Upper-Division

Principles of genetics and genomics focusing on how sequencing technologies enable us to understand gene function, genotype to phenotype relationships, and genetic inheritance.

Hands-on lectures and laboratory geared to teach basic tools and skills used in computational biology (genome browsers, sequence database searching, motif analysis, multiple sequence alignment, gene finders, phylogenetics analysis, protein structure visualization, and others). Web-based tools/databases are used on student laptops. Open to all science students; no prior programming or Unix experience required.

Investigates the mind as an adaptive system, the evolutionary history of the brain, and mathematical theories of knowledge representation and learning in humans and machines. Students build Jupyter notebooks that interact with human cerebral cortex organoids to explore adaptive processes in neural circuits. Taught in conjunction with BME 218. Students cannot receive credit for this course and BME 218.

Examines life in extreme environments with an emphasis on the viruses that live there. Integrates aspects of virology, molecular biology, and computational biology. Students investigate a high-salt, extreme environment at the Don Edwards National Wildlife Refuge, and use DNA extraction methods to find molecular evidence of the organisms that live there and describe the genetic content of viruses and the community living in those high-salt ponds.

For bioengineering senior thesis students, guidance in preparing a draft manuscript describing their senior research project. Students also practice conference-style oral or poster presentation.

For bioengineering, bioinformatics, and biology majors, focuses on engineering (i.e., changing) of proteins. Topics focus on practical aspects of protein engineering strategies that are crucial to modern biotechnology and biomedicinal applications.

Students address a current scientific question about protein stability using structure-guided protein engineering. Specifically, Students use recombinant DNA technology to produce an engineered protein that is predicted to have enhanced stability. Students then assess its stability with differential scanning fluorimetry. Students are billed a materials fee of $140.

First of a three-part series focused on senior design projects in biomolecular engineering. In this first part, students examine experiments that elucidated the function of biological macromolecules at the Angstrom scale, and how technologies related to those functions were invented and implemented. Guided by these examples, each student develops a senior design project concept or small business proposal and defends its utility, plausibility, and inventiveness in a written document and an oral presentation.

Second part of a three-course sequence that is the culmination of the bioengineering program for students who chose a senior design group project to fulfill their capstone requirement. Students apply knowledge and skills gained in biomolecular engineering coursework to articulate, organize, and plan a senior design group project. Student groups complete research, specification, planning, and procurement for their project. Includes technical discussions, design reviews, and formal presentations.

Final part of a three-course sequence that is the culmination of the bioengineering program for students who chose a senior design group project to fulfill their capstone requirement. Students apply knowledge and skills gained in biomolecular engineering coursework to articulate, organize, and plan a senior design group project. Student groups complete research, specification, planning, and procurement for their project. Includes technical discussions, design reviews, and formal presentations.

Advanced elective for biology majors, examining biology on the genome scale. Topics include genome sequencing; large scale computational and functional analysis; features specific to prokaryotic, eukaryotic, or mammalian genomes; proteomics; SNP analysis; medical genomics; and genome evolution.

Covers major recent advances in evolutionary genomics. Students learn to analyze and interpret scientific writing in depth. Students also present on work covered in the class and produce one research or review paper. Students cannot receive credit for this courses and course 232.

Introduces the fundamental aspects of bioinstrumentation that are essential for beginning-level employment in clinical, pharmaceutical , and biotechnology laboratories. The advantages and disadvantages of several instruments are discussed and demonstrated, such as thermocycler, polymerase chain reaction (PCR), next-generation DNA sequencing platforms, pyrosequencing, fabless nanofabrication, ion-sensitive measurements, microarray fabrication, and fluorescent-activated cell sorter (FACS).

Teaches programming while exploring object-oriented design, use of high-performance data containers (dictionaries and sets), and team-based development—all with the goal of producing reliable and usable research tools. No programming experience is required, but basic computer and molecular biology understanding is assumed. Students without prior programming experience may benefit from taking CSE 20 in preparation for this course. Students learn programming in Python to manipulate biological data. Programming assignments comprise the majority of the assignments, and a final project using skills developed in this course is required. Lab section registration is required. BioPython and other modules are introduced for use in the final project.

Python and its Numpy, Scipy, and Matplotlib packages as well as Inkscape are used on scientific data to generate publication-quality figures. Students cannot receive credit for this course and course 263.

Focuses on contemporary issues in commercializing biotechnology and genomics, emphasizing development of teamwork and communication skills. Topics include intellectual property management, fundraising, market analysis, and technology development as related to biotechnology start-ups. Students perform real-world tasks preparing for commercialization. Taught in conjunction with BME 275.

For bioengineering students interested in stem cells. Class uses project-based learning to discuss basic stem cell concepts and past breakthrough approaches to identify and design solutions for technological hurdles in stem cell research.

Introduces students to laboratory techniques for growing and differentiating embryonic stem cells, genetic manipulation of stem cells and imaging of stem cells. Students learn how to culture stem cells, count cells, transfect cells, image cells and analyze morphology of stem cells. In addition, students learn how to write lab reports and present their findings. Students are billed a materials fee of $175.

Basic concepts, experimental approaches, and therapeutic potential are discussed. Students gain experience in reading the primary scientific literature.

Seminar course where students develop a research proposal and the collaborative skills needed for independent research projects. Includes professional practice development in collaboration skills, project management, proposal development, and funding.

Writing by biomolecular engineers, not to general audiences, but to engineers, engineering managers, and technical writers. Exercises include job application and resume, library puzzle, graphics, laboratory protocols, document specification, progress report, survey article or research proposal, poster, and oral presentation.

This two-credit course is the first of three courses in a 12-credit collaborative research project available to students in physical sciences, and biomolecular engineering intended to satisfy the capstone requirement. Provides a multidisciplinary, collaborative research experience working on a project in synthetic biology. Working with one or more research faculty, student teams complete a substantial project. Multiple oral/written presentations are required, including a formal conference presentation. Prerequisite(s): BME 180. Enrollment is restricted to juniors and seniors. Enrollment is by instructor permission.

This five-credit course is the second of three courses in a 12-credit collaborative research project available to students in physical sciences and biomolecular engineering intended to satisfy the capstone requirement. Multiple oral/written presentations are required, including a formal conference presentation. Prerequisite(s): BME 188A. Enrollment is restricted to juniors and seniors. Enrollment is by instructor permission.

Third of three courses in a 12-credit collaborative research project available to students in physical sciences and biomolecular engineering intended to satisfy the capstone requirement. Students in this course sequence may be participating in the annual IGEM (International Genetically Engineered Machines) competition. Course includes training in specific skills relevant to the specific sub-team and overall project, including lab-specific training (pcr, DNA electrophoresis, gel documentation, standard reagent prep, lab safety, lab equipment, project specifics). Prerequisite(s): BME 188B. Enrollment is restricted to juniors and seniors. Enrollment is by instructor permission.

Provides for individual programs of study with specific aims and academic objectives carried out under the direction of a BME faculty member and a willing sponsor at a field site, using resources not normally available on campus. Credit is based upon written and oral presentations demonstrating the achievement of the objectives of the course. Students submit petition to sponsoring agency.

Provides for individual programs of study with specific aims and academic objectives carried out under the direction of a BME faculty member and a willing sponsor at a field site, using resources not normally available on campus. Credit is based upon written and oral presentations demonstrating the achievement of the objectives of the course. Students submit petition to sponsoring agency.

A program of study arranged between a group of students and a faculty member. Students submit petition to sponsoring agency.

A program of independent study arranged between a group of students and a faculty member. Students submit petition to sponsoring agency.

Students submit petition to sponsoring agency.

Students submit petition to sponsoring agency.

Students submit petition to sponsoring agency.

Students submit petition to sponsoring agency.

For fourth-year students majoring in bioinformatics or bioengineering.