Zill OA, Scannell DR, Kuei J, Sadhu M, Rine J. Evolutionary Analysis of Heterochromatin Protein Compatibility by Interspecies Complementation in Saccharomyces. Genetics. 2012 Aug 24.
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Zunder RM, Rine J. Direct Interplay among Histones, Histone Chaperones, and a Chromatin Boundary Protein in the Control of Histone Gene Expression. Mol Cell Biol. 2012 Nov.
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Mayfield JA, Davies MW, Dimster-Denk D, Pleskac N, McCarthy S, Boydston EA, Fink L, Lin XX, Narain AS, Meighan M, Rine J. Surrogate genetics and metabolic profiling for characterization of human disease alleles. Genetics. 2012 Apr.
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Zunder RM, Antczak AJ, Berger JM, Rine J. Two surfaces on the histone chaperone Rtt106 mediate histone binding, replication, and silencing. Proc Natl Acad Sci U S A. 2012 Jan 17.
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2011
Marini NJ, Hoffmann TJ, Lammer EJ, Hardin J, Lazaruk K, Stein JB, Gilbert DA, Wright C, Lipzen A, Pennacchio LA, Carmichael SL, Witte JS, Shaw GM, Rine J. A genetic signature of spina bifida risk from pathway-informed comprehensive gene-variant analysis. PLoS One. 2011 Nov 30.
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Lombardi LM, Ellahi A, Rine J. Direct regulation of nucleosome density by the conserved AAA-ATPase Yta7. Proc Natl Acad Sci U S A. 2011 Nov 9.
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Scannell DR, Zill OA, Rokas A, Payen C, Dunham MJ, Eisen MB, Rine J, Johnston M, Hittinger CT. The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus. G3. June 2011.
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Osborne EA, Hiraoka Y, Rine J. Symmetry, asymmetry, and kinetics of silencing establishment in Saccharomyces cerevisiae revealed by single-cell optical assays. Proc Natl Acad Sci U S A. 2011 Jan 25.
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2010
Zill OA, Scannell D, Teytelman L, Rine J. Co-evolution of transcriptional silencing proteins and the DNA elements specifying their assembly. PLoS Biol. 2010 Nov 30.
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Mayfield JA, Fontana MF, Rine J. Genetic control of immune cell types in fungal disease. Proc Natl Acad Sci U S A. 2010 Dec 21.
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Halley JE, Kaplan T, Wang AY, Kobor MS, Rine J. Roles for H2A.Z and Its Acetylation in GAL1 Transcription and Gene Induction, but Not GAL1-Transcriptional Memory. PLoS Biol. 2010 Jun 22.
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Marini NJ, Thomas PD, Rine J. The use of orthologous sequences to predict the impact of amino acid substitutions on protein function. PLoS Genet. 2010 May 27.
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Rusche LN, Rine J. Switching the mechanism of mating type switching: a domesticated transposase supplants a domesticated homing endonuclease. Genes Dev. 2010 Jan 1.
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Ozaydin B, Rine J. Expanded Roles of ORC in the Architecture and Function of Silenced Chromatin in Saccharomyces cerevisiae. Mol Cell Bio. 2010 Feb.
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2009
Wang AY, Schulze JM, Skordalakes E, Gin JW, Berger JM, Rine J, Kobor MS. Asf1-like structure of the conserved Yaf9 YEATS domain and role in H2A.Z deposition and acetylation. Proc Natl Acad Sci U S A. 2009 Dec 22.
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Teytelman L, Ozaydin B, Zill O, Lefrançois P, Snyder M, Rine J, Eisen MB. Impact of Chromatin Structures on DNA Processing for Genomic Analyses. PLoS ONE. 2009 Aug 20.
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Osborne EA, Dudoit S, Rine J. The establishment of silencing at single-cell resolution. Nature Genetics. 2009 Jun 21.
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Gallagher JE, Babiarz JE, Teytelman L, Wolfe KH, Rine J. Elaboration, diversification and regulation of the sir1 family of silencing proteins in Saccharomyces. Genetics. 2009 Apr.
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Teytelman L, Eisen MB, Rine J. Silent but not static: accelerated base-pair substitution in silenced chromatin of budding yeasts. PLoS Genet. 2008 Nov.
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Chao LY, Rine J, Marletta MA. Spectroscopic and kinetic studies of Nor1, a cytochrome P450 nitric oxide reductase from the fungal pathogen Histoplasma capsulatum. Arch Biochem Biophys. 2008 Sep 10.
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Zill O, Rine J. Interspecies variation reveals a conserved repressor of {alpha}-specific genes in Saccharomyces yeasts. Genes and Development. 2008 Jun 15.
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Chao LY, Marletta MA, Rine J. Sre1, an Iron-Modulated GATA DNA-Binding Protein of Iron-Uptake Genes in the Fungal Pathogen Histoplasma capsulatum. Biochemistry. 2008 Jun 13.
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Marini NJ, Gin J, Ziegle J, Keho KH, Ginzinger D, Gilbert DA, Rine J. The prevalence of folate-remedial MTHFR enzyme variants in humans. Proc Natl Acad Sci U S A. 2008 Jun 10.
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Hwang LH, Mayfield JA, Rine J, Sil A. Histoplasma requires SID1, a member of an iron-regulated siderophore gene cluster, for host colonization. PLoS Pathogens. 2008 Apr 11.
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Suter B, Pogoutse O, Guo X, Krogan N, Lewis P, Greenblatt JF, Rine J, Emili A. Association with the origin recognition complex suggests a novel role for histone acetyltransferase Hat1p/Hat2p. BMC Biol. 2007 Sep 19.
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Mayfield JA, Rine J. The genetic basis of variation in susceptibility to infection with Histoplasma capsulatum in the mouse. Genes Immun. 2007 Jul 12.
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Ashby MN, Rine J, Mongodin EF, Nelson KE, Dimster-Denk D. Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities. Appl Environ Microbiol. 2007 Jul;73(14):4532-42. Epub 2007 May 25.
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Jeong H, Herskowitz I, Kroetz DL, Rine J. Function-altering SNPs in the human multidrug transporter gene ABCB1 identified using a Saccharomyces-based assay. PLoS Genet. 2007 Mar 9;3(3):e39.
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Davies BS, Rine J. A role for sterol levels in oxygen sensing in Saccharomyces cerevisiae. Genetics. 2006 Sep;174(1):191-201. Epub 2006 Jun 18.
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Babiarz JE, Halley JE, Rine J. Telomeric heterochromatin boundaries require NuA4-dependent acetylation of histone variant H2A.Z in Saccharomyces cerevisiae. Genes Dev. 2006 Mar 15;20(6):700-10.
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Neff MW, Rine J. A fetching model organism. Cell. 2006 Jan 27;124(2):229-31. Review.
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Kirchmaier AL, Rine J. Cell cycle requirements in assembling silent chromatin in Saccharomyce cerevisiae. Mol Cell Biol. 2006 Feb;26(3):852-62.
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Roberts TM, Kobor MS, Bastin-Shanower SA, Ii M, Horte SA, Gin JW, Emili A,
Rine J, Brill SJ, Brown GW. Slx4 regulates DNA damage checkpoint-dependent phosphorylation of the BRCT domain protein Rtt107/Esc4. Mol Biol Cell. 2006 Jan;17(1):539-48. Epub 2005 Nov 2.
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Olaharski AJ, Rine J, Marshall BL, Babiarz J, Zhang L, Verdin E, Smith MT. The Flavoring Agent Dihydrocoumarin Reverses Epigenetic Silencing and Inhibits Sirtuin Deacetylases.
PLoS Genet. 2005 Dec 16;1(6):e77
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Rine J. Cell biology. Twists in the tale of the aging yeast.Science. 2005 Nov 18;310(5751):1124-5.
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Roberts TM, Kobor MS, Bastin-Shanower SA, Ii M, Horte SA, Gin JW, Emili A, Rine J, Brill SJ, Brown GW. Slx4 regulates DNA damage checkpoint-dependent phosphorylation of the BRCT
domain protein Rtt107/Esc4.Mol Biol Cell. 2006 Jan;17(1):539-48. Epub 2005 Nov 2.
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Davies BS, Wang HS, Rine J. Dual activators of the sterol biosynthetic pathway of Saccharomyces cerevisiae: similar activation/regulatory domains but different response mechanisms. Mol Cell Biol. 2005 Aug;25(16):7375-85.
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Lynch PJ, Fraser HB, Sevastopoulos E, Rine J, Rusche LN. Sum1p, the origin recognition complex, and the spreading of a promoter-specific repressor in Saccharomyces cerevisiae. Mol Cell Biol. 2005 Jul;25(14):5920-32.
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Pillus L, Rine J. SIR1 and the origin of epigenetic states in Saccharomyces cerevisiae.
Cold Spring Harb Symp Quant Biol. 2004;69:259-65. Review.
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Suter B, Tong A, Chang M, Yu L, Brown GW, Boone C, Rine J. The origin recognition complex links replication, sister chromatid cohesion and transcriptional silencing in Saccharomyces cerevisiae. Genetics. 2004 Jun;167(2):579-91.
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Beh CT, Rine J. A role for yeast oxysterol-binding protein homologs in endocytosis and in the maintenance of intracellular sterol-lipid distribution. J Cell Sci. 2004 Jun 15;117(Pt 14):2983-96. Epub 2004 Jun 1.
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Kobor MS, Venkatasubrahmanyam S, Meneghini MD, Gin JW, Jennings JL, Link AJ,
Madhani HD, Rine J. A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol. 2004 May;2(5):E131. Epub 2004 Mar 23.
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Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost
RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J,
Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Menard P,
Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J,
Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J,
Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey
H, Boone C. Global mapping of the yeast genetic interaction network. Science. 2004 Feb 6;303(5659):808-13.
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Hwang L, Hocking-Murray D, Bahrami AK, Andersson M, Rine J, Sil A. Identifying phase-specific genes in the fungal pathogen Histoplasma capsulatum using a genomic shotgun microarray. Mol Biol Cell. 2003 Jun;14(6):2314-26. Epub 2003 Mar 20.
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Rusche LN, Kirchmaier AL, Rine J. The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae.Annu Rev Biochem. 2003;72:481-516. Epub 2003 Mar 27. Review.
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Astrom SU, Cline TW, Rine J. The Drosophila melanogaster sir2+ gene is nonessential and has only minor effects on position-effect variegation. Genetics. 2003 Mar;163(3):931-7.
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Rusche LN, Kirchmaier AL, Rine J. Ordered nucleation and spreading of silenced chromatin in Saccharomyces cerevisiae. Mol Biol Cell. 2002 Jul;13(7):2207-22.
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Garber PM, Rine J. Overlapping roles of the spindle assembly and DNA damage checkpoints in the cell-cycle response to altered chromosomes in Saccharomyces cerevisiae. Genetics. 2002 Jun;161(2):521-34.
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Vik A, Rine J. Upc2p and Ecm22p, dual regulators of sterol biosynthesis in Saccharomyces cerevisiae. Mol Cell Biol. 2001 Oct;21(19):6395-405.
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Rusche LN, Rine J. Conversion of a gene-specific repressor to a regional silencer. Genes Dev. 2001 Apr 15;15(8):955-67.
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Beh CT, Cool L, Phillips J, Rine J. Overlapping functions of the yeast oxysterol-binding protein homologues. Genetics. 2001 Mar;157(3):1117-40. Erratum in: Genetics 2001 Jul;158(3):1387.
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Kirchmaier AL, Rine J. DNA replication-independent silencing in S. cerevisiae. Science. 2001 Jan 26;291(5504):646-50.
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Chang YW, Howard SC, Budovskaya YV, Rine J, Herman PK. The rye mutants identify a role for Ssn/Srb proteins of the RNA polymerase II holoenzyme during stationary phase entry in Saccharomyces cerevisiae. Genetics. 2001 Jan;157(1):17-26.
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Metallinos D, Rine J. Exclusion of EDNRB and KIT as the basis for white spotting in Border Collies. Genome Biol. 2000;1(2):RESEARCH0004. Epub 2000 Jul 28.
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Vik A, Rine J. Membrane biology: membrane-regulated transcription.
Curr Biol. 2000 Nov 30;10(23):R869-71.
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Astrom SU, Kegel A, Sjostrand JO, Rine J. Kluyveromyces lactis Sir2p regulates cation sensitivity and maintains a specialized chromatin structure at the cryptic alpha-locus. Genetics. 2000 Sep;156(1):81-91.
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Trueblood CE, Boyartchuk VL, Picologlou EA, Rozema D, Poulter CD, Rine J. The CaaX proteases, Afc1p and Rce1p, have overlapping but distinct substrate specificities. Mol Cell Biol. 2000 Jun;20(12):4381-92.
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Ehrenhofer-Murray AE, Kamakaka RT, Rine J. A role for the replication proteins PCNA, RF-C, polymerase epsilon and Cdc45 in transcriptional silencing in Saccharomyces cerevisiae. Genetics. 1999 Nov;153(3):1171-82.
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Xu EY, Kim S, Replogle K, Rine J, Rivier DH. Identification of SAS4 and SAS5, two genes that regulate silencing in Saccharomyces cerevisiae. Genetics. 1999 Sep;153(1):13-23.
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Rine J. On the mechanism of silencing in Escherichia coli. Proc Natl Acad Sci U S A. 1999 Jul 20;96(15):8309-11.
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Acland GM, Ray K, Mellersh CS, Langston AA, Rine J, Ostrander EA, Aguirre
GD. A novel retinal degeneration locus identified by linkage and comparative
mapping of canine early retinal degeneration. Genomics. 1999 Jul 15;59(2):134-42.
[abstract]
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Dimster-Denk D, Rine J, Phillips J, Scherer S, Cundiff P, DeBord K,
Gilliland D, Hickman S, Jarvis A, Tong L, Ashby M. Comprehensive evaluation of isoprenoid biosynthesis regulation in Saccharomyces cerevisiae utilizing the Genome Reporter Matrix. J Lipid Res. 1999 May;40(5):850-60.
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Donze D, Adams CR, Rine J, Kamakaka RT. The boundaries of the silenced HMR domain in Saccharomyces cerevisiae. Genes Dev. 1999 Mar 15;13(6):698-708.
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Astrom SU, Okamura SM, Rine J. Yeast cell-type regulation of DNA repair. Nature. 1999 Jan 28;397(6717):310. No abstract available.
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Neff MW, Broman KW, Mellersh CS, Ray K, Acland GM, Aguirre GD, Ziegle JS,
Ostrander EA, Rine J. A second-generation genetic linkage map of the domestic dog, Canis familiaris. Genetics. 1999 Feb;151(2):803-20.
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Rivier DH, Ekena JL, Rine J. HMR-I is an origin of replication and a silencer in Saccharomyces cerevisiae. Genetics. 1999 Feb;151(2):521-9.
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Gardner KA, Rine J, Fox CA. A region of the Sir1 protein dedicated to recognition of a silencer and required for interaction with the Orc1 protein in saccharomyces cerevisiae. Genetics. 1999 Jan;151(1):31-44.
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Gardner R, Cronin S, Leader B, Rine J, Hampton R. Sequence determinants for regulated degradation of yeast 3-hydroxy-3-methylglutaryl-CoA reductase, an integral endoplasmic reticulum membrane protein. Mol Biol Cell. 1998 Sep;9(9):2611-26. Erratum in: Mol Biol Cell 1999 Mar;10(3):precedi. Leder B [corrected to Leader B].
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Boyartchuk VL, Rine J. Roles of prenyl protein proteases in maturation of Saccharomyces cerevisiae a-factor. Genetics. 1998 Sep;150(1):95-101.
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Kamakaka RT, Rine J. Sir- and silencer-independent disruption of silencing in Saccharomyces by Sas10p. Genetics. 1998 Jun;149(2):903-14.
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Metallinos DL, Bowling AT, Rine J. A missense mutation in the endothelin-B receptor gene is associated with Lethal White Foal Syndrome: an equine version of Hirschsprung disease. Mamm Genome. 1998 Jun;9(6):426-31.
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Carver EA, Issel-Tarver L, Rine J, Olsen AS, Stubbs L. Location of mouse and human genes corresponding to conserved canine olfactory receptor gene subfamilies. Mamm Genome. 1998 May;9(5):349-54.
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Acland GM, Ray K, Mellersh CS, Gu W, Langston AA, Rine J, Ostrander EA,
Aguirre GD. Linkage analysis and comparative mapping of canine progressive rod-cone
degeneration (prcd) establishes potential locus homology with retinitis pigmentosa (RP17) in humans. Proc Natl Acad Sci U S A. 1998 Mar 17;95(6):3048-53.
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Astrom SU, Rine J. Theme and variation among silencing proteins in Saccharomyces cerevisiae and Kluyveromyces lactis. Genetics. 1998 Mar;148(3):1021-9.
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Dillin A, Rine J. Roles for ORC in M phase and S phase. Science. 1998 Mar 13;279(5357):1733-7.
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Dillin A, Rine J. Separable functions of ORC5 in replication initiation and silencing in Saccharomyces cerevisiae. Genetics. 1997 Nov;147(3):1053-62.
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Herman PK, Rine J. Yeast spore germination: a requirement for Ras protein activity during re-entry into the cell cycle. EMBO J. 1997 Oct 15;16(20):6171-81.
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Trueblood CE, Boyartchuk VL, Rine J. Substrate specificity determinants in the farnesyltransferase beta-subunit. Proc Natl Acad Sci U S A. 1997 Sep 30;94(20):10774-9.
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Whistler JL, Rine J. Ras2 and Ras1 protein phosphorylation in Saccharomyces cerevisiae. J Biol Chem. 1997 Jul 25;272(30):18790-800.
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Fox CA, Ehrenhofer-Murray AE, Loo S, Rine J. The origin recognition complex, SIR1, and the S phase requirement for silencing. Science. 1997 Jun 6;276(5318):1547-51.
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Yalovsky S, Trueblood CE, Callan KL, Narita JO, Jenkins SM, Rine J, Gruissem
W. Plant farnesyltransferase can restore yeast Ras signaling and mating. Mol Cell Biol. 1997 Apr;17(4):1986-94.
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Ehrenhofer-Murray AE, Rivier DH, Rine J. The role of Sas2, an acetyltransferase homologue of Saccharomyces cerevisiae, in silencing and ORC function. Genetics. 1997 Apr;145(4):923-34.
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Boyartchuk VL, Ashby MN, Rine J. Modulation of Ras and a-factor function by carboxyl-terminal proteolysis. Science. 1997 Mar 21;275(5307):1796-800.
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Moazed D, Kistler A, Axelrod A, Rine J, Johnson AD. Silent information regulator protein complexes in Saccharomyces cerevisiae: a SIR2/SIR4 complex and evidence for a regulatory domain in SIR4 that inhibits its interaction with SIR3. Proc Natl Acad Sci U S A. 1997 Mar 18;94(6):2186-91.
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Issel-Tarver L, Rine J. The evolution of mammalian olfactory receptor genes. Genetics. 1997 Jan;145(1):185-95.
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Hampton RY, Gardner RG, Rine J. Role of 26S proteasome and HRD genes in the degradation of 3-hydroxy-3-methylglutaryl-CoA reductase, an integral endoplasmic reticulum membrane protein. Mol Biol Cell. 1996 Dec;7(12):2029-44.
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Issel-Tarver L, Rine J. Organization and expression of canine olfactory receptor genes. Proc Natl Acad Sci U S A. 1996 Oct 1;93(20):10897-902.
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Dimster-Denk D, Rine J. Transcriptional regulation of a sterol-biosynthetic enzyme by sterol levels in Saccharomyces cerevisiae. Mol Cell Biol. 1996 Aug;16(8):3981-9.
[abstract]
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Fox CA, Rine J. Influences of the cell cycle on silencing. Curr Opin Cell Biol. 1996 Jun;8(3):354-7. Review.
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Hampton R, Dimster-Denk D, Rine J. The biology of HMG-CoA reductase: the pros of contra-regulation. Trends Biochem Sci. 1996 Apr;21(4):140-5. Review.
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Hampton RY, Koning A, Wright R, Rine J. In vivo examination of membrane protein localization and degradation with green fluorescent protein.Proc Natl Acad Sci U S A. 1996 Jan 23;93(2):828-33.
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1995 and earlier, go here.