Translational Medicine

University of California, Berkeley

About the Program

The Master of Translational Medicine (MTM) program links the Department of Bioengineering at Berkeley with the Department of Bioengineering and Therapeutic Sciences at UCSF and is designed to train students in applying translational research and engineering approaches to solve fundamental problems in healthcare delivery. The master’s program draws on the unique expertise and technological resources available at the two institutions to provide trainees with the tools necessary to address real-world problems in a creative, interdisciplinary team setting.

This program should appeal to engineers, scientists, and clinicians who seek to bring innovative treatments and devices into clinical use. Individuals with backgrounds in medicine, nursing, dentistry, and pharmacy are encouraged to apply. We anticipate that upon receiving their master’s degree or after further academic or clinical training, graduates will work in industries that deliver healthcare products or patient care. 

Coursework includes translational aspects of therapeutic science and principles of engineering design. Content covers the fundamentals of bioengineering, physiology and disease processes, along with core medical principles, clinical research methods, and clinical trials design, as well as basics of business and management. The program culminates in a capstone design project experience in which students work in interdisciplinary teams co-advised by an engineering faculty member and an MD, PharmD, or clinician.

The MTM program is focused specifically on training in translational medicine as opposed to basic research science. As such, this master’s degree is generally intended as a terminal degree for students interested in industry and entrepreneurship and is not a gateway to the Bioengineering PhD program.

Visit Program Website

Admissions

MTM Admissions

Please see the MTM Program website for detailed application instructions.

Admissions decisions are governed by committee, and are based on several factors in the application, including (but not limited to) test scores, academics, essays, letters of recommendation, and prior research and work experience. Students from all educational fields are eligible to apply, but all applicants should be aware that the masters curriculum includes required coursework in bioengineering fundamentals; applicants with a non-technical background should make it clear in their application why they feel that they will be able to handle the more rigorous technical components of the coursework. Applicants who already hold a master's degree in bioengineering (or a similar field) will need to carefully specify their reasons for pursuing this additional masters; duplicate degrees are not allowed.

Please note: Applicants who intend to pursue additional degrees beyond the MTM program should be prepared to explain their intended educational trajectory.

Admission to the University

Minimum Requirements for Admission

The following minimum requirements apply to all graduate programs and will be verified by the Graduate Division:

  1. A bachelor’s degree or recognized equivalent from an accredited institution;
  2. A grade point average of B or better (3.0);
  3. If the applicant comes from a country or political entity (e.g., Quebec) where English is not the official language, adequate proficiency in English to do graduate work, as evidenced by a TOEFL score of at least 90 on the iBT test, 570 on the paper-and-pencil test, or an IELTS Band score of at least 7 (note that individual programs may set higher levels for any of these); and
  4. Sufficient undergraduate training to do graduate work in the given field.

Applicants Who Already Hold a Graduate Degree

The Graduate Council views academic degrees not as vocational training certificates, but as evidence of broad training in research methods, independent study, and articulation of learning. Therefore, applicants who already have academic graduate degrees should be able to pursue new subject matter at an advanced level without need to enroll in a related or similar graduate program.

Programs may consider students for an additional academic master’s or professional master’s degree only if the additional degree is in a distinctly different field.

Applicants admitted to a doctoral program that requires a master’s degree to be earned at Berkeley as a prerequisite (even though the applicant already has a master’s degree from another institution in the same or a closely allied field of study) will be permitted to undertake the second master’s degree, despite the overlap in field.

The Graduate Division will admit students for a second doctoral degree only if they meet the following guidelines:

  1. Applicants with doctoral degrees may be admitted for an additional doctoral degree only if that degree program is in a general area of knowledge distinctly different from the field in which they earned their original degree. For example, a physics PhD could be admitted to a doctoral degree program in music or history; however, a student with a doctoral degree in mathematics would not be permitted to add a PhD in statistics.
  2. Applicants who hold the PhD degree may be admitted to a professional doctorate or professional master’s degree program if there is no duplication of training involved.

Applicants may apply only to one single degree program or one concurrent degree program per admission cycle.

Required Documents for Applications

  1. Transcripts: Applicants may upload unofficial transcripts with your application for the departmental initial review. If the applicant is admitted, then official transcripts of all college-level work will be required. Official transcripts must be in sealed envelopes as issued by the school(s) attended. If you have attended Berkeley, upload your unofficial transcript with your application for the departmental initial review. If you are admitted, an official transcript with evidence of degree conferral will not be required.
  2. Letters of recommendation: Applicants may request online letters of recommendation through the online application system. Hard copies of recommendation letters must be sent directly to the program, not the Graduate Division.
  3. Evidence of English language proficiency: All applicants from countries or political entities in which the official language is not English are required to submit official evidence of English language proficiency. This applies to applicants from Bangladesh, Burma, Nepal, India, Pakistan, Latin America, the Middle East, the People’s Republic of China, Taiwan, Japan, Korea, Southeast Asia, most European countries, and Quebec (Canada). However, applicants who, at the time of application, have already completed at least one year of full-time academic course work with grades of B or better at a US university may submit an official transcript from the US university to fulfill this requirement. The following courses will not fulfill this requirement:
    • courses in English as a Second Language,
    • courses conducted in a language other than English,
    • courses that will be completed after the application is submitted, and
    • courses of a non-academic nature.

If applicants have previously been denied admission to Berkeley on the basis of their English language proficiency, they must submit new test scores that meet the current minimum from one of the standardized tests.

Where to Apply

Visit the Berkeley Graduate Division application page

Admission to the Program

Applicants from countries in which the official language is not English must also demonstrate English language proficiency.

Master's Degree Requirements

Curriculum

Satisfactory completion of the MTM program requires the completion of 24 semester (or equivalent) units of upper division and graduate courses, including 6 semester (or equivalent) units of a master’s capstone project administered by the MTM faculty directors. At least 12 semester units (or equiv) must be in 200 series courses chosen from the outline below and from an approved elective list.

Please see the MTM curriculum website for more detail.

Bioengineering Courses (at least 10 semester units or equivalent)

Courses Required
BIO ENG 270: Translational Challenges: Diagnostics, Devices, and Therapeutics (UCSF course, 2 quarter units)
BIO ENG 280Ethical and Social Issues in Translational Medicine (Berkeley)1
BIO ENG 296MTM Capstone Project (UCSF or Berkeley)3
Bioengineering Electives per approved study list

Clinical Needs and Strategies Courses (at least 6 semester units or equivalent)

Courses Required
EPI 150.03: Designing Clinical Research (UCSF, online course, 2 quarter units)
BIO ENG 260: Translational Challenges as Medicine--"Anti-Medical School" (UCSF course, 1 quarter unit)
BIO ENG 285: Health Care Finance and Economics (UCSF course, 2 quarter units)
BIO ENG 296MTM Capstone Project (UCSF or Berkeley)3
Clinical needs and strategies electives per approved study list

Business, Entrepreneurship & Technology Courses

Courses Required
ENGIN 271Engineering Leadership I (Berkeley)3
ENGIN 272Engineering Leadership II (Berkeley)3
Business/Entrepreneurship Electives per approved study list

Courses

Translational Medicine

BIO ENG 200 The Graduate Group Introductory Seminar 1 Unit

Terms offered: Spring 2018, Fall 2017, Spring 2017
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 [+]

BIO ENG 201 Responsible Conduct in Bioengineering Research and in Practice 1 Unit

Terms offered: Spring 2018
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.



Responsible Conduct in Bioengineering Research and in Practice: Read More [+]

BIO ENG C208 Biological Performance of Materials 4 Units

Terms offered: Fall 2017, Fall 2015
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 biote
chnology.
Biological Performance of Materials: Read More [+]

BIO ENG C209 Advanced Orthopedic Biomechanics 4 Units

Terms offered: Fall 2017, Fall 2016, Fall 2015
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 [+]

BIO ENG 211 Cell and Tissue Mechanotransduction 3 Units

Terms offered: Fall 2017, Fall 2016, Fall 2015
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 [+]

BIO ENG C212 Heat and Mass Transport in Biomedical Engineering 3 Units

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 [+]

BIO ENG C213 Fluid Mechanics of Biological Systems 3 Units

Terms offered: Spring 2016, Spring 2014, Spring 2011
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 [+]

BIO ENG C214 Advanced Tissue Mechanics 3 Units

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 [+]

BIO ENG C215 Molecular Biomechanics and Mechanobiology of the Cell 4 Units

Terms offered: Spring 2016, Spring 2015, Spring 2014
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 [+]

BIO ENG C216 Macromolecular Science in Biotechnology and Medicine 4 Units

Terms offered: Spring 2018, Spring 2017, Spring 2015, Spring 2014
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 [+]

BIO ENG C217 Biomimetic Engineering -- Engineering from Biology 3 Units

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 [+]

BIO ENG C218 Stem Cells and Directed Organogenesis 3 Units

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 [+]

BIO ENG C219 Protein Engineering 3 Units

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 [+]

BIO ENG 220L Cells and Biomaterials Laboratory 4 Units

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 [+]

BIO ENG 221 Advanced BioMEMS and Bionanotechnology 4 Units

Terms offered: Spring 2018, Spring 2017, Fall 2016
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 [+]

BIO ENG 221L BioMEMS and BioNanotechnology Laboratory 4 Units

Terms offered: Fall 2016, Spring 2015, Spring 2014
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 [+]

BIO ENG C222 Advanced Structural Aspects of Biomaterials 4 Units

Terms offered: Spring 2018, Spring 2016, Fall 2013
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 [+]

BIO ENG C223 Polymer Engineering 3 Units

Terms offered: Fall 2017, Fall 2015, Fall 2014
A survey of the structure and mechanical properties of advanced engineering polymers. Topics include rubber elasticity, viscoelasticity, mechanical properties, yielding, deformation, and fracture mechanisms of various classes of polymers. The course will discuss degradation schemes of polymers and long-term performance issues. The class will include polymer applications in bioengineering and medicine.

Polymer Engineering: Read More [+]

BIO ENG 224 Basic Principles of Drug Delivery 3 Units

Terms offered: Fall 2017, Fall 2016, Fall 2015
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.

Basic Principles of Drug Delivery: Read More [+]

BIO ENG 225 Biomolecular Structure Determination 3 Units

Terms offered: Fall 2017
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.

Biomolecular Structure Determination: Read More [+]

BIO ENG C230 Implications and Applications of Synthetic Biology 3 Units

Terms offered: Prior to 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.,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 [+]

BIO ENG C230 Implications and Applications of Synthetic Biology 3 Units

Terms offered: Prior to 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.,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 [+]

BIO ENG C230 Implications and Applications of Synthetic Biology 3 Units

Terms offered: Prior to 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.,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 [+]

BIO ENG C230 Implications and Applications of Synthetic Biology 3 Units

Terms offered: Prior to 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.,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 [+]

BIO ENG 231 Introduction to Computational Molecular and Cellular Biology 4 Units

Terms offered: Fall 2017, Fall 2016, Fall 2015
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 [+]

BIO ENG 232 Genetic Devices 4 Units

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 fun
ctions.
Genetic Devices: Read More [+]

BIO ENG 235 Frontiers in Microbial Systems Biology 4 Units

Terms offered: Spring 2017, Fall 2009
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 [+]

BIO ENG C237 Adv Designing for the Human Body 3 Units

Terms offered: Fall 2017
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 [+]

BIO ENG 241 Probabilistic Modeling in Computational Biology 4 Units

Terms offered: Spring 2018, Spring 2017, Spring 2016
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 [+]

BIO ENG 243 Computational Methods in Biology 4 Units

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 [+]

BIO ENG 244 Introduction to Protein Informatics 4 Units

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 [+]

BIO ENG 244L Protein Informatics Laboratory 3 Units

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 [+]

BIO ENG 245 Intro to Machine Learning in Computational Biology 4 Units

Terms offered: Fall 2017
This course will review the fundamentals of Data Science and data mining techniques. We will begin by reviewing Data Science across the disciplines, including guest lectures from data scientists on campus. As the semester progresses, we will focus increasingly on data science techniques in computational biology and bioinformatics, illustrating major methods and issues from these fields. Finally, we will discuss ethical issues related to data from biomedical research
and genomics.


Intro to Machine Learning in Computational Biology: Read More [+]

BIO ENG 247 Principles of Synthetic Biology 4 Units

Terms offered: Fall 2016, Fall 2015, Fall 2014
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 [+]

BIO ENG 248 Bioenergy and Sustainable Chemical Synthesis: Metabolic Engineering and Synthetic Biology Approaches 3 Units

Terms offered: Fall 2017, Fall 2016, Fall 2015
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 [+]

BIO ENG C250 Nanomaterials in Medicine 3 Units

Terms offered: Fall 2017, Fall 2016, Fall 2015
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 [+]

BIO ENG 251 Micro/Nanofluidics for Bioengineering and Lab-On-A-Chip 4 Units

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 [+]

BIO ENG 252 Clinical Need-Based Therapy Solutions 2 Units

Terms offered: Fall 2017, Fall 2016
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 [+]

BIO ENG C261 Medical Imaging Signals and Systems 4 Units

Terms offered: Fall 2017, Fall 2016, Fall 2015
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 [+]

BIO ENG 263 Principles of Molecular and Cellular Biophotonics 4 Units

Terms offered: Fall 2017, Fall 2016, Fall 2015
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 [+]

BIO ENG 263L Molecular and Cellular Biophotonics Laboratory 4 Units

Terms offered: Spring 2018, Spring 2017, Spring 2015
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 [+]

BIO ENG C265 Principles of Magnetic Resonance Imaging 4 Units

Terms offered: Spring 2018, Spring 2017, Spring 2016, Spring 2015
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 [+]

BIO ENG 280 Ethical and Social Issues in Translational Medicine 1 Unit

Terms offered: Spring 2018, Spring 2017, Fall 2016
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.

Ethical and Social Issues in Translational Medicine: Read More [+]

BIO ENG C280 Introduction to Nano-Science and Engineering 3 Units

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 [+]

BIO ENG C281 The Berkeley Lectures on Energy: Energy from Biomass 3 Units

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 [+]

BIO ENG 282 Model-Based Design of Clinical Therapies 3 Units

Terms offered: Spring 2018
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 [+]

BIO ENG 290 Advanced Topics in Bioengineering 1 - 4 Units

Terms offered: Spring 2018, Spring 2017, Fall 2016
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 [+]

BIO ENG C290D Advanced Technical Communication: Proposals, Patents, and Presentations 3 Units

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 [+]

BIO ENG 295 Bringing Biomedical Devices to Market 3 Units

Terms offered: Spring 2017
Engineering design is the process by which an idea is generated, developed, constructed, tested, and managed. Typical bioengineering courses often focus on idea conception and construction. True engineering design integrates not only these two essential elements, but also the process of evaluating, planning, and testing a product. This course highlights the context and value of product development: the formalized process bridging the gap between device proof-of-concept
and an FDA approved biomedical product in the marketplace. Instructor led lectures and student led case studies and exercises will form the core of the coursework.
Bringing Biomedical Devices to Market: Read More [+]

BIO ENG 296 MTM Capstone Project 3 Units

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 [+]

BIO ENG 297 Bioengineering Department Seminar 1 Unit

Terms offered: Not yet offered
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 [+]

BIO ENG 298 Group Studies, Seminars, or Group Research 1 - 8 Units

Terms offered: Spring 2018, Fall 2017, Spring 2017
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 [+]

BIO ENG 299 Individual Study or Research 1 - 12 Units

Terms offered: Spring 2018, Fall 2017, Spring 2017
Investigations of advanced problems in bioengineering.

Individual Study or Research: Read More [+]

BIO ENG N299 Individual Study or Research 1 - 6 Units

Terms offered: Summer 2013 10 Week Session, Summer 2012 10 Week Session, Summer 2009 10 Week Session
Investigations of advanced problems in bioengineering.

Individual Study or Research: Read More [+]

BIO ENG 301 Teaching Techniques for Bioengineering 1 Unit

Terms offered: Fall 2017, Fall 2016, Fall 2015
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 [+]

Faculty and Instructors

+ Indicates this faculty member is the recipient of the Distinguished Teaching Award.

Faculty

John Anderson, Assistant Professor.

Martin S. Banks, Professor. Stereopsis, virtual reality, optometry, multisensory interactions, self-motion perception, vision, depth perception, displays, picture perception, visual ergonomics.
Research Profile

Steven Brenner, Professor. Molecular biology, computational biology, evolutionary biology, bioengineering, structural genomics, computational genomics, cellular activity, cellular functions, personal genomics.
Research Profile

John Canny, Professor. Computer science, activity-based computing, livenotes, mechatronic devices, flexonics.
Research Profile

Jose M. Carmena, Professor. Brain-machine interfaces, neural ensemble computation, neuroprosthetics, sensorimotor learning and control.
Research Profile

Michelle Chang, Associate Professor.

Irina M. Conboy, Associate Professor. Stem cell niche engineering, tissue repair, stem cell aging and rejuvenation.
Research Profile

Yang Dan, Professor. Neuronal circuits, mammalian visual system, electrophysiological, psychophysical and computational techniques, visual cortical circuits, visual neurons.
Research Profile

John Eugene Dueber, Assistant Professor. Synthetic biology, Metabolic Engineering.
Research Profile

+ Robert J. Full, Professor. Energetics, comparative biomechanics, arthropod, adhesion, comparative physiology, locomotion, neuromechanics, biomimicry, biological inspiration, reptile, gecko, amphibian, robots, artificial muscles.
Research Profile

Jack L. Gallant, Professor. Vision science, form vision, attention, fMRI, computational neuroscience, natural scene perception, brain encoding, brain decoding.
Research Profile

Xiaohua Gong, Professor. Optometry, vision science, eye development and diseases, lens development.
Research Profile

Amy Herr, Associate Professor. Microfluidics, bioanalytical separations, diagnostics, electrokinetic transport, engineering design.
Research Profile

Tony M. Keaveny, Professor. Biomechanics of bone, orthopaedic biomechanics, design of artificial joints, osteoporosis, finite element modeling, clinical biomechanics.
Research Profile

Stanley A. Klein, Professor. Optometry, vision science, spatial vision modeling, psychophysical methods and vision test design, corneal topography and contact lens design, source localization of evoked potentials, fMRI, amblyopia.
Research Profile

Luke Lee, Professor. Biophotonics, biophysics, bionanoscience, molecular imaging, single cell analysis, bio-nano interfaces, integrated microfluidic devices (iMD) for diagnostics and preventive personalized medicine.
Research Profile

Seung-Wuk Lee, Associate Professor. Nanotechnology, bio-inspired nanomaterials, synthetic viruses, regenerative tissue engineering materials, drug delivery vehicles.
Research Profile

Song Li, Professor. Bioengineering, vascular tissue engineering, stem cell engineering, mechano-chemical signal transduction, biomimetic matrix, molecules, bioinformatic applications in tissue engineering, molecular dynamics.
Research Profile

Michel Maharbiz, Associate Professor. Neural interfaces, bioMEMS, microsystems, MEMS, microsystems for the life sciences.
Research Profile

Gerard Marriott, Professor.

Richard Mathies, Professor. Genomics, biophysical, bioanalytical, physical chemistry; laser spectroscopy, resonance Raman, excited-state reaction dynamics photoactive proteins, rhodopsins, microfabricated chemical biochemical analysis devices, forensics, infectious disease detection.
Research Profile

Mohammad Mofrad, Professor. Nuclear pore complex and nucleocytoplasmic transport, mechanobiology of disease, cellular mechanotransduction, integrin-mediated focal adhesions.
Research Profile

Niren Murthy, Professor.

+ Alexander Pines, Professor. Theory and experiment in magnetic resonance spectroscopy and imaging, quantum coherence and decoherence, novel concepts and methods including molecular and biomolecular sensors and microfluidics, laser hyperpolarization and detection, laser and zero-field NMR, in areas from material science to biomedicine.
Research Profile

Austin John Roorda, Professor. Adaptive optics, eye, vision, ophthalmoscopy, scanning laser ophthalmoscope, ophthalmology.
Research Profile

Kimmen Sjolander, Professor. Computational biology, algorithms, phylogenetic tree reconstruction, protein structure prediction, multiple sequence alignment, evolution, bioinformatics, hidden Markov models, metagenomics, statistical modeling, phylogenomics, emerging and neglected diseases, machine-learning, genome annotation, metagenome annotation, systems biology, functional site prediction, ortholog identification.
Research Profile

Lydia Sohn, Associate Professor. Micro-nano engineering.
Research Profile

Danielle Tullman-Ercek, Assistant Professor. Bioenergy, synthetic biology, protein engineering, bionanotechnology.
Research Profile

Emeritus Faculty

Thomas F. Budinger, Professor Emeritus. Image processing, biomedical electronics, quantitative aging, cardiovascular physiology, bioastronautics, image reconstruction, nuclear magnetic resonance, positron emission, tomography, reconstruction tomography, inverse problem mathematics.
Research Profile

Contact Information

Bioengineering Graduate Group

306 Stanley Hall

MC 1762

Phone: 510-642-5833

Fax: 510-642-5835

bioeng@berkeley.edu

Visit Program Website

Department Chair

Daniel Fletcher, PhD

Phone: 510-642-5833

bioe_chair@berkeley.edu

Executive Director, MTM Program

Michael "Moose" O'Donnell, PhD

306B Stanley Hall, UC Berkeley

Phone: 510-664-4472

http://bioeng.berkeley.edu/mtm

mooseo@berkeley.edu

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