-
1
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, et al. The transcriptional landscape of the mammalian genome. Science 2005;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
Maeda, N.6
-
2
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
The ENCODE Project Consortium
-
The ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007;447: 799-816.
-
(2007)
Nature
, vol.447
, pp. 799-816
-
-
-
4
-
-
34248162440
-
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs
-
Ponjavic J, Ponting CP, Lunter G. Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res 2007;17:556-565.
-
(2007)
Genome Res
, vol.17
, pp. 556-565
-
-
Ponjavic, J.1
Ponting, C.P.2
Lunter, G.3
-
5
-
-
0142104045
-
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
-
Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 2002;420:563-573.
-
(2002)
Nature
, vol.420
, pp. 563-573
-
-
Okazaki, Y.1
Furuno, M.2
Kasukawa, T.3
Adachi, J.4
Bono, H.5
Kondo, S.6
-
6
-
-
84862188358
-
ModMine: Flexible access to modENCODE data
-
Contrino S, Smith RN, Butano D, Carr A, Hu F, Lyne R, et al. modMine: flexible access to modENCODE data. Nucleic Acids Res 2012;40:D1082-D1088.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. D1082-D1088
-
-
Contrino, S.1
Smith, R.N.2
Butano, D.3
Carr, A.4
Hu, F.5
Lyne, R.6
-
7
-
-
0035656688
-
Non-coding RNA genes and the modern RNA world
-
Eddy SR. Non-coding RNA genes and the modern RNA world. Nat Rev Genet 2001;2:919-929.
-
(2001)
Nat Rev Genet
, vol.2
, pp. 919-929
-
-
Eddy, S.R.1
-
9
-
-
60149099385
-
Evolution and functions of long noncoding RNAs
-
Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell 2009;136:629-641.
-
(2009)
Cell
, vol.136
, pp. 629-641
-
-
Ponting, C.P.1
Oliver, P.L.2
Reik, W.3
-
10
-
-
73949085491
-
Noncoding RNAs regulators of disease
-
Taft RJ, Pang KC, Mercer TR, Dinger M, Mattick JS. Noncoding RNAs: regulators of disease. J Pathol 2010;220: 126-139.
-
(2010)
J Pathol
, vol.220
, pp. 126-139
-
-
Taft, R.J.1
Pang, K.C.2
Mercer, T.R.3
Dinger, M.4
Mattick, J.S.5
-
11
-
-
81355142141
-
Non-coding RNAs in human disease
-
Esteller M. Non-coding RNAs in human disease. Nat Rev Genet 2011;12:861-874.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 861-874
-
-
Esteller, M.1
-
12
-
-
79957533104
-
Non-coding RNAs as regulators of gene expression and epigenetics
-
Kaikkonen MU, Lam MT, Glass CK. Non-coding RNAs as regulators of gene expression and epigenetics. Cardiovasc Res 2011;90:430-440.
-
(2011)
Cardiovasc Res
, vol.90
, pp. 430-440
-
-
Kaikkonen, M.U.1
Lam, M.T.2
Glass, C.K.3
-
13
-
-
26944495173
-
MicroRNA function in animal development
-
Wienholds E, Plasterk RH. MicroRNA function in animal development. FEBS Lett 2005;579:5911-5922.
-
(2005)
FEBS Lett
, vol.579
, pp. 5911-5922
-
-
Wienholds, E.1
Plasterk, R.H.2
-
14
-
-
33645124258
-
Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs
-
Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S, Inoue K, et al. Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 2006; 312:75-79.
-
(2006)
Science
, vol.312
, pp. 75-79
-
-
Giraldez, A.J.1
Mishima, Y.2
Rihel, J.3
Grocock, R.J.4
Van Dongen, S.5
Inoue, K.6
-
15
-
-
77953897182
-
A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity
-
Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, et al. A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity. Science 2010;328:1694-1698.
-
(2010)
Science
, vol.328
, pp. 1694-1698
-
-
Cifuentes, D.1
Xue, H.2
Taylor, D.W.3
Patnode, H.4
Mishima, Y.5
Cheloufi, S.6
-
16
-
-
84862778053
-
Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish
-
Bazzini AA, Lee MT, Giraldez AJ. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 2012;336:233-237.
-
(2012)
Science
, vol.336
, pp. 233-237
-
-
Bazzini, A.A.1
Lee, M.T.2
Giraldez, A.J.3
-
17
-
-
84871398891
-
Reverse genetics screen in zebrafish identifies a role of miR-142a-3p in vascular development and integrity
-
Lalwani MK, Sharma M, Singh AR, Chauhan RK, Patowary A, Singh N, et al. Reverse genetics screen in zebrafish identifies a role of miR-142a-3p in vascular development and integrity. PLoS One 2012;7:e52588.
-
(2012)
PLoS One
, vol.7
, pp. e52588
-
-
Lalwani, M.K.1
Sharma, M.2
Singh, A.R.3
Chauhan, R.K.4
Patowary, A.5
Singh, N.6
-
18
-
-
67649671961
-
Long noncoding RNAs: Functional surprises from the RNA world
-
Wilusz JE, Sunwoo H, Spector DL. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev 2009; 23:1494-1504.
-
(2009)
Genes Dev
, vol.23
, pp. 1494-1504
-
-
Wilusz, J.E.1
Sunwoo, H.2
Spector, D.L.3
-
19
-
-
0025809321
-
Parental imprinting of the mouse H19 gene
-
Bartolomei MS, Zemel S, Tilghman SM. Parental imprinting of the mouse H19 gene. Nature 1991;351:153-155.
-
(1991)
Nature
, vol.351
, pp. 153-155
-
-
Bartolomei, M.S.1
Zemel, S.2
Tilghman, S.M.3
-
20
-
-
0026456701
-
The human XIST gene: Analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus
-
Brown CJ, Hendrich BD, Rupert JL, Lafreniere RG, Xing Y, Lawrence J, et al. The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 1992;71:527-542.
-
(1992)
Cell
, vol.71
, pp. 527-542
-
-
Brown, C.J.1
Hendrich, B.D.2
Rupert, J.L.3
Lafreniere, R.G.4
Xing, Y.5
Lawrence, J.6
-
21
-
-
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, Feldser D, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009;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
Feldser, D.6
-
22
-
-
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, Regev A, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 2011;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
Regev, A.6
-
23
-
-
84870566023
-
Long noncoding RNAs in C elegans
-
Nam JW, Bartel DP. Long noncoding RNAs in C. elegans. Genome Res 2012;22:2529-2540.
-
(2012)
Genome Res
, vol.22
, pp. 2529-2540
-
-
Nam, J.W.1
Bartel, D.P.2
-
24
-
-
84864098110
-
Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome
-
Young RS, Marques AC, Tibbit C, Haerty W, Bassett AR, Liu JL, et al. Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome. Genome Biol Evol 2012;4:427-442.
-
(2012)
Genome Biol Evol
, vol.4
, pp. 427-442
-
-
Young, R.S.1
Marques, A.C.2
Tibbit, C.3
Haerty, W.4
Bassett, A.R.5
Liu, J.L.6
-
25
-
-
84865727393
-
The GENCODE v7 catalog of human long 506 HAQUE et AL noncoding RNAs: Analysis of their gene structure, evolution, and expression
-
Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, et al. The GENCODE v7 catalog of human long 506 HAQUE ET AL. noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 2012;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
Tilgner, H.6
-
26
-
-
84891798006
-
NONCODEv4: Exploring the world of long non-coding RNA genes
-
Xie C, Yuan J, Li H, Li M, Zhao G, Bu D, et al. NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res 2014;42:D98-D103.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D98-D103
-
-
Xie, C.1
Yuan, J.2
Li, H.3
Li, M.4
Zhao, G.5
Bu, D.6
-
27
-
-
78651314039
-
Update of the FANTOM web resource: From mammalian transcriptional landscape to its dynamic regulation
-
Kawaji H, Severin J, Lizio M, Forrest AR, van Nimwegen E, Rehli M, et al. Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Nucleic Acids Res 2011;39:D856-D860.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D856-D860
-
-
Kawaji, H.1
Severin, J.2
Lizio, M.3
Forrest, A.R.4
Van Nimwegen, E.5
Rehli, M.6
-
28
-
-
84455206362
-
Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution
-
Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP. Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 2011; 147:1537-1550.
-
(2011)
Cell
, vol.147
, pp. 1537-1550
-
-
Ulitsky, I.1
Shkumatava, A.2
Jan, C.H.3
Sive, H.4
Bartel, D.P.5
-
29
-
-
84857836107
-
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
-
Pauli A, Valen E, Lin MF, Garber M, Vastenhouw NL, Levin JZ, et al. Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res 2012;22:577-591.
-
(2012)
Genome Res
, vol.22
, pp. 577-591
-
-
Pauli, A.1
Valen, E.2
Lin, M.F.3
Garber, M.4
Vastenhouw, N.L.5
Levin, J.Z.6
-
30
-
-
84894226828
-
Dynamic expression of long non-coding RNAs (lncRNAs) in adult zebrafish
-
Kaushik K, Leonard VE, Shamsudheen KV, Lalwani MK, Jalali S, Patowary A, et al. Dynamic expression of long non-coding RNAs (lncRNAs) in adult zebrafish. PLoS One 2013;8:e83616.
-
(2013)
PLoS One
, vol.8
, pp. e83616
-
-
Kaushik, K.1
Leonard, V.E.2
Shamsudheen, K.V.3
Lalwani, M.K.4
Jalali, S.5
Patowary, A.6
-
32
-
-
84894532371
-
On the classification of long non-coding RNAs
-
Ma L, Bajic VB, Zhang Z. On the classification of long non-coding RNAs. RNA Biol 2013;10:925-933.
-
(2013)
RNA Biol
, vol.10
, pp. 925-933
-
-
Ma, L.1
Bajic, V.B.2
Zhang, Z.3
-
33
-
-
81055150443
-
Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer
-
Tahira AC, Kubrusly MS, Faria MF, Dazzani B, Fonseca RS, Maracaja-Coutinho V, et al. Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer. Mol Cancer 2011;10:141.
-
(2011)
Mol Cancer
, vol.10
, pp. 141
-
-
Tahira, A.C.1
Kubrusly, M.S.2
Faria, M.F.3
Dazzani, B.4
Fonseca, R.S.5
Maracaja-Coutinho, V.6
-
34
-
-
78650966670
-
Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA
-
Heo JB, Sung S. Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 2011;331: 76-79.
-
(2011)
Science
, vol.331
, pp. 76-79
-
-
Heo, J.B.1
Sung, S.2
-
35
-
-
84891870087
-
Comprehensive analysis of the transcriptional landscape of the human FMR1 gene reveals two new long noncoding RNAs differentially expressed in Fragile X syndrome and Fragile X-associated tremor/ataxia syndrome
-
Pastori C, Peschansky VJ, Barbouth D, Mehta A, Silva JP, Wahlestedt C. Comprehensive analysis of the transcriptional landscape of the human FMR1 gene reveals two new long noncoding RNAs differentially expressed in Fragile X syndrome and Fragile X-associated tremor/ataxia syndrome. Hum Genet 2014;133:59-67.
-
(2014)
Hum Genet
, vol.133
, pp. 59-67
-
-
Pastori, C.1
Peschansky, V.J.2
Barbouth, D.3
Mehta, A.4
Silva, J.P.5
Wahlestedt, C.6
-
36
-
-
24644472515
-
Antisense transcription in the mammalian transcriptome
-
Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, et al. Antisense transcription in the mammalian transcriptome. Science 2005;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
Nakamura, M.6
-
37
-
-
84868705910
-
Long noncoding RNAs in cardiac development and pathophysiology
-
Schonrock N, Harvey RP, Mattick JS. Long noncoding RNAs in cardiac development and pathophysiology. Circ Res 2012;111:1349-1362.
-
(2012)
Circ Res
, vol.111
, pp. 1349-1362
-
-
Schonrock, N.1
Harvey, R.P.2
Mattick, J.S.3
-
38
-
-
84879987789
-
LincRNAs: Genomics, evolution, and mechanisms
-
Ulitsky I, Bartel DP. lincRNAs: genomics, evolution, and mechanisms. Cell 2013;154:26-46.
-
(2013)
Cell
, vol.154
, pp. 26-46
-
-
Ulitsky, I.1
Bartel, D.P.2
-
39
-
-
2542542256
-
Ultraconserved elements in the human genome
-
Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, et al. Ultraconserved elements in the human genome. Science 2004;304:1321-1325.
-
(2004)
Science
, vol.304
, pp. 1321-1325
-
-
Bejerano, G.1
Pheasant, M.2
Makunin, I.3
Stephen, S.4
Kent, W.J.5
Mattick, J.S.6
-
40
-
-
84856805631
-
Expression levels of transcribed ultraconserved regions uc.73 and uc.388 are altered in colorectal cancer
-
Sana J, Hankeova S, Svoboda M, Kiss I, Vyzula R, Slaby O. Expression levels of transcribed ultraconserved regions uc.73 and uc.388 are altered in colorectal cancer. Oncology 2012;82:114-118.
-
(2012)
Oncology
, vol.82
, pp. 114-118
-
-
Sana, J.1
Hankeova, S.2
Svoboda, M.3
Kiss, I.4
Vyzula, R.5
Slaby, O.6
-
41
-
-
79953673245
-
Expression of distinct RNAs from 3¢ untranslated regions
-
Mercer TR, Wilhelm D, Dinger ME, Soldà G, Korbie DJ, Glazov EA, et al. Expression of distinct RNAs from 3¢ untranslated regions. Nucleic Acids Res 2011;39:2393-2403.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 2393-2403
-
-
Mercer, T.R.1
Wilhelm, D.2
Dinger, M.E.3
Soldà, G.4
Korbie, D.J.5
Glazov, E.A.6
-
42
-
-
77952367798
-
Widespread transcription at neuronal activity-regulated enhancers
-
Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 2010;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
Wu, J.6
-
43
-
-
84884928187
-
The Igf2/H19 muscle enhancer is an active transcriptional complex
-
Eun B, Sampley ML, Van Winkle MT, Good AL, Kachman MM, Pfeifer K. The Igf2/H19 muscle enhancer is an active transcriptional complex. Nucleic Acids Res 2013;41:8126-8134.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 8126-8134
-
-
Eun, B.1
Sampley, M.L.2
Van Winkle, M.T.3
Good, A.L.4
Kachman, M.M.5
Pfeifer, K.6
-
44
-
-
80053045739
-
Molecular mechanisms of long noncoding RNAs
-
Wang KC, Chang HY. Molecular mechanisms of long noncoding RNAs. Mol Cell 2011;43:904-914.
-
(2011)
Mol Cell
, vol.43
, pp. 904-914
-
-
Wang, K.C.1
Chang, H.Y.2
-
45
-
-
84864927713
-
Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs
-
Moran VA, Perera RJ, Khalil AM. Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs. Nucleic Acids Res 2012;40:6391-6400.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 6391-6400
-
-
Moran, V.A.1
Perera, R.J.2
Khalil, A.M.3
-
46
-
-
84875590101
-
Long noncoding RNAs: Past, present, and future
-
Kung JT, Colognori D, Lee JT. Long noncoding RNAs: past, present, and future. Genetics 2013;193:651-669.
-
(2013)
Genetics
, vol.193
, pp. 651-669
-
-
Kung, J.T.1
Colognori, D.2
Lee, J.T.3
-
47
-
-
77956927823
-
The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation
-
Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 2010;39:925-938.
-
(2010)
Mol Cell
, vol.39
, pp. 925-938
-
-
Tripathi, V.1
Ellis, J.D.2
Shen, Z.3
Song, D.Y.4
Pan, Q.5
Watt, A.T.6
-
48
-
-
84861491678
-
Conceptual approaches for lncRNA drug discovery and future strategies
-
Bhartiya D, Kapoor S, Jalali S, Sati S, Kaushik K, Sachidanandan C, et al. Conceptual approaches for lncRNA drug discovery and future strategies. Expert Opin Drug Discov 2012;7:503-513.
-
(2012)
Expert Opin Drug Discov
, vol.7
, pp. 503-513
-
-
Bhartiya, D.1
Kapoor, S.2
Jalali, S.3
Sati, S.4
Kaushik, K.5
Sachidanandan, C.6
-
49
-
-
84885912472
-
LncRNome: A comprehensive knowledgebase of human long noncoding RNAs
-
(Oxford) bat034
-
Bhartiya D, Pal K, Ghosh S, Kapoor S, Jalali S, Panwar B, et al. lncRNome: a comprehensive knowledgebase of human long noncoding RNAs. Database (Oxford) 2013;2013: bat034.
-
(2013)
Database
, pp. 2013
-
-
Bhartiya, D.1
Pal, K.2
Ghosh, S.3
Kapoor, S.4
Jalali, S.5
Panwar, B.6
-
50
-
-
84873550059
-
Systematic transcriptome wide analysis of lncRNA-miRNA interactions
-
Jalali S, Bhartiya D, Lalwani MK, Sivasubbu S, Scaria V. Systematic transcriptome wide analysis of lncRNA-miRNA interactions. PLoS One 2013;8:e53823.
-
(2013)
PLoS One
, vol.8
, pp. e53823
-
-
Jalali, S.1
Bhartiya, D.2
Lalwani, M.K.3
Sivasubbu, S.4
Scaria, V.5
-
51
-
-
84893441632
-
MicroRNA-9 targets the long non-coding RNA MALAT1 for degradation in the nucleus
-
Leucci E, Patella F, Waage J, Holmstrøm K, Lindow M, Porse B, et al. microRNA-9 targets the long non-coding RNA MALAT1 for degradation in the nucleus. Sci Rep 2013;3:2535.
-
(2013)
Sci Rep
, vol.3
, pp. 2535
-
-
Leucci, E.1
Patella, F.2
Waage, J.3
Holmstrøm, K.4
Lindow, M.5
Porse, B.6
-
52
-
-
61849133411
-
Long intronic noncoding RNA transcription: Expression noise or expression choice?
-
Louro R, Smirnova AS, Verjovski-Almeida S. Long intronic noncoding RNA transcription: expression noise or expression choice? Genomics 2009;93:291-298.
-
(2009)
Genomics
, vol.93
, pp. 291-298
-
-
Louro, R.1
Smirnova, A.S.2
Verjovski-Almeida, S.3
-
53
-
-
29444457713
-
Rapid evolution of noncoding RNAs: Lack of conservation does not mean lack of function
-
Pang KC, Frith MC, Mattick JS. Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet 2006;22:1-5.
-
(2006)
Trends Genet
, vol.22
, pp. 1-5
-
-
Pang, K.C.1
Frith, M.C.2
Mattick, J.S.3
-
54
-
-
84864739324
-
Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs
-
Jalali S, Jayaraj GG, Scaria V. Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs. Biol Direct 2012;7:25.
-
(2012)
Biol Direct
, vol.7
, pp. 25
-
-
Jalali, S.1
Jayaraj, G.G.2
Scaria, V.3
-
55
-
-
84876864345
-
Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs
-
Kapusta A, Kronenberg Z, Lynch VJ, Zhuo X, Ramsay L, Bourque G, et al. Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet 2013;9: e1003470.
-
(2013)
PLoS Genet
, vol.9
, pp. e1003470
-
-
Kapusta, A.1
Kronenberg, Z.2
Lynch, V.J.3
Zhuo, X.4
Ramsay, L.5
Bourque, G.6
-
56
-
-
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, et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA 2009; 106:11667-11672.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 11667-11672
-
-
Khalil, A.M.1
Guttman, M.2
Huarte, M.3
Garber, M.4
Raj, A.5
Rivea Morales, D.6
-
57
-
-
74949140605
-
A noncoding antisense RNA in tie-1 locus regulates tie-1 function in vivo
-
Li K, Blum Y, Verma A, Liu Z, Pramanik K, Leigh NR, et al. A noncoding antisense RNA in tie-1 locus regulates tie-1 function in vivo. Blood 2010;115:133-139.
-
(2010)
Blood
, vol.115
, pp. 133-139
-
-
Li, K.1
Blum, Y.2
Verma, A.3
Liu, Z.4
Pramanik, K.5
Leigh, N.R.6
-
58
-
-
84896695852
-
Knockdown of PU.1 mRNA and AS lncRNA regulates expression of immune-related genes in zebrafish Danio rerio
-
Wei N, Pang W, Wang Y, Xiong Y, Xu R, Wu W, et al. Knockdown of PU.1 mRNA and AS lncRNA regulates expression of immune-related genes in zebrafish Danio rerio. Dev Comp Immunol 2014;44:315-319.
-
(2014)
Dev Comp Immunol
, vol.44
, pp. 315-319
-
-
Wei, N.1
Pang, W.2
Wang, Y.3
Xiong, Y.4
Xu, R.5
Wu, W.6
-
59
-
-
84896385370
-
An evolutionarily conserved long noncoding RNA TUNA controls pluripotency and neural lineage commitment
-
Lin N, Chang KY, Li Z, Gates K, Rana ZA, Dang J, et al. An evolutionarily conserved long noncoding RNA TUNA controls pluripotency and neural lineage commitment. Mol Cell 2014;53:1005-1019.
-
(2014)
Mol Cell
, vol.53
, pp. 1005-1019
-
-
Lin, N.1
Chang, K.Y.2
Li, Z.3
Gates, K.4
Rana, Z.A.5
Dang, J.6
-
60
-
-
70350118664
-
Complex architecture and regulated expression of the Sox2ot locus during vertebrate development
-
Amaral PP, Neyt C, Wilkins SJ, Askarian-Amiri ME, Sunkin SM, Perkins AC, et al. Complex architecture and regulated expression of the Sox2ot locus during vertebrate development. RNA 2009;15:2013-2027.
-
(2009)
RNA
, vol.15
, pp. 2013-2027
-
-
Amaral, P.P.1
Neyt, C.2
Wilkins, S.J.3
Askarian-Amiri, M.E.4
Sunkin, S.M.5
Perkins, A.C.6
-
61
-
-
80052576353
-
The midblastula transition defines the onset of y RNA-dependent DNA replication in Xenopus laevis
-
Collart C, Christov CP, Smith JC, Krude T. The midblastula transition defines the onset of Y RNA-dependent DNA replication in Xenopus laevis. Mol Cell Biol 2011;31: 3857-3870.
-
(2011)
Mol Cell Biol
, vol.31
, pp. 3857-3870
-
-
Collart, C.1
Christov, C.P.2
Smith, J.C.3
Krude, T.4
-
62
-
-
45549090297
-
FishMap: A community resource for zebrafish genomics
-
Meli R, Prasad A, Patowary A, Lalwani MK, Maini J, Sharma M, et al. FishMap: a community resource for zebrafish genomics. Zebrafish 2008;5:125-130.
-
(2008)
Zebrafish
, vol.5
, pp. 125-130
-
-
Meli, R.1
Prasad, A.2
Patowary, A.3
Lalwani, M.K.4
Maini, J.5
Sharma, M.6
-
63
-
-
77953623103
-
FishMap Zv8 update - A genomic regulatory map of zebrafish
-
Bhartiya D, Maini J, Sharma M, Joshi P, Laddha SV, Jalali S, et al. FishMap Zv8 update-a genomic regulatory map of zebrafish. Zebrafish 2010;7:179-180.
-
(2010)
Zebrafish
, vol.7
, pp. 179-180
-
-
Bhartiya, D.1
Maini, J.2
Sharma, M.3
Joshi, P.4
Laddha, S.V.5
Jalali, S.6
-
64
-
-
84876273475
-
A sequence-based variation map of zebrafish
-
Patowary A, Purkanti R, Singh M, Chauhan R, Singh AR, Swarnkar M, et al. A sequence-based variation map of zebrafish. Zebrafish 2013;10:15-20.
-
(2013)
Zebrafish
, vol.10
, pp. 15-20
-
-
Patowary, A.1
Purkanti, R.2
Singh, M.3
Chauhan, R.4
Singh, A.R.5
Swarnkar, M.6
-
65
-
-
84876798186
-
The zebrafish reference genome sequence and its relationship to the human genome
-
Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature 2013; 496:498-503.
-
(2013)
Nature
, vol.496
, pp. 498-503
-
-
Howe, K.1
Clark, M.D.2
Torroja, C.F.3
Torrance, J.4
Berthelot, C.5
Muffato, M.6
-
66
-
-
30544437719
-
Transcriptome analysis of zebrafish embryogenesis using microarrays
-
Mathavan S, Lee SG, Mak A, Miller LD, Murthy KR, Govindarajan KR, et al. Transcriptome analysis of zebrafish embryogenesis using microarrays. PLoS Genet 2005;1:e29.
-
(2005)
PLoS Genet
, vol.1
, pp. e29
-
-
Mathavan, S.1
Lee, S.G.2
Mak, A.3
Miller, L.D.4
Murthy, K.R.5
Govindarajan, K.R.6
-
67
-
-
79955554921
-
Isolation and transcriptome analysis of adult zebrafish cells enriched for skeletal muscle progenitors
-
Alexander MS, Kawahara G, Kho AT, Howell MH, Pusack TJ, Myers JA, et al. Isolation and transcriptome analysis of adult zebrafish cells enriched for skeletal muscle progenitors. Muscle Nerve 2011;43:741-750.
-
(2011)
Muscle Nerve
, vol.43
, pp. 741-750
-
-
Alexander, M.S.1
Kawahara, G.2
Kho, A.T.3
Howell, M.H.4
Pusack, T.J.5
Myers, J.A.6
-
68
-
-
33646483032
-
The abundance of short proteins in the mammalian proteome
-
Frith MC, Forrest AR, Nourbakhsh E, Pang KC, Kai C, Kawai J, et al. The abundance of short proteins in the mammalian proteome. PLoS Genet 2006;2:e52.
-
(2006)
PLoS Genet
, vol.2
, pp. e52
-
-
Frith, M.C.1
Forrest, A.R.2
Nourbakhsh, E.3
Pang, K.C.4
Kai, C.5
Kawai, J.6
-
69
-
-
81055155799
-
Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
-
Ingolia NT, Lareau LF, Weissman JS. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 2011;147:789-802.
-
(2011)
Cell
, vol.147
, pp. 789-802
-
-
Ingolia, N.T.1
Lareau, L.F.2
Weissman, J.S.3
-
70
-
-
84878865619
-
Ribosome profiling reveals resemblance between long noncoding RNAs and 5¢ leaders of coding RNAs
-
Chew GL, Pauli A, Rinn JL, Regev A, Schier AF, Valen E. Ribosome profiling reveals resemblance between long noncoding RNAs and 5¢ leaders of coding RNAs. Development 2013;140:2828-2834.
-
(2013)
Development
, vol.140
, pp. 2828-2834
-
-
Chew, G.L.1
Pauli, A.2
Rinn, J.L.3
Regev, A.4
Schier, A.F.5
Valen, E.6
-
71
-
-
2442597244
-
The steroid receptor RNA activator is the first functional RNA encoding a protein
-
Chooniedass-Kothari S, Emberley E, Hamedani MK, Troup S, Wang X, Czosnek A, et al. The steroid receptor RNA activator is the first functional RNA encoding a protein. FEBS Lett 2004;566:43-47.
-
(2004)
FEBS Lett
, vol.566
, pp. 43-47
-
-
Chooniedass-Kothari, S.1
Emberley, E.2
Hamedani, M.K.3
Troup, S.4
Wang, X.5
Czosnek, A.6
-
72
-
-
80053572392
-
Steroid receptor RNA activator bi-faceted genetic system: Heads or tails?
-
Cooper C, Vincett D, Yan Y, Hamedani MK, Myal Y, Leygue E. Steroid receptor RNA activator bi-faceted genetic system: heads or tails? Biochimie 2011;93:1973-1980.
-
(2011)
Biochimie
, vol.93
, pp. 1973-1980
-
-
Cooper, C.1
Vincett, D.2
Yan, Y.3
Hamedani, M.K.4
Myal, Y.5
Leygue, E.6
-
73
-
-
84899884309
-
Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation
-
Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, et al. Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J 2014;33:981-993.
-
(2014)
EMBO J
, vol.33
, pp. 981-993
-
-
Bazzini, A.A.1
Johnstone, T.G.2
Christiano, R.3
MacKowiak, S.D.4
Obermayer, B.5
Fleming, E.S.6
-
74
-
-
84891749518
-
Toddler: An embryonic signal that promotes cell movement via Apelin receptors
-
Pauli A, Norris ML, Valen E, Chew GL, Gagnon JA, Zimmerman S, et al. Toddler: an embryonic signal that promotes cell movement via Apelin receptors. Science 2014;343: 1248636.
-
(2014)
Science
, vol.343
, pp. 1248636
-
-
Pauli, A.1
Norris, M.L.2
Valen, E.3
Chew, G.L.4
Gagnon, J.A.5
Zimmerman, S.6
-
75
-
-
84865609694
-
Whole transcriptome RNA sequencing detects multiple 1a,25-dihydroxyvitamin D3-sensitive metabolic pathways in developing zebrafish
-
Craig TA, Zhang Y, McNulty MS, Middha S, Ketha H, Singh RJ, et al. Whole transcriptome RNA sequencing detects multiple 1a,25-dihydroxyvitamin D3-sensitive metabolic pathways in developing zebrafish. Mol Endocrinol 2012;26:1630-1642.
-
(2012)
Mol Endocrinol
, vol.26
, pp. 1630-1642
-
-
Craig, T.A.1
Zhang, Y.2
McNulty, M.S.3
Middha, S.4
Ketha, H.5
Singh, R.J.6
-
76
-
-
84902305132
-
Detection of 1,25-dihydroxyvitamin D-regulated miRNAs in zebrafish by whole transcriptome sequencing
-
Craig TA, Zhang Y, Magis AT, Funk C, Price ND, Ekker SC, et al. Detection of 1,25-dihydroxyvitamin D-regulated miRNAs in zebrafish by whole transcriptome sequencing. Zebrafish 2014;11:207-218.
-
(2014)
Zebrafish
, vol.11
, pp. 207-218
-
-
Craig, T.A.1
Zhang, Y.2
Magis, A.T.3
Funk, C.4
Price, N.D.5
Ekker, S.C.6
-
77
-
-
79957840356
-
Long noncoding RNAs and human disease
-
Wapinski O, Chang HY. Long noncoding RNAs and human disease. Trends Cell Biol 2011;21:354-361.
-
(2011)
Trends Cell Biol
, vol.21
, pp. 354-361
-
-
Wapinski, O.1
Chang, H.Y.2
-
78
-
-
84876125829
-
LncRNADisease: A database for long-non-coding RNAassociated diseases
-
Chen G, Wang Z, Wang D, Qiu C, Liu M, Chen X, et al. LncRNADisease: a database for long-non-coding RNAassociated diseases. Nucleic Acids Res 2013;41:D983-D986.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D983-D986
-
-
Chen, G.1
Wang, Z.2
Wang, D.3
Qiu, C.4
Liu, M.5
Chen, X.6
-
79
-
-
33746817949
-
Gene-breaking transposon mutagenesis reveals an essential role for histone H2afza in zebrafish larval development
-
Sivasubbu S, Balciunas D, Davidson AE, Pickart MA, Hermanson SB, Wangensteen KJ, et al. Gene-breaking transposon mutagenesis reveals an essential role for histone H2afza in zebrafish larval development. Mech Dev 2006; 123:513-529.
-
(2006)
Mech Dev
, vol.123
, pp. 513-529
-
-
Sivasubbu, S.1
Balciunas, D.2
Davidson, A.E.3
Pickart, M.A.4
Hermanson, S.B.5
Wangensteen, K.J.6
-
81
-
-
84885413157
-
Inheritable and precise large genomic deletions of non-coding RNA genes in zebrafish using TALENs
-
Liu Y, Luo D, Zhao H, Zhu Z, Hu W, Cheng CH. Inheritable and precise large genomic deletions of non-coding RNA genes in zebrafish using TALENs. PLoS One 2013;8: e76387.
-
(2013)
PLoS One
, vol.8
, pp. e76387
-
-
Liu, Y.1
Luo, D.2
Zhao, H.3
Zhu, Z.4
Hu, W.5
Cheng, C.H.6
-
82
-
-
84900314611
-
CRISPR-Cas systems for editing, regulating and targeting genomes
-
Sander JD, Joung JK. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 2014;32: 347-355.
-
(2014)
Nat Biotechnol
, vol.32
, pp. 347-355
-
-
Sander, J.D.1
Joung, J.K.2
-
83
-
-
34547630727
-
Efficient genome-wide mutagenesis of zebrafish genes by retroviral insertions
-
Wang D, Jao LE, Zheng N, Dolan K, Ivey J, Zonies S, et al. Efficient genome-wide mutagenesis of zebrafish genes by retroviral insertions. Proc Natl Acad Sci USA 2007;104: 12428-12433.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 12428-12433
-
-
Wang, D.1
Jao, L.E.2
Zheng, N.3
Dolan, K.4
Ivey, J.5
Zonies, S.6
-
84
-
-
84875356531
-
The Zebrafish Insertion Collection (ZInC): A web based, searchable collection of zebrafish mutations generated by DNA insertion
-
Varshney GK, Huang H, Zhang S, Lu J, Gildea DE, Yang Z, et al. The Zebrafish Insertion Collection (ZInC): a web based, searchable collection of zebrafish mutations generated by DNA insertion. Nucleic Acids Res 2013;41:D861-D864.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D861-D864
-
-
Varshney, G.K.1
Huang, H.2
Zhang, S.3
Lu, J.4
Gildea, D.E.5
Yang, Z.6
|