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MARIS: method for analyzing RNA following intracellular sorting.
Hrvatin S, Deng F, O'Donnell CW, Gifford DK, Melton DA. Hrvatin S, et al. Among authors: gifford dk. PLoS One. 2014 Mar 3;9(3):e89459. doi: 10.1371/journal.pone.0089459. eCollection 2014. PLoS One. 2014. PMID: 24594682 Free PMC article.
Core transcriptional regulatory circuitry in human embryonic stem cells.
Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, Zucker JP, Guenther MG, Kumar RM, Murray HL, Jenner RG, Gifford DK, Melton DA, Jaenisch R, Young RA. Boyer LA, et al. Among authors: gifford dk. Cell. 2005 Sep 23;122(6):947-56. doi: 10.1016/j.cell.2005.08.020. Cell. 2005. PMID: 16153702 Free PMC article.
High-resolution computational models of genome binding events.
Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK. Qi Y, et al. Among authors: gifford dk. Nat Biotechnol. 2006 Aug;24(8):963-70. doi: 10.1038/nbt1233. Nat Biotechnol. 2006. PMID: 16900145
Control of transcription by cell size.
Wu CY, Rolfe PA, Gifford DK, Fink GR. Wu CY, et al. Among authors: gifford dk. PLoS Biol. 2010 Nov 2;8(11):e1000523. doi: 10.1371/journal.pbio.1000523. PLoS Biol. 2010. PMID: 21072241 Free PMC article.
Discovering regulatory overlapping RNA transcripts.
Danford T, Dowell R, Agarwala S, Grisafi P, Fink G, Gifford D. Danford T, et al. J Comput Biol. 2011 Mar;18(3):295-303. doi: 10.1089/cmb.2010.0267. J Comput Biol. 2011. PMID: 21385035
Embryonic stem cell-based mapping of developmental transcriptional programs.
Mazzoni EO, Mahony S, Iacovino M, Morrison CA, Mountoufaris G, Closser M, Whyte WA, Young RA, Kyba M, Gifford DK, Wichterle H. Mazzoni EO, et al. Among authors: gifford dk. Nat Methods. 2011 Nov 13;8(12):1056-8. doi: 10.1038/nmeth.1775. Nat Methods. 2011. PMID: 22081127 Free PMC article.
Ruler arrays reveal haploid genomic structural variation.
Rolfe PA, Bernstein DA, Grisafi P, Fink GR, Gifford DK. Rolfe PA, et al. Among authors: gifford dk. PLoS One. 2012;7(8):e43210. doi: 10.1371/journal.pone.0043210. Epub 2012 Aug 27. PLoS One. 2012. PMID: 22952647 Free PMC article.
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