-
1
-
-
57749195712
-
RNA-Seq: a revolutionary tool for transcriptomics
-
Wang,Z., Gerstein,M. and Snyder,M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
2
-
-
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, 621-628.
-
(2008)
Nat. Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
3
-
-
70449711243
-
Computation for ChIP-seq and RNA-seq studies
-
Pepke,S., Wold,B. and Mortazavi,A. (2009) Computation for ChIP-seq and RNA-seq studies. Nat. Methods, 6, S22-S32.
-
(2009)
Nat. Methods
, vol.6
-
-
Pepke, S.1
Wold, B.2
Mortazavi, A.3
-
4
-
-
70449516738
-
Transcript quantification with RNA-Seq data
-
Bohnert,R. Behr,J. and Rätsch,G. (2009) Transcript quantification with RNA-Seq data. BMC Bioinformatics, 10(Suppl. 13), P5.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.SUPPL. 13
-
-
Bohnert, R.1
Behr, J.2
Rätsch, G.3
-
6
-
-
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
-
-
Dohm, J.C.1
Lottaz, C.2
Borodina, T.3
Himmelbauer, H.4
-
7
-
-
77955883388
-
Biases in Illumina transcriptome sequencing caused by random hexamer priming
-
doi:10.1093/nar/gkq224 [14 April 2010, Epub ahead of print]
-
Hansen,K.D., Brenner,S.E. and Dudoit,S. (2010) Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res., doi:10.1093/nar/gkq224 [14 April 2010, Epub ahead of print].
-
(2010)
Nucleic Acids Res.
-
-
Hansen, K.D.1
Brenner, S.E.2
Dudoit, S.3
-
8
-
-
67649595548
-
Wyman,S.K., de Bruijn,E., Voest,E.E. et al. Limitations and possibilities of small RNA digital gene expression profiling
-
Linsen,S.E.V., de Wit,E., Janssens,G., Heater,S., Chapman,L., Parkin,R.K., Fritz,B., Wyman,S.K., de Bruijn,E., Voest,E.E. et al. (2009) Limitations and possibilities of small RNA digital gene expression profiling. Nat. Methods, 6, 474-476.
-
(2009)
Nat. Methods
, vol.6
, pp. 474-476
-
-
Linsen, S.E.V.1
de Wit, E.2
Janssens, G.3
Heater, S.4
Chapman, L.5
Parkin, R.K.6
Fritz, B.7
-
9
-
-
64549119707
-
Statistical inferences for isoform expression in RNA-Seq
-
Jiang,H. and Wong,W.H. (2009) Statistical inferences for isoform expression in RNA-Seq. Bioinformatics, 25, 1026-1032.
-
(2009)
Bioinformatics
, vol.25
, pp. 1026-1032
-
-
Jiang, H.1
Wong, W.H.2
-
10
-
-
77954127002
-
Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments
-
doi:10.1093/nar/gkq041 [11 February 2010, Epub ahead of print
-
Richard,H., Schulz,M.H., Sultan,M., Nurnberger,A., Schrinner,S., Balzereit,D., Dagand,E., Rasche,A., Lehrach,H., Vingron,M. et al. (2010) Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Res., doi:10.1093/nar/gkq041 [11 February 2010, Epub ahead of print].
-
(2010)
Nucleic Acids Res.
-
-
Richard, H.1
Schulz, M.H.2
Sultan, M.3
Nurnberger, A.4
Schrinner, S.5
Balzereit, D.6
Dagand, E.7
Rasche, A.8
Lehrach, H.9
Vingron, M.10
-
11
-
-
77949507153
-
RNA-Seq gene expression estimation with read mapping uncertainty
-
Li,B., Ruotti,V., Stewart,R.M., Thomson,J.A. and Dewey,C.N. (2010) RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics, 26, 493-500.
-
(2010)
Bioinformatics
, vol.26
, pp. 493-500
-
-
Li, B.1
Ruotti, V.2
Stewart, R.M.3
Thomson, J.A.4
Dewey, C.N.5
-
12
-
-
77954305297
-
-
(1 June 2010, date last accessed)
-
Sammeth,M. (2010) The Flux Capacitor. http://flux.sammeth.net/capacitor.html (1 June 2010, date last accessed).
-
(2010)
The Flux Capacitor
-
-
Sammeth, M.1
-
13
-
-
49549102475
-
Optimal spliced alignments of short sequence reads
-
De Bona,F., Ossowski,S., Schneeberger,K. and Rätsch,G. (2008) Optimal spliced alignments of short sequence reads. Bioinformatics, 24, i174-i180.
-
(2008)
Bioinformatics
, vol.24
-
-
De Bona, F.1
Ossowski, S.2
Schneeberger, K.3
Rätsch, G.4
-
14
-
-
76249113666
-
Simultaneous alignment of short reads against multiple genomes
-
Schneeberger,K., Hagmann,J., Ossowski,S., Warthmann,N., Gesing,S., Kohlbacher,O. and Weigel,D. (2009) Simultaneous alignment of short reads against multiple genomes. Genome Biol., 10, R98.
-
(2009)
Genome Biol
, vol.10
-
-
Schneeberger, K.1
Hagmann, J.2
Ossowski, S.3
Warthmann, N.4
Gesing, S.5
Kohlbacher, O.6
Weigel, D.7
-
15
-
-
70350708134
-
mGene: accurate SVM-based gene finding with an application to nematode genomes
-
Schweikert,G., Zien,A., Zeller,G., Behr,J., Dieterich,C., Ong,C.S., Philips,P., de Bona,F., Hartmann,L., Bohlen,A. et al. (2009) mGene: accurate SVM-based gene finding with an application to nematode genomes. Genome Res., 19, 2133-2143.
-
(2009)
Genome Res
, vol.19
, pp. 2133-2143
-
-
Schweikert, G.1
Zien, A.2
Zeller, G.3
Behr, J.4
Dieterich, C.5
Ong, C.S.6
Philips, P.7
de Bona, F.8
Hartmann, L.9
Bohlen, A.10
-
16
-
-
63849342015
-
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans
-
Hillier,L.W., Reinke,V., Green,P., Hirst,M., Marra,M.A. and Waterston,R.H. (2009) Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res., 19, 657-666.
-
(2009)
Genome Res
, vol.19
, pp. 657-666
-
-
Hillier, L.W.1
Reinke, V.2
Green, P.3
Hirst, M.4
Marra, M.A.5
Waterston, R.H.6
-
17
-
-
77954251933
-
-
(1 June 2010, date last accessed)
-
Sammeth,M. (2010) The Flux Simulator. http://flux.sammeth.net/simulator.html (1 June 2010, date last accessed).
-
(2010)
The Flux Simulator
-
-
Sammeth, M.1
-
18
-
-
25844449770
-
Galaxy: a platform for interactive large-scale genome analysis
-
Giardine,B., Riemer,C., Hardison,R.C., Burhans,R., Elnitski,L., Shah,P., Zhang,Y., Blankenberg,D., Albert,I., Taylor,J. et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res., 15, 1451-1455.
-
(2005)
Genome Res
, vol.15
, pp. 1451-1455
-
-
Giardine, B.1
Riemer, C.2
Hardison, R.C.3
Burhans, R.4
Elnitski, L.5
Shah, P.6
Zhang, Y.7
Blankenberg, D.8
Albert, I.9
Taylor, J.10
-
19
-
-
75949108066
-
Galaxy: a web-based genome analysis tool for experimentalists
-
Chapter 19:Unit 19.10.1-21
-
Blankenberg,D., Von Kuster,G., Coraor,N., Ananda,G., Lazarus,R., Mangan,M., Nekrutenko,A. and Taylor,J. (2010) Galaxy: a web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol., 10, 1-21, Chapter 19:Unit 19.10.1-21.
-
(2010)
Curr. Protoc. Mol. Biol
, vol.10
, pp. 1-21
-
-
Blankenberg, D.1
Von Kuster, G.2
Coraor, N.3
Ananda, G.4
Lazarus, R.5
Mangan, M.6
Nekrutenko, A.7
Taylor, J.8
-
20
-
-
67849099280
-
mGene.web: a web service for accurate computational gene finding
-
Schweikert,G., Behr,J., Zien,A., Zeller,G., Ong,C.S., Sonnenburg,S. and Rätsch,G. (2009) mGene.web: a web service for accurate computational gene finding. Nucleic Acids Res., 37(Suppl. 2), W312-W316.
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.SUPPL. 2
-
-
Schweikert, G.1
Behr, J.2
Zien, A.3
Zeller, G.4
Ong, C.S.5
Sonnenburg, S.6
Rä tsch, G.7
-
21
-
-
68549104404
-
1000 Genome Project Data Processing Sub group The sequence Alignment/Map format and SAMtools
-
Li,H., Handsaker,B., Wysoker,A., Fennell,T., Ruan,J., Homer,N., Marth,G., Abecasis,G. and Durbin,R. (2009) 1000 Genome Project Data Processing Sub group. The sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
-
(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
-
22
-
-
77954286509
-
-
Mosek version 6. Technical Report TR-2009-3. MOSEK ApS
-
Andersen,E.D., Jensen,B., Jensen,J., Sandvik,R. and Worsoe,U. (2009) Mosek version 6. Technical Report TR-2009-3. MOSEK ApS.
-
(2009)
-
-
Andersen, E.D.1
Jensen, B.2
Jensen, J.3
Sandvik, R.4
Worsoe, U.5
|