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.

Examinations

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.

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

A graduate student working towards a Ph.D. must pass a Ph.D. Qualifying Exam. The purpose of the Qualifying Exam is to test the student's basic preparation in researc and in topic areas that are considered core to computer science and engineering. Refer to the Ph.D. Qualifying Examination Process documentRegistration Form, and Qualifying Exam Grading Rubric for more details. 

A student admitted to the Computer Science and Engineering Ph.D. program with an M.S. received at the university or elsewhere must fulfill his/her Qualifying Examination requirement no later than the third semester after admission. A student admitted to the Computer Science and Engineering Ph.D. program without an MS must fulfill his/her Qualifying Examination requirement no later than the fourth semester after admission. A student may take the exam no more than twice.

A student cannot form his/her Ph.D. Supervisory Committee before passing the Qualifying Examination and thus the Program of Studies for the Ph.D. can not be approved before the student has passed the Qualifying Examination. Also, it should be noted that according to Graduate College requirements, a student should not be beyond the half-way mark (that is 45 credit hours applicable towards the degree) when her/his program of studies is approved.

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 which must consist of the following: 

  • 51 to 63 hours of regular course work compliant with the Breath Requirements, of which at most 9 credit hours of the following independent study type courses: CSCE 896 (when taken as an independent study), CSCE 897, CSCE 898, or CSCE 996. At most, 6 credit hours of CSCE 899 (master's thesis) can be counted towards regular non-independent study course work. 
  • 3 to 9 hours must be Directed Doctoral Research (CSCE 991)
  • 18 to 36 hours must be Dissertation Credits (CSCE 999)
  • No fewer than 45 credit hours must be completed at the University of Nebraska. 

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 Graduate Studies. The program of study cannot be filed until the student has cleared all the deficiency courses listed in his or her Certificate of Admission.

For more details, refer to the Ph.D. Requirements document

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.

Directed Doctoral Research course: CSCE 991

At least 3 hours of research (up to 9 credit hours) with chosen supervisor on a topic directly related to the dissertation. This course provides a directed research experience with a faculty advisor as a gateway to doctoral dissertation research. 

Every PhD student should take this course and pass *before* they take CSCE 999 dissertation credits. For a passing grade the student must (a) submit a written report which will be evaluated and graded by the supervisor, and (b) pass the PhD Qualifying Examination. 

Note: This course is a pre-requisite for CSCE 999.  

Comprehensive Examination

After a student has reached a point in their studies where they have substantially defined their Ph.D. research topic and completed preliminary work toward that topic, it is important that they demonstrate their readiness to conduct that research, and the sufficiency of their background preparation in that area. The comprehensive examination is the mechanism for achieving this.

The comprehensive examination shall be conducted by the Ph.D. Supervisory Committee. The examination will be conducted after the student has completed at least 54 hours of course work and has spent time working on one or more specific research problems that are expected lead to their dissertation. The exam must be completed no later than 7 months prior to the student's Ph.D. defense.

The comprehensive examination shall consist of two parts: a written dissertation proposal followed by an oral presentation. The written proposal shall contain a statement of the student's thesis topic and motivation for the work, a summary of preliminary work completed (ideally, with reference to one or more papers published), and a description of proposed work remaining. It is essential that the proposal demonstrate the student's breadth of understanding of the field of knowledge of which their research area is a part by providing a thorough discussion of background and related work in the topic area of the dissertation that is sufficient to allow the committee to evaluate the novelty of the student's own proposed work. The written proposal shall be sent to the student's Supervisory Committee at least 2 weeks prior to the date of the oral presentation.

The oral presentation shall involve a formal presentation of the proposal by the student, of duration between 30 and 45 minutes. The oral presentation will be followed by a question-and-answer period. The questions may pertain to any aspect of the student's proposal, oral presentation, and planned research.

The Supervisory Committee will report its decision to the student and, in writing, report results to the Graduate Secretary and Graduate Committee (these results will then be reported to the Graduate College).

If a student fails the Comprehensive Examination, the Supervisory committee may decide to give the student a second chance, making particular recommendations for improvements, or they may recommend termination of the student's graduate status. A second exam may not be attempted earlier than the following academic term.

Failure to pass the Comprehensive Examination in will result in the student's dismissal from the Ph.D. program. The letter of dismissal will be issued by the Graduate Committee and Graduate Chair, following receipt of a recommendation and report from the Supervisory Committee. The student will have the usual right to appeal dismissal decisions to the Graduate College.

No more than two attempts to pass the Comprehensive Exam will be allowed.

Candidacy

Upon the successful completion of the Comprehensive Examination, the Supervisory Committee will normally recommend the student for admission to candidacy. The Committee, however, may require additional examinations. The student must file the Application for Admission to Candidacy form with the Office of Graduate Studies. The term for candidacy is three years and the student is expected to complete the dissertation during this period. Following admission to Candidacy the student must register for graduate classes during each academic year semester until he/she receives the Ph.D. degree.

Dissertation

All Ph.D. students must complete a dissertation under the supervision of a fellow of graduate faculty. It is expected that the work done makes original contribution to the field. It is expected that the work is of a quality that can be published in refereed journals, if it has not already been published. The student is required to write the dissertation in a standard style (Use the "Guidebook for Preparing your Thesis or Dissertation" available from the Office of Graduate Studies.) LaTeX templates are also available on the departmental computers.

Following a thorough review by the advisor, copies of the dissertation are given to the members of the Reading Committee (a subset of the Supervisory Committee). The student must give the committee at least two weeks for review. Upon approval of the Reading Committee a copy of the completed "Application for Final Oral Examination" form (Appendix Q) and a copy of the dissertation is submitted to the Office of Graduate Studies, at least three weeks prior to the final oral examination.

Final Oral Examination (Thesis Defense)

The final oral examination is required for all Ph.D. students. The oral examination will be scheduled for two hours and consist of the presentation and defense of the research. The presentation is open to the public and the student is required to give an abstract (electronic copy) to the office to be used for advertising. After the public presentation and a question-and-answer period, the remainder of the examination is conducted privately by the supervisory committee. The supervisory committee may require the student to make changes to the dissertation and/or conduct additional research and the advisor is generally responsible for making sure that the work is completed. The advisor decides on the grade of the Ph.D. Dissertation.

Final Dissertation

After appropriate changes have been made to the dissertation based on the comments of the committee, and the supervisory committee has approved the final dissertation, the student must upload an electronic version of the dissertation to ProQuest and UNL Digital Commons. The student is required to make a hard-bound copy of the thesis/report to the advisor, unless the advisor chooses not to require one. It is also customary to offer each member of the supervisory committee a copy of the final report. The student must also submit two unbound copies to the Library.