-
1
-
-
84901639160
-
Trafficking of mRNAs containing ALREX-promoting elements through nuclear speckles
-
Akef, A., Zhang, H., Masuda, S., and Palazzo, A. F. (2013). Trafficking of mRNAs containing ALREX-promoting elements through nuclear speckles. Nucleus 4, 326-340. doi: 10.4161/nucl.26052
-
(2013)
Nucleus
, vol.4
, pp. 326-340
-
-
Akef, A.1
Zhang, H.2
Masuda, S.3
Palazzo, A.F.4
-
2
-
-
84897459814
-
An atlas of active enhancers across human cell types and tissues
-
Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M.,et al. (2014). An atlas of active enhancers across human cell types and tissues. Nature 507, 455-461. doi: 10.1038/nature12787
-
(2014)
Nature
, vol.507
, pp. 455-461
-
-
Andersson, R.1
Gebhard, C.2
Miguel-Escalada, I.3
Hoof, I.4
Bornholdt, J.5
Boyd, M.6
-
3
-
-
2342456308
-
Nonsense-mediated mRNA decay: terminating erroneous gene expression
-
Baker, K. E., and Parker, R. (2004). Nonsense-mediated mRNA decay: terminating erroneous gene expression. Curr. Opin. Cell Biol. 16, 293-299. doi: 10.1016/j.ceb.2004.03.003
-
(2004)
Curr. Opin. Cell Biol.
, vol.16
, pp. 293-299
-
-
Baker, K.E.1
Parker, R.2
-
4
-
-
84865839598
-
Long noncoding RNAs are rarely translated in two human cell lines
-
Bánfai, B., Jia, H., Khatun, J., Wood, E., Risk, B., Gundling, W. E.,et al. (2012). Long noncoding RNAs are rarely translated in two human cell lines. Genome Res. 22, 1646-1657. doi: 10.1101/gr.134767.111
-
(2012)
Genome Res.
, vol.22
, pp. 1646-1657
-
-
Bánfai, B.1
Jia, H.2
Khatun, J.3
Wood, E.4
Risk, B.5
Gundling, W.E.6
-
5
-
-
84899884309
-
Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation
-
Bazzini, A. A., Johnstone, T. G., Christiano, R., Mackowiak, S. D., Obermayer, B., Fleming, E. S.,et al. (2014). Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J. 33, 981-993. doi: 10.1002/embj.201488411
-
(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
-
6
-
-
80054728495
-
Animal transcription networks as highly connected, quantitative continua
-
Biggin, M. D. (2011). Animal transcription networks as highly connected, quantitative continua. Dev. Cell 21, 611-626. doi: 10.1016/j.devcel.2011. 09.008
-
(2011)
Dev. Cell
, vol.21
, pp. 611-626
-
-
Biggin, M.D.1
-
7
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
Birney, E., Stamatoyannopoulos, J. A., Dutta, A., Guigó, R., Gingeras, T. R., Margulies, E. H.,et al. (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816. doi: 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
-
8
-
-
73249118950
-
Absolute quantification of microRNAs by using a universal reference
-
Bissels, U., Wild, S., Tomiuk, S., Holste, A., Hafner, M., Tuschl, T.,et al. (2009). Absolute quantification of microRNAs by using a universal reference. RNA 15, 2375-2384. doi: 10.1261/rna.1754109
-
(2009)
RNA
, vol.15
, pp. 2375-2384
-
-
Bissels, U.1
Wild, S.2
Tomiuk, S.3
Holste, A.4
Hafner, M.5
Tuschl, T.6
-
9
-
-
0034161419
-
Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases
-
Blencowe, B. (2000). Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases. Trends Biochem. Sci. 25, 106-110. doi: 10.1016/S0968-0004(00)01549-8
-
(2000)
Trends Biochem. Sci.
, vol.25
, pp. 106-110
-
-
Blencowe, B.1
-
10
-
-
0014202530
-
Studies on free and membrane-bound ribosomes in rat liver. I. Distribution as related to total cellular RNA.
-
Blobel, G., and Potter, V. R. (1967). Studies on free and membrane-bound ribosomes in rat liver. I. Distribution as related to total cellular RNA. J. Mol. Biol. 26, 279-292. doi: 10.1016/0022-2836(67)90297-5
-
(1967)
J. Mol. Biol.
, vol.26
, pp. 279-292
-
-
Blobel, G.1
Potter, V.R.2
-
11
-
-
0026489906
-
The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus
-
Brockdorff, N., Ashworth, A., Kay, G. F., McCabe, V. M., Norris, D. P., Cooper, P. J.,et al. (1992). The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell 71, 515-526. doi: 10.1016/0092-8674(92)90519-I
-
(1992)
Cell
, vol.71
, pp. 515-526
-
-
Brockdorff, N.1
Ashworth, A.2
Kay, G.F.3
McCabe, V.M.4
Norris, D.P.5
Cooper, P.J.6
-
12
-
-
0028006781
-
Quantitative RT-PCR assays show Xist RNA levels are low in mouse female adult tissue, embryos and embryoid bodies
-
Buzin, C. H., Mann, J. R., and Singer-Sam, J. (1994). Quantitative RT-PCR assays show Xist RNA levels are low in mouse female adult tissue, embryos and embryoid bodies. Development 120, 3529-3536.
-
(1994)
Development
, vol.120
, pp. 3529-3536
-
-
Buzin, C.H.1
Mann, J.R.2
Singer-Sam, J.3
-
13
-
-
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.,et al. (2011). Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915-1927. doi: 10.1101/gad.17446611
-
(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
-
14
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N.,et al. (2005). The transcriptional landscape of the mammalian genome. Science 309, 1559-1563. doi: 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
-
15
-
-
33744805985
-
Genome-wide analysis of mammalian promoter architecture and evolution
-
Carninci, P., Sandelin, A., Lenhard, B., Katayama, S., Shimokawa, K., Ponjavic, J.,et al. (2006). Genome-wide analysis of mammalian promoter architecture and evolution. Nat. Genet. 38, 626-635. doi: 10.1038/ng1789
-
(2006)
Nat. Genet.
, vol.38
, pp. 626-635
-
-
Carninci, P.1
Sandelin, A.2
Lenhard, B.3
Katayama, S.4
Shimokawa, K.5
Ponjavic, J.6
-
16
-
-
33646878930
-
Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray
-
Carter, M. G., Sharov, A. A., VanBuren, V., Dudekula, D. B., Carmack, C. E., Nelson, C.,et al. (2005). Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray. Genome Biol. 6:R61. doi: 10.1186/gb-2005- 6-7-r61
-
(2005)
Genome Biol
, vol.6
-
-
Carter, M.G.1
Sharov, A.A.2
VanBuren, V.3
Dudekula, D.B.4
Carmack, C.E.5
Nelson, C.6
-
17
-
-
77955643151
-
Digital genome-wide ncRNA expression, including SnoRNAs, across 11 human tissues using polyA-neutral amplification
-
Castle, J. C., Armour, C. D., Löwer, M., Haynor, D., Biery, M., Bouzek, H.,et al. (2010). Digital genome-wide ncRNA expression, including SnoRNAs, across 11 human tissues using polyA-neutral amplification. PLoS ONE 5:e11779. doi: 10.1371/journal.pone.0011779
-
(2010)
PLoS ONE
, vol.5
-
-
Castle, J.C.1
Armour, C.D.2
Löwer, M.3
Haynor, D.4
Biery, M.5
Bouzek, H.6
-
18
-
-
84897128298
-
The noncoding RNA revolution-trashing old rules to forge new ones
-
Cech, T. R., and Steitz, J. A. (2014). The noncoding RNA revolution-trashing old rules to forge new ones. Cell 157, 77-94. doi: 10.1016/j.cell.2014.03.008
-
(2014)
Cell
, vol.157
, pp. 77-94
-
-
Cech, T.R.1
Steitz, J.A.2
-
19
-
-
60349093708
-
Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation
-
Charlesworth, B. (2009). Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation. Nat. Rev. Genet. 10, 195-205. doi: 10.1038/nrg2526
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 195-205
-
-
Charlesworth, B.1
-
20
-
-
37349038984
-
Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome
-
Chekanova, J. A., Gregory, B. D., Reverdatto, S. V., Chen, H., Kumar, R., Hooker, T.,et al. (2007). Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell 131, 1340-1353. doi: 10.1016/j.cell.2007.10.056
-
(2007)
Cell
, vol.131
, pp. 1340-1353
-
-
Chekanova, J.A.1
Gregory, B.D.2
Reverdatto, S.V.3
Chen, H.4
Kumar, R.5
Hooker, T.6
-
21
-
-
56849114880
-
Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome
-
Cheung, V., Chua, G., Batada, N. N., Landry, C. R., Michnick, S. W., Hughes, T. R.,et al. (2008). Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome. PLoS Biol. 6:e277. doi: 10.1371/journal.pbio.0060277
-
(2008)
PLoS Biol
, vol.6
-
-
Cheung, V.1
Chua, G.2
Batada, N.N.3
Landry, C.R.4
Michnick, S.W.5
Hughes, T.R.6
-
22
-
-
0141567459
-
Physical stability of proteins in aqueous solution: mechanism and driving forces in nonnative protein aggregation
-
Chi, E. Y., Krishnan, S., Randolph, T. W., and Carpenter, J. F. (2003). Physical stability of proteins in aqueous solution: mechanism and driving forces in nonnative protein aggregation. Pharm. Res. 20, 1325-1336. doi: 10.1023/A:10257714 21906
-
(2003)
Pharm. Res.
, vol.20
, pp. 1325-1336
-
-
Chi, E.Y.1
Krishnan, S.2
Randolph, T.W.3
Carpenter, J.F.4
-
23
-
-
0003779650
-
The Cell: A Molecular Approach
-
Washington, DC; Sunderland, MA: ASM Press; Sinauer Associates.
-
Cooper, G. M. (2000). The Cell: A Molecular Approach. Washington, DC; Sunderland, MA: ASM Press; Sinauer Associates.
-
(2000)
-
-
Cooper, G.M.1
-
24
-
-
33644784770
-
Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae
-
Davis, C. A., and Ares, M. Jr. (2006). Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 103, 3262-3267. doi: 10.1073/pnas.0507783103
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 3262-3267
-
-
Davis, C.A.1
Ares, M.2
-
25
-
-
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.,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. doi: 10.1101/gr.132159.111
-
(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
-
-
84877749322
-
Exaptation of transposable elements into novel cis-regulatory elements: is the evidence always strong
-
de Souza, F. S. J., Franchini, L. F., and Rubinstein, M. (2013). Exaptation of transposable elements into novel cis-regulatory elements: is the evidence always strong? Mol. Biol. Evol. 30, 1239-1251. doi: 10.1093/molbev/mst045
-
(2013)
Mol.Biol. Evol.
, vol.30
, pp. 1239-1251
-
-
de Souza, F.S.J.1
Franchini, L.F.2
Rubinstein, M.3
-
27
-
-
84865757142
-
Landscape of transcription in human cells
-
Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A.,et al. (2012). Landscape of transcription in human cells. Nature 489, 101-108. doi: 10.1038/nature11233
-
(2012)
Nature
, vol.489
, pp. 101-108
-
-
Djebali, S.1
Davis, C.A.2
Merkel, A.3
Dobin, A.4
Lassmann, T.5
Mortazavi, A.6
-
28
-
-
84875847924
-
Is junk DNA bunk? A critique of ENCODE
-
Doolittle, W. F. (2013). Is junk DNA bunk? A critique of ENCODE. Proc. Natl. Acad. Sci. U.S.A. 110, 5294-5300. doi: 10.1073/pnas.1221376110
-
(2013)
Proc. Natl. Acad. Sci. U.S.A.
, vol.110
, pp. 5294-5300
-
-
Doolittle, W.F.1
-
29
-
-
84902672358
-
Distinguishing between "function" and "effect" in genome biology
-
Doolittle, W. F., Brunet, T. D. P., Linquist, S., and Gregory, T. R. (2014). Distinguishing between "function" and "effect" in genome biology. Genome Biol. Evol. 6, 1234-1237. doi: 10.1093/gbe/evu098
-
(2014)
Genome Biol. Evol.
, vol.6
, pp. 1234-1237
-
-
Doolittle, W.F.1
Brunet, T.D.P.2
Linquist, S.3
Gregory, T.R.4
-
30
-
-
84913594397
-
Genome editing. The new frontier of genome engineering with CRISPR-Cas9
-
Doudna, J. A., and Charpentier, E. (2014). Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 346:1258096. doi: 10.1126/science.1258096
-
(2014)
Science
, vol.346
, pp. 1258096
-
-
Doudna, J.A.1
Charpentier, E.2
-
31
-
-
0021099528
-
Identification and quantitation of levels of protein synthesis initiation factors in crude HeLa cell lysates by two-dimensional polyacrylamide gel electrophoresis
-
Duncan, R., and Hershey, J. W. (1983). Identification and quantitation of levels of protein synthesis initiation factors in crude HeLa cell lysates by two-dimensional polyacrylamide gel electrophoresis. J. Biol. Chem. 258, 7228-7235.
-
(1983)
J. Biol. Chem
, vol.258
, pp. 7228-7235
-
-
Duncan, R.1
Hershey, J.W.2
-
32
-
-
84865772716
-
Genomics: ENCODE explained
-
Ecker, J. R., Bickmore, W. A., Barroso, I., Pritchard, J. K., Gilad, Y., and Segal, E. (2012). Genomics: ENCODE explained. Nature 489, 52-55. doi: 10.1038/48 9052a
-
(2012)
Nature
, vol.489
, pp. 52-55
-
-
Ecker, J.R.1
Bickmore, W.A.2
Barroso, I.3
Pritchard, J.K.4
Gilad, Y.5
Segal, E.6
-
33
-
-
84868550433
-
The C-value paradox, junk DNA and ENCODE
-
Eddy, S. R. (2012). The C-value paradox, junk DNA and ENCODE. Curr. Biol. 22, R898-R899. doi: 10.1016/j.cub.2012.10.002
-
(2012)
Curr. Biol.
, vol.22
, pp. R898-R899
-
-
Eddy, S.R.1
-
34
-
-
84876031068
-
The ENCODE project: missteps overshadowing a success
-
Eddy, S. R. (2013). The ENCODE project: missteps overshadowing a success. Curr. Biol. 23, R259-R261. doi: 10.1016/j.cub.2013.03.023
-
(2013)
Curr. Biol.
, vol.23
, pp. R259-R261
-
-
Eddy, S.R.1
-
35
-
-
84901645644
-
Conceptual and empirical challenges of ascribing functions to transposable elements
-
Elliott, T. A., Linquist, S., and Gregory, T. R. (2014). Conceptual and empirical challenges of ascribing functions to transposable elements. Am. Nat. 184, 14-24. doi: 10.1086/676588
-
(2014)
Am. Nat.
, vol.184
, pp. 14-24
-
-
Elliott, T.A.1
Linquist, S.2
Gregory, T.R.3
-
36
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
ENCODE Project Consortium,Bernstein, B. E., Birney, E., Dunham, I., Green, E. D., Gunter, C.,et al. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74. doi: 10.1038/ nature11247
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
Bernstein, B.E.1
Birney, E.2
Dunham, I.3
Green, E.D.4
Gunter, C.5
-
37
-
-
84911444179
-
Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes
-
Ezkurdia, I., Juan, D., Rodriguez, J. M., Frankish, A., Diekhans, M., Harrow, J.,et al. (2014). Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes. Hum. Mol. Genet. 23, 5866-5878. doi: 10.1093/hmg/ddu309
-
(2014)
Hum. Mol. Genet.
, vol.23
, pp. 5866-5878
-
-
Ezkurdia, I.1
Juan, D.2
Rodriguez, J.M.3
Frankish, A.4
Diekhans, M.5
Harrow, J.6
-
39
-
-
0018692402
-
The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme
-
Gould, S. J., and Lewontin, R. C. (1979). The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proc. R. Soc. Lond. Biol. Sci. 205, 581-598. doi: 10.1098/rspb.1979.0086
-
(1979)
Proc. R. Soc. Lond. Biol. Sci.
, vol.205
, pp. 581-598
-
-
Gould, S.J.1
Lewontin, R.C.2
-
40
-
-
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, R. B. R., Zufall, R. A., and 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. doi: 10.1093/gbe/evt028
-
(2013)
Genome Biol. Evol.
, vol.5
, pp. 578-590
-
-
Graur, D.1
Zheng, Y.2
Price, N.3
Azevedo, R.B.R.4
Zufall, R.A.5
Elhaik, E.6
-
41
-
-
84956906428
-
Expanded identification and characterization of mammalian circular RNAs
-
Guo, J. U., Agarwal, V., Guo, H., and Bartel, D. P. (2014). Expanded identification and characterization of mammalian circular RNAs. Genome Biol. 15:409. doi: 10.1186/s13059-014-0409-z
-
(2014)
Genome Biol
, vol.15
, Issue.409
-
-
Guo, J.U.1
Agarwal, V.2
Guo, H.3
Bartel, D.P.4
-
42
-
-
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.,et al. (2009). Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223-227. doi: 10.1038/nature07672
-
(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
-
43
-
-
84879969127
-
Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins
-
Guttman, M., Russell, P., Ingolia, N. T., Weissman, J. S., and Lander, E. S. (2013). Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell 154, 240-251. doi: 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
-
44
-
-
84879671055
-
Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs
-
Hangauer, M. J., Vaughn, I. W., and McManus, M. T. (2013). Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PLoS Genet. 9:e1003569. doi: 10.1371/journal.pgen.1003569
-
(2013)
PLoS Genet
, vol.9
-
-
Hangauer, M.J.1
Vaughn, I.W.2
McManus, M.T.3
-
45
-
-
0017220998
-
The expression of three abundance classes of messenger RNA in mouse tissues
-
Hastie, N. D., and Bishop, J. O. (1976). The expression of three abundance classes of messenger RNA in mouse tissues. Cell 9, 761-774. doi: 10.1016/0092-8674(76)90139-2
-
(1976)
Cell
, vol.9
, pp. 761-774
-
-
Hastie, N.D.1
Bishop, J.O.2
-
46
-
-
45249123859
-
Evidence against the energetic cost hypothesis for the short introns in highly expressed genes
-
Huang, Y.-F., and Niu, D.-K. (2008). Evidence against the energetic cost hypothesis for the short introns in highly expressed genes. BMC Evol. Biol. 8:154. doi: 10.1186/1471-2148-8-154
-
(2008)
BMC Evol. Biol
, vol.8
, Issue.154
-
-
Huang, Y.-F.1
Niu, D.-K.2
-
47
-
-
84922489184
-
Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes
-
Ingolia, N. T., Brar, G. A., Stern-Ginossar, N., Harris, M. S., Talhouarne, G. J. S., Jackson, S. E.,et al. (2014). Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. Cell Rep. 8, 1365-1379. doi: 10.1016/j.celrep.2014.07.045
-
(2014)
Cell Rep.
, vol.8
, pp. 1365-1379
-
-
Ingolia, N.T.1
Brar, G.A.2
Stern-Ginossar, N.3
Harris, M.S.4
Talhouarne, G.J.S.5
Jackson, S.E.6
-
48
-
-
81055155799
-
Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
-
Ingolia, N. T., Lareau, L. F., and Weissman, J. S. (2011). Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147, 789-802. doi: 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
-
49
-
-
84872531655
-
Circular RNAs are abundant, conserved, and associated with ALU repeats
-
Jeck, W. R., Sorrentino, J. A., Wang, K., Slevin, M. K., Burd, C. E., Liu, J.,et al. (2013). Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA 19, 141-157. doi: 10.1261/rna.035667.112
-
(2013)
RNA
, vol.19
, pp. 141-157
-
-
Jeck, W.R.1
Sorrentino, J.A.2
Wang, K.3
Slevin, M.K.4
Burd, C.E.5
Liu, J.6
-
50
-
-
77955110979
-
Genome-wide computational identification and manual annotation of human long noncoding RNA genes
-
Jia, H., Osak, M., Bogu, G. K., Stanton, L. W., Johnson, R., and Lipovich, L. (2010). Genome-wide computational identification and manual annotation of human long noncoding RNA genes. RNA 16, 1478-1487. doi: 10.1261/rna.19 51310
-
(2010)
RNA
, vol.16
, pp. 1478-1487
-
-
Jia, H.1
Osak, M.2
Bogu, G.K.3
Stanton, L.W.4
Johnson, R.5
Lipovich, L.6
-
51
-
-
78649847070
-
U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation
-
Kaida, D., Berg, M. G., Younis, I., Kasim, M., Singh, L. N., Wan, L.,et al. (2010). U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation. Nature 468, 664-668. doi: 10.1038/nature09479
-
(2010)
Nature
, vol.468
, pp. 664-668
-
-
Kaida, D.1
Berg, M.G.2
Younis, I.3
Kasim, M.4
Singh, L.N.5
Wan, L.6
-
52
-
-
84921908289
-
Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications
-
Kapusta, A., and Feschotte, C. (2014). Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications. Trends Genet. 30, 439-452. doi: 10.1016/j.tig.2014.08.004
-
(2014)
Trends Genet.
, vol.30
, pp. 439-452
-
-
Kapusta, A.1
Feschotte, C.2
-
53
-
-
84864315587
-
HP1Swi6 mediates the recognition and destruction of heterochromatic RNA transcripts
-
Keller, C., Adaixo, R., Stunnenberg, R., Woolcock, K. J., Hiller, S., and Bühler, M. (2012). HP1Swi6 mediates the recognition and destruction of heterochromatic RNA transcripts. Mol. Cell 47, 215-227. doi: 10.1016/j.molcel.2012.05.009
-
(2012)
Mol. Cell
, vol.47
, pp. 215-227
-
-
Keller, C.1
Adaixo, R.2
Stunnenberg, R.3
Woolcock, K.J.4
Hiller, S.5
Bühler, M.6
-
54
-
-
67650921949
-
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
-
Khalil, A. M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D.,et al. (2009). Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. U.S.A. 106, 11667-11672. doi: 10.1073/pnas.0904715106
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, 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
-
55
-
-
0014421064
-
Evolutionary rate at the molecular level
-
Kimura, M. (1968). Evolutionary rate at the molecular level. Nature 217, 624-626. doi: 10.1038/217624a0
-
(1968)
Nature
, vol.217
, pp. 624-626
-
-
Kimura, M.1
-
56
-
-
0004046696
-
The Neutral Theory of Molecular Evolution
-
Cambridge: Cambridge University Press.
-
Kimura, M. (1984). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
-
(1984)
-
-
Kimura, M.1
-
57
-
-
0014680905
-
Non-Darwinian evolution
-
King, J. L., and Jukes, T. H. (1969). Non-Darwinian evolution. Science 164, 788-798. doi: 10.1126/science.164.3881.788
-
(1969)
Science
, vol.164
, pp. 788-798
-
-
King, J.L.1
Jukes, T.H.2
-
58
-
-
0026694182
-
Evidence against a mitochondrial location of the 7-2/MRP RNA in mammalian cells
-
Kiss, T., and Filipowicz, W. (1992). Evidence against a mitochondrial location of the 7-2/MRP RNA in mammalian cells. Cell 70, 11-16. doi: 10.1016/0092-8674(92)90528-K
-
(1992)
Cell
, vol.70
, pp. 11-16
-
-
Kiss, T.1
Filipowicz, W.2
-
59
-
-
0026151349
-
A short leader sequence impairs the fidelity of initiation by eukaryotic ribosomes
-
Kozak, M. (1991). A short leader sequence impairs the fidelity of initiation by eukaryotic ribosomes. Gene Expr. 1, 111-115.
-
(1991)
Gene Expr
, vol.1
, pp. 111-115
-
-
Kozak, M.1
-
60
-
-
84874368349
-
Activating RNAs associate with Mediator to enhance chromatin architecture and transcription
-
Lai, F., Orom, U. A., Cesaroni, M., Beringer, M., Taatjes, D. J., Blobel, G. A.,et al. (2013). Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature 494, 497-501. doi: 10.1038/nature 11884
-
(2013)
Nature
, vol.494
, pp. 497-501
-
-
Lai, F.1
Orom, U.A.2
Cesaroni, M.3
Beringer, M.4
Taatjes, D.J.5
Blobel, G.A.6
-
61
-
-
40149095913
-
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm
-
Li, X., MacArthur, S., Bourgon, R., Nix, D., Pollard, D. A., Iyer, V. N.,et al. (2008). Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol. 6:e27. doi: 10.1371/journal.pbio.0060027
-
(2008)
PLoS Biol
, vol.6
-
-
Li, X.1
MacArthur, S.2
Bourgon, R.3
Nix, D.4
Pollard, D.A.5
Iyer, V.N.6
-
62
-
-
84859582058
-
Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function
-
Lickwar, C. R., Mueller, F., Hanlon, S. E., McNally, J. G., and Lieb, J. D. (2012). Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function. Nature 484, 251-255. doi: 10.1038/nature10985
-
(2012)
Nature
, vol.484
, pp. 251-255
-
-
Lickwar, C.R.1
Mueller, F.2
Hanlon, S.E.3
McNally, J.G.4
Lieb, J.D.5
-
63
-
-
0037407941
-
Analysis of the stimulatory effect of splicing on mRNA production and utilization in mammalian cells
-
Lu, S., and Cullen, B. R. (2003). Analysis of the stimulatory effect of splicing on mRNA production and utilization in mammalian cells. RNA 9, 618-630. doi: 10.1261/rna.5260303
-
(2003)
RNA
, vol.9
, pp. 618-630
-
-
Lu, S.1
Cullen, B.R.2
-
64
-
-
34250709215
-
The Origins of Genome Architecture
-
Sunderland MA: Sinauer Associates.
-
Lynch, M. (2007). The Origins of Genome Architecture. Sunderland MA: Sinauer Associates.
-
(2007)
-
-
Lynch, M.1
-
65
-
-
84883487014
-
Conserved regulation of cardiac calcium uptake by peptides encoded in small open reading frames
-
Magny, E. G., Pueyo, J. I., Pearl, F. M. G., Cespedes, M. A., Niven, J. E., Bishop, S. A.,et al. (2013). Conserved regulation of cardiac calcium uptake by peptides encoded in small open reading frames. Science 341, 1116-1120. doi: 10.1126/science.1238802
-
(2013)
Science
, vol.341
, pp. 1116-1120
-
-
Magny, E.G.1
Pueyo, J.I.2
Pearl, F.M.G.3
Cespedes, M.A.4
Niven, J.E.5
Bishop, S.A.6
-
66
-
-
84874780403
-
The vast, conserved mammalian lincRNome
-
Managadze, D., Lobkovsky, A. E., Wolf, Y. I., Shabalina, S. A., Rogozin, I. B., and Koonin, E. V. (2013). The vast, conserved mammalian lincRNome. PLoS Comput. Biol. 9:e1002917. doi: 10.1371/journal.pcbi.1002917
-
(2013)
PLoS Comput. Biol
, vol.9
-
-
Managadze, D.1
Lobkovsky, A.E.2
Wolf, Y.I.3
Shabalina, S.A.4
Rogozin, I.B.5
Koonin, E.V.6
-
67
-
-
84858798657
-
Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs
-
Managadze, D., Rogozin, I. B., Chernikova, D., Shabalina, S. A., and Koonin, E. V. (2011). Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs. Genome Biol. Evol. 3, 1390-1404. doi: 10.1093/gbe/evr116
-
(2011)
Genome Biol. Evol.
, vol.3
, pp. 1390-1404
-
-
Managadze, D.1
Rogozin, I.B.2
Chernikova, D.3
Shabalina, S.A.4
Koonin, E.V.5
-
68
-
-
33644783626
-
Introns and the origin of nucleus-cytosol compartmentalization
-
Martin, W., and Koonin, E. V. (2006). Introns and the origin of nucleus-cytosol compartmentalization. Nature 440, 41-45. doi: 10.1038/ nature04531
-
(2006)
Nature
, vol.440
, pp. 41-45
-
-
Martin, W.1
Koonin, E.V.2
-
69
-
-
84899637780
-
The extent of functionality in the human genome
-
Mattick, J. S., and Dinger, M. E. (2013). The extent of functionality in the human genome. HUGO J. 7:2. doi: 10.1186/1877-6566-7-2
-
(2013)
HUGO J
, vol.7
, Issue.2
-
-
Mattick, J.S.1
Dinger, M.E.2
-
70
-
-
72449129174
-
A global view of genomic information-moving beyond the gene and the master regulator
-
Mattick, J. S., Taft, R. J., and Faulkner, G. J. (2010). A global view of genomic information-moving beyond the gene and the master regulator. Trends Genet. 26, 21-28. doi: 10.1016/j.tig.2009.11.002
-
(2010)
Trends Genet.
, vol.26
, pp. 21-28
-
-
Mattick, J.S.1
Taft, R.J.2
Faulkner, G.J.3
-
71
-
-
84875369248
-
Circular RNAs are a large class of animal RNAs with regulatory potency
-
Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A.,et al. (2013). Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495, 333-338. doi: 10.1038/nature11928
-
(2013)
Nature
, vol.495
, pp. 333-338
-
-
Memczak, S.1
Jens, M.2
Elefsinioti, A.3
Torti, F.4
Krueger, J.5
Rybak, A.6
-
72
-
-
84881506759
-
Nascent-Seq reveals novel features of mouse circadian transcriptional regulation
-
Menet, J. S., Rodriguez, J., Abruzzi, K. C., and Rosbash, M. (2012). Nascent-Seq reveals novel features of mouse circadian transcriptional regulation. Elife 1:e00011. doi: 10.7554/eLife.00011
-
(2012)
Elife
, vol.1
-
-
Menet, J.S.1
Rodriguez, J.2
Abruzzi, K.C.3
Rosbash, M.4
-
73
-
-
50249112157
-
A yeast exosome cofactor, Mpp6, functions in RNA surveillance and in the degradation of noncoding RNA transcripts
-
Milligan, L., Decourty, L., Saveanu, C., Rappsilber, J., Ceulemans, H., Jacquier, A.,et al. (2008). A yeast exosome cofactor, Mpp6, functions in RNA surveillance and in the degradation of noncoding RNA transcripts. Mol. Cell. Biol. 28, 5446-5457. doi: 10.1128/MCB.00463-08
-
(2008)
Mol. Cell. Biol.
, vol.28
, pp. 5446-5457
-
-
Milligan, L.1
Decourty, L.2
Saveanu, C.3
Rappsilber, J.4
Ceulemans, H.5
Jacquier, A.6
-
74
-
-
84877111454
-
Widespread and extensive lengthening of 3'UTRs in the mammalian brain
-
Miura, P., Shenker, S., Andreu-Agullo, C., Westholm, J. O., and Lai, E. C. (2013). Widespread and extensive lengthening of 3'UTRs in the mammalian brain. Genome Res. 23, 812-825. doi: 10.1101/gr.146886.112
-
(2013)
Genome Res.
, vol.23
, pp. 812-825
-
-
Miura, P.1
Shenker, S.2
Andreu-Agullo, C.3
Westholm, J.O.4
Lai, E.C.5
-
75
-
-
58749097426
-
Small RNAs in transcriptional gene silencing and genome defence
-
Moazed, D. (2009). Small RNAs in transcriptional gene silencing and genome defence. Nature 457, 413-420. doi: 10.1038/nature07756
-
(2009)
Nature
, vol.457
, pp. 413-420
-
-
Moazed, D.1
-
76
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., and Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621-628. doi: 10.1038/nmeth.1226
-
(2008)
Nat. Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
77
-
-
60549114880
-
Widespread bidirectional promoters are the major source of cryptic transcripts in yeast
-
Neil, H., Malabat, C., d'Aubenton-Carafa, Y., Xu, Z., Steinmetz, L. M., and Jacquier, A. (2009). Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 457, 1038-1042. doi: 10.1038/ nature07747
-
(2009)
Nature
, vol.457
, pp. 1038-1042
-
-
Neil, H.1
Malabat, C.2
d'Aubenton-Carafa, Y.3
Xu, Z.4
Steinmetz, L.M.5
Jacquier, A.6
-
78
-
-
84872861423
-
Can ENCODE tell us how much junk DNA we carry in our genome? Biochem
-
Niu, D.-K., and Jiang, L. (2013). Can ENCODE tell us how much junk DNA we carry in our genome? Biochem. Biophys. Res. Commun. 430, 1340-1343. doi: 10.1016/j.bbrc.2012.12.074
-
(2013)
Biophys. Res. Commun.
, vol.430
, pp. 1340-1343
-
-
Niu, D.-K.1
Jiang, L.2
-
79
-
-
0015722319
-
Slightly deleterious mutant substitutions in evolution
-
Ohta, T. (1973). Slightly deleterious mutant substitutions in evolution. Nature 246, 96-98. doi: 10.1038/246096a0
-
(1973)
Nature
, vol.246
, pp. 96-98
-
-
Ohta, T.1
-
80
-
-
84860431158
-
Nuclear export as a key arbiter of "mRNA identity" in eukaryotes
-
Palazzo, A. F., and Akef, A. (2012). Nuclear export as a key arbiter of "mRNA identity" in eukaryotes. Biochim. Biophys. Acta 1819, 566-577. doi: 10.1016/j.bbagrm.2011.12.012
-
(2012)
Biochim. Biophys. Acta
, vol.1819
, pp. 566-577
-
-
Palazzo, A.F.1
Akef, A.2
-
81
-
-
84901596292
-
The case for junk DNA
-
Palazzo, A. F., and Gregory, T. R. (2014). The case for junk DNA. PLoS Genet. 10:e1004351. doi: 10.1371/journal.pgen.1004351
-
(2014)
PLoS Genet
, vol.10
-
-
Palazzo, A.F.1
Gregory, T.R.2
-
82
-
-
84882237496
-
ALREX-elements and introns: two identity elements that promote mRNA nuclear export
-
Palazzo, A., Mahadevan, K., and Tarnawsky, S. (2013). ALREX-elements and introns: two identity elements that promote mRNA nuclear export. Wiley Interdiscip. Rev. RNA 4, 523-533. doi: 10.1002/wrna.1176
-
(2013)
Wiley Interdiscip. Rev. RNA
, vol.4
, pp. 523-533
-
-
Palazzo, A.1
Mahadevanc, K.2
Tarnawsky, S.3
-
83
-
-
38549120240
-
The signal sequence coding region promotes nuclear export of mRNA
-
Palazzo, A. F., Springer, M., Shibata, Y., Lee, C.-S., Dias, A. P., and Rapoport, T. A. (2007). The signal sequence coding region promotes nuclear export of mRNA. PLoS Biol. 5:e322. doi: 10.1371/journal.pbio.0050322
-
(2007)
PLoS Biol
, vol.5
-
-
Palazzo, A.F.1
Springer, M.2
Shibata, Y.3
Lee, C.-S.4
Dias, A.P.5
Rapoport, T.A.6
-
84
-
-
84884698724
-
Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression
-
Paris, M., Kaplan, T., Li, X. Y., Villalta, J. E., Lott, S. E., and Eisen, M. B. (2013). Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression. PLoS Genet. 9:e1003748. doi: 10.1371/journal.pgen.1003748
-
(2013)
PLoS Genet
, vol.9
-
-
Paris, M.1
Kaplan, T.2
Li, X.Y.3
Villalta, J.E.4
Lott, S.E.5
Eisen, M.B.6
-
85
-
-
84865812140
-
Genomics. ENCODE project writes eulogy for junk DNA.
-
Pennisi, E. (2012). Genomics. ENCODE project writes eulogy for junk DNA. Science 337, 1159, 1161. doi: 10.1126/science.337.6099.1159
-
(2012)
Science
, vol.337
, pp. 1159-1161
-
-
Pennisi, E.1
-
86
-
-
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. doi: 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
-
87
-
-
57849123049
-
RNA exosome depletion reveals transcription upstream of active human promoters
-
Preker, P., Nielsen, J., Kammler, S., Lykke-Andersen, S., Christensen, M. S., Mapendano, C. K.,et al. (2008). RNA exosome depletion reveals transcription upstream of active human promoters. Science 322, 1851-1854. doi: 10.1126/science.1164096
-
(2008)
Science
, vol.322
, pp. 1851-1854
-
-
Preker, P.1
Nielsen, J.2
Kammler, S.3
Lykke-Andersen, S.4
Christensen, M.S.5
Mapendano, C.K.6
-
88
-
-
84946013175
-
LncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs
-
[Epub ahead of print].
-
Quek, X. C., Thomson, D. W., Maag, J. L. V., Bartonicek, N., Signal, B., Clark, M. B.,et al. (2014). lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res. doi: 10.1093/nar/gku988 [Epub ahead of print].
-
(2014)
Nucleic Acids Res
-
-
Quek, X.C.1
Thomson, D.W.2
Maag, J.L.V.3
Bartonicek, N.4
Signal, B.5
Clark, M.B.6
-
89
-
-
74549125753
-
An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data
-
Ramsköld, D., Wang, E. T., Burge, C. B., and Sandberg, R. (2009). An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput. Biol. 5:e1000598. doi: 10.1371/journal.pcbi.1000598
-
(2009)
PLoS Comput. Biol
, vol.5
-
-
Ramsköld, D.1
Wang, E.T.2
Burge, C.B.3
Sandberg, R.4
-
90
-
-
34247281027
-
Association of protein biogenesis factors at the yeast ribosomal tunnel exit is affected by the translational status and nascent polypeptide sequence
-
Raue, U., Oellerer, S., and Rospert, S. (2007). Association of protein biogenesis factors at the yeast ribosomal tunnel exit is affected by the translational status and nascent polypeptide sequence. J. Biol. Chem. 282, 7809-7816. doi: 10.1074/jbc.M611436200
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 7809-7816
-
-
Raue, U.1
Oellerer, S.2
Rospert, S.3
-
92
-
-
0017257102
-
Methyl labeling of HeLa cell hnRNA: a comparison with mRNA
-
Salditt-Georgieff, M., Jelinek, W., Darnell, J. E., Furuichi, Y., Morgan, M., and Shatkin, A. (1976). Methyl labeling of HeLa cell hnRNA: a comparison with mRNA. Cell 7, 227-237. doi: 10.1016/0092-8674(76)90022-2
-
(1976)
Cell
, vol.7
, pp. 227-237
-
-
Salditt-Georgieff, M.1
Jelinek, W.2
Darnell, J.E.3
Furuichi, Y.4
Morgan, M.5
Shatkin, A.6
-
93
-
-
84863045982
-
Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types
-
Salzman, J., Gawad, C., Wang, P. L., Lacayo, N., and Brown, P. O. (2012). Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS ONE 7:e30733. doi: 10.1371/journal.pone.0030733
-
(2012)
PLoS ONE
, vol.7
-
-
Salzman, J.1
Gawad, C.2
Wang, P.L.3
Lacayo, N.4
Brown, P.O.5
-
94
-
-
84943164143
-
The genomic challenge to adaptationism
-
[Epub ahead of print].
-
Sarkar, S. (2014). The genomic challenge to adaptationism. Br. J. Philos. Sci. doi: 10.1093/bjps/axu002 [Epub ahead of print].
-
(2014)
Br. J. Philos. Sci
-
-
Sarkar, S.1
-
95
-
-
70649088961
-
The peculiarities of large intron splicing in animals
-
Shepard, S., McCreary, M., and Fedorov, A. (2009). The peculiarities of large intron splicing in animals. PLoS ONE 4:e7853. doi: 10.1371/journal.pone.0007853
-
(2009)
PLoS ONE
, vol.4
-
-
Shepard, S.1
McCreary, M.2
Fedorov, A.3
-
96
-
-
84902374618
-
LncRNA and gene looping: what's the connection?
-
[Epub ahead of print].
-
Shibayama, Y., Fanucchi, S., Magagula, L., and Mhlanga, M. M. (2014). lncRNA and gene looping: what's the connection? Transcription doi: 10.4161/trns.28658 [Epub ahead of print].
-
(2014)
Transcription
-
-
Shibayama, Y.1
Fanucchi, S.2
Magagula, L.3
Mhlanga, M.M.4
-
97
-
-
0017855369
-
Ribonuclease P: an enzyme with an essential RNA component
-
Stark, B. C., Kole, R., Bowman, E. J., and Altman, S. (1978). Ribonuclease P: an enzyme with an essential RNA component. Proc. Natl. Acad. Sci. U.S.A. 75, 3717-3721. doi: 10.1073/pnas.75.8.3717
-
(1978)
Proc. Natl. Acad. Sci. U.S.A.
, vol.75
, pp. 3717-3721
-
-
Stark, B.C.1
Kole, R.2
Bowman, E.J.3
Altman, S.4
-
98
-
-
84869056823
-
Why transcription factor binding sites are ten nucleotides long
-
Stewart, A. J., Hannenhalli, S., and Plotkin, J. B. (2012). Why transcription factor binding sites are ten nucleotides long. Genetics 192, 973-985. doi: 10.1534/genetics.112.143370
-
(2012)
Genetics
, vol.192
, pp. 973-985
-
-
Stewart, A.J.1
Hannenhalli, S.2
Plotkin, J.B.3
-
99
-
-
33846984935
-
Transcriptional noise and the fidelity of initiation by RNA polymerase II
-
Struhl, K. (2007). Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat. Struct. Mol. Biol. 14, 103-105. doi: 10.1038/nsmb0207-103
-
(2007)
Nat. Struct. Mol. Biol.
, vol.14
, pp. 103-105
-
-
Struhl, K.1
-
100
-
-
84868193627
-
Gene loops enhance transcriptional directionality
-
Tan-Wong, S. M., Zaugg, J. B., Camblong, J., Xu, Z., Zhang, D. W., Mischo, H. E.,et al. (2012). Gene loops enhance transcriptional directionality. Science 338, 671-675. doi: 10.1126/science.1224350
-
(2012)
Science
, vol.338
, pp. 671-675
-
-
Tan-Wong, S.M.1
Zaugg, J.B.2
Camblong, J.3
Xu, Z.4
Zhang, D.W.5
Mischo, H.E.6
-
101
-
-
33748435751
-
Transcription termination and nuclear degradation of cryptic unstable transcripts: a role for the nrd1-nab3 pathway in genome surveillance
-
Thiebaut, M., Kisseleva-Romanova, E., Rougemaille, M., Boulay, J., and Libri, D. (2006). Transcription termination and nuclear degradation of cryptic unstable transcripts: a role for the nrd1-nab3 pathway in genome surveillance. Mol. Cell 23, 853-864. doi: 10.1016/j.molcel.2006.07.029
-
(2006)
Mol. Cell
, vol.23
, pp. 853-864
-
-
Thiebaut, M.1
Kisseleva-Romanova, E.2
Rougemaille, M.3
Boulay, J.4
Libri, D.5
-
102
-
-
84865777822
-
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs
-
Tilgner, H., Knowles, D. G., Johnson, R., Davis, C. A., Chakrabortty, S., Djebali, S.,et al. (2012). Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res. 22, 1616-1625. doi: 10.1101/gr.134445.111
-
(2012)
Genome Res.
, vol.22
, pp. 1616-1625
-
-
Tilgner, H.1
Knowles, D.G.2
Johnson, R.3
Davis, C.A.4
Chakrabortty, S.5
Djebali, S.6
-
103
-
-
80053569699
-
Pervasive transcription - lessons from yeast
-
Tisseur, M., Kwapisz, M., and Morillon, A. (2011). Pervasive transcription - lessons from yeast. Biochimie 93, 1889-1896. doi: 10.1016/j.biochi.2011. 07.001
-
(2011)
Biochimie
, vol.93
, pp. 1889-1896
-
-
Tisseur, M.1
Kwapisz, M.2
Morillon, A.3
-
104
-
-
69249203534
-
Focus on the centre: the role of chromatin on the regulation of centromere identity and function
-
Torras-Llort, M., Moreno-Moreno, O., and Azorín, F. (2009). Focus on the centre: the role of chromatin on the regulation of centromere identity and function. EMBO J. 28, 2337-2348. doi: 10.1038/emboj.2009.174
-
(2009)
EMBO J.
, vol.28
, pp. 2337-2348
-
-
Torras-Llort, M.1
Moreno-Moreno, O.2
Azorín, F.3
-
105
-
-
84879987789
-
LincRNAs: genomics, evolution, and mechanisms
-
Ulitsky, I., and Bartel, D. P. (2013). lincRNAs: genomics, evolution, and mechanisms. Cell 154, 26-46. doi: 10.1016/j.cell.2013.06.020
-
(2013)
Cell
, vol.154
, pp. 26-46
-
-
Ulitsky, I.1
Bartel, D.P.2
-
106
-
-
0021767937
-
Human genes and pseudogenes for the 7SL RNA component of signal recognition particle
-
Ullu, E., and Weiner, A. M. (1984). Human genes and pseudogenes for the 7SL RNA component of signal recognition particle. EMBO J. 3, 3303-3310.
-
(1984)
EMBO J
, vol.3
, pp. 3303-3310
-
-
Ullu, E.1
Weiner, A.M.2
-
107
-
-
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. doi: 10.1371/journal.pbio.1000371
-
(2010)
PLoS Biol
, vol.8
-
-
van Bakel, H.1
Nislow, C.2
Blencowe, B.J.3
Hughes, T.R.4
-
108
-
-
38949210998
-
Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin
-
Vasiljeva, L., Kim, M., Terzi, N., Soares, L. M., and Buratowski, S. (2008). Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin. Mol. Cell 29, 313-323. doi: 10.1016/j.molcel.2008.01.011
-
(2008)
Mol. Cell
, vol.29
, pp. 313-323
-
-
Vasiljeva, L.1
Kim, M.2
Terzi, N.3
Soares, L.M.4
Buratowski, S.5
-
109
-
-
84875530540
-
LNCipedia: a database for annotated human lncRNA transcript sequences and structures
-
Volders, P.-J., Helsens, K., Wang, X., Menten, B., Martens, L., Gevaert, K.,et al. (2013). LNCipedia: a database for annotated human lncRNA transcript sequences and structures. Nucleic Acids Res. 41, D246-D251. doi: 10.1093/nar/gks915
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D246-D251
-
-
Volders, P.-J.1
Helsens, K.2
Wang, X.3
Menten, B.4
Martens, L.5
Gevaert, K.6
-
110
-
-
0016730809
-
Effect of growth rate on the amounts of ribosomal and transfer ribonucleic acids in yeast
-
Waldron, C., and Lacroute, F. (1975). Effect of growth rate on the amounts of ribosomal and transfer ribonucleic acids in yeast. J. Bacteriol. 122, 855-865.
-
(1975)
J. Bacteriol
, vol.122
, pp. 855-865
-
-
Waldron, C.1
Lacroute, F.2
-
111
-
-
0019964240
-
Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum
-
Walter, P., and Blobel, G. (1982). Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum. Nature 299, 691-698. doi: 10.1038/299691a0
-
(1982)
Nature
, vol.299
, pp. 691-698
-
-
Walter, P.1
Blobel, G.2
-
112
-
-
80053045739
-
Molecular mechanisms of long noncoding RNAs
-
Wang, K. C., and Chang, H. Y. (2011). Molecular mechanisms of long noncoding RNAs. Mol. Cell 43, 904-914. doi: 10.1016/j.molcel.2011.08.018
-
(2011)
Mol. Cell
, vol.43
, pp. 904-914
-
-
Wang, K.C.1
Chang, H.Y.2
-
113
-
-
84923152199
-
Alternative splicing at GYNNGY 5' splice sites: more noise, less regulation
-
Wang, M., Zhang, P., Shu, Y., Yuan, F., Zhang, Y., Zhou, Y.,et al. (2014). Alternative splicing at GYNNGY 5' splice sites: more noise, less regulation. Nucleic Acids Res. 42, 13969-13980. doi: 10.1093/nar/gku1253
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 13969-13980
-
-
Wang, M.1
Zhang, P.2
Shu, Y.3
Yuan, F.4
Zhang, Y.5
Zhou, Y.6
-
114
-
-
84867234474
-
Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules
-
Wang, Y., Ma, M., Xiao, X., and Wang, Z. (2012). Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules. Nat. Struct. Mol. Biol. 19, 1044-1052. doi: 10.1038/nsmb.2377
-
(2012)
Nat. Struct. Mol. Biol.
, vol.19
, pp. 1044-1052
-
-
Wang, Y.1
Ma, M.2
Xiao, X.3
Wang, Z.4
-
115
-
-
0033613188
-
De novo amyloid proteins from designed combinatorial libraries
-
West, M. W., Wang, W., Patterson, J., Mancias, J. D., Beasley, J. R., and Hecht, M. H. (1999). De novo amyloid proteins from designed combinatorial libraries. Proc. Natl. Acad. Sci. U.S.A. 96, 11211-11216. doi: 10.1073/pnas.96.20. 11211
-
(1999)
Proc. Natl. Acad. Sci. U.S.A.
, vol.96
, pp. 11211-11216
-
-
West, M.W.1
Wang, W.2
Patterson, J.3
Mancias, J.D.4
Beasley, J.R.5
Hecht, M.H.6
-
116
-
-
84880362638
-
Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks
-
White, M. A., Myers, C. A., Corbo, J. C., and Cohen, B. A. (2013). Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks. Proc. Natl. Acad. Sci. U.S.A. 110, 11952-11957. doi: 10.1073/pnas.1307449110
-
(2013)
Proc. Natl. Acad. Sci. U.S.A.
, vol.110
, pp. 11952-11957
-
-
White, M.A.1
Myers, C.A.2
Corbo, J.C.3
Cohen, B.A.4
-
117
-
-
0021704598
-
A minimal intron length but no specific internal sequence is required for splicing the large rabbit beta-globin intron
-
Wieringa, B., Hofer, E., and Weissmann, C. (1984). A minimal intron length but no specific internal sequence is required for splicing the large rabbit beta-globin intron. Cell 37, 915-925. doi: 10.1016/0092-8674(84)90426-4
-
(1984)
Cell
, vol.37
, pp. 915-925
-
-
Wieringa, B.1
Hofer, E.2
Weissmann, C.3
-
119
-
-
67649671961
-
Long noncoding RNAs: functional surprises from the RNA world
-
Wilusz, J. E., Sunwoo, H., and Spector, D. L. (2009). Long noncoding RNAs: functional surprises from the RNA world. Genes Dev. 23, 1494-1504. doi: 10.1101/gad.1800909
-
(2009)
Genes Dev.
, vol.23
, pp. 1494-1504
-
-
Wilusz, J.E.1
Sunwoo, H.2
Spector, D.L.3
-
120
-
-
0017410444
-
Nuclear metabolism of ribosomal RNA in growing, methionine-limited, and ethionine-treated HeLa cells
-
Wolf, S. F., and Schlessinger, D. (1977). Nuclear metabolism of ribosomal RNA in growing, methionine-limited, and ethionine-treated HeLa cells. Biochemistry (Mosc.) 16, 2783-2791. doi: 10.1021/bi00631a031
-
(1977)
Biochemistry (Mosc.)
, vol.16
, pp. 2783-2791
-
-
Wolf, S.F.1
Schlessinger, D.2
-
121
-
-
79955788276
-
Naming "junk": human non-protein coding RNA (ncRNA) gene nomenclature
-
Wright, M. W., and Bruford, E. A. (2011). Naming "junk": human non-protein coding RNA (ncRNA) gene nomenclature. Hum. Genomics 5:90. doi: 10.1186/1479-7364-5-2-90
-
(2011)
Hum. Genomics
, vol.5
, Issue.90
-
-
Wright, M.W.1
Bruford, E.A.2
-
122
-
-
84879823671
-
Roles of long noncoding RNAs in brain development, functional diversification and neurodegenerative diseases
-
Wu, P., Zuo, X., Deng, H., Liu, X., Liu, L., and Ji, A. (2013). Roles of long noncoding RNAs in brain development, functional diversification and neurodegenerative diseases. Brain Res. Bull. 97, 69-80. doi: 10.1016/j.brainresbull.2013.06.001
-
(2013)
Brain Res. Bull.
, vol.97
, pp. 69-80
-
-
Wu, P.1
Zuo, X.2
Deng, H.3
Liu, X.4
Liu, L.5
Ji, A.6
-
123
-
-
20444368036
-
Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase
-
Wyers, F., Rougemaille, M., Badis, G., Rousselle, J.-C., Dufour, M.-E., Boulay, J.,et al. (2005). Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121, 725-737. doi: 10.1016/j.cell.2005.04.030
-
(2005)
Cell
, vol.121
, pp. 725-737
-
-
Wyers, F.1
Rougemaille, M.2
Badis, G.3
Rousselle, J.-C.4
Dufour, M.-E.5
Boulay, J.6
-
124
-
-
84896281082
-
Human coding RNA editing is generally nonadaptive
-
Xu, G., and Zhang, J. (2014). Human coding RNA editing is generally nonadaptive. Proc. Natl. Acad. Sci. U.S.A. 111, 3769-3774. doi: 10.1073/pnas.1321745111
-
(2014)
Proc. Natl. Acad. Sci. U.S.A.
, vol.111
, pp. 3769-3774
-
-
Xu, G.1
Zhang, J.2
-
125
-
-
60549108380
-
Bidirectional promoters generate pervasive transcription in yeast
-
Xu, Z., Wei, W., Gagneur, J., Perocchi, F., Clauder-Münster, S., Camblong, J.,et al. (2009). Bidirectional promoters generate pervasive transcription in yeast. Nature 457, 1033-1037. doi: 10.1038/nature07728
-
(2009)
Nature
, vol.457
, pp. 1033-1037
-
-
Xu, Z.1
Wei, W.2
Gagneur, J.3
Perocchi, F.4
Clauder-Münster, S.5
Camblong, J.6
-
126
-
-
0019499146
-
A small nuclear ribonucleoprotein is required for splicing of adenoviral early RNA sequences
-
Yang, V. W., Lerner, M. R., Steitz, J. A., and Flint, S. J. (1981). A small nuclear ribonucleoprotein is required for splicing of adenoviral early RNA sequences. Proc. Natl. Acad. Sci. U.S.A. 78, 1371-1375. doi: 10.1073/pnas.78. 3.1371
-
(1981)
Proc. Natl. Acad. Sci. U.S.A.
, vol.78
, pp. 1371-1375
-
-
Yang, V.W.1
Lerner, M.R.2
Steitz, J.A.3
Flint, S.J.4
|