PhD Program

Complex Biosystems


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.

Teaching

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

  • Annual progress evaluation
  • Weekly graduate seminar open to all
  • Annual research symposium open to all
  • Admissions and placement data maintenance

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. Quantitiative 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

Existing courses that will be part of the specialization are indicated in the Table below. 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". The list of possible courses in these three different categories is shown in the table below. 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)

Computational/Stats component:

AGRO 896: Bioinformatics Applications in Agriculture (3 credits)
AGRO/STAT 932: Biometrical genetics and plant breeding (3 credits)
BIOS 826: Computational Systems Biology (3 credits)
BIOS 827: Practical Bioinformatics Laboratory (3 credits)
BIOS 828: Perl Programming for Biological Applications (3 credits)
BIOS 829: Phylogenetic Biology (4 credits)
BIOS 877: Bioinformatics and Molecular Evolution (3 credits)
CSCE 871: Bioinformatics (3 credits)
CSCE 896: Computational Methods in Bioinformatics (3 credits)
STAT 801 (is a prereq of STAT 802 – I don't remember the title)
STAT 802: Experimental Design (4 credits
STAT 803: Ecological Statistics (4 credits)
STAT 842: Computational Biology (3 credits)

Organismal/Breeding component:

Botany (3 credits)
AGRO/HORT/NRES 826: Invasive Plants (3 credits)
AGRO/NRES 842: Wildland Plants (3 credits)
BIOS 855: Great Plains Flora (4 credits)
BIOS 871: Plant Systematics (4 credits)
BIOS 878: Plant Anatomy (4 credits)
BIOS 879: Plant Growth and Development (4 credits)
NRES 806: Plant Ecophysiology: Theory and Practice (4 credits)
AGRO/ASCI 931: Population Genetics (3 credits)
ENTO 827: Ecological Genetics (3 credits)

Genetics/Molecular/Cellular component:

BIOS 818: Advanced Genetics (3 credits)
AGRO 919: Plant Genetics (3 credits)
AGRO 810: Plant Molecular Biology (3 credits)
BIOS 820: Molecular Genetics (3 credits)
AGRO 807: Plant-Water Relations (3 credits)
AGRO/BIOC 834: Plant Biochemistry (3 credits)
AGRO 896: Biofortification (4 credits)
PLPT 867: Plant Associated Microbes (4 credits)

Environment/Ecology/Evolution component:

BIOS 803 Principles of Evolution (3 credits)
BIOS 805 Principles of Ecology (3 credits)
AGRO/HORT/NRES 806: Plant Ecophysiology: Theory and Practice (4 credits)
AGRO/NRES 807 / BIOS 817: Plant-Water Relations (3 credits)
AGRO/HORT/NRES 808: Microclimate: The Biological Environment (3 credits)
AGRO/HORT 832: Learning Plant Science (3 credits)
AGRO/HORT/NRES 835: Agroecology (3 credits)
AGRO/NRES 840: Great Plains Ecosystem (3 credits)
AGRO 843: Ecology of Invasive Species (3 credits)
AGRO 850 / NRES 852: Climate and Society (3 credits)
AGRO/NRES 877: Great Plains Field Pedology (4 credits)
HORT 812 / NRES 810: Landscape Ecology (3 credits)
BIOS/NRES 854: Ecological Interactions (3 credits)
BIOS 857: Ecosystem Ecology (4 credits)
BIOS 870: Prairie Ecology (4 credits)
NRES 824: Forest Ecology (4 credits)
NRES 868: Wetlands (4 credits)
NRES 867: Global Climate Change (3 credits)
NRES/HORT 817: Agroforestry Systems in Sustainable Agriculture (3 credits)

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

Required for all students in the specialization:

LIFEaaa, Life Sciences Research I: Big Questions (3cr)
LIFEbbb, Life Sciences Research II: Integrating discovery approaches into basic and applied research (3cr)
LIFEccc, Graduate Seminar (6cr total): Research and journal club presentations
LIFEddd, Rotation Research (3cr total)
LIFEeee, Professional Skills (1cr)
STAT 801 (4cr), Statistical methods in research

Macromolecules core, minimum 4cr, from among the following:

BIOC/BIOS/CHEM 932, Proteins (2cr)
BIOC/BIOS/CHEM 933, Enzymes (2cr)
BIOC/BIOS/CHEM 934, Genome dynamics and gene expression (3cr)
BIOC 848, Redox biochemistry (3cr)
BIOC/CHEM 836 (3cr), Physical basis of macromolecular function

Additional specialty courses appropriate for the specialization

ASCI/BIOS/VBMS 842, Endocrinology (3cr)
BIOC/BIOS/ASCI/NUTR 949, Biochemistry of Nutrition (3cr)
BIOC/BIOS/CHEM 935, Metabolic Function and Dysfunction (3cr)
BIOC/BIOS 837, Research Techniques in Biochemistry (4cr)
BIOS 802, Cancer Biology (3cr)
BIOS 807, Biology of cells and organelles (4cr)
BIOS 812, Human Genetics (3cr)
BIOS 818, Advanced Genetics (3cr)
BIOS/VBMS 840, Microbial Physiology (3cr)
BIOS/VBMS 841, Pathogenic Microbiology (3cr)
BIOS/VBMS 843, Immunology (3cr)
BIOS 897, Physical Biology of the Cell (3cr)
BIOS 945, RNA Biology (3cr)
BIOS/VBMS 964, Signal Transduction (3cr)
CHEM 835, Chemical Biology (3cr)

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.

BioinformaticsSystems Biology
AGRO896 Bioinfo App in Ag ANSCI896 Genomics and Sys Bio
BIOS427/827 Prac Bioinfo Lab    
BIOS477/877 Bioinfo and Mol Evol BIOS497/897 Comp Sys Bio
BIOS429/829 Phylo Biol    
BIOS942 Gen, Genom, and Bioinfo of Prok CSCE990 Mol and Nano Comm
BIOS/ STAT442/842 CompBio    
CSCE496/896 Comp Meth in Bioinfo STAT843 NGS and Sys Bio
CSCE971 Advanced Bioinfo    
ELEC452/852 Bioinfo    
MATH439/839 Math Mod in Biol    
BIOS/ NRES456/856 Math Mod in Biol    
MATH496/896 Math Aspects of Bioinfo    
STAT896A Stat Meth in Bioinfo    

Students must complete a total of 90 credits of study with a minimum of 45 credits of coursework [17 credits of coursework in the first year]. Of the 45 credits of coursework, at least 28 credits must be earned in graduate level quantitative courses. Graduate level life sciences courses approved by the other tracks in the Life Sciences PhD will count towards the remaining 17 credits. Other courses will count with permission of the student's Thesis Committee.

The following quantitative courses will count toward the 45 credits of course study.

Program Requirements:

  • First year program including LSRI and LSRII. Rotation credits do not count towards the 45 credits of coursework
  • At least two semesters of teaching
  • A total of 90 credits with at least 45 credits of coursework; at least 28 of these
  • 45 credits must be earned in quantitative courses (listed above)
  • Oral and written general exams
  • A thesis proposal that supports the goals of the specialization
  • Completion of thesis (progress overseen by thesis committee)

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).

The goals of this specialization are as follows:

  • Educate the next generation of leaders working to integrate organismal biology with higher levels of ecological organization
  • Develop expertise in novel empirical and quantitative approaches for scaling biological processes from individuals to ecosystems
  • Enable trainees to conduct research that addresses diverse and critical quantitative challenges in organismal biology, ecology and evolution

Required for all students in the specialization:

LIFE891, Life Sciences Research I: Big Questions (3cr)
LIFE891, Life Sciences Research II: Integrating discovery approaches into basic and applied research (3cr)
LIFE891c, Graduate Seminar (6cr total): Research and journal club presentations
LIFE891d, Rotation Research (3cr total)
LIFE891e, Professional Skills (1cr)
STAT 801 (4cr), Statistical methods in research
Biotechnology Core Facility instrumentation course (2cr)

Students must complete a total of 90 credits of study with a minimum of 35 credits of coursework [17 credits of coursework in the first year]. Of the 35 credits of coursework, at least 28 credits must be earned in graduate level quantitative courses. Graduate level courses approved by the other tracks in the Complex Biosystems PhD will count towards the remaining credits. Other courses will count with permission of the student’s supervisory Committee.The following courses will count toward the 35 credits of course study:

Organismal Biology

BIOS 406/806 Insect Ecology
BIOS 462/862 Animal Behavior
BIOS 468/868 Field Animal Behavior
BIOS 474/874 Herpetology
BIOS 825 Plant Biotech
NRES 406/806 Plant Ecophysiology
AGRO 426/826 Invasive Plants
NRES 489/889 Ichthyology
NRES 807 Plant-Water Relations
NRES 880 Vertebrate Population Analysis
BIOS 879 Plant Growth and Development
BIOS 475/875 Ornithology
BIOS 476/876 Mammology
BIOS 804 Principles of Behavioral Ecology
BIOS 813& 814 Animal Physiology I&II
BIOS 817 Plant-Water Relations
BIOS 955 Advanced Behavioral Ecology
BIOS 956 Biochemical Adaptation

Evolution

BIOS 803 Princ of Evolution
AGRO 919 Plant Genetics
ANSCI 932 Quant Animal Genetics
ANSCI 933 Quant Animal Genetics II
AGRO 931 Pop Gen
AGRO 932 Bio Gen and Plant Breeding
BIOS 818 Advanced Genetics
BIOS 958 Genetic Ecology
ANSCI 896 Genomics and Sys Bio
BIOS 829 Phylo Biol
BIOS 924 Molecular Phylogen
BIOS 952 Phylo Co-Evolution
BIOS 477/877 Bioinfo and Mol Evol
BIOS 427/827 Prac Bioinfo Lab
AGRO 896 Bioinfo App in Ag

Ecology

BIOS 805 Princ. Of Ecology
BIOS 824 Fund of Ecol and Evol Physiology
BIOS 958 Genetic Ecology
GEOL 438/838 Biogeochemical Cycles
NRES 810 Landscape Ecology
NRES 862 Conservation Biology
NRES 459/859 Limnology
NRES 481/881 Stream and River Ecology
GEOL 418/818 Chemistry of Natural Waters
NRES 424/824 Forest Ecology
NRES 450/850 Biology of Wildlife Populations
NRES 463/863 Fisheries Science
BIOS 454/854 Ecological Interactions
BIOS 457/857 Ecosystem Ecology
BIOS 452/852 Field Epidemiology
BIOS 453/853 Predator Ecology
BIOS 470/870 Prairie Ecology
BIOS 860 Advanced Limnology
BIOS 953 Advanced Population Ecology
BIOS 959 Advanced Community Ecology

Stat and Computation

BIOS 428/828 Perl Programming
MATH 439/839 Math Mod in Biol
BIOS 456/856 Math Mod in Biol
MATH 496/896 Math Aspects of Bioinfo
STAT 896A Stat Meth in Bioinfo
MATH 938 Math Modeling
STAT 802 Design and Analysis of Res Studies
STAT 803 Ecol Stat
CSCE 874 Data Mining
STAT 831 Spatial Stat
STAT 841 Stat Meth for HTB
STAT 884 Applied Stochastic Models
STAT 950 Bootstrap Methods and App
BIOS 951 Quantitative Analysis in Biology
   

How to Apply

Submit your application here

For general questions about applying contact:
Bob Hutkins at rhutkins1@unl.edu
Joshua Herr at 
Hollie Swanson at