(Image 1) Students examining a John Deere combine (Image 2) Dr. Troy Runge assessing lab sample (Image 3) Student tending to experiment in the field

Graduate work in the Department of Biological Systems Engineering (BSE) leads to the master of science and doctor of philosophy degrees. Graduates of the program help fill the need for highly educated engineers in industry, consulting firms, government agencies, and educational institutions.

Students who undertake graduate studies in BSE normally have as their goal a better understanding of the current theories, principles, issues, and problems in biological systems. They desire to learn how knowledge is generated, how it is critically evaluated, and how solutions to problems are generated and applied. Graduate studies improve the ability of students to think critically and creatively, and to synthesize, analyze, and integrate ideas for decision making and problem solving.

The department offers students an opportunity to undertake research and advanced study in different specializations such as biological systems, environmental quality and natural resource engineering, waste management, food and bioprocess engineering, nanotechnology and biosensing, machinery systems, bio-resources and bio-refining, and agricultural safety and health.

Graduate research assistantships, project assistantships, and fellowships are available on a highly competitive basis.

Please consult the table below for key information about this degree program’s admissions requirements. The program may have more detailed admissions requirements, which can be found below the table or on the program’s website.

Graduate admissions is a two-step process between academic programs and the Graduate School. Applicants must meet the minimum requirements of the Graduate School as well as the program(s). Once you have researched the graduate program(s) you are interested in, apply online.

Fall Deadline February 1
Spring Deadline September 1
Summer Deadline November 1
GRE (Graduate Record Examinations) Not required.
English Proficiency Test Every applicant whose native language is not English or whose undergraduate instruction was not in English must provide an English proficiency test score and meet the Graduate School minimum requirements (https://grad.wisc.edu/apply/requirements/#english-proficiency).
Other Test(s) (e.g., GMAT, MCAT) n/a
Letters of Recommendation Required 3

The department requires that students have a strong engineering background for admission to its graduate program. Most applicants have a bachelor of science degree from an ABET/EAC–accredited engineering program or an engineering undergraduate degree from an international institution. Applicants who do not have a bachelor of science degree from an ABET/EAC–accredited engineering program may be admitted with a stipulation that they complete supplemental work. Contact the department for details concerning additional requirements. Applicants are evaluated based on their academic record and educational objectives and letters of reference.

Graduate School Resources

Resources to help you afford graduate study might include assistantships, fellowships, traineeships, and financial aid. Further funding information is available from the Graduate School. Be sure to check with your program for individual policies and restrictions related to funding.

Program Information

Funding decisions are made by faculty supervisors of the admitted students based on the funding availability and project need.

Minimum Graduate School Requirements

Review the Graduate School minimum academic progress and degree requirements, in addition to the program requirements listed below.

Major Requirements


Face to Face Evening/Weekend Online Hybrid Accelerated
Yes No No No No

Mode of Instruction Definitions

Accelerated: Accelerated programs are offered at a fast pace that condenses the time to completion. Students are able to complete a program with minimal disruptions to careers and other commitments.

Evening/Weekend: ​Courses meet on the UW–Madison campus only in evenings and/or on weekends to accommodate typical business schedules.  Students have the advantages of face-to-face courses with the flexibility to keep work and other life commitments.

Face-to-Face: Courses typically meet during weekdays on the UW-Madison Campus.

Hybrid: These programs combine face-to-face and online learning formats.  Contact the program for more specific information.

Online: These programs are offered 100% online.  Some programs may require an on-campus orientation or residency experience, but the courses will be facilitated in an online format.


Minimum Credit Requirement 72 credits
Minimum Residence Credit Requirement 32 credits
Minimum Graduate Coursework Requirement At least 50% of credits applied toward the graduate degree credit requirement must be completed graduate-level coursework; courses with the Graduate Level Coursework attribute are identified and searchable in the university's Course Guide.
Overall Graduate GPA Requirement 3.00 GPA required.
Other Grade Requirements Graduate students in BSE must maintain a minimum overall B average (3.0 GPA) during their graduate studies. Seminars, research, or other special problems credits may not be used to offset BC or C grades. No grade below a C will be accepted for fulfilling course work requirements for the degree.
Assessments and Examinations Doctoral students are required to take a comprehensive preliminary/oral examination after they have cleared their record of all Incomplete and Progress grades (other than research and thesis). Deposit of the doctoral dissertation in the Graduate School is required.
Language Requirements n/a
Doctoral Minor/Breadth Requirements Doctoral students must complete a doctoral minor.


Course Credits 142-54
BSE 900 Seminar 21
BSE 901 Graduate Research Seminar 31
BSE 990 Research (Thesis) 41-12
Teaching Preparatory/Professional Communications Course 53
Students may choose from the following or select another course in consultation with their advisor:
Teaching in Science and Engineering
Practicum in Agricultural Engineering Teaching



At least 36 of the course credits must be taken in physical sciences. At least 9 credits must be from the 600 to 800 level classes from an engineering department and/or comparable technical area. All course credits need to be taken as a letter grade unless course is only offered for credit/no credit. Credit/no credit courses must get prior approval from advisor. Only 1 credit/no credit of the 9 credits can be used to fulfill your credits from 600- to 800-level classes. 


All graduate students are required to register for one credit of BSE 900 Seminar (only offered fall semesters) within the first three semesters as a graduate student in BSE. However, if you completed your master’s degree in BSE, you do not have to repeat the 1-credit seminar.


As a part of the seminar, all students are required to make an oral presentation reporting their research results, typically during the last semester of their graduate program (if you took this course as an M.S. student, you will need to repeat the course as a Ph.D. student to reflect your current research).


Graduate students should register for an appropriate number of credits of BSE 990 Research (Thesis Research). If the student’s progress is satisfactory, the student will receive a grade of P (progress) for each semester of BSE 990 Research until the final semester. At that time all of these credits will be given an S (satisfactory) grade by the major professor. 


The teaching course credits shall not be used to fulfill 9 credits of 600 to 800 level classes from an engineering department and/or comparable technical area. Teaching preparatory courses and seminar courses will NOT count toward the required 24 (42) course credits.

Graduate School Policies

The Graduate School’s Academic Policies and Procedures provide essential information regarding general university policies. Program authority to set degree policies beyond the minimum required by the Graduate School lies with the degree program faculty. Policies set by the academic degree program can be found below.

Major-Specific Policies

Prior Coursework

Graduate Work from Other Institutions

For well-prepared advanced students, the program may accept prior graduate coursework from other institutions toward the minimum graduate degree credit and minimum graduate coursework (50%) requirement. The minimum graduate residence credit requirement can be satisfied only with courses taken as a graduate student at UW–Madison. Coursework earned ten or more years prior to admission to a doctoral degree is not allowed to satisfy requirements. Up to 6 research credits received for the master’s degree may be transferred from another accredited institution. No other research credit may be transferred. Eighteen (18) Master’s course credits earned from another institution maybe transferred towards Ph.D. Additional credits need to be approved by the BSE Graduate Instruction and Research committee. 

UW–Madison Undergraduate

For well-prepared advanced students, the program may decide to accept up to 7 credits numbered 300 or above completed at UW–Madison toward fulfillment of minimum degree and minor credit requirements. This work would not be allowed to count toward the 50% graduate coursework minimum unless taken at the 700 level or above. Coursework earned ten or more years prior to admission to a doctoral degree is not allowed to satisfy requirements.

UW–Madison University Special

The program may decide to accept up to 15 University Special student credits as fulfillment of the minimum graduate residence, graduate degree, or minor credit requirements on occasion as an exception (on a case-by-case basis). UW–Madison coursework taken as a University Special student would not be allowed to count toward the 50% graduate coursework minimum unless taken at the 700 level or above. Coursework earned ten or more years prior to admission to a doctoral degree is not allowed to satisfy requirements.


The Graduate School regularly reviews the record of any student who earned grades of BC, C, D, F, or Incomplete in a graduate course (300 or above), or grade of U in research credits. This review could result in academic probation with a hold on future enrollment or in being suspended from the Graduate School.


Every graduate student is required to have an advisor. An advisor is a faculty member, or sometimes a committee, from the major department responsible for providing advice regarding graduate studies. An advisor generally serves as the thesis advisor. In many cases, an advisor is assigned to incoming students. Students can be suspended from the Graduate School if they do not have an advisor.

To ensure that students are making satisfactory progress toward a degree, the Graduate School expects them to meet with their advisor on a regular basis.

A committee often accomplishes advising for the students in the early stages of their studies.


15 credits

Time Constraints

Doctoral degree students who have been absent for ten or more consecutive years lose all credits that they have earned before their absence. Individual programs may count the coursework students completed prior to their absence for meeting program requirements; that coursework may not count toward Graduate School credit requirements.

A candidate for a doctoral degree who fails to take the final oral examination and deposit the dissertation within five years after passing the preliminary examination may by require to take another preliminary examination and to be admitted to candidacy a second time.

grievances and appeals

These resources may be helpful in addressing your concerns:

College of Agricultural and Life Sciences: Grievance Policy

In the College of Agricultural and Life Sciences (CALS), any student who feels unfairly treated by a member of the CALS faculty or staff has the right to complain about the treatment and to receive a prompt hearing. Some complaints may arise from misunderstandings or communication breakdowns and be easily resolved; others may require formal action. Complaints may concern any matter of perceived unfairness.

To ensure a prompt and fair hearing of any complaint, and to protect the rights of both the person complaining and the person at whom the complaint is directed, the following procedures are used in the College of Agricultural and Life Sciences. Any student, undergraduate or graduate, may use these procedures, except employees whose complaints are covered under other campus policies.

  1. The student should first talk with the person at whom the complaint is directed. Most issues can be settled at this level. Others may be resolved by established departmental procedures.
  2. If the student is unsatisfied, and the complaint involves any unit outside CALS, the student should seek the advice of the dean or director of that unit to determine how to proceed.
    1. If the complaint involves an academic department in CALS the student should proceed in accordance with item 3 below.
    2. If the grievance involves a unit in CALS that is not an academic department, the student should proceed in accordance with item 4 below.
  3. The student should contact the department’s grievance advisor within 120 calendar days of the alleged unfair treatment. The departmental administrator can provide this person’s name. The grievance advisor will attempt to resolve the problem informally within 10 working days of receiving the complaint, in discussions with the student and the person at whom the complaint is directed.
    1. If informal mediation fails, the student can submit the grievance in writing to the grievance advisor within 10 working days of the date the student is informed of the failure of the mediation attempt by the grievance advisor. The grievance advisor will provide a copy to the person at whom the grievance is directed.
    2. The grievance advisor will refer the complaint to a department committee that will obtain a written response from the person at whom the complaint is directed, providing a copy to the student. Either party may request a hearing before the committee. The grievance advisor will provide both parties a written decision within 20 working days from the date of receipt of the written complaint.
    3. If the grievance involves the department chairperson, the grievance advisor or a member of the grievance committee, these persons may not participate in the review.
    4. If not satisfied with departmental action, either party has 10 working days from the date of notification of the departmental committee action to file a written appeal to the CALS Equity and Diversity Committee. A subcommittee of this committee will make a preliminary judgement as to whether the case merits further investigation and review. If the subcommittee unanimously determines that the case does not merit further investigation and review, its decision is final. If one or more members of the subcommittee determine that the case does merit further investigation and review, the subcommittee will investigate and seek to resolve the dispute through mediation. If this mediation attempt fails, the subcommittee will bring the case to the full committee. The committee may seek additional information from the parties or hold a hearing. The committee will present a written recommendation to the dean who will provide a final decision within 20 working days of receipt of the committee recommendation.
  4. If the alleged unfair treatment occurs in a CALS unit that is not an academic department, the student should, within 120 calendar days of the alleged incident, take his/her grievance directly to the Associate Dean of Academic Affairs. The dean will attempt to resolve the problem informally within 10 working days of receiving the complaint. If this mediation attempt does not succeed the student may file a written complaint with the dean who will refer it to the CALS Equity and Diversity Committee. The committee will seek a written response from the person at whom the complaint is directed, subsequently following other steps delineated in item 3d above.


Funding decisions are made by faculty supervisors of the admitted students based on the funding availability and project need.

Graduate School Resources

Take advantage of the Graduate School's professional development resources to build skills, thrive academically, and launch your career. 

  1. Articulates research problems, potentials, and limits with respect to theory, knowledge, or practice within the field of study.
  2. Formulates ideas, concepts, designs, and/or techniques beyond the current boundaries of knowledge within the field of study.
  3. Creates research, scholarship, or performance that makes a substantive contribution.
  4. Demonstrates breadth within their learning experiences.
  5. Advances contributions of the field of study to society.
  6. Communicates complex ideas in a clear and understandable manner.
  7. Fosters ethical and professional conduct.

Professor Robert Anex

Biological systems analysis and assessment; life cycle assessment; techno-economic analysis

Professor Christopher Choi

Heat and mass transfer and computational fluid dynamics (CFD); controlled environments – livestock housing and greenhouse; water distribution system modeling and water quality; experimental methods, data acquisition, and systems optimization in biological systems

Assistant Professor Matthew Digman

Impact of autonomy on agricultural machine forms; application of sensors to predict chemical and physical properties of agricultural materials

Professor Sundaram Gunasekaran

Engineering properties and quality of food and biomaterials; rheology of food and other macromolecular systems and hydrogels; structure function relationships in foods; novel and value-added bioprocess engineering

Assistant Professor Margaret Kalcic

Watershed modeling; watershed management; conservation practice effectiveness; agricultural hydrology; nutrient transport; water quality; land use change; climate change

Professor K.G. Karthikeyan

Fate, removal, and transport of nutrients and contaminants in surface/subsurface environments; water quality chemistry; land application of agricultural/municipal/industrial waste; applications of GIS/water quality models; physical and chemical processes for water, wastewater, and waste treatment; soil decontamination

Associate Professor Rebecca Larson

Biological waste; manure management; handling and treatment of agricultural and food processing waste; agricultural sustainability; land application of various waste streams, including runoff and leaching; waste-to-energy technologies, including biogas production from anaerobic digestion; composting

Associate Professor Brian Luck

Machine management, variable rate technology; agricultural “Big Data” management; remote sensing

Professor Xuejun Pan

Development of innovative biorefining process for producing energy, fuels, chemicals, and materials from renewable resources (biomass) with specific research interests in pretreatment and fractionation of lignocellulosic biomass for bioconversion to chemicals and fuels; enzymatic and non-enzymatic saccharification of cellulose and lignocellulose; catalytic conversion of lignocellulose to drop-in hydrocarbon fuel; platform chemicals from biomass; functional materials from cellulose, lignin, hemicellulose, and extractives.

Professor Douglas Reinemann

Biomechanics of machine milking; sustainable development of bio-energy systems; renewable energy technology and policy; biosensors for milk quality analysis; effects of the electrical environment on farm animals; integral thought and philosophy

Associate Professor and Department Chair Troy Runge

Bioenergy – biomass composition impact on bioprocessing systems, including anaerobic digestion, combustion, gasification, and catalysis; Biomaterials – pulp, paper, bio-based chemicals, cellulose composites and nonwoven structures

Professor John Shutske

Safety engineering and education related to occupational and public health hazards in agricultural and food systems; multidisciplinary approaches for solving complex risk-related problems; design and evaluation of sensors and control systems to mitigate environmental and machine risks; risk communication methods and limitations.

Associate Professor Paul Stoy

Surface-atmosphere exchange; ecosystem ecology; natural resource management

Professor Anita Thompson

Hydrologic implications of land use change; urban hydrology and stormwater management; water quality impacts of biofuel crop production; cold regions hydrology; hydrologic modeling; sediment, nutrient and pathogen transport; polyacrylamides and biosolids for fertilizer and erosion management

 Assistant Professor Zhou Zhang

Multi-source remote sensing data fusion (e.g., hyperspectral, LiDAR, RGB); machine learning for high dimensional data analysis; UAV-based imaging platform developments for precision agriculture; crop yield prediction using remote sensing and machine learning; high-throughput image-based plant phenotyping.


Assistant Professor Grace Bulltail, Nelson Institute

Professor Awad Hanna, Dept. of Civil Engineering

Professor Richard Hartel, Dept. of Food Engineering

Professor John Ralph, Dept. of Biochemistry