Microbiology

  • Microbiology Ph.D. Bioinformatics Specialty

    Description and Purpose of Specialty

    The emerging field of bioinformatics has promoted a close working relationship between researchers in the life sciences and the computational sciences. The possible uses of bioinformatics technology in the microbiology field are immense. At The University of Iowa, many researchers in the Microbiology Department are now using bioinformatics to address questions such as how various microbes alter overall gene expression profiles in host cells, how microbes themselves alter their own gene expression in response to different stimuli and growth conditions, and how various pathogens affect expression of immune response pathways. It has become clear that the availability of more intense bioinformatics training is necessary for meeting the needs of microbiology students interested in bioinformatics. With the recently developed Center for Bioinformatics and Computational Biology (CBCB) at The University of Iowa, this has now become a possibility. We have therefore initiated a specialty within the Microbiology Ph.D. program that will lead to a Ph.D. in Microbiology with a focus on bioinformatics. The goals of this specialty will be two-fold:

    1. Offer a Microbiology Ph.D. training program involving coursework and Ph.D. thesis research opportunities in bioinformatics and microbiology for those incoming students who already have an interest in computational/computer sciences that would like to apply these interests and skills to microbiology-related topics.
    2. Provide students with microbiology/life sciences backgrounds exposure and training in bioinformatics.

    Although not required by the Microbiology PhD Program, for those students interested in earning a certificate in Bioinformatics and Computational Biology as part of their PhD training the requirements for completion of this certificate can be found on the Interdisciplinary Graduate Program in Informatics web site.

    Coursework

    Students will be required to take advanced level graduate course work in bioinformatics and/or computational studies. These courses will be offered by the Interdisciplinary Graduate Program in Informatics and will be designed to train and educate the student in methodologies focusing on bioinformatics. As with current policy, it will be up to the discretion of the Director of Graduate Studies (DGS) of the Microbiology PhD Program and/or the student's thesis committee to determine whether additional classes should be taken to make up for certain deficits or enhance training in this specific field. All students wishing to participate in the bioinformatics specialty, regardless of their original discipline, will be required to (1) master a sub-discipline of Microbiology (e.g. Virology, Pathogenesis, Immunology, Microbial Genetics); and (2) become familiar with bioinformatics tools and applications. It will also be expected that students will have taken courses in computing and statistics. These requirements can be met by either enrolling in upper level undergraduate courses prior to matriculation (e.g. as an undergraduate) or by enrolling in a combination of undergraduate and graduate courses selected to address individual student needs after matriculation as a graduate student.

    Examples of course work taken by students interested in the bioinformatics focus:

    Microbiology and Interdisciplinary Courses in Life Sciences: Same as those already approved and listed in the Graduate Student Handbook. See http://www.registrar.uiowa.edu/registrar/catalog/medicine/microbiology/.

    Computing: Coursework in practical computer science.

    Statistics (at least one semester equivalent): Biostatistics offered by Statistics and Actuarial Science or Biostatistics offered by the College of Public Health.

    Bioinformatics Tools and Applications: Two courses are generally required, the nature of which would depend upon interest and level of expertise when entering the program.

    Research Training

    The research training envisioned for Bioinformatics Specialty students is modeled after the program followed by students in the traditional Microbiology track, with modifications as noted above.

    Rotations

    The policies on rotations will be similar to those of the Microbiology Department. Specifically, all students will be required to rotate among three laboratories during their first year in graduate school. The choice of laboratories will be determined by the student in consultation with the Graduate Advisory Committee or the DGS and is subject to approval by the head of the laboratory.

    Choosing a Mentor/Co-mentor 

    For students in the Bioinformatics Specialty, both a mentor and co-mentor may be chosen representing the computational and biological aspects of the research project. The dual mentor system is meant to formally tie together the experimental and computational aspects of the Ph.D. thesis project. The co-mentor will be a member of the student's comprehensive and thesis committee each comprised of at least five faculty members. Three members of the Comprehensive Examination Committee must be from Microbiology and the Committee Chair must be from Microbiology. At least one member of the PhD advisory committee must be from outside the Department of Microbiology. In many cases the co-mentor is likely to be the outside committee member.

    Course Descriptions

    A complete list of bioinformatics courses and their descriptions can be found on the Interdisciplinary Graduate Program in Informatics web site and in The University of Iowa General Catalog. These courses are routinely reviewed and updated to reflect the continuing advances in this area.