-
1
-
-
57749195712
-
RNA-Seq: a revolutionary tool for transcriptomics
-
Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet, 2009, 10: 57-63.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
2
-
-
79957842166
-
Computational methods for transcriptome annotation and quantification using RNA-seq
-
Garber M, Grabherr M G, Guttman M, et al. Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods, 2011, 8: 469-477.
-
(2011)
Nat Methods
, vol.8
, pp. 469-477
-
-
Garber, M.1
Grabherr, M.G.2
Guttman, M.3
-
3
-
-
78549246241
-
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads
-
Martin J, Bruno V M, Fang Z, et al. Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. BMC Genomics, 2010, 11: 663.
-
(2010)
BMC Genomics
, vol.11
, pp. 663
-
-
Martin, J.1
Bruno, V.M.2
Fang, Z.3
-
4
-
-
80052960863
-
Next-generation transcriptome assembly
-
Martin J A, Wang Z. Next-generation transcriptome assembly. Nat Rev Genet, 2011, 12: 671-682.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 671-682
-
-
Martin, J.A.1
Wang, Z.2
-
5
-
-
84859885816
-
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
-
Trapnell C, Roberts A, Goff L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc, 2012, 7: 562-578.
-
(2012)
Nat Protoc
, vol.7
, pp. 562-578
-
-
Trapnell, C.1
Roberts, A.2
Goff, L.3
-
6
-
-
70350664649
-
De novo transcriptome assembly with ABySS
-
Birol I, Jackman S D, Nielsen C B, et al. De novo transcriptome assembly with ABySS. Bioinformatics, 2009, 25: 2872-2877.
-
(2009)
Bioinformatics
, vol.25
, pp. 2872-2877
-
-
Birol, I.1
Jackman, S.D.2
Nielsen, C.B.3
-
7
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino D R, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res, 2008, 18: 821-829.
-
(2008)
Genome Res
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
8
-
-
78049346632
-
De novo assembly and analysis of RNA-seq data
-
Robertson G, Schein J, Chiu R, et al. De novo assembly and analysis of RNA-seq data. Nat Methods, 2010, 7: 909-912.
-
(2010)
Nat Methods
, vol.7
, pp. 909-912
-
-
Robertson, G.1
Schein, J.2
Chiu, R.3
-
9
-
-
79960264362
-
Full-length transcriptome assembly from RNA-Seq data without a reference genome
-
Grabherr M G, Haas B J, Yassour M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol, 2011, 29: 644-652.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 644-652
-
-
Grabherr, M.G.1
Haas, B.J.2
Yassour, M.3
-
10
-
-
77952231080
-
Advancing RNA-Seq analysis
-
Haas B J, Zody M C. Advancing RNA-Seq analysis. Nat Biotechnol, 2010, 28: 421-423.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 421-423
-
-
Haas, B.J.1
Zody, M.C.2
-
11
-
-
84862914469
-
Overview of available methods for diverse RNA-Seq data analyses
-
Chen G, Wang C, Shi T. Overview of available methods for diverse RNA-Seq data analyses. Sci China Life Sci, 2011, 54: 1121-1128.
-
(2011)
Sci China Life Sci
, vol.54
, pp. 1121-1128
-
-
Chen, G.1
Wang, C.2
Shi, T.3
-
12
-
-
80051941094
-
Identification of novel transcripts in annotated genomes using RNA-Seq
-
Roberts A, Pimentel H, Trapnell C, et al. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics, 2011, 27: 2325-2329.
-
(2011)
Bioinformatics
, vol.27
, pp. 2325-2329
-
-
Roberts, A.1
Pimentel, H.2
Trapnell, C.3
-
13
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell C, Williams B A, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol, 2010, 28: 511-515.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
-
14
-
-
77952148742
-
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
-
Guttman M, Garber M, Levin J Z, et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol, 2010, 28: 503-510.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 503-510
-
-
Guttman, M.1
Garber, M.2
Levin, J.Z.3
-
15
-
-
84859768479
-
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
-
Schulz M H, Zerbino D R, Vingron M, et al. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics, 2012, 28: 1086-1092.
-
(2012)
Bioinformatics
, vol.28
, pp. 1086-1092
-
-
Schulz, M.H.1
Zerbino, D.R.2
Vingron, M.3
-
16
-
-
0023988195
-
Genomic mapping by fingerprinting random clones: a mathematical analysis
-
Lander E S, Waterman M S. Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics, 1988, 2: 231-239.
-
(1988)
Genomics
, vol.2
, pp. 231-239
-
-
Lander, E.S.1
Waterman, M.S.2
-
17
-
-
66449136667
-
ABySS: a parallel assembler for short read sequence data
-
Simpson J T, Wong K, Jackman S D, et al. ABySS: a parallel assembler for short read sequence data. Genome Res, 2009, 19: 1117-1123.
-
(2009)
Genome Res
, vol.19
, pp. 1117-1123
-
-
Simpson, J.T.1
Wong, K.2
Jackman, S.D.3
-
18
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol, 2009, 10: R25.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
-
19
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics, 2009, 25: 2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
-
20
-
-
65449136284
-
TopHat: discovering splice junctions with RNA-Seq
-
Trapnell C, Pachter L, Salzberg S L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 2009, 25: 1105-1111.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
21
-
-
0036226603
-
BLAT-the BLAST-like alignment tool
-
Kent W J. BLAT-the BLAST-like alignment tool. Genome Res, 2002, 12: 656-664.
-
(2002)
Genome Res
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
22
-
-
77951770756
-
BEDTools: a flexible suite of utilities for comparing genomic features
-
Quinlan A R, Hall I M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 2010, 26: 841-842.
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
23
-
-
33745634395
-
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 2006, 22: 1658-1659.
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
24
-
-
84861743958
-
RNA-SeQC: RNA-seq metrics for quality control and process optimization
-
DeLuca D S, Levin J Z, Sivachenko A, et al. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics, 2012, 28: 1530-1532.
-
(2012)
Bioinformatics
, vol.28
, pp. 1530-1532
-
-
DeLuca, D.S.1
Levin, J.Z.2
Sivachenko, A.3
-
25
-
-
33748674197
-
AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome
-
S11
-
Stanke M, Tzvetkova A, Morgenstern B. AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome. Genome Biol, 2006, 7(Suppl1): S11. 1-8.
-
(2006)
Genome Biol
, vol.7
, Issue.SUPPL. 1
, pp. 1-8
-
-
Stanke, M.1
Tzvetkova, A.2
Morgenstern, B.3
-
26
-
-
37249080658
-
-
Berlin Heidelberg: Springer
-
Medvedev P, Georgiou K, Myers G, et al. Computability of Models for Sequence Assembly, in Algorithms in Bioinformatics. Berlin Heidelberg: Springer, 2007. 289-301.
-
(2007)
Computability of Models for Sequence Assembly, in Algorithms in Bioinformatics
, pp. 289-301
-
-
Medvedev, P.1
Georgiou, K.2
Myers, G.3
-
27
-
-
70349212271
-
Parametric complexity of sequence assembly: theory and applications to next generation sequencing
-
Nagarajan N, Pop M. Parametric complexity of sequence assembly: theory and applications to next generation sequencing. J Comput Biol, 2009, 16: 897-908.
-
(2009)
J Comput Biol
, vol.16
, pp. 897-908
-
-
Nagarajan, N.1
Pop, M.2
-
28
-
-
77952886150
-
Assembly algorithms for next-generation sequencing data
-
Miller J R, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics, 2010, 95: 315-327.
-
(2010)
Genomics
, vol.95
, pp. 315-327
-
-
Miller, J.R.1
Koren, S.2
Sutton, G.3
-
29
-
-
0037606127
-
Generating consensus sequences from partial order multiple sequence alignment graphs
-
Lee C. Generating consensus sequences from partial order multiple sequence alignment graphs. Bioinformatics, 2003, 19: 999-1008.
-
(2003)
Bioinformatics
, vol.19
, pp. 999-1008
-
-
Lee, C.1
-
31
-
-
1542316923
-
The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures
-
Xing Y, Resch A, Lee C. The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures. Genome Res, 2004, 14: 426-441.
-
(2004)
Genome Res
, vol.14
, pp. 426-441
-
-
Xing, Y.1
Resch, A.2
Lee, C.3
-
34
-
-
82455162834
-
Revealing the missing expressed genes beyond the human reference genome by RNA-Seq
-
Chen G, Li R Y, Shi L M, et al. Revealing the missing expressed genes beyond the human reference genome by RNA-Seq. BMC Genomics, 2011, 12: 590.
-
(2011)
BMC Genomics
, vol.12
, pp. 590
-
-
Chen, G.1
Li, R.Y.2
Shi, L.M.3
-
35
-
-
84860485003
-
Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study
-
Zhao Q Y, Wang Y, Kong Y M, et al. Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics, 2011, 12: S2.
-
(2011)
BMC Bioinformatics
, vol.12
-
-
Zhao, Q.Y.1
Wang, Y.2
Kong, Y.M.3
-
36
-
-
84873727857
-
Trinity RNA-Seq assembler performance optimization
-
Chicago, Illinois, USA
-
Henschel R, Lieber M, Wu L S, et al. Trinity RNA-Seq assembler performance optimization. In: Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the Campus and Beyond, Chicago, Illinois, USA, 2012. 1-8.
-
(2012)
Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the Campus and Beyond
, pp. 1-8
-
-
Henschel, R.1
Lieber, M.2
Wu, L.S.3
|