-
1
-
-
60149099385
-
Evolution and functions of long noncoding RNAs
-
PMID:19239885
-
Ponting, CP, Oliver, PL, Reik, W. Evolution and functions of long noncoding RNAs. Cell 136, 629-41, (2009); PMID:19239885; http://dx.doi.org/10.1016/j.cell.2009.02.006
-
(2009)
Cell
, vol.136
, pp. 629-641
-
-
Ponting, C.P.1
Oliver, P.L.2
Reik, W.3
-
2
-
-
84879987789
-
LincRNAs: Genomics, evolution, and mechanisms
-
PMID:23827673
-
Ulitsky, I, Bartel, DP. lincRNAs: genomics, evolution, and mechanisms. Cell 154, 26-46, (2013); PMID:23827673; http://dx.doi.org/10.1016/j.cell.2013.06.020
-
(2013)
Cell
, vol.154
, pp. 26-46
-
-
Ulitsky, I.1
Bartel, D.P.2
-
3
-
-
79953858658
-
No-nonsense functions for long noncoding RNAs
-
PMID:21496640
-
Nagano, T, Fraser, P. No-nonsense functions for long noncoding RNAs. Cell 145, 178-81, (2011); PMID:21496640; http://dx.doi.org/10.1016/j.cell.2011.03.014
-
(2011)
Cell
, vol.145
, pp. 178-181
-
-
Nagano, T.1
Fraser, P.2
-
4
-
-
84875183056
-
Structure and function of long noncoding RNAs in epigenetic regulation
-
PMID:23463315
-
Mercer, TR, Mattick, JS. Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol 20, 300-7, (2013); PMID:23463315; http://dx.doi.org/10.1038/nsmb.2480
-
(2013)
Nat Struct Mol Biol
, vol.20
, pp. 300-307
-
-
Mercer, T.R.1
Mattick, J.S.2
-
5
-
-
60349120914
-
Long non-coding RNAs: Insights into functions
-
PMID:19188922
-
Mercer, TR, Dinger, ME, Mattick, JS. Long non-coding RNAs: insights into functions. Nat Rev Genet 10, 155-9, (2009); PMID:19188922; http://dx.doi.org/10.1038/nrg2521
-
(2009)
Nat Rev Genet
, vol.10
, pp. 155-159
-
-
Mercer, T.R.1
Dinger, M.E.2
Mattick, J.S.3
-
6
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
PMID:16141072
-
Carninci, P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, et al. The transcriptional landscape of the mammalian genome. Science 309, 1559-63, (2005); PMID:16141072; http://dx.doi.org/10.1126/science.1112014
-
(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
Oyama, R.7
Ravasi, T.8
Lenhard, B.9
Wells, C.10
-
7
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
PMID:17571346
-
Birney, E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816, (2007); PMID:17571346; http://dx.doi.org/10.1038/nature05874
-
(2007)
Nature
, vol.447
, pp. 799-816
-
-
Birney, E.1
Stamatoyannopoulos, J.A.2
Dutta, A.3
Guigó, R.4
Gingeras, T.R.5
Margulies, E.H.6
Weng, Z.7
Snyder, M.8
Dermitzakis, E.T.9
Thurman, R.E.10
-
8
-
-
84895908120
-
The evolution of lncRNA repertoires and expression patterns in tetrapods
-
PMID:24463510
-
Necsulea, A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature 505, 635-40, (2014); PMID:24463510; http://dx.doi.org/10.1038/nature 12943
-
(2014)
Nature
, vol.505
, pp. 635-640
-
-
Necsulea, A.1
Soumillon, M.2
Warnefors, M.3
Liechti, A.4
Daish, T.5
Zeller, U.6
Baker, J.C.7
Grützner, F.8
Kaessmann, H.9
-
9
-
-
24644472515
-
Antisense transcription in the mammalian transcriptome
-
PMID:16141073
-
Katayama, S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, et al. Antisense transcription in the mammalian transcriptome. Science 309, 1564-6, (2005); PMID:16141073; http://dx.doi.org/10.1126/science.1112009
-
(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
Nishida, H.7
Yap, C.C.8
Suzuki, M.9
Kawai, J.10
-
10
-
-
84902141800
-
Long Noncoding RNAs in Cell-Fate programming and reprogramming
-
PMID:24905165
-
Flynn, RA, Chang, HY, Long Noncoding RNAs in Cell-Fate programming and reprogramming. Cell Stem Cell 14, 752-61, (2014); PMID:24905165; http://dx.doi.org/10.1016/j.stem.2014.05.014
-
(2014)
Cell Stem Cell
, vol.14
, pp. 752-761
-
-
Flynn, R.A.1
Chang, H.Y.2
-
11
-
-
81055155799
-
Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
-
PMID:22056041
-
Ingolia, NT, Lareau, LF, Weissman, JS. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147, 789-802, (2011); PMID:22056041; http://dx.doi.org/10.1016/j.cell.2011.10.002
-
(2011)
Cell
, vol.147
, pp. 789-802
-
-
Ingolia, N.T.1
Lareau, L.F.2
Weissman, J.S.3
-
12
-
-
84879969127
-
Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins
-
PMID:23810193
-
Guttman, M, Russell, P, Ingolia, NT, Weissman, JS, Lander, ES. Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell 154, 240-51, (2013); PMID:23810193; http://dx.doi.org/10.1016/j.cell.2013.06.009
-
(2013)
Cell
, vol.154
, pp. 240-251
-
-
Guttman, M.1
Russell, P.2
Ingolia, N.T.3
Weissman, J.S.4
Lander, E.S.5
-
13
-
-
19344368188
-
Genomic analysis of mouse retinal development
-
PMID:15226823
-
Blackshaw, S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo WP, Weber G, Lee K, Fraioli RE, Cho SH, et al. Genomic analysis of mouse retinal development. PLoS Biol 2, E247, (2004); PMID:15226823; http://dx.doi.org/10.1371/journal.pbio.0020247
-
(2004)
Plos Biol
, vol.2
-
-
Blackshaw, S.1
Harpavat, S.2
Trimarchi, J.3
Cai, L.4
Huang, H.5
Kuo, W.P.6
Weber, G.7
Lee, K.8
Fraioli, R.E.9
Cho, S.H.10
-
14
-
-
84881511705
-
Identification and characterization of long non-coding RNAs related to mouse embryonic brain development from available transcriptomic data
-
PMID:23967161
-
Lv, J, Cui W, Liu H, He H, Xiu Y, Guo J, Liu H, Liu Q, Zeng T, Chen Y, et al. Identification and characterization of long non-coding RNAs related to mouse embryonic brain development from available transcriptomic data. PLoS One 8, e71152, (2013); PMID:23967161; http://dx.doi.org/10.1371/journal.pone.0071152
-
(2013)
Plos One
, vol.8
-
-
Lv, J.1
Cui, W.2
Liu, H.3
He, H.4
Xiu, Y.5
Guo, J.6
Liu, H.7
Liu, Q.8
Zeng, T.9
Chen, Y.10
-
15
-
-
38649114329
-
Specific expression of long noncoding RNAs in the mouse brain
-
PMID:18184812
-
Mercer, TR, Dinger, ME, Sunkin, SM, Mehler, MF, Mattick, JS. Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A 105, 716-21, (2008); PMID:18184812; http://dx.doi.org/10.1073/pnas.0706729105
-
(2008)
Proc Natl Acad Sci U S A
, 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
-
16
-
-
84880569773
-
Whole transcriptome sequencing of the aging rat brain reveals dynamic RNA changes in the dark matter of the genome
-
PMID:22555619
-
Wood, SH, Craig, T, Li, Y, Merry, B, de Magalhaes, JP. Whole transcriptome sequencing of the aging rat brain reveals dynamic RNA changes in the dark matter of the genome. Age 35, 763-76, (2013); PMID:22555619; http://dx.doi.org/10.1007/s11357-012-9410-1
-
(2013)
Age
, vol.35
, pp. 763-776
-
-
Wood, S.H.1
Craig, T.2
Li, Y.3
Merry, B.4
de Magalhaes, J.P.5
-
17
-
-
84877575447
-
Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo
-
PMID:23583100
-
Ramos, AD, Diaz A, Nellore A, Delgado RN, Park KY, Gonzales-Roybal G, Oldham MC, Song JS, Lim DA. et al. Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo. Cell Stem Cell 12, 616-28, (2013); PMID:23583100; http://dx.doi.org/10.1016/j.stem.2013.03.003
-
(2013)
Cell Stem Cell
, vol.12
, pp. 616-628
-
-
Ramos, A.D.1
Diaz, A.2
Nellore, A.3
Delgado, R.N.4
Park, K.Y.5
Gonzales-Roybal, G.6
Oldham, M.C.7
Song, J.S.8
Lim, D.A.9
-
18
-
-
84890567188
-
Transcriptome sequencing during mouse brain development identifies long non-coding RNAs functionally involved in neurogenic commitment
-
PMID:24240175
-
Aprea, J, Prenninger S, Dori M, Ghosh T, Monasor LS, Wessendorf E, Zocher S, Massalini S, Alexopoulou D, Lesche M., et al. Transcriptome sequencing during mouse brain development identifies long non-coding RNAs functionally involved in neurogenic commitment. EMBO J 32, 3145-60, (2013); PMID:24240175; http://dx.doi.org/10.1038/emboj.2013.245
-
(2013)
EMBO J
, vol.32
, pp. 3145-3160
-
-
Aprea, J.1
Prenninger, S.2
Dori, M.3
Ghosh, T.4
Monasor, L.S.5
Wessendorf, E.6
Zocher, S.7
Massalini, S.8
Alexopoulou, D.9
Lesche, M.10
-
19
-
-
1542297728
-
Neurons arise in the basal neuroepithelium of the early mammalian telencephalon: A major site of neurogenesis
-
PMID:14963232
-
Haubensak, W, Attardo, A, Denk, W, Huttner, WB. Neurons arise in the basal neuroepithelium of the early mammalian telencephalon: a major site of neurogenesis. Proc. Natl. Acad. Sci. USA 101, 3196-201 (2004); PMID:14963232
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 3196-3201
-
-
Haubensak, W.1
Attardo, A.2
Denk, W.3
Huttner, W.B.4
-
20
-
-
48649083476
-
Live imaging at the onset of cortical neurogenesis reveals differential appearance of the neuronal phenotype in apical vs. Basal progenitor progeny
-
PMID:18545663
-
Attardo, A, Calegari, F, Haubensak, W, Wilsch-Brauninger, M, Huttner, WB. Live imaging at the onset of cortical neurogenesis reveals differential appearance of the neuronal phenotype in apical vs. basal progenitor progeny. PLoS ONE 3, e2388, (2008); PMID:18545663; http://dx.doi.org/10.1371/journal. pone.0002388
-
(2008)
Plos ONE
, vol.3
-
-
Attardo, A.1
Calegari, F.2
Haubensak, W.3
Wilsch-Brauninger, M.4
Huttner, W.B.5
-
21
-
-
80052584757
-
Transcriptional programs in transient embryonic zones of the cerebral cortex defined by high-resolution mRNA sequencing
-
PMID:21873192
-
Ayoub, AE, Oh S, Xie Y, Leng J, Cotney J, Dominguez MH, Noonan JP, Rakic P. et al. Transcriptional programs in transient embryonic zones of the cerebral cortex defined by high-resolution mRNA sequencing. Proc Natl Acad Sci U S A 108, 14950-5, (2011); PMID:21873192; http://dx.doi.org/10.1073/pnas.1112213108
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 14950-14955
-
-
Ayoub, A.E.1
Oh, S.2
Xie, Y.3
Leng, J.4
Cotney, J.5
Dominguez, M.H.6
Noonan, J.P.7
Rakic, P.8
-
22
-
-
69149097967
-
Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing
-
PMID:19617558
-
Han, X, Wu X, Chung WY, Li T, Nekrutenko A, Altman NS, Chen G, Ma H. Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing. Proc Natl Acad Sci U S A 106, 12741-6, (2009); PMID:19617558; http://dx.doi.org/10.1073/pnas.0902417106
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 12741-12746
-
-
Han, X.1
Wu, X.2
Chung, W.Y.3
Li, T.4
Nekrutenko, A.5
Altman, N.S.6
Chen, G.7
Ma, H.8
-
23
-
-
84861994366
-
Transcriptome analysis of microRNAs in developing cerebral cortex of rat
-
PMID:22691069
-
Yao, MJ, Chen G, Zhao PP, Lu MH, Jian J, Liu MF, Yuan XB. Transcriptome analysis of microRNAs in developing cerebral cortex of rat. BMC genomics 13, 232, (2012); PMID:22691069; http://dx.doi.org/10.1186/1471-2164-13-232
-
(2012)
BMC Genomics
, vol.13
, pp. 232
-
-
Yao, M.J.1
Chen, G.2
Zhao, P.P.3
Lu, M.H.4
Jian, J.5
Liu, M.F.6
Yuan, X.B.7
-
24
-
-
84863946985
-
Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal
-
PMID:22753484
-
Fietz, SA, Lachmann R, Brandl H, Kircher M, Samusik N, Schröder R, Lakshmanaperumal N, Henry I, Vogt J, Riehn A, et al. Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal. Proc Natl Acad Sci U S A 109, 11836-41, (2012); PMID:22753484; http://dx.doi.org/10.1073/pnas. 1209647109
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 11836-11841
-
-
Fietz, S.A.1
Lachmann, R.2
Brandl, H.3
Kircher, M.4
Samusik, N.5
Schröder, R.6
Lakshmanaperumal, N.7
Henry, I.8
Vogt, J.9
Riehn, A.10
-
25
-
-
84926211934
-
Tox: A multifunctional transcription factor and novel regulator of mammalian corticogenesis
-
PMID:25527292
-
Artegiani B. de Jesus, Domingues AM, Bragado Alonso A, Brandl E, Massalini S, Dahl A. Calegari, F Tox.: A multifunctional transcription factor and novel regulator of mammalian corticogenesis. EMBO J (2014) PMID:25527292; DOI:10.15252/embj.201490061
-
(2014)
EMBO J
-
-
de Jesus, A.B.1
Domingues, A.M.2
Bragado Alonso, A.3
Brandl, E.4
Massalini, S.5
Dahl, A.6
Calegari, F.7
-
26
-
-
70449704529
-
Computational methods for discovering structural variation with nextgeneration sequencing
-
PMID:19844226
-
Medvedev, P, Stanciu, M, Brudno, M. Computational methods for discovering structural variation with nextgeneration sequencing. Nat Methods 6, S13-20, (2009); PMID:19844226; http://dx.doi.org/10.1038/nmeth.1374
-
(2009)
Nat Methods
, vol.6
, pp. S13-S20
-
-
Medvedev, P.1
Stanciu, M.2
Brudno, M.3
-
27
-
-
84883496216
-
Predicting long non-coding RNAs using RNA sequencing
-
PMID:23541739
-
Ilott, NE, Ponting, CP. Predicting long non-coding RNAs using RNA sequencing. Methods 63, 50-9, (2013); PMID:23541739; http://dx.doi.org/10.1016/j.ymeth.2013.03.019
-
(2013)
Methods
, vol.63
, pp. 50-59
-
-
Ilott, N.E.1
Ponting, C.P.2
-
28
-
-
80855128254
-
Deep proteome and transcriptome mapping of a human cancer cell line
-
PMID:22068331
-
Nagaraj, N, Wisniewski JR, Geiger T, Cox J, Kircher M, Kelso J, Pääbo S, Mann M. Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol 7, 548, (2011); PMID:22068331; http://dx.doi.org/10.1038/msb.2011.81
-
(2011)
Mol Syst Biol
, vol.7
, pp. 548
-
-
Nagaraj, N.1
Wisniewski, J.R.2
Geiger, T.3
Cox, J.4
Kircher, M.5
Kelso, J.6
Pääbo, S.7
Mann, M.8
-
29
-
-
70149123708
-
Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain
-
PMID:19696892
-
Ponjavic, J, Oliver, PL, Lunter, G, Ponting, CP, Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain. PLoS Genet 5, e1000617, (2009); PMID:19696892; http://dx.doi.org/10.1371/journal.pgen.1000617
-
(2009)
Plos Genet
, vol.5
-
-
Ponjavic, J.1
Oliver, P.L.2
Lunter, G.3
Ponting, C.P.4
-
30
-
-
79851473886
-
A high-resolution anatomical atlas of the transcriptome in the mouse embryo
-
PMID:21267068
-
Diez-Roux, G, Banfi S, Sultan M, Geffers L, Anand S, Rozado D, Magen A, Canidio E, Pagani M, Peluso I, et al. A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol 9, e1000582, (2011); PMID:21267068; http://dx.doi.org/10.1371/journal.pbio.1000582
-
(2011)
Plos Biol
, vol.9
-
-
Diez-Roux, G.1
Banfi, S.2
Sultan, M.3
Geffers, L.4
Anand, S.5
Rozado, D.6
Magen, A.7
Canidio, E.8
Pagani, M.9
Peluso, I.10
-
31
-
-
84859210032
-
Fast gapped-read alignment with bowtie 2
-
PMID:22388286
-
Langmead, B, Salzberg, SL. Fast gapped-read alignment with bowtie 2. Nat Methods 9, 357-9, (2012); PMID:22388286; http://dx.doi.org/10.1038/nmeth.1923
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
32
-
-
84876996918
-
TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
-
PMID:23618408
-
Kim, D. Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14, R36, (2013); PMID:23618408; http://dx.doi.org/10.1186/gb-2013-14-4-r36
-
(2013)
Genome Biol
, vol.14
-
-
Kim, D.1
Pertea, G.2
Trapnell, C.3
Pimentel, H.4
Kelley, R.5
Salzberg, S.L.6
-
33
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
PMID:20436464
-
Trapnell, C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28, 511-5, (2010); PMID:20436464; http://dx.doi.org/10.1038/nbt.1621
-
(2010)
Nat Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
Van Baren, M.J.6
Salzberg, S.L.7
Wold, B.J.8
Pachter, L.9
-
34
-
-
84897397058
-
Featurecounts: An efficient general purpose program for assigning sequence reads to genomic features
-
PMID:24227677
-
Liao, Y, Smyth, GK, Shi, W. Featurecounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923-30, (2014); PMID:24227677; http://dx.doi.org/10.1093/bioinformatics/btt656
-
(2014)
Bioinformatics
, vol.30
, pp. 923-930
-
-
Liao, Y.1
Smyth, G.K.2
Shi, W.3
-
35
-
-
79953009230
-
RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data
-
PMID:21357752
-
Washietl, S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N. et al. RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. RNA 17, 578-94, (2011); PMID:21357752; http://dx.doi.org/10.1261/rna.2536111
-
(2011)
RNA
, vol.17
, pp. 578-594
-
-
Washietl, S.1
Findeiss, S.2
Müller, S.A.3
Kalkhof, S.4
von Bergen, M.5
Hofacker, I.L.6
Stadler, P.F.7
Goldman, N.8
-
36
-
-
84868097156
-
A “forward genomics” approach links genotype to phenotype using independent phenotypic losses among related species
-
PMID:23022484
-
Hiller, M, Schaar BT, Indjeian VB, Kingsley DM, Hagey LR, Bejerano G. A “forward genomics” approach links genotype to phenotype using independent phenotypic losses among related species. Cell Rep 2, 817-23, (2012); PMID:23022484; http://dx.doi.org/10.1016/j.celrep.2012.08.032
-
(2012)
Cell Rep
, vol.2
, pp. 817-823
-
-
Hiller, M.1
Schaar, B.T.2
Indjeian, V.B.3
Kingsley, D.M.4
Hagey, L.R.5
Bejerano, G.6
-
37
-
-
58549112996
-
Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
-
PMID:19033363
-
Huang da, W, Sherman, BT, Lempicki, RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37, 1-13, (2009); PMID:19033363; http://dx.doi.org/10.1093/nar/gkn923
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 1-13
-
-
Huang da, W.1
Sherman, B.T.2
Lempicki, R.A.3
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