Doctor of Philosophy in Interdisciplinary Studies: Specialization in Bioinformatics

Major: IS_PHDINFO
Degree Awarded: Ph.D.
Unit: GI
Program Webpage: http://bioinformatics.louisville.edu/phd/

Program Information

Program Executive Committee Chair

Dr. Eric C. Rouchka, (502) 852-3060, Email Dr. Rouchka

General Information

The Interdisciplinary Ph.D. Program in Bioinformatics (the Bioinformatics Program) trains students in bioinformatics for careers in research, education, and industry.

Defined as “the field of science in which biology, computer science, and information technology merge to form a single discipline, bioinformatics is a broad and diverse domain, ranging from management of biological research databases to computational approaches to biomedical modeling and data analysis.

The Bioinformatics Program focuses on those aspects of bioinformatics that reflect the research interests and experience of the Program’s faculty.  These include basic research in biostatistical methodology, computer science and mathematical modeling with applications to biochemistry, cell biology and molecular biology.  The following areas have been identified and named by the Bioinformatics Program faculty to represent the focus application areas of the Program:

  • Biomedical and Natural Sciences
  • Computational Sciences
  • Mathematics and Statistics

Students in the Bioinformatics Program specialize in one of the three focus application areas and graduate with cutting-edge expertise in this area and working knowledge in the other two focus application areas.

Curriculum

Graduate Studies -- Ph.D.

To earn the Doctor of Philosophy in Interdisciplinary Studies: Concentration in Bioinformatics, a student is required to successfully complete the following:

  • Core coursework in the focus application areas

  • Required coursework in the student’s area of specialization

  • Elective courses in the student’s area of specialization

  • Qualifying examination

  • Dissertation

  • Presentation and defense of dissertation

Good standing requires that the student maintain a minimum 3.0 grade point average.Upon successful completion of the written and oral portions of the qualifying examination, the examination committee will recommend acceptance into Ph.D. candidacy. Successful completion of the dissertation and its presentation and defense is established by the approval of the student’s dissertation committee and the approval of the chair of the sponsoring department and the program chair.

Programs of Study

Course requirements for the Interdisciplinary Ph.D. Degree Program in Bioinformatics consist of 16 core credit hours (that will be conditional based upon focus area) and 21 credit hours derived from a combination of required courses from a chosen focus area and electives from each of the three focus areas. Students with an appropriate background in the biomedical and natural sciences may petition to substitute a course in either the Computational Sciences or Mathematics and Statistics focus for the core course BIOC 545 Biochemistry I, and a corresponding course in either the Computational Sciences or Mathematics and Statistics for MBIO 667 Graduate Cell Biology, thus maintaining 16 core credit hours.   Following acceptance into a focus area, students will be required to complete three courses totaling at least nine hours from the declared focus area.  At least four additional elective courses (12 credit hours) will be selected from available elective courses, with the provision that two elective courses must be selected in each of the other two focus areas.  The Program of Study will be determined by the student and approved by both an advisor residing in a declared focus area department and the Executive Committee.  The following tables list the required courses for the core as well as the required and elective courses in each of the focus areas.  Students must accumulate at least nine credit hours of dissertation.

Core Course Work

Department
Description
Credits
BIOCBiochemistry I
3
BIOCResponsible Conduct of Research: Survival Skills and Research Ethics
1
MBIO667*
3
PSYCH
571/609#Computational Cognitive Science I
3
CECS660*Introduction to Bioinformatics
3
PHBI750*
Statistical Methods for Bioinformatics
3

*All courses are required. CHEM 645 may be substituted.Students may take either the BIOC 545/BIOC547 or CHEM 645/647 sequence but are not allowed to take the sequence BIOC 545/CHEM647 or CHEM 645/BIOC547. #Cross-listed as CECS 590-02.

Courses in Mathematics and Statistics

DepartmentCourseDescriptionCredits
MATH505Introduction to Partial Differential Equations3
MATH507Fourier Series3
MATH561#Probability3
PHYS565Computational Physics3
MATH566Nonparametric Statistical Methods3
PHYS625Statistical Mechanics3
PHST630Applied Statistical Models3
MATH636Mathematical Modeling II3
MATH
660Probability Theory3
PHST
661#Probability3
PHST662#Mathematical Statistics3

MATH

562/662#Advanced Mathematical Statistics3
MATH665Advanced Linear Statistical Models3
MATH667*Methods of Classification3
MATH670Introduction to Stochastic Calculus3
MATH681Combinatorics and Graph Theory I3
MATH682Combinatorics and Graph Theory II3
PHST682Multivariate Statistical Analysis3
PHST691Bayesian Inference and Decision3
PHST710Advanced Statistical Computing3
PHST711Advanced Statistical Computing II
3
PHST725Design of Experiments3
PHBI751High-throughput Data Analysis3
PHBI752Statistical Genetics3
PHST762Advanced Statistical Inference3
PHST780Advanced Nonparametric Statistics
3
PHST781Advanced Linear Models3
PHST782Generalized Linear Models
3

#Credit only for one: MATH 561/PHST 661; MATH 562/PHST 662

Courses in Biomedical and Natural Sciences

DepartmentCourseDescriptionCredits
BIOL542Gene Structure and Function3
BIOL569Evolution3
BIOC680Biomolecular Interactions3
BIOC611Biochemical and Molecular Methods4
ASNB614Molecular Neuroscience4
BIOC641Advanced Eukaryotic Genetics3
BIOC647#Advanced Biochemistry II4
CHEM647Advanced Biochemistry II4
CHEM648Systems Biochemistry Principles and Practices3
CHEM652Practical Approaches to Metabolomics3
BIOC661Molecular Mechanisms of Toxicology3
BIOC668Molecular Biology3
BIOC670Protein Structure and Function4
CHEM684Biophysical Chemistry3

#Credit only for one: CHEM 645/BIOC 645, CHEM 647/BIOC 647.Students may take either the BIOC 545/BIOC547 or CHEM 645/647 sequence but are not allowed to take the sequence BIOC 545/CHEM647 or CHEM 645/BIOC547.

Courses in Computational Sciences

DepartmentCourseDescriptionCredits
CECS535Introduction to Databases3
CECS546Knowledge Engineering and Expert Systems3
CECS619Design and Analysis of Computer Algorithms3
CECS622Simulation and Modeling of Discrete Engineering Systems3
CECS624Advanced Simulation3
CECS627Digital Image Processing3
CECS628Computer Graphics3
CECS629Distributed System Design3
CECS630Advanced Databases and Data Warehousing3
CECS632Data Mining3
CECS641Introduction to Medical Imaging3
CECS643Introduction to Biomedical Computing3
CECS645Advanced Artificial Intelligence3
CECS646Intelligent Systems3

Faculty

Participating Faculty for the Bioinformatics Program have primary appointments in various departments across the University, including:

  • College of Arts and Sciences: Departments of Biology, Chemistry, Mathematics, and Psychological and Brian Sciences
  • J.B. Speed School of Engineering: Department of Computer Engineering and Computer Science
  • School of Medicine: Departments of Anatomical Sciences and Neurobiology and Biochemistry and Molecular Biology
  • School of Public Health and Information Sciences: Departments of Bioinformatics and Biostatistics, Environmental Health and Occupational Health Sciences, and Epidemiology and Population Health
Nigel G.F. Cooper

Professor of Anatomical Sciences and Neurobiology

Ryan Gill

Associate Professor of Mathematics

Gary Hoyle

Professor of Environmental and Occupational Health Sciences

Theodore S. Kalbfleisch
Assistant Professor of Biochemistry and Molecular Biology

Executive Committee Vice-Chair

Richard Kerber

Associate Professor of Epidemiology and Population Health

Ashok Kumar

Professor of Anatomical Sciences and Neurobiology

Jiaxu Li

Assistant Professor of Mathematics

Rachel Neal

Assistant Professor of Environmental and Occupational Health Sciences

Liz O'Brien

Assistant Professor of Epidemiology and Population Health

John Pani

Professor of Psychological and Brain Sciences

Juw Won Park

Assistant Professor of Computer Engineering and Computer Science

Michael Perlin

Professor of Biology

Jeffrey C. Petruska

Assistant Professor of Anatomical Sciences and Neurobiology

Shesh Rai

Professor of Bioinformatics and Biostatistics

Eric C. Rouchka
Associate Professor of Computer Engineering and Computer Science

Executive Committee Chair

David Schultz

Associate Professor of Biology

Patrick Shafto

Assistant Professor of Psychological and Brain Science

Xiang Zhang

Associate Professor of Chemistry