-
1
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
10.1126/science.1112014 16141072
-
Carninci P Kasukawa T Katayama S Gough J Frith MC Maeda N Oyama R Ravasi T Lenhard B Wells C Kodzius R Shimokawa K Bajic VB Brenner SE Batalov S Forrest AR Zavolan M Davis MJ Wilming LG Aidinis V Allen JE Ambesi-Impiombato A Apweiler R Aturaliya RN Bailey TL Bansal M Baxter L Beisel KW Bersano T Bono H Chalk AM Chiu KP Choudhary V Christoffels A Clutterbuck DR Crowe ML Dalla E Dalrymple BP de Bono B Della Gatta G di Bernardo D Down T Engstrom P Fagiolini M Faulkner G Fletcher CF Fukushima T Furuno M Futaki S Gariboldi M Georgii-Hemming P Gingeras TR Gojobori T Green RE Gustincich S Harbers M Hayashi Y Hensch TK 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 Krishnan SP Kruger A Kummerfeld SK Kurochkin IV Lareau LF 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 KC Pavan WJ Pavesi G Pesole G Petrovsky N Piazza S Reed J Reid JF Ring BZ Ringwald M Rost B Ruan Y Salzberg SL Sandelin A Schneider C Schonbach C Sekiguchi K Semple CA Seno S Sessa L Sheng Y Shibata Y Shimada H Shimada K Silva D Sinclair B Sperling S Stupka E Sugiura K Sultana R Takenaka Y Taki K Tammoja K Tan SL Tang S Taylor MS Tegner J Teichmann SA Ueda HR van Nimwegen E Verardo R Wei CL Yagi K Yamanishi H Zabarovsky E Zhu S Zimmer A Hide W Bult C Grimmond SM Teasdale RD Liu ET Brusic V Quackenbush J Wahlestedt C Mattick JS Hume DA Kai C Sasaki D Tomaru Y Fukuda S Kanamori-Katayama M Suzuki M Aoki J Arakawa T Iida J Imamura 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 The transcriptional landscape of the mammalian genome Science 2005, 309:1559-1563. 10.1126/ science.1112014 16141072
-
(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
Batalov, 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
Choudhary, V.33
Christoffels, A.34
Clutterbuck, D.R.35
Crowe, M.L.36
Dalla, E.37
Dalrymple, 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
Krishnan, 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
Schonbach, C.120
Sekiguchi, K.121
Semple, C.A.122
Seno, S.123
Sessa, L.124
Sheng, Y.125
Shibata, 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
Brusic, 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
Imamura, 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..
-
2
-
-
19944376457
-
Global identification of human transcribed sequences with genome tiling arrays
-
10.1126/science.1103388 15539566
-
Bertone P Stolc V Royce TE Rozowsky JS Urban AE Zhu X Rinn JL Tongprasit W Samanta M Weissman S Gerstein M Snyder M Global identification of human transcribed sequences with genome tiling arrays Science 2004, 306:2242-2246. 10.1126/science.1103388 15539566
-
(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
-
3
-
-
21044431735
-
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
-
10.1126/science.1108625 15790807
-
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 DK Ganesh M Ghosh S Bell I Gerhard DS Gingeras TR Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution Science 2005, 308:1149-1154. 10.1126/science.1108625 15790807
-
(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
-
5
-
-
0035313774
-
Open systems: Panoramic views of gene expression
-
10.1016/S0022-1759(01)00306-4 11251222
-
Green CD Simons JF Taillon BE Lewin DA Open systems: Panoramic views of gene expression J Immunol Methods 2001, 250:67-79. 10.1016/ S0022-1759(01)00306-4 11251222
-
(2001)
J Immunol Methods
, vol.250
, pp. 67-79
-
-
Green, C.D.1
Simons, J.F.2
Taillon, B.E.3
Lewin, D.A.4
-
6
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
1464427 16056220
-
Margulies M Egholm M Altman WE Attiya S Bader JS Bemben LA Berka J Braverman MS Chen YJ Chen Z Dewell SB Du L Fierro JM Gomes XV Godwin BC He W Helgesen S Ho CH Irzyk GP Jando SC Alenquer ML Jarvie TP Jirage KB Kim JB Knight JR Lanza JR Leamon JH Lefkowitz SM Lei M Li J Lohman KL Lu H Makhijani VB McDade KE McKenna MP Myers EW Nickerson E Nobile JR Plant R Puc BP Ronan MT Roth GT Sarkis GJ Simons JF Simpson JW Srinivasan M Tartaro KR Tomasz A Vogt KA Volkmer GA Wang SH Wang Y Weiner MP Yu P Begley RF Rothberg JM Genome sequencing in microfabricated high-density picolitre reactors Nature 2005, 437:376-380. 1464427 16056220
-
(2005)
Nature
, vol.437
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
Attiya, S.4
Bader, J.S.5
Bemben, L.A.6
Berka, J.7
Braverman, M.S.8
Chen, Y.J.9
Chen, Z.10
Dewell, S.B.11
Du, L.12
Fierro, J.M.13
Gomes, X.V.14
Godwin, B.C.15
He, W.16
Helgesen, S.17
Ho, C.H.18
Irzyk, G.P.19
Jando, S.C.20
Alenquer, M.L.21
Jarvie, T.P.22
Jirage, K.B.23
Kim, J.B.24
Knight, J.R.25
Lanza, J.R.26
Leamon, J.H.27
Lefkowitz, S.M.28
Lei, M.29
Li, J.30
Lohman, K.L.31
Lu, H.32
Makhijani, V.B.33
McDade, K.E.34
McKenna, M.P.35
Myers, E.W.36
Nickerson, E.37
Nobile, J.R.38
Plant, R.39
Puc, B.P.40
Ronan, M.T.41
Roth, G.T.42
Sarkis, G.J.43
Simons, J.F.44
Simpson, J.W.45
Srinivasan, M.46
Tartaro, K.R.47
Tomasz, A.48
Vogt, K.A.49
Volkmer, G.A.50
Wang, S.H.51
Wang, Y.52
Weiner, M.P.53
Yu, P.54
Begley, R.F.55
Rothberg, J.M.56
more..
-
7
-
-
33845984917
-
Gene discovery and annotation using LCM-454 transcriptome sequencing
-
1716268 17095711 10.1101/gr.5145806
-
Emrich SJ Barbazuk WB Li L Schnable PS Gene discovery and annotation using LCM-454 transcriptome sequencing Genome Res 2007, 17:69-73. 1716268 17095711 10.1101/gr.5145806
-
(2007)
Genome Res
, vol.17
, pp. 69-73
-
-
Emrich, S.J.1
Barbazuk, W.B.2
Li, L.3
Schnable, P.S.4
-
8
-
-
13444260761
-
Statistical analysis of MPSS measurements: Application to the study of LPS-activated macrophage gene expression
-
547838 15668391 10.1073/pnas.0406555102
-
Stolovitzky GA Kundaje A Held GA Duggar KH Haudenschild CD Zhou D Vasicek TJ Smith KD Aderem A Roach JC Statistical analysis of MPSS measurements: Application to the study of LPS-activated macrophage gene expression Proc Natl Acad Sci U S A 2005, 102:1402-1407. 547838 15668391 10.1073/pnas.0406555102
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 1402-1407
-
-
Stolovitzky, G.A.1
Kundaje, A.2
Held, G.A.3
Duggar, K.H.4
Haudenschild, C.D.5
Zhou, D.6
Vasicek, T.J.7
Smith, K.D.8
Aderem, A.9
Roach, J.C.10
-
9
-
-
12344315892
-
A rapid method for computationally inferring transcriptome coverage and microarray sensitivity
-
10.1093/bioinformatics/bth472 15308544
-
Reverter A McWilliam SM Barris W Dalrymple BP A rapid method for computationally inferring transcriptome coverage and microarray sensitivity Bioinformatics 2005, 21:80-89. 10.1093/bioinformatics/bth472 15308544
-
(2005)
Bioinformatics
, vol.21
, pp. 80-89
-
-
Reverter, A.1
McWilliam, S.M.2
Barris, W.3
Dalrymple, B.P.4
-
10
-
-
0036356994
-
Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip arrays
-
RESEARCH0005. 150452 11806828
-
Chudin E Walker R Kosaka A Wu SX Rabert D Chang TK Kreder DE Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip arrays Genome Biol 2002, 3:RESEARCH0005. 150452 11806828
-
(2002)
Genome Biol
, vol.3
-
-
Chudin, E.1
Walker, R.2
Kosaka, A.3
Wu, S.X.4
Rabert, D.5
Chang, T.K.6
Kreder, D.E.7
-
11
-
-
0028789793
-
Serial analysis of gene expression
-
10.1126/science.270.5235.484 7570003
-
Velculescu VE Zhang L Vogelstein B Kinzler KW Serial analysis of gene expression Science 1995, 270:484-487. 10.1126/science.270.5235.484 7570003
-
(1995)
Science
, vol.270
, pp. 484-487
-
-
Velculescu, V.E.1
Zhang, L.2
Vogelstein, B.3
Kinzler, K.W.4
-
12
-
-
23644460630
-
Tag-based approaches for transcriptome research and genome annotation
-
10.1038/nmeth768 15973418
-
Harbers M Carninci P Tag-based approaches for transcriptome research and genome annotation Nat Methods 2005, 2:495-502. 10.1038/nmeth768 15973418
-
(2005)
Nat Methods
, vol.2
, pp. 495-502
-
-
Harbers, M.1
Carninci, P.2
-
13
-
-
0036246030
-
Using the transcriptome to annotate the genome
-
10.1038/nbt0502-508 11981567
-
Saha S Sparks AB Rago C Akmaev V Wang CJ Vogelstein B Kinzler KW Velculescu VE Using the transcriptome to annotate the genome Nat Biotechnol 2002, 20:508-512. 10.1038/nbt0502-508 11981567
-
(2002)
Nat Biotechnol
, vol.20
, pp. 508-512
-
-
Saha, S.1
Sparks, A.B.2
Rago, C.3
Akmaev, V.4
Wang, C.J.5
Vogelstein, B.6
Kinzler, K.W.7
Velculescu, V.E.8
-
14
-
-
0034130561
-
Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays
-
10.1038/76469 10835600
-
Brenner S Johnson M Bridgham J Golda G Lloyd DH Johnson D Luo S McCurdy S Foy M Ewan M Roth R George D Eletr S Albrecht G Vermaas E Williams SR Moon K Burcham T Pallas M DuBridge RB Kirchner J Fearon K Mao J Corcoran K Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays Nat Biotechnol 2000, 18:630-634. 10.1038/ 76469 10835600
-
(2000)
Nat Biotechnol
, vol.18
, pp. 630-634
-
-
Brenner, S.1
Johnson, M.2
Bridgham, J.3
Golda, G.4
Lloyd, D.H.5
Johnson, D.6
Luo, S.7
McCurdy, S.8
Foy, M.9
Ewan, M.10
Roth, R.11
George, D.12
Eletr, S.13
Albrecht, G.14
Vermaas, E.15
Williams, S.R.16
Moon, K.17
Burcham, T.18
Pallas, M.19
DuBridge, R.B.20
Kirchner, J.21
Fearon, K.22
Mao, J.23
Corcoran, K.24
more..
-
15
-
-
21444456797
-
Toward the 1,000 dollars human genome
-
10.1517/14622416.6.4.373 16004555
-
Bennett ST Barnes C Cox A Davies L Brown C Toward the 1,000 dollars human genome Pharmacogenomics 2005, 6:373-382. 10.1517/14622416.6.4.373 16004555
-
(2005)
Pharmacogenomics
, vol.6
, pp. 373-382
-
-
Bennett, S.T.1
Barnes, C.2
Cox, A.3
Davies, L.4
Brown, C.5
-
16
-
-
70549109033
-
Protocol for Whole Genome Sequencing using Solexa Technology
-
Solexa_Inc Informa Life Sciences
-
Solexa_Inc Protocol for Whole Genome Sequencing using Solexa Technology Biotechniques Protocol Guide 2007, Informa Life Sciences 2006:29.
-
(2006)
Biotechniques Protocol Guide 2007
, pp. 29
-
-
-
17
-
-
34147098535
-
An expression atlas of rice mRNAs and small RNAs
-
10.1038/nbt1291 17351617
-
Nobuta K Venu RC Lu C Belo A Vemaraju K Kulkarni K Wang W Pillay M Green PJ Wang GL Meyers BC An expression atlas of rice mRNAs and small RNAs Nat Biotechnol 2007, 25:473-477. 10.1038/nbt1291 17351617
-
(2007)
Nat Biotechnol
, vol.25
, pp. 473-477
-
-
Nobuta, K.1
Venu, R.C.2
Lu, C.3
Belo, A.4
Vemaraju, K.5
Kulkarni, K.6
Wang, W.7
Pillay, M.8
Green, P.J.9
Wang, G.L.10
Meyers, B.C.11
-
18
-
-
0017220998
-
The expression of three abundance classes of messenger RNA in mouse tissues
-
10.1016/0092-8674(76)90139-2 1017013
-
Hastie ND Bishop JO The expression of three abundance classes of messenger RNA in mouse tissues Cell 1976, 9:761-774. 10.1016/ 0092-8674(76)90139-2 1017013
-
(1976)
Cell
, vol.9
, pp. 761-774
-
-
Hastie, N.D.1
Bishop, J.O.2
-
19
-
-
0042932789
-
The T cell surface - How well do we know it?
-
10.1016/S1074-7613(03)00198-5 12932355
-
Evans EJ Hene L Sparks LM Dong T Retiere C Fennelly JA Manso-Sancho R Powell J Braud VM Rowland-Jones SL McMichael AJ Davis SJ The T cell surface - how well do we know it? Immunity 2003, 19:213-223. 10.1016/ S1074-7613(03)00198-5 12932355
-
(2003)
Immunity
, vol.19
, pp. 213-223
-
-
Evans, E.J.1
Hene, L.2
Sparks, L.M.3
Dong, T.4
Retiere, C.5
Fennelly, J.A.6
Manso-Sancho, R.7
Powell, J.8
Braud, V.M.9
Rowland-Jones, S.L.10
McMichael, A.J.11
Davis, S.J.12
-
20
-
-
0034741125
-
Biological insights into TCRgammadelta+ and TCRalphabeta+ intraepithelial lymphocytes provided by serial analysis of gene expression (SAGE)
-
10.1016/S1074-7613(01)00192-3 11567632
-
Shires J Theodoridis E Hayday AC Biological insights into TCRgammadelta+ and TCRalphabeta+ intraepithelial lymphocytes provided by serial analysis of gene expression (SAGE) Immunity 2001, 15:419-434. 10.1016/ S1074-7613(01)00192-3 11567632
-
(2001)
Immunity
, vol.15
, pp. 419-434
-
-
Shires, J.1
Theodoridis, E.2
Hayday, A.C.3
-
21
-
-
0038386030
-
Gene expression profile in human leukocytes
-
10.1182/blood-2002-06-1866 12522010
-
Hashimoto S Nagai S Sese J Suzuki T Obata A Sato T Toyoda N Dong HY Kurachi M Nagahata T Shizuno K Morishita S Matsushima K Gene expression profile in human leukocytes Blood 2003, 101:3509-3513. 10.1182/ blood-2002-06-1866 12522010
-
(2003)
Blood
, vol.101
, pp. 3509-3513
-
-
Hashimoto, S.1
Nagai, S.2
Sese, J.3
Suzuki, T.4
Obata, A.5
Sato, T.6
Toyoda, N.7
Dong, H.Y.8
Kurachi, M.9
Nagahata, T.10
Shizuno, K.11
Morishita, S.12
Matsushima, K.13
-
22
-
-
26244435958
-
Stage-dependent gene expression profiles during natural killer cell development
-
10.1016/j.ygeno.2005.06.010 16054799
-
Kang HS Kim EM Lee S Yoon SR Kawamura T Lee YC Kim S Myung PK Wang SM Choi I Stage-dependent gene expression profiles during natural killer cell development Genomics 2005, 86:551-565. 10.1016/j.ygeno.2005.06.010 16054799
-
(2005)
Genomics
, vol.86
, pp. 551-565
-
-
Kang, H.S.1
Kim, E.M.2
Lee, S.3
Yoon, S.R.4
Kawamura, T.5
Lee, Y.C.6
Kim, S.7
Myung, P.K.8
Wang, S.M.9
Choi, I.10
-
23
-
-
0034802541
-
Signatures of the immune response
-
10.1016/S1074-7613(01)00194-7 11567628
-
Shaffer AL Rosenwald A Hurt EM Giltnane JM Lam LT Pickeral OK Staudt LM Signatures of the immune response Immunity 2001, 15:375-385. 10.1016/ S1074-7613(01)00194-7 11567628
-
(2001)
Immunity
, vol.15
, pp. 375-385
-
-
Shaffer, A.L.1
Rosenwald, A.2
Hurt, E.M.3
Giltnane, J.M.4
Lam, L.T.5
Pickeral, O.K.6
Staudt, L.M.7
-
24
-
-
29144486808
-
Identification of T cell-restricted genes, and signatures for different T cell responses, using a comprehensive collection of microarray datasets
-
16339519
-
Chtanova T Newton R Liu SM Weininger L Young TR Silva DG Bertoni F Rinaldi A Chappaz S Sallusto F Rolph MS Mackay CR Identification of T cell-restricted genes, and signatures for different T cell responses, using a comprehensive collection of microarray datasets J Immunol 2005, 175:7837-7847. 16339519
-
(2005)
J Immunol
, vol.175
, pp. 7837-7847
-
-
Chtanova, T.1
Newton, R.2
Liu, S.M.3
Weininger, L.4
Young, T.R.5
Silva, D.G.6
Bertoni, F.7
Rinaldi, A.8
Chappaz, S.9
Sallusto, F.10
Rolph, M.S.11
Mackay, C.R.12
-
25
-
-
0038813928
-
Transcript identification by analysis of short sequence tags - Influence of tag length, restriction site and transcript database
-
153741 12682372 10.1093/nar/gkg313
-
Unneberg P Wennborg A Larsson M Transcript identification by analysis of short sequence tags - influence of tag length, restriction site and transcript database Nucleic Acids Res 2003, 31:2217-2226. 153741 12682372 10.1093/nar/gkg313
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 2217-2226
-
-
Unneberg, P.1
Wennborg, A.2
Larsson, M.3
-
26
-
-
0035162594
-
RefSeq and LocusLink: NCBI gene-centered resources
-
29787 11125071 10.1093/nar/29.1.137
-
Pruitt KD Maglott DR RefSeq and LocusLink: NCBI gene-centered resources Nucleic Acids Res 2001, 29:137-140. 29787 11125071 10.1093/nar/29.1.137
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 137-140
-
-
Pruitt, K.D.1
Maglott, D.R.2
-
27
-
-
11144355460
-
A human immunodeficiency virus 1 (HIV-1) clade A vaccine in clinical trials: Stimulation of HIV-specific T-cell responses by DNA and recombinant modified vaccinia virus Ankara (MVA) vaccines in humans
-
10.1099/vir.0.19701-0 15039533
-
Mwau M Cebere I Sutton J Chikoti P Winstone N Wee EG Beattie T Chen YH Dorrell L McShane H Schmidt C Brooks M Patel S Roberts J Conlon C Rowland-Jones SL Bwayo JJ McMichael AJ Hanke T A human immunodeficiency virus 1 (HIV-1) clade A vaccine in clinical trials: Stimulation of HIV-specific T-cell responses by DNA and recombinant modified vaccinia virus Ankara (MVA) vaccines in humans J Gen Virol 2004, 85:911-919. 10.1099/vir.0.19701-0 15039533
-
(2004)
J Gen Virol
, vol.85
, pp. 911-919
-
-
Mwau, M.1
Cebere, I.2
Sutton, J.3
Chikoti, P.4
Winstone, N.5
Wee, E.G.6
Beattie, T.7
Chen, Y.H.8
Dorrell, L.9
McShane, H.10
Schmidt, C.11
Brooks, M.12
Patel, S.13
Roberts, J.14
Conlon, C.15
Rowland-Jones, S.L.16
Bwayo, J.J.17
McMichael, A.J.18
Hanke, T.19
-
28
-
-
18444402182
-
The Ensembl genome database project
-
99161 11752248 10.1093/nar/30.1.38
-
Hubbard T Barker D Birney E Cameron G Chen Y Clark L Cox T Cuff J Curwen V Down T Durbin R Eyras E Gilbert J Hammond M Huminiecki L Kasprzyk A Lehvaslaiho H Lijnzaad P Melsopp C Mongin E Pettett R Pocock M Potter S Rust A Schmidt E Searle S Slater G Smith J Spooner W Stabenau A Stalker J Stupka E Ureta-Vidal A Vastrik I Clamp M The Ensembl genome database project Nucleic Acids Res 2002, 30:38-41. 99161 11752248 10.1093/nar/ 30.1.38
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 38-41
-
-
Hubbard, T.1
Barker, D.2
Birney, E.3
Cameron, G.4
Chen, Y.5
Clark, L.6
Cox, T.7
Cuff, J.8
Curwen, V.9
Down, T.10
Durbin, R.11
Eyras, E.12
Gilbert, J.13
Hammond, M.14
Huminiecki, L.15
Kasprzyk, A.16
Lehvaslaiho, H.17
Lijnzaad, P.18
Melsopp, C.19
Mongin, E.20
Pettett, R.21
Pocock, M.22
Potter, S.23
Rust, A.24
Schmidt, E.25
Searle, S.26
Slater, G.27
Smith, J.28
Spooner, W.29
Stabenau, A.30
Stalker, J.31
Stupka, E.32
Ureta-Vidal, A.33
Vastrik, I.34
Clamp, M.35
more..
-
29
-
-
18544392723
-
MicroSAGE is highly representative and reproducible but reveals major differences in gene expression among samples obtained from similar tissues
-
153457 12620102 10.1186/gb-2003-4-3-r17
-
Blackshaw S Kuo WP Park PJ Tsujikawa M Gunnersen JM Scott HS Boon WM Tan SS Cepko CL MicroSAGE is highly representative and reproducible but reveals major differences in gene expression among samples obtained from similar tissues Genome Biol 2003, 4:R17. 153457 12620102 10.1186/ gb-2003-4-3-r17
-
(2003)
Genome Biol
, vol.4
-
-
Blackshaw, S.1
Kuo, W.P.2
Park, P.J.3
Tsujikawa, M.4
Gunnersen, J.M.5
Scott, H.S.6
Boon, W.M.7
Tan, S.S.8
Cepko, C.L.9
-
30
-
-
3242875708
-
Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms
-
10.1093/bfgp/1.1.95 15251069
-
Reinartz J Bruyns E Lin JZ Burcham T Brenner S Bowen B Kramer M Woychik R Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms Brief Funct Genomic Proteomic 2002, 1:95-104. 10.1093/bfgp/1.1.95 15251069
-
(2002)
Brief Funct Genomic Proteomic
, vol.1
, pp. 95-104
-
-
Reinartz, J.1
Bruyns, E.2
Lin, J.Z.3
Burcham, T.4
Brenner, S.5
Bowen, B.6
Kramer, M.7
Woychik, R.8
-
31
-
-
26444545538
-
Reproducibility, bioinformatic analysis and power of the SAGE method to evaluate changes in transcriptome
-
549424 15716308 10.1093/nar/gni025
-
Dinel S Bolduc C Belleau P Boivin A Yoshioka M Calvo E Piedboeuf B Snyder EE Labrie F St-Amand J Reproducibility, bioinformatic analysis and power of the SAGE method to evaluate changes in transcriptome Nucleic Acids Res 2005, 33:e26. 549424 15716308 10.1093/nar/gni025
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Dinel, S.1
Bolduc, C.2
Belleau, P.3
Boivin, A.4
Yoshioka, M.5
Calvo, E.6
Piedboeuf, B.7
Snyder, E.E.8
Labrie, F.9
St-Amand, J.10
-
32
-
-
0034800372
-
Detecting the impact of sequencing errors on SAGE data
-
10.1093/bioinformatics/17.9.840 11590101
-
Colinge J Feger G Detecting the impact of sequencing errors on SAGE data Bioinformatics 2001, 17:840-842. 10.1093/bioinformatics/17.9.840 11590101
-
(2001)
Bioinformatics
, vol.17
, pp. 840-842
-
-
Colinge, J.1
Feger, G.2
-
33
-
-
2942553957
-
The use of MPSS for whole-genome transcriptional analysis in Arabidopsis
-
509274 15289482 10.1101/gr.2275604
-
Meyers BC Tej SS Vu TH Haudenschild CD Agrawal V Edberg SB Ghazal H Decola S The use of MPSS for whole-genome transcriptional analysis in Arabidopsis Genome Res 2004, 14:1641-1653. 509274 15289482 10.1101/ gr.2275604
-
(2004)
Genome Res
, vol.14
, pp. 1641-1653
-
-
Meyers, B.C.1
Tej, S.S.2
Vu, T.H.3
Haudenschild, C.D.4
Agrawal, V.5
Edberg, S.B.6
Ghazal, H.7
Decola, S.8
-
34
-
-
0032706622
-
Analysis of human transcriptomes
-
10.1038/70487 10581018
-
Velculescu VE Madden SL Zhang L Lash AE Yu J Rago C Lal A Wang CJ Beaudry GA Ciriello KM Cook BP Dufault MR Ferguson AT Gao Y He TC Hermeking H Hiraldo SK Hwang PM Lopez MA Luderer HF Mathews B Petroziello JM Polyak K Zawel L Zhang W Zhang X Zhou W Haluska FG Jen J Sukumar S Landes GM Riggins GJ Vogelstein B Kinzler KW Analysis of human transcriptomes Nat Genet 1999, 23:387-388. 10.1038/70487 10581018
-
(1999)
Nat Genet
, vol.23
, pp. 387-388
-
-
Velculescu, V.E.1
Madden, S.L.2
Zhang, L.3
Lash, A.E.4
Yu, J.5
Rago, C.6
Lal, A.7
Wang, C.J.8
Beaudry, G.A.9
Ciriello, K.M.10
Cook, B.P.11
Dufault, M.R.12
Ferguson, A.T.13
Gao, Y.14
He, T.C.15
Hermeking, H.16
Hiraldo, S.K.17
Hwang, P.M.18
Lopez, M.A.19
Luderer, H.F.20
Mathews, B.21
Petroziello, J.M.22
Polyak, K.23
Zawel, L.24
Zhang, W.25
Zhang, X.26
Zhou, W.27
Haluska, F.G.28
Jen, J.29
Sukumar, S.30
Landes, G.M.31
Riggins, G.J.32
Vogelstein, B.33
Kinzler, K.W.34
more..
-
36
-
-
12344302543
-
A comprehensive transcript index of the human genome generated using microarrays and computational approaches
-
545593 15461792 10.1186/gb-2004-5-10-r73
-
Schadt EE Edwards SW GuhaThakurta D Holder D Ying L Svetnik V Leonardson A Hart KW Russell A Li G Cavet G Castle J McDonagh P Kan Z Chen R Kasarskis A Margarint M Caceres RM Johnson JM Armour CD Garrett-Engele PW Tsinoremas NF Shoemaker DD A comprehensive transcript index of the human genome generated using microarrays and computational approaches Genome Biol 2004, 5:R73. 545593 15461792 10.1186/gb-2004-5-10-r73
-
(2004)
Genome Biol
, vol.5
-
-
Schadt, E.E.1
Edwards, S.W.2
GuhaThakurta, D.3
Holder, D.4
Ying, L.5
Svetnik, V.6
Leonardson, A.7
Hart, K.W.8
Russell, A.9
Li, G.10
Cavet, G.11
Castle, J.12
McDonagh, P.13
Kan, Z.14
Chen, R.15
Kasarskis, A.16
Margarint, M.17
Caceres, R.M.18
Johnson, J.M.19
Armour, C.D.20
Garrett-Engele, P.W.21
Tsinoremas, N.F.22
Shoemaker, D.D.23
more..
-
37
-
-
21844454212
-
Detecting novel low-abundant transcripts in Drosophila
-
1370778 15923377 10.1261/rna.7239605
-
Lee S Bao J Zhou G Shapiro J Xu J Shi RZ Lu X Clark T Johnson D Kim YC Wing C Tseng C Sun M Lin W Wang J Yang H Du W Wu CI Zhang X Wang SM Detecting novel low-abundant transcripts in Drosophila Rna 2005, 11:939-946. 1370778 15923377 10.1261/rna.7239605
-
(2005)
Rna
, vol.11
, pp. 939-946
-
-
Lee, S.1
Bao, J.2
Zhou, G.3
Shapiro, J.4
Xu, J.5
Shi, R.Z.6
Lu, X.7
Clark, T.8
Johnson, D.9
Kim, Y.C.10
Wing, C.11
Tseng, C.12
Sun, M.13
Lin, W.14
Wang, J.15
Yang, H.16
Du, W.17
Wu, C.I.18
Zhang, X.19
Wang, S.M.20
more..
-
38
-
-
0024212067
-
Rapid production of full-length cDNAs from rare transcripts: Amplification using a single gene-specific oligonucleotide primer
-
282649 2461560 10.1073/pnas.85.23.8998
-
Frohman MA Dush MK Martin GR Rapid production of full-length cDNAs from rare transcripts: Amplification using a single gene-specific oligonucleotide primer Proc Natl Acad Sci U S A 1988, 85:8998-9002. 282649 2461560 10.1073/pnas.85.23.8998
-
(1988)
Proc Natl Acad Sci U S A
, vol.85
, pp. 8998-9002
-
-
Frohman, M.A.1
Dush, M.K.2
Martin, G.R.3
-
39
-
-
2942617034
-
Has the yo-yo stopped? An assessment of human protein-coding gene number
-
10.1002/pmic.200300700 15174140
-
Southan C Has the yo-yo stopped? An assessment of human protein-coding gene number Proteomics 2004, 4:1712-1726. 10.1002/pmic.200300700 15174140
-
(2004)
Proteomics
, vol.4
, pp. 1712-1726
-
-
Southan, C.1
-
40
-
-
7244245762
-
Finishing the euchromatic sequence of the human genome
-
10.1038/nature03001 15496913
-
Consortium IHGS Finishing the euchromatic sequence of the human genome Nature 2004, 431:931-945. 10.1038/nature03001 15496913
-
(2004)
Nature
, vol.431
, pp. 931-945
-
-
Consortium, I.H.G.S.1
-
41
-
-
0017119107
-
Complexity and characterization of polyadenylated RNA in the mouse brain
-
10.1016/0092-8674(76)90195-1 986249
-
Bantle JA Hahn WE Complexity and characterization of polyadenylated RNA in the mouse brain Cell 1976, 8:139-150. 10.1016/0092-8674(76)90195-1 986249
-
(1976)
Cell
, vol.8
, pp. 139-150
-
-
Bantle, J.A.1
Hahn, W.E.2
-
42
-
-
0028328719
-
Transcription of individual genes in eukaryotic cells occurs randomly and infrequently
-
10.1038/icb.1994.26 8200693
-
Ross IL Browne CM Hume DA Transcription of individual genes in eukaryotic cells occurs randomly and infrequently Immunol Cell Biol 1994, 72:177-185. 10.1038/icb.1994.26 8200693
-
(1994)
Immunol Cell Biol
, vol.72
, pp. 177-185
-
-
Ross, I.L.1
Browne, C.M.2
Hume, D.A.3
-
43
-
-
3543007130
-
Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing
-
10.1038/nbt992 15247925
-
Meyers BC Vu TH Tej SS Ghazal H Matvienko M Agrawal V Ning J Haudenschild CD Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing Nat Biotechnol 2004, 22:1006-1011. 10.1038/nbt992 15247925
-
(2004)
Nat Biotechnol
, vol.22
, pp. 1006-1011
-
-
Meyers, B.C.1
Vu, T.H.2
Tej, S.S.3
Ghazal, H.4
Matvienko, M.5
Agrawal, V.6
Ning, J.7
Haudenschild, C.D.8
-
44
-
-
33746981831
-
Analysis of tag-position bias in MPSS technology
-
1533822 16603069 10.1186/1471-2164-7-77
-
Chen J Rattray M Analysis of tag-position bias in MPSS technology BMC Genomics 2006, 7:77. 1533822 16603069 10.1186/1471-2164-7-77
-
(2006)
BMC Genomics
, vol.7
, pp. 77
-
-
Chen, J.1
Rattray, M.2
-
47
-
-
0031955518
-
Base-calling of automated sequencer traces using phred. I. Accuracy assessment
-
9521921
-
Ewing B Hillier L Wendl MC Green P Base-calling of automated sequencer traces using phred. I. Accuracy assessment Genome Res 1998, 8:175-185. 9521921
-
(1998)
Genome Res
, vol.8
, pp. 175-185
-
-
Ewing, B.1
Hillier, L.2
Wendl, M.C.3
Green, P.4
-
48
-
-
14644411828
-
Evaluation of window cohabitation of DNA sequencing errors and lowest PHRED quality values
-
15688315
-
Prosdocimi F Peixoto FC Ortega JM Evaluation of window cohabitation of DNA sequencing errors and lowest PHRED quality values Genet Mol Res 2004, 3:483-492. 15688315
-
(2004)
Genet Mol Res
, vol.3
, pp. 483-492
-
-
Prosdocimi, F.1
Peixoto, F.C.2
Ortega, J.M.3
-
49
-
-
2442706422
-
An overview of Ensembl
-
479121 15078858 10.1101/gr.1860604
-
Birney E Andrews TD Bevan P Caccamo M Chen Y Clarke L Coates G Cuff J Curwen V Cutts T Down T Eyras E Fernandez-Suarez XM Gane P Gibbins B Gilbert J Hammond M Hotz HR Iyer V Jekosch K Kahari A Kasprzyk A Keefe D Keenan S Lehvaslaiho H McVicker G Melsopp C Meidl P Mongin E Pettett R Potter S Proctor G Rae M Searle S Slater G Smedley D Smith J Spooner W Stabenau A Stalker J Storey R Ureta-Vidal A Woodwark KC Cameron G Durbin R Cox A Hubbard T Clamp M An overview of Ensembl Genome Res 2004, 14:925-928. 479121 15078858 10.1101/gr.1860604
-
(2004)
Genome Res
, vol.14
, pp. 925-928
-
-
Birney, E.1
Andrews, T.D.2
Bevan, P.3
Caccamo, M.4
Chen, Y.5
Clarke, L.6
Coates, G.7
Cuff, J.8
Curwen, V.9
Cutts, T.10
Down, T.11
Eyras, E.12
Fernandez-Suarez, X.M.13
Gane, P.14
Gibbins, B.15
Gilbert, J.16
Hammond, M.17
Hotz, H.R.18
Iyer, V.19
Jekosch, K.20
Kahari, A.21
Kasprzyk, A.22
Keefe, D.23
Keenan, S.24
Lehvaslaiho, H.25
McVicker, G.26
Melsopp, C.27
Meidl, P.28
Mongin, E.29
Pettett, R.30
Potter, S.31
Proctor, G.32
Rae, M.33
Searle, S.34
Slater, G.35
Smedley, D.36
Smith, J.37
Spooner, W.38
Stabenau, A.39
Stalker, J.40
Storey, R.41
Ureta-Vidal, A.42
Woodwark, K.C.43
Cameron, G.44
Durbin, R.45
Cox, A.46
Hubbard, T.47
Clamp, M.48
more..
-
50
-
-
2442707676
-
The Ensembl automatic gene annotation system
-
479124 15123590 10.1101/gr.1858004
-
Curwen V Eyras E Andrews TD Clarke L Mongin E Searle SM Clamp M The Ensembl automatic gene annotation system Genome Res 2004, 14:942-950. 479124 15123590 10.1101/gr.1858004
-
(2004)
Genome Res
, vol.14
, pp. 942-950
-
-
Curwen, V.1
Eyras, E.2
Andrews, T.D.3
Clarke, L.4
Mongin, E.5
Searle, S.M.6
Clamp, M.7
-
51
-
-
0035895502
-
The human transcriptome map: Clustering of highly expressed genes in chromosomal domains
-
10.1126/science.1056794 11181992
-
Caron H van Schaik B van der Mee M Baas F Riggins G van Sluis P Hermus MC van Asperen R Boon K Voute PA Heisterkamp S van Kampen A Versteeg R The human transcriptome map: Clustering of highly expressed genes in chromosomal domains Science 2001, 291:1289-1292. 10.1126/science.1056794 11181992
-
(2001)
Science
, vol.291
, pp. 1289-1292
-
-
Caron, H.1
van Schaik, B.2
van der Mee, M.3
Baas, F.4
Riggins, G.5
van Sluis, P.6
Hermus, M.C.7
van Asperen, R.8
Boon, K.9
Voute, P.A.10
Heisterkamp, S.11
van Kampen, A.12
Versteeg, R.13
-
52
-
-
84871106113
-
-
The_R_Foundation
-
The_R_Foundation The R project http://www.r-project.org
-
The R Project
-
-
-
53
-
-
28644451737
-
Analysis of host response to bacterial infection using error model based gene expression microarray experiments
-
1072804 15800204 10.1093/nar/gni050
-
Stekel DJ Sarti D Trevino V Zhang L Salmon M Buckley CD Stevens M Pallen MJ Penn C Falciani F Analysis of host response to bacterial infection using error model based gene expression microarray experiments Nucleic Acids Res 2005, 33:e53. 1072804 15800204 10.1093/nar/gni050
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Stekel, D.J.1
Sarti, D.2
Trevino, V.3
Zhang, L.4
Salmon, M.5
Buckley, C.D.6
Stevens, M.7
Pallen, M.J.8
Penn, C.9
Falciani, F.10
|