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Items: 1 to 20 of 67

1.

Paradigm shifts in genomics through the FANTOM projects.

de Hoon M, Shin JW, Carninci P.

Mamm Genome. 2015 Oct;26(9-10):391-402. doi: 10.1007/s00335-015-9593-8. Epub 2015 Aug 8.

2.

Loss of Foxm1 Results in Reduced Somatotrope Cell Number during Mouse Embryogenesis.

Calderon MJ, Ploegman AG, Bailey B, Jung DO, Navratil AM, Ellsworth BS.

PLoS One. 2015 Jun 15;10(6):e0128942. doi: 10.1371/journal.pone.0128942. eCollection 2015.

3.

Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.

Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin A, Tanzer A, Lagarde J, Zaleski C, See LH, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigó R, Gingeras TR.

Nat Commun. 2015 Jan 13;6:5903. doi: 10.1038/ncomms6903.

4.

Diversity and dynamics of the Drosophila transcriptome.

Brown JB, Boley N, Eisman R, May GE, Stoiber MH, Duff MO, Booth BW, Wen J, Park S, Suzuki AM, Wan KH, Yu C, Zhang D, Carlson JW, Cherbas L, Eads BD, Miller D, Mockaitis K, Roberts J, Davis CA, Frise E, Hammonds AS, Olson S, Shenker S, Sturgill D, Samsonova AA, Weiszmann R, Robinson G, Hernandez J, Andrews J, Bickel PJ, Carninci P, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Lai EC, Oliver B, Perrimon N, Graveley BR, Celniker SE.

Nature. 2014 Aug 28;512(7515):393-9.

5.

Notch/Rbpjκ signaling regulates progenitor maintenance and differentiation of hypothalamic arcuate neurons.

Aujla PK, Naratadam GT, Xu L, Raetzman LT.

Development. 2013 Sep;140(17):3511-21. doi: 10.1242/dev.098681. Epub 2013 Jul 24.

6.

The forkhead transcription factor, Foxd1, is necessary for pituitary luteinizing hormone expression in mice.

Gumbel JH, Patterson EM, Owusu SA, Kabat BE, Jung DO, Simmons J, Hopkins T, Ellsworth BS.

PLoS One. 2012;7(12):e52156. doi: 10.1371/journal.pone.0052156. Epub 2012 Dec 19.

7.

Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii).

Tan YY, Kodzius R, Tay BH, Tay A, Brenner S, Venkatesh B.

PLoS One. 2012;7(10):e47174. doi: 10.1371/journal.pone.0047174. Epub 2012 Oct 8.

8.

Disentangling the relationship between sex-biased gene expression and X-linkage.

Meisel RP, Malone JH, Clark AG.

Genome Res. 2012 Jul;22(7):1255-65. doi: 10.1101/gr.132100.111. Epub 2012 Apr 12.

9.

Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer.

Itoh M, Kojima M, Nagao-Sato S, Saijo E, Lassmann T, Kanamori-Katayama M, Kaiho A, Lizio M, Kawaji H, Carninci P, Forrest AR, Hayashizaki Y.

PLoS One. 2012;7(1):e30809. doi: 10.1371/journal.pone.0030809. Epub 2012 Jan 30.

10.

The reality of pervasive transcription.

Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Ponting CP, Stadler PF, Morris KV, Morillon A, Rozowsky JS, Gerstein MB, Wahlestedt C, Hayashizaki Y, Carninci P, Gingeras TR, Mattick JS.

PLoS Biol. 2011 Jul;9(7):e1000625; discussion e1001102. doi: 10.1371/journal.pbio.1000625. Epub 2011 Jul 12. No abstract available.

11.

Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling.

Łabaj PP, Leparc GG, Linggi BE, Markillie LM, Wiley HS, Kreil DP.

Bioinformatics. 2011 Jul 1;27(13):i383-91. doi: 10.1093/bioinformatics/btr247.

12.

Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome.

Mercer TR, Dinger ME, Bracken CP, Kolle G, Szubert JM, Korbie DJ, Askarian-Amiri ME, Gardiner BB, Goodall GJ, Grimmond SM, Mattick JS.

Genome Res. 2010 Dec;20(12):1639-50. doi: 10.1101/gr.112128.110. Epub 2010 Nov 2.

13.

Corepressors TLE1 and TLE3 interact with HESX1 and PROP1.

Carvalho LR, Brinkmeier ML, Castinetti F, Ellsworth BS, Camper SA.

Mol Endocrinol. 2010 Apr;24(4):754-65. doi: 10.1210/me.2008-0359. Epub 2010 Feb 24.

14.

Networks and pathways in pigmentation, health, and disease.

Baxter LL, Loftus SK, Pavan WJ.

Wiley Interdiscip Rev Syst Biol Med. 2009 Nov-Dec;1(3):359-71. doi: 10.1002/wsbm.20. Review.

15.

Molecular mechanisms of pituitary organogenesis: In search of novel regulatory genes.

Davis SW, Castinetti F, Carvalho LR, Ellsworth BS, Potok MA, Lyons RH, Brinkmeier ML, Raetzman LT, Carninci P, Mortensen AH, Hayashizaki Y, Arnhold IJ, Mendonça BB, Brue T, Camper SA.

Mol Cell Endocrinol. 2010 Jul 8;323(1):4-19. doi: 10.1016/j.mce.2009.12.012. Epub 2009 Dec 16. Review.

16.

Estimating the fraction of non-coding RNAs in mammalian transcriptomes.

Xin Y, Quarta G, Gan HH, Schlick T.

Bioinform Biol Insights. 2008 Mar 1;2:75-94.

17.

Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain.

Ponjavic J, Oliver PL, Lunter G, Ponting CP.

PLoS Genet. 2009 Aug;5(8):e1000617. doi: 10.1371/journal.pgen.1000617. Epub 2009 Aug 21.

18.

Genetics, gene expression and bioinformatics of the pituitary gland.

Davis SW, Potok MA, Brinkmeier ML, Carninci P, Lyons RH, MacDonald JW, Fleming MT, Mortensen AH, Egashira N, Ghosh D, Steel KP, Osamura RY, Hayashizaki Y, Camper SA.

Horm Res. 2009 Apr;71 Suppl 2:101-15. doi: 10.1159/000192447. Epub 2009 Apr 29.

19.

Promoter analysis: gene regulatory motif identification with A-GLAM.

Mariño-Ramírez L, Tharakaraman K, Spouge JL, Landsman D.

Methods Mol Biol. 2009;537:263-76. doi: 10.1007/978-1-59745-251-9_13.

20.

Discovery of transcriptional regulators and signaling pathways in the developing pituitary gland by bioinformatic and genomic approaches.

Brinkmeier ML, Davis SW, Carninci P, MacDonald JW, Kawai J, Ghosh D, Hayashizaki Y, Lyons RH, Camper SA.

Genomics. 2009 May;93(5):449-60. doi: 10.1016/j.ygeno.2008.11.010. Epub 2009 Feb 11.

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