Curriculum
Overview
Ph.D. students complete a flexible curriculum that includes core engineering and life science courses as well as advanced electives related to their research. A minimum of 21 hours of didactic coursework is required for graduation.
In addition to coursework, the curriculum for first-year students includes up to four laboratory rotations and training in responsible conduct of research.
Beginning in their second year, students 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 a qualifying exam (Exam I), usually given during the second year. A supervisory research committee is formed for each doctoral candidate after successful completion of their qualifying exam. This committee reviews and evaluates the student’s progress, provides expertise and guidance on their research, and participates in the proposal and dissertation defenses.
Degree Plans:
Course Descriptions:
BME Exam: Preparation Course
Credit hours: 1
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.
Professionalism, Responsible Conduct of Research, and Ethics I
Credit hours: 1
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
Credit hours: 1
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.
Advanced Engineering Design Principles
Credit hours: 3
This course introduces the student to human anatomy and physiology. It will also emphasize practical aspects of anatomy and physiology pertained to medical physics practice. After introducing basics in human anatomy and organ systems, anatomy will be discussed as seen in the transverse, coronal, and sagittal planes. Anatomy of the brain, thorax, abdomen, and pelvis will be studied using CT and MRI images. Normal anatomy, anatomic variants, and selected pathologies will be discussed in the various body regions.
Anatomy & Physiology for Engineers
Credit hours: 3
This course is designed to introduce students to the structures and functions of the human body, with an emphasis on topics of interest to biomedical engineers. Students will be introduced to the basic pathophysiology of major diseases and to technologies such as drug delivery systems and medical devices. The course includes a team project component where students will develop potential solutions to biomedical problems.
Anatomy and Physiology for Radiation Oncology
Credit hours: 3
This course introduces the student to human anatomy and physiology. It will also emphasize practical aspects of anatomy and physiology pertained to medical physics practice. After introducing basics in human anatomy and organ systems, anatomy will be discussed as seen in the transverse, coronal, and sagittal planes. Anatomy of the brain, thorax, abdomen, and pelvis will be studied using CT and MRI images. Normal anatomy, anatomic variants, and selected pathologies will be discussed in the various body regions.
Current Topics in Computational Biology
Credit hours: 1
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 own choosing per year, with assistance from the course director(s).
Current Topics in Neuroimaging
Credit hours: 3
This course provides an intensive lecture series on cutting-edge neuroimaging technologies, with a specific focus on magnetic resonance imaging (MRI) and other advanced imaging modalities developed and utilized by research groups at UT Southwestern. The first half of the semester will cover the fundamentals and advancements in MRI technology for brain research. The second half of the course will delve into Electroencephalogram (EEG), Magnetoencephalography (MEG), Positron emission tomography (PET), Near Infrared Spectroscopy (NIRS), and super high-resolution optical imaging technologies. Each module includes a background lecture and an in-depth exploration of the imaging modality's current state and applications in neuroscience and clinical practice.
Fundamentals of Imaging in Medicine
Credit hours: 3
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.
Introduction to Biomedical and Molecular Imaging
Credit hours: 3
By the end of this course, the 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 process 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
Credit hours: 3
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 forest, Bayesian inference and Bayesian graphic network, and support vector machines. We will also introduce the basics concepts of neural network models and introduce the basics of deep learning methods.
Mathematical Foundations of Quantitative Biology – Part I
Credit hours: 2
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 datasets, 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 – Part II
Credit hours: 2
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
Credit hours: 3
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
Credit hours: 3
Molecular imaging probe development and technique implementation represents 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 & biology roles in molecular imaging probe development. The concepts for imaging probe design, synthesis, and evaluation in diseased animal models will be introduced with focus on major imaging techniques and their biomedical applications.
Optical Imaging and Probe Engineering (OIPE)
Credit hours: 1.5
The elective on Optical Imaging and Probe Engineering (OIPE) is offered to graduate students who are interested in imaging, imaging probe development and their translational applications in medicine. The course spans a diverse array of topics in optical imaging, including fundamentals of fluorescence and microscopy; fluorescence dyes and probe design; various imaging modalities such as confocal, multi-photon and second harmonic, light-sheet microscopy, fiber optic, optical tomography, photoacoustic tomography, bioluminescence, optical coherence tomography and ultrasound imaging. In addition, the course will discuss translational applications of optical imaging in surgery and diagnosis, and showcase contemporary approaches for engineering probes or sensors for the in vivo targeting and deep tissue imaging. A few lectures also include laboratories for students to gain hands-on experience on imaging equipment and their operations on live cells or animals. Upon completion of the course, students are expected to learn the basic principles of various optical imaging modalities, and to understand their strengths and limitations. The course meets twice a week for half a semester, with each class lasting 90 minutes. Postdoctoral fellows are welcome to audit the class.
Principles of MRI
Credit hours: 3
Course will cover the principles of Magnetic Resonance Imaging. Topics include introduction to Radio-Frequency 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, echo planar imaging. In addition, students will demonstrate an understanding of advanced MRI imaging methods applied in research and clinical environments.
Quantitative Biology
Credit hours: 1.5
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 in a hierarchical manner 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 timescales from physiological to evolutionary time.
Radiobiology
Credit hours: 3
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.
Radiation Protection and Safety
Credit hours: 3
This course will cover the fundamental concepts of radiation protection and radiation safety. The main focus will be on 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, 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 Physics
Credit hours: 3
This course is designed to introduce students to the general concepts of medical physics applied in radiation therapy of cancer disease, 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.
Radiological Physics and Dosimetry
Credit hours: 3
This course will cover the fundamental concepts of radiation physics and radiation dosimetry. The main focus will be on 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
Credit hours: 3
Computational approaches have played key roles in analyzing a myriad of 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 month-long 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 process 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
Credit hours: 3
Computational approaches have played key roles in analyzing a myriad of 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 month-long 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 process 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
Credit hours: 1
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, have the ability to perform simple analyses of genetic data, and be able to understand research studies in human genetics.
Translational Nanomedicine I
Credit hours: 2
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.
Biological Sciences Core Course Modules
Genes
Credit hours: 2
Molecular genetics of model organisms; DNA replication, repair, and recombination; transcription; RNA catalysis, processing, and interference; translation; protein turnover; developmental biology; and genomics.
Proteins
Credit hours: 2
The energetic basis of protein structure; stability; ligand binding and regulation; enzyme mechanics and kinetics; methods of purification; and analysis by spectroscopic methods.
Cells
Credit hours: 2
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.
