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.
Instructor
The Staff, Todd Lowe, Angela Brooks, Russell Corbett-Detig, Daniel Kim, Joshua Stuart
Quarter offered
Winter, Spring
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.
Instructor
The Staff, David Bernick
General Education Code
TA
Quarter offered
Fall, Winter
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.
Instructor
Kevin Karplus, Mark Akeson, Terry Terhaar
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.
Instructor
The Staff, Rebecca Dubois
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.
Instructor
Rebecca Dubois
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.
Instructor
Mark Akeson, Nader Pourmand
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.
Instructor
Mark Akeson, Russell Corbett-Detig
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.
Instructor
David Bernick, Mark Akeson, Nader Pourmand
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.
Instructor
Richard Edward Green
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.
Instructor
Russell Corbett-Detig
General Education Code
TA
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).
Instructor
Nader Pourmand
No programming experience is required, but basic computer and molecular biology understanding is assumed. 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 introduced for use in the final project.
Instructor
The Staff, David Bernick, Joshua Stuart
General Education Code
MF
Quarter offered
Winter, Spring
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.
Instructor
Christopher Vollmers
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.
Instructor
Todd Lowe, Richard Edward Green
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.
Instructor
Ali Shariati, Camilla Forsberg, Daniel Kim
General Education Code
TA
Basic concepts, experimental approaches, and therapeutic potential are discussed. Students gain experience in reading the primary scientific literature.
Instructor
Camilla Forsberg, Daniel Kim
General Education Code
TA
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.
Instructor
The Staff, David Bernick
General Education Code
PR-E
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.
Instructor
Joy Hagen, Kevin Karplus
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.
Quarter offered
Fall, Winter, Spring
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.
Quarter offered
Fall, Winter, Spring
A program of study arranged between a group of students and a faculty member. Students submit petition to sponsoring agency.
Quarter offered
Fall, Winter, Spring
A program of independent study arranged between a group of students and a faculty member. Students submit petition to sponsoring agency.
Quarter offered
Fall, Winter, Spring
Students submit petition to sponsoring agency.
Quarter offered
Fall, Winter, Spring
Students submit petition to sponsoring agency.
Quarter offered
Fall, Winter, Spring
Students submit petition to sponsoring agency.
Quarter offered
Fall, Winter, Spring
Students submit petition to sponsoring agency.
Quarter offered
Fall, Winter, Spring
For fourth-year students majoring in bioinformatics or bioengineering.
Quarter offered
Fall, Winter, Spring
Cross-listed Courses
Lectures and case studies explore principles and approaches in drug discovery and development, emphasizing concepts in pharmacology; medicinal chemistry; and genomics- and bioinformatics-based approaches to drug discovery to illustrate pathways from discovery through development for clinical use. Cannot receive credit for this course and METX 270.
Cross Listed Courses
CHEM 170, BME 170
Lectures and case studies explore principles and approaches in drug discovery and development, emphasizing concepts in pharmacology; medicinal chemistry; and genomics- and bioinformatics-based approaches to drug discovery to illustrate pathways from discovery through development for clinical use. Cannot receive credit for this course and course 170. (Formerly Frontiers in Drug Action and Discovery.)
Cross Listed Courses
CHEM 270, BME 270
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.
Cross Listed Courses
BME 268A, FMST 268A, ANTH 267A
Instructor
James Doucet-Battle
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.
Cross Listed Courses
FMST 268B, BME 268B, ANTH 267B
Instructor
Julie Bettie, Rebecca London, Hiroshi Fukurai