Computational Molecular Biology 2014, Vol. 4, No. 5
http://cmb.biopublisher.ca
9
Dinger M.E., Amaral P.P., Mercer T.R., Pang K.C., Bruce S.J.,
Gardiner B.B., Askarian-Amiri M.E., Ru K., Solda G.,
Simons C., Sunkin S.M., Crowe M.L., Grimmond S.M.,
Perkins A.C., and Mattick J.S., 2008, Long noncoding
RNAs in mouse embryonic stem cell pluripotency and
differentiation, Genome Res, 18: 1433-1445
http://dx.doi.org/10.1101/gr.078378.108
Eberwine J., Sul J.Y., Bartfai T., and Kim J., 2014, The
promise of single-cell sequencing, Nat Methods, 11: 25-27
http://dx.doi.org/10.1038/nmeth.2769
Eissmann M., Gutschner T., Hammerle M., Gunther S.,
Caudron-Herger M., Gross M., Schirmacher P., Rippe K.,
Braun T., Zornig M., and Diederichs S., 2012, Loss of the
abundant nuclear non-coding RNA MALAT1 is
compatible with life and development, RNA Biol, 9:
1076-1087
http://dx.doi.org/10.4161/rna.21089
Faghihi M.A., Modarresi F., Khalil A.M., Wood D.E., Sahagan
B.G., Morgan T.E., Finch C.E., St Laurent G., 3rd, Kenny
P.J., and Wahlestedt C., 2008, Expression of a noncoding
RNA is elevated in Alzheimer's disease and drives rapid
feed-forward regulation of beta-secretase, Nat Med, 14:
723-730
http://dx.doi.org/10.1038/nm1784
Feng J., Bi C., Clark B.S., Mady R., Shah P., and Kohtz J.D.,
2006, The Evf-2 noncoding RNA is transcribed from the
Dlx-5/6 ultraconserved region and functions as a Dlx-2
transcriptional coactivator, Genes Dev, 20: 1470-1484
http://dx.doi.org/10.1101/gad.1416106
Ferretti E., De Smaele E., Po A., Di Marcotullio L., Tosi E.,
Espinola M.S., Di Rocco C., Riccardi R., Giangaspero F.,
Farcomeni A., Nofroni I., Laneve P., Gioia U., Caffarelli
E., Bozzoni I., Screpanti I., and Gulino A., 2009,
MicroRNA profiling in human medulloblastoma, Int J
Cancer, 124: 568-577
http://dx.doi.org/10.1002/ijc.23948
Friese M.A., and Fugger L., 2009, Pathogenic CD8(+) T cells
in multiple sclerosis, Ann Neurol, 66: 132-141
http://dx.doi.org/10.1002/ana.21744
Graff J., and Mansuy I.M., 2008, Epigenetic codes in cognition
and behaviour, Behav Brain Res, 192: 70-87
http://dx.doi.org/10.1016/j.bbr.2008.01.021
Gutschner T., Hammerle M., Eissmann M., Hsu J., Kim Y.,
Hung G., Revenko A., Arun G., Stentrup M., Gross M.,
Zornig M., Macleod A.R., Spector D.L., and Diederichs S.,
2013, The noncoding RNA MALAT1 is a critical
regulator of the metastasis phenotype of lung cancer cells,
Cancer Res, 73: 1180-1189
http://dx.doi.org/10.1158/0008-5472.CAN-12-2850
Guttman M., Amit I., Garber M., French C., Lin M.F., Feldser
D., Huarte M., Zuk O., Carey B.W., Cassady J.P., Cabili
M.N., Jaenisch R., Mikkelsen T.S., Jacks T., Hacohen N.,
Bernstein B.E., Kellis M., Regev A., Rinn J.L., and
Lander E.S., 2009, Chromatin signature reveals over a
thousand highly conserved large non-coding RNAs in
mammals, Nature, 458: 223-227
http://dx.doi.org/10.1038/nature07672
Guttman M., Garber M., Levin J.Z., Donaghey J., Robinson J.,
Adiconis X., Fan L., Koziol M.J., Gnirke A., Nusbaum C.,
Rinn J.L., Lander E.S., and Regev A., 2010, Ab initio
reconstruction of cell type-specific transcriptomes in
mouse reveals the conserved multi-exonic structure of
lincRNAs, Nat Biotechnol, 28: 503-510
http://dx.doi.org/10.1038/nbt.1633
Guttman M., and Rinn J.L., 2012, Modular regulatory
principles of large non-coding RNAs, Nature, 482:
339-346
http://dx.doi.org/10.1038/nature10887
Huseby E.S., Huseby P.G., Shah S., Smith R., and Stadinski
B.D., 2012, Pathogenic CD8 T cells in multiple sclerosis
and its experimental models, Front Immunol, 3: 64
http://dx.doi.org/10.3389/fimmu.2012.00064
Ilott N.E., and Ponting C.P., 2013, Predicting long non-coding
RNAs using RNA sequencing, Methods, 63: 50-59
http://dx.doi.org/10.1016/j.ymeth.2013.03.019
International Multiple Sclerosis Genetics C., Hafler D.A.,
Compston A., Sawcer S., Lander E.S., Daly M.J., De Jager
P.L., De Bakker P.I., Gabriel S.B., Mirel D.B., Ivinson
A.J., Pericak-Vance M.A., Gregory S.G., Rioux J.D.,
Mccauley J.L., Haines J.L., Barcellos L.F., Cree B.,
Oksenberg J.R., and Hauser S.L., 2007, Risk alleles for
multiple sclerosis identified by a genomewide study, N
Engl J Med, 357: 851-862
http://dx.doi.org/10.1056/NEJMoa073493
Johnson R., Teh C.H., Jia H., Vanisri R.R., Pandey T., Lu Z.H.,
Buckley N.J., Stanton L.W., and Lipovich L., 2009,
Regulation of neural macroRNAs by the transcriptional
repressor REST, RNA, 15: 85-96
http://dx.doi.org/10.1261/rna.1127009
Kaushik K., Leonard V.E., Kv S., Lalwani M.K., Jalali S.,
Patowary A., Joshi A., Scaria V., and Sivasubbu S., 2013,
Dynamic expression of long non-coding RNAs (lncRNAs)
in adult zebrafish, PLoS One, 8: e83616
http://dx.doi.org/10.1371/journal.pone.0083616
Kaut O., Ramirez A., Pieper H., Schmitt I., Jessen F., and
Wullner U., 2014, DNA Methylation of the TNF-alpha
Promoter Region in Peripheral Blood Monocytes and the
Cortex of Human Alzheimer's Disease Patients, Dement