-
1
-
-
60549115605
-
Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs
-
Affymetrix/CSHL ENCODE Project
-
Affymetrix/CSHL ENCODE Project. (2009). Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Nature 457,1028-1032.
-
(2009)
Nature
, vol.457
, pp. 1028-1032
-
-
-
2
-
-
78651325932
-
lncRNAdb: a reference database for long noncoding RNAs
-
Amaral, P. P., Clark, M. B., Gascoigne, D. K., Dinger, M. E., and Mattick, J. S. (2011). lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res. 39,D146-D151.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Amaral, P.P.1
Clark, M.B.2
Gascoigne, D.K.3
Dinger, M.E.4
Mattick, J.S.5
-
3
-
-
79955005458
-
SNORD-host RNAZfas1 is a regulator of mammary development and a potential marker for breast cancer
-
Askarian-Amiri, M. E., Crawford, J., French, J. D., Smart, C. E., Smith, M. A., Clark, M. B., Ru, K., Mercer, T. R., Thompson, E. R., Lakhani, S. R., Vargas, A. C., Campbell, I. G., Brown, M. A., Dinger, M. E., and Mattick, J. S. (2011). SNORD-host RNAZfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA 17, 878-891.
-
(2011)
RNA
, vol.17
, pp. 878-891
-
-
Askarian-Amiri, M.E.1
Crawford, J.2
French, J.D.3
Smart, C.E.4
Smith, M.A.5
Clark, M.B.6
Ru, K.7
Mercer, T.R.8
Thompson, E.R.9
Lakhani, S.R.10
Vargas, A.C.11
Campbell, I.G.12
Brown, M.A.13
Dinger, M.E.14
Mattick, J.S.15
-
4
-
-
81855178276
-
Somatic retro -transposition alters the genetic landscape of the human brain
-
Baillie, J. K., Barnett, M. W., Upton, K. R., Gerhardt, D. J., Richmond, T. A., De Sapio, F., Brennan, P. M., Rizzu, P., Smith, S., Fell, M., Talbot, R. T., Gustincich, S., Freeman, T. C., Mattick, J. S., Hume, D. A., Heutink, P., Carninci, P., Jeddeloh, J. A., and Faulkner, G. J. (2011). Somatic retro -transposition alters the genetic landscape of the human brain. Nature 479, 534-537.
-
(2011)
Nature
, vol.479
, pp. 534-537
-
-
Baillie, J.K.1
Barnett, M.W.2
Upton, K.R.3
Gerhardt, D.J.4
Richmond, T.A.5
De Sapio, F.6
Brennan, P.M.7
Rizzu, P.8
Smith, S.9
Fell, M.10
Talbot, R.T.11
Gustincich, S.12
Freeman, T.C.13
Mattick, J.S.14
Hume, D.A.15
Heutink, P.16
Carninci, P.17
Jeddeloh, J.A.18
Faulkner, G.J.19
-
5
-
-
19944376457
-
Global identification of human transcribed sequences with genome tiling arrays
-
Bertone, P., Stolc, V., Royce, T. E., Rozowsky, J. S., Urban, A. E., Zhu, X., Rinn, J. L., Tongprasit, W., Samanta, M., Weissman, S., Gerstein, M., and Snyder, M. (2004). Global identification of human transcribed sequences with genome tiling arrays. Science 306, 2242-2246.
-
(2004)
Science
, vol.306
, pp. 2242-2246
-
-
Bertone, P.1
Stolc, V.2
Royce, T.E.3
Rozowsky, J.S.4
Urban, A.E.5
Zhu, X.6
Rinn, J.L.7
Tongprasit, W.8
Samanta, M.9
Weissman, S.10
Gerstein, M.11
Snyder, M.12
-
6
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
Nisc Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute
-
Birney, E., Stamatoyannopoulos, J. A., Dutta, A., Guigo, R., Gingeras, T. R., Margulies, E. H., Weng, Z., Snyder, M., Dermitzakis, E. T., Thurman, R. E., Kuehn, M. S., Taylor, C. M., Neph, S., Koch, C. M., Asthana, S., Malhotra, A., Adzhubei, I., Green-baum, J. A., Andrews, R. M., Flicek, P., Boyle, P. J., Cao, H., Carter, N. P., Clelland, G. K., Davis, S., Day, N., Dhami, P., Dillon, S. C., Dorschner, M. O., Fiegler, H., Giresi, P. G., Goldy, J., Hawrylycz, M., Haydock, A., Humbert, R., James, K. D., Johnson, B. E., Johnson, E. M., Frum, T. T., Rosenzweig, E. R., Karnani, N., Lee, K., Lefebvre, G. C., Navas, P. A., Neri, F., Parker, S. C., Sabo, P. J., Sandstrom, R., Shafer, A., Vetrie, D., Weaver, M., Wilcox, S., Yu, M., Collins, F. S., Dekker, J., Lieb, J. D., Tullius, T. D., Crawford, G. E., Sun-yaev, S., Noble, W. S., Dunham, I., Denoeud, F., Reymond, A., Kapranov, P., Rozowsky, J., Zheng, D., Castelo, R., Frankish, A., Harrow, J., Ghosh, S., Sandelin, A., Hofacker, I. L., Baertsch, R., Keefe, D., Dike, S., Cheng, J., Hirsch, H. A., Sekinger, E. A., Lagarde, J., Abril, J. F., Sha-hab, A., Flamm, C., Fried, C., Hack-ermuller, J., Hertel, J., Lindemeyer, M., Missal, K., Tanzer, A., Washietl, S., Korbel, J., Emanuelsson, O., Ped-ersen, J. S., Holroyd, N., Taylor, R., Swarbreck, D., Matthews, N., Dick-son, M. C., Thomas, D. J., Weirauch, M. T., Gilbert, J., Drenkow, J., Bell, I., Zhao, X., Srinivasan, K. G., Sung, W. K., Ooi, H. S., Chiu, K. P., Fois-sac, S., Alioto, T., Brent, M., Pachter, L., Tress, M. L., Valencia, A., Choo, S. W., Choo, C. Y., Ucla, C., Manzano, C., Wyss, C., Cheung, E., Clark, T. G., Brown, J. B., Ganesh, M., Patel, S., Tammana, H., Chrast, J., Hen-richsen, C. N., Kai, C., Kawai, J., Nagalakshmi, U., Wu, J., Lian, Z., Lian, J., Newburger, P., Zhang, X., Bickel, P., Mattick, J. S., Carninci, P., Hayashizaki, Y., Weissman, S., Hub-bard, T., Myers, R. M., Rogers, J., Stadler, P. F., Lowe, T. M., Wei, C. L., Ruan, Y., Struhl, K., Gerstein, M., Antonarakis, S. E., Fu, Y., Green, E. D., Karaöz, U., Siepel, A., Taylor, J., Liefer, L. A., Wetterstrand, K. A., Good, P. J., Feingold, E. A., Guyer, M. S., Cooper, G. M., Asi-menos, G., Dewey, C. N., Hou, M., Nikolaev, S., Montoya-Burgos, J. I., Löytynoja, A., Whelan, S., Pardi, F., Massingham, T., Huang, H., Zhang, N. R., Holmes, I., Mullikin, J. C., Ureta-Vidal, A., Paten, B., Sering-haus, M., Church, D., Rosenbloom, K., Kent, W. J., Stone, E. A., NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, Batzoglou, S., Goldman, N., Hardison, R. C., Haussler, D., Miller, W., Sidow, A., Trinklein, N. D., Zhang, Z. D., Barrera, L., Stuart, R., King, D. C., Ameur, A., Enroth, S., Bieda, M. C., Kim, J., Bhinge, A. A., Jiang, N., Liu, J., Yao, F., Vega, V B., Lee, C. W., Ng, P., Shahab, A., Yang, A., Moqtaderi, Z., Zhu, Z., Xu, X., Squazzo, S., Oberley, M. J., Inman, D., Singer, M. A., Richmond, T. A., Munn, K. J., Rada-Iglesias, A., Wallerman, O., Komorowski, J., Fowler, J. C., Couttet, P., Bruce, A. W., Dovey, O. M., Ellis, P. D., Lang-ford, C. F., Nix, D. A., Euskirchen, G., Hartman, S., Urban, A. E., Kraus, P., Van Calcar, S., Heintzman, N., Kim, T. H., Wang, K., Qu, C., Hon, G., Luna, R., Glass, C. K., Rosenfeld, M. G., Aldred, S. F., Cooper, S. J., Halees, A., Lin, J. M., Shulha, H. P., Zhang, X.,Xu, M., Haidar, J. N., Yu, Y., Ruan, Y., Iyer, V R., Green, R. D., Wadelius, C., Farnham, P. J., Ren, B., Harte, R. A., Hinrichs, A. S., Trumbower, H., Clawson, H., Hillman-Jackson, J., Zweig, A. S., Smith, K., Thakka-pallayil, A., Barber, G., Kuhn, R. M., Karolchik, D., Armengol, L., Bird, C. P., de Bakker, P. I., Kern, A. D., Lopez-Bigas, N., Martin, J. D., Stranger, B. E., Woodroffe, A., Davydov, E., Dimas, A., Eyras, E., Hallgrímsdóttir, I. B., Huppert, J.,Zody, M. C., Abeca-sis, G. R., Estivill, X., Bouffard, G. G., Guan, X., Hansen, N. F., Idol, J. R., Maduro, V V, Maskeri, B., McDowell, J. C., Park, M., Thomas, P. J., Young, A. C., Blakesley, R. W., Muzny, D. M., Sodergren, E., Wheeler, D. A., Worley, K. C., Jiang, H., Wein-stock, G. M., Gibbs, R. A., Graves, T., Fulton, R., Mardis, E. R., Wilson, R. K., Clamp, M., Cuff, J., Gnerre, S., Jaffe, D. B., Chang, J. L., Lindblad-Toh, K., Lander, E. S., Koriabine, M., Nefedov, M., Osoegawa, K., Yoshi-naga, Y., Zhu, B., and de Jong, P. J. (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816.
-
(2007)
Nature
, vol.447
, pp. 799-816
-
-
Birney, E.1
Stamatoyannopoulos, J.A.2
Dutta, A.3
Guigo, R.4
Gingeras, T.R.5
Margulies, E.H.6
Weng, Z.7
Snyder, M.8
Dermitzakis, E.T.9
Thurman, R.E.10
Kuehn, M.S.11
Taylor, C.M.12
Neph, S.13
Koch, C.M.14
Asthana, S.15
Malhotra, A.16
Adzhubei, I.17
Green-baum, J.A.18
Andrews, R.M.19
Flicek, P.20
Boyle, P.J.21
Cao, H.22
Carter, N.P.23
Clelland, G.K.24
Davis, S.25
Day, N.26
Dhami, P.27
Dillon, S.C.28
Dorschner, M.O.29
Fiegler, H.30
Giresi, P.G.31
Goldy, J.32
Hawrylycz, M.33
Haydock, A.34
Humbert, R.35
James, K.D.36
Johnson, B.E.37
Johnson, E.M.38
Frum, T.T.39
Rosenzweig, E.R.40
Karnani, N.41
Lee, K.42
Lefebvre, G.C.43
Navas, P.A.44
Neri, F.45
Parker, S.C.46
Sabo, P.J.47
Sandstrom, R.48
Shafer, A.49
Vetrie, D.50
Weaver, M.51
Wilcox, S.52
Yu, M.53
Collins, F.S.54
Dekker, J.55
Lieb, J.D.56
Tullius, T.D.57
Crawford, G.E.58
Sun-yaev, S.59
Noble, W.S.60
Dunham, I.61
Denoeud, F.62
Reymond, A.63
Kapranov, P.64
Rozowsky, J.65
Zheng, D.66
Castelo, R.67
Frankish, A.68
Harrow, J.69
Ghosh, S.70
Sandelin, A.71
Hofacker, I.L.72
Baertsch, R.73
Keefe, D.74
Dike, S.75
Cheng, J.76
Hirsch, H.A.77
Sekinger, E.A.78
Lagarde, J.79
Abril, J.F.80
Sha-hab, A.81
Flamm, C.82
Fried, C.83
Hack-ermuller, J.84
Hertel, J.85
Lindemeyer, M.86
Missal, K.87
Tanzer, A.88
Washietl, S.89
Korbel, J.90
Emanuelsson, O.91
Ped-ersen, J.S.92
Holroyd, N.93
Taylor, R.94
Swarbreck, D.95
Matthews, N.96
Dick-son, M.C.97
Thomas, D.J.98
Weirauch, M.T.99
Gilbert, J.100
Drenkow, J.101
Bell, I.102
Zhao, X.103
Srinivasan, K.G.104
Sung, W.K.105
Ooi, H.S.106
Chiu, K.P.107
Fois-sac, S.108
Alioto, T.109
Brent, M.110
Pachter, L.111
Tress, M.L.112
Valencia, A.113
Choo, S.W.114
Choo, C.Y.115
Ucla, C.116
Manzano, C.117
Wyss, C.118
Cheung, E.119
Clark, T.G.120
Brown, J.B.121
Ganesh, M.122
Patel, S.123
Tammana, H.124
Chrast, J.125
Hen-richsen, C.N.126
Kai, C.127
Kawai, J.128
Nagalakshmi, U.129
Wu, J.130
Lian, Z.131
Lian, J.132
Newburger, P.133
Zhang, X.134
Bickel, P.135
Mattick, J.S.136
Carninci, P.137
Hayashizaki, Y.138
Weissman, S.139
Hub-bard, T.140
Myers, R.M.141
Rogers, J.142
Stadler, P.F.143
Lowe, T.M.144
Wei, C.L.145
Ruan, Y.146
Struhl, K.147
Gerstein, M.148
Antonarakis, S.E.149
Fu, Y.150
Green, E.D.151
Karaöz, U.152
Siepel, A.153
Taylor, J.154
Liefer, L.A.155
Wetterstrand, K.A.156
Good, P.J.157
Feingold, E.A.158
Guyer, M.S.159
Cooper, G.M.160
Asi-menos, G.161
Dewey, C.N.162
Hou, M.163
Nikolaev, S.164
Montoya-Burgos, J.I.165
Löytynoja, A.166
Whelan, S.167
Pardi, F.168
Massingham, T.169
Huang, H.170
Zhang, N.R.171
Holmes, I.172
Mullikin, J.C.173
Ureta-Vidal, A.174
Paten, B.175
Sering-haus, M.176
Church, D.177
Rosenbloom, K.178
Kent, W.J.179
Stone, E.A.180
Batzoglou, S.181
Goldman, N.182
Hardison, R.C.183
Haussler, D.184
Miller, W.185
Sidow, A.186
Trinklein, N.D.187
Zhang, Z.D.188
Barrera, L.189
Stuart, R.190
King, D.C.191
Ameur, A.192
Enroth, S.193
Bieda, M.C.194
Kim, J.195
Bhinge, A.A.196
Jiang, N.197
Liu, J.198
Yao, F.199
Vega, V.B.200
Lee, C.W.201
Ng, P.202
Shahab, A.203
Yang, A.204
Moqtaderi, Z.205
Zhu, Z.206
Xu, X.207
Squazzo, S.208
Oberley, M.J.209
Inman, D.210
Singer, M.A.211
Richmond, T.A.212
Munn, K.J.213
Rada-Iglesias, A.214
Wallerman, O.215
Komorowski, J.216
Fowler, J.C.217
Couttet, P.218
Bruce, A.W.219
Dovey, O.M.220
Ellis, P.D.221
Lang-ford, C.F.222
Nix, D.A.223
Euskirchen, G.224
Hartman, S.225
Urban, A.E.226
Kraus, P.227
Van Calcar, S.228
Heintzman, N.229
Kim, T.H.230
Wang, K.231
Qu, C.232
Hon, G.233
Luna, R.234
Glass, C.K.235
Rosenfeld, M.G.236
Aldred, S.F.237
Cooper, S.J.238
Halees, A.239
Lin, J.M.240
Shulha, H.P.241
Zhang, X.242
Xu, M.243
Haidar, J.N.244
Yu, Y.245
Ruan, Y.246
Iyer, V.R.247
Green, R.D.248
Wadelius, C.249
Farnham, P.J.250
Ren, B.251
Harte, R.A.252
Hinrichs, A.S.253
Trumbower, H.254
Clawson, H.255
Hillman-Jackson, J.256
Zweig, A.S.257
Smith, K.258
Thakka-pallayil, A.259
Barber, G.260
Kuhn, R.M.261
Karolchik, D.262
Armengol, L.263
Bird, C.P.264
de Bakker, P.I.265
Kern, A.D.266
Lopez-Bigas, N.267
Martin, J.D.268
Stranger, B.E.269
Woodroffe, A.270
Davydov, E.271
Dimas, A.272
Eyras, E.273
Hallgrímsdóttir, I.B.274
Huppert, J.275
Zody, M.C.276
Abeca-sis, G.R.277
Estivill, X.278
Bouffard, G.G.279
Guan, X.280
Hansen, N.F.281
Idol, J.R.282
Maduro, V.V.283
Maskeri, B.284
McDowell, J.C.285
Park, M.286
Thomas, P.J.287
Young, A.C.288
Blakesley, R.W.289
Muzny, D.M.290
Sodergren, E.291
Wheeler, D.A.292
Worley, K.C.293
Jiang, H.294
Wein-stock, G.M.295
Gibbs, R.A.296
Graves, T.297
Fulton, R.298
Mardis, E.R.299
Wilson, R.K.300
Clamp, M.301
Cuff, J.302
Gnerre, S.303
Jaffe, D.B.304
Chang, J.L.305
Lindblad-Toh, K.306
Lander, E.S.307
Koriabine, M.308
Nefedov, M.309
Osoegawa, K.310
Yoshi-naga, Y.311
Zhu, B.312
De Jong, P.J.313
more..
-
7
-
-
17644382616
-
Waste not, want not - transcript excess in multicel-lular eukaryotes
-
Brosius, J. (2005). Waste not, want not - transcript excess in multicel-lular eukaryotes. Trends Genet. 21, 287-288.
-
(2005)
Trends Genet
, vol.21
, pp. 287-288
-
-
Brosius, J.1
-
8
-
-
80052978224
-
Inte-grative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
-
Cabili, M. N., Trapnell, C., Goff, L., Koziol, M., Tazon-Vega, B., Regev, A., and Rinn, J. L. (2011). Inte-grative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25,1915-1927.
-
(2011)
Genes Dev
, vol.25
, pp. 1915-1927
-
-
Cabili, M.N.1
Trapnell, C.2
Goff, L.3
Koziol, M.4
Tazon-Vega, B.5
Regev, A.6
Rinn, J.L.7
-
9
-
-
9344235449
-
Human microRNAs are processed from capped, polyadeny-lated transcripts that can also function as mRNAs
-
Cai, X., Hagedorn, C. H., and Cullen, B. R. (2004). Human microRNAs are processed from capped, polyadeny-lated transcripts that can also function as mRNAs. RNA 10,1957-1966.
-
(2004)
RNA
, vol.10
, pp. 1957-1966
-
-
Cai, X.1
Hagedorn, C.H.2
Cullen, B.R.3
-
10
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
FANTOM Consortium and RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group)
-
Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C., Kodzius, R., Shimokawa, K., Bajic, V B., Brenner, S. E., Bat-alov, S., Forrest, A. R., Zavolan, M., Davis, M. J., Wilming, L. G., Aidinis, V., Allen, J. E., Ambesi-Impiombato, A., Apweiler, R., Aturaliya, R. N., Bailey, T. L., Bansal, M., Baxter, L., Beisel, K. W., Bersano, T., Bono, H., Chalk, A. M., Chiu, K. P., Choud-hary, V., Christoffels, A., Clutterbuck, D. R., Crowe, M. L., Dalla, E., Dal-rymple, B. P., De Bono, B., Della Gatta, G., Di Bernardo, D., Down, T., Engstrom, P., Fagiolini, M., Faulkner, G., Fletcher, C. F., Fukushima, T., Furuno, M., Futaki, S., Gariboldi, M., Georgii-Hemming, P., Gingeras, T. R., Gojobori, T., Green, R. E., Gustincich, S., Harbers, M., Hayashi, Y., Hensch, T. K., Hirokawa, N., Hill, D., Huminiecki, L., Iacono, M., Ikeo, K., Iwama, A., Ishikawa, T., Jakt, M., Kanapin, A., Katoh, M., Kawasawa, Y., Kelso, J., Kitamura, H., Kitano, H., Kollias, G., Krish-nan, S. P., Kruger, A., Kummerfeld, S. K., Kurochkin, I. V., Lareau, L. E, Lazarevic, D., Lipovich, L., Liu, J., Liuni, S., Mcwilliam, S., Madan Babu, M., Madera, M., Marchionni, L., Matsuda, H., Matsuzawa, S., Miki, H., Mignone, F., Miyake, S., Morris, K., Mottagui-Tabar, S., Mulder, N., Nakano, N., Nakauchi, H., Ng, P., Nilsson, R., Nishiguchi, S., Nishikawa, S., Nori, F., Ohara, O., Okazaki, Y., Orlando, V., Pang, K. C., Pavan, W. J., Pavesi, G., Pesole, G., Petrovsky, N., Piazza, S., Reed, J., Reid, J. F., Ring, B. Z., Ringwald, M., Rost, B., Ruan, Y., Salzberg, S. L., Sandelin, A., Schneider, C., Schön-bach, C., Sekiguchi, K., Semple, C. A., Seno, S., Sessa, L., Sheng, Y., Shi-bata, Y., Shimada, H., Shimada, K., Silva, D., Sinclair, B., Sperling, S., Stupka, E., Sugiura, K., Sultana, R., Takenaka, Y., Taki, K., Tammoja, K., Tan, S. L., Tang, S., Taylor, M. S., Tegner, J., Teichmann, S. A., Ueda, H. R., van Nimwegen, E., Verardo, R., Wei, C. L., Yagi, K., Yamanishi, H., Zabarovsky, E., Zhu, S., Zimmer, A., Hide, W., Bult, C., Grimmond, S. M., Teasdale, R. D., Liu, E. T., Bru-sic, V., Quackenbush, J., Wahlestedt, C., Mattick, J. S., Hume, D. A., Kai, C., Sasaki, D., Tomaru, Y., Fukuda, S., Kanamori-Katayama, M., Suzuki, M.,Aoki, J.,Arakawa, T.,Iida,J.,Ima-mura, K., Itoh, M., Kato, T., Kawaji, H., Kawagashira, N., Kawashima, T., Kojima, M., Kondo, S., Konno, H., Nakano, K., Ninomiya, N., Nishio, T., Okada, M., Plessy, C., Shibata, K., Shiraki, T., Suzuki, S., Tagami, M., Waki, K., Watahiki, A., Okamura-Oho, Y., Suzuki, H., Kawai, J., Hayashizaki, Y. FANTOM Consortium, and RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group). (2005). The transcriptional landscape of the mammalian genome. Science 309, 1559-1563.
-
(2005)
Science
, vol.309
, pp. 1559-1563
-
-
Carninci, P.1
Kasukawa, T.2
Katayama, S.3
Gough, J.4
Frith, M.C.5
Maeda, N.6
Oyama, R.7
Ravasi, T.8
Lenhard, B.9
Wells, C.10
Kodzius, R.11
Shimokawa, K.12
Bajic, V.B.13
Brenner, S.E.14
Bat-alov, S.15
Forrest, A.R.16
Zavolan, M.17
Davis, M.J.18
Wilming, L.G.19
Aidinis, V.20
Allen, J.E.21
Ambesi-Impiombato, A.22
Apweiler, R.23
Aturaliya, R.N.24
Bailey, T.L.25
Bansal, M.26
Baxter, L.27
Beisel, K.W.28
Bersano, T.29
Bono, H.30
Chalk, A.M.31
Chiu, K.P.32
Choud-hary, V.33
Christoffels, A.34
Clutterbuck, D.R.35
Crowe, M.L.36
Dalla, E.37
Dal-rymple, B.P.38
De Bono, B.39
Della Gatta, G.40
Di Bernardo, D.41
Down, T.42
Engstrom, P.43
Fagiolini, M.44
Faulkner, G.45
Fletcher, C.F.46
Fukushima, T.47
Furuno, M.48
Futaki, S.49
Gariboldi, M.50
Georgii-Hemming, P.51
Gingeras, T.R.52
Gojobori, T.53
Green, R.E.54
Gustincich, S.55
Harbers, M.56
Hayashi, Y.57
Hensch, T.K.58
Hirokawa, N.59
Hill, D.60
Huminiecki, L.61
Iacono, M.62
Ikeo, K.63
Iwama, A.64
Ishikawa, T.65
Jakt, M.66
Kanapin, A.67
Katoh, M.68
Kawasawa, Y.69
Kelso, J.70
Kitamura, H.71
Kitano, H.72
Kollias, G.73
Krish-nan, S.P.74
Kruger, A.75
Kummerfeld, S.K.76
Kurochkin, I.V.77
Lareau, L.F.78
Lazarevic, D.79
Lipovich, L.80
Liu, J.81
Liuni, S.82
Mcwilliam, S.83
Madan Babu, M.84
Madera, M.85
Marchionni, L.86
Matsuda, H.87
Matsuzawa, S.88
Miki, H.89
Mignone, F.90
Miyake, S.91
Morris, K.92
Mottagui-Tabar, S.93
Mulder, N.94
Nakano, N.95
Nakauchi, H.96
Ng, P.97
Nilsson, R.98
Nishiguchi, S.99
Nishikawa, S.100
Nori, F.101
Ohara, O.102
Okazaki, Y.103
Orlando, V.104
Pang, K.C.105
Pavan, W.J.106
Pavesi, G.107
Pesole, G.108
Petrovsky, N.109
Piazza, S.110
Reed, J.111
Reid, J.F.112
Ring, B.Z.113
Ringwald, M.114
Rost, B.115
Ruan, Y.116
Salzberg, S.L.117
Sandelin, A.118
Schneider, C.119
Schön-bach, C.120
Sekiguchi, K.121
Semple, C.A.122
Seno, S.123
Sessa, L.124
Sheng, Y.125
Shi-bata, Y.126
Shimada, H.127
Shimada, K.128
Silva, D.129
Sinclair, B.130
Sperling, S.131
Stupka, E.132
Sugiura, K.133
Sultana, R.134
Takenaka, Y.135
Taki, K.136
Tammoja, K.137
Tan, S.L.138
Tang, S.139
Taylor, M.S.140
Tegner, J.141
Teichmann, S.A.142
Ueda, H.R.143
van Nimwegen, E.144
Verardo, R.145
Wei, C.L.146
Yagi, K.147
Yamanishi, H.148
Zabarovsky, E.149
Zhu, S.150
Zimmer, A.151
Hide, W.152
Bult, C.153
Grimmond, S.M.154
Teasdale, R.D.155
Liu, E.T.156
Bru-sic, V.157
Quackenbush, J.158
Wahlestedt, C.159
Mattick, J.S.160
Hume, D.A.161
Kai, C.162
Sasaki, D.163
Tomaru, Y.164
Fukuda, S.165
Kanamori-Katayama, M.166
Suzuki, M.167
Aoki, J.168
Arakawa, T.169
Iida, J.170
Ima-mura, K.171
Itoh, M.172
Kato, T.173
Kawaji, H.174
Kawagashira, N.175
Kawashima, T.176
Kojima, M.177
Kondo, S.178
Konno, H.179
Nakano, K.180
Ninomiya, N.181
Nishio, T.182
Okada, M.183
Plessy, C.184
Shibata, K.185
Shiraki, T.186
Suzuki, S.187
Tagami, M.188
Waki, K.189
Watahiki, A.190
Okamura-Oho, Y.191
Suzuki, H.192
Kawai, J.193
Hayashizaki, Y.194
more..
-
11
-
-
44649151063
-
Multifaceted mammalian transcriptome
-
Carninci, P., Yasuda, J., and Hayashizaki, Y. (2008). Multifaceted mammalian transcriptome. Curr. Opin. Cell Biol. 20,274-280.
-
(2008)
Curr. Opin. Cell Biol.
, vol.20
, pp. 274-280
-
-
Carninci, P.1
Yasuda, J.2
Hayashizaki, Y.3
-
12
-
-
80053029196
-
Regulatory RNA: the new age
-
Chen, F., Evans, A., Gaskell, E., Pham, J., and Tsai, M. C. (2011). Regulatory RNA: the new age. Mol Cell 43, 851-852.
-
(2011)
Mol Cell
, vol.43
, pp. 851-852
-
-
Chen, F.1
Evans, A.2
Gaskell, E.3
Pham, J.4
Tsai, M.C.5
-
13
-
-
21044431735
-
Tran-scriptional maps of 10 human chromosomes at 5-nucleotide resolution
-
Cheng, J., Kapranov, P., Drenkow, J., Dike, S., Brubaker, S., Patel, S., Long, J., Stern, D., Tammana, H., Helt, G., Sementchenko, V.,Piccolboni, A., Bekiranov, S., Bailey, D. K., Ganesh, M., Ghosh, S., Bell, I., Gerhard, D. S., and Gingeras, T. R. (2005). Tran-scriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308, 1149-1154.
-
(2005)
Science
, vol.308
, pp. 1149-1154
-
-
Cheng, J.1
Kapranov, P.2
Drenkow, J.3
Dike, S.4
Brubaker, S.5
Patel, S.6
Long, J.7
Stern, D.8
Tammana, H.9
Helt, G.10
Sementchenko, V.11
Piccolboni, A.12
Bekiranov, S.13
Bailey, D.K.14
Ganesh, M.15
Ghosh, S.16
Bell, I.17
Gerhard, D.S.18
Gingeras, T.R.19
-
14
-
-
79960911703
-
The reality of pervasive transcription
-
discussion e1001102. doi:10.1371/journal.pbio.1000625
-
Clark, M. B., Amaral, P. P., Schlesinger, E J., Dinger, M. E., Taft, R. J., Rinn, J. L., Ponting, C. P., Stadler, P. F., Morris, K. V., Morillon, A., Rozowsky, J. S., Gerstein, M. B., Wahlestedt, C., Hayashizaki, Y., Carninci, P., Gingeras, T. R., and Mattick, J. S. (2011). The reality of pervasive transcription. PLoS Biol. 9, e1000625; discussion e1001102. doi:10.1371/journal.pbio.1000625
-
(2011)
PLoS Biol
, vol.9
-
-
Clark, M.B.1
Amaral, P.P.2
Schlesinger, E.J.3
Dinger, M.E.4
Taft, R.J.5
Rinn, J.L.6
Ponting, C.P.7
Stadler, P.F.8
Morris, K.V.9
Morillon, A.10
Rozowsky, J.S.11
Gerstein, M.B.12
Wahlestedt, C.13
Hayashizaki, Y.14
Carninci, P.15
Gingeras, T.R.16
Mattick, J.S.17
-
15
-
-
46249103973
-
Stem cell transcriptome profiling via massive-scale 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 massive-scale 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
-
16
-
-
58849107237
-
Transcriptome content and dynamics at single-nucleotide resolution
-
Cloonan, N., and Grimmond, S. M. (2008). Transcriptome content and dynamics at single-nucleotide resolution. Genome Biol. 9, 234.
-
(2008)
Genome Biol
, vol.9
, pp. 234
-
-
Cloonan, N.1
Grimmond, S.M.2
-
17
-
-
0000586458
-
The nature and mechanisms of human gene mutation
-
7th Edn, eds C. Scriver, A. L. Beaudet, W. S. Sly, and D. Valle (New York: McGraw-Hill)
-
Cooper, D. N., Krawczak, M., and Antonarakis, S. E. (1995). "The nature and mechanisms of human gene mutation," in The Metabolic and Molecular Bases of Inherited Disease, 7th Edn, eds C. Scriver, A. L. Beaudet, W. S. Sly, and D. Valle (New York: McGraw-Hill), 259-291.
-
(1995)
The Metabolic and Molecular Bases of Inherited Disease
, pp. 259-291
-
-
Cooper, D.N.1
Krawczak, M.2
Antonarakis, S.E.3
-
18
-
-
34250369629
-
Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions
-
Denoeud, F., Kapranov, P., Ucla, C., Frankish,A., Castelo, R.,Drenkow, J., Lagarde, J., Alioto, T., Manzano, C., Chrast, J., Dike, S., Wyss, C., Hen-richsen, C. N., Holroyd, N., Dick-son, M. C., Taylor, R., Hance, Z., Foissac, S., Myers, R. M., Rogers, J., Hubbard, T., Harrow, J., Guigo, R., Gingeras, T. R., Antonarakis, S. E., and Reymond, A. (2007). Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res. 17, 746-759.
-
(2007)
Genome Res
, vol.17
, pp. 746-759
-
-
Denoeud, F.1
Kapranov, P.2
Ucla, C.3
Frankish, A.4
Castelo, R.5
Drenkow, J.6
Lagarde, J.7
Alioto, T.8
Manzano, C.9
Chrast, J.10
Dike, S.11
Wyss, C.12
Hen-richsen, C.N.13
Holroyd, N.14
Dick-son, M.C.15
Taylor, R.16
Hance, Z.17
Foissac, S.18
Myers, R.M.19
Rogers, J.20
Hubbard, T.21
Harrow, J.22
Guigo, R.23
Gingeras, T.R.24
Antonarakis, S.E.25
Reymond, A.26
more..
-
19
-
-
46249089426
-
Efficient targeted transcript discovery via array-based normalization of RACE libraries
-
Djebali, S., Kapranov, P., Foissac, S., Lagarde, J., Reymond, A., Ucla, C., Wyss, C., Drenkow, J., Dumais, E., Murray, R. R., Lin, C., Szeto, D., Denoeud, F., Calvo, M., Frankish, A., Harrow, J., Makrythanasis, P., Vidal, M., Salehi-Ashtiani, K., Antonarakis, S. E., Gingeras, T. R., and Guigo, R. (2008). Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nat. Methods 5, 629-635.
-
(2008)
Nat. Methods
, vol.5
, pp. 629-635
-
-
Djebali, S.1
Kapranov, P.2
Foissac, S.3
Lagarde, J.4
Reymond, A.5
Ucla, C.6
Wyss, C.7
Drenkow, J.8
Dumais, E.9
Murray, R.R.10
Lin, C.11
Szeto, D.12
Denoeud, F.13
Calvo, M.14
Frankish, A.15
Harrow, J.16
Makrythanasis, P.17
Vidal, M.18
Salehi-Ashtiani, K.19
Antonarakis, S.E.20
Gingeras, T.R.21
Guigo, R.22
more..
-
20
-
-
67349173665
-
The regulated retrotransposon transcriptome of mammalian cells
-
Faulkner, G. J., Kimura, Y., Daub, C. O., Wani, S., Plessy, C., Irvine, K. M., Schroder, K., Cloonan, N., Step-toe, A. L., Lassmann, T., Waki, K., Hornig, N., Arakawa, T., Takahashi, H., Kawai, J., Forrest, A. R., Suzuki, H., Hayashizaki, Y., Hume, D. A., Orlando, V., Grimmond, S. M., and Carninci, P. (2009). The regulated retrotransposon transcriptome of mammalian cells. Nat. Genet. 41, 563-571.
-
(2009)
Nat. Genet.
, vol.41
, pp. 563-571
-
-
Faulkner, G.J.1
Kimura, Y.2
Daub, C.O.3
Wani, S.4
Plessy, C.5
Irvine, K.M.6
Schroder, K.7
Cloonan, N.8
Step-toe, A.L.9
Lassmann, T.10
Waki, K.11
Hornig, N.12
Arakawa, T.13
Takahashi, H.14
Kawai, J.15
Forrest, A.R.16
Suzuki, H.17
Hayashizaki, Y.18
Hume, D.A.19
Orlando, V.20
Grimmond, S.M.21
Carninci, P.22
more..
-
21
-
-
79953888460
-
The functional role of long non-coding RNA in human carcinomas
-
Gibb, E. A., Brown, C. J., and Lam, W. L. (2011). The functional role of long non-coding RNA in human carcinomas. Mol Cancer 10, 38.
-
(2011)
Mol Cancer
, vol.10
, pp. 38
-
-
Gibb, E.A.1
Brown, C.J.2
Lam, W.L.3
-
22
-
-
77951118936
-
Long non-coding RNA HOTAIR repro-grams chromatin state to promote cancer metastasis
-
Gupta, R. A., Shah, N., Wang, K. C., Kim, J., Horlings, H. M., Wong, D. J., Tsai, M. C., Hung, T., Argani, P., Rinn, J. L., Wang, Y., Brzoska, P., Kong, B., Li, R., West, R. B., Van De Vijver, M. J., Sukumar, S., and Chang, H. Y. (2010). Long non-coding RNA HOTAIR repro-grams chromatin state to promote cancer metastasis. Nature 464, 1071-1076.
-
(2010)
Nature
, vol.464
, pp. 1071-1076
-
-
Gupta, R.A.1
Shah, N.2
Wang, K.C.3
Kim, J.4
Horlings, H.M.5
Wong, D.J.6
Tsai, M.C.7
Hung, T.8
Argani, P.9
Rinn, J.L.10
Wang, Y.11
Brzoska, P.12
Kong, B.13
Li, R.14
West, R.B.15
Van De Vijver, M.J.16
Sukumar, S.17
Chang, H.Y.18
-
23
-
-
33748645500
-
GENCODE: pro ducing a reference annotation for ENCODE
-
Harrow, J., Denoeud, F., Frankish, A., Reymond, A., Chen, C. K., Chrast, J., Lagarde, J., Gilbert, J. G., Storey, R., Swarbreck, D., Rossier, C., Ucla, C., Hubbard, T., Antonarakis, S. E., and Guigo, R. (2006). GENCODE: pro ducing a reference annotation for ENCODE. Genome Biol. 7(Suppl. 1), S41-S49.
-
(2006)
Genome Biol
, vol.7
, Issue.SUPPL. 1
-
-
Harrow, J.1
Denoeud, F.2
Frankish, A.3
Reymond, A.4
Chen, C.K.5
Chrast, J.6
Lagarde, J.7
Gilbert, J.G.8
Storey, R.9
Swarbreck, D.10
Rossier, C.11
Ucla, C.12
Hubbard, T.13
Antonarakis, S.E.14
Guigo, R.15
-
24
-
-
0017220998
-
The expression of three abundance classes of messenger RNA in mouse tissues
-
Hastie, N. D., and Bishop, J. O. (1976). The expression of three abundance classes of messenger RNA in mouse tissues. Cell 9, 761-774.
-
(1976)
Cell
, vol.9
, pp. 761-774
-
-
Hastie, N.D.1
Bishop, J.O.2
-
25
-
-
81055155799
-
Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
-
Ingolia, N. T., Lareau, L. F., and Weiss-man, J. S. (2011). Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147, 789-802.
-
(2011)
Cell
, vol.147
, pp. 789-802
-
-
Ingolia, N.T.1
Lareau, L.F.2
Weiss-man, J.S.3
-
26
-
-
12344291073
-
Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments
-
Johnson, J. M., Edwards, S., Shoemaker, D., and Schadt, E. E. (2005). Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet. 21,93-102.
-
(2005)
Trends Genet
, vol.21
, pp. 93-102
-
-
Johnson, J.M.1
Edwards, S.2
Shoemaker, D.3
Schadt, E.E.4
-
27
-
-
0037012881
-
Large-scale transcriptional activity in chromosomes 21 and 22
-
Kapranov, P., Cawley, S. E., Drenkow, J., Bekiranov, S., Strausberg, R. L., Fodor, S. P., and Gingeras, T. R. (2002). Large-scale transcriptional activity in chromosomes 21 and 22. Science 296, 916-919.
-
(2002)
Science
, vol.296
, pp. 916-919
-
-
Kapranov, P.1
Cawley, S.E.2
Drenkow, J.3
Bekiranov, S.4
Strausberg, R.L.5
Fodor, S.P.6
Gingeras, T.R.7
-
28
-
-
34250160256
-
RNA maps reveal new RNA classes and a possible function for pervasive transcription
-
Kapranov, P., Cheng, J., Dike, S., Nix, D. A., Duttagupta, R., Willing-ham, A. T., Stadler, P. F., Her-tel, J., Hackermuller, J., Hofacker, I. L., Bell, I., Cheung, E., Drenkow, J., Dumais, E., Patel, S., Helt, G., Ganesh, M., Ghosh, S., Piccolboni, A., Sementchenko, V., Tammana, H., and Gingeras, T. R. (2007a). RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316,1484-1488.
-
(2007)
Science
, vol.316
, pp. 1484-1488
-
-
Kapranov, P.1
Cheng, J.2
Dike, S.3
Nix, D.A.4
Duttagupta, R.5
Willing-ham, A.T.6
Stadler, P.F.7
Her-tel, J.8
Hackermuller, J.9
Hofacker, I.L.10
Bell, I.11
Cheung, E.12
Drenkow, J.13
Dumais, E.14
Patel, S.15
Helt, G.16
Ganesh, M.17
Ghosh, S.18
Piccolboni, A.19
Sementchenko, V.20
Tammana, H.21
Gingeras, T.R.22
more..
-
29
-
-
34249088350
-
Genome-wide transcription and the implications for genomic organization
-
Kapranov, P., Willingham, A. T., and Gingeras, T. R. (2007b). Genome-wide transcription and the implications for genomic organization. Nat. Rev. Genet. 8,413-423.
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 413-423
-
-
Kapranov, P.1
Willingham, A.T.2
Gingeras, T.R.3
-
30
-
-
22244442468
-
Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays
-
Kapranov, P., Drenkow, J., Cheng, J., Long, J., Helt, G., Dike, S., and Gingeras, T. R. (2005). Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res. 15,987-997.
-
(2005)
Genome Res
, vol.15
, pp. 987-997
-
-
Kapranov, P.1
Drenkow, J.2
Cheng, J.3
Long, J.4
Helt, G.5
Dike, S.6
Gingeras, T.R.7
-
31
-
-
3242766188
-
Beyond expression profiling: next generation uses of high density oligonucleotide arrays
-
Kapranov, P., Sementchenko, V. I., and Gingeras, T. R. (2003). Beyond expression profiling: next generation uses of high density oligonucleotide arrays. Brief. Funct. Genomic. Pro-teomic. 2, 47-56.
-
(2003)
Brief. Funct. Genomic. Pro-teomic.
, vol.2
, pp. 47-56
-
-
Kapranov, P.1
Sementchenko, V.I.2
Gingeras, T.R.3
-
32
-
-
78650292831
-
The majority of total nuclear-encoded non-ribosomal RNA in a human cell is "dark matter" un-annotated RNA
-
doi:10.1186/1741-7007-8-149
-
Kapranov, P., St Laurent, G., Raz, T., Ozsolak, F., Reynolds, C. P., Sorensen, P. H., Reaman, G., Milos, P., Arceci, R. J., Thompson, J. F., and Triche, T. J. (2010). The majority of total nuclear-encoded non-ribosomal RNA in a human cell is "dark matter" un-annotated RNA. BMC Biol. 8, 149. doi:10.1186/1741-7007-8-149
-
(2010)
BMC Biol
, vol.8
, pp. 149
-
-
Kapranov, P.1
St Laurent, G.2
Raz, T.3
Ozsolak, F.4
Reynolds, C.P.5
Sorensen, P.H.6
Reaman, G.7
Milos, P.8
Arceci, R.J.9
Thompson, J.F.10
Triche, T.J.11
-
33
-
-
0019194020
-
Non-polyadenylated mRNAs from eukaryotes
-
Katinakis, P. K., Slater, A., and Burdon, R. H. (1980). Non-polyadenylated mRNAs from eukaryotes. FEBS Lett. 116, 1-7.
-
(1980)
FEBS Lett
, vol.116
, pp. 1-7
-
-
Katinakis, P.K.1
Slater, A.2
Burdon, R.H.3
-
34
-
-
0036079158
-
The human genome browser at UCSC
-
Kent, W J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., and Haussler, D. (2002). The human genome browser at UCSC. Genome Res. 12, 996-1006.
-
(2002)
Genome Res
, vol.12
, pp. 996-1006
-
-
Kent, W.J.1
Sugnet, C.W.2
Furey, T.S.3
Roskin, K.M.4
Pringle, T.H.5
Zahler, A.M.6
Haussler, D.7
-
35
-
-
79957907741
-
The melanoma-upregulated long non-coding RNA SPRY4-IT1 modulates apoptosis and invasion
-
Khaitan, D., Dinger, M. E., Mazar, J., Crawford, J., Smith, M. A., Mattick, J. S., and Perera, R. J. (2011). The melanoma-upregulated long non-coding RNA SPRY4-IT1 modulates apoptosis and invasion. Cancer Res. 71,3852-3862.
-
(2011)
Cancer Res
, vol.71
, pp. 3852-3862
-
-
Khaitan, D.1
Dinger, M.E.2
Mazar, J.3
Crawford, J.4
Smith, M.A.5
Mattick, J.S.6
Perera, R.J.7
-
36
-
-
84988044467
-
CAGE: cap analysis of gene expression
-
Kodzius, R., Kojima, M., Nishiyori, H., Nakamura, M., Fukuda, S., Tagami, M., Sasaki, D., Imamura, K., Kai, C., Harbers, M., Hayashizaki, Y., and Carninci, P. (2006). CAGE: cap analysis of gene expression. Nat. Methods 3,211-222.
-
(2006)
Nat. Methods
, vol.3
, pp. 211-222
-
-
Kodzius, R.1
Kojima, M.2
Nishiyori, H.3
Nakamura, M.4
Fukuda, S.5
Tagami, M.6
Sasaki, D.7
Imamura, K.8
Kai, C.9
Harbers, M.10
Hayashizaki, Y.11
Carninci, P.12
-
37
-
-
77954786287
-
Small pep-tides switch the transcriptional activity of Shavenbaby during Drosophila embryogenesis
-
Kondo, T., Plaza, S., Zanet, J., Benrabah, E., Valenti, P., Hashimoto, Y., Kobayashi, S., Payre, F., and Kageyama, Y. (2010). Small pep-tides switch the transcriptional activity of Shavenbaby during Drosophila embryogenesis. Science 329, 336-339.
-
(2010)
Science
, vol.329
, pp. 336-339
-
-
Kondo, T.1
Plaza, S.2
Zanet, J.3
Benrabah, E.4
Valenti, P.5
Hashimoto, Y.6
Kobayashi, S.7
Payre, F.8
Kageyama, Y.9
-
38
-
-
77449147610
-
FRT-seq: 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). FRT-seq: 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
-
39
-
-
0028631058
-
Introns: evolution and function
-
Mattick, J. S. (1994). Introns: evolution and function. Curr. Opin. Genet. Dev. 4, 823-831.
-
(1994)
Curr. Opin. Genet. Dev.
, vol.4
, pp. 823-831
-
-
Mattick, J.S.1
-
40
-
-
0141867857
-
Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms
-
Mattick, J. S. (2003). Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. Bioessays 25, 930-939.
-
(2003)
Bioessays
, vol.25
, pp. 930-939
-
-
Mattick, J.S.1
-
41
-
-
1842584883
-
RNA regulation: a new genetics?
-
Mattick, J. S. (2004). RNA regulation: a new genetics? Nat. Rev. Genet. 5, 316-323.
-
(2004)
Nat Rev. Genet.
, vol.5
, pp. 316-323
-
-
Mattick, J.S.1
-
42
-
-
65649092633
-
The genetic signatures of noncoding RNAs
-
doi:10.1371/journal.pgen.1000459
-
Mattick, J. S. (2009). The genetic signatures of noncoding RNAs. PLoS Genet. 5, e1000459. doi:10.1371/journal.pgen.1000459
-
(2009)
PLoS Genet
, vol.5
-
-
Mattick, J.S.1
-
43
-
-
79957537160
-
The central role of RNA in human development and cognition
-
Mattick, J. S. (2011). The central role of RNA in human development and cognition. FEBS Lett. 585, 1600-1616.
-
(2011)
FEBS Lett
, vol.585
, pp. 1600-1616
-
-
Mattick, J.S.1
-
44
-
-
78650051452
-
Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome
-
Mercer, T. R., Dinger, M. E., Bracken, C. P., Kolle, G., Szubert, J. M., Korbie, D. J., Askarian-Amiri, M. E., Gardiner, B. B., Goodall, G. J., Grimmond, S. M., and Mattick, J. S. (2010). Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome. Genome Res. 20, 1639-1650.
-
(2010)
Genome Res
, vol.20
, pp. 1639-1650
-
-
Mercer, T.R.1
Dinger, M.E.2
Bracken, C.P.3
Kolle, G.4
Szubert, J.M.5
Korbie, D.J.6
Askarian-Amiri, M.E.7
Gardiner, B.B.8
Goodall, G.J.9
Grimmond, S.M.10
Mattick, J.S.11
-
45
-
-
84855539848
-
Targeted RNA sequencing reveals the deep complexity of the human transcriptome
-
Mercer, T. R., Gerhardt, D. J., Dinger, M. E., Crawford, J., Trapnell, C., Jeddeloh, J. A., Mattick, J. S., and Rinn, J. L. (2011a). Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat. Biotechnol. 30, 99-104.
-
(2011)
Nat. Biotechnol
, vol.30
, pp. 99-104
-
-
Mercer, T.R.1
Gerhardt, D.J.2
Dinger, M.E.3
Crawford, J.4
Trapnell, C.5
Jeddeloh, J.A.6
Mattick, J.S.7
Rinn, J.L.8
-
46
-
-
79953673245
-
Expression of distinct RNAs from 3' untranslated regions
-
Mercer, T. R., Wilhelm, D., Dinger, M. E., Solda, G., Korbie, D. J., Glazov, E. A., Truong, V., Schwenke, M., Simons, C., Matthaei, K. I., Saint, R., Koop-man, P., and Mattick, J. S. (2011b). Expression of distinct RNAs from 3' untranslated regions. Nucleic Acids Res. 39, 2393-2403.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 2393-2403
-
-
Mercer, T.R.1
Wilhelm, D.2
Dinger, M.E.3
Solda, G.4
Korbie, D.J.5
Glazov, E.A.6
Truong, V.7
Schwenke, M.8
Simons, C.9
Matthaei, K.I.10
Saint, R.11
Koop-man, P.12
Mattick, J.S.13
-
47
-
-
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
-
48
-
-
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
-
49
-
-
0018857680
-
Selfish DNA: the ultimate parasite
-
Orgel, L. E., and Crick, F. H. (1980). Selfish DNA: the ultimate parasite. Nature 284, 604-607.
-
(1980)
Nature
, vol.284
, pp. 604-607
-
-
Orgel, L.E.1
Crick, F.H.2
-
50
-
-
64649087770
-
Identification of a cytoplasmic complex that adds a cap onto 5'-monophosphate RNA
-
Otsuka, Y., Kedersha, N. L., and Schoen-berg, D. R. (2009). Identification of a cytoplasmic complex that adds a cap onto 5'-monophosphate RNA. Mol. Cell. Biol. 29,2155-2167.
-
(2009)
Mol. Cell. Biol.
, vol.29
, pp. 2155-2167
-
-
Otsuka, Y.1
Kedersha, N.L.2
Schoen-berg, D.R.3
-
52
-
-
33745319337
-
RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse
-
Rassoulzadegan, M., Grandjean, V., Gounon, P., Vincent, S., Gillot, I., and Cuzin,F. (2006). RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse. Nature 441,469-474.
-
(2006)
Nature
, vol.441
, pp. 469-474
-
-
Rassoulzadegan, M.1
Grandjean, V.2
Gounon, P.3
Vincent, S.4
Gillot, I.5
Cuzin, F.6
-
53
-
-
79955858869
-
Protocol dependence of sequencing-based gene expression measurements
-
doi:10.1371/journal.pone.0019287
-
Raz, T., Kapranov, P., Lipson, D., Letovsky, S., Milos, P. M., and Thompson, J. F. (2011). Protocol dependence of sequencing-based gene expression measurements. PLoS ONE 6, e19287. doi:10.1371/journal.pone.0019287
-
(2011)
PLoS ONE
, vol.6
-
-
Raz, T.1
Kapranov, P.2
Lipson, D.3
Letovsky, S.4
Milos, P.M.5
Thompson, J.F.6
-
54
-
-
0037442493
-
The transcriptional activity of human chromosome 22
-
Rinn, J. L., Euskirchen, G., Bertone, P., Martone, R., Luscombe, N. M., Hart-man, S., Harrison, P. M., Nelson, F. K., Miller, P., Gerstein, M., Weiss-man, S., and Snyder, M. (2003). The transcriptional activity of human chromosome 22. Genes Dev. 17, 529-540.
-
(2003)
Genes Dev
, vol.17
, pp. 529-540
-
-
Rinn, J.L.1
Euskirchen, G.2
Bertone, P.3
Martone, R.4
Luscombe, N.M.5
Hart-man, S.6
Harrison, P.M.7
Nelson, F.K.8
Miller, P.9
Gerstein, M.10
Weiss-man, S.11
Snyder, M.12
-
55
-
-
0019524412
-
Large heterogeneous nuclear ribonucleic acid has three times as many 5' caps as polyadenylic acid segments, and most caps do not enter polyribosomes
-
Salditt-Georgieff, M., Harpold, M. M., Wilson, M. C., and Darnell, J. E. Jr. (1981). Large heterogeneous nuclear ribonucleic acid has three times as many 5' caps as polyadenylic acid segments, and most caps do not enter polyribosomes. Mol. Cell. Biol. 1,179-187.
-
(1981)
Mol. Cell. Biol.
, vol.1
, pp. 179-187
-
-
Salditt-Georgieff, M.1
Harpold, M.M.2
Wilson, M.C.3
Darnell Jr., J.E.4
-
56
-
-
79952301722
-
A comparison of single molecule and amplification based sequencing of cancer tran-scriptomes
-
doi:10.1371/journal.pone.0017305
-
Sam, L. T., Lipson, D., Raz, T., Cao, X., Thompson, J., Milos, P. M., Robinson, D., Chinnaiyan, A. M., Kumar-Sinha, C., and Maher, C. A. (2011). A comparison of single molecule and amplification based sequencing of cancer tran-scriptomes. PLoS ONE 6, e17305. doi:10.1371/journal.pone.0017305
-
(2011)
PLoS ONE
, vol.6
-
-
Sam, L.T.1
Lipson, D.2
Raz, T.3
Cao, X.4
Thompson, J.5
Milos, P.M.6
Robinson, D.7
Chinnaiyan, A.M.8
Kumar-Sinha, C.9
Maher, C.A.10
-
57
-
-
36049020719
-
Noncoding RNAs: couplers of analog and digital information in nervous system function?
-
St Laurent, G. III, and Wahlestedt, C. (2007). Noncoding RNAs: couplers of analog and digital information in nervous system function? Trends Neurosci. 30,612-621.
-
(2007)
Trends Neurosci
, vol.30
, pp. 612-621
-
-
St Laurent III, G.1
Wahlestedt, C.2
-
58
-
-
33846984935
-
Transcriptional noise and the fidelity of initiation by RNA polymerase II
-
Struhl, K. (2007). Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat. Struct. Mol. Biol. 14, 103-105.
-
(2007)
Nat. Struct. Mol. Biol.
, vol.14
, pp. 103-105
-
-
Struhl, K.1
-
59
-
-
79551642322
-
Aberrant overexpression of satellite repeats in pancreatic and other epithelial cancers
-
Ting, D. T., Lipson, D., Paul, S., Bran-nigan, B. W., Akhavanfard, S., Coff-man, E. J., Contino, G., Desh-pande, V., Iafrate, A. J., Letovsky, S., Rivera, M. N., Bardeesy, N., Maheswaran, S., and Haber, D. A. (2011). Aberrant overexpression of satellite repeats in pancreatic and other epithelial cancers. Science 331, 593-596.
-
(2011)
Science
, vol.331
, pp. 593-596
-
-
Ting, D.T.1
Lipson, D.2
Paul, S.3
Bran-nigan, B.W.4
Akhavanfard, S.5
Coff-man, E.J.6
Contino, G.7
Desh-pande, V.8
Iafrate, A.J.9
Letovsky, S.10
Rivera, M.N.11
Bardeesy, N.12
Maheswaran, S.13
Haber, D.A.14
-
60
-
-
84455206362
-
Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution
-
Ulitsky, I., Shkumatava, A., Jan, C. H., Sive, H., and Bartel, D. P. (2011). Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 147, 1537-1550.
-
(2011)
Cell
, vol.147
, pp. 1537-1550
-
-
Ulitsky, I.1
Shkumatava, A.2
Jan, C.H.3
Sive, H.4
Bartel, D.P.5
-
61
-
-
70449723389
-
Establishing legitimacy and function in the new transcriptome
-
van Bakel, H., and Hughes, T. R. (2009). Establishing legitimacy and function in the new transcriptome. Brief. Funct. Genomic. Proteomic. 8, 424-436.
-
(2009)
Brief. Funct. Genomic. Proteomic.
, vol.8
, pp. 424-436
-
-
Van Bakel, H.1
Hughes, T.R.2
-
62
-
-
77952905505
-
Most "dark matter" transcripts are associated with known genes
-
doi:10.1371/jour-nal.pbio. 1000371
-
van Bakel, H., Nislow, C., Blencowe, B. J., and Hughes, T. R. (2010). Most "dark matter" transcripts are associated with known genes. PLoS Biol. 8, e1000371. doi:10.1371/jour-nal.pbio. 1000371
-
(2010)
PLoS Biol
, vol.8
-
-
Van Bakel, H.1
Nislow, C.2
Blencowe, B.J.3
Hughes, T.R.4
-
63
-
-
79960921433
-
Response to "the reality of pervasive transcription"
-
doi:10.1371/journal.pbio.1001102
-
van Bakel, H., Nislow, C., Blencowe, B. J., and Hughes, T. R. (2011). Response to "the reality of pervasive transcription." PLoS Biol. 9, e1001102. doi:10.1371/journal.pbio.1001102
-
(2011)
PLoS Biol
, vol.9
-
-
Van Bakel, H.1
Nislow, C.2
Blencowe, B.J.3
Hughes, T.R.4
-
64
-
-
0018629557
-
Complex population of nonpolyadenylated messenger RNA in mouse brain
-
van Ness, J., Maxwell, I. H., and Hahn, W E. (1979). Complex population of nonpolyadenylated messenger RNA in mouse brain. Cell 18, 1341-1349.
-
(1979)
Cell
, vol.18
, pp. 1341-1349
-
-
Van Ness, J.1
Maxwell, I.H.2
Hahn, W.E.3
-
65
-
-
80053045739
-
Molecular mechanisms of long non-coding RNAs
-
Wang, K. C., and Chang, H. Y. (2011). Molecular mechanisms of long non-coding RNAs. Mol. Cell 43,904-914.
-
(2011)
Mol. Cell
, vol.43
, pp. 904-914
-
-
Wang, K.C.1
Chang, H.Y.2
-
66
-
-
57749195712
-
RNA-seq: a revolutionary tool for transcriptomics
-
Wang, Z., Gerstein, M., and Snyder, M. (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
Gerstein, M.2
Snyder, M.3
|