Upper-Division

BME 105 Genetics in the Genomics Era

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

Credits

5

Instructor

Angela Brooks

Requirements

Prerequisite(s): BIOL 20A. Enrollment is restricted to bioengineering, biomolecular engineering and bioinformatics, biotechnology, and bioinformatics majors and proposed majors and bioinformatics minors.

Quarter offered

Spring

BME 110 Computational Biology Tools

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.

Credits

5

Instructor

The Staff, Todd Lowe, Angela Brooks, Russell Corbett-Detig, Daniel Kim, Joshua Stuart

Requirements

Prerequisite(s): BME 105, or BIOL 100, or BIOL 105, or BIOC 100A, or CHEM 103, or bioinformatics majors, or biomolecular engineering and bioinformatics majors.

Quarter offered

Fall, Winter, Spring

BME 122H Extreme Environmental Virology

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.

Credits

5

Instructor

The Staff, David Bernick

Requirements

Enrollment is restricted to College Scholar Students, and or by permission of the instructor.

General Education Code

TA

Quarter offered

Fall, Winter

BME 123T Senior Thesis Writing

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.

Credits

5

Instructor

Kevin Karplus, Mark Akeson, Terry Terhaar, Dianne Hendricks

Requirements

Prerequisite(s): BME 185 or CSE 185E. Concurrent enrollment in BME 193F or BME 195F or BME 198F or CSE 193F or CSE 195F or CSE 198F or ECE 193F or ECE 195F or ECE 198F is required. Enrollment is restricted to senior biomolecular engineering and bioinformatics and bioengineering majors.

Quarter offered

Winter

BME 128 Protein Engineering

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.

Credits

5

Instructor

The Staff, Rebecca Dubois

Requirements

Prerequisite(s): BIOL 20A; and BIOL 100 or BIOC 100A, or by permission of instructor.

Quarter offered

Winter

BME 128L Protein Engineering Laboratory

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.

Credits

2

Instructor

Rebecca Dubois

Requirements

Prerequisite(s): BME 128; and BIOL 101L, or BIOL 20L, or BME 21L. Enrollment is restricted to junior and senior bioengineering, biomolecular engineering, and bioinformatics majors; other majors by permission of instructor.

Quarter offered

Spring

BME 129A Project Design and Implementation in Biomolecular Engineering I

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.

Credits

5

Instructor

Mark Akeson, Nader Pourmand, Rebecca Dubois

Requirements

Prerequisite(s): BIOL 20A; BME 23L or BIOL 20L or BIOL 101L; BIOL 100 or BIOC 100A; and previous or concurrent enrollment in BME 185 or CSE 185E. Enrollment is restricted to junior and senior bioengineering and biomolecular engineering and bioinformatics majors or by permission of the instructor.

Quarter offered

Fall

BME 129B Project Design and Implementation in Biomolecular Engineering II

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.

Credits

5

Instructor

Mark Akeson, Russell Corbett-Detig

Requirements

Prerequisite(s): BME 129A or BME 150. Enrollment is restricted to senior bioengineering or biomolecular engineering and bioinformatics majors.

Quarter offered

Winter

BME 129C Project Design and Implementation in Biomolecular Engineering III

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.

Credits

5

Instructor

David Bernick, Mark Akeson, Nader Pourmand, Kim Daniel, Stuart Joshua

Requirements

Prerequisite(s): BME 129A and BME 129B. Enrollment is restricted to senior bioengineering or biomolecular engineering and bioinformatics majors.

Quarter offered

Spring

BME 130 Genomes

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.

Credits

5

Instructor

Richard Edward Green

Requirements

Prerequisite(s): BIOL 105 or BME 105; or permission of the instructor.

Quarter offered

Fall

BME 132 Evolutionary Genomics

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.

Credits

5

Instructor

Russell Corbett-Detig

Requirements

Prerequisite(s): BME 105 or BIOL 105 or METX 140. Enrollment is restricted to juniors and seniors.

General Education Code

TA

Quarter offered

Fall

BME 140 Bioinstrumentation

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).

Credits

5

Instructor

Nader Pourmand

Requirements

Prerequisite(s): BME 5; or BME 51A and BME 51B; or EE 101 and EE 101L; or BIOL 100; or BIOC 100A.

Quarter offered

Fall

BME 160 Research Programming in the Life Sciences

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 will be introduced for use in the final project.

Credits

6

Instructor

The Staff, David Bernick, Joshua Stuart

Requirements

Prerequisite(s): BIOL 20A or BIOL 21A.

General Education Code

MF

Quarter offered

Winter, Spring

BME 163 Applied Visualization and Analysis of Scientific Data

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.

Credits

3

Instructor

Christopher Vollmers

Requirements

Prerequisite(s): BME 160 or BME 205. Prerequisites can be waived in cases where students have the required programming skills. Enrollment is restricted to juniors and seniors.

Quarter offered

Spring

BME 175 Entrepreneurship in Biotechnology

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.

Credits

5

Instructor

Todd Lowe, Richard Edward Green

Quarter offered

Winter

BME 177 Engineering Stem Cells

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.

Credits

5

Instructor

Ali Shariati, Camilla Forsberg, Daniel Kim

Requirements

Prerequisite(s): BIOL 20A or by consent of instructor. Basic knowledge of molecular and cellular biology is required.

General Education Code

TA

Quarter offered

Spring

BME 178 Stem Cell Biology

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

Credits

5

Instructor

Camilla Forsberg, Daniel Kim

Requirements

Prerequisite(s): BIOL 110; BIOL 115 recommended.

General Education Code

TA

Quarter offered

Winter

BME 180 Professional Practice in Bioengineering

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.

Credits

2

Instructor

The Staff, David Bernick

Requirements

Prerequisite(s): previous or concurrent enrollment in BME 185 or CSE 185E. Enrollment is restricted to junior and senior bioengineering, biomolecular engineering and bioinformatics, and bioinformatics majors or by permission.

General Education Code

PR-E

Quarter offered

Winter

BME 185 Technical Writing for Biomolecular Engineers

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.

Credits

5

Instructor

Joy Hagen, Kevin Karplus, Dianne Hendricks

Requirements

Prerequisite(s): BIOL 20A; satisfaction of Entry Level Writing and Composition requirements; Enrollment restricted to junior and senior bioengineering, biomolecular engineering and bioinformatics, and biotechnology majors.

Quarter offered

Fall

BME 188A Synthetic Biology--Mentored Research A

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.

Credits

2

Instructor

David Bernick

Repeatable for credit

Yes

Quarter offered

Spring

BME 188B Synthetic Biology--Mentored Research B

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.

Credits

5

Instructor

David Bernick

Repeatable for credit

Yes

Quarter offered

Summer

BME 188C Synthetic Biology Mentored Research C

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.

Credits

5

Instructor

David Bernick

Quarter offered

Summer

BME 193 Field Study

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.

Credits

5

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

BME 193F Field Study

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.

Credits

2

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

BME 194 Group Tutorial

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

Credits

5

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

BME 194F Group Tutorial

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

Credits

2

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

BME 195 Senior Thesis Research

Students submit petition to sponsoring agency.

Credits

5

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

BME 195F Senior Thesis or Research

Students submit petition to sponsoring agency.

Credits

2

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

BME 198 Individual Study or Research

Students submit petition to sponsoring agency.

Credits

5

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

BME 198F Individual Study or Research

Students submit petition to sponsoring agency.

Credits

2

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

BME 199 Tutorial

For fourth-year students majoring in bioinformatics or bioengineering.

Credits

5

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

Cross-listed courses that are managed by another department are listed at the bottom.

Cross-listed Courses

BIOL 247 Stem Cell Research: Scientific, Ethical, Social, and Legal Issues

Investigates the scientific, ethical, social, and legal dimensions of human embryonic stem-cell research, including the moral status of the embryo; the concept of respect for life; ethical constraints on oocyte procurement; creation of embryonic chimeras; federal policies; and political realities. (Also offered as Biomolecular Engineering 247. Students cannot receive credit for both courses.) Prerequisite(s): Course in stem cell biology (ex: BME 278 Stem Cell Research) or the equivalent knowledge. Enrollment is restricted to graduate students.

Credits

2

Cross Listed Courses

BME 247

Instructor

Lindsay Hinck

Requirements

Prerequisite(s): Course in stem cell biology (ex: BME 278 Stem Cell Research) or the equivalent knowledge. Enrollment is restricted to graduate students.

SOCY 268A Science and Justice: Experiments in Collaboration

Considers the practical and epistemological necessity of collaborative research in the development of new sciences and technologies that are attentive to questions of ethics and justice. Enrollment is by permission of instructor. Enrollment is restricted to graduate students.

Credits

5

Cross Listed Courses

BME 268A, FMST 268A, ANTH 267A

Instructor

James Doucet-Battle

SOCY 268B Science and Justice Research Seminar

Provides in-depth instruction in conducting collaborative interdisciplinary research. Students produce a final research project that explores how this training might generate research that is more responsive to the links between questions of knowledge and questions of justice. Prerequisite(s): SOCY 268A, BME 268A, FMST 268A, or ANTH 267A. Enrollment is restricted to graduate students and by permission of the instructor.

Credits

5

Cross Listed Courses

FMST 268B, BME 268B, ANTH 267B

Instructor

Julie Bettie, Rebecca London, Hiroshi Fukurai