Biomedical Informatics-PhD

School of Interdisciplinary Informatics, College of Information Science & Technology

 

 

Vision Statement

The Doctor of Philosophy in Biomedical Informatics (BMI) degree is designed to prepare the next generation of biomedical informatics researchers who are uniquely positioned to advance research and practice in contemporary information and knowledge management that impact biomedical, clinical and translational research, healthcare services, healthcare practice, public health care, and healthcare delivery in general.  Graduates will be able to use their preparation to investigate and apply information and computer technologies to solve problems in the biomedical domain.

 

The mission of the Ph.D. program is to prepare students with the following abilities:

  • Understand the theory and application of biomedical informatics focused around the core areas of computer science, medicine, biology, and healthcare
  • Knowledge of the analysis, design, development, and implementation of current and future biomedical informatics systems & technologies
  • Competence in conducting and managing high quality, basic and applied research in the BMI domain
  • Solid grounding in the fundamentals of academic teaching
  • Strong foundation in multidisciplinary and emergent areas in biomedical informatics

 

 

Program Contact Information:

 

Dr. Dhundy (Kiran) Bastola, Graduate Program Committee Chair

College of Information Science & Technology, PKI 173A

402-554-4899 dkbastola@unomaha.edu

 

 

Ms. Carla Frakes, Advisor

College of Information Science & Technology, 176C

402-554-2073

cfrakes@unomaha.edu

 

Program website:

http://Si2.ist.unomaha.edu

 

Application Deadlines:

  • Fall: March 1
  • Spring: October 1
  • Summer: April 1

Application Requirements:

  • Online Application
  • One official copy of transcripts for ALL institutions previously attended
  • Application Fee
  • If English is not the language of nurture, official test scores from the TOEFL,   IELTS, or PTE exam are required
    • 500 on the written TOEFL
    • 173 on the computer-based TOEFL
    • 61 on the internet-based TOEFL
    • 5.5 on the IELTS
    • 44 on the PTE
  • Minimum GPA of at least 3.0 in undergraduate courses related to proposed major

 

 

Program-Specific Requirements:

  • For applicants who are required to take the TOEFL, a score of at least 577 (paper-based), 90 (iBT), or 7.0 IELTS is required. 
  • Graduate Record Exam (GRE) score of 310 out of 336, or a GMAT score above the 80th percentile.
  • Three (3) letters of recommendation from references who are able to give an in-depth evaluation of your strengths and weaknesses with respect to academic work, and who are competent to judge your probablilty of success in graduate school.
  • Statement of Purpose (not to exceed two pages) that address the following questions:
    • What you hope to accomplish with a Ph.D. in Biomedical Informatics?
    • Why you are applying to this specific program?
    • What background or qualifications do you have that you believe are essential to success in this program?
    • What general area or topics do you hope to study?
    • What you expect to be doing five to ten years after completion of the Ph.D. program?
  • Writing Sample
    • Evidence of graduate potential in the form of academic papers, publications, thesis or project reports done in an academic or industrial setting.
  • Resume
    • Submit a detailed resume indicating your work experience and background.

Applicants must follow the formal procedures established for admission to the graduate program at the appropriate NU campus.  Applicants must have:

  • successfully completed a baccalaureate degree from an accredited institution: preference wil be given to student's with a master's or doctoral degree from a related field
  • demonstrate superior performance in mathematics, including calculus, discrete mathematics and statistics, and a sequence of courses in the theory and practice of one or more information technology areas
  • documented test aptitude, interest and commitment to scholarly activities and research
  • proficiency in English, sufficient to engage in advanced studies

Evaluation for admission will be based on a portfolio approach that will include the following:

  • class standing during the applicant's bacclaureate and amster level studies.
  • grade point average in the undergraduate degree that is equivalent to 3.0 or higher.
  • verbal, quantitative, and analytic scores on the aptitude tests of the Graduate Record Examination (GRE)
  • letters of recommendation
  • other evidence of graduate potential, such as a portfolio of quality of papers or publications, projects, etc., completed by the applicant either in an academic or industrial setting. 
  • A personal interview, if warranted and feasible.

International students may be assessed for English proficiency and asked to take courses in English as a second language.  All students will be encouraged to take courses to improve their technical writing and professional communciation skills. 

Biomedical Informatics-PhD Degree Requirements

The doctoral BMI program is typically requires 90 credit hours beyond a baccalaureate degree and consists of a common required foundation/core courses to include doctoral seminars and colloquia, a major field of study, and a minor field of study in a related discipline. 

The doctoral program is divided into four phases from a student's perspective: foundation/core coursework, major-field-of-study/research coursework, additional elective coursework in an associated field minor-field-of-study (as advised by the student's supervisory committee), and doctoral research and dissertation. 

 

 

Foundation Requirements-bioinformatics track

Applicants should have background in programming languages, data structures & algorithms, statistics, math or experimental methods (any engineering, computer science related degree). Students with degrees in other disciplines will usually have to take foundation courses. Occasionally, a student's work experience may be sufficient to waive one or more foundation courses.

CIST 1400Introduction to Computer Programming

3 credits

CIST 2500Introduction to Applied Statistics for IS&T.

3 credits

CSCI 1620Introduction to Computer Science II

3 credits

CSCI 8325Data Structures

3 credits

ISQA 8040An Overview of Systems Development

3 credits

Total Credit Hours:15

Foundation Requirements-health informatics track

Applicants should have background in anatomy, physiology, cell biology or equivalent (any health science degree). Students with degrees in other disciplines will usually have to take foundation courses. Occasionally, a student's work experience may be sufficient to waive one or more foundation courses.

BIOL 2140Genetics

4 credits

BIOL 2740Human Physiology and Anatomy I

4 credits

BIOL 2840Human Physiology and Anatomy II

4 credits

BIOL 3020Molecular Biology of the Cell

3 credits

BMI 8005Medical Science for Non-Medical Professionals

3

CIST 2500Introduction to Applied Statistics for IS&T.

3 credits

Total Credit Hours:21

Core Courses-24 hours

Fulfilled from the master's degree program at UNO or elsewhere;

 

BMI 8100Introduction to Biomedical Informatics

3 credits

or a GPC approved equivalent is required

Research Foundations-Seminars-Tools-18 hours

CIST 9080Research Directions in IT

3 credits

ISQA 8156Advanced Statistical Methods for IS&T

3 credits

ISQA 8160Applied Distribution Free Statistics

3 credits

ISQA 8340Applied Regression Analysis

3 credits

ISQA 9010Foundations of Information Systems Research

3 credits

ISQA 9120Applied Experimental Design and Analysis

3 credits

ISQA 9130Applied Multivariate Analysis

3 credits

 

Track Option-18 hours from either the Bioinformatics or Health Informatics Track

At least 3 courses (9 credits) must be in 9000-level BMI courses. The remaining courses should include at least one 8000-level graduate only course. The supervisory committee should determine the remaining 6 credits and allow at most only 6 hours of cross-listed 8xx6 courses.

Bioinformatics Track-18 hours

BMI 8866/BIOI 4860/BIOI 8866Bioinformatics Algorithms

3 credits

BMI 8896Genetic Sequence Analysis

3 credits

9050Advanced Algorithmic Graph Theory

-3

BMI 9200Advances in Biomedical Technology

-3

BMI 9900Advanced Research in Biomedical Informatics

-3

CSCI 8156/MATH 8156Graph Theory & Applications

3 credits

CSCI 8456Introduction to Artificial Intelligence

3 credits

CSCI 8876Database Search and Pattern Discovery in Bioinformatics

3 credits

BMI 8080Seminar in Biomedical Informatics

1 - 3 credits

BMI 9980Independent Research in Biomedical Informatics

-3

CIST 9900Special Topics in Information Technology

1 - 3 credits

ISQA 8410Database Management

3 credits

ISQA 8700Data Warehousing: Theory and Practice

3 credits

ISQA 9020Technical & Process Issues in Information Systems Research

3 credits

ISQA 9030Behavioral & Organizational Issues in Information Systems

3 credits

Health Informatics Track

BMI 9300Public Health Genomics

-3

ISQA 8060Research in MIS

3 credits

ISQA 8106Information Systems Architecture and Organization

3 credits

ISQA 8196Process Reengineering with Information Technology

3 credits

ISQA 8220Advanced Systems Analysis and Design

3 credits

ISQA 8400Clinical Systems Architecture and Function

3 credits

ISQA 8500Readings in Clinical Informatics

3 credits

ISQA 8736Decision Support Systems

3 credits

ISQA 8810Information Technology Project Fundamentals

3 credits

BMI 8080Seminar in Biomedical Informatics

1 - 3 credits

BMI 9980Independent Research in Biomedical Informatics

-3

CIST 9900Special Topics in Information Technology

1 - 3 credits

ISQA 8700Data Warehousing: Theory and Practice

3 credits

ISQA 9020Technical & Process Issues in Information Systems Research

3 credits

ISQA 9030Behavioral & Organizational Issues in Information Systems

3 credits

Cognate Field-9 hours

Graduate courses (8000 or higher) in the areas of Biology, ISQA, Information Assurance, Neuroscience, Public Health, Computer Science, and Pathology are determined with faculty advisement. 

Colloquia-3 hours

CIST 9040Colloquium on IT Research

1 credit

CIST 9050Colloquium on IT Teaching

1 credit

CIST 9060Colloquium on IT Profession and Ethics

1 credit

Exit Requirement

Comprehensive Examination

BMI 9990Dissertation

 

Doctoral Program Supervisory Committee  

For each doctoral student, the Dean of Graduate Studies will appoint a supervisory committee (also called the formal dissertation committee).  The supervisory committee shall be formally established after completing at least 18 credit hours of course work or two years (whichever comes first) in the doctoral program. This committee will have responsibility for planning and supervision of the student's doctoral program in coordination with the BMI Graduate Program Committee, including the development of the comprehensive exam, defense of the doctoral dissertation proposal, the approval of the completed dissertation, and the final oral examination. At least one member on the committee shall be from another discipline. The student’s dissertation advisor will nominate the individual to serve on the supervisory committee in consultation with the student.  The responsibilities, procedures, and actions of the supervisory committee are regulated by the rules and bylaws of the Graduate College as established in the UNO Graduate Bulletins. 

Within three weeks of its appointment, the supervisory committee will meet to designate and subsequently file in the Office of Graduate Studies a complete program of studies conforming to the requirements for the degree.  At least half of the total hours for the degree must be completed at the University of Nebraska after the filing of the program of studies.  Any subsequent change in the program or in the dissertation topic must be approved by the supervisory committee and recommended to the Dean of Graduate Studies. 

 

Academic Requirements

Up to 36 credit hours of the coursework in the preparatory and advanced studies of the doctoral program may be accepted if from an accredited institution. Academic requirements for the doctorate degree include:

  • Doctoral research seminars in one or more of the thematic areas of the program.
  • Advanced courses (subject to dissertation advisor and Graduate Committee approvals) related to the student’s expected field of study/research area. 
  • Courses in an associated field of study.
  • Courses or colloquia relating to teaching, ethics and research.
  • Participation in relevant graduate research seminars each semester.
  • Successful passing of qualifying (comprehensive) examination.
  • Presentation and defense of a dissertation research proposal on a topic in the approved major field of study/research area.
  • Submission of the final dissertation manuscript in appropriate format after a successful dissertation defense.

Requirements for Admission to Candidacy

Students will follow the general candidacy requirements in the UNO Graduate College.  Admission to the graduate program does not necessarily imply admission to candidacy for a higher degree.

To be admitted to candidacy for the doctorate degree, a doctoral student must:

  • Pass the written qualifying (comprehensive) examination.
  • Successfully complete all coursework with satisfactory grades.
  • Receive the approval of his/her dissertation proposal before the supervisory committee (oral examination). 

After the student has met these requirements, the supervisory committee will recommend to the Office of Graduate Studies his/her admission to candidacy for the doctorate degree, the recommendation will note the dates of completing the comprehensive exam. Such a recommendation must be filed at least seven months prior to the final oral examination for defending his/her dissertation in the presence of his/her supervisory committee. A student is formally recognized as a candidate as of the date of completing the comprehensive exam. Following admission to candidacy, the student must register during each academic year semester until he/she receives the doctorate degree. Students not in residence may register for a minimum of one semester hour credit in dissertation. Failure to register during each academic year semester will result in termination of candidacy.  The term of candidacy is limited to three years.

 

Dissertation and Final Examination

The dissertation should treat a subject in-depth from the candidate’s major field of study/research area and as approved by his/her supervisory committee. The student’s dissertation should show his/her technical mastery of the field and create novel material by advancing or modifying knowledge, creating new material, finding new results, drawing new conclusions, or interpret old material in a new light. 

If the dissertation proposal is approved, the student may conduct the dissertation research under the guidance of the dissertation advisor. The student is advised to consult informally and continuously with his/her supervisory committee until the committee accepts the dissertation. After the dissertation research is completed, the dissertation document and/or product must be presented to all the members of the supervisory committee in time to permit review and approval, and the manuscripts must be turned in at least thirty days in advance of the final oral examination over the dissertation. The dissertation will be defended at an open meeting of the faculty, conducted by the student's supervisory committee.

Grade Requirements

In addition to maintaining at least a 3.0 GPA for all course work, all doctoral students must obtain a grade of B or better in any of the required courses. Any student failing the grade requirements will be denied from taking the comprehensive examination and/or dismissed from the program.

Comprehensive Examination & Admission to Candidacy

The comprehensive examination can be taken after the student has completed all course work according to his or her plan of study and formed a supervisory committee.  The comprehensive exam consists of a written part and an oral part. The written part of the exam is divided into two sub-parts that will be scheduled over two consecutive days.

 

  • Written Part I Examination Format and Procedure

Before taking the written part of the exam, students will provide a selection of 4 - 5 topics from the areas covered in the CIST 9080 Research Directions in IT course. The selected topics should not have significant overlap within the major or minor area of study given in the student’s plan of study. The topics should be selected so that they express a breadth in the areas in the core disciplines of the program in computer science, information systems and integrated informatics. The doctoral program committee will select two topics from the set of 4-5 topics and inform the student in advance of the exam.   The material related to the topic for preparing for the comprehensive exam (e.g., paper reading list) will already have been provided to the student when the student took the CIST 9080 course. Questions on the selected topics will be set by the faculty presenter(s) of the topic in CIST 9080. The answer s will also be evaluated by the topic’s presenter(s), either individually or by a group of faculty members selected by the topic’s presenter(s).

 

  • Written Part II Examination Format and Procedure

The questions for the second part of the written comprehensive exam evaluate the student’s understanding of his or her major field of study. The questions are set and evaluated by members of the student’s supervisory committee.

 

  • Oral Examination Procedure

The oral component of the comprehensive exam is the defense of the student’s dissertation proposal. The oral portion cannot be taken without successfully passing both written parts of the exam.  A Ph.D. student advances to candidacy after successfully passing all parts of the comprehensive examination.

 

Dissertation

  • Dissertation Credits

The dissertation of a Ph.D. candidate is supervised by the chair or co-chairs of the student’s supervisory committee in consultation with other members of the supervisory committee. While doing his or her dissertation, the candidate should take hours for the course BMI 9990 Dissertation in BMI. A minimum of 18 hours of this course is required for graduation. Dissertation course credits should be taken only after the doctoral student advances to candidacy. Under special circumstances, doctoral students can take dissertation credits during the semester they apply for candidacy, but the dissertation credits taken under these circumstances should be kept to a minimum. Dissertation credits cannot be taken if the student does not pass the written part of the comprehensive exam.

 

IMPORTANT NOTE: The Graduate Catalog mentions that a minimum of seven months must elapse between the date of the doctoral student’s advancement to candidacy and the date of dissertation defense. 

  • Scheduling Dissertation Defense

When the supervisory committee deems it appropriate for the Ph.D. candidate to defend their dissertation, the Ph.D. candidate should prepare a dissertation thesis and submit it to the supervisory committee members. While submitting the dissertation thesis to the supervisory committee, the candidate should also submit a final oral exam form to the Office of Graduate Studies. The final oral exam form requires the signatures of the supervisory committee members and the doctoral program committee chair, and should be submitted at least four weeks before the desired date of the dissertation defense. Supervisory committee members should sign this form after receiving the final draft of the dissertation.

 

IMPORTANT NOTE: Before scheduling his or her dissertation defense, the student should refer to the Office of Graduate Studies website and/or the current Graduate Catalog for the graduation checklist, thesis filing deadlines and commencement dates for the semester in which they plan to graduate.  

 

BMI-PHD Exit Requirements

  • Completing Graduation Requirements

After successfully defending his or her dissertation, the student should complete a Report on Completion of Degree form and contact the Office of Graduate Studies to apply for graduation.

 

  • Teaching Requirements

All Ph.D. students are required to teach at least ONE course/lab while studying in the program.  Students who are assigned to teach a course will be designated as the instructor for a section of the course, and will be trained and evaluated by a mentor before teaching the course.

 

Method of Allocation:

The steps for a student being allocated as a teaching assistant for a course are:

  • The student will inform the DPC chair about the plan to teach a course along with a list of preferred courses.
  • If the student is teaching a course for the first time, this information should be sent TWO semesters before the semester in which the planned course is intended to be offered.
  • If the student has taught the course in the past, this information should be sent ONE semester before the semester in which the planned course is intended to be offered.
  • The DPC chair will consult with the unit chairs responsible for course scheduling to determine the need of instructors for different courses to make a suitable allocation.
  • The student will undergo mentorship under the faculty member responsible for teaching the course by attending the lectures and doing additional duties as determined by the mentor, ONE semester BEFORE the semester in which the planned course will be offered.
  • The student will be assigned as an instructor for the planned course, if, after undergoing the mentorship, the mentor determines the student is suitable for teaching the course.

Timing of Teaching Activities: 

Teaching a course is an intense activity and can usually consume considerable time and effort. To avoid interference with his or her research work, a student should plan to teach a course, especially if teaching it for the first time, toward the beginning or mid-point of their doctoral studies. Students should plan to teach a course usually in the second or third year of studies.

 

  • Residency Requirements

All full-time doctoral students must complete 24 hours within 18 months in order to meet the residency requirement of the University. Part-time students must complete 18 hours during the same period. The residency requirement ensures that progress toward the degree occurs within a reasonably compact time frame, enabling the doctoral student to integrate his or her course work with the dissertation.

 

  • Progress Report

At the end of each semester, every doctoral student (full-time or part-time) must complete the Progress Report form and submit it to the Director of the Doctoral Committee.  An electronic copy of this form is available at http://phd.ist.unomaha.edu/index.php?p=currentforms

 

  • Satisfactory Progress

A minimum of three years of full-time graduate study is normally required to complete a doctoral program. The maximum time allowed by the Graduate School is eight years from the filing of the student’s program of study in the Office of Graduate Studies. Students not making satisfactory progress will be counseled out of the program.

 

  • Leave of Absence

Under extraordinary circumstances, e.g., medical problems, a student may request a leave of absence from the program for a period of no more than one year. The request must be submitted to and approved by the student’s supervisory committee and/or Doctoral Program Committee. The request should include necessary modifications to the Plan of Study as a result of the leave. The leave of absence stops the clock for the total time required for the program and the time required to meet the residency requirement. If a student withdraws in mid-semester and is approved for a leave of absence, the clock starts at the beginning of the following semester. A student does not have to have met the residency requirement in order to apply for a leave of absence. If a student does not return to the program within the one year approved for the leave of absence, then the student must submit an application to re-apply to the program. Re-admission to the program is not guaranteed at that point. Please refer to the Graduate Catalog for the complete policy on a leave of absence.