-
1
-
-
33646478817
-
Discrimination of non-protein-coding transcripts from protein-coding mRNA
-
Frith MC, Bailey TL, Kasukawa T, Mignone F, Kummerfeld SK, et al. (2006) Discrimination of non-protein-coding transcripts from protein-coding mRNA. RNA Biol 3: 40-48.
-
(2006)
RNA Biol
, vol.3
, pp. 40-48
-
-
Frith, M.C.1
Bailey, T.L.2
Kasukawa, T.3
Mignone, F.4
Kummerfeld, S.K.5
-
2
-
-
33646486093
-
Genome Network and FANTOM3: Assessing the complexity of the transcriptome
-
Hayashizaki Y, Carninci P (2006) Genome Network and FANTOM3: assessing the complexity of the transcriptome. PLoS Genet 2: e63.
-
(2006)
PLoS Genet
, vol.2
-
-
Hayashizaki, Y.1
Carninci, P.2
-
3
-
-
24644472515
-
Antisense transcription in the mammalian transcriptome
-
Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, et al. (2005) Antisense transcription in the mammalian transcriptome. Science 309: 1564-1566.
-
(2005)
Science
, vol.309
, pp. 1564-1566
-
-
Katayama, S.1
Tomaru, Y.2
Kasukawa, T.3
Waki, K.4
Nakanishi, M.5
-
4
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, et al. (2005) The transcriptional landscape of the mammalian genome. Science 309: 1559-1563.
-
(2005)
Science
, vol.309
, pp. 1559-1563
-
-
Carninci, P.1
Kasukawa, T.2
Katayama, S.3
Gough, J.4
Frith, M.C.5
-
5
-
-
21044431735
-
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
-
Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, et al. (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308: 1149-1154.
-
(2005)
Science
, vol.308
, pp. 1149-1154
-
-
Cheng, J.1
Kapranov, P.2
Drenkow, J.3
Dike, S.4
Brubaker, S.5
-
6
-
-
34250683058
-
Transcriptional landscape of the human and fly genomes: Nonlinear and multifunctional modular model of transcriptomes
-
Willingham AT, Dike S, Cheng J, Manak JR, Bell I, et al. (2006) Transcriptional landscape of the human and fly genomes: nonlinear and multifunctional modular model of transcriptomes. Cold Spring Harb Symp Quant Biol 71: 101-110.
-
(2006)
Cold Spring Harb Symp Quant Biol
, vol.71
, pp. 101-110
-
-
Willingham, A.T.1
Dike, S.2
Cheng, J.3
Manak, J.R.4
Bell, I.5
-
7
-
-
56949091456
-
Noncoding RNA in development
-
Mamm Genome
-
Amaral PP, Mattick JS (2008) Noncoding RNA in development. Mamm Genome.
-
(2008)
-
-
Amaral, P.P.1
Mattick, J.S.2
-
8
-
-
0037012881
-
Large-scale transcriptional activity in chromosomes 21 and 22
-
Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, et al. (2002) Large-scale transcriptional activity in chromosomes 21 and 22. Science 296: 916-919.
-
(2002)
Science
, vol.296
, pp. 916-919
-
-
Kapranov, P.1
Cawley, S.E.2
Drenkow, J.3
Bekiranov, S.4
Strausberg, R.L.5
-
9
-
-
34250160256
-
RNA maps reveal new RNA classes and a possible function for pervasive transcription
-
Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, et al. (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316: 1484-1488.
-
(2007)
Science
, vol.316
, pp. 1484-1488
-
-
Kapranov, P.1
Cheng, J.2
Dike, S.3
Nix, D.A.4
Duttagupta, R.5
-
10
-
-
10744226888
-
Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
-
Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, et al. (2004) Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116: 499-509.
-
(2004)
Cell
, vol.116
, pp. 499-509
-
-
Cawley, S.1
Bekiranov, S.2
Ng, H.H.3
Kapranov, P.4
Sekinger, E.A.5
-
11
-
-
12244275645
-
Widespread occurrence of antisense transcription in the human genome
-
Yelin R, Dahary D, Sorek R, Levanon EY, Goldstein O, et al. (2003) Widespread occurrence of antisense transcription in the human genome. Nat Biotechnol 21: 379-386.
-
(2003)
Nat Biotechnol
, vol.21
, pp. 379-386
-
-
Yelin, R.1
Dahary, D.2
Sorek, R.3
Levanon, E.Y.4
Goldstein, O.5
-
12
-
-
0037158780
-
Computational discovery of sense-antisense transcription in the human and mouse genomes
-
RESEARCH0044
-
Shendure J, Church GM (2002) Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biol 3: RESEARCH0044.
-
(2002)
Genome Biol
, vol.3
-
-
Shendure, J.1
Church, G.M.2
-
15
-
-
69249217649
-
Regulatory roles of natural antisense transcripts
-
Faghihi MA, Wahlestedt C (2009) Regulatory roles of natural antisense transcripts. Nat Rev Mol Cell Biol 10: 637-643.
-
(2009)
Nat Rev Mol Cell Biol
, vol.10
, pp. 637-643
-
-
Faghihi, M.A.1
Wahlestedt, C.2
-
16
-
-
33646473694
-
Complex Loci in human and mouse genomes
-
Engstrom PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, et al. (2006) Complex Loci in human and mouse genomes. PLoS Genet 2: e47.
-
(2006)
PLoS Genet
, vol.2
-
-
Engstrom, P.G.1
Suzuki, H.2
Ninomiya, N.3
Akalin, A.4
Sessa, L.5
-
17
-
-
36049020719
-
Noncoding RNAs: Couplers of analog and digital information in nervous system function?
-
St Laurent G, 3rd, Wahlestedt C (2007) Noncoding RNAs: couplers of analog and digital information in nervous system function? Trends Neurosci 30: 612-621.
-
(2007)
Trends Neurosci
, vol.30
, pp. 612-621
-
-
St Laurent III, G.1
Wahlestedt, C.2
-
18
-
-
46749083733
-
Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase
-
Faghihi MA, Modarresi F, Khalil AM, Wood DE, Sahagan BG, et al. (2008) Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase. Nat Med 14: 723-730.
-
(2008)
Nat Med
, vol.14
, pp. 723-730
-
-
Faghihi, M.A.1
Modarresi, F.2
Khalil, A.M.3
Wood, D.E.4
Sahagan, B.G.5
-
19
-
-
33751018566
-
Human sat III and Drosophila hsr omega transcripts: A common paradigm for regulation of nuclear RNA processing in stressed cells
-
Jolly C, Lakhotia SC (2006) Human sat III and Drosophila hsr omega transcripts: a common paradigm for regulation of nuclear RNA processing in stressed cells. Nucleic Acids Res 34: 5508-5514.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 5508-5514
-
-
Jolly, C.1
Lakhotia, S.C.2
-
20
-
-
2442576104
-
Natural antisense transcripts of hypoxiainducible factor 1alpha are detected in different normal and tumour human tissues
-
Rossignol F, Vache C, Clottes E (2002) Natural antisense transcripts of hypoxiainducible factor 1alpha are detected in different normal and tumour human tissues. Gene 299: 135-140.
-
(2002)
Gene
, vol.299
, pp. 135-140
-
-
Rossignol, F.1
Vache, C.2
Clottes, E.3
-
21
-
-
24644481406
-
A strategy for probing the function of noncoding RNAs finds a repressor of NFAT
-
Willingham AT, Orth AP, Batalov S, Peters EC, Wen BG, et al. (2005) A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 309: 1570-1573.
-
(2005)
Science
, vol.309
, pp. 1570-1573
-
-
Willingham, A.T.1
Orth, A.P.2
Batalov, S.3
Peters, E.C.4
Wen, B.G.5
-
22
-
-
33846252240
-
Genomewide atlas of gene expression in the adult mouse brain
-
Lein ES, Hawrylycz MJ, Ao N, Ayres M, Bensinger A, et al. (2007) Genomewide atlas of gene expression in the adult mouse brain. Nature 445: 168-176.
-
(2007)
Nature
, vol.445
, pp. 168-176
-
-
Lein, E.S.1
Hawrylycz, M.J.2
Ao, N.3
Ayres, M.4
Bensinger, A.5
-
23
-
-
38649114329
-
Specific expression of long noncoding RNAs in the mouse brain
-
Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS (2008) Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A 105: 716-721.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 716-721
-
-
Mercer, T.R.1
Dinger, M.E.2
Sunkin, S.M.3
Mehler, M.F.4
Mattick, J.S.5
-
24
-
-
38049155825
-
Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA
-
Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J, et al. (2008) Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451: 202-206.
-
(2008)
Nature
, vol.451
, pp. 202-206
-
-
Yu, W.1
Gius, D.2
Onyango, P.3
Muldoon-Jacobs, K.4
Karp, J.5
-
25
-
-
72049133207
-
Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target
-
Swiezewski S, Liu F, Magusin A, Dean C (2009) Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462: 799-802.
-
(2009)
Nature
, vol.462
, pp. 799-802
-
-
Swiezewski, S.1
Liu, F.2
Magusin, A.3
Dean, C.4
-
26
-
-
36749016685
-
Genomescale RNAi profiling of cell division in human tissue culture cells
-
Kittler R, Pelletier L, Heninger AK, Slabicki M, Theis M, et al. (2007) Genomescale RNAi profiling of cell division in human tissue culture cells. Nat Cell Biol 9: 1401-1412.
-
(2007)
Nat Cell Biol
, vol.9
, pp. 1401-1412
-
-
Kittler, R.1
Pelletier, L.2
Heninger, A.K.3
Slabicki, M.4
Theis, M.5
-
28
-
-
39349097864
-
Identification of host proteins required for HIV infection through a functional genomic screen
-
Brass AL, Dykxhoorn DM, Benita Y, Yan N, Engelman A, et al. (2008) Identification of host proteins required for HIV infection through a functional genomic screen. Science 319: 921-926.
-
(2008)
Science
, vol.319
, pp. 921-926
-
-
Brass, A.L.1
Dykxhoorn, D.M.2
Benita, Y.3
Yan, N.4
Engelman, A.5
-
29
-
-
41649115887
-
Discovery of novel targets with high throughput RNA interference screening
-
Kassner PD (2008) Discovery of novel targets with high throughput RNA interference screening. Comb Chem High Throughput Screen 11: 175-188.
-
(2008)
Comb Chem High Throughput Screen
, vol.11
, pp. 175-188
-
-
Kassner, P.D.1
-
31
-
-
10744225153
-
Asymmetry in the assembly of the RNAi enzyme complex
-
Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, et al. (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115: 199-208.
-
(2003)
Cell
, vol.115
, pp. 199-208
-
-
Schwarz, D.S.1
Hutvagner, G.2
Du, T.3
Xu, Z.4
Aronin, N.5
-
32
-
-
33749023011
-
Minimizing the risk of reporting false positives in large-scale RNAi screens
-
Echeverri CJ, Beachy PA, Baum B, Boutros M, Buchholz F, et al. (2006) Minimizing the risk of reporting false positives in large-scale RNAi screens. Nat Methods 3: 777-779.
-
(2006)
Nat Methods
, vol.3
, pp. 777-779
-
-
Echeverri, C.J.1
Beachy, P.A.2
Baum, B.3
Boutros, M.4
Buchholz, F.5
-
33
-
-
70350490057
-
Epac1-induced cellular proliferation in prostate cancer cells is mediated by B-Raf/ERK and mTOR signaling cascades
-
Misra UK, Pizzo SV (2009) Epac1-induced cellular proliferation in prostate cancer cells is mediated by B-Raf/ERK and mTOR signaling cascades. J Cell Biochem 108: 998-1011.
-
(2009)
J Cell Biochem
, vol.108
, pp. 998-1011
-
-
Misra, U.K.1
Pizzo, S.V.2
-
34
-
-
34548067637
-
Differentially expressed genes in radioresistant nasopharyngeal cancer cells: Gp96 and GDF15
-
Chang JT, Chan SH, Lin CY, Lin TY, Wang HM, et al. (2007) Differentially expressed genes in radioresistant nasopharyngeal cancer cells: gp96 and GDF15. Mol Cancer Ther 6: 2271-2279.
-
(2007)
Mol Cancer Ther
, vol.6
, pp. 2271-2279
-
-
Chang, J.T.1
Chan, S.H.2
Lin, C.Y.3
Lin, T.Y.4
Wang, H.M.5
-
35
-
-
0032126179
-
Finemapping, genomic organization, and transcript analysis of the human ubiquitinconjugating enzyme gene UBE2L3
-
Moynihan TP, Cole CG, Dunham I, O'Neil L, Markham AF, et al. (1998) Finemapping, genomic organization, and transcript analysis of the human ubiquitinconjugating enzyme gene UBE2L3. Genomics 51: 124-127.
-
(1998)
Genomics
, vol.51
, pp. 124-127
-
-
Moynihan, T.P.1
Cole, C.G.2
Dunham, I.3
O'Neil, L.4
Markham, A.F.5
-
36
-
-
16544380610
-
Mouse transcriptome: Neutral evolution of 'non-coding' complementary DNAs
-
1 p following 757; discussion following 757
-
Wang J, Zhang J, Zheng H, Li J, Liu D, et al. (2004) Mouse transcriptome: neutral evolution of 'non-coding' complementary DNAs. Nature 431: 1 p following 757; discussion following 757.
-
(2004)
Nature
, vol.431
-
-
Wang, J.1
Zhang, J.2
Zheng, H.3
Li, J.4
Liu, D.5
-
37
-
-
34248162440
-
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs
-
Ponjavic J, Ponting CP, Lunter G (2007) Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res 17: 556-565.
-
(2007)
Genome Res
, vol.17
, pp. 556-565
-
-
Ponjavic, J.1
Ponting, C.P.2
Lunter, G.3
-
38
-
-
34250743796
-
Transcriptional interferences in cis natural antisense transcripts of humans and mice
-
Osato N, Suzuki Y, Ikeo K, Gojobori T (2007) Transcriptional interferences in cis natural antisense transcripts of humans and mice. Genetics 176: 1299-1306.
-
(2007)
Genetics
, vol.176
, pp. 1299-1306
-
-
Osato, N.1
Suzuki, Y.2
Ikeo, K.3
Gojobori, T.4
-
39
-
-
44349130233
-
Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes
-
Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S, et al. (2008) Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature.
-
(2008)
Nature
-
-
Watanabe, T.1
Totoki, Y.2
Toyoda, A.3
Kaneda, M.4
Kuramochi-Miyagawa, S.5
-
40
-
-
51349095532
-
Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster
-
Okamura K, Balla S, Martin R, Liu N, Lai EC (2008) Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster. Nat Struct Mol Biol 15: 998.
-
(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
-
41
-
-
50149095122
-
Endogenous small interfering RNAs in animals
-
Okamura K, Lai EC (2008) Endogenous small interfering RNAs in animals. Nat Rev Mol Cell Biol 9: 673-678.
-
(2008)
Nat Rev Mol Cell Biol
, vol.9
, pp. 673-678
-
-
Okamura, K.1
Lai, E.C.2
-
43
-
-
24644443227
-
The functional genomics of noncoding RNA
-
Mattick JS (2005) The functional genomics of noncoding RNA. Science 309: 1527-1528.
-
(2005)
Science
, vol.309
, pp. 1527-1528
-
-
Mattick, J.S.1
-
45
-
-
13744254695
-
A large-scale analysis of mRNA polyadenylation of human and mouse genes
-
Tian B, Hu J, Zhang H, Lutz CS (2005) A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res 33: 201-212.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 201-212
-
-
Tian, B.1
Hu, J.2
Zhang, H.3
Lutz, C.S.4
-
46
-
-
60149099385
-
Evolution and functions of long noncoding RNAs
-
Ponting CP, Oliver PL, Reik W (2009) Evolution and functions of long noncoding RNAs. Cell 136: 629-641.
-
(2009)
Cell
, vol.136
, pp. 629-641
-
-
Ponting, C.P.1
Oliver, P.L.2
Reik, W.3
-
47
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15: 1034-1050.
-
(2005)
Genome Res
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
Bejerano, G.2
Pedersen, J.S.3
Hinrichs, A.S.4
Hou, M.5
-
48
-
-
29444457713
-
Rapid evolution of noncoding RNAs: Lack of conservation does not mean lack of function
-
Pang KC, Frith MC, Mattick JS (2006) Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet 22: 1-5.
-
(2006)
Trends Genet
, vol.22
, pp. 1-5
-
-
Pang, K.C.1
Frith, M.C.2
Mattick, J.S.3
-
49
-
-
33748675254
-
An RNA gene expressed during cortical development evolved rapidly in humans
-
Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, et al. (2006) An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443: 167-172.
-
(2006)
Nature
, vol.443
, pp. 167-172
-
-
Pollard, K.S.1
Salama, S.R.2
Lambert, N.3
Lambot, M.A.4
Coppens, S.5
-
50
-
-
31844455816
-
Primate-specific endogenous cis-antisense transcription in the human 5q31 protocadherin gene cluster
-
Lipovich L, Vanisri RR, Kong SL, Lin CY, Liu ET (2006) Primate-specific endogenous cis-antisense transcription in the human 5q31 protocadherin gene cluster. J Mol Evol 62: 73-88.
-
(2006)
J Mol Evol
, vol.62
, pp. 73-88
-
-
Lipovich, L.1
Vanisri, R.R.2
Kong, S.L.3
Lin, C.Y.4
Liu, E.T.5
-
51
-
-
44949246486
-
A novel RNA transcript with antiapoptotic function is silenced in fragile x syndrome
-
Khalil AM, Faghihi MA, Modarresi F, Brothers SP, Wahlestedt C (2008) A novel RNA transcript with antiapoptotic function is silenced in fragile x syndrome. PLoS ONE 3: e1486.
-
(2008)
PLoS ONE
, vol.3
-
-
Khalil, A.M.1
Faghihi, M.A.2
Modarresi, F.3
Brothers, S.P.4
Wahlestedt, C.5
-
52
-
-
31144467231
-
Rodent BDNF genes, novel promoters, novel splice variants, and regulation by cocaine
-
Liu QR, Lu L, Zhu XG, Gong JP, Shaham Y, et al. (2006) Rodent BDNF genes, novel promoters, novel splice variants, and regulation by cocaine. Brain Res 1067: 1-12.
-
(2006)
Brain Res
, vol.1067
, pp. 1-12
-
-
Liu, Q.R.1
Lu, L.2
Zhu, X.G.3
Gong, J.P.4
Shaham, Y.5
-
53
-
-
34547499702
-
Dissecting the human BDNF locus: Bidirectional transcription, complex splicing, and multiple promoters
-
Pruunsild P, Kazantseva A, Aid T, Palm K, Timmusk T (2007) Dissecting the human BDNF locus: bidirectional transcription, complex splicing, and multiple promoters. Genomics 90: 397-406.
-
(2007)
Genomics
, vol.90
, pp. 397-406
-
-
Pruunsild, P.1
Kazantseva, A.2
Aid, T.3
Palm, K.4
Timmusk, T.5
-
54
-
-
34948906343
-
antiCODE: A natural senseantisense transcripts database
-
Yin Y, Zhao Y, Wang J, Liu C, Chen S, et al. (2007) antiCODE: a natural senseantisense transcripts database. BMC Bioinformatics 8: 319.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 319
-
-
Yin, Y.1
Zhao, Y.2
Wang, J.3
Liu, C.4
Chen, S.5
-
56
-
-
35748962289
-
Tools for visually exploring biological networks
-
Suderman M, Hallett M (2007) Tools for visually exploring biological networks. Bioinformatics 23: 2651-2659.
-
(2007)
Bioinformatics
, vol.23
, pp. 2651-2659
-
-
Suderman, M.1
Hallett, M.2
|