Mark Eppinger

Mark Eppinger, Ph.D.

Associate Professor

Phone: (210) 458-6276
Email: Mark.Eppinger@utsa.edu
Lab website

Areas of Specialization
  • Bioinformatics
  • Infectious Diseases
  • Microbial Genomics

South Texas Center for Emerging Infectious Diseases


Ph.D. in Microbial Genetics; Max-Planck Institute for Developmental Biology, University of Tuebingen, Germany
B.S. in Biology; University of Tuebingen, Germany

Research Interests


research image

The focus of Dr. Eppinger's research is on the application of microbial genomics to address fundamental questions in emerging infectious diseases research. His current interests are directed towards large-scale sequencing and phylogenomic studies investigating major public health threats, such as Shiga toxin producing Escherichia coli and multidrug resistant (MDR) enteric bacteria of clinical importance. Experimental approaches include:

  1. Microbial Genome Sequencing – the gathering of additional sequence data as prerequisite to capture the genome architecture and genomic diversity in environmental or clinical settings
  2. Phylogenomics – the development of bioinformatics tools to survey the plasticity within pathogen populations and elucidate the ancestry of microbial species
  3. Microbial Diversity – the discovery of subtle yet important genetic variations in gene content and activity
  4. Pathogenicity – the study of virulence determinants and dynamic host-pathogen interactions

Data from this research provides crucial insights into the make-up of bacterial pathogens and how genomic variants relate to differences in evolutionary and ecological niches that underlie human transmissibility, infectivity and disease outcome. Most importantly, this research can help to initiate countermeasures in an attempt to decrease human morbidity rates.

Training Opportunities

Dr. Eppinger's research program offers an opportunity for students to be trained in a high-throughput microbial genomics and infectious disease laboratory. The research program, which is focused on microbial genomics, incorporates several fields of science, and has exposed students to aspects of microbiology, ecology, (patho-) genomics, epidemiology, molecular biology, and bioinformatics and has provided individual projects for students, which have been completed within the scope of a Work Study, Research Volunteer, MS thesis, or Ph.D dissertation project.


» list of publications

Book Chapters

S.M. Shah, T.H. Hazen, D.A. Rasko, M. Eppinger (2015): EHEC genomics: Past, present and future in "Enterohemorrhagic Escherichia coli and Other Shiga Toxin-Producing E. coli," in V. Sperandio, C.J. Hovde-Bohach (Editors). ASM Press (Publisher); 1st edition (May 1st, 2015) (ISBN-10: 1555818781, ISBN-13: 978-1555818784)

M. Eppinger, J. Ravel and L.E. Lindler (2012): Pathogenic Yersinia, in X.Yan, V.K. Juneja, P.M. Fratamico, J.L. Smith, (Editors): Omics, Microbial Modeling and Technologies for Food-borne Pathogens. DEStech Publications, Inc. (Publisher); 1st edition (January 10th, 2012) (ISBN-10: 1605950475ISBN-13: 978-1605950471)