-
1
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol., 11, R106
-
(2010)
Genome Biol
, vol.11
-
-
Anders, S.1
Huber, W.2
-
2
-
-
84865527768
-
Detecting differential usage of exons from RNA-seq data
-
Anders, S. et al. (2012) Detecting differential usage of exons from RNA-seq data. Genome Res., 22, 2008-2017
-
(2012)
Genome Res
, vol.22
, pp. 2008-2017
-
-
Anders, S.1
-
3
-
-
84855320189
-
Accurate identification of a-To-i rna editing in human by transcriptome sequencing
-
Bahn, J.H. et al. (2012) Accurate identification of a-To-i rna editing in human by transcriptome sequencing. Genome Res., 22, 142-50
-
(2012)
Genome Res
, vol.22
, pp. 142-150
-
-
Bahn, J.H.1
-
5
-
-
70449516738
-
Transcript quantification with rna-seq data
-
Bohnert, R. et al. (2009) Transcript quantification with RNA-Seq data. BMC Bioinformatics, 10 (Suppl. 13), P5
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.SUPPL. 13
-
-
Bohnert, R.1
-
6
-
-
84856480471
-
Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution
-
Bradley, R.K. et al. (2012) Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution. PLoS Biol., 10, e1001229
-
(2012)
PLoS Biol
, vol.10
-
-
Bradley, R.K.1
-
7
-
-
67649292737
-
Unlocking the secrets of the genome
-
Celniker, S. et al. (2009) Unlocking the secrets of the genome. Nature, 459, 927-930
-
(2009)
Nature
, vol.459
, pp. 927-930
-
-
Celniker, S.1
-
8
-
-
79959201528
-
The gencode exome: Sequencing the complete human exome
-
Coffey, A.J. et al. (2011) The gencode exome: Sequencing the complete human exome. Eur. J. Hum. Genet., 19, 827-31
-
(2011)
Eur. J. Hum. Genet
, vol.19
, pp. 827-831
-
-
Coffey, A.J.1
-
9
-
-
49549102475
-
Optimal spliced alignments of short sequence reads
-
De Bona, F. et al. (2008) Optimal spliced alignments of short sequence reads. Bioinformatics, 24, i174-i180
-
(2008)
Bioinformatics
, vol.24
-
-
De Bona, F.1
-
10
-
-
58149513263
-
Annotating genomes with massive-scale RNA sequencing
-
Denoeud, F. et al. (2008) Annotating genomes with massive-scale RNA sequencing. Genome Biol., 9, R175
-
(2008)
Genome Biol
, vol.9
-
-
Denoeud, F.1
-
11
-
-
84871809302
-
Star: Ultrafast universal RNA-Seq aligner
-
Dobin, A. et al. (2012) Star: Ultrafast universal RNA-Seq aligner. Bioinformatics, 29, 15-21
-
(2012)
Bioinformatics
, vol.29
, pp. 15-21
-
-
Dobin, A.1
-
12
-
-
84878539435
-
Accurate detection of differential rna processing
-
Drewe, P. et al. (2012) Accurate detection of differential rna processing. Nucleic Acids Res., 41, 5189-5198
-
(2012)
Nucleic Acids Res
, vol.41
, pp. 5189-5198
-
-
Drewe, P.1
-
13
-
-
84865790047
-
An integrated encyclopedia of dna elements in the human genome
-
ENCODE Project Consortium et al.
-
ENCODE Project Consortium et al. (2012) An integrated encyclopedia of dna elements in the human genome. Nature, 489, 57-74
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
14
-
-
84858221706
-
Ensembl 2012
-
Flicek, P. et al. (2012) Ensembl 2012. Nucleic Acids Res., 40, D84-D90
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Flicek, P.1
-
15
-
-
79960264362
-
Full-length transcriptome assembly from RNA-Seq data without a reference genome
-
Grabherr, M.G. et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol., 29, 644-652
-
(2011)
Nat. Biotechnol
, vol.29
, pp. 644-652
-
-
Grabherr, M.G.1
-
16
-
-
84869036699
-
Modelling and simulating generic RNA-Seq experiments with the flux simulator
-
Griebel, T. et al. (2012) Modelling and simulating generic RNA-Seq experiments with the flux simulator. Nucleic Acids Res., 40, 10073-10083
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 10073-10083
-
-
Griebel, T.1
-
17
-
-
77952148742
-
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
-
Guttman, M. et al. (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol., 28, 503-510
-
(2010)
Nat. Biotechnol
, vol.28
, pp. 503-510
-
-
Guttman, M.1
-
18
-
-
33748645500
-
Gencode: Producing a reference annotation for encode
-
Harrow, J. et al. (2006) Gencode: Producing a reference annotation for encode. Genome Biol., 7 (Suppl. 1), S41-9
-
(2006)
Genome Biol
, vol.7
, Issue.SUPPL. 1
-
-
Harrow, J.1
-
19
-
-
0013159620
-
Splicing graphs and est assembly problem
-
Heber, S. et al. (2002) Splicing graphs and est assembly problem. Bioinformatics, 18 (Suppl. 1), S181-S188
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Heber, S.1
-
20
-
-
84885584740
-
Simultaneous isoform discovery and quantification from RNA-Seq
-
Hiller, D. and Wong, W. (2012) Simultaneous isoform discovery and quantification from RNA-Seq. Stat. Biosci., 1-19
-
(2012)
Stat. Biosci
, pp. 1-19
-
-
Hiller, D.1
Wong, W.2
-
21
-
-
0031436890
-
Phylogeny estimation and hypothesis testing using maximum likelihood
-
Huelsenbeck, J.P. and Crandall, K.A. (1997) Phylogeny estimation and hypothesis testing using maximum likelihood. Annu. Revi. Ecol. Syst., 28, 437-466
-
(1997)
Annu. Revi. Ecol. Syst
, vol.28
, pp. 437-466
-
-
Huelsenbeck, J.P.1
Crandall, K.A.2
-
22
-
-
79952360093
-
RNA-Seq read alignments with palmapper
-
Jean, G. et al. (2010) RNA-Seq read alignments with palmapper. Curr. Protoc. Bioinform., 32, 11.6.1-11.6.38
-
(2010)
Curr. Protoc. Bioinform
, vol.32
, pp. 1161-11638
-
-
Jean, G.1
-
23
-
-
78649714014
-
Analysis and design of rna sequencing experiments for identifying isoform regulation
-
Katz, Y. et al. (2010) Analysis and design of rna sequencing experiments for identifying isoform regulation. Nat. Methods, 7, 1009-1015
-
(2010)
Nat. Methods
, vol.7
, pp. 1009-1015
-
-
Katz, Y.1
-
24
-
-
56649100471
-
Exact transcriptome reconstruction from short sequence reads
-
WABI 08. Springer-Verlag Berlin Heidelberg
-
Lacroix, V. et al. (2008) Exact transcriptome reconstruction from short sequence reads. In: Proceedings of the 8th International Workshop on Algorithms in Bioinformatics. WABI 08. Springer-Verlag, Berlin, Heidelberg, pp. 50-63
-
(2008)
Proceedings of the 8th International Workshop on Algorithms in Bioinformatics
, pp. 50-63
-
-
Lacroix, V.1
-
25
-
-
79953186446
-
Isolasso: A lasso regression approach to RNA-Seq based transcriptome assembly
-
Bafna, V. and Sahinalp, S. (eds, Lecture Notes in Computer Science. Springer, Berlin Heidelberg
-
Li, W. et al. (2011) Isolasso: A lasso regression approach to RNA-Seq based transcriptome assembly. In: Bafna, V. and Sahinalp, S. (eds) Research in Computational Molecular Biology. Vol. 6577, Lecture Notes in Computer Science. Springer, Berlin Heidelberg, pp. 168-188
-
(2011)
Research in Computational Molecular Biology
, vol.6577
, pp. 168-188
-
-
Li, W.1
-
26
-
-
84866700434
-
Cliiq: Accurate comparative detection and quantification of expressed isoforms in a population
-
Raphael, B. and Tang, J. (eds Lecture Notes in Computer Science. Springer, Berlin, Heidelberg
-
Lin, Y.Y. et al. (2012) Cliiq: Accurate comparative detection and quantification of expressed isoforms in a population. In: Raphael, B. and Tang, J. (eds) Algorithms in Bioinformatics. Vol 7534 Lecture Notes in Computer Science. Springer, Berlin, Heidelberg. pp. 178-189
-
(2012)
Algorithms in Bioinformatics
, vol.7534
, pp. 178-189
-
-
Lin, Y.Y.1
-
27
-
-
84874597027
-
Ireckon: Simultaneous isoform discovery and abundance estimation from rna-seq
-
Mezlini, A.M. et al. (2012) iReckon: Simultaneous isoform discovery and abundance estimation from RNA-Seq. Genome Res., 23, 519-529
-
(2012)
Genome Res
, vol.23
, pp. 519-529
-
-
Mezlini, A.M.1
-
28
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi, A. et al. (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
-
30
-
-
75849145292
-
Expansion of the eukaryotic proteome by alternative splicing
-
Nilsen, T.W. and Graveley, B.R. (2010) Expansion of the eukaryotic proteome by alternative splicing. Nature, 463, 457-463
-
(2010)
Nature
, vol.463
, pp. 457-463
-
-
Nilsen, T.W.1
Graveley, B.R.2
-
31
-
-
80052150179
-
Origins of the e coli strain causing an outbreak of hemolytic-uremic syndrome in Germany
-
Rasko, D.A. et al. (2011) Origins of the e. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N. Engl. J. Med., 365, 709-17
-
(2011)
N. Engl. J. Med
, vol.365
, pp. 709-717
-
-
Rasko, D.A.1
-
32
-
-
79551489429
-
Gaussian processes for machine learning (gpml) toolbox
-
Rasmusen, C.E. and Nickisch, H. (2010) Gaussian processes for machine learning (gpml) toolbox. J. Mach. Learn. Res., 11, 3011-3015
-
(2010)
J. Mach. Learn. Res
, vol.11
, pp. 3011-3015
-
-
Rasmusen, C.E.1
Nickisch, H.2
-
33
-
-
33847268161
-
Improving the caenorhabditis elegans genome annotation using machine learning
-
Rätsch G et al. 2007 Improving the caenorhabditis elegans genome annotation using machine learning PLoS Comput. Biol. 3 e20
-
(2007)
PLoS Comput. Biol
, vol.3
-
-
Rätsch, G.1
-
34
-
-
78049346632
-
De novo assembly and analysis of RNA-Seq data
-
Robertson, G. et al. (2010) De novo assembly and analysis of RNA-Seq data. Nat. Methods, 7, 909-912
-
(2010)
Nat. Methods
, vol.7
, pp. 909-912
-
-
Robertson, G.1
-
35
-
-
84859768479
-
Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels
-
Schulz, M.H. et al. (2012) Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics, 28, 1086-1092
-
(2012)
Bioinformatics
, vol.28
, pp. 1086-1092
-
-
Schulz, M.H.1
-
36
-
-
70350708134
-
MGene: Accurate SVM-based gene finding with an application to nematode genomes
-
Schweikert, G. 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
-
37
-
-
33644864739
-
Inferring global levels of alternative splicing isoforms using a generative model of microarray data
-
Shai, O. et al. (2006) Inferring global levels of alternative splicing isoforms using a generative model of microarray data. Bioinformatics, 22, 606-13
-
(2006)
Bioinformatics
, vol.22
, pp. 606-613
-
-
Shai, O.1
-
38
-
-
66449136667
-
ABySS: A parallel assembler for short read sequence data
-
Simpson, J.T. et al. (2009) ABySS: A parallel assembler for short read sequence data. Genome Res., 19, 1117-1123
-
(2009)
Genome Res
, vol.19
, pp. 1117-1123
-
-
Simpson, J.T.1
-
39
-
-
84862184527
-
Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes
-
Smith, L. et al. (2012) Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes. RNA Biol., 9, 596-609
-
(2012)
RNA Biol
, vol.9
, pp. 596-609
-
-
Smith, L.1
-
40
-
-
84885579558
-
Practical bayesian optimization of machine learning algorithms
-
Snoek, J. et al. (2012) Practical bayesian optimization of machine learning algorithms. Technical Report arXiv: 1206.2944, arXiv
-
(2012)
Technical Report arXiv: 1206.2944, arXiv
-
-
Snoek, J.1
-
41
-
-
42149137369
-
Accurate splice site prediction using support vector machines
-
Sonnenburg, S. et al. (2007) Accurate splice site prediction using support vector machines. BMC Bioinformatics, 8 (Suppl. 10), S7
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL. 10
-
-
Sonnenburg, S.1
-
42
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-Seq
-
Trapnell, C. et al. (2009) TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
-
43
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell, C. et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 28, 511-515
-
(2010)
Nat. Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
-
44
-
-
0242700119
-
Gene structure-based splice variant deconvolution using a microarry platform
-
Wang, H. et al. (2003) Gene structure-based splice variant deconvolution using a microarry platform. Bioinformatics, 19 (Suppl. 1), i315-i322
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 1
-
-
Wang, H.1
-
45
-
-
57749195712
-
RNA-Seq: A revolutionary tool for transcriptomics
-
Wang, Z. et al. (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
-
46
-
-
78649345104
-
MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
-
Wang, K. et al. (2010) MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res., 38, e178
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Wang, K.1
-
47
-
-
77951820899
-
Fast and SNP-Tolerant detection of complex variants and splicing in short reads
-
Wu, T.D. and Nacu, S. (2010) Fast and SNP-Tolerant detection of complex variants and splicing in short reads. Bioinformatics, 26, 873-81
-
(2010)
Bioinformatics
, vol.26
, pp. 873-881
-
-
Wu, T.D.1
Nacu, S.2
-
48
-
-
79955914959
-
Nsmap: A method for spliced isoforms identification and quantification from rna-seq
-
Xia, Z. et al. (2011) NSMAP: A method for spliced isoforms identification and quantification from RNA-Seq. BMC Bioinformatics, 12, 162
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 162
-
-
Xia, Z.1
-
49
-
-
1542316923
-
The multiassembly problem: Reconstructing multiple transcript isoforms from est fragment mixtures
-
Xing, Y. et al. (2004) The multiassembly problem: Reconstructing multiple transcript isoforms from est fragment mixtures. Genome Res., 14, 426-441
-
(2004)
Genome Res
, vol.14
, pp. 426-441
-
-
Xing, Y.1
|