Graduate

BME 201 Scientific Writing

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.

Credits

3

Instructor

Richard Edward Green, Joshua Stuart

Requirements

Enrollment is restricted to graduate students.

Quarter offered

Winter

BME 205 Bioinformatics Models and Algorithms

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.

Credits

5

Instructor

The Staff, David Bernick, Kevin Karplus

Requirements

Enrollment is restricted to graduate students. Undergraduates may enroll with prerequisite(s): BME 160; and CSE 107 or STAT 131; and concurrent enrollment in BIOC 100A.

Quarter offered

Fall

BME 215 Applied Gene Technology

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.

Credits

5

Instructor

Nader Pourmand

Requirements

Enrollment is restricted to graduate students.

BME 229 Protein and Cell Engineering

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.

Credits

5

Instructor

Camilla Forsberg, Rebecca Dubois

Requirements

Enrollment is restricted to graduate students. Undergraduates by permission of instructor.

BME 230A Introduction to Computational Genomics and Systems Biology

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.

Credits

5

Instructor

Joshua Stuart, David Haussler, Benedict Paten

Requirements

Prerequisite(s): BME 205. Enrollment is restricted to juniors, seniors, and graduate students.

Quarter offered

Winter

BME 230B Advanced Computational Genomics and Systems Biology

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.

Credits

5

Instructor

Joshua Stuart, David Haussler, Benedict Paten

Requirements

Prerequisite(s): BME 230A. Enrollment is restricted to juniors, seniors, and graduate students.

BME 232 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 may not receive credit for this course and course 132.

Credits

5

Instructor

Russell Corbett-Detig

Requirements

Enrollment is restricted to graduate students. BME 105 or BIOL 105 or equivalent courses in higher-level genetic processes are highly recommended.

Quarter offered

Fall

BME 237 Applied RNA Bioinformatics

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.

Credits

5

Instructor

The Staff, Todd Lowe, Angela Brooks

Requirements

Enrollment is restricted to seniors and graduate students.

BME 263 Applied Visualization and Analysis of Scientific Data

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.

Credits

5

Instructor

Christopher Vollmers

Requirements

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

Quarter offered

Spring

BME 272 Precision Medicine

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.

Credits

5

Instructor

Daniel Kim

Requirements

Enrollment restricted to juniors, seniors, and graduate students.

Quarter offered

Fall

BME 275 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 Biomolecular Engineering 175.

Credits

5

Instructor

Todd Lowe, Richard Edward Green

Quarter offered

Winter

BME 278 Stem Cell Biology

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.

Credits

5

Instructor

Camilla Forsberg

Requirements

Enrollment is restricted to graduate students in PBSE program (Program in Biomedical Science and Engineering: Biomolecular Engineering and Bioinformatics (BMEB), Microbial Biology and Pathogenesis (MICRO), Chemical Biology, Biochemistry and Biophysics (CB3), Molecular, Cell and Developmental Biology (MCDB)) or consent of instructor.

Quarter offered

Winter

BME 280B Seminar on Bioinformatics and Bioengineering

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.

Credits

2

Instructor

Camilla Forsberg, Josh Stuart, Richard Edward Green, Angela Brooks, Daniel Kim, Shariati Ali, Todd Lowe, Christopher Vollmers

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

BME 281A Seminar on Processive Enzymes and Nanopores

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.

Credits

2

Instructor

Mark Akeson

Requirements

Enrollment is restricted to graduate students. Qualified undergraduates may enroll with permission of instructor.

Repeatable for credit

Yes

Quarter offered

Winter, Spring

BME 281C Seminar in Cancer Genomics

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.

Credits

2

Instructor

Joshua Stuart, David Haussler

Requirements

Enrollment is restricted to graduate students.

Repeatable for credit

Yes

Quarter offered

Winter, Spring

BME 281D Seminar on Protein Engineering

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.

Credits

2

Instructor

Rebecca Dubois

Requirements

Enrollment is restricted to graduate students.

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

BME 281E Seminar in Genomics

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.

Credits

2

Instructor

Richard Edward Green

Requirements

Enrollment is restricted to graduate students

Repeatable for credit

Yes

Quarter offered

Spring

BME 281F Blood Cell Development

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.

Credits

2

Instructor

Camilla Forsberg

Requirements

Enrollment is restricted to graduate students. Undergraduates may enroll with permission of instructor.

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

BME 281H Seminar in Comparative Genomics

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

Credits

2

Instructor

David Haussler

Requirements

Enrollment is restricted to graduate students; qualified undergraduates may enroll with permission of instructor.

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

BME 281J Seminar in Computational Genomics and Biomedicine

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.

Credits

2

Instructor

Benedict Paten

Requirements

Enrollment is restricted to graduate students.

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

BME 281L Seminar in Computational Genetics

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.

Credits

2

Instructor

Todd Lowe

Requirements

Enrollment is restricted to graduate students; qualified undergraduates may enroll with permission of instructor.

Repeatable for credit

Yes

Quarter offered

Fall

BME 281N Seminar in Transcriptomics

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.

Credits

2

Instructor

Angela Brooks

Requirements

Enrollment is restricted to graduate students.

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

BME 281P Seminar on Nanotechnology and Biosensors

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.

Credits

2

Instructor

Nader Pourmand

Requirements

Enrollment is restricted to graduate students; qualified undergraduates may enroll with permission of instructor.

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

BME 281R Seminar in Stem Cell Genomics

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.

Credits

2

Instructor

Daniel Kim

Requirements

Enrollment restricted to graduate students; qualified undergraduates may enroll with instructor permission.

Quarter offered

Fall, Winter, Spring

BME 281S Seminar in Computational Functional Genomics

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.

Credits

2

Instructor

Joshua Stuart

Requirements

Enrollment is restricted to graduate students; qualified undergraduates may enroll with permission of instructor.

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

BME 281V Immunogenomics Seminar

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

Credits

2

Instructor

Christopher Vollmers

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

BME 281Z Seminar in Population and Evolutionary Genomics

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.

Credits

2

Instructor

Russell Corbett-Detig

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

BME 293 Seminar in Biomolecular Engineering

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.

Credits

5

Requirements

Enrollment is restricted to graduate students; qualified undergraduates may enroll with permission of instructor.

BME 296 Research in Bioinformatics

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.

Credits

5

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

BME 297A Independent Study or Research

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.

Credits

5

Repeatable for credit

Yes

Quarter offered

Fall

BME 297B Independent Study or Research

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.

Credits

10

Repeatable for credit

Yes

Quarter offered

Winter

BME 297C Independent Study or Research

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.

Credits

15

Repeatable for credit

Yes

Quarter offered

Spring

BME 297F Independent Study or Research

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.

Credits

2

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

BME 299A Thesis Research

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.

Credits

5

Repeatable for credit

Yes

Quarter offered

Fall

BME 299B Thesis Research

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.

Credits

10

Repeatable for credit

Yes

Quarter offered

Winter

BME 299C Thesis Research

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.

Credits

15

Repeatable for credit

Yes

Quarter offered

Spring

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

Cross-listed Courses

METX 170 Drug Action and Development

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.

Credits

5

Cross Listed Courses

CHEM 170, BME 170

Instructor

Don Smith

Requirements

Prerequisite(s): BIOL 100 or CHEM 103 or BIOC 100A; BIOL 110, and BIOL 130 and BIOL 130L or BIOE 131 and BIOE 131L are recommended. Enrollment restricted to juniors and seniors.

METX 270 Drug Action and Development

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.)

Credits

5

Cross Listed Courses

CHEM 270, BME 270

Instructor

Don Smith

Requirements

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

Quarter offered

Winter

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