-
1
-
-
70349910898
-
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
-
Degner JF, Marioni JC, Pai AA et al. (2009) Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics, 25, 3207-3212.
-
(2009)
Bioinformatics
, vol.25
, pp. 3207-3212
-
-
Degner, J.F.1
Marioni, J.C.2
Pai, A.A.3
-
2
-
-
79957842166
-
Computational methods for transcriptome annotation and quantification using RNA-seq
-
Garber M, Grabherr MG, Guttman M, Trapnell C (2011) Computational methods for transcriptome annotation and quantification using RNA-seq. Nature Methods, 8, 469-477.
-
(2011)
Nature Methods
, vol.8
, pp. 469-477
-
-
Garber, M.1
Grabherr, M.G.2
Guttman, M.3
Trapnell, C.4
-
3
-
-
80052745094
-
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
-
Grant GR, Farkas MH, Pizarro AD et al. (2011) Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics, 27, 2518-2528.
-
(2011)
Bioinformatics
, vol.27
, pp. 2518-2528
-
-
Grant, G.R.1
Farkas, M.H.2
Pizarro, A.D.3
-
4
-
-
84861365328
-
Allelic imbalance in drosophila hybrid heads: exons, isoforms, and evolution
-
Graze RM, Novelo LL, Amin V et al. (2012) Allelic imbalance in drosophila hybrid heads: exons, isoforms, and evolution. Molecular Biology and Evolution, 29, 1521-1532.
-
(2012)
Molecular Biology and Evolution
, vol.29
, pp. 1521-1532
-
-
Graze, R.M.1
Novelo, L.L.2
Amin, V.3
-
5
-
-
79251557454
-
PoPoolation: A toolbox for population genetic analysis of next generation sequencing data from pooled individuals
-
Kofler R, Orozco-terWengel P, De Maio N et al. (2011) PoPoolation: A toolbox for population genetic analysis of next generation sequencing data from pooled individuals. PLoS ONE, 6, e15925.
-
(2011)
PLoS ONE
, vol.6
-
-
Kofler, R.1
Orozco-terWengel, P.2
De Maio, N.3
-
6
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL (2009b) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10, 25.
-
(2009)
Genome Biology
, vol.10
, pp. 25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
7
-
-
78751570979
-
RNA sequencing: advances, challenges and opportunities
-
Ozsolak F, Milos PM, (2011) RNA sequencing: advances, challenges and opportunities. Nature Reviews Genetics, 12, 87-98.
-
(2011)
Nature Reviews Genetics
, vol.12
, pp. 87-98
-
-
Ozsolak, F.1
Milos, P.M.2
-
8
-
-
84867055719
-
Evaluation of different reference based annotation strategies using RNA-Seq - a case study in Drosophila pseudoobscura
-
Palmieri N, Nolte V, Suvorov A, Kosiol C, Schlötterer C (2012) Evaluation of different reference based annotation strategies using RNA-Seq - a case study in Drosophila pseudoobscura. PLoS ONE, 7, e46415.
-
(2012)
PLoS ONE
, vol.7
-
-
Palmieri, N.1
Nolte, V.2
Suvorov, A.3
Kosiol, C.4
Schlötterer, C.5
-
9
-
-
77953176036
-
A scaling normalization method for differential expression analysis of RNA-seq data
-
Robinson MD, Oshlack A (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology, 11, R25.
-
(2010)
Genome Biology
, vol.11
-
-
Robinson, M.D.1
Oshlack, A.2
-
10
-
-
80051489977
-
AlleleSeq: analysis of allele-specific expression and binding in a network framework
-
Rozowsky J, Abyzov A, Wang J et al. (2011) AlleleSeq: analysis of allele-specific expression and binding in a network framework. Molecular Systems Biology, 7, 522.
-
(2011)
Molecular Systems Biology
, vol.7
, pp. 522
-
-
Rozowsky, J.1
Abyzov, A.2
Wang, J.3
-
12
-
-
0028806048
-
Quantitative monitoring of gene expression patterns with a complementary DNA microarray
-
Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270, 467-470.
-
(1995)
Science
, vol.270
, pp. 467-470
-
-
Schena, M.1
Shalon, D.2
Davis, R.W.3
Brown, P.O.4
-
14
-
-
80053522581
-
A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
-
Skelly DA, Johansson M, Madeoy J, Wakefield J, Akey JM (2011) A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data. Genome Research, 21, 1728-1737.
-
(2011)
Genome Research
, vol.21
, pp. 1728-1737
-
-
Skelly, D.A.1
Johansson, M.2
Madeoy, J.3
Wakefield, J.4
Akey, J.M.5
-
15
-
-
77953911178
-
Inferring combined CNV/SNP haplotypes from genotype data
-
Su SY, Asher JE, Jarvelin MR et al. (2010) Inferring combined CNV/SNP haplotypes from genotype data. Bioinformatics, 26, 1437-1445.
-
(2010)
Bioinformatics
, vol.26
, pp. 1437-1445
-
-
Su, S.Y.1
Asher, J.E.2
Jarvelin, M.R.3
-
16
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell C, Williams BA, Pertea G et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology, 28, 511-515.
-
(2010)
Nature Biotechnology
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
-
17
-
-
79751531332
-
Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads
-
Turro E, Su SY, Gonçalves Â, Coin LJ, Richardson S, Lewin A (2011) Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads. Genome Biology, 12, R13.
-
(2011)
Genome Biology
, vol.12
-
-
Turro, E.1
Su, S.Y.2
Gonçalves, A.3
Coin, L.J.4
Richardson, S.5
Lewin, A.6
-
18
-
-
77951820899
-
Fast and SNP-tolerant detection of complex variants and splicing in short reads
-
Wu TD, Nacu S (2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics, 26, 873-881.
-
(2010)
Bioinformatics
, vol.26
, pp. 873-881
-
-
Wu, T.D.1
Nacu, S.2
|