-
1
-
-
57749195712
-
RNA-seq: A revolutionary tool for transcriptomics
-
Z. Wang, M. Gerstein, and M. Snyder RNA-seq: a revolutionary tool for transcriptomics Nat. Rev. Genet. 10 2009 57 63
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
2
-
-
46249096804
-
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution
-
B.T. Wilhelm, S. Marguerat, S. Watt, F. Schubert, V. Wood, I. Goodhead, C.J. Penkett, J. Rogers, and J. Bahler Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution Nature 453 2008 1239 1243
-
(2008)
Nature
, vol.453
, pp. 1239-1243
-
-
Wilhelm, B.T.1
Marguerat, S.2
Watt, S.3
Schubert, F.4
Wood, V.5
Goodhead, I.6
Penkett, C.J.7
Rogers, J.8
Bahler, J.9
-
3
-
-
79957842166
-
Computational methods for transcriptome annotation and quantification using RNA-seq
-
M. Garber, M.G. Grabherr, M. Guttman, and C. Trapnell Computational methods for transcriptome annotation and quantification using RNA-seq Nat. Methods 8 2011 469 477
-
(2011)
Nat. Methods
, vol.8
, pp. 469-477
-
-
Garber, M.1
Grabherr, M.G.2
Guttman, M.3
Trapnell, C.4
-
4
-
-
62549126083
-
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing
-
M. Yassour, T. Kaplan, H.B. Fraser, J.Z. Levin, J. Pfiffner, X. Adiconis, G. Schroth, S. Luo, I. Khrebtukova, A. Gnirke, C. Nusbaum, D.A. Thompson, N. Friedman, and A. Regev Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing Proc. Natl. Acad. Sci. USA 106 2009 3264 3269
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 3264-3269
-
-
Yassour, M.1
Kaplan, T.2
Fraser, H.B.3
Levin, J.Z.4
Pfiffner, J.5
Adiconis, X.6
Schroth, G.7
Luo, S.8
Khrebtukova, I.9
Gnirke, A.10
Nusbaum, C.11
Thompson, D.A.12
Friedman, N.13
Regev, A.14
-
5
-
-
58149513263
-
Annotating genomes with massive-scale RNA sequencing
-
F. Denoeud, J.M. Aury, C. Da Silva, B. Noel, O. Rogier, M. Delledonne, M. Morgante, G. Valle, P. Wincker, C. Scarpelli, O. Jaillon, and F. Artiguenave Annotating genomes with massive-scale RNA sequencing Genome Biol. 9 2008 R175
-
(2008)
Genome Biol.
, vol.9
, pp. 175
-
-
Denoeud, F.1
Aury, J.M.2
Da Silva, C.3
Noel, B.4
Rogier, O.5
Delledonne, M.6
Morgante, M.7
Valle, G.8
Wincker, P.9
Scarpelli, C.10
Jaillon, O.11
Artiguenave, F.12
-
6
-
-
58749096360
-
On the road to reading the RNA-interference code
-
H. Siomi, and M.C. Siomi On the road to reading the RNA-interference code Nature 457 2009 396 404
-
(2009)
Nature
, vol.457
, pp. 396-404
-
-
Siomi, H.1
Siomi, M.C.2
-
8
-
-
41849084855
-
Discovering microRNAs from deep sequencing data using miRDeep
-
M.R. Friedlander, W. Chen, C. Adamidi, J. Maaskola, R. Einspanier, S. Knespel, and N. Rajewsky Discovering microRNAs from deep sequencing data using miRDeep Nat. Biotechnol. 26 2008 407 415
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 407-415
-
-
Friedlander, M.R.1
Chen, W.2
Adamidi, C.3
Maaskola, J.4
Einspanier, R.5
Knespel, S.6
Rajewsky, N.7
-
9
-
-
78651293534
-
MiRBase: Integrating microRNA annotation and deep-sequencing data
-
A. Kozomara, and S. Griffiths-Jones miRBase: integrating microRNA annotation and deep-sequencing data Nucleic Acids Res. 39 2011 D152 D157
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Kozomara, A.1
Griffiths-Jones, S.2
-
10
-
-
75649135574
-
RNA-seq: From technology to biology
-
S. Marguerat, and J. Bahler RNA-seq: from technology to biology Cell. Mol. Life Sci. 67 2010 569 579
-
(2010)
Cell. Mol. Life Sci.
, vol.67
, pp. 569-579
-
-
Marguerat, S.1
Bahler, J.2
-
12
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-seq
-
A. Mortazavi, B.A. Williams, K. McCue, L. Schaeffer, and B. Wold Mapping and quantifying mammalian transcriptomes by RNA-seq Nat. Methods 5 2008 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
-
13
-
-
77952123055
-
Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation
-
C. Trapnell, B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M.J. van Baren, S.L. Salzberg, B.J. Wold, and L. Pachter Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation Nat. Biotechnol. 28 2010 511 515
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
Van Baren, M.J.6
Salzberg, S.L.7
Wold, B.J.8
Pachter, L.9
-
14
-
-
80054075400
-
Cleavage of rRNA in ensures translational cessation to prepare sperm for fertilization
-
PMID:21831882.
-
G.D. Johnson, E. Sendler, C. Lalancette, R. Hauser, M.P. Diamond, S.A. Krawetz, Cleavage of rRNA in ensures translational cessation to prepare sperm for fertilization, Mol. Hum. Reprod. (2011) PMID:21831882.
-
(2011)
Mol. Hum. Reprod.
-
-
Johnson, G.D.1
Sendler, E.2
Lalancette, C.3
Hauser, R.4
Diamond, M.P.5
Krawetz, S.A.6
-
15
-
-
50649089207
-
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
-
J.C. Marioni, C.E. Mason, S.M. Mane, M. Stephens, and Y. Gilad RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays Genome Res. 18 2008 1509 1517
-
(2008)
Genome Res.
, vol.18
, pp. 1509-1517
-
-
Marioni, J.C.1
Mason, C.E.2
Mane, S.M.3
Stephens, M.4
Gilad, Y.5
-
16
-
-
78650748904
-
The sperm nucleus: Chromatin, RNA, and the nuclear matrix
-
G.D. Johnson, C. Lalancette, A.K. Linnemann, F. Leduc, G. Boissonneault, and S.A. Krawetz The sperm nucleus: chromatin, RNA, and the nuclear matrix Reproduction 141 2011 21 36
-
(2011)
Reproduction
, vol.141
, pp. 21-36
-
-
Johnson, G.D.1
Lalancette, C.2
Linnemann, A.K.3
Leduc, F.4
Boissonneault, G.5
Krawetz, S.A.6
-
17
-
-
52649157765
-
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
-
J.C. Dohm, C. Lottaz, T. Borodina, and H. Himmelbauer Substantial biases in ultra-short read data sets from high-throughput DNA sequencing Nucleic Acids Res. 36 2008 e105
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 105
-
-
Dohm, J.C.1
Lottaz, C.2
Borodina, T.3
Himmelbauer, H.4
-
18
-
-
79951694175
-
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
-
D. Aird, M.G. Ross, W.S. Chen, M. Danielsson, T. Fennell, C. Russ, D.B. Jaffe, C. Nusbaum, and A. Gnirke Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries Genome Biol. 12 2011 R18
-
(2011)
Genome Biol.
, vol.12
, pp. 18
-
-
Aird, D.1
Ross, M.G.2
Chen, W.S.3
Danielsson, M.4
Fennell, T.5
Russ, C.6
Jaffe, D.B.7
Nusbaum, C.8
Gnirke, A.9
-
19
-
-
77449147610
-
FRT-seq: Amplification-free, strand-specific transcriptome sequencing
-
L. Mamanova, R.M. Andrews, K.D. James, E.M. Sheridan, P.D. Ellis, C.F. Langford, T.W. Ost, J.E. Collins, and D.J. Turner FRT-seq: amplification-free, strand-specific transcriptome sequencing Nat. Methods 7 2010 130 132
-
(2010)
Nat. Methods
, vol.7
, pp. 130-132
-
-
Mamanova, L.1
Andrews, R.M.2
James, K.D.3
Sheridan, E.M.4
Ellis, P.D.5
Langford, C.F.6
Ost, T.W.7
Collins, J.E.8
Turner, D.J.9
-
20
-
-
0035205327
-
Reverse transcription slippage over the mRNA secondary structure of the LIP1 gene
-
Y.J. Zhang, H.Y. Pan, and S.J. Gao Reverse transcription slippage over the mRNA secondary structure of the LIP1 gene BioTechniques 31 2001 1286 1290
-
(2001)
BioTechniques
, vol.31
, pp. 1286-1290
-
-
Zhang, Y.J.1
Pan, H.Y.2
Gao, S.J.3
-
21
-
-
0018801281
-
Methylmercury hydroxide enhancement of translation and transcription of ovalbumin and conalbumin mRNA's
-
F. Payvar, and R.T. Schimke Methylmercury hydroxide enhancement of translation and transcription of ovalbumin and conalbumin mRNA's J. Biol. Chem. 254 1979 7636 7642
-
(1979)
J. Biol. Chem.
, vol.254
, pp. 7636-7642
-
-
Payvar, F.1
Schimke, R.T.2
-
22
-
-
0029134549
-
Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes
-
N. Sugimoto, S. Nakano, M. Katoh, A. Matsumura, H. Nakamuta, T. Ohmichi, M. Yoneyama, and M. Sasaki Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes Biochemistry 34 1995 11211 11216
-
(1995)
Biochemistry
, vol.34
, pp. 11211-11216
-
-
Sugimoto, N.1
Nakano, S.2
Katoh, M.3
Matsumura, A.4
Nakamuta, H.5
Ohmichi, T.6
Yoneyama, M.7
Sasaki, M.8
-
23
-
-
0032729689
-
Predicting oligonucleotide affinity to nucleic acid targets
-
D.H. Mathews, M.E. Burkard, S.M. Freier, J.R. Wyatt, and D.H. Turner Predicting oligonucleotide affinity to nucleic acid targets RNA 5 1999 1458 1469
-
(1999)
RNA
, vol.5
, pp. 1458-1469
-
-
Mathews, D.H.1
Burkard, M.E.2
Freier, S.M.3
Wyatt, J.R.4
Turner, D.H.5
-
24
-
-
77949447172
-
RNAstructure: Software for RNA secondary structure prediction and analysis
-
J.S. Reuter, and D.H. Mathews RNAstructure: software for RNA secondary structure prediction and analysis BMC Bioinf. 11 2010 129
-
(2010)
BMC Bioinf.
, vol.11
, pp. 129
-
-
Reuter, J.S.1
Mathews, D.H.2
-
25
-
-
77955883388
-
Biases in Illumina transcriptome sequencing caused by random hexamer priming
-
K.D. Hansen, S.E. Brenner, and S. Dudoit Biases in Illumina transcriptome sequencing caused by random hexamer priming Nucleic Acids Res. 38 2010 e131
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 131
-
-
Hansen, K.D.1
Brenner, S.E.2
Dudoit, S.3
-
26
-
-
0343308108
-
Patterns of cleavages induced by lead ions in defined RNA secondary structure motifs
-
J. Ciesiolka, D. Michalowski, J. Wrzesinski, J. Krajewski, and W.J. Krzyzosiak Patterns of cleavages induced by lead ions in defined RNA secondary structure motifs J. Mol. Biol. 275 1998 211 220
-
(1998)
J. Mol. Biol.
, vol.275
, pp. 211-220
-
-
Ciesiolka, J.1
Michalowski, D.2
Wrzesinski, J.3
Krajewski, J.4
Krzyzosiak, W.J.5
-
27
-
-
57049122389
-
A large genome center's improvements to the Illumina sequencing system
-
M.A. Quail, I. Kozarewa, F. Smith, A. Scally, P.J. Stephens, R. Durbin, H. Swerdlow, and D.J. Turner A large genome center's improvements to the Illumina sequencing system Nat. Methods 5 2008 1005 1010
-
(2008)
Nat. Methods
, vol.5
, pp. 1005-1010
-
-
Quail, M.A.1
Kozarewa, I.2
Smith, F.3
Scally, A.4
Stephens, P.J.5
Durbin, R.6
Swerdlow, H.7
Turner, D.J.8
-
28
-
-
77951940273
-
Modeling non-uniformity in short-read rates in RNA-seq data
-
J. Li, H. Jiang, and W.H. Wong Modeling non-uniformity in short-read rates in RNA-seq data Genome Biol. 11 2010 R50
-
(2010)
Genome Biol.
, vol.11
, pp. 50
-
-
Li, J.1
Jiang, H.2
Wong, W.H.3
-
29
-
-
79952709611
-
Improving RNA-seq expression estimates by correcting for fragment bias
-
A. Roberts, C. Trapnell, J. Donaghey, J.L. Rinn, and L. Pachter Improving RNA-seq expression estimates by correcting for fragment bias Genome Biol. 12 2011 R22
-
(2011)
Genome Biol.
, vol.12
, pp. 22
-
-
Roberts, A.1
Trapnell, C.2
Donaghey, J.3
Rinn, J.L.4
Pachter, L.5
|