-
1
-
-
12344291073
-
Dark matter in the genome: Evidence of widespread transcription detected by microarray tiling experiments
-
DOI 10.1016/j.tig.2004.12.009, PII S0168952504003373
-
Johnson, J.M., Edwards, S., Shoemaker, D. and Schadt, E.E. (2005) Dark matter in the genome: Evidence of widespread transcription detected by microarray tiling experiments. Trends Genet., 21, 93-102. (Pubitemid 40127353
-
(2005)
Trends in Genetics
, vol.21
, Issue.2
, pp. 93-102
-
-
Johnson, J.M.1
Edwards, S.2
Shoemaker, D.3
Schadt, E.E.4
-
2
-
-
33745286231
-
TUF love for 'Junk DNA
-
Willingham, A.T. and Gingeras, T.R. (2006) TUF love for 'Junk' DNA. Cell, 125, 1215-1220.
-
(2006)
Cell
, vol.125
, pp. 1215-1220
-
-
Willingham, A.T.1
Gingeras, T.R.2
-
3
-
-
34250330777
-
What is a gene, post-ENCODE? History and updated definition
-
DOI 10.1101/gr.6339607
-
Gerstein, M.B., Bruce, C., Rozowsky, J.S., Zheng, D., Du, J., Korbel, J.O., Emanuelsson, O., Zhang, Z.D., Weissman, S. and Snyder, M. (2007) What is a gene, post-ENCODE? History and updated definition. Genome Res., 17, 669-681. (Pubitemid 46919705
-
(2007)
Genome Research
, vol.17
, Issue.6
, pp. 669-681
-
-
Gerstein, M.B.1
Bruce, C.2
Rozowsky, J.S.3
Zheng, D.4
Du, J.5
Korbel, J.O.6
Emanuelsson, O.7
Zhang, Z.D.8
Weissman, S.9
Snyder, M.10
-
4
-
-
34250160256
-
RNA maps reveal new RNA classes and a possible function for pervasive transcription
-
Kapranov, P., Cheng, J., Dike, S., Nix, D.A., Duttagupta, R., Willingham, A.T., Stadler, P.F., Hertel, J., Hackermüller, J., Hofacker, I.L. 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
Willingham, A.T.6
Stadler, P.F.7
Hertel, J.8
Hackermüller, J.9
Hofacker, I.L.10
-
5
-
-
84864927713
-
Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs
-
Moran, V.A., Perera, R.J. and Khalil, A.M. (2012) Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs. Nucleic Acids Res., 40, 6391-6400.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 6391-6400
-
-
Moran, V.A.1
Perera, R.J.2
Khalil, A.M.3
-
6
-
-
77952905505
-
Most 'Dark Matter' transcripts are associated with known genes
-
Van Bakel, H., Nislow, C., Blencowe, B.J. and Hughes, T.R. (2010) Most 'Dark Matter' transcripts are associated with known genes. PLoS Biol., 8, e1000371.
-
(2010)
PLoS Biol.
, vol.8
-
-
Van Bakel, H.1
Nislow, C.2
Blencowe, B.J.3
Hughes, T.R.4
-
7
-
-
79960911703
-
The reality of pervasive transcription
-
Clark, M.B., Amaral, P.P., Schlesinger, F.J., Dinger, M.E., Taft, R.J., Rinn, J.L., Ponting, C.P., Stadler, P.F., Morris, K.V., Morillon, A. et al. (2011) The Reality of Pervasive Transcription. PLoS Biol., 9, e1000625.
-
(2011)
PLoS Biol.
, vol.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
Ponting, C.P.7
Stadler, P.F.8
Morris, K.V.9
Morillon, A.10
-
8
-
-
78650292831
-
The Majority Of Total Nuclear-encoded Non-ribosomal RNA In A Human Cell Is 'dark matter' un-Annotated RNA
-
Kapranov, P., St Laurent, G., Raz, T., Ozsolak, F., Reynolds, C.P., Sorensen, P.H., Reaman, G., Milos, P., Arceci, R.J., Thompson, J.F. et al. (2010) The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-Annotated RNA. BMC Biol., 8, 149.
-
(2010)
BMC Biol.
, vol.8
, pp. 149
-
-
Kapranov, P.1
St Laurent, G.2
Raz, T.3
Ozsolak, F.4
Reynolds, C.P.5
Sorensen, P.H.6
Reaman, G.7
Milos, P.8
Arceci, R.J.9
Thompson, J.F.10
-
9
-
-
84865727393
-
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
-
Derrien, T., Johnson, R., Bussotti, G., Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D.G. et al. (2012) The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res., 22, 1775-1789.
-
(2012)
Genome Res.
, Issue.22
, pp. 1775-1789
-
-
Derrien, T.1
Johnson, R.2
Bussotti, G.3
Tanzer, A.4
Djebali, S.5
Tilgner, H.6
Guernec, G.7
Martin, D.8
Merkel, A.9
Knowles, D.G.10
-
10
-
-
80052978224
-
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
-
Cabili, M.N., Trapnell, C., Goff, L., Koziol, M., Tazon-Vega, B., Regev, A. and Rinn, J.L. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev., 25, 1915-1927.
-
(2011)
Genes Dev.
, pp. 25
-
-
Cabili, M.N.1
Trapnell, C.2
Goff, L.3
Koziol, M.4
Tazon-Vega, B.5
Regev, A.6
Rinn, J.L.7
-
11
-
-
34250729138
-
Functional demarcation of active and silent chromatin domains in human hox loci by noncoding rnas
-
DOI 10.1016/j.cell.2007.05.022, PII S0092867407006599
-
Rinn, J.L., Kertesz, M., Wang, J.K., Squazzo, S.L., Xu, X., Brugmann, S.A., Goodnough, L.H., Helms, J.A., Farnham, P.J., Segal, E. et al. (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell, 129, 1311-1323. (Pubitemid 46962090
-
(2007)
Cell
, vol.129
, Issue.7
, pp. 1311-1323
-
-
Rinn, J.L.1
Kertesz, M.2
Wang, J.K.3
Squazzo, S.L.4
Xu, X.5
Brugmann, S.A.6
Goodnough, L.H.7
Helms, J.A.8
Farnham, P.J.9
Segal, E.10
Chang, H.Y.11
-
12
-
-
62249133709
-
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
-
Guttman, M., Amit, I., Garber, M., French, C., Lin, M.F., Feldser, D., Huarte, M., Zuk, O., Carey, B.W., Cassady, J.P. 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
Feldser, D.6
Huarte, M.7
Zuk, O.8
Carey, B.W.9
Cassady, J.P.10
-
13
-
-
60349120914
-
Long non-coding RNAs: Insights into functions
-
Mercer, T.R., Dinger, M.E. and Mattick, J.S. (2009) Long non-coding RNAs: Insights into functions. Nat. Rev. Genet., 10, 155-159.
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 155-159
-
-
Mercer, T.R.1
Dinger, M.E.2
Mattick, J.S.3
-
14
-
-
60149099385
-
Evolution and functions of long noncoding RNAs
-
Ponting, C.P., Oliver, P.L. and Reik, W. (2009) Evolution and functions of long noncoding RNAs. Cell, 136, 629-641.
-
(2009)
Cell
, vol.136
, pp. 629-641
-
-
Ponting, C.P.1
Oliver, P.L.2
Reik, W.3
-
15
-
-
84875858020
-
RNA-Seq: Revelation of the messengers
-
Van Verk, M.C., Hickman, R., Pieterse, C.M.J. and Van Wees, S.C.M. (2013) RNA-Seq: Revelation of the messengers. Trends Plant Sci., 18, 175-179.
-
(2013)
Trends Plant Sci.
, vol.18
, pp. 175-179
-
-
Van Verk, M.C.1
Hickman, R.2
Pieterse, C.M.J.3
Van Wees, S.C.M.4
-
16
-
-
84876031547
-
Genomic 'dark matter': Implications for understanding human disease mechanisms, diagnostics, and cures
-
Kapranov, P. and Laurent, G.S. (2012) Genomic 'dark matter': Implications for understanding human disease mechanisms, diagnostics, and cures. Front. Genet., 3, 95.
-
(2012)
Front. Genet.
, vol.3
, pp. 95
-
-
Kapranov, P.1
Laurent, G.S.2
-
17
-
-
84857074361
-
Molecular biology: RNA discrimination
-
Kowalczyk, M.S., Higgs, D.R. and Gingeras, T.R. (2012) Molecular biology: RNA discrimination. Nature, 482, 310-311.
-
(2012)
Nature
, vol.482
, pp. 310-311
-
-
Kowalczyk, M.S.1
Higgs, D.R.2
Gingeras, T.R.3
-
18
-
-
84866952775
-
Dark matter RNA: An intelligent scaffold for the dynamic regulation of the nuclear information landscape
-
St Laurent, G., Savva, Y.A. and Kapranov, P. (2012) Dark matter RNA: An intelligent scaffold for the dynamic regulation of the nuclear information landscape. Front. Genet., 3, 57.
-
(2012)
Front. Genet.
, vol.3
, pp. 57
-
-
St Laurent, G.1
Savva, Y.A.2
Kapranov, P.3
-
19
-
-
69849093232
-
Using reads to annotate the genome: Influence of length, background distribution, and sequence errors on prediction capacity
-
Philippe, N., Boureux, A., Bréhé lin, L., Tarhio, J., Commes, T. and Rivals, E. (2009) Using reads to annotate the genome: Influence of length, background distribution, and sequence errors on prediction capacity. Nucleic Acids Res., 37, e104-e104.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Philippe, N.1
Boureux, A.2
Bréhélin, L.3
Tarhio, J.4
Commes, T.5
Rivals, E.6
-
20
-
-
84875292779
-
CRAC: An integrated approach to the analysis of RNA-seq reads
-
Philippe, N., Salson, M., Commes, T. and Rivals, E. (2013) CRAC: An integrated approach to the analysis of RNA-seq reads. Genome Biol., 14, R30.
-
(2013)
Genome Biol.
, vol.14
-
-
Philippe, N.1
Salson, M.2
Commes, T.3
Rivals, E.4
-
21
-
-
84858221706
-
Ensembl 2012
-
Flicek, P., Amode, M.R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S. et al. (2012) Ensembl 2012. Nucleic Acids Res., 40, D84-D90.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Flicek, P.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Brent, S.5
Carvalho-Silva, D.6
Clapham, P.7
Coates, G.8
Fairley, S.9
Fitzgerald, S.10
-
22
-
-
34848885253
-
Transcriptome annotation using tandem sage tags
-
Rivals, E., Boureux, A., Lejeune, M., Ottones, F., Pérez, O.P., Tarhio, J., Pierrat, F., Ruffle, F., Commes, T. and Marti, J. (2007) Transcriptome annotation using tandem SAGE tags. Nucleic Acids Res., 35, e108-e108.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Rivals, E.1
Boureux, A.2
Lejeune, M.3
Ottones, F.4
Pérez, O.P.5
Tarhio, J.6
Pierrat, F.7
Ruffle, F.8
Commes, T.9
Marti, J.10
-
23
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
Huang, D.W., Sherman, B.T. and Lempicki, R.A. (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
-
-
Huang, D.W.1
Sherman, B.T.2
Lempicki, R.A.3
-
24
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95, 14863-14868.
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 14863-14868
-
-
Eisen, M.B.1
Spellman, P.T.2
Brown, P.O.3
Botstein, D.4
-
25
-
-
58849123232
-
A gene expression signature shared by human mature oocytes and embryonic stem cells
-
Assou, S., Cerecedo, D., Tondeur, S., Pantesco, V., Hovatta, O., Klein, B., Hamamah, S. and De Vos, J. (2009) A gene expression signature shared by human mature oocytes and embryonic stem cells. BMC Genomics, 10, 10.
-
(2009)
BMC Genomics
, vol.10
, pp. 10
-
-
Assou, S.1
Cerecedo, D.2
Tondeur, S.3
Pantesco, V.4
Hovatta, O.5
Klein, B.6
Hamamah, S.7
De Vos, J.8
-
26
-
-
84857658568
-
Dissecting the first transcriptional divergence during human embryonic development
-
Bai, Q., Assou, S., Haouzi, D., Ramirez, J.-M., Monzo, C., Becker, F., Gerbal-Chaloin, S., Hamamah, S. and De Vos, J. (2012) Dissecting the first transcriptional divergence during human embryonic development. Stem. Cell Rev., 8, 150-162.
-
(2012)
Stem. Cell Rev.
, vol.8
, pp. 150-162
-
-
Bai, Q.1
Assou, S.2
Haouzi, D.3
Ramirez, J.-M.4
Monzo, C.5
Becker, F.6
Gerbal-Chaloin, S.7
Hamamah, S.8
De Vos, J.9
-
27
-
-
0035710746
-
-CT method
-
DOI 10.1006/meth.2001.1262
-
Livak, K.J. and Schmittgen, T.D. (2001) Analysis of relative gene expression data using real-Time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods, 25, 402-408. (Pubitemid 34164012
-
(2001)
Methods
, vol.25
, Issue.4
, pp. 402-408
-
-
Livak, K.J.1
Schmittgen, T.D.2
-
28
-
-
52649157765
-
Substantial biases in ultra-short read data sets from highthroughput DNA sequencing
-
Dohm, J.C., Lottaz, C., Borodina, T. and Himmelbauer, H. (2008) Substantial biases in ultra-short read data sets from highthroughput DNA sequencing. Nucleic Acids Res., 36, e105.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Dohm, J.C.1
Lottaz, C.2
Borodina, T.3
Himmelbauer, H.4
-
29
-
-
70349636603
-
Nextgeneration tag sequencing for cancer gene expression profiling
-
Morrissy, A.S., Morin, R.D., Delaney, A., Zeng, T., McDonald, H., Jones, S., Zhao, Y., Hirst, M. and Marra, M.A. (2009) Nextgeneration tag sequencing for cancer gene expression profiling. Genome Res., 19, 1825-1835.
-
(2009)
Genome Res.
, vol.19
, pp. 1825-1835
-
-
Morrissy, A.S.1
Morin, R.D.2
Delaney, A.3
Zeng, T.4
McDonald, H.5
Jones, S.6
Zhao, Y.7
Hirst, M.8
Marra, M.A.9
-
30
-
-
79955858869
-
Protocol dependence of sequencing-based gene expression measurements
-
Raz, T., Kapranov, P., Lipson, D., Letovsky, S., Milos, P.M. and Thompson, J.F. (2011) Protocol dependence of sequencing-based gene expression measurements. PLoS One, 6, e19287.
-
(2011)
PLoS One
, vol.6
-
-
Raz, T.1
Kapranov, P.2
Lipson, D.3
Letovsky, S.4
Milos, P.M.5
Thompson, J.F.6
-
31
-
-
0036731713
-
Transcriptome analysis of monocytic leukemia cell differentiation
-
Piquemal, D., Commes, T., Manchon, L., Lejeune, M., Ferraz, C., Pugnère, D., Demaille, J., Elalouf, J.-M. and Marti, J. (2002) Transcriptome analysis of monocytic leukemia cell differentiation. Genomics, 80, 361-371.
-
(2002)
Genomics
, vol.80
, pp. 361-371
-
-
Piquemal, D.1
Commes, T.2
Manchon, L.3
Lejeune, M.4
Ferraz, C.5
Pugnère, D.6
Demaille, J.7
Elalouf, J.-M.8
Marti, J.9
-
32
-
-
80053523254
-
The evolution of RNAs with multiple functions
-
Dinger, M.E., Gascoigne, D.K. and Mattick, J.S. (2011) The evolution of RNAs with multiple functions. Biochimie, 93, 2013-2018.
-
(2011)
Biochimie
, vol.93
, pp. 2013-2018
-
-
Dinger, M.E.1
Gascoigne, D.K.2
Mattick, J.S.3
-
33
-
-
34248212337
-
Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human
-
Zhang, Z., Pang, A. and Gerstein, M. (2007) Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human. BMC Evol. Biol., 7, S14.
-
(2007)
BMC Evol. Biol.
, vol.7
-
-
Zhang, Z.1
Pang, A.2
Gerstein, M.3
|