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University of Louisville Bioinformatics

Doctor of Philosophy in Interdisciplinary Studies: Specialization in Bioinformatics

Program Information


Program Executive Committee Chair

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

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"[1], 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:

  1. Biomedical and Natural Sciences
  2. Computational Sciences
  3. 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.


[1] "Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources." National Center for Biotechnology Information. http://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html. Revised: March 29, 2004

Curriculum


Graduate Studies -- Ph.D.

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

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

DepartmentCourse NumberDescriptionCredits
BIOC
545*,+
Biochemistry I
3
BIOC
630*
Responsible Conduct of Research:
Survival Skills and Research Ethics
1
MBIO
667*
Graduate Cell Biology
3
PSYCH
571/609#
Computational Cognitive Science I
3
CECS
660*
Introduction to Bioinformatics
3
PHBI
750*
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.

Elective Courses in Mathematics and Statistics

DepartmentCourse NumberDescriptionCredits
MATH
505
Introduction to Partial Differential Equations
3
MATH
507
Fourier Series
3
MATH
561#
Probability
3
PHYS
565
Computational Physics
3
MATH
566
Nonparametric Statistical Methods
3
PHYS
625
Statistical Mechanics
3
PHST
630
Applied Statistical Models
3
MATH
636
Mathematical Modeling II
3
MATH
660
Probability Theory
3
PHST
661#
Probability
3
PHST
662#
Mathematical Statistics
3
MATH
562/662#
Advanced Mathematical Statistics
3
MATH
665
Advanced Linear Statistical Models
3
MATH
667*
Methods of Classification
3
MATH
670
Introduction to Stochastic Calculus
3
MATH
681
Combinatorics and Graph Theory I
3
MATH
682
Combinatorics and Graph Theory II
3
PHST
682
Multivariate Statistical Analysis
3
PHST
691
Bayesian Inference and Decision
3
PHST
710
Advanced Statistical Computing
3
PHST
711
Advanced Statistical Computing II
3
PHST
724
Advanced Clinical Trials
3
PHST
725
Design of Experiments
3
PHBI
751
High-throughput Data Analysis
3
PHBI
752
Statistical Genetics
3
PHST
762
Advanced Statistical Inference
3
PHST
780
Advanced Nonparametric Statistics
3
PHST
781
Advanced Linear Models
3
PHST
782
Generalized Linear Models
3

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

Elective Courses in Biomedical and Natural Sciences

Department
Course Number
Description
Credits
BIOL
542
Gene Structure and Function
3
BIOL
569
Evolution
3
BIOC
680
Biomolecular Interactions
3
BIOC
611
Biochemical and Molecular Methods
4
ASNB
614
Molecular Neuroscience
4
BIOC
641
Advanced Eukaryotic Genetics
3
BIOC
647#
Advanced Biochemistry II
4
CHEM
647
Advanced Biochemistry II
4
CHEM
648
Systems Biochemistry Principles and Practices
3
CHEM
652
Practical Approaches to Metabolomics
3
BIOC
661
Molecular Mechanisms of Toxicology
3
BIOC
668
Molecular Biology
3
BIOC
670
Protein Structure and Function
4
CHEM
684
Biophysical Chemistry
3

#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.

Elective Courses in Computational Sciences

Department
Course Number
Description
Credits
CECS
535
Introduction to Databases
3
CECS
546
Knowledge Engineering and Expert Systems
3
CECS
619
Design and Analysis of Computer Algorithms
3
CECS
622
Simulation and Modeling of Discrete Engineering Systems
3
CECS
624
Advanced Simulation
3
CECS
627
Digital Image Processing
3
CECS
628
Computer Graphics
3
CECS
629
Distributed System Design
3
CECS
630
Advanced Databases and Data Warehousing
3
CECS
632
Data Mining
3
CECS
641
Introduction to Medical Imaging
3
CECS
643
Introduction to Biomedical Computing
3
CECS
645
Advanced Artificial Intelligence
3
CECS
646
Intelligent Systems
3

Departmental Faculty


Departments

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

Faculty

Eric C. Rouchka, Executive Committee Chair
D.Sc., Washington University in St. Louis
Associate Professor, Computer Engineering and Computer Science

Theodore S. Kalbfleisch, Executive Committee Vice-Chair
Ph.D., Boston University
Assistant Professor, Biochemistry and Molecular Biology

Guy Brock
Ph.D., University of New Mexico
Assistant Professor, Bioinformatics and Biostatistics

Nigel G.F. Cooper
Ph.D., University of Tennessee Health Sciences Center
Professor, Anatomical Sciences and Neurobiology

Somnath Datta
Ph.D., Michigan State University
Professor, Bioinformatics and Biostatistics

Susmita Datta
Ph.D., University of Georgia
Professor, Bioinformatics and Biostatistics

Ryan Gill
Ph.D., The University of Texas at Dallas
Associate Professor, Mathematics

Gary Hoyle
Ph.D., Duke University
Professor, Environmental and Occupational Health Sciences

Richard Kerber
Ph.D., Northwestern University
Associate Professor, Epidemiology and Population Health

Jiaxu Li
Ph.D., Arizona State University
Assistant Professor, Mathematics

Rachel Neal
Ph.D., University of Missouri-Rolla
Assistant Professor, Environmental and Occupational Health Sciences

Liz O'Brien
Ph.D., Northwestern University
Assistant Professor, Epidemiology and Population Health

John Pani
Ph.D., University of Illinois
Professor, Psychological and Brain Sciences

Michael Perlin
Ph.D., University of Chicago
Professor, Biology

Jeffrey C. Petruska
Ph.D., University of Florida
Assistant Professor, Anatomical Sciences and Neurobiology

Shesh Rai
Ph.D., University of Waterloo
Professor, Bioinformatics and Biostatistics

Patrick Shafto
Ph.D., Northeastern University
Assistant Professor, Psychological and Brain Science

David Schultz
Ph.D., Pennsylvania State University
Associate Professor, Biology

Xiang Zhang
Ph.D., Purdue University
Associate Professor, Chemistry

Executive Committee Members

Eric Rouchka, D.Sc.
Executive Committee Chair (8/15/2011-6/30/2014)
Speed School of Engineering Representative (8/15/2011-6/30/2016)

Ted Kalbfleisch, Ph.D.
Executive Commmittee Vice-Chair (8/15/2011-6/30/2014)
School Of Medicine Representative (8/15/2011-6/30/2016)

Nigel Cooper, Ph.D.
School of Medicine Representative (8/15/2011-6/30/2015)

Susmita Datta, Ph.D.
School of Public Health Representative (8/15/2011-6/30/2014)

Rachel Neal, Ph.D.
School of Public Health Representative (8/15/2011-6/30/2015)

David Schultz, Ph.D.
College of Arts and Sciences Representative (8/15/2011-6/30/2015)

VACANT
College of Arts and Sciences Representative (8/15/2011-6/30/2014)

Apply Now


Ph.D. students are encouraged to apply for the program through the School of Interdisciplinary and Graduate Studies.

Application information can be found at: http://graduate.louisville.edu/apply

For more information about the Ph.D. program, contact Eric Rouchka


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