Ph.D. in Computer Science (Bioinformatics Specialization)

The objective of the Ph.D. program in Computer Science with a Bioinformatics Specialization is to provide qualified candidates with the opportunity to pursue a course of study that will bring them to the frontiers of knowledge in an area of bioinformatics and engage them in high quality research under the direction of a Supervisory Committee. This research should culminate in a dissertation presenting significant results, which are publishable in recognized refereed journals.

Admission Requirements

To enter the Ph.D. program a student must have completed the equivalent of our Master's degree in Computer Science. Background courses must include: in Mathematics - calculus, linear algebra, and probability and statistics; in Computer Science - programming languages, computer organization, discrete structures, algorithms and information structures, computer architecture and operating systems. The student must have the equivalent of 36 semester hours (30 with thesis option) of graduate course work including at least 18 hours of advanced courses in Computer Science & Engineering. Students entering the Ph.D. program must have adequate background to successfully take the Qualifying Examination within a year.


Students are generally admitted to the Ph.D. program on a provisional basis. Every Ph.D. student must take the Bioinformatics Qualifying Examination no later than one year after completing requirements for an M.S. degree. Once the student has passed the Qualifying Examination, he/she is no longer considered provisional. Each student must also pass a written Comprehensive Examination after the student has substantially finished the course work for the Ph.D. After the student has decided on a dissertation topic and obtained preliminary results, an oral Candidacy Examination must be scheduled for approval of the research topic by the student's Supervisory Committee. After the dissertation research work is complete and written up, a public defense of this work must take place during the Final Oral Examination.

Breadth Requirements

At least three courses in each of the following tracks:

  1. Theory
  2. Systems/Applications
  3. Biosciences/Bioinformatics

Note: For details see the Bioinformatics Track Listing.

Additionally, the student must attend at least 30 departmental colloquia, doctoral oral presentations, and/or master's thesis presentations during the Ph.D. program. A sign-up sheet is used during these events as proof of attendance. Note that master's project presentations may not be used to fulfill this requirement.

Depth Requirements

  • Decided by student, research advisor, and the supervisory committee
  • No fewer than 45 credit hours must be completed at the University of Nebraska–Lincoln
  • 24 to 30 credit hours may be for dissertation
  • Total = 90 credit hours

Choosing an Advisor

The choice of an advisor is based on a student’s goal for a Ph.D. It is important to realize that the research program is a cooperative effort between the student and the advisor. The advisor has the overall responsibility for the direction and course of the student's research program. The advisor must be a Fellow of the Graduate Faculty in CSE. The Bioinformatics Graduate Advisory Committee, in consultation with the graduate student, will recommend the appointment of the advisor for the Supervisory Committee to the Chair of the departmental Graduate Committee.

Qualifying Examination

Effective Fall 2018 the department has adopted the following new Qualifying Examination format

The Qualifying Exam shall be composed of 16 questions from 4 topic areas (4 questions per area), corresponding to core courses in Bioinformatics and Biosciences, and classified into two groups as follows:

Group A:

  • Theory of Computation (CSCE 428/828)
  • Algorithms (CSCE 423/823)

Group B:

  • Molecular Genetics (BIOS 420/820)
  • Introduction to Bioinformatics (CSCE 471/871)

The student must select and answer 8 questions, at least 3 of which must be chosen from Group A and at least 3 of which must be chosen from Group B with the additional condition that the student must select at least 1 question from each topic areas. The questions comprising an exam are meant to be questions that a student well-prepared in the central 400/800-level course in the area might find on a final exam in that course and be able to answer correctly, in approximately 20 minutes. The Examination period will be 3 hours. The Qualifying Examination will be offered in the second week of both the Fall and Spring semesters. Please, see Ph.D. in Computer Science for further details including information on comprehensive exam, dissertation, and final exam.

Supervisory Committee

The purpose of the Supervisory Committee is to assist the students in preparing a program to enable success in the Ph.D. program and in evaluating the research. The Supervisory committee for the PhD degree in Computer Science with the bioinformatics specialization follows the same guidelines as for the regular CSE PhD program. The Supervisory Committee can be formed only after the student has passed the Qualifying Examination. The Supervisory Committee for a student should consist of at least four Graduate Faculty Fellows including one from a life-sciences department. The advisor acts as the chair of the committee. The advisor generally helps the student in forming the supervisory committee. The student and the advisor must then submit the “Recommendation for Appointment of a Supervisory Committee for the Doctoral Degree” form (Appendix N) to the Bioinformatics Graduate Advisory Committee chair for his/her signature. After the approval by the Graduate Advisory Committee Chair, the form is forwarded to the Departmental Graduate Committee Chair for approval and then to the Dean of Graduate Studies for final approval of the Supervisory Committee.

A Reading Committee consisting of two members of the Supervisory Committee will be appointed by the Supervisory Committee. The chair of the committee must not be a member of the Reading Committee. The dissertation must be approved by the Reading Committee before the final oral examination can be scheduled.

Program of Study

A total of 90 credit hours are required, of which 24 to 30 may be for dissertation. The remainder must reflect course work that shows certain breadth as well as depth in the following three tracks: CSE Theory, Biosciences/Bioinformatics, and CSE Applications. For breadth, 3 courses in each track must be taken. The depth courses are determined by the student in consultation with his/her research advisor. At least 30 semester hours of course work must be in advanced courses open only to graduate students. Among 30 hours, at least 20 must be in Computer Science and 10 in Biosciences/Bioinformatics.

No fewer than 45 credit hours must be completed at the University of Nebraska-Lincoln. A minimum residency at Nebraska is also required (Consult the Graduate Catalog for details).

The program of study must be filed with the Graduate Studies office before the student has completed 45 credit hours. The supervisory committee should meet to review and approve the program of study and general area of research for the dissertation. A “Report of the Supervisory Committee on Program of Studies for the Doctoral Degree” is then forwarded to the Graduate Studies office. Any subsequent change in the program or in the dissertation topic must be approved by the supervisory committee and the action reported to the Graduate Studies. The program of study cannot be filed until the student has cleared all the deficiency courses listed in his/her Certificate of Admission.