-
2
-
-
79955005458
-
SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer
-
Askarian-Amiri ME, Crawford J, French JD, Smart CE, Smith MA, Clark MB, Mattick JS (2011) SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA 17:878–891
-
(2011)
RNA
, vol.17
, pp. 878-891
-
-
Askarian-Amiri, M.E.1
Crawford, J.2
French, J.D.3
Smart, C.E.4
Smith, M.A.5
Clark, M.B.6
Mattick, J.S.7
-
3
-
-
81855178276
-
Somatic retrotransposition alters the genetic landscape of the human brain
-
Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, Faulkner GJ (2011) Somatic retrotransposition alters the genetic landscape of the human brain. Nature 479:534–537
-
(2011)
Nature
, vol.479
, pp. 534-537
-
-
Baillie, J.K.1
Barnett, M.W.2
Upton, K.R.3
Gerhardt, D.J.4
Richmond, T.A.5
De Sapio, F.6
Faulkner, G.J.7
-
5
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, de Jong PJ (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816
-
(2007)
Nature
, vol.447
, pp. 799-816
-
-
Birney, E.1
Stamatoyannopoulos, J.A.2
Dutta, A.3
Guigo, R.4
Gingeras, T.R.5
Margulies, E.H.6
De Jong, P.J.7
-
6
-
-
0032865868
-
RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements
-
Brosius J (1999) RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238:115–134
-
(1999)
Gene
, vol.238
, pp. 115-134
-
-
Brosius, J.1
-
7
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Hayashizaki Y (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
Maeda, N.6
Hayashizaki, Y.7
-
8
-
-
46149104377
-
Evo-devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution
-
Carroll SB (2008) Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 134:25–36
-
(2008)
Cell
, vol.134
, pp. 25-36
-
-
Carroll, S.B.1
-
9
-
-
21044431735
-
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
-
Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Gingeras TR (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
Patel, S.6
Gingeras, T.R.7
-
10
-
-
79960911703
-
The reality of pervasive transcription
-
Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Mattick JS (2011) The reality of pervasive transcription. PLoS Biol 9:e1000625
-
(2011)
Plos Biol
, pp. 9
-
-
Clark, M.B.1
Amaral, P.P.2
Schlesinger, F.J.3
Dinger, M.E.4
Taft, R.J.5
Rinn, J.L.6
Mattick, J.S.7
-
13
-
-
50649118350
-
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
-
Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Mattick JS (2008) Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 18:1433–1445
-
(2008)
Genome Res
, vol.18
, 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
Mattick, J.S.7
-
15
-
-
84875847924
-
Is junk DNA bunk? A critique of ENCODE
-
Doolittle WF (2013) Is junk DNA bunk? A critique of ENCODE. Proc Natl Acad Sci USA 110:5294–5300
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, pp. 5294-5300
-
-
Doolittle, W.F.1
-
16
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Birney E (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
Dunham, I.1
Kundaje, A.2
Aldred, S.F.3
Collins, P.J.4
Davis, C.A.5
Doyle, F.6
Birney, E.7
-
17
-
-
67349173665
-
The regulated retrotransposon transcriptome of mammalian cells
-
Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Carninci P (2009) The regulated retrotransposon transcriptome of mammalian cells. Nat Genet 41:563–571
-
(2009)
Nat Genet
, vol.41
, pp. 563-571
-
-
Faulkner, G.J.1
Kimura, Y.2
Daub, C.O.3
Wani, S.4
Plessy, C.5
Irvine, K.M.6
Carninci, P.7
-
18
-
-
33645833857
-
Conservation of RET regulatory function from human to zebrafish without sequence similarity
-
Fisher S, Grice EA, Vinton RM, Bessling SL, McCallion AS (2006) Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science 312:276–279
-
(2006)
Science
, vol.312
, pp. 276-279
-
-
Fisher, S.1
Grice, E.A.2
Vinton, R.M.3
Bessling, S.L.4
McCallion, A.S.5
-
19
-
-
33744824906
-
Evolutionary turnover of mammalian transcription start sites
-
Frith MC, Ponjavic J, Fredman D, Kai C, Kawai J, Carninci P, Sandelin A (2006) Evolutionary turnover of mammalian transcription start sites. Genome Res 16:713–722
-
(2006)
Genome Res
, vol.16
, pp. 713-722
-
-
Frith, M.C.1
Ponjavic, J.2
Fredman, D.3
Kai, C.4
Kawai, J.5
Carninci, P.6
Sandelin, A.7
-
20
-
-
84875275808
-
On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE
-
Graur D, Zheng Y, Price N, Azevedo RB, Zufall RA, Elhaik E (2013) On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol 5:578–590
-
(2013)
Genome Biol Evol
, vol.5
, pp. 578-590
-
-
Graur, D.1
Zheng, Y.2
Price, N.3
Azevedo, R.B.4
Zufall, R.A.5
Elhaik, E.6
-
21
-
-
77951118936
-
Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis
-
Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Chang HY (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464:1071–1076
-
(2010)
Nature
, vol.464
, pp. 1071-1076
-
-
Gupta, R.A.1
Shah, N.2
Wang, K.C.3
Kim, J.4
Horlings, H.M.5
Wong, D.J.6
Chang, H.Y.7
-
22
-
-
80052869283
-
Lander ES (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation
-
Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Lander ES (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477:295–300
-
Nature
, vol.477
, pp. 295-300
-
-
Guttman, M.1
Donaghey, J.2
Carey, B.W.3
Garber, M.4
Grenier, J.K.5
Munson, G.6
-
23
-
-
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, Perera RJ (2011) The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion. Cancer Res 71:3852–3862
-
(2011)
Cancer Res
, vol.71
, 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
-
24
-
-
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, Rinn JL (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA 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
Rinn, J.L.7
-
25
-
-
77952212771
-
RNA traffic control of chromatin complexes
-
Koziol MJ, Rinn JL (2010) RNA traffic control of chromatin complexes. Curr Opin Genet Dev 20:142–148
-
(2010)
Curr Opin Genet Dev
, vol.20
, pp. 142-148
-
-
Koziol, M.J.1
Rinn, J.L.2
-
26
-
-
3943107461
-
Role of a neuronal small non-messenger RNA: Behavioural alterations in BC1 RNA-deleted mice
-
Lewejohann L, Skryabin BV, Sachser N, Prehn C, Heiduschka P, Thanos S, Prior H (2004) Role of a neuronal small non-messenger RNA: behavioural alterations in BC1 RNA-deleted mice. Behav Brain Res 154:273–289
-
(2004)
Behav Brain Res
, vol.154
, pp. 273-289
-
-
Lewejohann, L.1
Skryabin, B.V.2
Sachser, N.3
Prehn, C.4
Heiduschka, P.5
Thanos, S.6
Prior, H.7
-
27
-
-
84879758121
-
A meta-analysis of the genomic and transcriptomic composition of complex life
-
Liu G, Mattick JS, Taft RJ (2013) A meta-analysis of the genomic and transcriptomic composition of complex life. Cell Cycle 12:127–138
-
(2013)
Cell Cycle
, vol.12
, pp. 127-138
-
-
Liu, G.1
Mattick, J.S.2
Taft, R.J.3
-
28
-
-
33645798112
-
Genome-wide identification of human functional DNA using a neutral indel model
-
Lunter G, Ponting CP, Hein J (2006) Genome-wide identification of human functional DNA using a neutral indel model. PLoS Comput Biol 2:e5
-
(2006)
Plos Comput Biol
, vol.2
, pp. 5
-
-
Lunter, G.1
Ponting, C.P.2
Hein, J.3
-
29
-
-
0028631058
-
Mattick JS (1994) Introns: Evolution and function
-
Mattick JS (1994) Introns: evolution and function. Curr Opin Genet Dev 4:823–831
-
Curr Opin Genet Dev
, vol.4
, pp. 823-831
-
-
-
30
-
-
1842584883
-
RNA regulation: A new genetics?
-
Mattick JS (2004) RNA regulation: a new genetics? Nat Rev Genet 5:316–323
-
(2004)
Nat Rev Genet
, vol.5
, pp. 316-323
-
-
Mattick, J.S.1
-
31
-
-
34249740942
-
A new paradigm for developmental biology
-
Mattick JS (2007) A new paradigm for developmental biology. J Exp Biol 210:1526–1547
-
(2007)
J Exp Biol
, vol.210
, pp. 1526-1547
-
-
Mattick, J.S.1
-
32
-
-
70350460793
-
Deconstructing the dogma: A new view of the evolution and genetic programming of complex organisms
-
Mattick JS (2009a) Deconstructing the dogma: a new view of the evolution and genetic programming of complex organisms. Ann N Y Acad Sci 1178:29–46
-
(2009)
Ann N Y Acad Sci
, vol.1178
, pp. 29-46
-
-
Mattick, J.S.1
-
33
-
-
65649092633
-
The genetic signatures of noncoding RNAs
-
Mattick JS (2009b) The genetic signatures of noncoding RNAs. PLoS Genet 5:e1000459
-
(2009)
Plos Genet
, pp. 5
-
-
Mattick, J.S.1
-
34
-
-
67650091292
-
Has evolution learnt how to learn?
-
Mattick JS (2009c) Has evolution learnt how to learn? EMBO Rep 10:665
-
(2009)
EMBO Rep
, vol.10
, pp. 665
-
-
Mattick, J.S.1
-
35
-
-
79957537160
-
The central role of RNA in human development and cognition
-
Mattick JS (2011) The central role of RNA in human development and cognition. FEBS Lett 585:1600–1616
-
(2011)
FEBS Lett
, vol.585
, pp. 1600-1616
-
-
Mattick, J.S.1
-
36
-
-
0034882101
-
The evolution of controlled multitasked gene networks: The role of introns and other noncoding RNAs in the development of complex organisms
-
Mattick JS, Gagen MJ (2001) The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms. Mol Biol Evol 18:1611–1630
-
(2001)
Mol Biol Evol
, vol.18
, pp. 1611-1630
-
-
Mattick, J.S.1
Gagen, M.J.2
-
37
-
-
59849088220
-
RNA regulation of epigenetic processes
-
Mattick JS, Amaral PP, Dinger ME, Mercer TR, Mehler MF (2009) RNA regulation of epigenetic processes. Bioessays 31:51–59
-
(2009)
Bioessays
, vol.31
, pp. 51-59
-
-
Mattick, J.S.1
Amaral, P.P.2
Dinger, M.E.3
Mercer, T.R.4
Mehler, M.F.5
-
38
-
-
72449129174
-
A global view of genomic information–moving beyond the gene and the master regulator
-
Mattick JS, Taft RJ, Faulkner GJ (2010) A global view of genomic information–moving beyond the gene and the master regulator. Trends Genet 26:21–28
-
(2010)
Trends Genet
, vol.26
, pp. 21-28
-
-
Mattick, J.S.1
Taft, R.J.2
Faulkner, G.J.3
-
39
-
-
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 USA 105:716–721
-
(2008)
Proc Natl Acad Sci USA
, 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
-
40
-
-
76649122999
-
Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation
-
Mercer TR, Qureshi IA, Gokhan S, Dinger ME, Li G, Mattick JS, Mehler MF (2010) Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. BMC Neurosci 11:14
-
(2010)
BMC Neurosci
, vol.11
, pp. 14
-
-
Mercer, T.R.1
Qureshi, I.A.2
Gokhan, S.3
Dinger, M.E.4
Li, G.5
Mattick, J.S.6
Mehler, M.F.7
-
41
-
-
84855539848
-
Targeted RNA sequencing reveals the deep complexity of the human transcriptome
-
Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Rinn JL (2012) Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotech 30:99–104
-
(2012)
Nat Biotech
, vol.30
, pp. 99-104
-
-
Mercer, T.R.1
Gerhardt, D.J.2
Dinger, M.E.3
Crawford, J.4
Trapnell, C.5
Jeddeloh, J.A.6
Rinn, J.L.7
-
42
-
-
56549111129
-
The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin
-
Nagano T, Mitchell JA, Sanz LA, Pauler FM, Ferguson-Smith AC, Feil R, Fraser P (2008) The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 322:1717–1720
-
(2008)
Science
, vol.322
, pp. 1717-1720
-
-
Nagano, T.1
Mitchell, J.A.2
Sanz, L.A.3
Pauler, F.M.4
Ferguson-Smith, A.C.5
Feil, R.6
Fraser, P.7
-
43
-
-
84856492490
-
Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors
-
Ng SY, Johnson R, Stanton LW (2012) Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors. Embo J 31:522–533
-
(2012)
Embo J
, vol.31
, pp. 522-533
-
-
Ng, S.Y.1
Johnson, R.2
Stanton, L.W.3
-
44
-
-
84872861423
-
Can ENCODE tell us how much junk DNA we carry in our genome?
-
Niu DK, Jiang L (2013) Can ENCODE tell us how much junk DNA we carry in our genome? Biochem Biophys Res Commun 430:1340–1343
-
(2013)
Biochem Biophys Res Commun
, vol.430
, pp. 1340-1343
-
-
Niu, D.K.1
Jiang, L.2
-
46
-
-
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, Kanduri C (2008) Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell 32:232–246
-
(2008)
Mol Cell
, vol.32
, pp. 232-246
-
-
Pandey, R.R.1
Mondal, T.2
Mohammad, F.3
Enroth, S.4
Redrup, L.5
Komorowski, J.6
Kanduri, C.7
-
47
-
-
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
-
48
-
-
67649160600
-
Genome-wide identification of long noncoding RNAs in CD8+ T cells
-
Pang KC, Dinger ME, Mercer TR, Malquori L, Grimmond SM, Chen W, Mattick JS (2009) Genome-wide identification of long noncoding RNAs in CD8+ T cells. J Immunol 182:7738–7748
-
(2009)
J Immunol
, vol.182
, pp. 7738-7748
-
-
Pang, K.C.1
Dinger, M.E.2
Mercer, T.R.3
Malquori, L.4
Grimmond, S.M.5
Chen, W.6
Mattick, J.S.7
-
49
-
-
34548432104
-
Raising the estimate of functional human sequences
-
Pheasant M, Mattick JS (2007) Raising the estimate of functional human sequences. Genome Res 17:1245–1253
-
(2007)
Genome Res
, vol.17
, pp. 1245-1253
-
-
Pheasant, M.1
Mattick, J.S.2
-
50
-
-
81555208922
-
RNA-Seq and find: Entering the RNA deep field
-
Roberts A, Pachter L (2011) RNA-Seq and find: entering the RNA deep field. Genome Med 3:74
-
(2011)
Genome Med
, vol.3
, pp. 74
-
-
Roberts, A.1
Pachter, L.2
-
52
-
-
4744370251
-
Evidence for turnover of functional noncoding DNA in mammalian genome evolution
-
Smith NG, Brandstrom M, Ellegren H (2004) Evidence for turnover of functional noncoding DNA in mammalian genome evolution. Genomics 84:806–813
-
(2004)
Genomics
, vol.84
, pp. 806-813
-
-
Smith, N.G.1
Brandstrom, M.2
Ellegren, H.3
-
53
-
-
79957538539
-
RNA templating the epigenome: Long noncoding RNAs as molecular scaffolds
-
Spitale RC, Tsai MC, Chang HY (2011) RNA templating the epigenome: Long noncoding RNAs as molecular scaffolds. Epigenetics 6:539–43
-
(2011)
Epigenetics
, vol.6
, pp. 539-543
-
-
Spitale, R.C.1
Tsai, M.C.2
Chang, H.Y.3
-
54
-
-
61849113891
-
MEN ε/β 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, Spector DL (2009) MEN ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 19:347–359
-
(2009)
Genome Res
, vol.19
, 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
-
55
-
-
33847698971
-
The relationship between non-protein-coding DNA and eukaryotic complexity
-
Taft RJ, Pheasant M, Mattick JS (2007) The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 29:288–299
-
(2007)
Bioessays
, vol.29
, pp. 288-299
-
-
Taft, R.J.1
Pheasant, M.2
Mattick, J.S.3
-
56
-
-
33646489947
-
Heterotachy in mammalian promoter evolution
-
Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Semple CA (2006) Heterotachy in mammalian promoter evolution. PLoS Genet 2:e30
-
(2006)
Plos Genet
, vol.30
, pp. 2
-
-
Taylor, M.S.1
Kai, C.2
Kawai, J.3
Carninci, P.4
Hayashizaki, Y.5
Semple, C.A.6
-
58
-
-
84857153213
-
-
Discovery Institute Press, Seattle
-
Wells J (2011) The Myth of Junk DNA. Discovery Institute Press, Seattle
-
(2011)
The Myth of Junk DNA
-
-
Wells, J.1
|