-
1
-
-
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..
-
2
-
-
45549088326
-
The transcriptional landscape of the yeast genome defined by RNA sequencing
-
10.1126/science.1158441, 2951732, 18451266
-
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008, 320:1344-1349. 10.1126/science.1158441, 2951732, 18451266.
-
(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
-
3
-
-
24644490196
-
Elucidation of the small RNA component of the transcriptome
-
10.1126/science.1114112, 16141074
-
Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ. Elucidation of the small RNA component of the transcriptome. Science 2005, 309:1567-1569. 10.1126/science.1114112, 16141074.
-
(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
-
4
-
-
43449091567
-
Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome
-
10.1016/j.cub.2008.04.042, 2583427, 18472421
-
Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ. Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol 2008, 18:758-762. 10.1016/j.cub.2008.04.042, 2583427, 18472421.
-
(2008)
Curr Biol
, vol.18
, pp. 758-762
-
-
Addo-Quaye, C.1
Eshoo, T.W.2
Bartel, D.P.3
Axtell, M.J.4
-
5
-
-
49449118943
-
Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends
-
10.1038/nbt1417, 18542052
-
German MA, Pillay M, Jeong DH, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis LA, Nobuta K, German R, De Paoli E, Lu C, Schroth G, Meyers BC, Green PJ. Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 2008, 26:941-946. 10.1038/nbt1417, 18542052.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 941-946
-
-
German, M.A.1
Pillay, M.2
Jeong, D.H.3
Hetawal, A.4
Luo, S.5
Janardhanan, P.6
Kannan, V.7
Rymarquis, L.A.8
Nobuta, K.9
German, R.10
De Paoli, E.11
Lu, C.12
Schroth, G.13
Meyers, B.C.14
Green, P.J.15
-
6
-
-
44449142226
-
A link between RNA metabolism and silencing affecting Arabidopsis development
-
10.1016/j.devcel.2008.04.005, 18486559
-
Gregory BD, O'Malley RC, Lister R, Urich MA, Tonti-Filippini J, Chen H, Millar AH, Ecker JR. A link between RNA metabolism and silencing affecting Arabidopsis development. Dev Cell 2008, 14:854-866. 10.1016/j.devcel.2008.04.005, 18486559.
-
(2008)
Dev Cell
, vol.14
, pp. 854-866
-
-
Gregory, B.D.1
O'Malley, R.C.2
Lister, R.3
Urich, M.A.4
Tonti-Filippini, J.5
Chen, H.6
Millar, A.H.7
Ecker, J.R.8
-
7
-
-
77956306662
-
Genome-wide measurement of RNA secondary structure in yeast
-
10.1038/nature09322, 20811459
-
Kertesz M, Wan Y, Mazor E, Rinn JL, Nutter RC, Chang HY, Segal E. Genome-wide measurement of RNA secondary structure in yeast. Nature 2010, 467:103-107. 10.1038/nature09322, 20811459.
-
(2010)
Nature
, vol.467
, pp. 103-107
-
-
Kertesz, M.1
Wan, Y.2
Mazor, E.3
Rinn, J.L.4
Nutter, R.C.5
Chang, H.Y.6
Segal, E.7
-
8
-
-
78049445573
-
Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis
-
pii, 10.1371/journal.pgen.1001141, 2947979, 20941385
-
Zheng Q, Ryvkin P, Li F, Dragomir I, Valladares O, Yang J, Cao K, Wang LS, Gregory BD. Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. PLoS Genet 2010, 6:e1001141. pii, 10.1371/journal.pgen.1001141, 2947979, 20941385.
-
(2010)
PLoS Genet
, vol.6
-
-
Zheng, Q.1
Ryvkin, P.2
Li, F.3
Dragomir, I.4
Valladares, O.5
Yang, J.6
Cao, K.7
Wang, L.S.8
Gregory, B.D.9
-
9
-
-
78751659330
-
Nascent transcript sequencing visualizes transcription at nucleotide resolution
-
10.1038/nature09652, 21248844
-
Churchman LS, Weissman JS. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 2011, 469:368-373. 10.1038/nature09652, 21248844.
-
(2011)
Nature
, vol.469
, pp. 368-373
-
-
Churchman, L.S.1
Weissman, J.S.2
-
10
-
-
62549134121
-
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
-
10.1126/science.1168978, 2746483, 19213877
-
Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 2009, 324:218-223. 10.1126/science.1168978, 2746483, 19213877.
-
(2009)
Science
, vol.324
, pp. 218-223
-
-
Ingolia, N.T.1
Ghaemmaghami, S.2
Newman, J.R.3
Weissman, J.S.4
-
11
-
-
34547633677
-
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
-
10.1038/nmeth1068, 17558387
-
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 2007, 4:651-657. 10.1038/nmeth1068, 17558387.
-
(2007)
Nat Methods
, vol.4
, pp. 651-657
-
-
Robertson, G.1
Hirst, M.2
Bainbridge, M.3
Bilenky, M.4
Zhao, Y.5
Zeng, T.6
Euskirchen, G.7
Bernier, B.8
Varhol, R.9
Delaney, A.10
Thiessen, N.11
Griffith, O.L.12
He, A.13
Marra, M.14
Snyder, M.15
Jones, S.16
-
12
-
-
40749109894
-
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
-
10.1038/nature06745, 2377394, 18278030
-
Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 2008, 452:215-219. 10.1038/nature06745, 2377394, 18278030.
-
(2008)
Nature
, vol.452
, pp. 215-219
-
-
Cokus, S.J.1
Feng, S.2
Zhang, X.3
Chen, Z.4
Merriman, B.5
Haudenschild, C.D.6
Pradhan, S.7
Nelson, S.F.8
Pellegrini, M.9
Jacobsen, S.E.10
-
13
-
-
55549089660
-
Accurate whole human genome sequencing using reversible terminator chemistry
-
10.1038/nature07517, 2581791, 18987734
-
Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456:53-59. 10.1038/nature07517, 2581791, 18987734.
-
(2008)
Nature
, vol.456
, pp. 53-59
-
-
Bentley, D.R.1
Balasubramanian, S.2
Swerdlow, H.P.3
Smith, G.P.4
Milton, J.5
Brown, C.G.6
Hall, K.P.7
Evers, D.J.8
Barnes, C.L.9
Bignell, H.R.10
Boutell, J.M.11
Bryant, J.12
Carter, R.J.13
Keira Cheetham, R.14
Cox, A.J.15
Ellis, D.J.16
Flatbush, M.R.17
Gormley, N.A.18
Humphray, S.J.19
Irving, L.J.20
Karbelashvili, M.S.21
Kirk, S.M.22
Li, H.23
Liu, X.24
Maisinger, K.S.25
Murray, L.J.26
Obradovic, B.27
Ost, T.28
Parkinson, M.L.29
Pratt, M.R.30
more..
-
14
-
-
55549097849
-
The diploid genome sequence of an Asian individual
-
10.1038/nature07484, 2716080, 18987735
-
Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Zhang J, Guo Y, Feng B, Li H, Lu Y, Fang X, Liang H, Du Z, Li D, Zhao Y, Hu Y, Yang Z, Zheng H, Hellmann I, Inouye M, Pool J, Yi X, Zhao J, Duan J, Zhou Y, Qin J, et al. The diploid genome sequence of an Asian individual. Nature 2008, 456:60-65. 10.1038/nature07484, 2716080, 18987735.
-
(2008)
Nature
, vol.456
, pp. 60-65
-
-
Wang, J.1
Wang, W.2
Li, R.3
Li, Y.4
Tian, G.5
Goodman, L.6
Fan, W.7
Zhang, J.8
Li, J.9
Zhang, J.10
Guo, Y.11
Feng, B.12
Li, H.13
Lu, Y.14
Fang, X.15
Liang, H.16
Du, Z.17
Li, D.18
Zhao, Y.19
Hu, Y.20
Yang, Z.21
Zheng, H.22
Hellmann, I.23
Inouye, M.24
Pool, J.25
Yi, X.26
Zhao, J.27
Duan, J.28
Zhou, Y.29
Qin, J.30
more..
-
15
-
-
42249087308
-
The complete genome of an individual by massively parallel DNA sequencing
-
10.1038/nature06884, 18421352
-
Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM. The complete genome of an individual by massively parallel DNA sequencing. Nature 2008, 452:872-876. 10.1038/nature06884, 18421352.
-
(2008)
Nature
, vol.452
, pp. 872-876
-
-
Wheeler, D.A.1
Srinivasan, M.2
Egholm, M.3
Shen, Y.4
Chen, L.5
McGuire, A.6
He, W.7
Chen, Y.J.8
Makhijani, V.9
Roth, G.T.10
Gomes, X.11
Tartaro, K.12
Niazi, F.13
Turcotte, C.L.14
Irzyk, G.P.15
Lupski, J.R.16
Chinault, C.17
Song, X.Z.18
Liu, Y.19
Yuan, Y.20
Nazareth, L.21
Qin, X.22
Muzny, D.M.23
Margulies, M.24
Weinstock, G.M.25
Gibbs, R.A.26
Rothberg, J.M.27
more..
-
16
-
-
9444269217
-
A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization
-
10.1186/1471-2164-4-38, 239980, 14499002
-
Talla E, Tekaia F, Brino L, Dujon B. A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization. BMC Genomics 2003, 4:38. 10.1186/1471-2164-4-38, 239980, 14499002.
-
(2003)
BMC Genomics
, vol.4
, pp. 38
-
-
Talla, E.1
Tekaia, F.2
Brino, L.3
Dujon, B.4
-
17
-
-
9944226811
-
Sensitivity of microarray oligonucleotide probes: variability and effect of base composition
-
Binder H, Kirsten T, Loeffler M, Stadler PF. Sensitivity of microarray oligonucleotide probes: variability and effect of base composition. J Phys Chem B 2004, 108:18003-18014.
-
(2004)
J Phys Chem B
, vol.108
, pp. 18003-18014
-
-
Binder, H.1
Kirsten, T.2
Loeffler, M.3
Stadler, P.F.4
-
18
-
-
7944220031
-
Determinants of sensitivity and specificity in spotted DNA microarrays with unmodified oligonucleotides
-
10.1266/ggs.79.189, 15514438
-
Kucho K, Yoneda H, Harada M, Ishiura M. Determinants of sensitivity and specificity in spotted DNA microarrays with unmodified oligonucleotides. Genes Genet Syst 2004, 79:189-197. 10.1266/ggs.79.189, 15514438.
-
(2004)
Genes Genet Syst
, vol.79
, pp. 189-197
-
-
Kucho, K.1
Yoneda, H.2
Harada, M.3
Ishiura, M.4
-
19
-
-
34249730556
-
Assessing the need for sequence-based normalization in tiling microarray experiments
-
10.1093/bioinformatics/btm052, 17387113
-
Royce TE, Rozowsky JS, Gerstein MB. Assessing the need for sequence-based normalization in tiling microarray experiments. Bioinformatics 2007, 23:988-997. 10.1093/bioinformatics/btm052, 17387113.
-
(2007)
Bioinformatics
, vol.23
, pp. 988-997
-
-
Royce, T.E.1
Rozowsky, J.S.2
Gerstein, M.B.3
-
20
-
-
55449117619
-
Removal of AU bias from microarray mRNA expression data enhances computational identification of active microRNAs
-
10.1371/journal.pcbi.1000189, 2533120, 18833292
-
Elkon R, Agami R. Removal of AU bias from microarray mRNA expression data enhances computational identification of active microRNAs. PLoS Comput Biol 2008, 4:e1000189. 10.1371/journal.pcbi.1000189, 2533120, 18833292.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Elkon, R.1
Agami, R.2
-
21
-
-
0142121516
-
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
-
10.1093/biostatistics/4.2.249, 12925520
-
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4:249-264. 10.1093/biostatistics/4.2.249, 12925520.
-
(2003)
Biostatistics
, vol.4
, pp. 249-264
-
-
Irizarry, R.A.1
Hobbs, B.2
Collin, F.3
Beazer-Barclay, Y.D.4
Antonellis, K.J.5
Scherf, U.6
Speed, T.P.7
-
22
-
-
77953553548
-
Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays
-
10.1186/1471-2164-11-383, 20565764
-
Agarwal A, Koppstein D, Rozowsky J, Sboner A, Habegger L, Hillier LW, Sasidharan R, Reinke V, Waterston RH, Gerstein M. Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays. BMC Genomics 2010, 11:383. 10.1186/1471-2164-11-383, 20565764.
-
(2010)
BMC Genomics
, vol.11
, pp. 383
-
-
Agarwal, A.1
Koppstein, D.2
Rozowsky, J.3
Sboner, A.4
Habegger, L.5
Hillier, L.W.6
Sasidharan, R.7
Reinke, V.8
Waterston, R.H.9
Gerstein, M.10
-
23
-
-
77951777930
-
A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling
-
10.1186/1471-2164-11-282, 2877694, 20444259
-
Bradford JR, Hey Y, Yates T, Li Y, Pepper SD, Miller CJ. A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling. BMC Genomics 2010, 11:282. 10.1186/1471-2164-11-282, 2877694, 20444259.
-
(2010)
BMC Genomics
, vol.11
, pp. 282
-
-
Bradford, J.R.1
Hey, Y.2
Yates, T.3
Li, Y.4
Pepper, S.D.5
Miller, C.J.6
-
24
-
-
38049176566
-
A comparison of microarray and MPSS technology platforms for expression analysis of Arabidopsis
-
10.1186/1471-2164-8-414, 2190774, 17997849
-
Chen J, Agrawal V, Rattray M, West MA, St Clair DA, Michelmore RW, Coughlan SJ, Meyers BC. A comparison of microarray and MPSS technology platforms for expression analysis of Arabidopsis. BMC Genomics 2007, 8:414. 10.1186/1471-2164-8-414, 2190774, 17997849.
-
(2007)
BMC Genomics
, vol.8
, pp. 414
-
-
Chen, J.1
Agrawal, V.2
Rattray, M.3
West, M.A.4
St Clair, D.A.5
Michelmore, R.W.6
Coughlan, S.J.7
Meyers, B.C.8
-
25
-
-
2942527215
-
A comparison of global gene expression measurement technologies in Arabidopsis thaliana
-
10.1002/cfg.397, 2447440, 18629150
-
Coughlan SJ, Agrawal V, Meyers B. A comparison of global gene expression measurement technologies in Arabidopsis thaliana. Comp Funct Genomics 2004, 5:245-252. 10.1002/cfg.397, 2447440, 18629150.
-
(2004)
Comp Funct Genomics
, vol.5
, pp. 245-252
-
-
Coughlan, S.J.1
Agrawal, V.2
Meyers, B.3
-
26
-
-
0034283071
-
Direct comparison of GeneChip and SAGE on the quantitative accuracy in transcript profiling analysis
-
10.1006/geno.2000.6284, 10964511
-
Ishii M, Hashimoto S, Tsutsumi S, Wada Y, Matsushima K, Kodama T, Aburatani H. Direct comparison of GeneChip and SAGE on the quantitative accuracy in transcript profiling analysis. Genomics 2000, 68:136-143. 10.1006/geno.2000.6284, 10964511.
-
(2000)
Genomics
, vol.68
, pp. 136-143
-
-
Ishii, M.1
Hashimoto, S.2
Tsutsumi, S.3
Wada, Y.4
Matsushima, K.5
Kodama, T.6
Aburatani, H.7
-
27
-
-
34347241740
-
Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates
-
10.1186/1471-2164-8-153, 1899500, 17555589
-
Liu F, Jenssen TK, Trimarchi J, Punzo C, Cepko CL, Ohno-Machado L, Hovig E, Kuo WP. Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates. BMC Genomics 2007, 8:153. 10.1186/1471-2164-8-153, 1899500, 17555589.
-
(2007)
BMC Genomics
, vol.8
, pp. 153
-
-
Liu, F.1
Jenssen, T.K.2
Trimarchi, J.3
Punzo, C.4
Cepko, C.L.5
Ohno-Machado, L.6
Hovig, E.7
Kuo, W.P.8
-
28
-
-
57149085481
-
Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms
-
2588528, 18927111
-
'tHoen PA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, de Menezes RX, Boer JM, van Ommen GJ, den Dunnen JT. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res 2008, 36:e141. 2588528, 18927111.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
'tHoen, P.A.1
Ariyurek, Y.2
Thygesen, H.H.3
Vreugdenhil, E.4
Vossen, R.H.5
de Menezes, R.X.6
Boer, J.M.7
van Ommen, G.J.8
den Dunnen, J.T.9
-
29
-
-
0034536614
-
Analyzing high-density oligonucleotide gene expression array data
-
10.1002/1097-4644(20010201)80:2<192::AID-JCB50>3.0.CO;2-W, 11074587
-
Schadt EE, Li C, Su C, Wong WH. Analyzing high-density oligonucleotide gene expression array data. J Cell Biochem 2000, 80:192-202. 10.1002/1097-4644(20010201)80:2<192::AID-JCB50>3.0.CO;2-W, 11074587.
-
(2000)
J Cell Biochem
, vol.80
, pp. 192-202
-
-
Schadt, E.E.1
Li, C.2
Su, C.3
Wong, W.H.4
-
30
-
-
0036161083
-
Correcting for signal saturation errors in the analysis of microarray data
-
334, 336
-
Hsiao LL, Jensen RV, Yoshida T, Clark KE, Blumenstock JE, Gullans SR. Correcting for signal saturation errors in the analysis of microarray data. Biotechniques 2002, 32:330-332. 334, 336.
-
(2002)
Biotechniques
, vol.32
, pp. 330-332
-
-
Hsiao, L.L.1
Jensen, R.V.2
Yoshida, T.3
Clark, K.E.4
Blumenstock, J.E.5
Gullans, S.R.6
-
31
-
-
33645326509
-
Comparison of Affymetrix GeneChip expression measures
-
10.1093/bioinformatics/btk046, 16410320
-
Irizarry RA, Wu Z, Jaffee HA. Comparison of Affymetrix GeneChip expression measures. Bioinformatics 2006, 22:789-794. 10.1093/bioinformatics/btk046, 16410320.
-
(2006)
Bioinformatics
, vol.22
, pp. 789-794
-
-
Irizarry, R.A.1
Wu, Z.2
Jaffee, H.A.3
-
32
-
-
9144268360
-
Empirical evaluation of data transformations and ranking statistics for microarray analysis
-
10.1093/nar/gkh866, 524279, 15479783
-
Qin LX, Kerr KF. Empirical evaluation of data transformations and ranking statistics for microarray analysis. Nucleic Acids Res 2004, 32:5471-5479. 10.1093/nar/gkh866, 524279, 15479783.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 5471-5479
-
-
Qin, L.X.1
Kerr, K.F.2
-
33
-
-
35748949257
-
A comparison of background correction methods for two-colour microarrays
-
10.1093/bioinformatics/btm412, 17720982
-
Ritchie ME, Silver J, Oshlack A, Holmes M, Diyagama D, Holloway A, Smyth GK. A comparison of background correction methods for two-colour microarrays. Bioinformatics 2007, 23:2700-2707. 10.1093/bioinformatics/btm412, 17720982.
-
(2007)
Bioinformatics
, vol.23
, pp. 2700-2707
-
-
Ritchie, M.E.1
Silver, J.2
Oshlack, A.3
Holmes, M.4
Diyagama, D.5
Holloway, A.6
Smyth, G.K.7
-
34
-
-
0035863097
-
RNA interference is mediated by 21- and 22-nucleotide RNAs
-
10.1101/gad.862301, 312613, 11157775
-
Elbashir SM, Lendeckel W, Tuschl T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev 2001, 15:188-200. 10.1101/gad.862301, 312613, 11157775.
-
(2001)
Genes Dev
, vol.15
, pp. 188-200
-
-
Elbashir, S.M.1
Lendeckel, W.2
Tuschl, T.3
-
35
-
-
0035955374
-
Identification of novel genes coding for small expressed RNAs
-
10.1126/science.1064921, 11679670
-
Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T. Identification of novel genes coding for small expressed RNAs. Science 2001, 294:853-858. 10.1126/science.1064921, 11679670.
-
(2001)
Science
, vol.294
, pp. 853-858
-
-
Lagos-Quintana, M.1
Rauhut, R.2
Lendeckel, W.3
Tuschl, T.4
-
36
-
-
0035955361
-
An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans
-
10.1126/science.1065062, 11679671
-
Lau NC, Lim LP, Weinstein EG, Bartel DP. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 2001, 294:858-862. 10.1126/science.1065062, 11679671.
-
(2001)
Science
, vol.294
, pp. 858-862
-
-
Lau, N.C.1
Lim, L.P.2
Weinstein, E.G.3
Bartel, D.P.4
-
37
-
-
0035955366
-
An extensive class of small RNAs in Caenorhabditis elegans
-
10.1126/science.1065329, 11679672
-
Lee RC, Ambros V. An extensive class of small RNAs in Caenorhabditis elegans. Science 2001, 294:862-864. 10.1126/science.1065329, 11679672.
-
(2001)
Science
, vol.294
, pp. 862-864
-
-
Lee, R.C.1
Ambros, V.2
-
38
-
-
0036645146
-
MicroRNAs in plants
-
10.1101/gad.1004402, 186362, 12101121
-
Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP. MicroRNAs in plants. Genes Dev 2002, 16:1616-1626. 10.1101/gad.1004402, 186362, 12101121.
-
(2002)
Genes Dev
, vol.16
, pp. 1616-1626
-
-
Reinhart, B.J.1
Weinstein, E.G.2
Rhoades, M.W.3
Bartel, B.4
Bartel, D.P.5
-
39
-
-
0035984059
-
Endogenous and silencing-associated small RNAs in plants
-
10.1105/tpc.003210, 150710, 12119378
-
Llave C, Kasschau KD, Rector MA, Carrington JC. Endogenous and silencing-associated small RNAs in plants. Plant Cell 2002, 14:1605-1619. 10.1105/tpc.003210, 150710, 12119378.
-
(2002)
Plant Cell
, vol.14
, pp. 1605-1619
-
-
Llave, C.1
Kasschau, K.D.2
Rector, M.A.3
Carrington, J.C.4
-
40
-
-
0027751663
-
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
-
10.1016/0092-8674(93)90529-Y, 8252621
-
Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993, 75:843-854. 10.1016/0092-8674(93)90529-Y, 8252621.
-
(1993)
Cell
, vol.75
, pp. 843-854
-
-
Lee, R.C.1
Feinbaum, R.L.2
Ambros, V.3
-
41
-
-
0037144546
-
A microRNA in a multiple-turnover RNAi enzyme complex
-
10.1126/science.1073827, 12154197
-
Hutvagner G, Zamore PD. A microRNA in a multiple-turnover RNAi enzyme complex. Science 2002, 297:2056-2060. 10.1126/science.1073827, 12154197.
-
(2002)
Science
, vol.297
, pp. 2056-2060
-
-
Hutvagner, G.1
Zamore, P.D.2
-
42
-
-
0037144457
-
Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA
-
10.1126/science.1076311, 12242443
-
Llave C, Xie Z, Kasschau KD, Carrington JC. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 2002, 297:2053-2056. 10.1126/science.1076311, 12242443.
-
(2002)
Science
, vol.297
, pp. 2053-2056
-
-
Llave, C.1
Xie, Z.2
Kasschau, K.D.3
Carrington, J.C.4
-
43
-
-
0027730383
-
Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans
-
10.1016/0092-8674(93)90530-4, 8252622
-
Wightman B, Ha I, Ruvkun G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 1993, 75:855-862. 10.1016/0092-8674(93)90530-4, 8252622.
-
(1993)
Cell
, vol.75
, pp. 855-862
-
-
Wightman, B.1
Ha, I.2
Ruvkun, G.3
-
44
-
-
0032545933
-
Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans
-
10.1038/35888, 9486653
-
Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998, 391:806-811. 10.1038/35888, 9486653.
-
(1998)
Nature
, vol.391
, pp. 806-811
-
-
Fire, A.1
Xu, S.2
Montgomery, M.K.3
Kostas, S.A.4
Driver, S.E.5
Mello, C.C.6
-
45
-
-
0033615491
-
A species of small antisense RNA in posttranscriptional gene silencing in plants
-
10.1126/science.286.5441.950, 10542148
-
Hamilton AJ, Baulcombe DC. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 1999, 286:950-952. 10.1126/science.286.5441.950, 10542148.
-
(1999)
Science
, vol.286
, pp. 950-952
-
-
Hamilton, A.J.1
Baulcombe, D.C.2
-
46
-
-
0034737298
-
RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals
-
10.1016/S0092-8674(00)80620-0, 10778853
-
Zamore PD, Tuschl T, Sharp PA, Bartel DP. RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 2000, 101:25-33. 10.1016/S0092-8674(00)80620-0, 10778853.
-
(2000)
Cell
, vol.101
, pp. 25-33
-
-
Zamore, P.D.1
Tuschl, T.2
Sharp, P.A.3
Bartel, D.P.4
-
47
-
-
31044452870
-
Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways
-
10.1016/j.cell.2005.11.036, 16439208
-
Duchaine TF, Wohlschlegel JA, Kennedy S, Bei Y, Conte D, Pang K, Brownell DR, Harding S, Mitani S, Ruvkun G, Yates JR, Mello C. Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways. Cell 2006, 124:343-354. 10.1016/j.cell.2005.11.036, 16439208.
-
(2006)
Cell
, vol.124
, pp. 343-354
-
-
Duchaine, T.F.1
Wohlschlegel, J.A.2
Kennedy, S.3
Bei, Y.4
Conte, D.5
Pang, K.6
Brownell, D.R.7
Harding, S.8
Mitani, S.9
Ruvkun, G.10
Yates, J.R.11
Mello, C.12
-
48
-
-
33645464445
-
Interacting endogenous and exogenous RNAi pathways in Caenorhabditis elegans
-
10.1261/rna.2231506, 1421084, 16489184
-
Lee RC, Hammell CM, Ambros V. Interacting endogenous and exogenous RNAi pathways in Caenorhabditis elegans. RNA 2006, 12:589-597. 10.1261/rna.2231506, 1421084, 16489184.
-
(2006)
RNA
, vol.12
, pp. 589-597
-
-
Lee, R.C.1
Hammell, C.M.2
Ambros, V.3
-
49
-
-
0035900651
-
On the role of RNA amplification in dsRNA-triggered gene silencing
-
10.1016/S0092-8674(01)00576-1, 11719187
-
Sijen T, Fleenor J, Simmer F, Thijssen KL, Parrish S, Timmons L, Plasterk RH, Fire A. On the role of RNA amplification in dsRNA-triggered gene silencing. Cell 2001, 107:465-476. 10.1016/S0092-8674(01)00576-1, 11719187.
-
(2001)
Cell
, vol.107
, pp. 465-476
-
-
Sijen, T.1
Fleenor, J.2
Simmer, F.3
Thijssen, K.L.4
Parrish, S.5
Timmons, L.6
Plasterk, R.H.7
Fire, A.8
-
50
-
-
0035999373
-
Spreading of RNA targeting and DNA methylation in RNA silencing requires transcription of the target gene and a putative RNA-dependent RNA polymerase
-
10.1105/tpc.010480, 150687, 11971140
-
Vaistij FE, Jones L, Baulcombe DC. Spreading of RNA targeting and DNA methylation in RNA silencing requires transcription of the target gene and a putative RNA-dependent RNA polymerase. Plant Cell 2002, 14:857-867. 10.1105/tpc.010480, 150687, 11971140.
-
(2002)
Plant Cell
, vol.14
, pp. 857-867
-
-
Vaistij, F.E.1
Jones, L.2
Baulcombe, D.C.3
-
51
-
-
33846527241
-
Distinct populations of primary and secondary effectors during RNAi in C. elegans
-
10.1126/science.1132839, 17124291
-
Pak J, Fire A. Distinct populations of primary and secondary effectors during RNAi in C. elegans. Science 2007, 315:241-244. 10.1126/science.1132839, 17124291.
-
(2007)
Science
, vol.315
, pp. 241-244
-
-
Pak, J.1
Fire, A.2
-
52
-
-
33846524902
-
Secondary siRNAs result from unprimed RNA synthesis and form a distinct class
-
10.1126/science.1136699, 17158288
-
Sijen T, Steiner FA, Thijssen KL, Plasterk RH. Secondary siRNAs result from unprimed RNA synthesis and form a distinct class. Science 2007, 315:244-247. 10.1126/science.1136699, 17158288.
-
(2007)
Science
, vol.315
, pp. 244-247
-
-
Sijen, T.1
Steiner, F.A.2
Thijssen, K.L.3
Plasterk, R.H.4
-
53
-
-
0034596989
-
Transcriptional silencing and promoter methylation triggered by double-stranded RNA
-
10.1093/emboj/19.19.5194, 302106, 11013221
-
Mette MF, Aufsatz W, van der Winden J, Matzke MA, Matzke AJ. Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J 2000, 19:5194-5201. 10.1093/emboj/19.19.5194, 302106, 11013221.
-
(2000)
EMBO J
, vol.19
, pp. 5194-5201
-
-
Mette, M.F.1
Aufsatz, W.2
van der Winden, J.3
Matzke, M.A.4
Matzke, A.J.5
-
54
-
-
0037009520
-
Two classes of short interfering RNA in RNA silencing
-
10.1093/emboj/cdf464, 125409, 12198169
-
Hamilton A, Voinnet O, Chappell L, Baulcombe D. Two classes of short interfering RNA in RNA silencing. EMBO J 2002, 21:4671-4679. 10.1093/emboj/cdf464, 125409, 12198169.
-
(2002)
EMBO J
, vol.21
, pp. 4671-4679
-
-
Hamilton, A.1
Voinnet, O.2
Chappell, L.3
Baulcombe, D.4
-
55
-
-
0037072660
-
Small RNAs correspond to centromere heterochromatic repeats
-
10.1126/science.1077183, 12193644
-
Reinhart BJ, Bartel DP. Small RNAs correspond to centromere heterochromatic repeats. Science 2002, 297:1831. 10.1126/science.1077183, 12193644.
-
(2002)
Science
, vol.297
, pp. 1831
-
-
Reinhart, B.J.1
Bartel, D.P.2
-
56
-
-
29244490062
-
Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis
-
10.1016/j.cell.2005.11.035, 16377568
-
Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 2005, 123:1279-1291. 10.1016/j.cell.2005.11.035, 16377568.
-
(2005)
Cell
, vol.123
, pp. 1279-1291
-
-
Borsani, O.1
Zhu, J.2
Verslues, P.E.3
Sunkar, R.4
Zhu, J.K.5
-
57
-
-
47249107415
-
Processing of naturally occurring sense/antisense transcripts of the vertebrate Slc34a gene into short RNAs
-
10.1152/physiolgenomics.00004.2008, 18413783
-
Carlile M, Nalbant P, Preston-Fayers K, McHaffie GS, Werner A. Processing of naturally occurring sense/antisense transcripts of the vertebrate Slc34a gene into short RNAs. Physiol Genomics 2008, 34:95-100. 10.1152/physiolgenomics.00004.2008, 18413783.
-
(2008)
Physiol Genomics
, vol.34
, pp. 95-100
-
-
Carlile, M.1
Nalbant, P.2
Preston-Fayers, K.3
McHaffie, G.S.4
Werner, A.5
-
58
-
-
44349104241
-
An endogenous small interfering RNA pathway in Drosophila
-
10.1038/nature07007, 2895258, 18463631
-
Czech B, Malone CD, Zhou R, Stark A, Schlingeheyde C, Dus M, Perrimon N, Kellis M, Wohlschlegel JA, Sachidanandam R, Hannon GJ, Brennecke J. An endogenous small interfering RNA pathway in Drosophila. Nature 2008, 453:798-802. 10.1038/nature07007, 2895258, 18463631.
-
(2008)
Nature
, vol.453
, pp. 798-802
-
-
Czech, B.1
Malone, C.D.2
Zhou, R.3
Stark, A.4
Schlingeheyde, C.5
Dus, M.6
Perrimon, N.7
Kellis, M.8
Wohlschlegel, J.A.9
Sachidanandam, R.10
Hannon, G.J.11
Brennecke, J.12
-
59
-
-
44349130233
-
Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes
-
10.1038/nature06908, 18404146
-
Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S, Obata Y, Chiba H, Kohara Y, Kono T, Nakano T, Surani MA, Sakaki Y, Sasaki H. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 2008, 453:539-543. 10.1038/nature06908, 18404146.
-
(2008)
Nature
, vol.453
, pp. 539-543
-
-
Watanabe, T.1
Totoki, Y.2
Toyoda, A.3
Kaneda, M.4
Kuramochi-Miyagawa, S.5
Obata, Y.6
Chiba, H.7
Kohara, Y.8
Kono, T.9
Nakano, T.10
Surani, M.A.11
Sakaki, Y.12
Sasaki, H.13
-
60
-
-
44349101881
-
Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster
-
10.1038/nsmb0908-998c, 18769470
-
Okamura K, Balla S, Martin R, Liu N, Lai EC. Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster. Nat Struct Mol Biol 2008, 15:998. 10.1038/nsmb0908-998c, 18769470.
-
(2008)
Nat Struct Mol Biol
, vol.15
, pp. 998
-
-
Okamura, K.1
Balla, S.2
Martin, R.3
Liu, N.4
Lai, E.C.5
-
61
-
-
4644286235
-
SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis
-
10.1101/gad.1231804, 522987, 15466488
-
Peragine A, Yoshikawa M, Wu G, Albrecht HL, Poethig RS. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev 2004, 18:2368-2379. 10.1101/gad.1231804, 522987, 15466488.
-
(2004)
Genes Dev
, vol.18
, pp. 2368-2379
-
-
Peragine, A.1
Yoshikawa, M.2
Wu, G.3
Albrecht, H.L.4
Poethig, R.S.5
-
62
-
-
4944225347
-
Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs
-
10.1016/j.molcel.2004.09.028, 15469823
-
Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory AC, Hilbert JL, Bartel DP, Crete P. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell 2004, 16:69-79. 10.1016/j.molcel.2004.09.028, 15469823.
-
(2004)
Mol Cell
, vol.16
, pp. 69-79
-
-
Vazquez, F.1
Vaucheret, H.2
Rajagopalan, R.3
Lepers, C.4
Gasciolli, V.5
Mallory, A.C.6
Hilbert, J.L.7
Bartel, D.P.8
Crete, P.9
-
63
-
-
24944491201
-
A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis
-
10.1101/gad.1352605, 1221887,1221887, 16131612
-
Yoshikawa M, Peragine A, Park MY, Poethig RS. A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev 2005, 19:2164-2175. 10.1101/gad.1352605, 1221887,1221887, 16131612.
-
(2005)
Genes Dev
, vol.19
, pp. 2164-2175
-
-
Yoshikawa, M.1
Peragine, A.2
Park, M.Y.3
Poethig, R.S.4
-
64
-
-
17444430392
-
MicroRNA-directed phasing during trans-acting siRNA biogenesis in plants
-
10.1016/j.cell.2005.04.004, 15851028
-
Allen E, Xie Z, Gustafson AM, Carrington JC. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 2005, 121:207-221. 10.1016/j.cell.2005.04.004, 15851028.
-
(2005)
Cell
, vol.121
, pp. 207-221
-
-
Allen, E.1
Xie, Z.2
Gustafson, A.M.3
Carrington, J.C.4
-
65
-
-
33745402414
-
A novel class of small RNAs bind to MILI protein in mouse testes
-
Aravin A, Gaidatzis D, Pfeffer S, Lagos-Quintana M, Landgraf P, Iovino N, Morris P, Brownstein MJ, Kuramochi-Miyagawa S, Nakano T, Chien M, Russo JJ, Ju J, Sheridan R, Sander C, Zavolan M, Tuschl T. A novel class of small RNAs bind to MILI protein in mouse testes. Nature 2006, 442:203-207.
-
(2006)
Nature
, vol.442
, pp. 203-207
-
-
Aravin, A.1
Gaidatzis, D.2
Pfeffer, S.3
Lagos-Quintana, M.4
Landgraf, P.5
Iovino, N.6
Morris, P.7
Brownstein, M.J.8
Kuramochi-Miyagawa, S.9
Nakano, T.10
Chien, M.11
Russo, J.J.12
Ju, J.13
Sheridan, R.14
Sander, C.15
Zavolan, M.16
Tuschl, T.17
-
66
-
-
33745336617
-
A germline-specific class of small RNAs binds mammalian Piwi proteins
-
Girard A, Sachidanandam R, Hannon GJ, Carmell MA. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 2006, 442:199-202.
-
(2006)
Nature
, vol.442
, pp. 199-202
-
-
Girard, A.1
Sachidanandam, R.2
Hannon, G.J.3
Carmell, M.A.4
-
67
-
-
33745621037
-
A novel class of small RNAs in mouse spermatogenic cells
-
10.1101/gad.1434406, 1522066, 16766680
-
Grivna ST, Beyret E, Wang Z, Lin H. A novel class of small RNAs in mouse spermatogenic cells. Genes Dev 2006, 20:1709-1714. 10.1101/gad.1434406, 1522066, 16766680.
-
(2006)
Genes Dev
, vol.20
, pp. 1709-1714
-
-
Grivna, S.T.1
Beyret, E.2
Wang, Z.3
Lin, H.4
-
68
-
-
33746527679
-
Characterization of the piRNA complex from rat testes
-
10.1126/science.1130164, 16778019
-
Lau NC, Seto AG, Kim J, Kuramochi-Miyagawa S, Nakano T, Bartel DP, Kingston RE. Characterization of the piRNA complex from rat testes. Science 2006, 313:363-367. 10.1126/science.1130164, 16778019.
-
(2006)
Science
, vol.313
, pp. 363-367
-
-
Lau, N.C.1
Seto, A.G.2
Kim, J.3
Kuramochi-Miyagawa, S.4
Nakano, T.5
Bartel, D.P.6
Kingston, R.E.7
-
69
-
-
33745599586
-
Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes
-
10.1101/gad.1425706, 1522070, 16766679
-
Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N, Imai H. Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev 2006, 20:1732-1743. 10.1101/gad.1425706, 1522070, 16766679.
-
(2006)
Genes Dev
, vol.20
, pp. 1732-1743
-
-
Watanabe, T.1
Takeda, A.2
Tsukiyama, T.3
Mise, K.4
Okuno, T.5
Sasaki, H.6
Minami, N.7
Imai, H.8
-
70
-
-
33747369856
-
Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome
-
10.1101/gad.1454806, 1553205, 16882972
-
Saito K, Nishida KM, Mori T, Kawamura Y, Miyoshi K, Nagami T, Siomi H, Siomi MC. Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome. Genes Dev 2006, 20:2214-2222. 10.1101/gad.1454806, 1553205, 16882972.
-
(2006)
Genes Dev
, vol.20
, pp. 2214-2222
-
-
Saito, K.1
Nishida, K.M.2
Mori, T.3
Kawamura, Y.4
Miyoshi, K.5
Nagami, T.6
Siomi, H.7
Siomi, M.C.8
-
71
-
-
33746502166
-
A distinct small RNA pathway silences selfish genetic elements in the germline
-
10.1126/science.1129333, 16809489
-
Vagin VV, Sigova A, Li C, Seitz H, Gvozdev V, Zamore PD. A distinct small RNA pathway silences selfish genetic elements in the germline. Science 2006, 313:320-324. 10.1126/science.1129333, 16809489.
-
(2006)
Science
, vol.313
, pp. 320-324
-
-
Vagin, V.V.1
Sigova, A.2
Li, C.3
Seitz, H.4
Gvozdev, V.5
Zamore, P.D.6
-
72
-
-
72749089855
-
A novel class of small RNAs: tRNA-derived RNA fragments (tRFs)
-
10.1101/gad.1837609, 2779758, 19933153
-
Lee YS, Shibata Y, Malhotra A, Dutta A. A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev 2009, 23:2639-2649. 10.1101/gad.1837609, 2779758, 19933153.
-
(2009)
Genes Dev
, vol.23
, pp. 2639-2649
-
-
Lee, Y.S.1
Shibata, Y.2
Malhotra, A.3
Dutta, A.4
-
73
-
-
71549169628
-
Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs
-
10.1261/rna.1738409, 2779667, 19850906
-
Cole C, Sobala A, Lu C, Thatcher SR, Bowman A, Brown JW, Green PJ, Barton GJ, Hutvagner G. Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA 2009, 15:2147-2160. 10.1261/rna.1738409, 2779667, 19850906.
-
(2009)
RNA
, vol.15
, pp. 2147-2160
-
-
Cole, C.1
Sobala, A.2
Lu, C.3
Thatcher, S.R.4
Bowman, A.5
Brown, J.W.6
Green, P.J.7
Barton, G.J.8
Hutvagner, G.9
-
74
-
-
52949145277
-
TRNA cleavage is a conserved response to oxidative stress in eukaryotes
-
10.1261/rna.1232808, 2553748, 18719243
-
Thompson DM, Lu C, Green PJ, Parker R. tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA 2008, 14:2095-2103. 10.1261/rna.1232808, 2553748, 18719243.
-
(2008)
RNA
, vol.14
, pp. 2095-2103
-
-
Thompson, D.M.1
Lu, C.2
Green, P.J.3
Parker, R.4
-
75
-
-
21844449964
-
Human mitochondrial tRNAMet is exported to the cytoplasm and associates with the Argonaute 2 protein
-
10.1261/rna.2210805, 1370769, 15872185
-
Maniataki E, Mourelatos Z. Human mitochondrial tRNAMet is exported to the cytoplasm and associates with the Argonaute 2 protein. RNA 2005, 11:849-852. 10.1261/rna.2210805, 1370769, 15872185.
-
(2005)
RNA
, vol.11
, pp. 849-852
-
-
Maniataki, E.1
Mourelatos, Z.2
-
76
-
-
77957799907
-
Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control
-
10.1038/msb.2010.76, 2990639, 20924354
-
Jiao Y, Meyerowitz EM. Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control. Mol Syst Biol 2010, 6:419. 10.1038/msb.2010.76, 2990639, 20924354.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 419
-
-
Jiao, Y.1
Meyerowitz, E.M.2
-
77
-
-
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, et al. 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
more..
-
78
-
-
41749104588
-
Single-molecule DNA sequencing of a viral genome
-
10.1126/science.1150427, 18388294
-
Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z. Single-molecule DNA sequencing of a viral genome. Science 2008, 320:106-109. 10.1126/science.1150427, 18388294.
-
(2008)
Science
, vol.320
, pp. 106-109
-
-
Harris, T.D.1
Buzby, P.R.2
Babcock, H.3
Beer, E.4
Bowers, J.5
Braslavsky, I.6
Causey, M.7
Colonell, J.8
Dimeo, J.9
Efcavitch, J.W.10
Giladi, E.11
Gill, J.12
Healy, J.13
Jarosz, M.14
Lapen, D.15
Moulton, K.16
Quake, S.R.17
Steinmann, K.18
Thayer, E.19
Tyurina, A.20
Ward, R.21
Weiss, H.22
Xie, Z.23
more..
-
79
-
-
67650500019
-
Quantification of the yeast transcriptome by single-molecule sequencing
-
10.1038/nbt.1551, 19581875
-
Lipson D, Raz T, Kieu A, Jones DR, Giladi E, Thayer E, Thompson JF, Letovsky S, Milos P, Causey M. Quantification of the yeast transcriptome by single-molecule sequencing. Nat Biotechnol 2009, 27:652-658. 10.1038/nbt.1551, 19581875.
-
(2009)
Nat Biotechnol
, vol.27
, pp. 652-658
-
-
Lipson, D.1
Raz, T.2
Kieu, A.3
Jones, D.R.4
Giladi, E.5
Thayer, E.6
Thompson, J.F.7
Letovsky, S.8
Milos, P.9
Causey, M.10
-
80
-
-
58149234737
-
Real-time DNA sequencing from single polymerase molecules
-
10.1126/science.1162986, 19023044
-
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Dewinter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong X, Kuse R, Lacroix Y, Lin S, et al. Real-time DNA sequencing from single polymerase molecules. Science 2009, 323:133-138. 10.1126/science.1162986, 19023044.
-
(2009)
Science
, vol.323
, pp. 133-138
-
-
Eid, J.1
Fehr, A.2
Gray, J.3
Luong, K.4
Lyle, J.5
Otto, G.6
Peluso, P.7
Rank, D.8
Baybayan, P.9
Bettman, B.10
Bibillo, A.11
Bjornson, K.12
Chaudhuri, B.13
Christians, F.14
Cicero, R.15
Clark, S.16
Dalal, R.17
Dewinter, A.18
Dixon, J.19
Foquet, M.20
Gaertner, A.21
Hardenbol, P.22
Heiner, C.23
Hester, K.24
Holden, D.25
Kearns, G.26
Kong, X.27
Kuse, R.28
Lacroix, Y.29
Lin, S.30
more..
-
81
-
-
46449103738
-
A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
-
10.1101/gr.076463.108, 2493394, 18477713
-
Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, Johnson SM. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 2008, 18:1051-1063. 10.1101/gr.076463.108, 2493394, 18477713.
-
(2008)
Genome Res
, vol.18
, pp. 1051-1063
-
-
Valouev, A.1
Ichikawa, J.2
Tonthat, T.3
Stuart, J.4
Ranade, S.5
Peckham, H.6
Zeng, K.7
Malek, J.A.8
Costa, G.9
McKernan, K.10
Sidow, A.11
Fire, A.12
Johnson, S.M.13
-
82
-
-
24644462173
-
Accurate multiplex polony sequencing of an evolved bacterial genome
-
10.1126/science.1117389, 16081699
-
Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 2005, 309:1728-1732. 10.1126/science.1117389, 16081699.
-
(2005)
Science
, vol.309
, pp. 1728-1732
-
-
Shendure, J.1
Porreca, G.J.2
Reppas, N.B.3
Lin, X.4
McCutcheon, J.P.5
Rosenbaum, A.M.6
Wang, M.D.7
Zhang, K.8
Mitra, R.D.9
Church, G.M.10
-
83
-
-
44349191457
-
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing
-
10.1038/ng.128, 2705838, 18438408
-
Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, Santarius T, Stebbings LA, Leroy C, Edkins S, Hardy C, Teague JW, Menzies A, Goodhead I, Turner DJ, Clee CM, Quail MA, Cox A, Brown C, Durbin R, Hurles ME, Edwards PA, Bignell GR, Stratton MR, Futreal PA. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 2008, 40:722-729. 10.1038/ng.128, 2705838, 18438408.
-
(2008)
Nat Genet
, vol.40
, pp. 722-729
-
-
Campbell, P.J.1
Stephens, P.J.2
Pleasance, E.D.3
O'Meara, S.4
Li, H.5
Santarius, T.6
Stebbings, L.A.7
Leroy, C.8
Edkins, S.9
Hardy, C.10
Teague, J.W.11
Menzies, A.12
Goodhead, I.13
Turner, D.J.14
Clee, C.M.15
Quail, M.A.16
Cox, A.17
Brown, C.18
Durbin, R.19
Hurles, M.E.20
Edwards, P.A.21
Bignell, G.R.22
Stratton, M.R.23
Futreal, P.A.24
more..
-
84
-
-
33746207763
-
Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes
-
10.1093/nar/gkl444, 1524903, 16840528
-
Ng P, Tan JJ, Ooi HS, Lee YL, Chiu KP, Fullwood MJ, Srinivasan KG, Perbost C, Du L, Sung WK, Wei CL, Ruan Y. Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes. Nucleic Acids Res 2006, 34:e84. 10.1093/nar/gkl444, 1524903, 16840528.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Ng, P.1
Tan, J.J.2
Ooi, H.S.3
Lee, Y.L.4
Chiu, K.P.5
Fullwood, M.J.6
Srinivasan, K.G.7
Perbost, C.8
Du, L.9
Sung, W.K.10
Wei, C.L.11
Ruan, Y.12
-
85
-
-
58149200962
-
Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing
-
10.1371/journal.pone.0004012, 2603312, 19107202
-
Shen Y, Sarin S, Liu Y, Hobert O, Pe'er I. Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing. PLoS One 2008, 3:e4012. 10.1371/journal.pone.0004012, 2603312, 19107202.
-
(2008)
PLoS One
, vol.3
-
-
Shen, Y.1
Sarin, S.2
Liu, Y.3
Hobert, O.4
Pe'er, I.5
-
86
-
-
67649595548
-
Limitations and possibilities of small RNA digital gene expression profiling
-
10.1038/nmeth0709-474, 19564845
-
Linsen SE, de Wit E, Janssens G, Heater S, Chapman L, Parkin RK, Fritz B, Wyman SK, de Bruijn E, Voest EE, Kuersten S, Tewari M, Cuppen E. Limitations and possibilities of small RNA digital gene expression profiling. Nat Methods 2009, 6:474-476. 10.1038/nmeth0709-474, 19564845.
-
(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
-
87
-
-
0017889065
-
Enzymatic oligoribonucleotide synthesis with T4 RNA ligase
-
10.1021/bi00604a008, 667012
-
England TE, Uhlenbeck OC. Enzymatic oligoribonucleotide synthesis with T4 RNA ligase. Biochemistry 1978, 17:2069-2076. 10.1021/bi00604a008, 667012.
-
(1978)
Biochemistry
, vol.17
, pp. 2069-2076
-
-
England, T.E.1
Uhlenbeck, O.C.2
-
88
-
-
0017885868
-
Addition of mononucleotides to oligoribonucleotide acceptors with T4 RNA ligase
-
10.1073/pnas.75.3.1270, 411452, 274717
-
Kikuchi Y, Hishinuma F, Sakaguchi K. Addition of mononucleotides to oligoribonucleotide acceptors with T4 RNA ligase. Proc Natl Acad Sci USA 1978, 75:1270-1273. 10.1073/pnas.75.3.1270, 411452, 274717.
-
(1978)
Proc Natl Acad Sci USA
, vol.75
, pp. 1270-1273
-
-
Kikuchi, Y.1
Hishinuma, F.2
Sakaguchi, K.3
-
89
-
-
0022425388
-
Donor activation in the T4 RNA ligase reaction
-
10.1021/bi00323a005, 3978074
-
McLaughlin LW, Piel N, Graeser E. Donor activation in the T4 RNA ligase reaction. Biochemistry 1985, 24:267-273. 10.1021/bi00323a005, 3978074.
-
(1985)
Biochemistry
, vol.24
, pp. 267-273
-
-
McLaughlin, L.W.1
Piel, N.2
Graeser, E.3
-
90
-
-
0017153836
-
Joining of ribooligonucleotides with T4 RNA ligase and identification of the oligonucleotide-adenylate intermediate
-
343018, 183186
-
Ohtsuka E, Nishikawa S, Sugiura M, Ikehara M. Joining of ribooligonucleotides with T4 RNA ligase and identification of the oligonucleotide-adenylate intermediate. Nucleic Acids Res 1976, 3:1613-1623. 343018, 183186.
-
(1976)
Nucleic Acids Res
, vol.3
, pp. 1613-1623
-
-
Ohtsuka, E.1
Nishikawa, S.2
Sugiura, M.3
Ikehara, M.4
-
91
-
-
0020164793
-
The effect of acceptor oligoribonucleotide sequence on the T4 RNA ligase reaction
-
10.1111/j.1432-1033.1982.tb06730.x, 7117259
-
Romaniuk E, McLaughlin LW, Neilson T, Romaniuk PJ. The effect of acceptor oligoribonucleotide sequence on the T4 RNA ligase reaction. Eur J Biochem 1982, 125:639-643. 10.1111/j.1432-1033.1982.tb06730.x, 7117259.
-
(1982)
Eur J Biochem
, vol.125
, pp. 639-643
-
-
Romaniuk, E.1
McLaughlin, L.W.2
Neilson, T.3
Romaniuk, P.J.4
-
92
-
-
43049096410
-
The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members
-
10.1242/dev.005629, 18287206
-
Farazi TA, Juranek SA, Tuschl T. The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members. Development 2008, 135:1201-1214. 10.1242/dev.005629, 18287206.
-
(2008)
Development
, vol.135
, pp. 1201-1214
-
-
Farazi, T.A.1
Juranek, S.A.2
Tuschl, T.3
-
93
-
-
26444540413
-
Extensive 3' modification of plant small RNAs is modulated by helper component-proteinase expression
-
10.1073/pnas.0506597102, 1224661, 16157869
-
Ebhardt HA, Thi EP, Wang MB, Unrau PJ. Extensive 3' modification of plant small RNAs is modulated by helper component-proteinase expression. Proc Natl Acad Sci USA 2005, 102:13398-13403. 10.1073/pnas.0506597102, 1224661, 16157869.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 13398-13403
-
-
Ebhardt, H.A.1
Thi, E.P.2
Wang, M.B.3
Unrau, P.J.4
-
94
-
-
32644454064
-
HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2' OH of the 3' terminal nucleotide
-
10.1093/nar/gkj474, 1356533, 16449203
-
Yang Z, Ebright YW, Yu B, Chen X. HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2' OH of the 3' terminal nucleotide. Nucleic Acids Res 2006, 34:667-675. 10.1093/nar/gkj474, 1356533, 16449203.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 667-675
-
-
Yang, Z.1
Ebright, Y.W.2
Yu, B.3
Chen, X.4
-
95
-
-
78649668009
-
Optimization of enzymatic reaction conditions for generating representative pools of cDNA from small RNA
-
2995414, 20921270
-
Munafó DB, Robb GB. Optimization of enzymatic reaction conditions for generating representative pools of cDNA from small RNA. RNA 2010, 16:2537-2552. 2995414, 20921270.
-
(2010)
RNA
, vol.16
, pp. 2537-2552
-
-
Munafó, D.B.1
Robb, G.B.2
-
96
-
-
0032213293
-
Incorporation of terminal phosphorothioates into oligonucleotides
-
10.1093/nar/26.21.4983, 147945, 9776763
-
Alefelder S, Patel BK, Eckstein F. Incorporation of terminal phosphorothioates into oligonucleotides. Nucleic Acids Res 1998, 26:4983-4988. 10.1093/nar/26.21.4983, 147945, 9776763.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 4983-4988
-
-
Alefelder, S.1
Patel, B.K.2
Eckstein, F.3
-
97
-
-
0035800521
-
A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA
-
Hutvágner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, Zamore PD. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 2001, 293:834-838.
-
(2001)
Science
, vol.293
, pp. 834-838
-
-
Hutvágner, G.1
McLachlan, J.2
Pasquinelli, A.E.3
Balint, E.4
Tuschl, T.5
Zamore, P.D.6
-
98
-
-
13644256193
-
Methylation as a crucial step in plant microRNA biogenesis
-
10.1126/science.1107130, 15705854
-
Yu B, Yang Z, Li J, Minakhina S, Yang M, Padgett RW, Steward R, Chen X. Methylation as a crucial step in plant microRNA biogenesis. Science 2005, 307:932-935. 10.1126/science.1107130, 15705854.
-
(2005)
Science
, vol.307
, pp. 932-935
-
-
Yu, B.1
Yang, Z.2
Li, J.3
Minakhina, S.4
Yang, M.5
Padgett, R.W.6
Steward, R.7
Chen, X.8
-
99
-
-
57149118220
-
Small RNAs with 5'-polyphosphate termini associate with a Piwi-related protein and regulate gene expression in the single-celled eukaryote Entamoeba histolytica
-
10.1371/journal.ppat.1000219, 2582682, 19043551
-
Zhang H, Ehrenkaufer GM, Pompey JM, Hackney JA, Singh U. Small RNAs with 5'-polyphosphate termini associate with a Piwi-related protein and regulate gene expression in the single-celled eukaryote Entamoeba histolytica. PLoS Pathog 2008, 4:e1000219. 10.1371/journal.ppat.1000219, 2582682, 19043551.
-
(2008)
PLoS Pathog
, vol.4
-
-
Zhang, H.1
Ehrenkaufer, G.M.2
Pompey, J.M.3
Hackney, J.A.4
Singh, U.5
-
100
-
-
46449086130
-
Capped small RNAs and MOV10 in human hepatitis delta virus replication
-
10.1038/nsmb.1440, 2876191, 18552826
-
Haussecker D, Cao D, Huang Y, Parameswaran P, Fire AZ, Kay MA. Capped small RNAs and MOV10 in human hepatitis delta virus replication. Nat Struct Mol Biol 2008, 15:714-721. 10.1038/nsmb.1440, 2876191, 18552826.
-
(2008)
Nat Struct Mol Biol
, vol.15
, pp. 714-721
-
-
Haussecker, D.1
Cao, D.2
Huang, Y.3
Parameswaran, P.4
Fire, A.Z.5
Kay, M.A.6
-
101
-
-
60549115605
-
Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs
-
10.1038/nature07759, 2719882, 19169241, Affymetrix ENCODE Transcriptome Project; Cold Spring Harbor Laboratory ENCODE Transcriptome Project
-
Affymetrix ENCODE Transcriptome Project; Cold Spring Harbor Laboratory ENCODE Transcriptome Project Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Nature 2009, 457:1028-1032. 10.1038/nature07759, 2719882, 19169241, Affymetrix ENCODE Transcriptome Project; Cold Spring Harbor Laboratory ENCODE Transcriptome Project.
-
(2009)
Nature
, vol.457
, pp. 1028-1032
-
-
-
102
-
-
0028949935
-
Classical and novel approaches to the detection and localization of the numerous modified nucleotides in eukaryotic ribosomal RNA
-
10.1016/0300-9084(96)88100-4, 7599273
-
Maden BE, Corbett ME, Heeney PA, Pugh K, Ajuh PM. Classical and novel approaches to the detection and localization of the numerous modified nucleotides in eukaryotic ribosomal RNA. Biochimie 1995, 77:22-29. 10.1016/0300-9084(96)88100-4, 7599273.
-
(1995)
Biochimie
, vol.77
, pp. 22-29
-
-
Maden, B.E.1
Corbett, M.E.2
Heeney, P.A.3
Pugh, K.4
Ajuh, P.M.5
-
103
-
-
63949083912
-
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes
-
10.1038/nmeth.1311, 2664327, 19287394
-
Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods 2009, 6:291-295. 10.1038/nmeth.1311, 2664327, 19287394.
-
(2009)
Nat Methods
, vol.6
, pp. 291-295
-
-
Kozarewa, I.1
Ning, Z.2
Quail, M.A.3
Sanders, M.J.4
Berriman, M.5
Turner, D.J.6
-
104
-
-
77449147610
-
FRT-seq: amplification-free, strand-specific transcriptome sequencing
-
10.1038/nmeth.1417, 2861772, 20081834
-
Mamanova L, Andrews RM, James KD, Sheridan EM, Ellis PD, Langford CF, Ost TW, Collins JE, Turner DJ. FRT-seq: amplification-free, strand-specific transcriptome sequencing. Nat Methods 2010, 7:130-132. 10.1038/nmeth.1417, 2861772, 20081834.
-
(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
-
105
-
-
34250201129
-
Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy
-
10.1126/science.1137325, 17556586
-
Kim JB, Porreca GJ, Song L, Greenway SC, Gorham JM, Church GM, Seidman CE, Seidman JG. Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science 2007, 316:1481-1484. 10.1126/science.1137325, 17556586.
-
(2007)
Science
, vol.316
, pp. 1481-1484
-
-
Kim, J.B.1
Porreca, G.J.2
Song, L.3
Greenway, S.C.4
Gorham, J.M.5
Church, G.M.6
Seidman, C.E.7
Seidman, J.G.8
-
106
-
-
33947236065
-
Genome-wide profiling and analysis of Arabidopsis siRNAs
-
10.1371/journal.pbio.0050057, 1820830, 17298187
-
Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Carrington JC. Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol 2007, 5:e57. 10.1371/journal.pbio.0050057, 1820830, 17298187.
-
(2007)
PLoS Biol
, vol.5
-
-
Kasschau, K.D.1
Fahlgren, N.2
Chapman, E.J.3
Sullivan, C.M.4
Cumbie, J.S.5
Givan, S.A.6
Carrington, J.C.7
-
107
-
-
39449089394
-
Parallel tagged sequencing on the 454 platform
-
10.1038/nprot.2007.520, 18274529
-
Meyer M, Stenzel U, Hofreiter M. Parallel tagged sequencing on the 454 platform. Nat Protoc 2008, 3:267-278. 10.1038/nprot.2007.520, 18274529.
-
(2008)
Nat Protoc
, vol.3
, pp. 267-278
-
-
Meyer, M.1
Stenzel, U.2
Hofreiter, M.3
-
108
-
-
40149103278
-
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
-
10.1038/nmeth.1184, 18264105
-
Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 2008, 5:235-237. 10.1038/nmeth.1184, 18264105.
-
(2008)
Nat Methods
, vol.5
, pp. 235-237
-
-
Hamady, M.1
Walker, J.J.2
Harris, J.K.3
Gold, N.J.4
Knight, R.5
-
109
-
-
53249132629
-
Identification of genetic variants using bar-coded multiplexed sequencing
-
10.1038/nmeth.1251, 18794863
-
Craig DW, Pearson JV, Szelinger S, Sekar A, Redman M, Corneveaux JJ, Pawlowski TL, Laub T, Nunn G, Stephan DA, Homer N, Huentelman MJ. Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods 2008, 5:887-893. 10.1038/nmeth.1251, 18794863.
-
(2008)
Nat Methods
, vol.5
, pp. 887-893
-
-
Craig, D.W.1
Pearson, J.V.2
Szelinger, S.3
Sekar, A.4
Redman, M.5
Corneveaux, J.J.6
Pawlowski, T.L.7
Laub, T.8
Nunn, G.9
Stephan, D.A.10
Homer, N.11
Huentelman, M.J.12
-
110
-
-
77955237447
-
Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples
-
10.1093/nar/gkq368, 2910071, 20460461
-
Smith AM, Heisler LE, St Onge RP, Farias-Hesson E, Wallace IM, Bodeau J, Harris AN, Perry KM, Giaever G, Pourmand N, Nislow C. Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples. Nucleic Acids Res 2010, 38:e142. 10.1093/nar/gkq368, 2910071, 20460461.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Smith, A.M.1
Heisler, L.E.2
St Onge, R.P.3
Farias-Hesson, E.4
Wallace, I.M.5
Bodeau, J.6
Harris, A.N.7
Perry, K.M.8
Giaever, G.9
Pourmand, N.10
Nislow, C.11
-
111
-
-
34547834963
-
The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing
-
10.1371/journal.pone.0000197, 1797623, 17299583
-
Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev E. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One 2007, 2:e197. 10.1371/journal.pone.0000197, 1797623, 17299583.
-
(2007)
PLoS One
, vol.2
-
-
Binladen, J.1
Gilbert, M.T.2
Bollback, J.P.3
Panitz, F.4
Bendixen, C.5
Nielsen, R.6
Willerslev, E.7
-
112
-
-
34548588390
-
Targeted high-throughput sequencing of tagged nucleic acid samples
-
10.1093/nar/gkm566, 1976447, 17670798
-
Meyer M, Stenzel U, Myles S, Prufer K, Hofreiter M. Targeted high-throughput sequencing of tagged nucleic acid samples. Nucleic Acids Res 2007, 35:e97. 10.1093/nar/gkm566, 1976447, 17670798.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Meyer, M.1
Stenzel, U.2
Myles, S.3
Prufer, K.4
Hofreiter, M.5
-
113
-
-
69549139892
-
Direct multiplex sequencing (DMPS): a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA
-
10.1101/gr.095760.109, 2765274, 19635845
-
Stiller M, Knapp M, Stenzel U, Hofreiter M, Meyer M. Direct multiplex sequencing (DMPS): a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA. Genome Res 2009, 19:1843-1848. 10.1101/gr.095760.109, 2765274, 19635845.
-
(2009)
Genome Res
, vol.19
, pp. 1843-1848
-
-
Stiller, M.1
Knapp, M.2
Stenzel, U.3
Hofreiter, M.4
Meyer, M.5
-
114
-
-
56149096455
-
Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology
-
10.1093/nar/gkn502, 2577356, 18753151
-
Cronn R, Liston A, Parks M, Gernandt DS, Shen R, Mockler T. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res 2008, 36:e122-e122. 10.1093/nar/gkn502, 2577356, 18753151.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Cronn, R.1
Liston, A.2
Parks, M.3
Gernandt, D.S.4
Shen, R.5
Mockler, T.6
-
115
-
-
65349094759
-
Computational and analytical framework for small RNA profiling by high-throughput sequencing
-
10.1261/rna.1473809, 2673065, 19307293
-
Fahlgren N, Sullivan CM, Kasschau KD, Chapman EJ, Cumbie JS, Montgomery TA, Gilbert SD, Dasenko M, Backman TWH, Givan SA, Carrington JC. Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA 2009, 15:992-1002. 10.1261/rna.1473809, 2673065, 19307293.
-
(2009)
RNA
, vol.15
, pp. 992-1002
-
-
Fahlgren, N.1
Sullivan, C.M.2
Kasschau, K.D.3
Chapman, E.J.4
Cumbie, J.S.5
Montgomery, T.A.6
Gilbert, S.D.7
Dasenko, M.8
Backman, T.W.H.9
Givan, S.A.10
Carrington, J.C.11
-
116
-
-
50649089207
-
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
-
10.1101/gr.079558.108, 2527709, 18550803
-
Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Research 2008, 18:1509-1517. 10.1101/gr.079558.108, 2527709, 18550803.
-
(2008)
Genome Research
, vol.18
, pp. 1509-1517
-
-
Marioni, J.C.1
Mason, C.E.2
Mane, S.M.3
Stephens, M.4
Gilad, Y.5
-
117
-
-
77955562856
-
Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes
-
10.1016/j.ajhg.2010.07.014, 2917713, 20696290
-
Li M, Schonberg A, Schaefer M, Schroeder R, Nasidze I, Stoneking M. Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes. Am J Hum Genet 2010, 87:237-249. 10.1016/j.ajhg.2010.07.014, 2917713, 20696290.
-
(2010)
Am J Hum Genet
, vol.87
, pp. 237-249
-
-
Li, M.1
Schonberg, A.2
Schaefer, M.3
Schroeder, R.4
Nasidze, I.5
Stoneking, M.6
-
118
-
-
78249274213
-
Digital gene expression signatures for maize development
-
10.1104/pp.110.159673, 20833728
-
Eveland AL, Satoh-Nagasawa N, Goldshmidt A, Meyer S, Beatty M, Sakai H, Ware D, Jackson D. Digital gene expression signatures for maize development. Plant Physiol 2010, 154:1024-1039. 10.1104/pp.110.159673, 20833728.
-
(2010)
Plant Physiol
, vol.154
, pp. 1024-1039
-
-
Eveland, A.L.1
Satoh-Nagasawa, N.2
Goldshmidt, A.3
Meyer, S.4
Beatty, M.5
Sakai, H.6
Ware, D.7
Jackson, D.8
-
119
-
-
77955778246
-
Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens
-
10.1093/nar/gkq510, 2919738, 20525786
-
Wood HM, Belvedere O, Conway C, Daly C, Chalkley R, Bickerdike M, McKinley C, Egan P, Ross L, Hayward B, Morgan J, Davidson L, MacLennan K, Ong TK, Papagiannopoulos K, Cook I, Adams DJ, Taylor GR, Rabbitts P. Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens. Nucleic Acids Res 2010, 38:e151. 10.1093/nar/gkq510, 2919738, 20525786.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Wood, H.M.1
Belvedere, O.2
Conway, C.3
Daly, C.4
Chalkley, R.5
Bickerdike, M.6
McKinley, C.7
Egan, P.8
Ross, L.9
Hayward, B.10
Morgan, J.11
Davidson, L.12
MacLennan, K.13
Ong, T.K.14
Papagiannopoulos, K.15
Cook, I.16
Adams, D.J.17
Taylor, G.R.18
Rabbitts, P.19
-
120
-
-
77953176036
-
A scaling normalization method for differential expression analysis of RNA-seq data
-
10.1186/gb-2010-11-3-r25, 2864565, 20196867
-
Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 2010, 11:R25. 10.1186/gb-2010-11-3-r25, 2864565, 20196867.
-
(2010)
Genome Biol
, vol.11
-
-
Robinson, M.D.1
Oshlack, A.2
-
121
-
-
40049104732
-
SOAP: short oligonucleotide alignment program
-
10.1093/bioinformatics/btn025, 18227114
-
Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24:713-714. 10.1093/bioinformatics/btn025, 18227114.
-
(2008)
Bioinformatics
, vol.24
, pp. 713-714
-
-
Li, R.1
Li, Y.2
Kristiansen, K.3
Wang, J.4
-
122
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
10.1186/gb-2009-10-3-r25, 2690996, 19261174
-
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
123
-
-
60149112271
-
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
-
10.1038/nbt.1518, 2924752, 19122651
-
Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol 2009, 27:66-75. 10.1038/nbt.1518, 2924752, 19122651.
-
(2009)
Nat Biotechnol
, vol.27
, pp. 66-75
-
-
Rozowsky, J.1
Euskirchen, G.2
Auerbach, R.K.3
Zhang, Z.D.4
Gibson, T.5
Bjornson, R.6
Carriero, N.7
Snyder, M.8
Gerstein, M.B.9
-
124
-
-
70149095956
-
Genome-wide analysis of small RNA and novel microRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach
-
10.1371/journal.pone.0006849, 2731166, 19724645
-
Zhang H, Yang JH, Zheng YS, Zhang P, Chen X, Wu J, Xu L, Luo XQ, Ke ZY, Zhou H, Qu LH, Chen YQ. Genome-wide analysis of small RNA and novel microRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach. PLoS One 2009, 4:e6849. 10.1371/journal.pone.0006849, 2731166, 19724645.
-
(2009)
PLoS One
, vol.4
-
-
Zhang, H.1
Yang, J.H.2
Zheng, Y.S.3
Zhang, P.4
Chen, X.5
Wu, J.6
Xu, L.7
Luo, X.Q.8
Ke, Z.Y.9
Zhou, H.10
Qu, L.H.11
Chen, Y.Q.12
-
125
-
-
75649089335
-
Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries
-
10.1101/gr.095273.109, 2813481, 20051556
-
de Hoon MJL, Taft RJ, Hashimoto T, Kanamori-Katayama M, Kawaji H, Kawano M, Kishima M, Lassmann T, Faulkner GJ, Mattick JS, Daub CO, Carninci P, Kawai J, Suzuki H, Hayashizaki Y. Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Res 2010, 20:257-264. 10.1101/gr.095273.109, 2813481, 20051556.
-
(2010)
Genome Res
, vol.20
, pp. 257-264
-
-
de Hoon, M.J.L.1
Taft, R.J.2
Hashimoto, T.3
Kanamori-Katayama, M.4
Kawaji, H.5
Kawano, M.6
Kishima, M.7
Lassmann, T.8
Faulkner, G.J.9
Mattick, J.S.10
Daub, C.O.11
Carninci, P.12
Kawai, J.13
Suzuki, H.14
Hayashizaki, Y.15
-
126
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-seq
-
10.1038/nmeth.1226, 18516045
-
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods 2008, 5:621-628. 10.1038/nmeth.1226, 18516045.
-
(2008)
Nat Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
127
-
-
77949507153
-
RNA-seq gene expression estimation with read mapping uncertainty
-
10.1093/bioinformatics/btp692, 2820677, 20022975
-
Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN. RNA-seq gene expression estimation with read mapping uncertainty. Bioinformatics 2010, 26:493-500. 10.1093/bioinformatics/btp692, 2820677, 20022975.
-
(2010)
Bioinformatics
, vol.26
, pp. 493-500
-
-
Li, B.1
Ruotti, V.2
Stewart, R.M.3
Thomson, J.A.4
Dewey, C.N.5
-
128
-
-
65849172363
-
Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications
-
10.1093/nar/gkp093, 2677864, 19255090
-
Ebhardt HA, Tsang HH, Dai DC, Liu Y, Bostan B, Fahlman RP. Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications. Nucleic Acids Res 2009, 37:2461-2470. 10.1093/nar/gkp093, 2677864, 19255090.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 2461-2470
-
-
Ebhardt, H.A.1
Tsang, H.H.2
Dai, D.C.3
Liu, Y.4
Bostan, B.5
Fahlman, R.P.6
-
129
-
-
65449131636
-
Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana
-
10.1186/1471-2164-10-155, 2674459, 19358740
-
Iida K, Jin H, Zhu JK. Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana. BMC Genomics 2009, 10:155. 10.1186/1471-2164-10-155, 2674459, 19358740.
-
(2009)
BMC Genomics
, vol.10
, pp. 155
-
-
Iida, K.1
Jin, H.2
Zhu, J.K.3
-
130
-
-
0036202577
-
Normalizing DNA microarray data
-
Bilban M, Buehler LK, Head S, Desoye G, Quaranta V. Normalizing DNA microarray data. Curr Issues Mol Biol 2002, 4:57-64.
-
(2002)
Curr Issues Mol Biol
, vol.4
, pp. 57-64
-
-
Bilban, M.1
Buehler, L.K.2
Head, S.3
Desoye, G.4
Quaranta, V.5
-
131
-
-
60849113704
-
Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations
-
10.1186/1471-2105-10-S1-S24, 2648747, 19208124
-
Autio R, Kilpinen S, Saarela M, Kallioniemi O, Hautaniemi S, Astola J. Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations. BMC Bioinformatics 2009, 10(Suppl 1):S24. 10.1186/1471-2105-10-S1-S24, 2648747, 19208124.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.SUPPL. 1
-
-
Autio, R.1
Kilpinen, S.2
Saarela, M.3
Kallioniemi, O.4
Hautaniemi, S.5
Astola, J.6
-
132
-
-
0035793042
-
Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection
-
10.1073/pnas.011404098, 14539, 11134512
-
Li C, Wong WH. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 2001, 98:31-36. 10.1073/pnas.011404098, 14539, 11134512.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 31-36
-
-
Li, C.1
Wong, W.H.2
-
133
-
-
60849121405
-
Global rank-invariant set normalization (GRSN) to reduce systematic distortions in microarray data
-
10.1186/1471-2105-9-520, 2644708, 19055840
-
Pelz CR, Kulesz-Martin M, Bagby G, Sears RC. Global rank-invariant set normalization (GRSN) to reduce systematic distortions in microarray data. BMC Bioinformatics 2008, 9:520. 10.1186/1471-2105-9-520, 2644708, 19055840.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 520
-
-
Pelz, C.R.1
Kulesz-Martin, M.2
Bagby, G.3
Sears, R.C.4
-
134
-
-
0035752668
-
Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data
-
10.1002/jcb.10073, 11842437
-
Schadt EE, Li C, Ellis B, Wong WH. Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. J Cell Biochem Suppl 2001, (Suppl 37):120-125. 10.1002/jcb.10073, 11842437.
-
(2001)
J Cell Biochem Suppl
, Issue.SUPPL. 37
, pp. 120-125
-
-
Schadt, E.E.1
Li, C.2
Ellis, B.3
Wong, W.H.4
-
135
-
-
0035875553
-
Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects
-
10.1093/nar/29.12.2549, 55725, 11410663
-
Tseng GC, Oh MK, Rohlin L, Liao JC, Wong WH. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res 2001, 29:2549-2557. 10.1093/nar/29.12.2549, 55725, 11410663.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 2549-2557
-
-
Tseng, G.C.1
Oh, M.K.2
Rohlin, L.3
Liao, J.C.4
Wong, W.H.5
-
136
-
-
0032883806
-
Housekeeping genes as internal standards: use and limits
-
10.1016/S0168-1656(99)00163-7, 10617337
-
Thellin O, Zorzi W, Lakaye B, De Borman B, Coumans B, Hennen G, Grisar T, Igout A, Heinen E. Housekeeping genes as internal standards: use and limits. J Biotechnol 1999, 75:291-295. 10.1016/S0168-1656(99)00163-7, 10617337.
-
(1999)
J Biotechnol
, vol.75
, pp. 291-295
-
-
Thellin, O.1
Zorzi, W.2
Lakaye, B.3
De Borman, B.4
Coumans, B.5
Hennen, G.6
Grisar, T.7
Igout, A.8
Heinen, E.9
-
138
-
-
0036178995
-
Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies
-
10.1101/gr.217802, 155273, 11827948
-
Lee PD, Sladek R, Greenwood CM, Hudson TJ. Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies. Genome Res 2002, 12:292-297. 10.1101/gr.217802, 155273, 11827948.
-
(2002)
Genome Res
, vol.12
, pp. 292-297
-
-
Lee, P.D.1
Sladek, R.2
Greenwood, C.M.3
Hudson, T.J.4
-
139
-
-
0037129827
-
Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
-
10.1186/gb-2002-3-7-research0034, 126239, 12184808
-
Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002, 3:RESEARCH0034. 10.1186/gb-2002-3-7-research0034, 126239, 12184808.
-
(2002)
Genome Biol
, vol.3
-
-
Vandesompele, J.1
De Preter, K.2
Pattyn, F.3
Poppe, B.4
Van Roy, N.5
De Paepe, A.6
Speleman, F.7
-
140
-
-
32644481938
-
Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis
-
10.1104/pp.105.063743, 1203353, 16166256
-
Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible WR. Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol 2005, 139:5-17. 10.1104/pp.105.063743, 1203353, 16166256.
-
(2005)
Plant Physiol
, vol.139
, pp. 5-17
-
-
Czechowski, T.1
Stitt, M.2
Altmann, T.3
Udvardi, M.K.4
Scheible, W.R.5
-
141
-
-
20844458965
-
Housekeeping genes in cancer: normalization of array data
-
10.2144/05385ST04, 15948292
-
Khimani AH, Mhashilkar AM, Mikulskis A, O'Malley M, Liao J, Golenko EE, Mayer P, Chada S, Killian JB, Lott ST. Housekeeping genes in cancer: normalization of array data. Biotechniques 2005, 38:739-745. 10.2144/05385ST04, 15948292.
-
(2005)
Biotechniques
, vol.38
, pp. 739-745
-
-
Khimani, A.H.1
Mhashilkar, A.M.2
Mikulskis, A.3
O'Malley, M.4
Liao, J.5
Golenko, E.E.6
Mayer, P.7
Chada, S.8
Killian, J.B.9
Lott, S.T.10
-
142
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
10.1093/bioinformatics/19.2.185, 12538238
-
Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:185-193. 10.1093/bioinformatics/19.2.185, 12538238.
-
(2003)
Bioinformatics
, vol.19
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
143
-
-
0012572299
-
A variance-stabilizing transformation for gene-expression microarray data
-
Durbin BP, Hardin JS, Hawkins DM, Rocke DM. A variance-stabilizing transformation for gene-expression microarray data. Bioinformatics 2002, 18(Suppl 1):S105-S110.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Durbin, B.P.1
Hardin, J.S.2
Hawkins, D.M.3
Rocke, D.M.4
-
144
-
-
11244346557
-
Variance stabilization applied to microarray data calibration and to the quantification of differential expression
-
Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 2002, 18(Suppl 1):S96-S104.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Huber, W.1
von Heydebreck, A.2
Sultmann, H.3
Poustka, A.4
Vingron, M.5
-
145
-
-
0042589211
-
A 'consistency' test for determining the significance of gene expression changes on replicate samples and two-convenient variance-stabilizing transformations
-
Bethesda, MD, Speed T
-
Munson P. A 'consistency' test for determining the significance of gene expression changes on replicate samples and two-convenient variance-stabilizing transformations. Proceedings of the GeneLogic Workshop on Low Level Analysis of Affymetrix GeneChip Data 2001, Bethesda, MD, Speed T., http://oz.berkeley.edu/users/terry/zarray/Affy/GL_Workshop/genelogic2001.html
-
(2001)
Proceedings of the GeneLogic Workshop on Low Level Analysis of Affymetrix GeneChip Data
-
-
Munson, P.1
-
146
-
-
33846561627
-
Effect of various normalization methods on Applied Biosystems expression array system data
-
10.1186/1471-2105-7-533, 1764432, 17173684
-
Barbacioru CC, Wang Y, Canales RD, Sun YA, Keys DN, Chan F, Poulter KA, Samaha RR. Effect of various normalization methods on Applied Biosystems expression array system data. BMC Bioinformatics 2006, 7:533. 10.1186/1471-2105-7-533, 1764432, 17173684.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 533
-
-
Barbacioru, C.C.1
Wang, Y.2
Canales, R.D.3
Sun, Y.A.4
Keys, D.N.5
Chan, F.6
Poulter, K.A.7
Samaha, R.R.8
-
147
-
-
74049120413
-
Calibration of microarray gene-expression data
-
full_text, 19882273
-
Binder H, Preibisch S, Berger H. Calibration of microarray gene-expression data. Methods Mol Biol 2010, 576:375-407. full_text, 19882273.
-
(2010)
Methods Mol Biol
, vol.576
, pp. 375-407
-
-
Binder, H.1
Preibisch, S.2
Berger, H.3
-
148
-
-
32644439684
-
Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons
-
10.1093/nar/gnj010, 1345700, 16432259
-
Harr B, Schlotterer C. Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons. Nucleic Acids Res 2006, 34:e8. 10.1093/nar/gnj010, 1345700, 16432259.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Harr, B.1
Schlotterer, C.2
-
149
-
-
33645651236
-
How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results
-
10.1186/1471-2105-7-137, 1431565, 16539732
-
Millenaar FF, Okyere J, May ST, van Zanten M, Voesenek LA, Peeters AJ. How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results. BMC Bioinformatics 2006, 7:137. 10.1186/1471-2105-7-137, 1431565, 16539732.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 137
-
-
Millenaar, F.F.1
Okyere, J.2
May, S.T.3
van Zanten, M.4
Voesenek, L.A.5
Peeters, A.J.6
-
150
-
-
77952123055
-
Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation
-
10.1038/nbt.1621, 20436464
-
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010, 28:511-515. 10.1038/nbt.1621, 20436464.
-
(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
-
151
-
-
49449118943
-
Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends
-
10.1038/nbt1417, 18542052
-
German MA, Pillay M, Jeong DH, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis LA, Nobuta K, German R, De Paoli E, Lu C, Schroth G, Meyers BC, Green PJ. Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 2008, 26:941-946. 10.1038/nbt1417, 18542052.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 941-946
-
-
German, M.A.1
Pillay, M.2
Jeong, D.H.3
Hetawal, A.4
Luo, S.5
Janardhanan, P.6
Kannan, V.7
Rymarquis, L.A.8
Nobuta, K.9
German, R.10
De Paoli, E.11
Lu, C.12
Schroth, G.13
Meyers, B.C.14
Green, P.J.15
-
152
-
-
78650514497
-
SiRNAs from miRNA sites mediate DNA methylation of target genes
-
10.1093/nar/gkq590, 2978365, 20621980
-
Chellappan P, Xia J, Zhou X, Gao S, Zhang X, Coutino G, Vazquez F, Zhang W, Jin H. siRNAs from miRNA sites mediate DNA methylation of target genes. Nucleic Acids Res 2010, 38:6883-6894. 10.1093/nar/gkq590, 2978365, 20621980.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 6883-6894
-
-
Chellappan, P.1
Xia, J.2
Zhou, X.3
Gao, S.4
Zhang, X.5
Coutino, G.6
Vazquez, F.7
Zhang, W.8
Jin, H.9
-
153
-
-
77956989755
-
From the cover: 22-nucleotide RNAs trigger secondary siRNA biogenesis in plants
-
10.1073/pnas.1001738107, 2930544, 20643946
-
Chen HM, Chen LT, Patel K, Li YH, Baulcombe DC, Wu SH. From the cover: 22-nucleotide RNAs trigger secondary siRNA biogenesis in plants. Proc Natl Acad Sci 2010, 107:15269-15274. 10.1073/pnas.1001738107, 2930544, 20643946.
-
(2010)
Proc Natl Acad Sci
, vol.107
, pp. 15269-15274
-
-
Chen, H.M.1
Chen, L.T.2
Patel, K.3
Li, Y.H.4
Baulcombe, D.C.5
Wu, S.H.6
-
154
-
-
77949481052
-
Evaluation of statistical methods for normalization and differential expression in mRNA-seq experiments
-
10.1186/1471-2105-11-94, 2838869, 20167110
-
Bullard JH, Purdom E, Hansen KD, Dudoit S. Evaluation of statistical methods for normalization and differential expression in mRNA-seq experiments. BMC Bioinformatics 2010, 11:94. 10.1186/1471-2105-11-94, 2838869, 20167110.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 94
-
-
Bullard, J.H.1
Purdom, E.2
Hansen, K.D.3
Dudoit, S.4
-
155
-
-
51449109568
-
Characterization of unique small RNA populations from rice grain
-
10.1371/journal.pone.0002871, 2518513, 18716673
-
Heisel SE, Zhang Y, Allen E, Guo L, Reynolds TL, Yang X, Kovalic D, Roberts JK. Characterization of unique small RNA populations from rice grain. PLoS One 2008, 3:e2871. 10.1371/journal.pone.0002871, 2518513, 18716673.
-
(2008)
PLoS One
, vol.3
-
-
Heisel, S.E.1
Zhang, Y.2
Allen, E.3
Guo, L.4
Reynolds, T.L.5
Yang, X.6
Kovalic, D.7
Roberts, J.K.8
-
156
-
-
69849103628
-
Comparative study on ChIP-seq data: normalization and binding pattern characterization
-
10.1093/bioinformatics/btp384, 2800347, 19561022
-
Taslim C, Wu J, Yan P, Singer G, Parvin J, Huang T, Lin S, Huang K. Comparative study on ChIP-seq data: normalization and binding pattern characterization. Bioinformatics 2009, 25:2334-2340. 10.1093/bioinformatics/btp384, 2800347, 19561022.
-
(2009)
Bioinformatics
, vol.25
, pp. 2334-2340
-
-
Taslim, C.1
Wu, J.2
Yan, P.3
Singer, G.4
Parvin, J.5
Huang, T.6
Lin, S.7
Huang, K.8
-
157
-
-
0030681260
-
The significance of digital gene expression profiles
-
Audic S, Claverie JM. The significance of digital gene expression profiles. Genome Res 1997, 7:986-995.
-
(1997)
Genome Res
, vol.7
, pp. 986-995
-
-
Audic, S.1
Claverie, J.M.2
-
158
-
-
70449338987
-
Basic properties and information theory of Audic-Claverie statistic for analyzing cDNA arrays
-
2761412, 19775462
-
Tiňo P. Basic properties and information theory of Audic-Claverie statistic for analyzing cDNA arrays. BMC Bioinformatics 2009, 10:310. 2761412, 19775462.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 310
-
-
Tiňo, P.1
-
159
-
-
47649124124
-
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
-
10.1126/science.1160342, 18599741
-
Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O'Keeffe S, Haas S, Vingron M, Lehrach H, Yaspo ML. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 2008, 321:956-960. 10.1126/science.1160342, 18599741.
-
(2008)
Science
, vol.321
, pp. 956-960
-
-
Sultan, M.1
Schulz, M.H.2
Richard, H.3
Magen, A.4
Klingenhoff, A.5
Scherf, M.6
Seifert, M.7
Borodina, T.8
Soldatov, A.9
Parkhomchuk, D.10
Schmidt, D.11
O'Keeffe, S.12
Haas, S.13
Vingron, M.14
Lehrach, H.15
Yaspo, M.L.16
-
160
-
-
41649106136
-
Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells
-
10.1101/gr.7179508, 2279248, 18285502
-
Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL, Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res 2008, 18:610-621. 10.1101/gr.7179508, 2279248, 18285502.
-
(2008)
Genome Res
, vol.18
, pp. 610-621
-
-
Morin, R.D.1
O'Connor, M.D.2
Griffith, M.3
Kuchenbauer, F.4
Delaney, A.5
Prabhu, A.L.6
Zhao, Y.7
McDonald, H.8
Zeng, T.9
Hirst, M.10
Eaves, C.J.11
Marra, M.A.12
-
161
-
-
77951940273
-
Modeling non-uniformity in short-read rates in RNA-seq data
-
10.1186/gb-2010-11-5-r50, 2898062, 20459815
-
Li J, Jiang H, Wong W. Modeling non-uniformity in short-read rates in RNA-seq data. Genome Biol 2010, 11:R50. 10.1186/gb-2010-11-5-r50, 2898062, 20459815.
-
(2010)
Genome Biol
, vol.11
-
-
Li, J.1
Jiang, H.2
Wong, W.3
-
162
-
-
75249087100
-
EdgeR: a Bioconductor package for differential expression analysis of digital gene expression data
-
10.1093/bioinformatics/btp616, 2796818, 19910308
-
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2009, 26:139-140. 10.1093/bioinformatics/btp616, 2796818, 19910308.
-
(2009)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
|