-
1
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, et al. The transcriptional landscape of the mammalian genome. Science. 2005; 309(5740):1559-1563.
-
(2005)
Science
, vol.309
, Issue.5740
, pp. 1559-1563
-
-
Carninci, P.1
Kasukawa, T.2
Katayama, S.3
Gough, J.4
Frith, M.C.5
Maeda, N.6
Oyama, R.7
Ravasi, T.8
Lenhard, B.9
Wells, C.10
Kodzius, R.11
Shimokawa, K.12
Bajic, V.B.13
Brenner, S.E.14
Batalov, S.15
Forrest, A.R.16
-
2
-
-
21044431735
-
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
-
Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, Sementchenko V, Piccolboni A, Bekiranov S, Bailey DK, Ganesh M, Ghosh S, et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science. 2005; 308(5725):1149-1154.
-
(2005)
Science
, vol.308
, Issue.5725
, pp. 1149-1154
-
-
Cheng, J.1
Kapranov, P.2
Drenkow, J.3
Dike, S.4
Brubaker, S.5
Patel, S.6
Long, J.7
Stern, D.8
Tammana, H.9
Helt, G.10
Sementchenko, V.11
Piccolboni, A.12
Bekiranov, S.13
Bailey, D.K.14
Ganesh, M.15
Ghosh, S.16
-
3
-
-
60349120914
-
Long non-coding RNAs: insights into functions
-
Mercer TR, Dinger ME and Mattick JS. Long non-coding RNAs: insights into functions. Nat Rev Genet. 2009; 10(3):155-159.
-
(2009)
Nat Rev Genet
, vol.10
, Issue.3
, pp. 155-159
-
-
Mercer, T.R.1
Dinger, M.E.2
Mattick, J.S.3
-
4
-
-
84864927713
-
Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs
-
Moran VA, Perera RJ and Khalil AM. Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs. Nucleic Acids Res. 2012; 40(14):6391-6400.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.14
, pp. 6391-6400
-
-
Moran, V.A.1
Perera, R.J.2
Khalil, A.M.3
-
5
-
-
59849088220
-
RNA regulation of epigenetic processes
-
Mattick JS, Amaral PP, Dinger ME, Mercer TR and Mehler MF. RNA regulation of epigenetic processes. Bioessays. 2009; 31(1):51-59.
-
(2009)
Bioessays
, vol.31
, Issue.1
, pp. 51-59
-
-
Mattick, J.S.1
Amaral, P.P.2
Dinger, M.E.3
Mercer, T.R.4
Mehler, M.F.5
-
6
-
-
84875183056
-
Structure and function of long noncoding RNAs in epigenetic regulation
-
Mercer TR and Mattick JS. Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol. 2013; 20(3):300-307.
-
(2013)
Nat Struct Mol Biol
, vol.20
, Issue.3
, pp. 300-307
-
-
Mercer, T.R.1
Mattick, J.S.2
-
7
-
-
84865839598
-
Long noncoding RNAs are rarely translated in two human cell lines
-
Banfai B, Jia H, Khatun J, Wood E, Risk B, Gundling WE, Jr., Kundaje A, Gunawardena HP, Yu Y, Xie L, Krajewski K, Strahl BD, Chen X, Bickel P, Giddings MC, Brown JB, et al. Long noncoding RNAs are rarely translated in two human cell lines. Genome research. 2012; 22(9):1646-1657.
-
(2012)
Genome research
, vol.22
, Issue.9
, pp. 1646-1657
-
-
Banfai, B.1
Jia, H.2
Khatun, J.3
Wood, E.4
Risk, B.5
Gundling, W.E.6
Kundaje, A.7
Gunawardena, H.P.8
Yu, Y.9
Xie, L.10
Krajewski, K.11
Strahl, B.D.12
Chen, X.13
Bickel, P.14
Giddings, M.C.15
Brown, J.B.16
-
8
-
-
84870417305
-
Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes
-
Gascoigne DK, Cheetham SW, Cattenoz PB, Clark MB, Amaral PP, Taft RJ, Wilhelm D, Dinger ME and Mattick JS. Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes. Bioinformatics. 2012; 28(23):3042-3050.
-
(2012)
Bioinformatics
, vol.28
, Issue.23
, pp. 3042-3050
-
-
Gascoigne, D.K.1
Cheetham, S.W.2
Cattenoz, P.B.3
Clark, M.B.4
Amaral, P.P.5
Taft, R.J.6
Wilhelm, D.7
Dinger, M.E.8
Mattick, J.S.9
-
9
-
-
79960911703
-
The reality of pervasive transcription
-
discussion e1001102
-
Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Ponting CP, Stadler PF, Morris KV, Morillon A, Rozowsky JS, Gerstein MB, Wahlestedt C, Hayashizaki Y, Carninci P, Gingeras TR, et al. The reality of pervasive transcription. PLoS Biol. 2011; 9(7):e1000625; discussion e1001102.
-
(2011)
PLoS Biol
, vol.9
, Issue.7
-
-
Clark, M.B.1
Amaral, P.P.2
Schlesinger, F.J.3
Dinger, M.E.4
Taft, R.J.5
Rinn, J.L.6
Ponting, C.P.7
Stadler, P.F.8
Morris, K.V.9
Morillon, A.10
Rozowsky, J.S.11
Gerstein, M.B.12
Wahlestedt, C.13
Hayashizaki, Y.14
Carninci, P.15
Gingeras, T.R.16
-
10
-
-
73949085491
-
Non-coding RNAs: regulators of disease
-
Taft RJ, Pang KC, Mercer TR, Dinger M and Mattick JS. Non-coding RNAs: regulators of disease. J Pathol. 2010; 220(2):126-139.
-
(2010)
J Pathol
, vol.220
, Issue.2
, pp. 126-139
-
-
Taft, R.J.1
Pang, K.C.2
Mercer, T.R.3
Dinger, M.4
Mattick, J.S.5
-
11
-
-
56949091456
-
Noncoding RNA in development
-
Amaral PP and Mattick JS. Noncoding RNA in development. Mamm Genome. 2008; 19(7-8):454-492.
-
(2008)
Mamm Genome
, vol.19
, Issue.7-8
, pp. 454-492
-
-
Amaral, P.P.1
Mattick, J.S.2
-
12
-
-
38649114329
-
Specific expression of long noncoding RNAs in the mouse brain
-
Mercer TR, Dinger ME, Sunkin SM, Mehler MF and Mattick JS. Specific expression of long noncoding RNAs in the mouse brain. Proceedings of the National Academy of Sciences of the United States of America. 2008; 105(2):716-721.
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.2
, pp. 716-721
-
-
Mercer, T.R.1
Dinger, M.E.2
Sunkin, S.M.3
Mehler, M.F.4
Mattick, J.S.5
-
13
-
-
61849113891
-
MEN varepsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles
-
Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS and Spector DL. MEN varepsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome research. 2009; 19(3):347-359.
-
(2009)
Genome research
, vol.19
, Issue.3
, pp. 347-359
-
-
Sunwoo, H.1
Dinger, M.E.2
Wilusz, J.E.3
Amaral, P.P.4
Mattick, J.S.5
Spector, D.L.6
-
14
-
-
79957907741
-
The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion
-
Khaitan D, Dinger ME, Mazar J, Crawford J, Smith MA, Mattick JS and Perera RJ. The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion. Cancer Res. 2011; 71(11):3852-3862.
-
(2011)
Cancer Res
, vol.71
, Issue.11
, pp. 3852-3862
-
-
Khaitan, D.1
Dinger, M.E.2
Mazar, J.3
Crawford, J.4
Smith, M.A.5
Mattick, J.S.6
Perera, R.J.7
-
15
-
-
54049138948
-
Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation
-
Pandey RR, Mondal T, Mohammad F, Enroth S, Redrup L, Komorowski J, Nagano T, Mancini-Dinardo D and Kanduri C. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell. 2008; 32(2):232-246.
-
(2008)
Mol Cell
, vol.32
, Issue.2
, pp. 232-246
-
-
Pandey, R.R.1
Mondal, T.2
Mohammad, F.3
Enroth, S.4
Redrup, L.5
Komorowski, J.6
Nagano, T.7
Mancini-Dinardo, D.8
Kanduri, C.9
-
16
-
-
44649152934
-
The role of long non-coding RNAs in chromatin structure and gene regulation: variations on a theme
-
Umlauf D, Fraser P and Nagano T. The role of long non-coding RNAs in chromatin structure and gene regulation: variations on a theme. Biol Chem. 2008; 389(4):323-331.
-
(2008)
Biol Chem
, vol.389
, Issue.4
, pp. 323-331
-
-
Umlauf, D.1
Fraser, P.2
Nagano, T.3
-
17
-
-
84861904178
-
Genome regulation by long noncoding RNAs
-
Rinn JL and Chang HY. Genome regulation by long noncoding RNAs. Annu Rev Biochem. 2012; 81:145-166.
-
(2012)
Annu Rev Biochem
, vol.81
, pp. 145-166
-
-
Rinn, J.L.1
Chang, H.Y.2
-
18
-
-
50649118350
-
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
-
Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Askarian-Amiri ME, Ru K, Solda G, Simons C, Sunkin SM, Crowe ML, Grimmond SM, Perkins AC and Mattick JS. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res. 2008; 18(9):1433-1445.
-
(2008)
Genome Res
, vol.18
, Issue.9
, pp. 1433-1445
-
-
Dinger, M.E.1
Amaral, P.P.2
Mercer, T.R.3
Pang, K.C.4
Bruce, S.J.5
Gardiner, B.B.6
Askarian-Amiri, M.E.7
Ru, K.8
Solda, G.9
Simons, C.10
Sunkin, S.M.11
Crowe, M.L.12
Grimmond, S.M.13
Perkins, A.C.14
Mattick, J.S.15
-
19
-
-
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, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, Regev A, Lander ES and Rinn JL. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A. 2009; 106(28):11667-11672.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, Issue.28
, pp. 11667-11672
-
-
Khalil, A.M.1
Guttman, M.2
Huarte, M.3
Garber, M.4
Raj, A.5
Rivea Morales, D.6
Thomas, K.7
Presser, A.8
Bernstein, B.E.9
van Oudenaarden, A.10
Regev, A.11
Lander, E.S.12
Rinn, J.L.13
-
20
-
-
77954572735
-
Long noncoding RNA as modular scaffold of histone modification complexes
-
Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E and Chang HY. Long noncoding RNA as modular scaffold of histone modification complexes. Science. 2010; 329(5992):689-693.
-
(2010)
Science
, vol.329
, Issue.5992
, pp. 689-693
-
-
Tsai, M.C.1
Manor, O.2
Wan, Y.3
Mosammaparast, N.4
Wang, J.K.5
Lan, F.6
Shi, Y.7
Segal, E.8
Chang, H.Y.9
-
21
-
-
50649118350
-
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
-
Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Askarian-Amiri ME, Ru K, Solda G, Simons C, Sunkin SM, Crowe ML, Grimmond SM, Perkins AC and Mattick JS. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome research. 2008; 18(9):1433-1445.
-
(2008)
Genome research
, vol.18
, Issue.9
, pp. 1433-1445
-
-
Dinger, M.E.1
Amaral, P.P.2
Mercer, T.R.3
Pang, K.C.4
Bruce, S.J.5
Gardiner, B.B.6
Askarian-Amiri, M.E.7
Ru, K.8
Solda, G.9
Simons, C.10
Sunkin, S.M.11
Crowe, M.L.12
Grimmond, S.M.13
Perkins, A.C.14
Mattick, J.S.15
-
22
-
-
81355142141
-
Non-coding RNAs in human disease
-
Esteller M. Non-coding RNAs in human disease. Nat Rev Genet. 2011; 12(12):861-874.
-
(2011)
Nat Rev Genet
, vol.12
, Issue.12
, pp. 861-874
-
-
Esteller, M.1
-
23
-
-
84875891842
-
HOTAIR is a negative prognostic factor and exhibits pro-oncogenic activity in pancreatic cancer
-
Kim K, Jutooru I, Chadalapaka G, Johnson G, Frank J, Burghardt R, Kim S and Safe S. HOTAIR is a negative prognostic factor and exhibits pro-oncogenic activity in pancreatic cancer. Oncogene. 2012.
-
(2012)
Oncogene
-
-
Kim, K.1
Jutooru, I.2
Chadalapaka, G.3
Johnson, G.4
Frank, J.5
Burghardt, R.6
Kim, S.7
Safe, S.8
-
24
-
-
70449562559
-
Prostate cancer gene expression marker 1 (PCGEM1): a patented prostate-specific non-coding gene and regulator of prostate cancer progression
-
Ifere GO and Ananaba GA. Prostate cancer gene expression marker 1 (PCGEM1): a patented prostate-specific non-coding gene and regulator of prostate cancer progression. Recent Pat DNA Gene Seq. 2009; 3(3):151-163.
-
(2009)
Recent Pat DNA Gene Seq
, vol.3
, Issue.3
, pp. 151-163
-
-
Ifere, G.O.1
Ananaba, G.A.2
-
25
-
-
77952454961
-
Protein-coding and non-coding gene expression analysis in differentiating human keratinocytes using a three-dimensional epidermal equivalent
-
Mazar J, Sinha S, Dinger ME, Mattick JS and Perera RJ. Protein-coding and non-coding gene expression analysis in differentiating human keratinocytes using a three-dimensional epidermal equivalent. Mol Genet Genomics. 2010; 284(1):1-9.
-
(2010)
Mol Genet Genomics
, vol.284
, Issue.1
, pp. 1-9
-
-
Mazar, J.1
Sinha, S.2
Dinger, M.E.3
Mattick, J.S.4
Perera, R.J.5
-
26
-
-
9144252038
-
Complete sequencing and characterization of 21,243 full-length human cDNAs
-
Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie R, Wakamatsu A, Hayashi K, Sato H, Nagai K, Kimura K, Makita H, Sekine M, Obayashi M, Nishi T, Shibahara T, et al. Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet. 2004; 36(1):40-45.
-
(2004)
Nat Genet
, vol.36
, Issue.1
, pp. 40-45
-
-
Ota, T.1
Suzuki, Y.2
Nishikawa, T.3
Otsuki, T.4
Sugiyama, T.5
Irie, R.6
Wakamatsu, A.7
Hayashi, K.8
Sato, H.9
Nagai, K.10
Kimura, K.11
Makita, H.12
Sekine, M.13
Obayashi, M.14
Nishi, T.15
Shibahara, T.16
-
27
-
-
0032719944
-
Vertebrate Sprouty genes are induced by FGF signaling and can cause chondrodysplasia when overexpressed
-
Minowada G, Jarvis LA, Chi CL, Neubuser A, Sun X, Hacohen N, Krasnow MA and Martin GR. Vertebrate Sprouty genes are induced by FGF signaling and can cause chondrodysplasia when overexpressed. Development. 1999; 126(20):4465-4475.
-
(1999)
Development
, vol.126
, Issue.20
, pp. 4465-4475
-
-
Minowada, G.1
Jarvis, L.A.2
Chi, C.L.3
Neubuser, A.4
Sun, X.5
Hacohen, N.6
Krasnow, M.A.7
Martin, G.R.8
-
28
-
-
84864453787
-
The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
-
Ingolia NT, Brar GA, Rouskin S, McGeachy AM and Weissman JS. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nature protocols. 2012; 7(8):1534-1550.
-
(2012)
Nature protocols
, vol.7
, Issue.8
, pp. 1534-1550
-
-
Ingolia, N.T.1
Brar, G.A.2
Rouskin, S.3
McGeachy, A.M.4
Weissman, J.S.5
-
29
-
-
65449172036
-
Lipin 2 is a liver-enriched phosphatidate phosphohydrolase enzyme that is dynamically regulated by fasting and obesity in mice
-
Gropler MC, Harris TE, Hall AM, Wolins NE, Gross RW, Han X, Chen Z and Finck BN. Lipin 2 is a liver-enriched phosphatidate phosphohydrolase enzyme that is dynamically regulated by fasting and obesity in mice. The Journal of biological chemistry. 2009; 284(11):6763-6772.
-
(2009)
The Journal of biological chemistry
, vol.284
, Issue.11
, pp. 6763-6772
-
-
Gropler, M.C.1
Harris, T.E.2
Hall, A.M.3
Wolins, N.E.4
Gross, R.W.5
Han, X.6
Chen, Z.7
Finck, B.N.8
-
30
-
-
56349113455
-
3' end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA
-
Wilusz JE, Freier SM and Spector DL. 3' end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell. 2008; 135(5):919-932.
-
(2008)
Cell
, vol.135
, Issue.5
, pp. 919-932
-
-
Wilusz, J.E.1
Freier, S.M.2
Spector, D.L.3
-
31
-
-
77956411754
-
Mining mammalian transcript data for functional long non-coding RNAs
-
Khachane AN and Harrison PM. Mining mammalian transcript data for functional long non-coding RNAs. PLoS One. 2010; 5(4):e10316.
-
(2010)
PLoS One
, vol.5
, Issue.4
, pp. e10316
-
-
Khachane, A.N.1
Harrison, P.M.2
-
33
-
-
65449172036
-
Lipin 2 is a liver-enriched phosphatidate phosphohydrolase enzyme that is dynamically regulated by fasting and obesity in mice
-
Gropler MC, Harris TE, Hall AM, Wolins NE, Gross RW, Han X, Chen Z and Finck BN. Lipin 2 is a liver-enriched phosphatidate phosphohydrolase enzyme that is dynamically regulated by fasting and obesity in mice. J Biol Chem. 2009; 284(11):6763-6772.
-
(2009)
J Biol Chem
, vol.284
, Issue.11
, pp. 6763-6772
-
-
Gropler, M.C.1
Harris, T.E.2
Hall, A.M.3
Wolins, N.E.4
Gross, R.W.5
Han, X.6
Chen, Z.7
Finck, B.N.8
-
34
-
-
33846438568
-
Regulation of mTOR by phosphatidic acid?
-
Foster DA. Regulation of mTOR by phosphatidic acid? Cancer Res. 2007; 67(1):1-4.
-
(2007)
Cancer Res
, vol.67
, Issue.1
, pp. 1-4
-
-
Foster, D.A.1
-
35
-
-
79953691809
-
NCI60 cancer cell line panel data and RNAi analysis help identify EAF2 as a modulator of simvastatin and lovastatin response in HCT-116 cells
-
Savas S, Azorsa DO, Jarjanazi H, Ibrahim-Zada I, Gonzales IM, Arora S, Henderson MC, Choi YH, Briollais L, Ozcelik H and Tuzmen S. NCI60 cancer cell line panel data and RNAi analysis help identify EAF2 as a modulator of simvastatin and lovastatin response in HCT-116 cells. PLoS One. 2011; 6(4):e18306.
-
(2011)
PLoS One
, vol.6
, Issue.4
, pp. e18306
-
-
Savas, S.1
Azorsa, D.O.2
Jarjanazi, H.3
Ibrahim-Zada, I.4
Gonzales, I.M.5
Arora, S.6
Henderson, M.C.7
Choi, Y.H.8
Briollais, L.9
Ozcelik, H.10
Tuzmen, S.11
|