Lafleur, B., Lee, W., Billheimer, D., Lockhart, C., Liu, J., & Merchant, N. (2011). Statistical methods for assays with limits of detection: Serum bile acid as a differentiator between patients with normal colons, adenomas, and colore. J Carcinog, 10, 12.
Sanders, M. E., Dias, E. C., Xu, B. J., Mobley, J. A., Billheimer, D., Roder, H., Grigorieva, J., Dowsett, M., Arteaga, C. L., & Caprioli, R. M. (2008). Differentiating Proteomic Biomarkers in Breast Cancer by Laser Capture Microdissection and MALDI MS. Journal of Proteome Research, 7(4), 1500-1507.
PMID: 18386930;PMCID: PMC2738605;Abstract:
We assessed proteomic patterns in breast cancer using MALDI MS and laser capture microdissected cells. Protein and peptide expression in invasive mammary carcinoma versus normal mammary epithelium and estrogen-receptor positive versus estrogen-receptor negative tumors were compared. Biomarker candidates were identified by statistical analysis and classifiers were developed and validated in blinded test sets. Several of the mlz features used in the classifiers were identified by LC-MS/MS and two were confirmed by immunohistochemistry. © 2008 American Chemical Society.
Gomez-Rubio, P., Gomez-Rubio, P., Klimentidis, Y., Klimentidis, Y., Cantu-Soto, E., Cantu-Soto, E., Meza-Montenegro, M., Meza-Montenegro, M., Billheimer, D., Billheimer, D., Lu, Z., Lu, Z., Chen, Z., Chen, Z., Klimecki, W., & Klimecki, W. (2012). Indigenous American Ancestry is Associated with Arsenic Methylation Efficiency in an Admixed Population of Northwest Mexico. J Toxicol Environ Health A, 75(1), 36-49.
BIO5 Collaborators
Dean Billheimer, Walter Klimecki
Jacquemin, J., Ammiraju, J. S., Haberer, G., Billheimer, D. D., Yu, Y., Liu, L. C., Rivera, L. F., Mayer, K., Chen, M., & Wing, R. A. (2013). Fifteen Million Years of Evolution in the Oryza Genus Shows Extensive Gene Family Expansion. Molecular plant.
In analyzing gene families in the whole-genome sequences available for O. sativa (AA), O. glaberrima (AA), and O. brachyantha (FF), we observed large size expansions in the AA genomes compared to FF genomes for the super-families F-box and NB-ARC, and five additional families: the Aspartic proteases, BTB/POZ proteins (BTB), Glutaredoxins, Trypsin α-amylase inhibitor proteins, and Zf-Dof proteins. Their evolutionary dynamic was investigated to understand how and why such important size variations are observed between these closely related species. We show that expansions resulted from both amplification, largely by tandem duplications, and contraction by gene losses. For the F-box and NB-ARC gene families, the genes conserved in all species were under strong purifying selection while expanded orthologous genes were under more relaxed purifying selection. In F-box, NB-ARC, and BTB, the expanded groups were enriched in genes with little evidence of expression, in comparison with conserved groups. We also detected 87 loci under positive selection in the expanded groups. These results show that most of the duplicated copies in the expanded groups evolve neutrally after duplication because of functional redundancy but a fraction of these genes were preserved following neofunctionalization. Hence, the lineage-specific expansions observed between Oryza species were partly driven by directional selection.
Hanusch, K., Janssen, C. H., Billheimer, D., Jenkins, I., Spurgeon, E., Lowry, C. A., & Raison, C. L. (2013). Whole-body hyperthermia for the treatment of major depression: Associations with thermoregulatory cooling. American Journal of Psychiatry, 170(7), 802-804.
