Related Documents and Articles

• Nature magazine featured work by the Genome Sequencing Center in a section called The Chimpanzee Genome. Also, some of the people from Elaine Mardis’ and Rick Wilson’s labs were authors on a companion paper in the same issue, with David Page’s lab at MIT on the chimp Y chromosome comparison to human Y. Three articles from the issue (The chimpanzee genome, Timeline: A brief history of chimp, and News & Views: The chimpanzee and us) may be found at: http://www.nature.com/nature/journal/v437/n7055/index.html#The-Chimpanzee-Genome
• Evidence for Domesticated and Wild Populations of Saccharomyces cerevisiae. Justin C. Fay, Joseph A. Benavides: http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pgen.0010005
• C. elegans Noncoding RNA Genes. S. L. Stricklin, S. Griffiths-Jones, S. R. Eddy.WormBook, in press, 2005. http://selab.wustl.edu/publications/Stricklin05/Stricklin05-preprint.pdf
  (Please see additional Eddy Lab publications at http://selab.wustl.edu/publications.)
• Jason Gertz, Linda Riles, Peter Turnbaugh, Su-Wen Ho and Barak A. Cohen. Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics. http://www.genome.org/cgi/content/full/15/8/1145
• Liu, J., Stormo, G.D. (2005) Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein. BMC Bioinformatics 6:176 http://www.biomedcentral.com/1471-2105/6/176
• Agarwal, R. and Stormo, G.D. (2005) Differences in editing of a Drosophila gene correlate with a change in distant splice site selection. RNA 11:563-6.
• Ley, R. E., Backhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., and Gordon, J. I. Obesity alters gut microbial ecology, Proc. Natl. Acad. Sci. USA, 102: 11070-11075 (2005). http://www.pnas.org/cgi/content/full/102/31/11070
• Ippolito, J. E., Xu, J., Jain, S., Moulder, K.L., Mennerick, S., Crowley, J. R., Townsend, R. R., and Gordon, J. I. An integrated functional genomics and metabolomics approach for defining poor prognosis in human neuroendocrine cancers, Proc. Natl. Acad. Sci. USA 102: 9901-9906 (2005). http://www.pnas.org/cgi/content/full/102/28/9901
• Zhang, X., Stappenbeck, T.S., White, A. C., Lavine, K. J., Gordon, J. I., and Ornitz, D. M Reciprocal epithelial-mesenchymal FGF signaling is required for cecal development Development 133: 173-180 (2006).
• Oh, J., Backhed-Kling, H., Giannakis, M., Engstrand L. G., and Gordon, J.I. Gastric epithelial stem cells and Helicobacter pylori: dangerous liaisons in the setting of chronic atrophic gastritis. Curr. Opin. Micro Biol. 9: 21-27 (2006).
• Ley, R., Peterson, D. A., and Gordon, J.I Ecological and evolutionary forces that shape microbial diversity and genome content in the human intestine. Cell 124: 837-848 (2006).
• Giannakis, M., Stappenbeck, T., Mills, J.C., Leip, D. G., Lovett, M., Clifton, S.W. Ippolito, J. E., Glasscock, J. I., Arumugam, M., Brent, M. R., and Gordon, J. I. Molecular properties of adult mouse gastric and intestinal epithelial progenitors in their niches, J. Biol. Chem. 281: 11292-11300 (2006).
• Chen, S. L., Hung C-S,, Xu, J., Reigstad, C. S., Magrini, V., Sabo, A., Blasiar, D., Bieri, T., Meyer, R. R., Ozersky, P., Armstrong, J.R., Fulton, R. S., Latreille, J. P., Spieth, J., Hooton, T. M., Mardis, E. R., Hultgren, S. J., and Gordon, J. I., Identification of genes subject to positive selection in uropathogenic strains of E. Coli: a comparative genomics approach. Proc. Natl. Acad. Sci. USA 103: 5977-5982 (2006).
• Gill, S.R., Pop, M., DeBoy, R. T., Eckburg, P.B., Turnbaugh, P. Samuel, B.S., Gordon, J.I., Relman, D. A., Fraser, C.M., and Nelson, K. E. Metagenomic analysis of the human gutmicrobiome. Science. 2006 Jun 2;312(5778):1355-9 http://www.sciencemag.org/cgi/content/full/312/5778/1355
• Sonnenburg, E.D., Sonnenburg, J.L., Manchester, J.K., Hansen, E.E., Chiang, H.C., and Gordon, J.I. A hybrid two component system protein of a prominent human gut symbiont couples glycan sensing in vivo to carbohydrate metabolism. In press.
• Chang, L.-W., Nagarajan, R., Magee, J.A., Milbrandt, J. and Stormo, G.D. (2006) Predicting Transcriptional Regulatory Mechanisms by Systematic Promoter Analysis. Genome Res 16:405-13.
• MacIsaac, K.D., Wang, T., Gordon, D.B., Gifford, D.K., Stormo, G.D. and Fraenkel, E. (2006) An Improved Genome-Wide Map of Regulatory Sites for Saccharomyces cerevisiae. BMC BIoinformatics 7:113.
• Magee, J.A., Chang, L., Stormo, G.D. and Milbrandt, J. (2006) Direct, Androgen Receptor Mediated Regulation of the FKBP5 Gene via a Distal Enhancer Element. Endocrinology 147(1):590-8.
• Ong C, Cheng H, Chang LW, Ohtsuka T, Kageyama R, Stormo GD, Kopan R. (2006) Collaboration between discrete protein domains and binding site architecture on the promoter determine target selectivity of vertebrate notch proteins. J Biol Chem. 281:5106-19.
• Agrawal, R, and Stormo, G.D. (2006) Using mRNAs Lengths to Accurately Predict the Alternatively Spliced Gene Products in Caenorhabditis elegans. Bioinformatics, in press.
• Kim J-H, Brachet V, Moriya H, and JOHNSTON M: Integration of transcriptional and post-translational regulation in a glucose signal transduction pathway in/ Saccharomyces cerevisiae. / Eukaryotic Cell 2006; 5:167-73 http://www.pubmedcentral.gov/articlerender.fcgi?artid=1360249
• Cliften PF, Fulton RS, Wilson RK, and JOHNSTON M: After the duplication: gene loss and adaptation in/ Saccharomyces/ genomes. Genetics 2006; 172:863-872. http://www.genetics.org/cgi/reprint/172/2/863