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Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same.
Weirauch MT, Hughes TR. Weirauch MT, et al. Among authors: hughes tr. Trends Genet. 2010 Feb;26(2):66-74. doi: 10.1016/j.tig.2009.12.002. Epub 2010 Jan 18. Trends Genet. 2010. PMID: 20083321 Review.
Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors.
Grigull J, Mnaimneh S, Pootoolal J, Robinson MD, Hughes TR. Grigull J, et al. Among authors: hughes tr. Mol Cell Biol. 2004 Jun;24(12):5534-47. doi: 10.1128/MCB.24.12.5534-5547.2004. Mol Cell Biol. 2004. PMID: 15169913 Free PMC article.
Exploration of essential gene functions via titratable promoter alleles.
Mnaimneh S, Davierwala AP, Haynes J, Moffat J, Peng WT, Zhang W, Yang X, Pootoolal J, Chua G, Lopez A, Trochesset M, Morse D, Krogan NJ, Hiley SL, Li Z, Morris Q, Grigull J, Mitsakakis N, Roberts CJ, Greenblatt JF, Boone C, Kaiser CA, Andrews BJ, Hughes TR. Mnaimneh S, et al. Among authors: hughes tr. Cell. 2004 Jul 9;118(1):31-44. doi: 10.1016/j.cell.2004.06.013. Cell. 2004. PMID: 15242642
Transcriptional networks: reverse-engineering gene regulation on a global scale.
Chua G, Robinson MD, Morris Q, Hughes TR. Chua G, et al. Among authors: hughes tr. Curr Opin Microbiol. 2004 Dec;7(6):638-46. doi: 10.1016/j.mib.2004.10.009. Curr Opin Microbiol. 2004. PMID: 15556037 Review.
The functional landscape of mouse gene expression.
Zhang W, Morris QD, Chang R, Shai O, Bakowski MA, Mitsakakis N, Mohammad N, Robinson MD, Zirngibl R, Somogyi E, Laurin N, Eftekharpour E, Sat E, Grigull J, Pan Q, Peng WT, Krogan N, Greenblatt J, Fehlings M, van der Kooy D, Aubin J, Bruneau BG, Rossant J, Blencowe BJ, Frey BJ, Hughes TR. Zhang W, et al. Among authors: hughes tr. J Biol. 2004;3(5):21. doi: 10.1186/jbiol16. Epub 2004 Dec 6. J Biol. 2004. PMID: 15588312 Free PMC article.
Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform.
Pan Q, Shai O, Misquitta C, Zhang W, Saltzman AL, Mohammad N, Babak T, Siu H, Hughes TR, Morris QD, Frey BJ, Blencowe BJ. Pan Q, et al. Among authors: hughes tr. Mol Cell. 2004 Dec 22;16(6):929-41. doi: 10.1016/j.molcel.2004.12.004. Mol Cell. 2004. PMID: 15610736
Alternative splicing of conserved exons is frequently species-specific in human and mouse.
Pan Q, Bakowski MA, Morris Q, Zhang W, Frey BJ, Hughes TR, Blencowe BJ. Pan Q, et al. Among authors: hughes tr. Trends Genet. 2005 Feb;21(2):73-7. doi: 10.1016/j.tig.2004.12.004. Trends Genet. 2005. PMID: 15661351
A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription.
Babak T, Blencowe BJ, Hughes TR. Babak T, et al. Among authors: hughes tr. BMC Genomics. 2005 Aug 5;6:104. doi: 10.1186/1471-2164-6-104. BMC Genomics. 2005. PMID: 16083503 Free PMC article.
The synthetic genetic interaction spectrum of essential genes.
Davierwala AP, Haynes J, Li Z, Brost RL, Robinson MD, Yu L, Mnaimneh S, Ding H, Zhu H, Chen Y, Cheng X, Brown GW, Boone C, Andrews BJ, Hughes TR. Davierwala AP, et al. Among authors: hughes tr. Nat Genet. 2005 Oct;37(10):1147-52. doi: 10.1038/ng1640. Epub 2005 Sep 11. Nat Genet. 2005. PMID: 16155567
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF. Krogan NJ, et al. Among authors: hughes tr. Nature. 2006 Mar 30;440(7084):637-43. doi: 10.1038/nature04670. Epub 2006 Mar 22. Nature. 2006. PMID: 16554755
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