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Curriculum

Overview

The Biomedical Engineering (BME) Graduate Program has five core research areas: Biomedical and Molecular Imaging, Biomaterials, Mechanics, and Tissue Engineering, Computational Biology, Medical Physics, and Molecular and Translational Nanomedicine. Ph.D. students complete a flexible curriculum that typically includes track-specific engineering and life science courses as well as several advanced electives related to their research. In addition to coursework, the curriculum for first-year students includes three or four laboratory rotations and training in responsible conduct of research. Beginning in their second year, students also participate in a Works-in-Progress course in which they present and receive feedback on their dissertation research. The curriculum is further enhanced by numerous seminar series and journal clubs offered across the UTSW campus.

All doctoral students must pass three examinations. Exam I is the qualifying exam, usually given during the second year. It consists of a written examination, based on a broad problem in the area of the student’s research, and an oral examination in which the student critiques and defends his or her written response. Successful completion of the qualifying examination is required to advance to candidacy for the Ph.D. Exam II consists of a detailed written prospectus of the proposed dissertation research and an oral defense of this proposal. Exam III is the final defense of the completed dissertation.

A supervisory research committee is formed for each doctoral candidate after successful completion of Exam I. This committee reviews and evaluates the student’s progress and participates in the proposal and dissertation defenses.

Degree Plans

Course Descriptions

Courses from all of the core research areas within the BME PhD Program are listed below. Note that in addition to these courses, students often take elective courses from other Graduate Programs in the Division of Basic Science at UT Southwestern, as well as graduate level BME courses offered at UT Arlington and UT Dallas.

Biomechanics in Human Disease

3 credit hours
The objective is to provide bioengineering students with a quantitative understanding of the biomechanical properties of hard and soft human tissues in their physiological and pathological aspects and methods to measure and analyze these properties. The fundamental principles of solid mechanics are introduced and applied to selected human tissues. Normal tissue biomechanical characteristics are presented and contrasted with changes due to pathological conditions. Current corrective treatments are described by guest clinicians. Students are expected to provide critical reviews on current challenges and novel developments in selected topics.

Biomedical Image Processing

(Offered by UT DAllas)
3 credit hours
This course covers basic digital image processing techniques used for the analysis of images. Topics include spatial and frequency domain filtering, image restoration, morphological operators (e.g., erosion and dilation) and their uses (e.g., boundary extraction, extraction of connected components), image segmentation and pattern recognition. A percentage of the course grade is based on projects, which require students to program image processing techniques and apply them to images.

Cells

(Division of Basic Sciences Course)
2 credit hours
Cell structure; membrane biology; intracellular membrane and protein trafficking; energy conversion; signal transduction and second messengers; cytoskeleton; cell cycle; and introductory material in microbiology, immunology, and neurobiology.

Current Topics in Computational Biology

1 credit hour
Starting with the second year, all students of the Computational Biology track will participate in a journal club that covers landmark papers as well as the latest publications across a wide spectrum of the field. The journal club will be coordinated with invitations of speakers in the Computational Biology seminar series. Speakers will be encouraged to lead the journal club on one of their papers of choice, which can be their own work or a publication they deem as seminal to their current line of study. Students of the track will be allowed to invite two speakers of their choosing per year with assistance from the course director(s).

Developmental Principles in Regenerative Science and Medicine

(Offered by Genetics, Development, and Disease graduate program)
3 credit hours
The Developmental Principles in Regenerative Science and Medicine course integrates the fundamental concepts of development and stem cell biology. We will explore the interrelated themes of pluripotency, cell fate specification, differentiation, organogenesis, regeneration, patterning, and morphogenesis with an emphasis on model systems and in vitro rodent and human models. The first part of the course will survey developmental principles and discuss classic papers in embryology. The second part of the course will discuss pluripotent stem cells and the factors that regulate their growth and development into tissue-specific stem cells. Subsequently, adult stem cells will be discussed to provide examples of the various types of tissue-specific stem cells. The final part of the course will discuss how advances in cellular and molecular biology can be applied to regenerative science and medicine, with a focus on emerging “hot” topics such as human iPSC disease models and direct reprogramming.

Exam I Preparation Course

1 credit hour
This course prepares students for the BME qualifying exam (Exam I). It provides an overview of the Exam I process, followed by interactive workshops focused on developing and presenting a concise research summary, identifying appropriate committee members, reviewing previous exam I questions and written responses, formulating a hypothesis, and drafting a specific aims page. The course includes question and answer sessions with both faculty and senior PhD students.

Fundamentals of Imaging in Medicine

3 credit hours
This course is designed to introduce students to the general concepts of image science, including the inverse problem, signal processing, system performance, linear system theory, digital image processing, stochastic processes, image reconstruction, quantification, and decision theory. The covered material will conform to the curriculum of the American Association of Physicists in Medicine to cover the essential medical physics didactic elements related to radiation protection and radiation safety for individuals entering the medical physics profession through an alternative pathway as published in AAPM report number 197.

Genes

(Division of Basic Sciences Course)
2 credit hours
Molecular genetics of model organisms; DNA replication, repair, and recombination; transcription; RNA catalysis, processing, and interference; translation; protein turnover; developmental biology; and genomics.

Human Physiology

3 credits
A comprehensive study of the basic functions of the body systems and their interrelationships is offered in this course.

Intro to Nuclear Magnetic Resonance (NMR)

3 credit hours
Introduction to NMR is intended to provide a fundamental understanding of magnetic resonance and the associated phenomena of relaxation and coherence excitation. Using both a vector model and product operators, a general method for describing the current state-of-the-art magnetic resonance experiments is developed. Students will demonstrate working knowledge about the underlying principles and in vivo applications of several multi-nuclei magnetic resonance spectroscopy (MRS) modalities, including conventional MRS, spectral editing, 2D NMR, spectroscopic imaging, etc. The students will demonstrate the ability to describe the radiofrequency and gradient pulse actions and the NMR consequences, using mathematical and quantum-mechanical tools (e.g., product operator formalism). By the end of the course, the students will demonstrate the ability to track the NMR coherence evolution over any type of NMR sequence and will demonstrate the capability of designing new MRS techniques and interpreting the spectroscopic results for evaluation of certain physiological or pathological processes at cellular and molecular levels in the living body. Students will demonstrate the ability to design an MRS protocol for studying some physiological or pathological processes.

Introduction to Biomedical and Molecular Imaging

3 credit hours
By the end of this course, students will demonstrate working knowledge about individual imaging modalities including X-ray, CT, ultrasound, optical imaging, MRI, and nuclear imaging, which are the most commonly used in clinical or preclinical research. The students will demonstrate proficiency in the underlying mathematic and physical mechanisms of each imaging modality. By the end of the course, the students will demonstrate the ability to design imaging techniques and imaging sequences, process imaging data, and interpret imaging findings for evaluation of certain physiological or pathological processes at cellular and molecular levels, such as vascular perfusion and permeability, water diffusion change, etc. Students will demonstrate the ability to propose imaging techniques for some specific physiological or pathological process.

Machine Learning

3 credit hours
From the discovery of hidden subtypes in cancer patients to the identification of unknown patterns in imaging data, machine learning has rapidly advanced almost all fields of bioinformatics and biomedical engineering. In this course, we will cover the classic topics in traditional machine learning, including linear/logistic regression, classification/regression trees and random forests, Bayesian inference and Bayesian graphic network, and support vector machines. We will also introduce the basic concepts of neural network models and introduce the basics of deep learning methods.

Mathematical Biostatistics

3 credit hours
This course is a traditional, mathematical approach to statistical analysis of biomedical data. Topics include data description, summary statistics, elements of probability, distributions of random variables including applications of the binomial and normal distributions, estimation and confidence intervals, hypothesis testing, analysis of variance, correlation and regression, and contingency tables. Additional topics include statistical power, sample size, and study design.

Mathematical Foundations of Quantitative Biology – Part I

2 credit hours
As scientists, we make careful but often indirect, incomplete, or noisy experimental measurements and use these to model the world around us. Mathematics gives us a language to quantitatively compare experiments, assess and model error, describe large data sets, abstract complex processes, and build predictive models. This course – the first in a two-part series – focuses on the math behind physics-based modeling of biological systems. We will cover: series and combinatorics, differential equations, transform theory, and linear algebra. These ideas are integrated in a final section on multivariable calculus. Students will build comfort and familiarity with these techniques through both pencil-and-paper assignments and programming exercises in MATLAB. Students will practice abstracting and representing biological systems in mathematical terms and develop familiarity with numerical (computational) strategies in differential equations and transform theory.

Mathematical Foundations of Quantitative Biology – II

2 credit hours
Much of modern computational biology is rooted in ideas from probability theory and information theory. In this second mathematics course, we discuss the quantification and representation of information. This course will cover concepts from probability theory, noise analysis, statistical hypothesis testing, information theory, graph theory, and the foundations of computing. As in MFQB-I, students will practice abstracting and representing biological systems in mathematical terms and develop familiarity with numerical (computational) strategies. This course includes a final project in which students will apply concepts from the course to a biological problem of interest. MFQB-I is a prerequisite (this can be waived with instructor consent).

Metabolic Imaging of Disease

3 credit hours
Many human diseases are associated with disruption of cell metabolism. Understanding the principles of metabolism is valuable for designing and interpreting diagnostic studies as well as understanding the effects of many therapies. In this course, the fundamentals of intermediary metabolism and bioenergetics will be presented. The links between abnormal metabolism and disease will be emphasized. Although the focus is not on technology, research and diagnostic methods to probe metabolism, including radiotracers, mass spectrometry, NMR, magnetic resonance imaging, and positron tomography will be introduced.

Molecular Imaging & Probe Development

3 credit hours
Molecular imaging probe development and technique implementation represent one of the "New Pathways to Discovery" in the NIH Roadmap for medical research (http://nihroadmap.nih.gov/initiatives.asp). The purpose of this course is to provide students with a basic understanding of the chemistry and biology roles in molecular imaging probe development. The concepts for imaging probe design, synthesis, and evaluation in diseased animal models will be introduced with a focus on major imaging techniques and their biomedical applications.

Principles of MRI

3 credit hours
The course will cover the principles of magnetic resonance imaging. Topics include an introduction to radiofrequency pulses, spatial information end-coding using gradients, signal acquisition, and processing. Students will demonstrate a working knowledge of basic MRI imaging techniques including gradient and spin echo, fast spin echo, and echo planar imaging. In addition, students will demonstrate an understanding of advanced MRI imaging methods applied in research and clinical environments.

Professionalism, Responsible Conduct of Research, and Ethics I

1 credit hour
Topics covered through lectures and small group discussions: goals of education in RCR; professionalism; collaboration; teambuilding and professional behaviors; everyday practice of ethical science; mentorship; data management and reproducibility; animal research; genetics; and human research.

Professionalism, Responsible Conduct of Research, and Ethics II

1 credit hour
Topics covered through lectures and small group discussions: codes of ethics and misconduct; building interprofessional teams; conflict of interest; sexual boundaries and professional behavior; applications of genetic testing; technology transfer and intellectual property; plagiarism, authorship, and citation; peer review; image and data manipulation.

Proteins

(Division of Basic Sciences Course)
2 credit hours
The energetic basis of protein structure; stability; ligand binding and regulation; enzyme mechanics and kinetics; methods of purification; and analysis by spectroscopic methods.

Quantitative Biology

1.5 credit hours
This course aims to provide the conceptual framework and mathematical techniques to predict the behavior of “complex” biological systems from first principles. Complexity will be defined hierarchically in terms of three orthogonal characteristics: linear/nonlinear, equilibrium/nonequilibrium, and static/time-varying. All categories of problems within the complexity hierarchy will be described intuitively and mathematically before being made manifest as a specific problem in biology. The goal is to foster a deep understanding of what makes different types of collective problems easy or hard and which techniques/properties are generally applicable for a given problem. The examples of biological systems will span length scales from proteins to populations and operate on time scales from physiological to evolutionary time.

Radiation Protection and Safety

3 credit hours
This course will cover the fundamental concepts of radiation protection and radiation safety. The main focus will be on the physics of radiation protection, instrumentation used in radiation protection, shielding and relevant regulatory requirements, statistical methods used in radiation protection, protection against non-ionizing and ultrasound radiation, and internal exposure due during nuclear medicine applications. The covered material will conform to the curriculum of the American Association of Physicists in Medicine to cover the essential medical physics didactic elements related to radiation protection and radiation safety for individuals entering the medical physics profession through an alternative pathway as published in AAPM report number 197.

Radiation Therapy

3 credit hours
This course is designed to introduce students to the general concepts of medical physics applied in radiation therapy of cancer, including external beam radiation therapy, brachytherapy, treatment planning, radiation therapy devices, and radiation therapy with neutrons, protons, and heavy ions. The covered material will conform to the curriculum of the American Association of Physicists in Medicine to cover the essential medical physics didactic elements related to therapeutic medical physics for individuals entering the medical physics profession through an alternative pathway as published in AAPM report number 197.

Radiobiology

3 credit hours
This course covers the fundamental concepts of radiobiology: the physical interaction of ionizing radiation with matter with a focus on biological responses from the molecular level to the whole organism; and the consequences of such interactions including carcinogenic risk, hereditary risk, non-cancer risks, and anti-tumor effects. There is a strong emphasis placed on the understanding of the underlying principles of therapeutic uses of ionizing radiation in modern radiation oncology practice.

Radiological Physics and Dosimetry

3 credit hours
This course will cover the fundamental concepts of radiation physics and radiation dosimetry. The main focus will be on a quantitative description of the interaction of ionizing radiation with matter and on how to theoretically predict and experimentally measure the absorbed energy in matter. The covered material will conform to the curriculum of the American Association of Physicists in Medicine to cover the essential medical physics didactic elements related to radiological physics and dosimetry for individuals entering the medical physics profession through an alternative pathway as published in AAPM report number 197.

Software engineering for research computing – Part I

3 credit hours
Computational approaches have played key roles in analyzing myriad biological data to elicit underlying principles and mechanisms. While we expect that all students on the Computational Biology track will bring solid programming skills from their undergraduate training, we offer a monthlong intensive workshop where we study computer science with an emphasis on software engineering methods: algorithms, data structures, object-oriented programming, high-performance computing, software engineering processes and techniques, and database design. Upon successful completion of this course, students will be equipped with the capability to develop efficient, functional, easy-to-use software and to design reusable and extendable software architecture that ensures reproducibility, stability, and robustness.

Software engineering for research computing – Part II

3 credit hours
Computational approaches have played key roles in analyzing myriad biological data to elicit underlying principles and mechanisms. While we expect that all students on the Computational Biology track will bring solid programming skills from their undergraduate training, we offer a monthlong intensive workshop where we study computer science with an emphasis on software engineering methods: algorithms, data structures, object-oriented programming, high-performance computing, software engineering processes and techniques, and database design. Upon successful completion of this course, students will be equipped with the capability to develop efficient, functional, easy-to-use software and to design reusable and extendable software architecture that ensures reproducibility, stability, and robustness.

Statistical Analysis of Genetic Data

1 credit hour
Students have the option to take an additional course focused on genetic data analysis. This class covers the principles underlying classical genetic study designs. Then we describe how these principles apply to the design and analysis of modern genetic studies involving high-throughput DNA sequencing data. By the end of this course, students will have acquired a basic understanding of the principles underlying genetic association and linkage studies, can perform simple analyses of genetic data, and be able to understand research studies in human genetics.

Translational Nanomedicine I

1.5 credit hours
This course presents the fundamentals underlying molecular design of nanomedicine platforms to help translate basic biological science to clinical medicine. Molecular design and nanoengineering will be closely integrated with pathophysiology and biological rationales to establish emerging precision paradigms for disease diagnosis and therapy.