I received my Ph.D. under the mentorship of Prof. Dr. Gerhard Gottschalk in 2005 at the Georg-August University in Göttingen, Germany, where I got introduced to microbial genomics and applied bioinformatics. I continued to work in this field as a post-doc at The Institute for Genomic Research (TIGR) in Rockville, Maryland, in the group of Dr. Jacques Ravel. In 2007 I moved to the newly founded Institute for Genome Sciences at the University of Maryland where I became Assistant Professor in the Department of Microbiology & Immunology in 2010.
My research evolves around the characterization of host-microbe interactions using genomic and bioinformatic approaches. This work includes single-genome projects on human commensal and pathogenic organisms, e.g. Salmonella enterica and Helicobacter pylori, as well as metagenomic projects on microbial communities from the gastrointestinal tract. I am especially interested in studying the dynamics of host-microbe interactions in the context of altered immune responses or microbiota manipulations, for example through fecal transplantation.
The CloVR project aims to provide bioinformatics support for researchers new to the genomics field by building automated sequence analysis pipelines. Using pre-installed software in combination with a framework for optional access to online cloud computing services, CloVR supports even large-scale genome projects without requiring extensive local bioinformatics infrastructures or experience. Taking advantage of the CloVR framework, we are currently developing automated bioinformatics pipelines for whole-genome sequencing-based diagnostic applications in clinical microbiology.
von Rosenvinge E.C., White J.R., Cain C., Blanchard T., and Fricke W.F. (2013) Immune status, antibiotic medication and pH are associated with changes in the stomach fluid microbiota. ISME (accepted for publication)
White J.R., Cain C., White O., Angiuoli S.F., and Fricke W.F. (2013) CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota. Microbiome 1:6
Sellitto M., Bai. G, Serena G., Fricke W.F., Sturgeon C., Gajer P., White J.R., Koenig S.S., Sakamoto J., Boothe D., Gicquelais R., Kryszak D., Puppa E., Catassi C., Ravel J., and Fasano A. (2012). Proof of concept of microbiome-metabolome analysis and delayed gluten exposure on celiac disease autoimmunity in genetically at-risk infants. PLoS One. 2012;7(3):e33387
Angiuoli S.V., Matalka M., Gussman A., Galens K., Vangala M., Riley D., Arze C., White J.R., White O., and Fricke W.F. (2011). CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics, 12(1):356.
Angiuoli S.V., White, J.R., Matalka M., White, O. and Fricke W.F. (2011). Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing. PLoS One, 6(10):e26624
Donia M.S., Fricke W.F., Partensky F., Cox J., Elshahawi S.I., White J.R., Phillippy A.M., Schatz M.C., Piel J., Haygood M.G., Ravel J., and Schmidt E.W. (2011). Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis. Proc Natl Acad Sci U S A. 108(51):E1423-32.
Fricke W.F., Mammel M.K., McDermott P.F., Tartera C., White D.G., LeClerc J.E, Ravel J., and Cebula T.A. (2011). Comparative genomics of 17 non-typhoidal Salmonella enterica isolates: CRISPR-mediated adaptive sublineage evolution via gene acquisition and loss? J Bacteriol. 193(14):3556-68
W.F. Fricke, D. Rasko, and J. Ravel (2009). The role of genomics in the identification, prediction, and prevention of biological threats. PLoS Biol 7(10): e1000217
W.F. Fricke, P.F. McDermott, M.K. Mammel, S. Zhao, T.J. Johnson, D.A. Rasko, P.J. Fedorka-Cray, A. Pedroso, J.M. Whichard, J.E. LeClerc, D.G. White, T.A. Cebula, and J. Ravel (2009). Antimicrobial resistance-encoding APEC plasmids in Salmonella enterica serovar Kentucky from poultry. Appl Environ Microbiol 75(18):5963-71.
W.F. Fricke, T. Welch, P.F. McDermott, M.K. Mammel, D.A. Rasko, D.G. White, and J. Ravel (2009). The evolution of IncA/C resistance plasmids: Comparative analysis of recent and historic isolates. Journal of Bacteriology 191(15):4750-57.
W.F. Fricke, B. Kusian and B. Bowien (2008). The genome organization of Ralstonia eutropha strain H16 and related species of the Burkholderiaceae. Journal of Molecular Microbiology and Biotechnology, 16(1):124-35.
W.F. Fricke, M.S. Wright, A.H. Lindell, D.M. Harkins, C. Baker-Austin, J. Ravel and R. Stepanauskas (2008). Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5. Journal of Bacteriology 190(20):6779-94.
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