-
1
-
-
70350664649
-
De novo transcriptome assembly with ABySS
-
Birol, I., Jackman, S.D., Nielsen, C.B., Qian, J.Q., Varhol, R., Stazyk, G., Morin, R.D., Zhao, Y., Hirst, M., Schein, J.E.,Horsman,D.E., Connors, J.M., Gascoyne, R.D., Marra, M.A., and Jones, S.J. 2009. De novo transcriptome assembly with ABySS. Bioinformatics 25:2872-2877.
-
(2009)
Bioinformatics
, vol.25
, pp. 2872-2877
-
-
Birol, I.1
Jackman, S.D.2
Nielsen, C.B.3
Qian, J.Q.4
Varhol, R.5
Stazyk, G.6
Morin, R.D.7
Zhao, Y.8
Hirst, M.9
Schein, J.E.10
Horsman, D.E.11
Connors, J.M.12
Gascoyne, R.D.13
Marra, M.A.14
Jones, S.J.15
-
2
-
-
84865420834
-
RNA sequencing: Platform selection, experimental design, and data interpretation
-
Chu, Y. and Corey, D.R. 2012. RNA sequencing: Platform selection, experimental design, and data interpretation. Nucleic Acid Ther. 22:271-274.
-
(2012)
Nucleic Acid Ther.
, vol.22
, pp. 271-274
-
-
Chu, Y.1
Corey, D.R.2
-
3
-
-
46249103973
-
Stem cell transcriptome profiling via massivescale mRNA sequencing
-
Cloonan, N., Forrest, A.R., Kolle, G., Gardiner, B.B., Faulkner, G.J., Brown,M.K., Taylor, D.F., Steptoe, A.L., Wani, S., Bethel, G., Robertson, A.J., Perkins, A.C., Bruce, S.J., Lee, C.C., Ranade, S.S., Peckham, H.E., Manning, J.M., McKernan, K.J., and Grimmond, S.M. 2008. Stem cell transcriptome profiling via massivescale mRNA sequencing. Nat. Methods 5:613-619.
-
(2008)
Nat. Methods
, vol.5
, pp. 613-619
-
-
Cloonan, N.1
Forrest, A.R.2
Kolle, G.3
Gardiner, B.B.4
Faulkner, G.J.5
Brown, M.K.6
Taylor, D.F.7
Steptoe, A.L.8
Wani, S.9
Bethel, G.10
Robertson, A.J.11
Perkins, A.C.12
Bruce, S.J.13
Lee, C.C.14
Ranade, S.S.15
Peckham, H.E.16
Manning, J.M.17
McKernan, K.J.18
Grimmond, S.M.19
-
4
-
-
84865757142
-
Landscape of transcription in human cells
-
Djebali, S., Davis, C.A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin,W., Schlesinger, F.,Xue, C., Marinov, G.K., Khatun, J., Williams, B.A., Zaleski, C., Rozowsky, J., Röder, M., Kokocinski, F., Abdelhamid, R.F., Alioto, T., Antoshechkin, I., Baer,M.T., Bar, N.S., Batut, P., Bell, K., Bell I., Chakrabortty, S., Chen, X., Chrast, J., Curado, J., Derrien, T., Drenkow, J., Dumais, E., Dumais, J., Duttagupta, R., Falconnet, E., Fastuca, M., Fejes-Toth, K., Ferreira, P., Foissac, S., Fullwood, M.J., Gao, H., Gonzalez, D., Gordon, A., Gunawardena, H., Howald, C., Jha, S., Johnson, R., Kapranov, P., King, B., Kingswood, C., Luo, O.J., Park, E., Persaud, K., Preall, J.B., Ribeca, P., Risk, B., Robyr, D., Sammeth, M., Schaffer, L., See, L.H., Shahab, A., Skancke, J., Suzuki, A.M., Takahashi,H., Tilgner, H., Trout,D.,Walters, N., Wang, H., Wrobel, J., Yu, Y., Ruan, X., Hayashizaki, Y., Harrow, J., Gerstein, M., Hubbard, T., Reymond, A., Antonarakis, S.E., Hannon, G., Giddings, M.C., Ruan, Y., Wold, B., Carninci, P., Guigó, R., and Gingeras, T.R. 2012. Landscape of transcription in human cells. Nature 489:101-108.
-
(2012)
Nature
, vol.489
, pp. 101-108
-
-
Djebali, S.1
Davis, C.A.2
Merkel, A.3
Dobin, A.4
Lassmann, T.5
Mortazavi, A.6
Tanzer, A.7
Lagarde, J.8
Lin, W.9
Schlesinger, F.10
Xue, C.11
Marinov, G.K.12
Khatun, J.13
Williams, B.A.14
Zaleski, C.15
Rozowsky, J.16
Röder, M.17
Kokocinski, F.18
Abdelhamid, R.F.19
Alioto, T.20
Antoshechkin, I.21
Baer, M.T.22
Bar, N.S.23
Batut, P.24
Bell, K.25
Bell, I.26
Chakrabortty, S.27
Chen, X.28
Chrast, J.29
Curado, J.30
Derrien, T.31
Drenkow, J.32
Dumais, E.33
Dumais, J.34
Duttagupta, R.35
Falconnet, E.36
Fastuca, M.37
Fejes-Toth, K.38
Ferreira, P.39
Foissac, S.40
Fullwood, M.J.41
Gao, H.42
Gonzalez, D.43
Gordon, A.44
Gunawardena, H.45
Howald, C.46
Jha, S.47
Johnson, R.48
Kapranov, P.49
King, B.50
Kingswood, C.51
Luo, O.J.52
Park, E.53
Persaud, K.54
Preall, J.B.55
Ribeca, P.56
Risk, B.57
Robyr, D.58
Sammeth, M.59
Schaffer, L.60
See, L.H.61
Shahab, A.62
Skancke, J.63
Suzuki, A.M.64
Takahashi, H.65
Tilgner, H.66
Trout, D.67
Walters, N.68
Wang, H.69
Wrobel, J.70
Yu, Y.71
Ruan, X.72
Hayashizaki, Y.73
Harrow, J.74
Gerstein, M.75
Hubbard, T.76
Reymond, A.77
Antonarakis, S.E.78
Hannon, G.79
Giddings, M.C.80
Ruan, Y.81
Wold, B.82
Carninci, P.83
Guigó, R.84
Gingeras, T.R.85
more..
-
5
-
-
77952231080
-
Advancing RNASeq analysis
-
Haas, B.J. and Zody, M.C. 2010. Advancing RNASeq analysis. Nat. Biotechnol. 28:421-423.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 421-423
-
-
Haas, B.J.1
Zody, M.C.2
-
6
-
-
77956340995
-
Comprehensive comparative analysis of strand-specific RNA sequencing methods
-
Levin, J.Z., Yassour, M., Adiconis, X., Nusbaum, C., Thompson, D.A., Friedman, N., Gnirke, A., and Regev, A. 2010. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat. Methods 7:709-715.
-
(2010)
Nat. Methods
, vol.7
, pp. 709-715
-
-
Levin, J.Z.1
Yassour, M.2
Adiconis, X.3
Nusbaum, C.4
Thompson, D.A.5
Friedman, N.6
Gnirke, A.7
Regev, A.8
-
7
-
-
67649595548
-
Limitations and possibilities of small RNA digital gene expression profiling
-
Linsen, S.E., de Wit, E., Janssens, G., Heater, S., Chapman, L., Parkin, R.K., Fritz, B., Wyman, S.K., de Bruijn, E., Voest, E.E., Kuersten, S., Tewari, M., and Cuppen, E. 2009. Limitations and possibilities of small RNA digital gene expression profiling. Nat. Methods 6:474-476.
-
(2009)
Nat. Methods
, vol.6
, pp. 474-476
-
-
Linsen, S.E.1
de Wit, E.2
Janssens, G.3
Heater, S.4
Chapman, L.5
Parkin, R.K.6
Fritz, B.7
Wyman, S.K.8
de Bruijn, E.9
Voest, E.E.10
Kuersten, S.11
Tewari, M.12
Cuppen, E.13
-
8
-
-
84893682902
-
Next generation sequencing for profiling expression of miRNAs: Technical progress and applications in drug development
-
Liu, J., Jennings, S.F., Tong, W., and Hong, H. 2011. Next generation sequencing for profiling expression of miRNAs: Technical progress and applications in drug development. J. Biomed. Sci. Eng. 4:666-676.
-
(2011)
J. Biomed. Sci. Eng.
, vol.4
, pp. 666-676
-
-
Liu, J.1
Jennings, S.F.2
Tong, W.3
Hong, H.4
-
9
-
-
24644490196
-
Elucidation of the small RNA component of the transcriptome
-
Lu, C., Tej, S.S., Luo, S., Haudenschild, C.D., Meyers, B.C., and Green, P.J. 2005. Elucidation of the small RNA component of the transcriptome. Science 309:1567-1569.
-
(2005)
Science
, vol.309
, pp. 1567-1569
-
-
Lu, C.1
Tej, S.S.2
Luo, S.3
Haudenschild, C.D.4
Meyers, B.C.5
Green, P.J.6
-
10
-
-
77449147610
-
FRTseq: Amplification-free, strand-specific, transcriptome sequencing
-
Mamanova, L., Andrews, R.M., James,K.D., Sheridan, E.M., Ellis, P.D., Langford, C.F., Ost, T.W., Collins, J.E., and Turner, D.J. 2010. FRTseq: Amplification-free, strand-specific, transcriptome sequencing. Nat. Methods 7:130-132.
-
(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
-
11
-
-
47949084846
-
Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing
-
Morin, R., Bainbridge, M., Fejes, A., Hirst, M., Krzywinski, M., Pugh, T., McDonald, H., Varhol,R., Jones, S., and Marra,M. 2008. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques 45:81-94.
-
(2008)
Biotechniques
, vol.45
, pp. 81-94
-
-
Morin, R.1
Bainbridge, M.2
Fejes, A.3
Hirst, M.4
Krzywinski, M.5
Pugh, T.6
McDonald, H.7
Varhol, R.8
Jones, S.9
Marra, M.10
-
12
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi, A.,Williams, B.A., McCue, K., Schaeffer, L., and Wold, B. 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
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
13
-
-
45549088326
-
The transcriptional landscape of the yeast genome defined by RNA sequencing
-
Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., and Snyder, M. 2008. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344-1349.
-
(2008)
Science
, vol.320
, pp. 1344-1349
-
-
Nagalakshmi, U.1
Wang, Z.2
Waern, K.3
Shou, C.4
Raha, D.5
Gerstein, M.6
Snyder, M.7
-
14
-
-
52949093215
-
Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes
-
Reid, J.G., Nagaraja, A.K., Lynn, F.C., Drabek, R.B., Muzny, D.M., Shaw, C.A., Weiss, M.K., Naghavi, A.O., Khan, M., Zhu, H., Tennakoon, J., Gunaratne, G.H., Corry, D.B., Miller, J., McManus, M.T., German, M.S., Gibbs, R.A., Matzuk, M.M., and Gunaratne, P.H. 2008. Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes. Genome Res. 18:1571-1581.
-
(2008)
Genome Res.
, vol.18
, pp. 1571-1581
-
-
Reid, J.G.1
Nagaraja, A.K.2
Lynn, F.C.3
Drabek, R.B.4
Muzny, D.M.5
Shaw, C.A.6
Weiss, M.K.7
Naghavi, A.O.8
Khan, M.9
Zhu, H.10
Tennakoon, J.11
Gunaratne, G.H.12
Corry, D.B.13
Miller, J.14
McManus, M.T.15
German, M.S.16
Gibbs, R.A.17
Matzuk, M.M.18
Gunaratne, P.H.19
-
15
-
-
80051489977
-
Allele-Seq: Analysis of allele-specific expression and binding in a network framework
-
Rozowsky, J., Abyzov, A., Wang, J., Alves, P., Raha, D., Harmanci, A., Leng, J., Bjornson, R., Kong, Y., Kitabayashi, N., Bhardwaj, N., Rubin, M., Snyder, M., and Gerstein, M. 2011. Allele-Seq: Analysis of allele-specific expression and binding in a network framework. Mol. Syst. Biol. 7:522.
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 522
-
-
Rozowsky, J.1
Abyzov, A.2
Wang, J.3
Alves, P.4
Raha, D.5
Harmanci, A.6
Leng, J.7
Bjornson, R.8
Kong, Y.9
Kitabayashi, N.10
Bhardwaj, N.11
Rubin, M.12
Snyder, M.13
Gerstein, M.14
-
16
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell, C.,Williams, B.A., Pertea, G.,Mortazavi, A., Kwan, G., van Baren, M.J., Salzberg, S.L., Wold, B.J., and Pachter, L. 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
Mortazavi, A.4
Kwan, G.5
van Baren, M.J.6
Salzberg, S.L.7
Wold, B.J.8
Pachter, L.9
-
17
-
-
57749195712
-
RNASeq: A revolutionary tool for transcriptomics
-
Wang, Z., Gerstein, M., and Snyder, M. 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
Gerstein, M.2
Snyder, M.3
-
18
-
-
46249096804
-
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution
-
Wilhelm, B.T., Marguerat, S., Watt, S., Schubert, F., Wood, V., Goodhead, I., Penkett, C.J., Rogers, J., and Bähler, J. 2008. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453:1239-1243.
-
(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
Bähler, J.9
-
19
-
-
84860198538
-
Structural bias in T4 RNA ligase-mediated 3'-adapter ligation
-
Zhuang, F., Fuchs, R.T., Sun, Z., Zheng, Y., and Robb, G.B. 2012. Structural bias in T4 RNA ligase-mediated 3'-adapter ligation. Nucleic Acids Res. 40:e54.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Zhuang, F.1
Fuchs, R.T.2
Sun, Z.3
Zheng, Y.4
Robb, G.B.5
|