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Dilworth, D.J., Saleem, R.A. Rogers, R.S., Mirzaei, H., Boyle, J., Aitchison, J.D. QTIPS: A novel method of unsupervised determination of isotopic amino acid distribution in SILAC experiments. Journal of the American Society for Mass Spectrometry, (2010) Article in Press, Accepted Manuscript Saleem RA, Rogers RS, Ratushny AV, Dilworth DJ, Shannon PT, Shteynberg D, Wan Y, Moritz RL, Nesvizhskii AI, Rachubinski RA, Aitchison JD. (2010) Integrated phosphoproteomic analysis of a signaling network governing nutrient response and peroxisome induction, Mol Cell Proteomics. 2010 Apr 15. [Epub ahead of print]. Sekedat MD, Fenyö D, Rogers RS, Tackett AJ, Aitchison JD, Chait BT. (2010) GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome, Mol Syst Biol. 2010;6:353. Epub 2010 Mar 9. PMCID: PMC2858444 Jung, S., Marelli, M., Rachubinski, R. A., Goodlett, D. R. and Aitchison, J. D. (2010) Dynamic changes in the subcellular distribution of Gpd1p in response to cell stress, J Biol Chem, 285: 6739-6749. PMCID: PMC2825468 Shmulevich, I. and Aitchison, J. D. (2009) Deterministic and stochastic models of genetic regulatory networks, Methods Enzymol, 467: 335-356 Wan, Y., Chiang, J. H., Lin, C. H., Arens, C. E., Saleem, R. A., Smith, J. J. and Aitchison, J. D. (2009) Histone chaperone Chz1p regulates H2B ubiquitination and subtelomeric anti-silencing, Nucleic Acids Res, 2010 Mar 1;38(5):1431-40. Epub 2009 Dec 14.. PMCID: PMC2836552 Smith, J. J. and Aitchison, J. D. (2009) Regulation of peroxisome dynamics, Curr Opin Cell Biol. Feb;21(1):119-26. Epub 2009 Jan 31. Wan, Y., Saleem, R. A., Ratushny, A. V., Roda, O., Smith, J. J., Lin, C. H., Chiang, J. H. and Aitchison, J. D. (2009) Role of the histone variant H2A.Z/Htz1p in TBP recruitment, chromatin dynamics, and regulated expression of oleate-responsive genes, Mol Cell Biol, 29: 2346-2358, PMCID: PMC2668375 Fagarasanu, A., Mast, F. D., Knoblach, B., Jin, Y., Brunner, M. J., Logan, M. R., Glover, J. N., Eitzen, G. A., Aitchison, J. D., Weisman, L. S. and Rachubinski, R. A. (2009) Myosin-driven peroxisome partitioning in S. cerevisiae, J Cell Biol, 186: 541-554. PMC2733749 Ptak, C., Anderson, A. M., Scott, R. J., Van de Vosse, D., Rogers, R. S., Sydorskyy, Y., Aitchison, J. D. and Wozniak, R. W. (2009) A role for the karyopherin Kap123p in microtubule stability, Traffic, 10: 1619-1634 Saleem RA, Aitchison JD. (2009) Quantitative Phosphoproteomics in Fatty Acid Stimulated Saccharomyces cerevisiae. J Vis Exp. 2009 Oct 12;(32). pii: 1474. doi: 10.3791/1474. Gradolatto, A., Rogers, R. S., Lavender, H., Taverna, S. D., Allis, C. D., Aitchison, J. D. and Tackett, A. J. (2008) Saccharomyces cerevisiae Yta7 regulates histone gene expression, Genetics, 179: 291-304. PMCID: PMC2390607 Marelli, M., Nesvizhskii, A. I. and Aitchison, J. D. (2008) Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions : an example in peroxisomes, Methods Mol Biol, 432: 357-371 Ratushny, A. V., Ramsey, S. A., Roda, O., Wan, Y., Smith, J. J. and Aitchison, J. D. (2008) Control of transcriptional variability by overlapping feed-forward regulatory motifs, Biophys J, 95: 3715-3723 Saleem, R. A., Knoblach, B., Mast, F. D., Smith, J. J., Boyle, J., Dobson, C. M., Long-O'Donnell, R., Rachubinski, R. A. and Aitchison, J. D. (2008) Genome-wide analysis of signaling networks regulating fatty acid-induced gene expression and organelle biogenesis, J Cell Biol, 181: 281-292