-
1
-
-
33747322165
-
Tagging mammalian transcription complexity
-
Carninci P, ((2006)) Tagging mammalian transcription complexity. Trends Genet 22: 501-510.
-
(2006)
Trends Genet
, vol.22
, pp. 501-510
-
-
Carninci, P.1
-
2
-
-
33747712023
-
The complexity of the mammalian transcriptome
-
Gustincich S, Sandelin A, Plessy C, Katayama S, Simone R, et al. ((2006)) The complexity of the mammalian transcriptome. J Physiol 575: 321-332.
-
(2006)
J Physiol
, vol.575
, pp. 321-332
-
-
Gustincich, S.1
Sandelin, A.2
Plessy, C.3
Katayama, S.4
Simone, R.5
-
3
-
-
23644443393
-
The amazing complexity of the human transcriptome
-
Frith MC, Pheasant M, Mattick JS, ((2005)) The amazing complexity of the human transcriptome. Eur J Hum Genet 13: 894-897.
-
(2005)
Eur J Hum Genet
, vol.13
, pp. 894-897
-
-
Frith, M.C.1
Pheasant, M.2
Mattick, J.S.3
-
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
-
-
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, et al. ((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
-
7
-
-
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
-
8
-
-
77955323879
-
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response
-
Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, et al. ((2010)) A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142: 409-419.
-
(2010)
Cell
, vol.142
, pp. 409-419
-
-
Huarte, M.1
Guttman, M.2
Feldser, D.3
Garber, M.4
Koziol, M.J.5
-
9
-
-
77957243921
-
Long noncoding RNAs with enhancer-like function in human cells
-
Orom 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
-
-
Orom, U.A.1
Derrien, T.2
Beringer, M.3
Gumireddy, K.4
Gardini, A.5
-
10
-
-
67349157682
-
Tiny RNAs associated with transcription start sites in animals
-
Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, et al. ((2009)) Tiny RNAs associated with transcription start sites in animals. Nat Genet 41: 572-578.
-
(2009)
Nat Genet
, vol.41
, pp. 572-578
-
-
Taft, R.J.1
Glazov, E.A.2
Cloonan, N.3
Simons, C.4
Stephen, S.5
-
11
-
-
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
-
12
-
-
77955140071
-
New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism
-
Kapranov P, Ozsolak F, Kim SW, Foissac S, Lipson D, et al. ((2010)) New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism. Nature 466: 642-646.
-
(2010)
Nature
, vol.466
, pp. 642-646
-
-
Kapranov, P.1
Ozsolak, F.2
Kim, S.W.3
Foissac, S.4
Lipson, D.5
-
13
-
-
69149106357
-
Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome
-
Adelson DL, Raison JM, Edgar RC, ((2009)) Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome. Proc Natl Acad Sci U S A 106: 12855-12860.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 12855-12860
-
-
Adelson, D.L.1
Raison, J.M.2
Edgar, R.C.3
-
15
-
-
33846224659
-
Improved repeat identification and masking in Dipterans
-
Smith CD, Edgar RC, Yandell MD, Smith DR, Celniker SE, et al. ((2007)) Improved repeat identification and masking in Dipterans. Gene 389: 1-9.
-
(2007)
Gene
, vol.389
, pp. 1-9
-
-
Smith, C.D.1
Edgar, R.C.2
Yandell, M.D.3
Smith, D.R.4
Celniker, S.E.5
-
18
-
-
38549132347
-
NONCODE v2.0: decoding the non-coding
-
He S, Liu C, Skogerbo G, Zhao H, Wang J, et al. ((2008)) NONCODE v2.0: decoding the non-coding. Nucleic Acids Res 36: D170-172.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
He, S.1
Liu, C.2
Skogerbo, G.3
Zhao, H.4
Wang, J.5
-
19
-
-
0030854739
-
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
-
Lowe TM, Eddy SR, ((1997)) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
20
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
Huang da W, Sherman BT, Lempicki RA, ((2009)) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
-
(2009)
Nat Protoc
, vol.4
, pp. 44-57
-
-
da Huang, W.1
Sherman, B.T.2
Lempicki, R.A.3
-
21
-
-
58549112996
-
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
-
Huang da W, Sherman BT, Lempicki RA, ((2009)) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37: 1-13.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 1-13
-
-
da Huang, W.1
Sherman, B.T.2
Lempicki, R.A.3
-
22
-
-
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
-
23
-
-
78651237647
-
Identifying a high fraction of the human genome to be under selective constraint using GERP++
-
Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, et al. ((2010)) Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol 6: e1001025.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Davydov, E.V.1
Goode, D.L.2
Sirota, M.3
Cooper, G.M.4
Sidow, A.5
-
24
-
-
77957991364
-
An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation
-
Harhay GP, Smith TP, Alexander LJ, Haudenschild CD, Keele JW, et al. ((2010)) An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation. Genome Biol 11: R102.
-
(2010)
Genome Biol
, vol.11
-
-
Harhay, G.P.1
Smith, T.P.2
Alexander, L.J.3
Haudenschild, C.D.4
Keele, J.W.5
-
25
-
-
35348955882
-
A universal framework for regulatory element discovery across all genomes and data types
-
Elemento O, Slonim N, Tavazoie S, ((2007)) A universal framework for regulatory element discovery across all genomes and data types. Mol Cell 28: 337-350.
-
(2007)
Mol Cell
, vol.28
, pp. 337-350
-
-
Elemento, O.1
Slonim, N.2
Tavazoie, S.3
-
27
-
-
83755163018
-
Detecting novel associations in large data sets
-
Reshef DN, Reshef YA, Finucane HK, Grossman SR, McVean G, et al. ((2011)) Detecting novel associations in large data sets. Science 334: 1518-1524.
-
(2011)
Science
, vol.334
, pp. 1518-1524
-
-
Reshef, D.N.1
Reshef, Y.A.2
Finucane, H.K.3
Grossman, S.R.4
McVean, G.5
-
28
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, et al. ((2008)) Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476.
-
(2008)
Nature
, vol.456
, pp. 470-476
-
-
Wang, E.T.1
Sandberg, R.2
Luo, S.3
Khrebtukova, I.4
Zhang, L.5
-
29
-
-
60549115605
-
Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs
-
Fejes-Toth K, Sotirova V, Sachidanandam R, Assaf G, Hannon GJ, et al. ((2009)) Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs. Nature 457: 1028-1032.
-
(2009)
Nature
, vol.457
, pp. 1028-1032
-
-
Fejes-Toth, K.1
Sotirova, V.2
Sachidanandam, R.3
Assaf, G.4
Hannon, G.J.5
-
30
-
-
79953673245
-
Expression of distinct RNAs from 3′ untranslated regions
-
Mercer TR, Wilhelm D, Dinger ME, Solda G, Korbie DJ, et al. ((2011)) Expression of distinct RNAs from 3′ untranslated regions. Nucleic Acids Res 39: 2393-2403.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 2393-2403
-
-
Mercer, T.R.1
Wilhelm, D.2
Dinger, M.E.3
Solda, G.4
Korbie, D.J.5
-
31
-
-
75549083389
-
UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs
-
Grillo G, Turi A, Licciulli F, Mignone F, Liuni S, et al. ((2010)) UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res 38: D75-80.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Grillo, G.1
Turi, A.2
Licciulli, F.3
Mignone, F.4
Liuni, S.5
-
32
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. ((2000)) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
-
33
-
-
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, et al. ((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
-
34
-
-
0003157183
-
Noncoding RNA gene detection using comparative sequence analysis
-
Rivas E, Eddy SR, ((2001)) Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2: 8.
-
(2001)
BMC Bioinformatics
, vol.2
, pp. 8
-
-
Rivas, E.1
Eddy, S.R.2
-
36
-
-
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 Res 35: W345-349.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Kong, L.1
Zhang, Y.2
Ye, Z.Q.3
Liu, X.Q.4
Zhao, S.Q.5
-
37
-
-
33845986334
-
Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA
-
Freyhult EK, Bollback JP, Gardner PP, ((2007)) Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Res 17: 117-125.
-
(2007)
Genome Res
, vol.17
, pp. 117-125
-
-
Freyhult, E.K.1
Bollback, J.P.2
Gardner, P.P.3
-
39
-
-
44849084714
-
Finding noncoding RNA transcripts from low abundance expressed sequence tags
-
Xue C, Li F, ((2008)) Finding noncoding RNA transcripts from low abundance expressed sequence tags. Cell Res 18: 695-700.
-
(2008)
Cell Res
, vol.18
, pp. 695-700
-
-
Xue, C.1
Li, F.2
-
40
-
-
36049029123
-
Detection of RNA structures in porcine EST data and related mammals
-
Seemann SE, Gilchrist MJ, Hofacker IL, Stadler PF, Gorodkin J, ((2007)) Detection of RNA structures in porcine EST data and related mammals. BMC Genomics 8: 316.
-
(2007)
BMC Genomics
, vol.8
, pp. 316
-
-
Seemann, S.E.1
Gilchrist, M.J.2
Hofacker, I.L.3
Stadler, P.F.4
Gorodkin, J.5
-
41
-
-
79953020169
-
Critical association of ncRNA with introns
-
Rearick D, Prakash A, McSweeny A, Shepard SS, Fedorova L, et al. ((2011)) Critical association of ncRNA with introns. Nucleic Acids Res.
-
(2011)
Nucleic Acids Res
-
-
Rearick, D.1
Prakash, A.2
McSweeny, A.3
Shepard, S.S.4
Fedorova, L.5
-
42
-
-
77954399763
-
Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes
-
Chodroff RA, Goodstadt L, Sirey TM, Oliver PL, Davies KE, et al. ((2010)) Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes. Genome Biol 11: R72.
-
(2010)
Genome Biol
, vol.11
-
-
Chodroff, R.A.1
Goodstadt, L.2
Sirey, T.M.3
Oliver, P.L.4
Davies, K.E.5
-
43
-
-
34250189924
-
Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription
-
Nakaya HI, Amaral PP, Louro R, Lopes A, Fachel AA, et al. ((2007)) Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription. Genome Biol 8: R43.
-
(2007)
Genome Biol
, vol.8
-
-
Nakaya, H.I.1
Amaral, P.P.2
Louro, R.3
Lopes, A.4
Fachel, A.A.5
-
44
-
-
56949091456
-
Noncoding RNA in development
-
Amaral PP, Mattick JS, ((2008)) Noncoding RNA in development. Mamm Genome 19: 454-492.
-
(2008)
Mamm Genome
, vol.19
, pp. 454-492
-
-
Amaral, P.P.1
Mattick, J.S.2
-
45
-
-
77956411754
-
Mining mammalian transcript data for functional long non-coding RNAs
-
Khachane AN, Harrison PM, ((2010)) Mining mammalian transcript data for functional long non-coding RNAs. PLoS One 5: e10316.
-
(2010)
PLoS One
, vol.5
-
-
Khachane, A.N.1
Harrison, P.M.2
-
46
-
-
26444576847
-
Gene factories, microfunctionalization and the evolution of gene families
-
Hancock JM, ((2005)) Gene factories, microfunctionalization and the evolution of gene families. Trends Genet 21: 591-595.
-
(2005)
Trends Genet
, vol.21
, pp. 591-595
-
-
Hancock, J.M.1
-
47
-
-
50849129426
-
Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation
-
Li JT, Zhang Y, Kong L, Liu QR, Wei L, ((2008)) Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation. Nucleic Acids Res 36: 4833-4844.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 4833-4844
-
-
Li, J.T.1
Zhang, Y.2
Kong, L.3
Liu, Q.R.4
Wei, L.5
-
48
-
-
33745123379
-
A role for the catalytic ribonucleoprotein RNase P in RNA polymerase III transcription
-
Reiner R, Ben-Asouli Y, Krilovetzky I, Jarrous N, ((2006)) A role for the catalytic ribonucleoprotein RNase P in RNA polymerase III transcription. Genes Dev 20: 1621-1635.
-
(2006)
Genes Dev
, vol.20
, pp. 1621-1635
-
-
Reiner, R.1
Ben-Asouli, Y.2
Krilovetzky, I.3
Jarrous, N.4
-
49
-
-
55549098872
-
Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs
-
Hirota K, Miyoshi T, Kugou K, Hoffman CS, Shibata T, et al. ((2008)) Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs. Nature 456: 130-134.
-
(2008)
Nature
, vol.456
, pp. 130-134
-
-
Hirota, K.1
Miyoshi, T.2
Kugou, K.3
Hoffman, C.S.4
Shibata, T.5
-
50
-
-
33744805985
-
Genome-wide analysis of mammalian promoter architecture and evolution
-
Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, et al. ((2006)) Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 38: 626-635.
-
(2006)
Nat Genet
, vol.38
, pp. 626-635
-
-
Carninci, P.1
Sandelin, A.2
Lenhard, B.3
Katayama, S.4
Shimokawa, K.5
-
51
-
-
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
-
52
-
-
34547626629
-
Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells
-
Han J, Kim D, Morris KV, ((2007)) Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells. Proc Natl Acad Sci U S A 104: 12422-12427.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 12422-12427
-
-
Han, J.1
Kim, D.2
Morris, K.V.3
-
53
-
-
77958576363
-
Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes
-
Schmitz KM, Mayer C, Postepska A, Grummt I, ((2010)) Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes Dev 24: 2264-2269.
-
(2010)
Genes Dev
, vol.24
, pp. 2264-2269
-
-
Schmitz, K.M.1
Mayer, C.2
Postepska, A.3
Grummt, I.4
-
54
-
-
15244358503
-
Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals
-
Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, et al. ((2005)) Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434: 338-345.
-
(2005)
Nature
, vol.434
, pp. 338-345
-
-
Xie, X.1
Lu, J.2
Kulbokas, E.J.3
Golub, T.R.4
Mootha, V.5
-
55
-
-
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
-
56
-
-
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. Nat Biotechnol 28: 503-510.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 503-510
-
-
Guttman, M.1
Garber, M.2
Levin, J.Z.3
Donaghey, J.4
Robinson, J.5
-
57
-
-
34250735674
-
RNA regulons: coordination of post-transcriptional events
-
Keene JD, ((2007)) RNA regulons: coordination of post-transcriptional events. Nat Rev Genet 8: 533-543.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 533-543
-
-
Keene, J.D.1
|