-
1
-
-
57749195712
-
RNASeq: A revolutionary tool for transcriptomics
-
Wang Z, Gerstein M, SnyderM(2009) RNASeq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57-63
-
(2009)
Nat Rev Genet
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Snyderm, G.M.2
-
2
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
DOI 10.1038/nature07509, PII NATURE07509
-
Wang ET, Sandberg R, Luo S et al (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456:470-476 (Pubitemid 352759009)
-
(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
-
3
-
-
56749098074
-
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
-
Pan Q, Shai O, Lee L et al (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40:1413-1415
-
(2008)
Nat Genet
, vol.40
, pp. 1413-1415
-
-
Pan, Q.1
Shai, O.2
Lee, L.3
-
4
-
-
62649160909
-
Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing
-
Yoder-Himes DR, Chain PSG, Zhu Y et al (2009) Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci USA 106:3976-3981
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 3976-3981
-
-
Yoder-Himes, D.R.1
Psg, C.2
Zhu, Y.3
-
5
-
-
69549112743
-
Digital transcriptome profiling using selective hexamer priming for cDNA synthesis
-
Armour CD, Castle JC, Chen R et al (2009) Digital transcriptome profiling using selective hexamer priming for cDNA synthesis. Nat Methods 6:647-649
-
(2009)
Nat Methods
, vol.6
, pp. 647-649
-
-
Armour, C.D.1
Castle, J.C.2
Chen, R.3
-
6
-
-
57849109058
-
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
-
Core LJ, Waterfall JJ and Lis JT (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322:1845-1848
-
(2008)
Science
, vol.322
, pp. 1845-1848
-
-
Core, L.J.1
Waterfall, J.J.2
Lis, J.T.3
-
7
-
-
62549134121
-
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
-
Ingolia NT, Ghaemmaghami S, Newman JRS et al (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324:218-223
-
(2009)
Science
, vol.324
, pp. 218-223
-
-
Ingolia, N.T.1
Ghaemmaghami, S.2
Jrs, N.3
-
8
-
-
72849144434
-
Sequencing technologies-The next generation
-
Metzker ML (2010) Sequencing technologies-the next generation. Nat Rev Genet 11:31-46
-
(2010)
Nat Rev Genet
, vol.11
, pp. 31-46
-
-
Metzker, M.L.1
-
9
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
DOI 10.1038/nmeth.1226, PII NMETH.1226
-
Mortazavi A, Williams BA, McCue K et al (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621-628 (Pubitemid 351911867)
-
(2008)
Nature Methods
, vol.5
, Issue.7
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
10
-
-
77952148742
-
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
-
Guttman M, Garber M, Levin JZ 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
Garber, M.2
Levin, J.Z.3
-
11
-
-
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. Nat Biotechnol 28:511-515
-
(2010)
Nat Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
-
12
-
-
84860883182
-
-
Sequence Read Archive
-
Sequence Read Archive. http://www.ncbi.nlm.nih.gov/sra.
-
-
-
-
13
-
-
84860888289
-
-
Gene Expression Omnibus
-
Gene Expression Omnibus. http://www.ncbi.nlm.nih.gov/geo.
-
-
-
-
14
-
-
0031955518
-
Base-calling of automated sequencer traces using phred. I. Accuracy assessment
-
Ewing B, Hillier L, Wendl MC et al (1998) Base-calling of automated sequencer traces using phred I accuracy assessment. Genome Res 8:175-185 (Pubitemid 28177229)
-
(1998)
Genome Research
, vol.8
, Issue.3
, pp. 175-185
-
-
Ewing, B.1
Hillier, L.2
Wendl, M.C.3
Green, P.4
-
15
-
-
77951226627
-
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
-
Cock PJA, Fields CJ, Goto N et al (2010) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 38:1767-1771
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 1767-1771
-
-
Pja, C.1
Fields, C.J.2
Goto, N.3
-
16
-
-
25844449770
-
Galaxy: A platform for interactive large-scale genome analysis
-
DOI 10.1101/gr.4086505
-
Giardine B, Riemer C, Hardison RC et al (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res 15:1451-1455 (Pubitemid 41400913)
-
(2005)
Genome Research
, vol.15
, Issue.10
, 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
Miller, W.11
Kent, W.J.12
Nekrutenko, A.13
-
17
-
-
18644368714
-
The Bioperl toolkit: Perl modules for the life sciences
-
DOI 10.1101/gr.361602
-
Stajich JE, Block D, Boulez K et al (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12:1611-1618 (Pubitemid 35175100)
-
(2002)
Genome Research
, vol.12
, Issue.10
, pp. 1611-1618
-
-
Stajich, J.E.1
Block, D.2
Boulez, K.3
Brenner, S.E.4
Chervitz, S.A.5
Dagdigian, C.6
Fuellen, G.7
Gilbert, J.G.R.8
Korf, I.9
Lapp, H.10
Lehvaslaiho, H.11
Matsalla, C.12
Mungall, C.J.13
Osborne, B.I.14
Pocock, M.R.15
Schattner, P.16
Senger, M.17
Stein, L.D.18
Stupka, E.19
Wilkinson, M.D.20
Birney, E.21
more..
-
18
-
-
65649092976
-
Biopython: Freely available Python tools for computational molecular biology and bioinformatics
-
Cock PJA, Antao T, Chang JT et al (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25:1422-1423
-
(2009)
Bioinformatics
, vol.25
, pp. 1422-1423
-
-
Pja, C.1
Antao, T.2
Chang, J.T.3
-
19
-
-
84860887554
-
-
NCBI, Accessed 2 Nov 2010
-
NCBI (2010) Sequence Read Archive Submission Guidelines. http://www.ncbi.nlm. nih.gov/Traces/sra/static/SRA-Submission-Guidelines.pdf. Accessed 2 Nov 2010
-
(2010)
Sequence Read Archive Submission Guidelines
-
-
-
20
-
-
84860888290
-
-
SOLiD Sequence Read Format package
-
SOLiD Sequence Read Format package. http://solidsoftwaretools.com/gf/ project/srf/
-
-
-
-
21
-
-
84860883180
-
-
Staden IO module
-
Staden IO module. http://staden.sourceforge. net/
-
-
-
-
22
-
-
84860888421
-
-
Sequenceread package
-
Sequenceread package http://sourceforge.net/projects/sequenceread/
-
-
-
-
23
-
-
70449711243
-
Computation for ChIP-seq and RNA-seq studies
-
Pepke S, Wold B, 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
-
24
-
-
52649157765
-
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
-
Dohm JC, Lottaz C, Borodina T et al (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
-
25
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M et al (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
-
26
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-Seq
-
Trapnell C, Pachter L and Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105-1111
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
27
-
-
70349886587
-
PerM: Efficient mapping of short sequencing reads with periodic full sensitive spaced seeds
-
Chen Y, Souaiaia T and Chen T (2009) PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. Bioinformatics 25:2514-2521
-
(2009)
Bioinformatics
, vol.25
, pp. 2514-2521
-
-
Chen, Y.1
Souaiaia, T.2
Chen, T.3
-
28
-
-
84860882788
-
-
Galaxy
-
Galaxy. http://g2.bx.psu.edu
-
-
-
-
29
-
-
84860888418
-
-
Galaxy Experimental Features
-
Galaxy Experimental Features. http://test.g2.bx.psu.edu
-
-
-
-
30
-
-
84860883179
-
-
Novoalign
-
Novoalign. http://www.novocraft.com
-
-
-
-
31
-
-
70450177746
-
BFAST: An alignment tool for large scale genome resequencing
-
Homer N, Merriman B, Nelson SF (2009) BFAST: an alignment tool for large scale genome resequencing. PLoS ONE 4:e7767
-
(2009)
PLoS ONE
, vol.4
-
-
Homer, N.1
Merriman, B.2
Nelson, S.F.3
-
32
-
-
84860883177
-
-
Mosaik
-
Mosaik. http://bioinformatics.bc.edu/marthlab/Mosaik
-
-
-
-
34
-
-
84860888419
-
-
Tophat
-
Tophat. http://tophat.cbcb.umd.edu/index.html
-
-
-
-
35
-
-
84860882787
-
-
UCSC Genome Browser FAQ File Formats
-
UCSC Genome Browser FAQ File Formats. http://genome.ucsc.edu/FAQ/ FAQformathtml#format1
-
-
-
-
36
-
-
84555210896
-
-
Bowtie http://bowtie-bio.sourceforge.net
-
Bowtie. http://bowtie-bio.sourceforge.net
-
-
-
-
37
-
-
84860888420
-
-
RNA-Seq files at sandberg lab homepage
-
RNA-Seq files at sandberg lab homepage. http://sandberg.cmb.ki.se/rnaseq/
-
-
-
-
38
-
-
84860883178
-
-
PerM
-
PerM. http://code.google.com/p/perm/
-
-
-
-
39
-
-
84860883176
-
-
Python
-
Python. http://www.python.org
-
-
-
-
40
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li H, Handsaker B, Wysoker A et al (2009) 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
-
41
-
-
84860888416
-
-
UCSC Genome Browser Downloads
-
UCSC Genome Browser Downloads. http://hgdownload.cse.ucsc.edu/downloads. html
-
-
-
-
42
-
-
77952905505
-
Most "dark matter" transcripts are associated with known genes
-
van Bakel H, Nislow C, Blencowe BJ et al (2010) Most "dark matter" transcripts are associated with known genes. PLoS Biol 8: e1000371
-
(2010)
PLoS Biol
, vol.8
-
-
Van Bakel, H.1
Nislow, C.2
Blencowe, B.J.3
-
43
-
-
84860888417
-
-
Integrative Genome Browser
-
Integrative Genome Browser. http://www.broadinstitute.org/igv
-
-
-
-
44
-
-
46249092601
-
Proliferating cells express mRNAs with shortened 30 untranslated regions and fewer microRNA target sites
-
DOI 10.1126/science.1155390
-
Sandberg R, Neilson JR, Sarma A et al (2008) Proliferating cells express mRNAs with shortened 30 untranslated regions and fewer micro-RNA target sites. Science 320:1643-7 (Pubitemid 351931255)
-
(2008)
Science
, vol.320
, Issue.5883
, pp. 1643-1647
-
-
Sandberg, R.1
Neilson, J.R.2
Sarma, A.3
Sharp, P.A.4
Burge, C.B.5
-
45
-
-
77952576233
-
Heterogeneity in mammalian RNA 30 end formation
-
Neilson JR and Sandberg R (2010) Heterogeneity in mammalian RNA 30 end formation. Exp Cell Res 316:1357-1364
-
(2010)
Exp Cell Res
, vol.316
, pp. 1357-1364
-
-
Neilson, J.R.1
Sandberg, R.2
-
46
-
-
74549125753
-
An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data
-
Ramsköld D,Wang ET, Burge CB et al (2009) An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol 5:e1000598
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Ramsköld, D.1
Wang, E.T.2
Burge, C.B.3
-
47
-
-
77950458649
-
Transcriptome genetics using second generation sequencing in a Caucasian population
-
Montgomery SB, Sammeth M, Gutierrez-Arcelus M et al (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464:773-777
-
(2010)
Nature
, vol.464
, pp. 773-777
-
-
Montgomery, S.B.1
Sammeth, M.2
Gutierrez-Arcelus, M.3
-
48
-
-
84860883173
-
-
NumPy
-
NumPy. http://numpy.scipy.org
-
-
-
-
49
-
-
77955895425
-
BigWig and BigBed: Enabling browsing of large distributed datasets
-
Kent WJ, Zweig AS, Barber G et al (2010) BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics 26:2204-2207
-
(2010)
Bioinformatics
, vol.26
, pp. 2204-2207
-
-
Kent, W.J.1
Zweig, A.S.2
Barber, G.3
-
50
-
-
84860883174
-
-
UCSC stand-alone bioinformatic programs
-
UCSC stand-alone bioinformatic programs. http://hgdownload.cse.ucsc.edu/ admin/exe/linux.x86-64/
-
-
-
-
51
-
-
84860883175
-
-
UCSC Mappability Data
-
UCSC Mappability Data. http://hgdownload. cse.ucsc.edu/goldenPath/hg19/ encodeDCC/wgEncodeMapability/
-
-
-
-
52
-
-
50649089207
-
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
-
Marioni JC,Mason CE, Mane SMet al (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18:1509-1517
-
(2008)
Genome Res
, vol.18
, pp. 1509-1517
-
-
Marioni Jcmason, C.E.1
Smet Al, M.2
-
53
-
-
29244448340
-
Microarray data analysis: From disarray to consolidation and consensus
-
DOI 10.1038/nrg1749
-
Allison DB, Cui X, Page GP et al (2006) Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet 7:55-65 (Pubitemid 41828948)
-
(2006)
Nature Reviews Genetics
, vol.7
, Issue.1
, pp. 55-65
-
-
Allison, D.B.1
Cui, X.2
Page, G.P.3
Sabripour, M.4
-
54
-
-
75249087100
-
EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson MD, McCarthy DJ and Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139-140
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
55
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders S, 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
-
56
-
-
84860888415
-
-
Scripture
-
Scripture. http://www.broadinstitute.org/software/scripture
-
-
-
-
57
-
-
84860883170
-
-
R
-
R, http://www.r-project.org/
-
-
-
-
58
-
-
84860883171
-
-
Bioconductor
-
Bioconductor, http://www.bioconductor. org/
-
-
-
-
59
-
-
55549097836
-
Mapping short DNA sequencing reads and calling variants using mapping quality scores
-
Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18:1851-1858
-
(2008)
Genome Res
, vol.18
, pp. 1851-1858
-
-
Li, H.1
Ruan, J.2
Durbin, R.3
|