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Program Requirements

GRADUATE PROGRAM REQUIREMENTS AND CURRICULUM

A. Candidates for the Doctor of Philosophy degree are required to complete a minimum of 72 credits. Specific course requirements are ENGR 452, BIOS 411, two additional core courses from an approved list of courses, twelve credits of adviser-approved technical electives at the 300-level or higher, and six credits of dissertation research. An additional 48 credits of electives and/or dissertation research are required to reach the required 72 credits. Students who have earned a previous master’s degree are required to complete a minimum of 48 credits, which include the specific course requirements listed above, and an additional 24 credits of electives and/or dissertation research.

All Ph.D. students undergo a first year evaluation, and must pass a qualification exam (taken after the completion of the core class requirements), a thesis research proposal, a final written dissertation, and an oral defense of the dissertation.

B. Candidates for the thesis-based Master of Science degree are required to complete a minimum of 30 credits. Specific course requirements are ENGR 452, BioS 411, two additional core courses from an approved list of courses, twelve credits of adviser-approved technical electives at the 300-level or higher, and six credits of thesis research, culminating in a written thesis. An oral defense of thesis research is dependent upon the requirements of the student’s adviser.

C. Candidates for the non-thesis Master of Science degree program are required to complete a minimum of 30 credits. Specific course requirements are ENGR 452, BioS 411, two additional core courses from an approved list of courses, and eighteen (18) credits of adviser-approved technical electives at the 300-level or higher.

APPROVED CORE CLASS OPTIONS

BIOE 408 -- Bioinformatics: Issues and Algorithms
BIOE 420 -- Biomedical Image Computing and Modeling
BIOE 421 -- Biomolecular and Cellular Mechanics
BIOE 424 -- Organic Biomaterials
BIOE 425 -- Inorganic Biomaterials
BIOE 426 -- Biomimetic and Bio-enabled Materials
BIOE 439 -- Neuronal Modeling and Computation
BIOE 441 -- Biotechnology 1
BIOE 442 -- Biotechnology 2
BIOE 449 -- Metabolic Engineering
BIOE 496 -- Introduction to Biophotonics/Optics
BIOE 498 -- Neural Engineering

GRADUATE CORE COURSE DESCRIPTIONS

BIOE 408/CSE 408 -- Bioinformatics: Issues and Algorithms
Computational problems and their associated algorithms arising from the creation, analysis, and management of bioinformatics data. Genetic sequence comparison and alignment, physical mapping, genome sequencing and assembly, clustering of DNA microarray results in gene expression studies, computation of genomic rearrangements and evolutionary trees. This course, a version of 308 for graduate students requires advanced assignments. Credit will not be given for both CSE 308 and CSE 408. No prior background in biology is assumed. Prerequisites: CSE 17 or permission of the instructor. | BACK TO COURSE LIST

BIOE 420 -- Biomedical Image Computing and Modeling
This course aims to give students the background on various biomedical imaging modalities and the knowledge needed to understand, develop, and use algorithms and software on biomedical image data and to extract useful quantitative information. Topics on biomedical imaging are organized into three parts: Part I. Imaging modalities (physics, signals and systems) such as X-ray, CT, MRI, Ultrasound, Nuclear Medicine, and Microscopy; Part II: Image computing, and modeling of objects and processes in images; Part III: PACS (Picture Archiving and Communication System) and imaging informatics systems in biomedicine. | BACK TO COURSE LIST

BIOE 421 -- Biomolecular and Cellular Mechanics
Mechanics and physics of the components of the cell, ranging in length scale from fundamental biomolecules to the entire cell. The course covers entropic elasticity of biopolymers, mechanics of 2D and 3D protein networks, shapes of cells driven by bending of membranes, electrostatic forces, and the mechanics of the entire cell.  Students should be familiar with basic solid and fluid mechanics, statistics, differential equations, and programming in an environment such as Matlab or Mathematica. | BACK TO COURSE LIST

BIOE 424 -- Organic Biomaterials
This course will provide an overview of the field of Biomaterials. Upon completing the class, all student should be familiar with the basic concepts in biomaterials, major types of organic biomaterials and their properties, biological response to biomaterials and applications of biomaterials in medicine and biology. The graduate level students are expected to become familiar with state-of-the-art literature in the biomaterials area through additional reading and paper critique assignment. | BACK TO COURSE LIST

BIOE 425 -- Inorganic Biomaterials
Fabrication methods for biomedical implants and devices. Selection of metals and ceramics with specific bulk and surface physical as well as chemical properties. Role of materials chemistry and microstructure. Biocompatibility. Case studies (dental and orthopedic mplants, stents, nanoporous ceramic filters for kidney dialysis). Graduate version of BIOE 325 requiring additional assignments. Credit is not given for both BIOE 325 (MAT 325) and BIOE 425 (MAT 425). Prerequisites: MAT 033 | BACK TO COURSE LIST

BIOE 426 -- Biomimetic and Bio-enabled Materials
The structure, function, properties and use of biopolymers, biocomposites, and biominerals. Chemical structure and macromolecular architecture of these materials, including collagen, tissue, silk, wool, spider’s thread, shell, etc. The marriage of structure and function and how this marriage can be manipulated in the development of "intelligent" materials (materials which can adapt to their environment or have the ability to alter their properties as required). Biomimetic materials design, including colloids, interfaces, macromolecules, and applications of such materials. Environmental and ethical considerations, such as degradation products when using biomimetic materials. | BACK TO COURSE LIST

BIOE 439 -- Neuronal Modeling and Computation
The course is aimed at understanding computational aspects of information processing within the nervous system by focusing on single neuron modeling. The course will emphasize single neurons and how their biological properties relate to neuronal coding, i.e., how information is actually represented in the brain at the level of action potentials. Topics include biophysics of single neurons, signal detection and signal reconstruction, information theory, population coding and temporal coding. Students are required to hand in homework assignments, discuss at least two papers in class, and participate in the class discussions. Graduate students registering for the 400 level class will be expected to complete an independent term project. | BACK TO COURSE LIST

BIOE 441 -- Biotechnology I (J. Hsu)
Applications of material and energy balances; heat, mass, and momentum transfer; enzyme and microbial kinetics; and mathematical modeling to the engineering design and scaleup of bioreactor systems. Prerequisites: BioS 41, ChE31, and CHM 31; the consent of the instructor. In order to receive 400-level credits, the student must do an additional, more advanced term project, as defined by the instructor at the beginning of the course. Closed to students who have taken CHE 441. | BACK TO COURSE LIST

BIOE 442/CHE 442 -- Biotechnology II (J. Hsu)
Engineering design and analysis of the unit operations used in the recovery and purification of products manufactured by the biotechnology industries. Requirements for product finishing and waste handling will be addressed. Prerequisite: ChE 31 and CHM 31; and the consent of the instructor. In order to receive 400-level credits, the student must do an additional, more advanced term project, as defined by the instructor at the beginning of the course. Closed to students who have taken CHE 442. | BACK TO COURSE LIST

BIOE 449 -- Metabolic Engineering
This course will focus on cellular metabolism and metabolic pathways from a quantitative perspective. Topics include metabolic flux in reaction networks, enzyme kinetics, metabolic control analysis, kinetic modeling, and the metabolic basis for disease. Prerequisites: Math 205 and Math 231, or equivalent. | BACK TO COURSE LIST

BIOE 496 -- Introduction to Biophotonics/Optics
This course covers the optical principles, techniques, and instruments used in biomedical research and clinical medicine. It includes in-depth coverage of fundamental concepts of optical imaging and spectroscopy systems, and details of light-tissue interaction. The course describes commercial devices and instruments as well as novel optical imaging technologies under development. This course is intended for graduate students and senior undergraduate students in Electrical Engineering, Physics or Engineering with a suitable background in optics and imaging. | BACK TO COURSE LIST

BIOE 498 -- Neural Engineering
This course focuses on neural system interfaces for scientific and health applications.  Topics include the basic properties of neurons, signal detection and stimulation, instrumentation and microfabricated electrode arrays.  In addition, fundamentals of peripheral and central neural signals and EEG, and applications such as neural prostheses and implants, brain-computer interfaces and deep brain stimulation will be examined.  Prerequisites: ECE 81 or consent of instructor. | BACK TO COURSE LIST