The Department of Bioengineering offers a Master of Engineering (MEng) in Bioengineering, PhD in Bioengineering, and a Master of Translational Medicine (MTM). The PhD and MTM are operated in partnership with UC San Francisco, and degrees are granted jointly by UCSF and UC Berkeley.
The Master of Engineering is a one-year master’s degree with a strong emphasis on engineering and entrepreneurship designed for students planning to move directly into industry after completing the program.
The PhD in Bioengineering is granted jointly by Berkeley and UCSF, two of the top public universities in the world in engineering and health sciences. Our interdisciplinary program combines the outstanding resources in biomedical and clinical sciences at UCSF with the excellence in engineering, physical, and life sciences at Berkeley.
Administered by the Department of Bioengineering at UC Berkeley and the Department of Bioengineering and Therapeutic Sciences at UCSF, all students in the program are simultaneously enrolled in the graduate divisions of both the San Francisco and Berkeley campuses and are free to take advantage of courses and research opportunities on both campuses. The program awards the PhD in Bioengineering degree from both campuses.
The MTM program is a cross-campus collaboration between the Department of Bioengineering at UC Berkeley and the Department of Bioengineering and Therapeutic Sciences at UCSF. The MTM program is an intense year of coursework designed around the main content themes of engineering, clinical needs & strategies, and business, entrepreneurship & technology. The centerpiece of the curriculum is the capstone project course. The MTM program is specifically designed for students seeking to build a career in medical-technology innovation and development. Through our highly specialized curriculum, students are provided with the fundamental skills necessary to become experts at transforming new biomedical discoveries into real-world clinical products. The MTM program is best suited for students who intend to pursue a professional career developing new medical technologies, and who wish to become leaders in the emerging field of translational medicine.
Thank you for considering UC Berkeley for graduate study! UC Berkeley offers more than 120 graduate programs representing the breadth and depth of interdisciplinary scholarship. A complete list of graduate academic departments, degrees offered, and application deadlines can be found on the Graduate Division website.
Prospective students must submit an online application to be considered for admission, in addition to any supplemental materials specific to the program for which they are applying. The online application can be found on the Graduate Division website.
Admission Requirements
The minimum graduate admission requirements are:
A bachelor’s degree or recognized equivalent from an accredited institution;
A satisfactory scholastic average, usually a minimum grade-point average (GPA) of 3.0 (B) on a 4.0 scale; and
Enough undergraduate training to do graduate work in your chosen field.
For a list of requirements to complete your graduate application, please see the Graduate Division’s Admissions Requirements page. It is also important to check with the program or department of interest, as they may have additional requirements specific to their program of study and degree. Department contact information can be found here.
The course requirements are designed to develop a strong and useful knowledge base in both biology and engineering. In general, the program of study includes a major and a minor field of study. Due to the wide variety of topics included in bioengineering and the variety of student interests, major and minor subfields will be chosen by the student in consultation with their primary graduate adviser, taking into account the student’s prior training, research interests, and career goals. Students who already hold a master’s or other professional degree (MD, DDS, or DVM) may not be required to complete minor coursework.
All students in the Program must complete the following course requirements:
Area Requirements (see below)
Major Area and Minor Area Major = 16 semester (24 quarter) units. Minor = 8 semester (12 quarter) units.
First Year Seminars: Bioengineering 200 (UCB) and Bioengineering 280/281 (UCSF)
Ethics: Bioengineering 201 (UCB) or equivalent, taken in the first and fourth years
Racism in Science: Grad 202 (UCSF)
All students in the Ph.D. program are required to have completed, at some time during their academic career, the Area Requirements described below. Most students will have completed some of these courses prior to initiating the Ph.D. program; any remaining coursework will be integrated into the graduate program of study.
Anatomy, physiology, and biology: 9 semester or 13.5 quarter units of upper division or graduate level coursework.
Biochemistry and/or intermediate chemistry: 3 semester or 4.5 quarter units of upper division or graduate level coursework.
Engineering and/or computer science: 7 semester or 10.5 quarter units of upper division or graduate level coursework.
Mathematics and/or statistics: 2 semester or 3 quarter units of upper division or graduate level coursework.
Laboratory Rotations
Students should perform three 12-week rotations in different graduate group faculty laboratories during the first year. The objective of the research rotation is to allow students to become familiar with different areas of research, learn new experimental techniques, obtain experience in unique research laboratories, and ultimately to identify a lab in which to conduct dissertation research. The research being performed during a rotation may correspond to the initial stages of a thesis project or may be on an entirely different topic.
Teaching
Anticipating future careers which may include teaching, all graduate students participate in undergraduate instruction by serving as a Graduate Student Instructor for at least one semester.
Qualifying Examination
An oral qualifying examination must be taken in the spring of the second year or the fall of the third year. In this examination, students demonstrate their ability to recognize research problems of fundamental importance, to propose appropriate experimental approaches to address these problems and to display comprehensive knowledge of their disciplinary area and related subjects.
Dissertation Work
After advancing to candidacy, a student meets each fall semester with his or her thesis committee to discuss the dissertation project, to review results, and to chart directions for their third and subsequent years. In the final years in the program, students complete a dissertation based on original laboratory research. It generally takes five and a half years to complete the doctoral program.
The Bioengineering MEng Degree requires a minimum 25 total units of course credit, a capstone report and presentation, and passing the leadership and technical comprehensive exams. Coursework requirements fall across three areas – technical bioengineering (12 units), leadership (8 units), and capstone (5 units).
Students must take a minimum of 12 credits of 200-level Bioengineering courses for a letter grade, selected within any of our 7 technical concentrations, or any Bioengineering courses across those concentrations.
Two units of boot camp short courses in early January. Select two of any of the one-unit electives (Note: Electives listed below are subject to change)
Professional Ethics in Technology, Law and Business [1]
3. Capstone Experience [5 units]
Students must be enrolled in ENGIN 296MA in the fall (1-2 units) and ENGIN 296MB in the spring (3-4 units), for a total of 5 units total over both semesters.
4. Comprehensive Exams – Leadership & Technical
Leadership: The Fung Institute will administer a written exam for the fall leadership portion of the curriculum. Students should be prepared to spend a designated day to complete the degree requirement Leadership Comprehensive Exam.
Technical: The Bioengineering Technical Comprehensive Exam will take place late in the Spring semester (generally during RRR week) and will consist of a 20 minute minimum presentation on your Capstone project. The presentation will be assessed by a BioE faculty member and an allied field member (for example, if a project is in ME, the second assessor must be in ME). Students will be asked probing questions during the presentation and answers given will determine a pass. If a student fails the presentation requirement, they will be given the option to give the presentation again the following Fall semester. Failure to pass the exam on the third attempt will constitute a failure of the comprehensive exam requirement for the MEng degree.
Students earning this degree will choose a track (concentration) of coursework in one of these seven fields. Please see the requirements for each concentration below:
Bioenergy and Sustainable Chemical Synthesis: Metabolic Engineering and Synthetic Biology Approaches
3
Courses
Bioengineering
Terms offered: Fall 2024, Fall 2023, Fall 2022
An introduction to research in bioengineering including specific case studies and organization of this rapidly expanding and diverse field. The Graduate Group Introductory Seminar: Read More [+]
Rules & Requirements
Prerequisites: Enrollment in PhD Program in Bioengineering or consent of instructor
Repeat rules: Course may be repeated for credit without restriction.
Hours & Format
Fall and/or spring: 15 weeks - 1 hour of seminar per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Offered for satisfactory/unsatisfactory grade only.
Terms offered: Spring 2024, Spring 2023, Spring 2022
This course will explore ethical issues likely to be faced by a bioengineer, and consider them in the context of responsible engineering. The content of the class is designed considering the NSF Standards of Ethical Conduct and the NIH Ethical Guidelines & Regulations in mind, and to serve as the Responsible Conduct of Research training for our PhD program.
Course Objectives: The content of the class is designed considering the NSF Standards of Ethical Conduct and the NIH Ethical Guidelines & Regulations in mind, and to serve as the Responsible Conduct of Research training for our PhD program.
Student Learning Outcomes: To prepare bioengineering PhD students to perform their research and design responsibly.
Rules & Requirements
Prerequisites: Open only to Bioengineering graduate students
Hours & Format
Fall and/or spring: 10 weeks - 1 hour of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Offered for satisfactory/unsatisfactory grade only.
Terms offered: Fall 2024, Fall 2023, Fall 2022
This course will teach the main concepts and current views on key attributes of animal cells (somatic, embryonic, pluripotent, germ-line; with the focus on mammalian cells), will introduce theory of the regulation of cell function, methods for deliberate control of cell properties and resulting biomedical and bioengineering technologies. Cell Engineering: Read More [+]
Objectives & Outcomes
Course Objectives: The goal of this course to establish fundamental understanding of cell engineering technologies and of the key biological paradigms, upon which cell engineering is based, with the focus on biomedical applications of cell engineering.
Student Learning Outcomes: At the completion of this course students will understand how bioengineering technologies address the deliberate control of cell properties (and how this advances biomedicine); and students will learn the main concepts and current views on key attributes of animal cells (somatic, embryonic, pluripotent, germ-line; with the focus on mammalian cells).
Terms offered: Prior to 2007
This class provides a conceptual and practical understanding of cell and tissue bioengineering that is vital for careers in medicine, biotechnology, and bioengineering. Students are introduced to cell biology laboratory techniques, including immunofluorescence, quantitative image analysis, protein quantification, protein expression, gene expression, and cell culture. Tissue Engineering lab: Read More [+]
Objectives & Outcomes
Course Objectives: The goal of this course to provide students with conceptual and practical understanding of cell and tissue bioengineering.
Student Learning Outcomes: At the completion of this course, students will learn key cellular bioengineering laboratory techniques, will develop a conceptual and theoretical understanding of the reliability and limitations of these techniques and will enhance their skills in quantitative data analysis, interpretation and integration.
Terms offered: Fall 2024, Fall 2023, Fall 2022
This course is intended to give students the opportunity to expand their knowledge of topics related to biomedical materials selection and design. Structure-property relationships of biomedical materials and their interaction with biological systems will be addressed. Applications of the concepts developed include blood-materials compatibility, biomimetic materials, hard and soft tissue-materials interactions, drug delivery, tissue engineering, and biotechnology. Biological Performance of Materials: Read More [+]
Objectives & Outcomes
Course Objectives: The course is separated into four parts spanning the principles of synthetic materials and surfaces, principles of biological materials, biological performance of materials and devices, and state-of-the-art materials design. Students are required to attend class and master the material therein. In addition, readings from the clinical, life and materials science literature are assigned. Students are encouraged to seek out additional reference material to complement the readings assigned. A mid-term examination is given on basic principles (parts 1 and 2 of the outline). A comprehensive final examination is given as well. The purpose of this course is to introduce students to problems associated with the selection and function of biomaterials. Through class lectures and readings in both the physical and life science literature, students will gain broad knowledge of the criteria used to select biomaterials, especially in devices where the material-tissue or material-solution interface dominates performance. Materials used in devices for medicine, dentistry, tissue engineering, drug delivery, and the biotechnology industry will be addressed.
This course also has a significant design component (~35%). Students will form small teams (five or less) and undertake a semester-long design project related to the subject matter of the course. The project includes the preparation of a paper and a 20 minute oral presentation critically analyzing a current material-tissue or material-solution problem. Students will be expected to design improvements to materials and devices to overcome the problems identified in class with existing materials.
Student Learning Outcomes: Work independently and function on a team, and develop solid communication skills (oral, graphic & written) through the class design project.
•
Develop an understanding of the social, safety and medical consequences of biomaterial use and regulatory issues associated with the selection of biomaterials in the context of the silicone breast implant controversy and subsequent biomaterials crisis.
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Design experiments and analyze data from the literature in the context of the class design project.
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Understanding of the origin of surface forces and interfacial free energy, and how they contribute to the development of the biomaterial interface and ultimately biomaterial performance.
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Apply math, science & engineering principles to the understanding of soft materials, surface chemistry, DLVO theory, protein adsorption kinetics, viscoelasticity, mass diffusion, and molecular (i.e., drug) delivery kinetics.
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Apply core concepts in materials science to solve engineering problems related to the selection biomaterials, especially in devices where the material-tissue or material-solution interface dominates performance.
Terms offered: Fall 2024, Fall 2023, Fall 2022
Students will learn the application of engineering concepts including statics, dynamics, optimization theory, composite beam theory, beam-on-elastic foundation theory, Hertz contact theory, and materials behavior. Topics will include forces and moments acting on human joints; composition and mechanical behavior of orthopedic biomaterials; design/analysis of artificial joint, spine, and fracture fixation prostheses; musculoskeletal tissues including bone, cartilage, tendon, ligament, and muscle; osteoporosis and fracture-risk predication of bones; and bone adaptation. Students will be challenged in a MATLAB-based project to integrate the course material in an attempt to gain insight into contemporary design/analysis/problems. Advanced Orthopedic Biomechanics: Read More [+]
Objectives & Outcomes
Course Objectives: The purpose of this course is twofold:
•
to learn the fundamental concepts of orthopaedic biomechanics;
•
to enhance skills in mechanical engineering and bioengineering by analyzing the mechanical behavior of various complex biomedical problems.
Student Learning Outcomes: Working knowledge of various engineering concepts such as composite beam theory, beam-on-elastic-foundation theory, Hertz contact theory and MATLAB-based optimization design analysis. Understanding of basic concepts in orthopaedic biomechanics and the ability to apply the appropriate engineering concepts to solve realistic biomechanical problems, knowing clearly the assumptions involved.
Rules & Requirements
Prerequisites: ME C85/CE C30 or Bio Eng 102; concurrent enrollment OK. Proficiency in MatLab or equivalent. Prior knowledge of biology or anatomy is not assumed
Credit Restrictions: Students will not receive credit for this course if they have taken ME C176/Bio E C119.
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture, 1 hour of discussion, and 1 hour of laboratory per week
Terms offered: Fall 2024, Fall 2023, Fall 2018
This course will focus on biophysical and bioengineering aspects of mechanotransduction, the process through which living cells sense and respond to their mechanical environment. Students will learn how mechanical inputs to cells influence both subcellular biochemistry and whole-cell behavior. They will also study newly-engineered technologies for force manipulation and measurement in living cells, and synthetic strategies to control the mechanics and chemistry of the extracellular matrix. Finally, students will learn about the role of mechanotransduction in selected human organ systems and how these mechanisms may go awry in the setting of the disease. Instruction will feature lectures, discussions, analysis of relevant research papers, assembly of a literature review and a research proposal, and an oral presentation. Cell and Tissue Mechanotransduction: Read More [+]
Rules & Requirements
Prerequisites: Undergraduate cell biology or consent of instructor
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Terms offered: Spring 2008, Fall 2007, Spring 2006, Spring 2005
Fundamental processes of heat and mass transport in biological systems; organic molecules, cells, biological organs, whole animals. Derivation of mathematical models and discussion of experimental procedures. Applications to biomedical engineering. Heat and Mass Transport in Biomedical Engineering: Read More [+]
Rules & Requirements
Prerequisites: 106 and 109 (106 and 109 may be taken concurrently)
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Terms offered: Fall 2023, Spring 2019, Spring 2016
Fluid mechanical aspects of various physiological systems, the circulatory, respiratory, and renal systems. Motion in large and small blood vessels. Pulsatile and peristaltic flows. Other biofluidmechanical flows: the ear, eye, etc. Instrumentation for fluid measurements in biological systems and for medical diagnosis and applications. Artificial devices for replacement of organs and/or functions, e.g. blood oxygenators, kidney dialysis machines, artificial hearts/circulatory assist devices. Fluid Mechanics of Biological Systems: Read More [+]
Rules & Requirements
Prerequisites: 106 or equivalent; 265A or consent of instructor
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Terms offered: Spring 2018, Spring 2017, Spring 2015
The goal of this course is to provide a foundation for characterizing and understanding the mechanical behavior of load-bearing tissues. A variety of mechanics topics will be introduced, including anisotropic elasticity and failure, cellular solid theory, biphasic theory, and quasi-linear viscoelasticity (QLV) theory. Building from this theoretical basis, we will explore the constitutive behavior of a wide variety of biological tissues. After taking this course, students should have sufficient background to independently study the mechanical behavior of most biological tissues. Formal discussion section will include a seminar series with external speakers. Advanced Tissue Mechanics: Read More [+]
Rules & Requirements
Prerequisites: 102A, 176, 185; graduate standing or consent of instructor
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Terms offered: Spring 2023, Spring 2022, Spring 2021, Spring 2020
This course develops and applies scaling laws and the methods of continuum and statistical mechanics to understand micro- and nano-scale mechanobiological phenomena involved in the living cell with particular attention the nucleus and the cytoskelton as well as the interactions of the cell with the extracellular matrix and how these interactions may cause changes in cell architecture and biology, consequently leading to functional adaptation or pathological conditions. Molecular Biomechanics and Mechanobiology of the Cell: Read More [+]
Objectives & Outcomes
Course Objectives: This course, which is open to graduate students in diverse disciplines ranging from engineering to biology to chemistry and physics, is aimed at exposing students to subcellular biomechanical phenomena spanning scales from molecules to the whole cell.
Student Learning Outcomes: The students will develop tools and skills to (1) understand and analyze subcelluar biomechanics and transport phenomena, and (2) ultimately apply these skills to novel biological and biomedical applications.
Terms offered: Spring 2024, Spring 2023, Spring 2022
Overview of the problems associated with the selection and function of polymers used in biotechnology and medicine. Principles of polymer science, polymer synthesis, and structure-property-performance relationships of polymers. Particular emphasis is placed on the performance of polymers in biological environments. Interactions between macromolecular and biological systems for therapy and diagnosis. Specific applications will include drug delivery, gene therapy, tissue engineering, and surface engineering. Macromolecular Science in Biotechnology and Medicine: Read More [+]
Rules & Requirements
Prerequisites:BIO ENG 115. Open to seniors with consent of instructor
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Terms offered: Fall 2017, Spring 2014, Fall 2010
Study of nature's solutions to specific problems with the aim of determining appropriate engineering analogs. Morphology, scaling, and design in organisms applied to engineering structures. Mechanical principles in nature and their application to engineering devices. Mechanical behavior of biological materials as governed by underlying microstructure, with the potential for synthesis into engineered materials. Trade-offs between redundancy and efficiency. Students will work in teams on projects where they will take examples of designs, concepts, and models from biology and determine their potential in specific engineering applications. Biomimetic Engineering -- Engineering from Biology: Read More [+]
Rules & Requirements
Prerequisites: Graduate standing in engineering or consent of instructor
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Terms offered: Spring 2015, Spring 2014, Spring 2013
This course will provide an overview of basic and applied embryonic stem cell (ESC) biology. Topics will include early embryonic development, ESC laboratory methods, biomaterials for directed differentiation and other stem cell manipulations, and clinical uses of stem cells. Stem Cells and Directed Organogenesis: Read More [+]
Rules & Requirements
Prerequisites: Consent of instructor
Hours & Format
Fall and/or spring: 15 weeks - 6 hours of laboratory and 1 hour of lecture per week
Terms offered: Fall 2015, Fall 2014, Fall 2010
An in-depth study of the current methods used to design and engineer proteins. Emphasis on how strategies can be applied in the laboratory. Relevant case studies presented to illustrate method variations and applications. Intended for graduate students. Protein Engineering: Read More [+]
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Terms offered: Prior to 2007
The objective of this course is to teach graduate students the essential laboratory techniques in the design and characterization and analysis of cells and biomaterials. The course will cover basics on synthetic biomaterials and native matrix, cellular responses to biomaterials, three-dimensional culture, and tissue engineering. The course includes a lecture and a laboratory section each week. There will be a midterm exam, final exam, and a tissue engineering group project. Cells and Biomaterials Laboratory: Read More [+]
Rules & Requirements
Prerequisites: Cell and tissue engineering; upper division cell biology course or consent of instructor
Hours & Format
Fall and/or spring: 15 weeks - 2 hours of lecture and 6 hours of laboratory per week
Terms offered: Fall 2023, Fall 2022, Fall 2021
Biophysical and chemical principles of biomedical devices, bionanotechnology, bionanophotonics, and biomedical microelectromechanical systems (BioMEMS). Topics include basics of nano-& microfabrication, soft-lithography, DNA arrays, protein arrays, electrokinetics, electrochemical transducers, microfluidic devices, biosensor, point of care diagnostics, lab-on-a-chip, drug delivery microsystems, clinical lab-on-a-chip, advanced biomolecular probes, biomolecular spectroscopy, and etc. Advanced BioMEMS and Bionanotechnology: Read More [+]
Rules & Requirements
Prerequisites: Chemistry 3A, Physics 7A and 7B, Electrical Engineering 143 or equivalent
Repeat rules: Course may be repeated for credit without restriction.
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Summer: 6 weeks - 7.5 hours of lecture per week 8 weeks - 5.5 hours of lecture per week 10 weeks - 4.5 hours of lecture per week
Terms offered: Spring 2024, Spring 2023, Fall 2022
Students will become familiar with BioMEMS and Lab-on-a-Chip research. Students will design and fabricate their own novel micro- or nano-scale device to address a specific problem in biotechnology using the latest micro- and nano-technological tools and fabrication techniques. This will involve an intensive primary literature review, experimental design, and quantitative data analysis. Results will be presented during class presentations and at a final poster symposium. BioMEMS and BioNanotechnology Laboratory: Read More [+]
Objectives & Outcomes
Course Objectives: Students will become familiar with research associated with BioMEMS and Lab-on-a-Chip technologies. Students will gain experience in using creative design to solve a technological problem. Students will learn basic microfabrication techniques. Working in engineering teams, students will learn how to properly characterize a novel device
by choosing and collecting informative metrics. Students will design and carry out carefully controlled experiments that will result in the analysis of quantitative data.
Student Learning Outcomes: Students will learn how to critically read BioMEMS and Lab-on-a-Chip primary literature. Students will learn how to use AutoCAD software to design microscale device features. Students will gain hands-on experience in basic photolithography and soft lithography. Students will get experience with a variety of fluid loading interfaces and
microscopy techniques. Students will learn how to design properly controlled uantitative experiments. Students will gain experience in presenting data to their peers in the form of powerpoint presentations and also at a poster symposium.
Terms offered: Fall 2024, Spring 2023, Fall 2020
This course covers the structure and mechanical functions of load bearing tissues and their replacements. Biocompatibility of biomaterials and host response to structural implants are examined. Quantitative treatment of biomechanical issues and constitutive relationships of materials are covered in order to design implants for structural function. Material selection for load bearing applications including reconstructive surgery, orthopedics, dentistry, and cardiology are addressed. Advanced Structural Aspects of Biomaterials: Read More [+]
Rules & Requirements
Credit Restrictions: Students should not receive credit if they've taken ME ME C117 or Bio Eng C117.
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Terms offered: Fall 2023, Fall 2021, Fall 2019
This course provides an overview of engineering polymers and an introduction to polymer physics. The molecular variables that play a role in structural performance of polymer systems are examined. The assessment of structural behavior of macromolecules and engineering polymers are addressed for functional design in broad applications including medical devices as well as product design. Environmental impact and novel applications of plastics are evaluated. Polymer Engineering: Read More [+]
Rules & Requirements
Prerequisites: MECENG 108, BIOENG 102, MATSCI 113 or equivalent
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Terms offered: Fall 2024, Fall 2023, Fall 2021
This course focuses on providing students with the foundations needed to understand contemporary literature in drug delivery. Concepts in organic chemistry, biochemistry, and physical chemistry needed to understand current problems in drug delivery are emphasized.
Course Objectives: The goal of this course is to give students the ability to understand problems in drug delivery. Emphasis is placed on the design and synthesis of new molecules for drug delivery.
Student Learning Outcomes: At the completion of this course students should be able to design new molecules to solve drug delivery problems.
Terms offered: Spring 2023, Spring 2021, Spring 2020
The detailed, atomic-level structure of biomolecules is at the basis of our understanding of many biochemical processes. The knowledge of these 3D structures has provided fundamental insights in the organization and inner workings of the living cell and has directly impacted the daily lives of many through the development of novel therapeutic agents. This graduate level course is designed to provide students with an in-depth understanding of
crystallography for macromolecular structure determination. The underlying theory, computational approaches, and practical considerations for each step in the process will be discussed.
Course Objectives: (1) Introduce students to the atomic structure of macromolecules,
2) review methods for structure determination, (3) describe the basic theory of diffraction, and (4) provide students with a detailed knowledge of macromolecular crystallography. At the end of the course students will have a solid theoretical and practical understanding of how macromolecular structures are determined to atomic resolution using crystallographic methods. The application of the method to problems in biomolecular engineering will be reviewed.
Student Learning Outcomes: The students will be able to (1) interpret diffraction data to determine reciprocal and real space parameters, (2) plan diffraction experiments, (3) use computational methods to solve the crystallographic phase problem (an inverse problem), (4) interpret complex 3-dimensional maps to build atomic models, (5) determine which optimization methods are appropriate for obtaining a refined, validated model, and (6) apply the knowledge to the engineering of biomolecules.
Rules & Requirements
Prerequisites: Consent of instructor
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Terms offered: Spring 2007
Explore strategies for maximizing the economic and societal benefits of synthetic biology and minimizing the risks; create "seedlings" for future research projects in synthetic biology at UC Berkeley; increase multidisciplinary collaborations at UC Berkeley on synthetic biology; and introduce students to a wide perspective of SB projects and innovators as well as policy, legal, and ethical experts. Implications and Applications of Synthetic Biology: Read More [+]
Rules & Requirements
Prerequisites: Consent of instructor
Hours & Format
Fall and/or spring: 15 weeks - 2 hours of lecture and 1 hour of discussion per week
Terms offered: Fall 2018, Fall 2017, Fall 2016
Topics include computational approaches and techniques to gene structure and genome annotation, sequence alignment using dynamic programming, protein domain analysis, RNA folding and structure prediction, RNA sequence design for synthetic biology, genetic and biochemical pathways and networks, UNIX and scripting languages, basic probability and information theory. Various "case studies" in these areas are reviewed and web-based computational biology tools will be used by students and programming projects will be given. Introduction to Computational Molecular and Cellular Biology: Read More [+]
Terms offered: Fall 2024, Fall 2023, Fall 2022, Fall 2021, Fall 2020
This class teaches basic bioinformatics and computational biology, with an emphasis on alignment, phylogeny, and ontologies. Supporting foundational topics are also reviewed with an emphasis on bioinformatics topics, including basic molecular biology, probability theory, and information theory. Introduction to Computational Molecular and Cell Biology: Read More [+]
Terms offered: Spring 2018, Fall 2014, Fall 2013
This graduate-level course is a comprehensive survey of genetic devices. These DNA-based constructs are comprised of multiple "parts" that together encode a higher-level biological behavior and perform useful human-defined functions. Such constructs are the engineering target for most projects in synthetic biology. Included within this class of constructs are genetic circuits, sensors, biosynthetic pathways, and microbiological functions. Genetic Devices: Read More [+]
Objectives & Outcomes
Course Objectives: (1) To introduce the basic biology and engineering principles for constructing genetic devices including biochemical devices, microbiological devices, genetic circuits, eukaryotic devices, and developmental devices, (2) To familiarize students with current literature examples of genetic devices and develop literature searching skills; (3) To develop the students' ability to apply computational tools to the design of genetic devices.
Student Learning Outcomes: Students will be able to (1) use mathematical models to describe the dynamics of genetic devices, (2) comprehend and evaluate publications related to any type of genetic device, (3) perform a thorough literature search, (4) evaluate the technical plausibility of a proposed genetic device, (5) analyze a design challenge and propose a plausible solution to it in the form of a genetic device, and (6) assess any ethical or safety issues associated with a proposed genetic device.
Terms offered: Spring 2024, Spring 2022, Spring 2021
This course is aimed at graduate and advanced undergraduate students from the (bio) engineering and chemo-physical sciences interested in a research-oriented introduction to current topics in systems biology. Focusing mainly on two well studied microbiological model systems--the chemotaxis network and Lambda bacteriophage infection--the class systematically introduces key concepts and techniques for biological network deduction, modelling, analysis, evolution and synthetic network design. Students analyze the impact of approaches from the quantitative sciences--such as deterministic modelling, stochastic processes, statistics, non-linear dynamics, control theory, information theory, graph theory, etc.--on understanding biological processes, including (stochastic) gene regulation, signalling, network evolution, and synthetic network design. The course aims identify unsolved problems and discusses possible novel approaches while encouraging students to develop ideas to explore new directions in their own research. Frontiers in Microbial Systems Biology: Read More [+]
Rules & Requirements
Prerequisites: Designed for graduates with background in differential equations and probability. Course work in molecular cell biology or biochemistry helpful
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Terms offered: Fall 2024, Fall 2019, Fall 2018
The course provides project-based learning experience in understanding product design, with a focus on the human body as a mechanical machine. Students will learn the design of external devices used to aid or protect the body. Topics will include forces acting on internal materials (e.g., muscles and total replacement devices), forces acting on external materials (e.g., prothetics and crash pads), design/analysis of devices aimed to improve or fix the human body, muscle adaptation, and soft tissue injury. Weekly laboratory projects will incorporate EMG sensing, force plate analysis, and interpretation of data collection (e.g., MATLAB analysis) to integrate course material to better understand contemporary design/analysis/problems. Adv Designing for the Human Body: Read More [+]
Objectives & Outcomes
Course Objectives: The purpose of this course is twofold:
•
to learn the fundamental concepts of designing devices that interact with the human body;
•
to enhance skills in mechanical engineering and bioengineering by analyzing the behavior of various complex biomedical problems;
•
To explore the transition of a device or discovery as it goes from “benchtop to bedside”.
•
Three separate written projects evaluating devices that interact with the body. Projects will focus on 1) biomechanical analysis, 2) FDA regulations and procedures, and 3) design lifecycle.
Student Learning Outcomes: Working knowledge of design considerations for creating a device to protect or aid the human body, force transfer and distribution, data analysis, and FDA approval process for new devices. Understanding of basic concepts in orthopaedic biomechanics and the ability to apply the appropriate engineering concepts to solve realistic biomechanical problems, knowing clearly the assumptions involved. Critical analysis of current literature and technology.
Rules & Requirements
Prerequisites: Proficiency in MatLab or equivalent. Prior knowledge of biology or anatomy is not assumed
Credit Restrictions: There will be no credit given for MEC ENG C178 / BIO ENG C137 after taking MEC ENG 178.
Hours & Format
Fall and/or spring: 15 weeks - 1-3 hours of lecture per week
Terms offered: Spring 2023, Spring 2022, Spring 2021
This course covers applications of probabilistic modeling to topics in bioinformatics, with an emphasis on literature study and novel tool development. Areas covered vary from year to year but typically include finite-state Markov models as models of point substitution processes; graphical models and dynamic programming; basic coalescent theory; grammar theory; birth-death processes and the Thorne-Kishino-Felsenstein model of indels; general PDE methods and applications to continuous-state models; the Chinese restaurant process in population genetics and ecology; data compression algorithms; general techniques including conjugate priors, MCMC, and variational methods. Probabilistic Modeling in Computational Biology: Read More [+]
Objectives & Outcomes
Course Objectives: To introduce the most commonly used statistical models and associated inference techniques for the analysis and organization of biological sequences, with a focus on models based on evolutionary theory.
Student Learning Outcomes: Students will be familiar with the bioinformatics literature and underyling theory for discrete Markov processes, Bayesian networks, stochastic grammars, birth-death processes, Chinese restaurant processes, data compression algorithms, and related methods such as dynamic programming and MCMC.
Rules & Requirements
Prerequisites: Recommended preparation: MATH 53 (multivariable calculus), MATH 54 (linear algebra), MATH 126 (partial differential equations); or consent of instructor
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 3 hours of laboratory per week
Terms offered: Spring 2024, Spring 2023
An introduction to mathematical optimization, statistical models, and advances in machine learning for the physical sciences. Machine learning prerequisites are introduced including local and global optimization, various statistical and clustering models, and early meta-heuristic methods such as genetic algorithms and artificial neural networks. Building on this foundation, current machine learning techniques are covered including deep learning artificial neural networks, Convolutional neural networks, Recurrent and long short term memory (LSTM) networks, graph neural networks, decision trees. Machine Learning, Statistical Models, and Optimization for Molecular Problems: Read More [+]
Objectives & Outcomes
Course Objectives: To build on optimization and statistical modeling to the field of machine learning techniques To introduce the basics of optimization and statistical modeling techniques relevant to chemistry students To utilize these concepts on problems relevant to the chemical sciences.
Student Learning Outcomes: Students will be able to understand the landscape and connections between numerical optimization, stand-alone statistical models, and machine learning techniques, and its relevance for chemical problems.
Rules & Requirements
Prerequisites: Math 53 and Math 54; Chem 120A or 120B or BioE 103; or consent of intructor
Credit Restrictions: Students will receive no credit for BIO ENG C242 after completing BIO ENG 242. A deficient grade in BIO ENG C242 may be removed by taking BIO ENG 242.
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Teresa Head-Gordon
Formerly known as: Bioengineering C242/Chemistry C242
Terms offered: Fall 2011, Fall 2010, Fall 2009
An introduction to biophysical simulation methods and algorithms, including molecular dynamics, Monte Carlo, mathematical optimization, and "non-algorithmic" computation such as neural networks. Various case studies in applying these areas in the areas of protein folding, protein structure prediction, drug docking, and enzymatics will be covered. Core Specialization: Core B (Informatics and Genomics); Core D (Computational Biology); Bioengineering Content: Biological. Computational Methods in Biology: Read More [+]
Rules & Requirements
Prerequisites:MATH 53 and MATH 54; and programming experience preferred but not required
Credit Restrictions: Students will receive no credit for 243 after taking 143.
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture, 1 hour of discussion, and 2 hours of laboratory per week
Terms offered: Spring 2017, Fall 2008, Fall 2007
This course will introduce students to the bioinformatics algorithms used by biologists to identify homologs, construct multiple sequence alignments, predict protein structure, estimate phylogenetic trees, identify orthologs, predict protein-protein interaction, and build hidden Markov models. The focus is on the algorithms used, and on the sources of various types of errors in these methods. This class includes no programming, and no programming background is required. Introduction to Protein Informatics: Read More [+]
Objectives & Outcomes
Course Objectives: This course is designed to provide a theoretical framework for protein sequence and structure analysis using bioinformatics software tools. Students completing this course will be prepared for subsequent in-depth studies in bioinformatics, for algorithm development, and for the use of bioinformatics methods for biological discovery. It is aimed at two populations: students in the life sciences who need to become expert users of bioinformatics tools, and students in engineering and mathematics/computer science who wish to become the developers of the next generation of bioinformatics methods. As virtually all the problems in this field are very complex, there are many opportunities for research and development of new methods.
Student Learning Outcomes: Students completing this course are likely to find several potential areas of research of interest, which they may want to work on as independent study projects during undergraduate work, or take on as Master’s or Ph.D. thesis topics for advanced work.
Rules & Requirements
Prerequisites: Prior coursework in algorithms (e.g., COMPSCI 170) is highly recommended. The class does not include programming, and no prior programming experience is required, although students need to be comfortable reading and writing pseudocode (precise text descriptions of algorithms
Credit Restrictions: BioE 144 or previous BioE/PMB C144
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Sjolander
Formerly known as: Bioengineering C244/Plant and Microbial Biology C244
Terms offered: Prior to 2007
This course is intended to provide hands-on experience with a variety of bioinformatics tools, web servers and databases that are used to predict protein function and structure. This course will cover numerous bioinformatics tasks including: homolog detection using BLAST and PSI-BLAST, hidden Markov model construction and use, multiple sequence alignment, phylogenetic tree construction, ortholog identification, protein structure prediction, active site prediction, cellular localization, protein-protein interaction and phylogenomic analysis. Some minimal programming/scripting skills (e.g., Perl or Python) are required to complete some of the labs. Protein Informatics Laboratory: Read More [+]
Rules & Requirements
Prerequisites: One upper-division course in molecular biology or biochemistry (e.g., MCELLBI C100A/CHEM C130). Python programming (e.g., COMPSCI 61A) and experience using command-line tools in a Unix environment
Credit Restrictions: BioE 144L or BioE C144L/PMB C144L
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of laboratory and 2 hours of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Sjolander
Formerly known as: Bioengineering C244L/Plant and Microbial Biology C244L
Terms offered: Spring 2024, Spring 2023, Spring 2022
Genome-scale experimental data and modern machine learning methods have transformed our understanding of biology.This course investigates classical approaches and recent machine learning advances in genomics including:
1)Computational models for genome analysis.
2)Applications of machine learning to high throughput biological data.
3)Machine learning for genomic data in health.
This course builds on existing skills to introduce methodologies for probabilistic modeling, statistical learning, and dimensionality reduction, while grounding these methods in understanding genomic information.
Course Objectives: This course aims to equip students with a foundational understanding of computational and machine learning techniques used in genomics and computational biology.
Student Learning Outcomes: Students completing this course should have a better understanding of some of the challenges in machine learning as applied to biology
Students completing this course should have stronger programming skills.
Students completing this course should have the ability to apply simple statistical and machine learning techniques to complex genomics data
Rules & Requirements
Prerequisites: Bio 1A or BioE 11, Math 54, CS61B; CS70 or Math 55 recommended
Credit Restrictions: Students will receive no credit for BIO ENG 245 after completing BIO ENG 145.
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 3 hours of laboratory per week
Terms offered: Fall 2024, Fall 2023, Fall 2021
The field of synthetic biology is quickly emerging as potentially one of the most important and profound ways by which we can understand and manipulate our physical world for desired purposes. In this course, the field and its natural scientific and engineering basis are introduced. Relevant topics in cellular and molecular biology and biophysics, dynamical and engineering systems, and design and operation of natural and synthetic circuits are covered in a concise manner that then allows the student to begin to design new biology-based systems. Principles of Synthetic Biology: Read More [+]
Objectives & Outcomes
Course Objectives: (1) To introduce the basics of Synthetic Biology, including quantitative cellular network characterization and modeling, (2) to introduce the principles of discovery and genetic factoring of useful cellular activities into reusable functions for design, (3) to inculcate the principles of biomolecular system design and diagnosis of designed systems, and (4) to illustrate cutting-edge applications in Synthetic Biology and to enhance skull sin analyzing and designing synthetic biological applications.
Student Learning Outcomes: The goals of this course are to enable students to: (1) design simple cellular circuitry to meet engineering specification using both rational/model-based and library-based approaches, (2) design experiments to characterize and diagnose operation of natural and synthetic biomolecular network functions, and (3) understand scientific, safety and ethical issues of synthetic biology.
Terms offered: Fall 2024, Fall 2023, Fall 2022
This course will cover metabolic engineering and the various synthetic biology approaches for optimizing pathway performance. Use of metabolic engineering to produce biofuels and general "green technology" will be emphasized since these aims are currently pushing these fields. The course is meant to be a practical guide for metabolic engineering and the related advances in synthetic biology as well the related industrial research and opportunities. Bioenergy and Sustainable Chemical Synthesis: Metabolic Engineering and Synthetic Biology Approaches: Read More [+]
Terms offered: Fall 2024, Fall 2023
This course provides a survey of the computational analysis of genomic data, introducing the material through lectures on biological concepts and computational methods, presentations of primary literature, and practical bioinformatics exercises. The emphasis is on measuring the output of the genome and its regulation. Topics include modern computational and statistical methods for analyzing data from genomics experiments: high-throughput RNA sequencing data, single-cell data, and other genome-scale measurements of biological processes. Students will perform original analyses with Python and command-line tools. Computational Functional Genomics: Read More [+]
Objectives & Outcomes
Course Objectives: This course aims to equip students with practical proficiency in bioinformatics analysis of genomic data, as well as understanding of the biological, statistical, and computational underpinnings of this field.
Student Learning Outcomes: Students completing this course should have stronger programming skills, practical proficiency with essential bioinformatics methods that are applicable to genomics research, understanding of the statistics underlying these methods, and awareness of key aspects of genome function and challenges in the field of genomics.
Rules & Requirements
Prerequisites: Math 54 or EECS 16A/B; CS 61A or another course in python; BioE 11 or Bio 1a; and BioE 131. Introductory statistics or data science is recommended
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Terms offered: Fall 2022, Fall 2021, Fall 2020
The course is designed for graduate students interested in the emerging field of nanomedicine. The course will involve lectures, literature reviews and proposal writing. Students will be required to formulate a nanomedicine research project and write an NIH-style proposal during the course. The culmination of this project will involve a mock review panel in which students will serve as peer reviewers to read and evaluate the proposals. Nanomaterials in Medicine: Read More [+]
Objectives & Outcomes
Course Objectives: To review the current literature regarding the use of nanomaterials in medical applications; (2) To describe approaches to nanomaterial synthesis and surface modification; (3) To understand the interaction of nanomaterials with proteins, cells and biological systems; (4) To familiarize students with proposal writing and scientific peer review.
Student Learning Outcomes: Students should be able to (1) identify the important properties of metal, polymer and ceramic nanomaterials used in healthcare; (2) understand the role of size, shape and surface chemistry of nanomaterials in influencing biological fate and performance; (3) understand common methods employed for surface modification of nanomaterials; (4) comprehend the range of cell-nanomaterial interactions and methods for assaying these interactions; (5) read and critically review the scientific literature relating to nanomedicine; (6) formulate and design an experimental nanomedicine research project; (7) understand the principles of the peer review system.
Rules & Requirements
Prerequisites: Graduate Standing
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Terms offered: Spring 2015, Spring 2014, Spring 2013
Introduction and in-depth treatment of theory relevant to fluid flow in microfluidic and nanofluidic systems supplemented by critical assessment of recent applications drawn from the literature. Topics include low Reynolds Number flow, mass transport including diffusion phenomena, and emphasis on electrokinetic systems and bioanalytical applications of said phenomena. Micro/Nanofluidics for Bioengineering and Lab-On-A-Chip: Read More [+]
Objectives & Outcomes
Course Objectives: The course is an introduction to the physicochemical dynamics associated with fluid flow in nanoscale and microscale devices for graduate students and advance undergraduate students. The course has been created in response to the active field of microfluidics and nanofluidics, as well as the associated interest from industry, government, and academic research groups. The course provides an theoretical treatment of micro/nanofluidic phenomena that complements the well-established laboratory and research content offered in the Department. We will study mass and momentum transport phenomena of microscale and nanoscale flow devices. Throughout the course, we will place an emphasis on bioanalytical microfluidic system applications where electrophoresis, electroosmosis, molecular diffusion, and/or Brownian motion effects dominate. Successful completion of the course will prepare students to design micro/nanofluidic engineering solutions, as well as critically assess academic and industrial developments in these areas.
Student Learning Outcomes: 1.
To introduce students to the governing principles of fluid flow in microfluidic and nanofluidic regimes, with emphasis on phenomena relevant to bioanalytical devices.
2.
To provide students with an understanding of scaling laws that define the performance of microfluidic and nanofluidic systems.
3.
To provide students with a detailed investigation of applications that do and do not benefit from miniaturization.
4.
To give students adequate didactic background for critical assessment of literature reports and conference presentations regarding advances in the topical areas of microfluidics and nanofluidics.
Terms offered: Fall 2024, Fall 2023, Fall 2022
Students will be introduced to clinical areas with unmet needs, be introduced to the current standard of care or state of the art solutions for those needs, and learn to methodically conceptualize potential alternatives. The course will emphasize interaction between students and subject matter experts in these clinical areas and in the related fields of medtech and biotech innovation. Open innovative ideas from students are encouraged during the course. Clinical Need-Based Therapy Solutions: Read More [+]
Objectives & Outcomes
Course Objectives: (1) To expose students to clinical areas with major unmet need; (2) Expose students to current state of the art in therapy solutions for the above clinical need; (3) Stimulate innovation concept targeting high-impact clinical needs
Student Learning Outcomes: Students will be able to (1) Immerse in an enabling innovation environment stemming from the solution ideas by the students and mentor faculties; (2) Obtain potential avenues to enable capstone projects, UCSF collaborations, SBIR, etc.
Hours & Format
Fall and/or spring: 15 weeks - 2 hours of lecture per week
Terms offered: Spring 2024, Spring 2023, Spring 2021
This course is designed for students interested in an introduction to the biotechnology entrepreneurship, biotherapeutics R and D, and careers in the industry. Students should be interested in the impact of biotechnology on medicine and society, the history of the field (including individual scientists, entrepreneurs and companies), key methodologies, therapeutic product classes, entrepreneurship and innovation within the life sciences. Students will learn principles of drug and biologics discovery, development and commercialization, and will be exposed to the range of careers in the biopharmaceutical industry. Students should be considering careers in the biopharmaceutical and life sciences fields. Biotechnology Entrepreneurship: Impact, History, Therapeutics R&D, Entrepreneurship & Careers: Read More [+]
Objectives & Outcomes
Course Objectives: To educate students on careers in the biopharmaceutical industry To educate students on the history of the field and industry, including key methodologies, technologies, scientists, entrepreneurs, and companies To foster understanding and appreciation for the medical and societal impact of the biopharmaceutical field and industry To introduce the key steps in the process of discovery, development and commercialization of novel therapeutics o educate students on biopharmaceutical company entrepreneurship and innovation through team-based hands on virtual company creation
Student Learning Outcomes: Entrepreneurship principles, including those defined by the Lean Launchpad approach (including the Business Model Canvas, the Minimum Viable Product and Customer Discovery)
The history of the biotech industry
The impact of the biopharmaceutical industry on medicine and society
The methods, product technologies and development methodologies that have driven the evolution of the field
The nature of the ecosystem and specific careers in the biopharmaceutical industry
The product design and development process (with a focus on biotherapeutics), including opportunities and challenges
Hours & Format
Fall and/or spring: 15 weeks - 2 hours of lecture per week
Terms offered: Fall 2024, Fall 2023, Fall 2022
Biomedical imaging is a clinically important application of engineering, applied mathematics, physics, and medicine. In this course, we apply linear systems theory and basic physics to analyze X-ray imaging, computerized tomography, nuclear medicine, and MRI. We cover the basic physics and instrumentation that characterizes medical image as an ideal perfect-resolution image blurred by an impulse response. This material could prepare the student for a career in designing new medical imaging systems that reliably detect small tumors or infarcts. Medical Imaging Signals and Systems: Read More [+]
Objectives & Outcomes
Course Objectives: •
understand how 2D impulse response or 2D spatial frequency transfer function (or Modulation Transfer Function) allow one to quantify the spatial resolution of an imaging system.
•
understand 2D sampling requirements to avoid aliasing
•
understand 2D filtered backprojection reconstruction from projections based on the projection-slice theorem of Fourier Transforms
•
understand the concept of image reconstruction as solving a mathematical inverse problem.
•
understand the limitations of poorly conditioned inverse problems and noise amplification
•
understand how diffraction can limit resolution---but not for the imaging systems in this class
•
understand the hardware components of an X-ray imaging scanner
• •
understand the physics and hardware limits to spatial resolution of an X-ray imaging system
•
understand tradeoffs between depth, contrast, and dose for X-ray sources
•
understand resolution limits for CT scanners
•
understand how to reconstruct a 2D CT image from projection data using the filtered backprojection algorithm
•
understand the hardware and physics of Nuclear Medicine scanners
•
understand how PET and SPECT images are created using filtered backprojection
•
understand resolution limits of nuclear medicine scanners
•
understand MRI hardware components, resolution limits and image reconstruction via a 2D FFT
•
understand how to construct a medical imaging scanner that will achieve a desired spatial resolution specification.
Student Learning Outcomes: •
students will be tested for their understanding of the key concepts above
•
undergraduate students will apply to graduate programs and be admitted
•
students will apply this knowledge to their research at Berkeley, UCSF, the national labs or elsewhere
•
students will be hired by companies that create, sell, operate or consult in biomedical imaging
Rules & Requirements
Prerequisites: Undergraduate level course work covering integral and differential calculus, two classes in engineering-level physics, introductory level linear algebra, introductory level statistics, at least 1 course in LTI system theory including (analog convolution, Fourier transforms, and Nyquist sampling theory). The recommended undergrad course prerequisites are introductory level skills in Python or Matlab and either EECS 16A, EECS 16B and EL ENG 120, or MATH 54, BIO ENG 101, and BIO ENG 105
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Terms offered: Fall 2024, Fall 2022, Fall 2018
Topics in the emerging field of biophotonics with an emphasis on fluorescence spectroscopy, biosensors, and devices for optical imaging and detection of biomolecules. The course will cover the photophysics and photochemistry of organic molecules, the design and characterization of biosensors, and their applications within diverse environments, ranging from the detection of single molecules in vitro and in cells to studies of detection, diagnosis, and monitoring of specific health conditions and disease. Principles of Molecular and Cellular Biophotonics: Read More [+]
Rules & Requirements
Prerequisites: 102 or consent of instructor, and Chemistry 3A and Physics 7B
Credit Restrictions: Students will receive no credit for 263 after taking 163.
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Terms offered: Spring 2024, Spring 2023, Spring 2022
This course provides undergraduate and graduate bioengineering students with an opportunity to acquire essential experimental skills in fluorescence spectroscopy and the design, evaluation, and optimization of optical biosensors for quantitative measurements of proteins and their targets. Groups of students will be responsible for the research, design, and development of a biosensor or diagnostic device for the detection, diagnosis, and monitoring of a specific biomarker(s). Molecular and Cellular Biophotonics Laboratory: Read More [+]
Rules & Requirements
Prerequisites:BIO ENG 263; experience in a research lab; and consent of instructor
Credit Restrictions: Students will receive no credit for 263L after taking 163L.
Hours & Format
Fall and/or spring: 15 weeks - 6 hours of laboratory and 2 hours of discussion per week
Terms offered: Spring 2023, Spring 2021, Spring 2020, Spring 2019
Fundamentals of MRI including signal-to-noise ratio, resolution, and contrast as dictated by physics, pulse sequences, and instrumentation. Image reconstruction via 2D FFT methods. Fast imaging reconstruction via convolution-back projection and gridding methods and FFTs. Hardware for modern MRI scanners including main field, gradient fields, RF coils, and shim supplies. Software for MRI including imaging methods such as 2D FT, RARE, SSFP, spiral and echo planar imaging methods. Principles of Magnetic Resonance Imaging: Read More [+]
Objectives & Outcomes
Course Objectives: Graduate level understanding of physics, hardware, and systems engineering description of image formation, and image reconstruction in MRI. Experience in Imaging with different MR Imaging systems. This course should enable students to begin graduate level research at Berkeley (Neuroscience labs, EECS and Bioengineering), LBNL or at UCSF (Radiology and Bioengineering) at an advanced level and make research-level contribution
Credit Restrictions: Students will receive no credit for Bioengineering C265/El Engineering C225E after taking El Engineering 265.
Repeat rules: Course may be repeated for credit under special circumstances: Students can only receive credit for 1 of the 2 versions of the class,BioEc265 or EE c225e, not both
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture, 1 hour of discussion, and 3 hours of laboratory per week
Terms offered: Spring 2024, Spring 2023, Spring 2022
This course is designed as an introduction to the growing world of molecular imaging in medicine and research. The course is divided into five modules based on common imaging modalities (optical imaging, ultrasound methods, radiography, nuclear imaging, and magnetic resonance approaches). Within each module the fundamental physics and engineering behind each modality, corresponding methods for targeted molecular imaging including contrast mechanisms and probe design, and signal and image processing algorithms are covered. Homework assignments will utilize imaging data from either clinical or research studies in order to provide training in MATLAB based image analysis techniques.
Course Objectives: Discuss limitations to each targeted approach including non-specific binding, unbound probe clearance, signal decay, etc Discuss the design of targeted molecular contrast agents for each modality across myriad biological applications Establish a foundational understanding of MRI (multi-spectral), PET/SPECT, Ultrasound (including photo-acoustic imaging), and emerging methods including MPI Establish proficiency in the use of MATLAB as a tool for analyzing biomedical imaging data Reinforce mathematical principles relevant to image analysis including linear algebra, convolution and differential equations To discuss imaging ethics in the context of data interpretation To expose students interested in biomedical research or clinical practice to fundamentals of modern imaging methods and interpretation To learn quantitative approaches to analyze biomedical images (includes pharmacokinetic models, attenuation correction, cross modality registration, etc.)
Student Learning Outcomes: Analyze imaging data derived from imaging studies using commonly utilized image processing techniques
Critically evaluate scientific publications in the molecular imaging space.
Understand the devices, techniques and protocols used for in vivo imaging in research and clinical settings
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Terms offered: Spring 2023, Spring 2021
The course will provide students with an overview of the tight interface between neural engineering and neuroethological approaches in the field of neuroscience. This course will also discuss the concepts of causal manipulations, such as the control of brain circuits using optics and genetic engineering. Lastly, students will also inquire and discuss what discoveries have yet to be made and how neuroethological approaches can inform neural engineering designs that will revolutionize the future of neural medicine. Interface Between Neuroethology & Neural Engineering: Read More [+]
Objectives & Outcomes
Course Objectives: Understand the close interface between studies of the nervous system and technology
Student Learning Outcomes: The course will review the utilization, development and implementation of a wide diversity of neural engineering technologies to the study of the brain. Students will discuss the bidirectional road between the two approaches
The overreaching goal of this course is to expose student interested in neural engineering to the remarkable history of neuroethological approaches that have been a foundation of discoveries in the field.
Terms offered: Spring 2024, Spring 2023, Spring 2022
This class is designed to introduce MTM students to their professional responsibilities
as engineers and translational scientists. By the end of it, students will have
experience communicating their ideas appropriately and effectively to their peers,
their superiors, and those whom they manage or mentor. We will also discuss
methods for having a successful graduate school experience - choosing and working
on a project and preparing to meet post-graduate goals. Finally, some of the ethical
challenges likely to be met by a working bioengineer will be explored.
While this syllabus is meant to be an accurate description of the course and its content,
it may be modified at the instructor’s discretion.
Course Objectives: Objectives
● Communications skills and best practices
● Research ethics in translational medicine
● Professional development for MTM graduate students
Student Learning Outcomes: MTM students will become aware of ethical issues commonly confronted in
translational medicine and learn how to evaluate and act accordingly. They will also
leave capable of independently considering new ethical issues that arise during their
careers.
Rules & Requirements
Prerequisites: Open only to students in the Masters of Translational Medicine Graduate program
Hours & Format
Fall and/or spring: 15 weeks - 1 hour of lecture per week
Terms offered: Spring 2015, Spring 2013, Spring 2012
A three-module introduction to the fundamental topics of Nano-Science and Engineering (NSE) theory and research within chemistry, physics, biology, and engineering. This course includes quantum and solid-state physics; chemical synthesis, growth fabrication, and characterization techniques; structures and properties of semiconductors, polymer, and biomedical materials on nanoscales; and devices based on nanostructures. Students must take this course to satisfy the NSE Designated Emphasis core requirement. Introduction to Nano-Science and Engineering: Read More [+]
Rules & Requirements
Prerequisites: Major in physical science such as chemistry, physics, etc., or engineering; consent of advisor or instructor
Repeat rules: Course may be repeated for credit without restriction.
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructors: Gronsky, S.W. Lee, Wu
Also listed as: MAT SCI C261/NSE C201/PHYSICS C201
Terms offered: Fall 2015, Fall 2014, Fall 2013
After an introduction to the different aspects of our global energy consumption, the course will focus on the role of biomass. The course will illustrate how the global scale of energy guides the biomass research. Emphasis will be places on the integration of the biological aspects (crop selection, harvesting, storage, and distribution, and chemical composition of biomass) with the chemical aspects to convert biomass to energy. The course aims to engage students in state-of-art research. The Berkeley Lectures on Energy: Energy from Biomass: Read More [+]
Rules & Requirements
Prerequisites: Biology 1A; Chemistry 1B or 4B, Mathematics 1B
Repeat rules: Course may be repeated for credit under special circumstances: Repeatable when topic changes with consent of instructor.
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructors: Bell, Blanch, Clark, Smit, C. Somerville
Also listed as: CHEM C238/CHM ENG C295A/PLANTBI C224
Terms offered: Spring 2024, Spring 2023, Spring 2022
Students will learn how to translate a clinically relevant physical system into a governing equation with boundary conditions, and how to use this mathematical model to test and improve the design of medical devices and therapies. Problems of mass, heat, and momentum transport; the interaction of electromagnetic fields with materials (including tissue); and the mechanics of fluids and solids will be explored. Model-Based Design of Clinical Therapies: Read More [+]
Objectives & Outcomes
Course Objectives: •
Develop skills in translating physical problem statement into quantitative applied math construction
•
Emphasis will be on constructing problems statements into mathematical equations and boundary conditions.
Student Learning Outcomes: •
Use quantitative applied math construction to estimate dominant parameters or dimensionless groups in cutting-edge, industry-relevant problem statements
•
Students become well-versed in quantitative analysis of real life products and therapeutic applications
Rules & Requirements
Prerequisites: Calculus (MATH 54); BIO ENG 104 (preferred but not required); and/or consent of instructor
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Terms offered: Fall 2024, Spring 2024, Fall 2023
This course covers current topics of research interest in bioengineering. The course content may vary from semester to semester. Advanced Topics in Bioengineering: Read More [+]
Rules & Requirements
Prerequisites: Consent of instructor
Credit Restrictions: One hour of lecture per week per unit.
Repeat rules: Course may be repeated for credit without restriction.
Hours & Format
Fall and/or spring: 15 weeks - 1-4 hours of lecture per week
Terms offered: Spring 2018, Spring 2016, Spring 2012, Spring 2011
This course will help the advanced Ph.D. student further develop critically important technical communication traits via a series of lectures, interactive workshops, and student projects that will address the structure and creation of effective research papers, technical reports, patents, proposals, business plans, and oral presentations. One key concept will be the emphasis on focus and clarity--achieved through critical thinking regarding objectives and context. Examples will be drawn primarily from health care and bioengineering multidisciplinary applications. Advanced Technical Communication: Proposals, Patents, and Presentations: Read More [+]
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Offered for satisfactory/unsatisfactory grade only.
Terms offered: Not yet offered
This course emphasizes practical examples of medical innovation projects. The classroom pedagogy draws on industry professionals sharing real-world experiences. The goal is twofold: first, for students to get a better appreciation for why health innovation projects need to be managed differently to successfully navigate the clinical world; second, to gain familiarity with specific aspects and topics in medical product development that need to be done for successful implementation. Some speakers will provide insights into relevant careers in project management for medical technology. Project Management for Translational Medicine: Read More [+]
Hours & Format
Fall and/or spring: 15 weeks - 2 hours of lecture per week
Terms offered: Spring 2016, Fall 2015, Spring 2015
Members of the MTM Program Committee will help design several capstone projects in collaboration with clinical, academic, and/or industry partners, aiming to incorporate emerging technologies, industry requirements, and the potential for significant economic or social impact with regard to medicine and health care. All projects will be designed and vetted by the MTM Program Committee and in consultation with the MTM Advisory Board. For each selected project, an Academic Senate member from the Department of Bioengineering or BTS will serve as research adviser. MTM Capstone Project: Read More [+]
Objectives & Outcomes
Course Objectives: The objective of the one year professional MTM program is to develop engineering leaders who can synthesize the technical, environmental, economic, and social issues involved in the design and operation of complex engineering devices, systems, and organizations. Students will develop and demonstrate this skill at synthesis through the capstone project.
Student Learning Outcomes: Projects will provide practical instruction and experience in solving real problems in translational medicine, and it is anticipated that some will lead to innovations with commercial potential. This experience, undertaken by each student as a member of a team and marked by extensive interaction with faculty, peers, and industry partners, enables the student to integrate the leadership and technical dimensions of the professional MTM curriculum.
Rules & Requirements
Prerequisites: Graduate status in the MTM program
Repeat rules: Course may be repeated for credit without restriction.
Hours & Format
Fall and/or spring: 15 weeks - 9-9 hours of independent study per week
Terms offered: Fall 2024, Spring 2024, Fall 2023
This weekly seminar series invites speakers from the bioengineering community, as well as those in related fields, to share their work with our department and other interested parties on the Berkeley campus. The series includes our annual Bioengineering Distinguished Lecture and Rising Star lecture. Bioengineering Department Seminar: Read More [+]
Objectives & Outcomes
Course Objectives: •
To introduce students to bioengineering research as it is performed at Berkeley and at other institutions
•
To give students opportunities to connect their own work to work in the field overall
•
To give students an opportunity to meet with speakers who can inform and contribute to their post-graduation career paths
Student Learning Outcomes: To introduce students to the breadth of bioengineering research, both here at Berkeley and at other institutions, and help them to connect their work here at Berkeley to the field overall.
Rules & Requirements
Repeat rules: Course may be repeated for credit without restriction.
Hours & Format
Fall and/or spring: 15 weeks - 1 hour of seminar per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Offered for satisfactory/unsatisfactory grade only.
Terms offered: Fall 2024, Spring 2024, Fall 2023
Advanced studies in various subjects through special seminars on topics to be selected each year. Informal group studies of special problems, group participation in comprehensive design problems, or group research on complete problems for analysis and experimentation. Group Studies, Seminars, or Group Research: Read More [+]
Rules & Requirements
Repeat rules: Course may be repeated for credit without restriction.
Hours & Format
Fall and/or spring: 15 weeks - 1-8 hours of directed group study per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Offered for satisfactory/unsatisfactory grade only.
Terms offered: Fall 2024, Fall 2022, Fall 2021
Weekly seminars and discussions of effective teaching techniques. Use of educational objectives, alternative forms of instruction, and special techniques for teaching key concepts and techniques in bioengineering. Course is intended to orient new graduate student instructors to teaching in the Bioengineering department at Berkeley. Teaching Techniques for Bioengineering: Read More [+]
Rules & Requirements
Prerequisites: Graduate standing
Repeat rules: Course may be repeated for credit without restriction.
Hours & Format
Fall and/or spring: 15 weeks - 1 hour of seminar per week
Additional Details
Subject/Course Level: Bioengineering/Professional course for teachers or prospective teachers
Grading: Offered for satisfactory/unsatisfactory grade only.
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