Staff Scientist

425G Henry Mall Suite 4400V
Madison, Wisconsin 53706

Phone: (608) 320-4171
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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 initiated 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 and comparative genomic software to undergraduate educators as tools for inquiry-based exercises to integrate bioinformatics throughout the undergraduate biology curriculum.

From August 2008- Sept 2010, I was a postdoctoral fellow through the BACTER (Bringing Advanced Computational Techniques to Energy Research) program here at UW-Madison, working in the area of systems biology in collaboration with Prof. Jennie Reed (Chemical and Biological Engineering, UW-Madison).  Through a combination of genome annotation and comparative genomics techniques, an E. coli pangenome metabolic network was constructed and used to rapidly construct genome-scale computational models representing reconstructed metabolic networks for six strains of E. coli.  Our findings demonstrated that through use of the pangenome metabolic network, additional E. coli strain-specific models can be rapidly constructed, and that quantitative models of pathogenic and non-pathogenic strains of E. coli can accurately predict strain-specific phenotypes and offer bioengineers a larger suite of metabolic capabilities with which to work with for designing new industrial E. coli strains.

Since October 2010, I was awarded a postdoctoral fellowship through the Computational and Informatics for Biology and Medicine (CIBM) program at UW-Madison.  This work focused on constructing the first in silico representation of the metabolic network containing the collective information of all sequenced enterobacterial genomes referred to as the pangenome. I am examining metabolic requirements of pathogenic bacteria during host-interaction through conservation of essential genes while controlling for the environmental parameters.  The necessary metabolic networks that result for each host environmental condition examined will be compared to real evolutionary outcomes of genomes of sequenced enterobacteria that cause disease in the respective region in the human host.  Computational modeling of human-pathogen interactions is a promising approach since experiments with humans is not an option.  Expected outcomes are that predictions of metabolic and gene content of an organism with knowledge of its distant ancestors and its current lifestyle will lead to a better understanding of human pathogenic bacteria and could contribute to new treatments, diagnostics, and antibiotics to combat human disease.

Publications

• Baumler, D.J., Peplinski, R.M., Glasner, J.D., Reed, J.L, and N.T. Perna. 2011. The Evolution of Metabolic Networks of E. coli. BMC Systems Biology journal (in press).
  
• Baumler, D.J., Banta, L.M., Hung, K.F., Schwarz, J.A., Cabot, E.L., Glasner, J.D., and N.T. Perna. 2011. Use of comparative genomics for inquiry-based learning to dissect virulence of Escherichia coli O157:H7 and Yersinia pestis. Cell Biology Education-Life Science Education (CBE-LSE) journal (in press). 
• Jeong, K.C, Kang, M.Y, Kang, J., Baumler, D.J., and C.W. Kaspar. 2011.  Feeding chitosan microparticles reduces Escherichia coli O157:H7 shedding in cattle. Applied and Environmental Microbiology Apr;77(8):2611-6. Epub 2011 Feb 18.PMID: 21335379.
• 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.