-
1
-
-
81355142141
-
Non-coding RNAs in human disease
-
Esteller M, (2011) Non-coding RNAs in human disease. Nat Rev Genet 12: 861-874.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 861-874
-
-
Esteller, M.1
-
2
-
-
79751484450
-
Identification of miRNomes in human liver and hepatocellular carcinoma reveals miR-199a/b-3p as therapeutic target for hepatocellular carcinoma
-
Hou J, Lin L, Zhou W, Wang Z, Ding G, et al. (2011) Identification of miRNomes in human liver and hepatocellular carcinoma reveals miR-199a/b-3p as therapeutic target for hepatocellular carcinoma. Cancer Cell 19: 232-243.
-
(2011)
Cancer Cell
, vol.19
, pp. 232-243
-
-
Hou, J.1
Lin, L.2
Zhou, W.3
Wang, Z.4
Ding, G.5
-
3
-
-
78751570979
-
RNA sequencing: advances, challenges and opportunities
-
Ozsolak F, Milos PM, (2011) RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 12: 87-98.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 87-98
-
-
Ozsolak, F.1
Milos, P.M.2
-
4
-
-
62249133709
-
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
-
Guttman M, Amit I, Garber M, French C, Lin MF, et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458: 223-227.
-
(2009)
Nature
, vol.458
, pp. 223-227
-
-
Guttman, M.1
Amit, I.2
Garber, M.3
French, C.4
Lin, M.F.5
-
5
-
-
67650921949
-
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
-
Khalil AM, Guttman M, Huarte M, Garber M, Raj A, et al. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A 106: 11667-11672.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 11667-11672
-
-
Khalil, A.M.1
Guttman, M.2
Huarte, M.3
Garber, M.4
Raj, A.5
-
6
-
-
77957243921
-
Long noncoding RNAs with enhancer-like function in human cells
-
Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, et al. (2010) Long noncoding RNAs with enhancer-like function in human cells. Cell 143: 46-58.
-
(2010)
Cell
, vol.143
, pp. 46-58
-
-
Ørom, U.A.1
Derrien, T.2
Beringer, M.3
Gumireddy, K.4
Gardini, A.5
-
7
-
-
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
-
9
-
-
84876152425
-
Systematic study of human long intergenic non-coding RNAs and their impact on cancer
-
Sun L, Luo H, Liao Q, Bu D, Zhao G, et al. (2013) Systematic study of human long intergenic non-coding RNAs and their impact on cancer. Sci China Life Sci 56: 324-334.
-
(2013)
Sci China Life Sci
, vol.56
, pp. 324-334
-
-
Sun, L.1
Luo, H.2
Liao, Q.3
Bu, D.4
Zhao, G.5
-
10
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci P, Kasukawa T, Katayama S, Gough J, Frith M, et al. (2005) The transcriptional landscape of the mammalian genome. Science 309: 1559.
-
(2005)
Science
, vol.309
, pp. 1559
-
-
Carninci, P.1
Kasukawa, T.2
Katayama, S.3
Gough, J.4
Frith, M.5
-
11
-
-
77952148742
-
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
-
Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, et al. (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nature biotechnology 28: 503-510.
-
(2010)
Nature Biotechnology
, vol.28
, pp. 503-510
-
-
Guttman, M.1
Garber, M.2
Levin, J.Z.3
Donaghey, J.4
Robinson, J.5
-
12
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature biotechnology 28: 511-515.
-
(2010)
Nature Biotechnology
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
-
13
-
-
80052851950
-
Mouse genomic variation and its effect on phenotypes and gene regulation
-
Keane TM, Goodstadt L, Danecek P, White MA, Wong K, et al. (2011) Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 477: 289-294.
-
(2011)
Nature
, vol.477
, pp. 289-294
-
-
Keane, T.M.1
Goodstadt, L.2
Danecek, P.3
White, M.A.4
Wong, K.5
-
14
-
-
65449136284
-
TopHat: discovering splice junctions with RNA-Seq
-
Trapnell C, Pachter L, Salzberg SL, (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
15
-
-
33846057724
-
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
-
Pruitt KD, Tatusova T, Maglott DR, (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35: D61-65.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Pruitt, K.D.1
Tatusova, T.2
Maglott, D.R.3
-
16
-
-
80052978224
-
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
-
Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, et al. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes & Development 25: 1915-1927.
-
(2011)
Genes & Development
, vol.25
, pp. 1915-1927
-
-
Cabili, M.N.1
Trapnell, C.2
Goff, L.3
Koziol, M.4
Tazon-Vega, B.5
-
17
-
-
84860742355
-
NONCODE v3. 0: integrative annotation of long noncoding RNAs
-
Bu D, Yu K, Sun S, Xie C, Skogerbø G, et al. (2011) NONCODE v3. 0: integrative annotation of long noncoding RNAs. Nucleic acids research.
-
(2011)
Nucleic acids research
-
-
Bu, D.1
Yu, K.2
Sun, S.3
Xie, C.4
Skogerbø, G.5
-
19
-
-
84858221706
-
Ensembl 2012
-
Flicek P, Amode MR, Barrell D, Beal K, Brent S, et al. (2012) Ensembl 2012. Nucleic Acids Res 40: D84-90.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Flicek, P.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Brent, S.5
-
20
-
-
34547582418
-
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine
-
Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, et al. (2007) CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic acids research 35: W345-W349.
-
(2007)
Nucleic Acids Research
, vol.35
-
-
Kong, L.1
Zhang, Y.2
Ye, Z.Q.3
Liu, X.Q.4
Zhao, S.Q.5
-
21
-
-
79957842166
-
Computational methods for transcriptome annotation and quantification using RNA-seq
-
Garber M, Grabherr MG, Guttman M, Trapnell C, (2011) Computational methods for transcriptome annotation and quantification using RNA-seq. Nature methods 8: 469-477.
-
(2011)
Nature Methods
, vol.8
, pp. 469-477
-
-
Garber, M.1
Grabherr, M.G.2
Guttman, M.3
Trapnell, C.4
-
22
-
-
30044434769
-
Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome
-
Ravasi T, Suzuki H, Pang KC, Katayama S, Furuno M, et al. (2006) Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome research 16: 11-19.
-
(2006)
Genome Research
, vol.16
, pp. 11-19
-
-
Ravasi, T.1
Suzuki, H.2
Pang, K.C.3
Katayama, S.4
Furuno, M.5
-
23
-
-
79956010263
-
Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network
-
Liao Q, Liu C, Yuan X, Kang S, Miao R, et al. (2011) Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic Acids Res 39: 3864-3878.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 3864-3878
-
-
Liao, Q.1
Liu, C.2
Yuan, X.3
Kang, S.4
Miao, R.5
-
24
-
-
79959949911
-
ncFANs: a web server for functional annotation of long non-coding RNAs
-
Liao Q, Xiao H, Bu D, Xie C, Miao R, et al. (2011) ncFANs: a web server for functional annotation of long non-coding RNAs. Nucleic Acids Res 39: W118-124.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Liao, Q.1
Xiao, H.2
Bu, D.3
Xie, C.4
Miao, R.5
-
25
-
-
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 research 17: 556-565.
-
(2007)
Genome Research
, vol.17
, pp. 556-565
-
-
Ponjavic, J.1
Ponting, C.P.2
Lunter, G.3
-
26
-
-
80052869283
-
lincRNAs act in the circuitry controlling pluripotency and differentiation
-
Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, et al. (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477: 295-300.
-
(2011)
Nature
, vol.477
, pp. 295-300
-
-
Guttman, M.1
Donaghey, J.2
Carey, B.W.3
Garber, M.4
Grenier, J.K.5
-
27
-
-
84865727393
-
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression
-
Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, et al. (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22: 1775-1789.
-
(2012)
Genome Res
, vol.22
, pp. 1775-1789
-
-
Derrien, T.1
Johnson, R.2
Bussotti, G.3
Tanzer, A.4
Djebali, S.5
-
28
-
-
77952367798
-
Widespread transcription at neuronal activity-regulated enhancers
-
Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, et al. (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature 465: 182-187.
-
(2010)
Nature
, vol.465
, pp. 182-187
-
-
Kim, T.K.1
Hemberg, M.2
Gray, J.M.3
Costa, A.M.4
Bear, D.M.5
-
29
-
-
76249108851
-
Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness
-
Marques AC, Ponting CP, (2009) Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness. Genome Biol 10: R124.
-
(2009)
Genome Biol
, vol.10
-
-
Marques, A.C.1
Ponting, C.P.2
-
30
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
Bernstein, B.E.1
Birney, E.2
Dunham, I.3
Green, E.D.4
Gunter, C.5
-
31
-
-
84865757142
-
Landscape of transcription in human cells
-
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, et al. (2012) Landscape of transcription in human cells. Nature 489: 101-108.
-
(2012)
Nature
, vol.489
, pp. 101-108
-
-
Djebali, S.1
Davis, C.A.2
Merkel, A.3
Dobin, A.4
Lassmann, T.5
-
32
-
-
84865839598
-
Long noncoding RNAs are rarely translated in two human cell lines
-
Banfai B, Jia H, Khatun J, Wood E, Risk B, et al. (2012) Long noncoding RNAs are rarely translated in two human cell lines. Genome Res 22: 1646-1657.
-
(2012)
Genome Res
, vol.22
, pp. 1646-1657
-
-
Banfai, B.1
Jia, H.2
Khatun, J.3
Wood, E.4
Risk, B.5
-
33
-
-
84865728918
-
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome
-
Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, et al. (2012) Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res 22: 1698-1710.
-
(2012)
Genome Res
, vol.22
, pp. 1698-1710
-
-
Howald, C.1
Tanzer, A.2
Chrast, J.3
Kokocinski, F.4
Derrien, T.5
-
34
-
-
84867070330
-
Human beta Cell Transcriptome Analysis Uncovers lncRNAs That Are Tissue-Specific, Dynamically Regulated, and Abnormally Expressed in Type 2 Diabetes
-
Moran I, Akerman I, van de Bunt M, Xie R, Benazra M, et al. (2012) Human beta Cell Transcriptome Analysis Uncovers lncRNAs That Are Tissue-Specific, Dynamically Regulated, and Abnormally Expressed in Type 2 Diabetes. Cell Metab 16: 435-448.
-
(2012)
Cell Metab
, vol.16
, pp. 435-448
-
-
Moran, I.1
Akerman, I.2
van de Bunt, M.3
Xie, R.4
Benazra, M.5
-
35
-
-
84876848171
-
Genome-Wide Analysis of Human SNPs at Long Intergenic Noncoding RNAs
-
Chen G, Qiu C, Zhang Q, Liu B, Cui Q (2012) Genome-Wide Analysis of Human SNPs at Long Intergenic Noncoding RNAs. Hum Mutat.
-
(2012)
Hum Mutat
-
-
Chen, G.1
Qiu, C.2
Zhang, Q.3
Liu, B.4
Cui, Q.5
-
36
-
-
38549148703
-
The vertebrate genome annotation (Vega) database
-
Wilming LG, Gilbert JG, Howe K, Trevanion S, Hubbard T, et al. (2008) The vertebrate genome annotation (Vega) database. Nucleic Acids Res 36: D753-760.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Wilming, L.G.1
Gilbert, J.G.2
Howe, K.3
Trevanion, S.4
Hubbard, T.5
-
37
-
-
33745614319
-
PseudoPipe: an automated pseudogene identification pipeline
-
Zhang Z, Carriero N, Zheng D, Karro J, Harrison PM, et al. (2006) PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics 22: 1437-1439.
-
(2006)
Bioinformatics
, vol.22
, pp. 1437-1439
-
-
Zhang, Z.1
Carriero, N.2
Zheng, D.3
Karro, J.4
Harrison, P.M.5
-
38
-
-
80052978224
-
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
-
Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, et al. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25: 1915-1927.
-
(2011)
Genes Dev
, vol.25
, pp. 1915-1927
-
-
Cabili, M.N.1
Trapnell, C.2
Goff, L.3
Koziol, M.4
Tazon-Vega, B.5
|