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Roger Bumgarner
Associate Professor of Microbiology

Email: rogerb@u.washington.edu
Phone: (206) 732-6137
Office Location: 262B Rosen
Campus Box: 358070




A fundamental issue facing modern biology is the development of methods and tools to convert genomics and function genomics data into mechanistic understanding. Genome sequences and computational methods have provided us with tools to identify and annotate genes and other functional sequences with varying degrees of accuracy. Annotated sequence information in turn enables tools such as microarrays, 2-D gels, protein mass spectrometry and yeast 2-hybrids to measure RNA and protein levels and physical interactions on genome-wide or near genome-wide scales. Genome information has also enable high-throughput genetic mapping technologies that allow one to rapidly trace a given phenotype or trait to specific genetic regions. However, in most cases there is still a major gap between the collection of large-scale genomic/genetic data and the inference of biological mechanism for a particular state, disease, or clinical outcome. This gap between large-scale data collection and biological understanding has become extremely apparent in the last several years during which an increasing number of microarray-based works have been published which made little contribution to new biological understanding. The focus of my research efforts is on the creation of tools to connect expression data to biological meaning and the application of these tools to understanding host-virus interactions and the host innate immune response.

Selected Publications:

Bumgarner. For a More Complete List of Pubs Querry Pubmed as this List of Pubs Is Incomplete. , 13 May 2005

Wei C,Li J,Bumgarner RE. Sample Size for Detecting Differentially Expressed Genes in Microarray Experiments.. Bmc Genomics [electronic Resource]. 5(1): 87, Nov 2004

Medvedovic M,Yeung KY,Bumgarner RE. Bayesian Mixture Model Based Clustering of Replicated Microarray Data.. Bioinformatics (oxford, England). 20(8): 1222-32, May 2004

Yeung KY,Medvedovic M,Bumgarner RE. From Co-expression to Co-regulation: How Many Microarray Experiments Do We Need?. Genome Biology. 5(7): R48, 2004

Xia M, Bumgarner RE, Lampe MF, Stamm WE. Chlamydia trachomatis infection alters host cell transcription in diverse cellular pathways. Journal of Infectious Diseases. 187(3): 424-34, February 2003

Smith MW, Yue ZN, Geiss GK, Sadovnikova NY, Carter VS, Boix L, Lazaro CA, Rosenberg GB, Bumgarner RE, Fausto N, Bruix J, Katze MG. Identification of novel tumor markers in hepatitis C virus-associated hepatocellular carcinoma. Cancer Research. 63(4): 859-64, February 2003

Van't Wout AB, Lehrman GK, Mikheeva SA, O'Keeffe GC, Katze MG, Bumgarner RE, Geiss GK, Mullins JI. Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4(+)-T-cell lines. Journal of Virology. 77(2): 1392-402, January 2003

Yeung KY,Bumgarner RE. Multiclass Classification of Microarray Data With Repeated Measurements: Application to Cancer.. Genome Biology. 4(12): R83, 2003





Department of Microbiology · University of Washington · Box 357735 · Seattle WA 98195-7735

phone: (206) 543-5824 · fax: (206) 543-8297 · micro@u.washington.edu