649126066
-
Transcript length bias in RNA-seq data confounds systems biology
-
Oshlack, A. and Wakefield, M.J. (2009) Transcript length bias in RNA-seq data confounds systems biology. Biol. Direct, 4, 14.
-
(2009)
Biol. Direct
, vol.4
, pp. 14
-
-
Oshlack, A.1
Wakefield, M.J.2
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