Staff Scientist

425G Henry Mall Suite 4400V
Madison, Wisconsin 53706

Phone: 608-890-0172
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Curriculum Vitae

Degrees and Training

• B.S., Biochemistry; 1996, University of Wisconsin-Madison
  
• M.S., Food Microbiology and Safety; 2000, University of Wisconsin-Madison
• Ph.D., Cellular and Molecular Biology ; 2006, University of Wisconsin-Madison
  

Description

I joined the Enteropathogen Resource Integration Center ERIC in the fall of 2006. Having previously elucidated the sulfur pathway of an acidophilic archaeon and various acid tolerance mechanisms in E. coli O157:H7, I was focused on curation, analysis, and conservation of biochemical pathways and subsystems of the organisms  whose genomes comprise the ERIC database.  Additionally, I conduct various aspects of genome curation including: feature identification and creation, establishment of feature coordinates, analyzing and approving orthology and other sequence similarity-related relationships between features, and functional annotation of features using literature as well as other sources.  I was also the facilitator for educational outreach on the ERIC project.  I worked in collaboration with the division of education of the American Society of Microbiology and the Scientific Education Alliance of the Howard Hughes Medical Institute to extend the use of the ERIC database to undergraduate educators as a tool for inquiry-based exercises to integrate bioinformatics throughout the undergraduate biology curriculum.

Since August 2008, I was awarded a postdoctoral fellowship through the BACTER (Bringing Advanced Computational Techniques to Energy Research) program here at UW-Madison.  I am working in the area of systems biology in collaboration with Prof. Jennie Reed (Chemical and Biological Engineering, UW-Madison).  Currently my work involves constructing and validating computational models that represent the reconstructed metabolic network of E. coli K12.  Future plans of my project focus on the extension of genome annotation and comparative genomics to generate computational models of additional Enterobacteria to aid in the bioengineering of an ideal ethanologen.   

Publications

• Baumler, D.J., Hung, K.F., Jeong, K.C., and C.W. Kaspar. 2008. Molybdate treatment and sulfate starvation decrease levels of ATP and DNA in "Ferroplasma acidarmanus". Archaea Dec;2(3):205-209.
• Jeong, K.C., Hung, K.F., Baumler, D.J., Byrd, J.J., and C.W. Kaspar. 2008. Acid stress damage of DNA is prevented by Dps binding in Escherichia coli O157:H7. BMC Microbiology "Highly accessed" Oct 15:8;181.
• Baumler, D.J., Hung, K.F., Cabot, E.C., Glasner, J.D., Greene, J.M., and N.T. Perna. 2008. Annotation of the bacteriophage 933W genome: an in-class interactive web-based exercise. Curriculum Resources Collection; http://www.microbelibrary.org/
• Glasner, J.D., G. Plunkett III, B.D. Anderson,  D.J. Baumler, B.S. Biehl, V. Burland,  E.C. Cabot, A.E. Darling, B. Mau, E.C. Neeno-Eckwall, D. Pot, Y. Qiu, A.I. Rissman, S. Worzella, S. Zaremba, J. Fedorko, P. Liss, M. Rusch, M. Shaker, L. Shaull, P. Shetty, J. Whitmore, F.R. Blattner, J.M. Greene, and N.T. Perna. 2007. Enteropathogen resource integration center (ERIC)-bioinformatics support for research on biodefense-relevant enterobacteria. Nucleic Acids Research 36:D519-523.  
  
• Baumler, D.J. and C.W. Kaspar. 2007. Morphology of the acidophilic archaeon "Ferroplasma acidarmanus" strain fer1. Visual Collection; http://www.microbelibrary.org/ 
• Baumler, D.J., K.F. Hung, K.C. Jeong, C.W. Kaspar. 2007. Production of methanethiol and volatile sulfur compounds by the archaeon "Ferroplasma acidarmanus". Extremophiles 11(6):841-851. 
• Erol, I., K.C Jeong, D.J. Baumler, B. Vykhodets, S.H. Choi, and C.W. Kaspar.  2006.  H-NS controls metabolism and stress tolerance in Escherichia coli O157:H7 that influence mouse passage. BMC Microbiology 6(1):72.
• Baumler, D.J., K.F. Hung, J.L. Bose, B.M. Vykhodets, C.-M. Cheng, K.C. Jeong, and C.W. Kaspar.  2006. Enhancement of acid tolerance in Zymomonas mobilis by a proton-buffering peptide. Applied Biochemistry and Biotechnology 134(1):15-26.
• Jeong, K.-C., D.J. Baumler, and C.W. Kaspar. 2006. dps expression in Escherichia coli O157:H7 requires an extended -10 region and is affected by the cAMP receptor protein.  Biochim Biophys Acta. 1759(1-2): 51-59.
  
• Baumler, D.J., K.C. Jeong, B.G. Fox, J.F. Banfield, and C.W. Kaspar. 2005. Sulfate requirement for heterotrophic growth of the acidophilic archaeon “Ferroplasma acidarmanus” strain fer1.  Research in Microbiology 156(4): 492-498.
• Macalady, J.L., M.M. Vestling, D.J. Baumler, N. Boekelheide, C.W. Kaspar, and J.F. Banfield.  2004. Tetraether-linked membrane monolayers in Ferroplasma spp.: a key to survival in acid. Extremophiles 8:411-419.
• Choi, S-H., D.J. Baumler, and C. W. Kaspar.  2000.  Contribution of dps to Acid Stress Tolerance and oxidative stress tolerance in Escherichia coli O157:H7.  Applied and Environmental Microbiology. 66: 3911-3916.