Publications

2008

Lee, T., G. Yao, J. Nevins, and L. You, "Sensing and integration of Erk and PI3K signals by Myc.", PLoS Comput Biol, vol. 4, issue 2, pp. e1000013, 2008 Feb 29. PMCID: PMC2265471  PMID: 18463697
Casey, F. P., J. J. Waterfall, R. N. Gutenkunst, C. R. Myers, and J. P. Sethna, "Variational method for estimating the rate of convergence of Markov-chain Monte Carlo algorithms.", Phys Rev E Stat Nonlin Soft Matter Phys, vol. 78, issue 4 Pt 2, pp. 046704, 2008 Oct. PMID: 18999558
Babic, A. C., E. J. Little, V. M. Manohar, J. Bitinaite, and N. C. Horton, "DNA distortion and specificity in a sequence-specific endonuclease.", J Mol Biol, vol. 383, issue 1, pp. 186-204, 2008 Oct 31. PMCID: PMC2605692  PMID: 18762194
Bolger, T. A., A. W. Folkmann, E. J. Tran, and S. R. Wente, "The mRNA export factor Gle1 and inositol hexakisphosphate regulate distinct stages of translation.", Cell, vol. 134, issue 4, pp. 624-33, 2008 Aug 22. PMCID: PMC2601711  PMID: 18724935
Steinkraus, K. A., E. D. Smith, C. Davis, D. Carr, W. R. Pendergrass, G. L. Sutphin, B. K. Kennedy, and M. Kaeberlein, "Dietary restriction suppresses proteotoxicity and enhances longevity by an hsf-1-dependent mechanism in Caenorhabditis elegans.", Aging Cell, vol. 7, issue 3, pp. 394-404, 2008 Jun. PMCID: PMC2709959  PMID: 18331616

2007

Casey, F. P., D. Baird, Q. Feng, R. N. Gutenkunst, J. J. Waterfall, C. R. Myers, K. S. Brown, R. A. Cerione, and J. P. Sethna, "Optimal experimental design in an epidermal growth factor receptor signalling and down-regulation model.", IET Syst Biol, vol. 1, issue 3, pp. 190-202, 2007 May. PMID: 17591178
Buchan, J.R., and I. Stansfield, "Halting a cellular production line: responses to ribosomal pausing during translation.", Biol Cell, vol. 99, issue 9, pp. 475-87, 2007 Sep. PMID: 17696878
Pochampalli, M. R., B. G. Bitler, and J. A. Schroeder, "Transforming growth factor alpha dependent cancer progression is modulated by Muc1.", Cancer Res, vol. 67, issue 14, pp. 6591-8, 2007 Jul 15. PMID: 17638868
Tran, E. J., T. A. Bolger, and S. R. Wente, "SnapShot: nuclear transport.", Cell, vol. 131, issue 2, pp. 420, 2007 Oct 19. PMID: 17956740
Gutenkunst, R., N. Newlands, M. Lutcavage, and L. Edelstein-Keshet, "Inferring resource distributions from Atlantic bluefin tuna movements: an analysis based on net displacement and length of track.", J Theor Biol, vol. 245, issue 2, pp. 243-57, 2007 Mar 21. PMID: 17140603
Gutenkunst, R. N., F. P. Casey, J. J. Waterfall, C. R. Myers, and J. P. Sethna, "Extracting falsifiable predictions from sloppy models.", Ann N Y Acad Sci, vol. 1115, pp. 203-11, 2007 Dec. PMID: 17925353
Pochampalli, M. R., R. M. el Bejjani, and J. A. Schroeder, "MUC1 is a novel regulator of ErbB1 receptor trafficking.", Oncogene, vol. 26, issue 12, pp. 1693-701, 2007 Mar 15. PMID: 16983337
Bolger, T. A., X. Zhao, T. J. Cohen, C-C. Tsai, and T-P. Yao, "The neurodegenerative disease protein ataxin-1 antagonizes the neuronal survival function of myocyte enhancer factor-2.", J Biol Chem, vol. 282, issue 40, pp. 29186-92, 2007 Oct 05. PMID: 17646162
Gutenkunst, R. N., J. J. Waterfall, F. P. Casey, K. S. Brown, C. R. Myers, and J. P. Sethna, "Universally sloppy parameter sensitivities in systems biology models.", PLoS Comput Biol, vol. 3, issue 10, pp. 1871-78, 2007 Oct. PMCID: PMC2000971  PMID: 17922568
Buchan, J.R., and R. Parker, "Molecular biology. The two faces of miRNA.", Science, vol. 318, issue 5858, pp. 1877-8, 2007 Dec 21. PMID: 18096794

2006

Bild, A. H., G. Yao, J. T. Chang, Q. Wang, A. Potti, D. Chasse, M-B. Joshi, D. Harpole, J. M. Lancaster, A. Berchuck, et al., "Oncogenic pathway signatures in human cancers as a guide to targeted therapies.", Nature, vol. 439, issue 7074, pp. 353-7, 2006 Jan 19. PMID: 16273092
Joshi, H. K., C. Etzkorn, L. Chatwell, J. Bitinaite, and N. C. Horton, "Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism.", J Biol Chem, vol. 281, issue 33, pp. 23852-69, 2006 Aug 18. PMID: 16675462
Buchan, J.R., L. S. Aucott, and I. Stansfield, "tRNA properties help shape codon pair preferences in open reading frames.", Nucleic Acids Res, vol. 34, issue 3, pp. 1015-27, 2006. PMCID: PMC1363775  PMID: 16473853
Waterfall, J. J., F. P. Casey, R. N. Gutenkunst, K. S. Brown, C. R. Myers, P. W. Brouwer, V. Elser, and J. P. Sethna, "Sloppy-model universality class and the Vandermonde matrix.", Phys Rev Lett, vol. 97, issue 15, pp. 150601, 2006 Oct 13. PMID: 17155311
Segal, D. J., J. W. Crotty, M. S. Bhakta, C. F. Barbas, and N. C. Horton, "Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA.", J Mol Biol, vol. 363, issue 2, pp. 405-21, 2006 Oct 20. PMID: 16963084

2005

Zhao, X., T. Sternsdorf, T. A. Bolger, R. M. Evans, and T-P. Yao, "Regulation of MEF2 by histone deacetylase 4- and SIRT1 deacetylase-mediated lysine modifications.", Mol Cell Biol, vol. 25, issue 19, pp. 8456-64, 2005 Oct. PMCID: PMC1265742  PMID: 16166628
Delong, M., G. Yao, Q. Wang, A. Dobra, E. P. Black, J. T. Chang, A. Bild, M. West, J. R. Nevins, and H. Dressman, "DIG--a system for gene annotation and functional discovery.", Bioinformatics, vol. 21, issue 13, pp. 2957-9, 2005 Jul 01. PMID: 15870167
Crotty, J. W., C. Etzkorn, C. F. Barbas, D. J. Segal, and N. C. Horton, "Crystallization and preliminary X-ray crystallographic analysis of Aart, a designed six-finger zinc-finger peptide, bound to DNA.", Acta Crystallogr Sect F Struct Biol Cryst Commun, vol. 61, issue Pt 6, pp. 573-6, 2005 Jun 01. PMCID: PMC1952332  PMID: 16511099
Little, E. J., and N. C. Horton, "DNA-induced conformational changes in type II restriction endonucleases: the structure of unliganded HincII.", J Mol Biol, vol. 351, issue 1, pp. 76-88, 2005 Aug 05. PMID: 15993893
Lopez, J. I., T. D. Camenisch, M. V. Stevens, B. J. Sands, J. McDonald, and J. A. Schroeder, "CD44 attenuates metastatic invasion during breast cancer progression.", Cancer Res, vol. 65, issue 15, pp. 6755-63, 2005 Aug 01. PMID: 16061657

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