BME - Biomolecular Engineering

Introduces the tools and applications of biotechnology in the fields of medicine, agriculture, the environment, and industry.

The principles of life as it exists on this planet and how they generalize. Darwinian evolution, genomes, scientific theories of life (mechanistic, thermodynamic, information theoretic). Future of life: Internet, machine learning and adaptation, artificial intelligence, genome editing, fully artificial life.

Laboratory course providing hands-on training in fundamental techniques used to express, isolate, and analyze genes in prokaryotic cells. Introduction to common laboratory instruments and fundamental skills required for basic research in molecular biology and biomolecular engineering.

Project-based laboratory course providing hands-on training in fundamental molecular biology and biomolecular engineering techniques used to manipulate expression of DNA and proteins in prokaryotic cells. Students are introduced to essential processes in experimental design.

Laboratory-based course extending the wet lab skills developed in the first two quarters of the BME 2x series with bioinformatics skills that form the foundation of biomolecular engineering. Focuses on sequencing of low-diversity environmental samples, including: field sampling, DNA extraction from those samples, library preparation, hands-on sequencing using a Nanopore device, base-calling of the raw data, assembly of contigs, quality assessment, contig assignment to species/bins, automated annotation of a single assemblage from collection genome publication.

Lab-based course that introduces measuring, modeling, and designing electronics circuits, emphasizing voltage dividers and complex impedance culminating in simple, negative-feedback op amp circuits for amplifying audio signals.

Lab-based course that introduces designing, measuring, and modeling electronics circuits, emphasizing RC filters and negative-feedback amplifiers for various sensors circuits for amplifying audio signals, design of multi-stage amplifiers, instrumentation amplifiers, and class-D power amplifiers.

Course intended to assist second-year biomolecular engineering and bioinformatics undergraduates find research labs that they might join. Students sit in on different lab group meetings, read papers recommended by the lab groups, and report back to other students in the class both verbally and in writing. Course is offered for pass/no pass only.

Serves science and non-science majors interested in bioethics. Guest speakers and instructors lead discussions of major ethical questions having arisen from research in genetics, medicine, and industries supported by this knowledge.

Course will focus on understanding human genes. Accessible to non-science majors. Will cover principles of human inheritance and techniques used in gene analysis. The evolutionary, social, ethical, and legal issues associated with knowledge of the human genome will be discussed.

Provides a means for a small group of students to study a particular topic in consultation with a faculty sponsor. Students submit petition to sponsoring agency.

Provides a means for a small group of students to study a particular topic in consultation with a faculty sponsor. Students submit petition to sponsoring agency.

Students submit petition to sponsoring agency.

Students submit petition to sponsoring agency.

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.

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.

Covers effective writing styles for scientific communication for bio-science and engineering graduate students. Covers instruction for writing grant applications, scientific manuscripts, and thesis proposals. Students practice by preparing, editing, and evaluating each of these documents.

Covers bioinformatics models and algorithms: the use of computational techniques to convert the masses of information from biochemical experiments (DNA sequencing, DNA chips, and other high-throughput experimental methods) into useful information. Emphasis is on DNA and protein sequence alignment and analysis.

Detailed insight into the techniques and technological trends in genomics and transcriptomics, building the necessary foundations for further research in genetic association studies, population genetic association studies, population genetics, diagnostics, medicine, and drug development. Students should already have a deeper understanding of the basic tools of molecular biotechnology than acquired in introductory courses in biotechnology, biochemistry, and molecular biotechnology.

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 118. Students cannot receive credit for this course and BME 118.

Focuses on established and novel strategies for protein and cell engineering. Explores concepts, design, and practical applications of engineered proteins, cells, and organisms as research tools and in therapeutic applications. Recommended for graduate students with interests in bioengineering.

Introductory and intermediate-level topics in computational genomics, DNA and RNA sequence analysis, mapping, quantification, detection of variants and their associations with disease. Covers topics in machine-learning, probabilistic graphical models, gene regulatory network inference, and single cell analysis. Students conduct related independent research.

Covers advanced topics in computational genomics, DNA and RNA sequence analysis, mapping, quantification, detection of variants and their associations with disease. Topics include machine-learning, probabilistic graphical models, gene regulatory network inference, and single cell analysis. Students participate in teams in a computational analysis competition.

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 may not receive credit for this course and course 132.

Teaches methods for RNA gene discovery; gene expression quantification; probabalistic modeling, secondary structure/trans-interaction prediction; mRNA splicing; and functional analysis. Emphasis on leveraging comparative genomics and employing high-throughput RNA sequencing data. Includes lectures, scientific literature discussion, problem sets, and final gene-discovery project.

Python and its Numpy, Scipy, and Matplotlib packages as well as Inkscape are used to generate publication quality figures from scientific data. Students cannot receive credit for this course and course 163.

Focuses on modern "precision" approaches to understanding human health, where every patient is unique. Explores basic and clinical discoveries and 'omics-based medicine for the prevention, diagnosis, and treatment of disease. Emphasis is on genomic approaches and applications to cancer.

Course focuses on the application of epi/genomic technologies of stem cells. Topics include 'omics to interrogate pluripotency, cell lineages, hierarchies, trajectories, epigenomic reprogramming. Class includes hands-on computational analysis of epi/genomics data. For graduate/postdoctoral trainees engaged in stem cell research. Enrollment is restricted to graduate students and by permission of the instructor. Basic programming knowledge is recommended.

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 Biomolecular Engineering 175.

Basic stem cell concepts, experimental approaches, and therapeutic potential are discussed. Students gain experience in reading and critically evaluating the primary scientific literature. Students cannot receive credit for this course and BME 178.

Weekly seminar series covering topics of current research in computational biology, and bioinformatics. Current research work and literature in these areas are discussed. Short papers reflecting on presentations required. Available for Satisfactory/Unsatisfactory (or Pass/No Pass) grading only.

Weekly seminar series covering experimental research in nanopore technology and single-molecule analysis of polymerase function. Current research work and literature is discussed. Students lead some discussions and participate in all meetings.

Presents current computational biology research to identify genomics-based signatures of cancer onset, progression, and treatment response. Examples of such investigations include: genetic pathway interpretation of multivariate high-throughput datasets; discovery of mutations in whole-genome sequence; identifications and quantification of gene isoforms, alleles, and copy number variants; and machine-learning tools to predict clinical outcomes. Students present their own research, host journal clubs, and attend lectures and teleconferences to learn about research conducted by national and international projects.

Weekly seminar series covering experimental research in protein structure, function, and engineering. Current research work and literature in this area are discussed. Students lead some discussions and participate in all meetings.

Current topics in genomics including high-throughput sequencing, genome assembly, and comparative genomics. Students design and implement independent research projects. Weekly laboratory meetings are held to discuss these projects and related research in the field.

Weekly seminar covering topics in current research on blood cell development and stem cell biology. Current research and literature in these areas discussed. Students lead some discussions and participate in all meetings.

Weekly seminar series covering experimental research in cell fate decisions. Current research work and literature in this area is discussed. Students lead some discussions and participate in all meetings. Available for Satisfactory/Unsatisfactory or Pass/No Pass grading only.

Weekly seminar series covering topics of current computational and experimental research in live cell biotechnology. Current research work and literature in this area are discussed. Students lead some discussions and participate in all meetings. (Formerly offered as Seminar in Comparative Genomics.)

Research seminar of the UCSC Computational Genomic Laboratory and Platform Teams. Students receive hands-on instruction in modern computational methods to address research questions. Topics include: genomic and transcriptomic sequence analysis methods, comparative and evolutionary genomics, big-data genomic analysis, biomedical data sharing, and precision medicine. Students attend and participate in monthly lab meetings, monthly all-hands meetings, where students give a quick report on their progress and the next month's goals, and a bi-weekly journal club, where pairs of students present and discuss a paper of their choosing with the lab. Students also participate in hands-on, active computational laboratory-based research. Student evaluation is based on suitable progress toward research goals and graduate program progress.

Weekly seminar series covering topics and experimental research in computational genetics. Current research work and literature in this area discussed. Students lead some discussions and participate in all meetings.

Weekly seminar series covering experimental research in chromosome structure and repeat biology. Current research work and literature in this area is discussed. Students lead some discussions and participate in all meetings. Available for Satisfactory/Unsatisfactory or Pass/No Pass grading only.

Covers current topics in computational and experimental research in transcriptomics. Current research work and literature discussed. Weekly laboratory meetings held to discuss these projects and related research in the field.

Weekly seminar covering topics of research in the development of new tools and technologies to detect and study genes and proteins. Latest research work and literature in these areas are discussed. Students lead some discussions and participate in all meetings.

Weekly seminar series covering topics in research on stem cell genomics. Current research and literature in this area is discussed. Students lead some discussions and participate in all meetings.

Weekly seminar series covering topics of current computational and experimental research in computational functional genomics. Current research work and literature in this area discussed. Students lead some discussions and participate in all meetings.

Discusses research topics in 3D stem cell-derived brain organoid models, neuroengineering and systems neuroscience. Students lead some discussions and participate in all meetings. Available for Satisfactory/Unsatisfactory or Pass/No Pass grading only. Enrollment is restricted to graduate students; qualified undergraduate students may enroll with permission of the instructor.

Journal club and research presentations in immunogenomics. Enrollment is by consent of the instructor and is restricted to graduate students, juniors, and seniors.

Seminar course consisting of the Russell Lab's weekly meeting to cover lab business, present and discuss new results, practice presentations, and read recent scientific literature. May be repeated for credit. Enrollment is restricted to graduate students and is by permission of the instructor.

Includes the Yeh Lab’s weekly group meeting to discuss new data, present research paper, pitch new scientific idea, cover lab business, and practice presentations. Available for Satisfactory/Unsatisfactory or Pass/No Pass grading only.

Covers major recent topics in evolutionary and population genomics. Consists primarily of discussions of recent literature and updates on group members' research. Enrollment is available only to members of the Corbett-Detig laboratory.

Weekly seminar series covering topics of bioinformatics and biomolecular engineering research. Current research work and literature in this area discussed. Students lead some discussions and participate in all meetings.

Independent research in bioinformatics under faculty supervision. Although this course may be repeated for credit, not every degree program accepts a repeated course toward degree requirements. Students submit petition to sponsoring agency.

Independent study or research under faculty supervision. Although course may be repeated for credit, not every degree program accepts a repeated course toward degree requirements. Students submit petition to sponsoring agency.

Independent study or research under faculty supervision. Although course may be repeated for credit, not every degree program accepts a repeated course toward degree requirements. Students submit petition to sponsoring agency.

Independent study or research under faculty supervision. Although course may be repeated for credit, not every degree program accepts a repeated course toward degree requirements. Students submit petition to sponsoring agency.

Independent study or research under faculty supervision. Although course may be repeated for credit, not every degree program accepts a repeated course toward degree requirements. Students submit petition to sponsoring agency. Enrollment is restricted to graduate students.

Thesis research conducted under faculty supervision. Although course may be repeated for credit, not every degree program accepts a repeated course towards degree requirements.Students submit petition to sponsoring agency.

Thesis research conducted under faculty supervision. Although course may be repeated for credit, not every degree program accepts a repeated course towards degree requirements.Students submit petition to sponsoring agency.

Thesis research conducted under faculty supervision. Although course may be repeated for credit, not every degree program accepts a repeated course towards degree requirements.Students submit petition to sponsoring agency.