The Plant Systems Biology Graduate Program aims to train each student to span the full range from molecular biology and genomics research at the bench to computer-based data analysis and model building. Research training clusters emphasize five rapidly emerging and important areas of plant cellular signaling, with meaningful integration of each to a nuclear cluster of bioinformatics, biostatistics, and computational biology. The five plant systems we emphasize are Plant Defense, Organelle Biology, Epigenetic Signals, Metabolite Signals, and Plant Development.

The capability to fully integrate molecular biology and genomics research with excellent training in computational biology and bioinformatics prepares students for future academic and industrial research job markets. A systems biology approach to understanding an organism encompasses the future of biological research, providing powerful means for modulating gene expression with the ability to predict outcome. We envision that students from this program will be highly competitive for research opportunities in academia and in industrial research areas ranging from agricultural to pharmaceutical.

Our students will be equipped for positions ranging from laboratory research and teaching to computational biology and computer program development. This PhD degree is conferred through the School of Biological Sciences.

Apply to the Plant Systems Biology Program.

Xinrong Ma in Dr. Cerutti's lab

Xinrong Ma in Dr. Cerutti's lab.

Guidance Interview for New Students

The guidance interview will be held before the beginning of the first semester of classes. At least three Graduate faculty, including the potential adviser or faculty sponsor, should be present. The meeting should be instructive with respect to guiding the student to register for appropriate classes for the first semester and providing a copy and some explanation of the PSP program requirements.
The student's interests should be discussed in the context of the diversity of graduate program expertise. The Graduate Committee will conduct an orientation meeting for all new entering students at the beginning of each semester to explain the guidelines and general expectations of the School of Biological Sciences graduate program.

 

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Exams
M.S. written comprehensive exam

The Examining Committee administers the exam to the student; it covers the student's approved program of study and should be done no later than one month before the Final Oral Examination (Defense). The Faculty Adviser notifies the Graduate Committee in writing of the outcome along with a copy of the written exam. Answers and scores from the written comprehensive exam must be made available at the Final Oral Examination.

Ph.D. preliminary exam

The Preliminary Examination, a written exam focused mainly on topics covered in Year 1 coursework, will be administered at the end of Year 1. The results of this examination, together with Year 1 coursework grades and written evaluations by laboratory rotation mentors, will be used to assess student performance. This three-way evaluation at the end of Year 1 permits us to redirect students unsuitable to the program to other opportunities early in the process, and to identify particular weaknesses in otherwise well qualified students in order to make recommendations on Year 2 coursework or laboratory practices. Three rotating faculty members will be assigned the task annually of administering the qualifying examination, and the program Executive Committee will assess overall student performance and make recommendations on continued funding.

Ph.D. comprehensive exam

At the end of Year 2, the Comprehensive Examination will be administered. This exam includes a written research proposal prepared by the student and an oral examination by the student's Advisory Committee. This examination evaluates a student's ability to design and conduct research, and to understand and integrate information related to the research topic. An unsatisfactory performance may require the fellow to perform additional work on the proposal, take additional coursework, or, perhaps on occasion, be discontinued for funding by the program.

 

 

 

Suggested Coursework

A student will hold annual progress meetings with the Advisory Committee
in order to develop a suitable curriculum. Upon completion of the student’s program,
the dissertation must be accompanied by at least one publication or manuscript suitable
for publication in a refereed journal.

Category I
Biology
  • BIOC 431/831 Biomolecules & Metabolism
  • BIOC 432/832 Gene Expression & Replication
  • BIOC 839 Graduate Survey of Biochemistry
  • BIOS 418/818 Advanced Genetics
  • BIOS 420/820 Molecular Genetics
  • * BIOS 206 General Genetics
  • * BIOS 207 Ecology and Evolution
  • * BIOC 321 Elements of Biochemistry
Category II
Computer & Mathematical Methods
  • MATH/CSCE 340/840 Numerical Analysis I
  • MATH/CSCE 441/841 Approximation of Functions
  • MATH/CSCE 447/847 Numerical Analysis II
  • * CSCE 155 Introduction to Computer Science I
  • * CSCE 156 Introduction to Computer Science II
  • * CSCE 235 Introduction to Discrete Structures
  • * CSCE 310 Data Structures and Algorithms
 
Category III
Bioinformatics & Computational Biology
  • ASCI 896 Genomics & Systems Biology
  • BIOS 427/827 Practical Bioinformatics Laboratory
  • BIOS 477/877 Bioinformatics & Molecular Evolution
  • BIOS 942 Genetics, Genomics, & Bioinformatics of Prokaryotes
  • CSCE 496/896 Special Topics: Bioinformatics
  • STAT 896A Statistical Methods in Bioinformatics
  • MATH 439/839 Mathematical Models in Biology
  • MATH 842 Methods of Applied Mathematics I
  • MATH 496/896 Mathematical Aspects of Bioinformatics
Category IV
Advanced Plant Biology
  • BIOC 834 Plant Biochemistry
  • AGRO 919 Advanced Plant Genetics
  • BIOS 825 Plant Biotechnology
  • BIOS 897 Fungal Genetics and Cell Biology
  • AGRO 810 Plant Molecular Biology
  • BIOS 963 Genetics of Plant-Pathogen Interactions
  • BIOS 964 Signal Transduction
  • BIOS 910 Developmental Genetics/Epigenetics
  • BIOS 879 Advanced Plant Physiology
  • BIOS 878 Plant Anatomy & Development

 

 

 

 

Rotations

Julie Stone with StudentStudents entering the program will be encouraged to complete two or three laboratory rotations in Year 1 before deciding on a home laboratory in which to pursue their research. During this period, they will acquire a temporary adviser, with whom they will develop a Student Advisory Committee that will ultimately include the primary adviser (non-voting member), co-adviser, and three additional faculty members.

Seminars

Students are expected to participate in monthly Group Meetings, which will feature lab research presentations. In addition, students and faculty will meet on a weekly basis for a lunch time Bioinformatics Seminar Series, with presentations by local laboratories and outside guests. A two-day annual retreat will also provide students with the opportunity to interact with fellow students and faculty.

Student Mentoring

Students will have the opportunity to participate in a Student-Mentoring program. This will be for students that feel they would benefit from a mentor. We will match up students with faculty advisers in a culturally and racially sensitive manner. The adviser will be someone other than those that have contact with students in an academic capacity.

Students will meet weekly with their mentor. Discussion topics could include course grades and other academic matters, progress and achievements made, personal issues that may have arisen, feelings of isolation or any other subject that either party deems important. Either person can make changes if they are uncomfortable for any reason. Meetings will be mutually scheduled. After a comfortable amount of time, and by mutual agreement, the meetings can be scheduled monthly. The coordinator will receive reports from each person participating in this program (even if it is just a few sentences). We hope this program and experience will give our students an opportunity for positive growth, personally and professionally, and lend a hand in welcoming students to UNL.