PhD Program

Program Flier pdf

Complex Biosystems Student Receives Milton E. Mohr Fellowship

New doctoral program links life sciences with big data (October 28, 2016)

Courses, Specializations, Faculty & Research

Description & courses Specialization Tracks Faculty & research

Program Description

The PhD Program in Complex Biosystems is designed to prepare students for both academic and industrial careers. It is directed toward students interested in applying quantitative statistical and computational approaches to data acquisition and analysis in multiple life sciences fields including human health and medical biochemistry, plant phenomics, and host-microbial metagenomics.

In this interdisciplinary program, graduate students participate in a full year of laboratory rotations (three total) on diverse topics, with one semester of laboratory teaching experience. In the first year of study, students consider "big questions" in the life sciences, and learn current technical and analytical approaches to answer them.

Program Requirements

Core course requirements

  • Biosystems Research I (3 credit hours)
  • Biosystems Research II (3 credit hours)
  • Statistics 801 or equivalent (4 credit hours)
  • Professional Development (1 credit hour)
  • Biotechnology instrumentation short course (1 credit hour)

Mandatory specialization

To earn the degree, each student will enter a program of studies approved by his/her supervisory committee within one of the Complex Biosystems specializations. Currently, these specializations are (1) Systems analysis; (2) Integrated plant biology; (3) Pathobiology and biomedical science; (4) Microbial interaction; and (5) Computational organismal biology, ecology and evolution. The specializations are designed to complete a minimum of 35 hours of formal graduate coursework (including the required courses above), consistent with requirements for a PhD degree set by the Office of Graduate Studies.


Each student will complete one semester of teaching within the first year, either in LIFE 120 Lab or LIFE 121 Lab as needed. Approximately half of the students will teach in the fall and the remainder will teach in the spring.

Research requirements

Students complete two semesters of research rotation in the first year (three total rotations for 6 credit hours total). One rotation will span the full semester that the student is teaching. The other two rotations will be completed in two 8-week blocks during the semester the student is not teaching. Upon entering their respective specializations, students will complete an additional minimum of 55 hours of dissertation research.

Comprehensive examinations

All students will complete a written and oral examination at least seven months before applying to graduate. The format of the written examination will consist of an original research proposal in a style and on a topic approved by the supervisory committee. The oral examination will consist of a defense of the proposal and concepts important to the student's demonstration of interdisciplinary scientific knowledge.

External proposal submission

Each student in the program will be required to identify an external fellowship opportunity and work with the program's director and coordinating committee to develop and submit the proposal. In the case of National Science Foundation fellowships, the proposal will be submitted in the first year. For other agencies, the specific agency requirements will be followed and the proposal will be submitted with support from the student's research advisor as sponsor, and advice or critical review as needed from the supervisory committee.

Dissertation, final oral examination, and public seminar

All students will complete a written dissertation describing their original graduate research. Students will present a public seminar summarizing their research, and will defend the research in a final oral examination before the supervisory committee.

10-12 students per year

PhD Program Features

  • Weekly graduate seminar open to all
  • Choose research in human, plant, microbial, and ecological systems
  • Flexible curriculum centered around your goals
  • Rotate through multiple lab experiences to inform your choice of research topic
  • Faculty advisors who lead multidisciplinary projects funded by federal agencies
  • Strong emphasis on career preparation
  • Competitive tuition & benefits package

Core Curriculum

Year 1 Core Curriculum

Semester 1Semester 2
Rotation 1 Rotation 2 Rotation 3
LIFE 120 teaching assistant  
Rotation 1 Rotation 2 Rotation 3
  LIFE 121 teaching assistant
Complex Biosystems Graduate Seminar (1 cr. all 4 years)

Program faculty research presentations with student evaluation of research publications and a seminar evaluation; as the program is fully implemented in later years, student research presentations and journal club discussions will be integrated into the seminar rotation.
Professional Development (1 cr):
Data analysis and presentation
Literature critique
Scientific communication: seminars, posters, journal publications and grant proposals
Ethics in research and publication

Elective Course (3-4 cr)

Professional Development (1 cr)

Statistics 801 (4 cr):
Statistical methods in research
OR Statistics 801 (4 cr):
Statistical methods in research (or appropriate alternative course if student can document equivalent knowledge of statistics)

Center for Biotechnology Instrumentation Core Course (1 cr)

Elective Course (3 cr)

Center for Biotechnology Instrumentation Core Course (1 cr)
Life Sciences Research 1:
Big Questions (3 cr)

Five modules featuring a coordinated, systems-level examination of a key research question in each specialization using primary literature:

1. Pathobiology and Biomedical Science
2. Microbial Interactions
3. Systems Analysis
4. Integrated Plant Biology
5. Computational Organismal Biology, Ecology, Evolution
OR Life Sciences Research II: Integrating quantitative discovery into basic and applied research (3 cr)

Five modules featuring in-depth examinations of key challenges in computational and quantitative biology:

1. Genomics
2. Systems and Networks
3. Sequence analysis
4. Phylogenic inference
5. Quantitative ecology

Year 2 Requirements

Select mandatory specialization for program of study.

Choose research mentor(s) and supervisory committee:

  1. Pathobiology and Biomedical Science
  2. Microbial Interactions
  3. Systems Analysis
  4. Integrated Plant Biology
  5. Computational Organismal Biology, Ecology, and Evolution

Specialization Tracks

Microbial Interactions

The Microbial Interactions specialization is designed to provide students with a broad array of training necessary to study complex interactions that occur between mammals and the massive populations of microorganisms that live in and on them. After completing the program, students should:

  1. Understand ecological principles that drive assemblages of microbes (the microbiome) that occupy various niches in and on mammalian hosts
  2. Understand how microbial assemblages relate to health, performance, and disease susceptibility of the host
  3. Understand the host factors (immune system, host genetics) that influence microbial ecosystems
  4. Understand the role of diet in shaping microbial communities
  5. Understand the applications of quantitative data sciences to analyze microbiome data and complex data sets

The first year of courses will consist of the Interdisciplinary Life Sciences PhD Core Curriculum. The remaining 25-30 credit hours will come from a combination of courses that fall into the categories of "host processes", "microbial processes" and "bioinformatics and systems biology". Students will take courses in all three of the categories, with the program of study based on the student's research project and their career goals.

View Microbial Interactions Courses

Integrated Plant Biology

The Integrative Plant Biology specialization within the Complex Biosystems Ph.D. Program is designed to prepare graduate students to address complex problems in plant biology that require interdisciplinary research approaches and effectively assimilate laboratory to field-based studies. The program and the specialization feature a systems-oriented curriculum and cutting edge collaborative research. Graduates in this program will have rigorous training in the application and underlying concepts of quantitative research methods, critical literature evaluation, grantsmanship, and statistics. Through this program, students will have exposure to teaching in the life sciences and mentored laboratory research at the cutting edge of the discipline. 
The complexity of contemporary challenges in hypothesis testing in a transdisciplinary fashion involving integration across levels of organization from gene to organism to ecosystem, necessitates disciplines, technologies and strategies from a diversified knowledge base. Hence, to be successful in understanding and solving research problems, and for our graduate students to be competitive in the job market, training programs must combine proficiency and breadth across the broad range of scientific fields required to meet the future needs of research in plant biology. 

Upon successful completion of the Specialization in Integrative Plant Biology, students will have mastered the skills and concepts necessary to • Formulate and experimentally test new hypotheses about relationships between genes, organisms, and ecosystems  • Demonstrate competence, proficiency and breadth in quantitative plant research  • Apply theories and methodologies related to plant biological systems • Conduct and provide leadership in basic and applied research in plant biology.

IPB student's core course selection options (minimum of 3 credits per topic area)

View Integrated Plant Biology Courses

Pathobiology and Biomedical Science

The Pathobiology and Biomedical Science specialization within the Interdisciplinary Life Sciences Ph.D. Program is designed to prepare graduate students to address complex problems in normal and pathogenic processes through systems-oriented curriculum and cutting edge collaborative research. Graduates in this program will have received rigorous training in the application and underlying concepts of quantitative research methods, critical literature evaluation, grantsmanship, and statistics. Through this program, students will have exposure to teaching in the life sciences and mentored laboratory research at the cutting edge of the discipline.

Upon successful completion of the Specialization in Pathobiology and Biomedical Science, students will have mastered the skills and concepts necessary to •Formulate and experimentally test new hypotheses about normal and pathogenic processes •Demonstrate competence in quantitative biology •Apply theories and methodologies related to biological systems •Conduct and provide leadership in basic and applied research.

View Pathobiology and Biomedical Science Courses

Systems Analysis

This pathway involves students and researchers in the areas of bioinformatics and computational biology; genetics and genomics; and systems biology. We define bioinformatics as investigating questions about biology and evolution using primarily informatics and statistics; and computational biology as investigating questions about biology and evolution using primarily mathematical modeling and computational simulation Researchers in genetics and genomics apply bioinformatics and computational techniques using data from current and novel biotechnological methods. Systems biology seeks to explain how biological units (genes, pathways, cells, tissues, organisms) function from the perspective of a biological system. These perspectives on research are viewed as inherently compatible, complementary, and reciprocal approaches to scientific inquiry.

View Systems Analysis Courses

Computational Organismal Biology, Ecology and Evolution

The specialization in Computational Organismal Biology, Ecology and Evolution (COBEE) will train students with the objective of using combined computational and empirical approaches at the interface of ecology, evolution and organismal biology with the aim of modeling how processes at different scales of biology – from individual to populations to communities and ecosystems – impact each other. While each of these fields has a rich tradition of quantitative methods, new computational approaches are required to bridge process-based individual models with population, community, and ecosystem phenomena. This includes reciprocal interactions between the evolution and expression of individual traits with population dynamics and the myriad of pathways through which organisms engage and respond to their environment. Making these links will benefit from expertise in a variety of adjacent disciplines including mathematics, statistics, computer science, and biomechanics. This program will expect students to conduct research at the interface of at least two of these focal fields (organismal biology, ecology and evolution).

View Computational Organismal Biology, Ecology and Evolution Courses

How to Apply

Submit your application here

For general questions about applying contact:
Jennifer Clarke at 
Amanda Ramer-Tait at
Joshua Herr at
Hollie Swanson at