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BIOE 131: Ethics in Bioengineering (ETHICSOC 131X)

Bioengineering focuses on the development and application of new technologies in the biology and medicine. These technologies often have powerful effects on living systems at the microscopic and macroscopic level. They can provide great benefit to society, but they also can be used in dangerous or damaging ways. These effects may be positive or negative, and so it is critical that bioengineers understand the basic principles of ethics when thinking about how the technologies they develop can and should be applied. On a personal level, every bioengineer should understand the basic principles of ethical behavior in the professional setting. This course will involve substantial writing, and will use case-study methodology to introduce both societal and personal ethical principles, with a focus on practical applications.
Terms: Spr | Units: 3 | UG Reqs: GER:EC-EthicReas, WAY-ER

BIOE 191: Bioengineering Problems and Experimental Investigation

Directed study and research for undergraduates on a subject of mutual interest to student and instructor. Prerequisites: consent of instructor and adviser. (Staff)
Terms: Aut, Win, Spr, Sum | Units: 1-5 | Repeatable for credit

BIOE 212: Introduction to Biomedical Informatics Research Methodology (BIOMEDIN 212, CS 272, GENE 212)

Capstone Biomedical Informatics (BMI) experience. Hands-on software building. Student teams conceive, design, specify, implement, evaluate, and report on a software project in the domain of biomedicine. Creating written proposals, peer review, providing status reports, and preparing final reports. Issues related to research reproducibility. Guest lectures from professional biomedical informatics systems builders on issues related to the process of project management. Software engineering basics. Because the team projects start in the first week of class, attendance that week is strongly recommended. Prerequisites: BIOMEDIN 210 or 214 or 215 or 217 or 260. Preference to BMI graduate students. Consent of instructor required.
Terms: Spr | Units: 3-5
Instructors: Altman, R. (PI)

BIOE 214: Representations and Algorithms for Computational Molecular Biology (BIOMEDIN 214, CS 274, GENE 214)

Topics: This is a graduate level introduction to bioinformatics and computational biology, algorithms for alignment of biological sequences and structures, computing with strings, phylogenetic tree construction, hidden Markov models, basic structural computations on proteins, protein structure prediction, molecular dynamics and energy minimization, statistical analysis of 3D biological data, integration of data sources, knowledge representation and controlled terminologies for molecular biology, microarray analysis, chemoinformatics, pharmacogenetics, network biology. Note: For Fall 2021, Dr. Altman will be away on sabbatical and so class will be taught from lecture videos recorded in fall of 2018. The class will be entirely online, with no scheduled meeting times. Lectures will be released in batches to encourage pacing. A team of TAs will manage all class logistics and grading. Firm prerequisite: CS 106B.
Terms: Aut | Units: 3-4

BIOE 299B: Practical Training

Educational opportunities in high technology research and development labs in industry. Students engage in internship work and integrate that work into their academic program. Following internship work, students complete a research report outlining work activity, problems investigated, key results, and follow-up projects they expect to perform. Meets the requirements for curricular practical training for students on F-1 visas. Student is responsible for arranging own internship/employment and faculty sponsorship. Register under faculty sponsor's section number. All paperwork must be completed by student and faculty sponsor, as the student services office does not sponsor CPT. Students are allowed only two quarters of CPT per degree program. Course may be repeated twice.
Terms: Aut, Sum | Units: 1 | Repeatable 2 times (up to 2 units total)

BIOE 391: Directed Study

May be used to prepare for research during a later quarter in 392. Faculty sponsor required. May be repeated for credit.
Terms: Aut, Win, Spr, Sum | Units: 1-6 | Repeatable for credit
Instructors: Altman, R. (PI) ; Appel, E. (PI) ; Bammer, R. (PI) ; Barron, A. (PI) ; Batzoglou, S. (PI) ; Bintu, L. (PI) ; Boahen, K. (PI) ; Bowden, A. (PI) ; Brophy, J. (PI) ; Bryant, Z. (PI) ; Butte, A. (PI) ; Camarillo, D. (PI) ; Carter, D. (PI) ; Chaudhari, A. (PI) ; Chiu, W. (PI) ; Cochran, J. (PI) ; Covert, M. (PI) ; Curtis, C. (PI) ; Davis, M. (PI) ; Deisseroth, K. (PI) ; Delp, S. (PI) ; Endy, D. (PI) ; Ennis, D. (PI) ; Fahrig, R. (PI) ; Feinstein, J. (PI) ; Fischbach, M. (PI) ; Fordyce, P. (PI) ; Fuller, G. (PI) ; Gambhir, S. (PI) ; Gevaert, O. (PI) ; Giaccia, A. (PI) ; Gold, G. (PI) ; Goodman, S. (PI) ; Graves, E. (PI) ; Gurtner, G. (PI) ; Hargreaves, B. (PI) ; Heilshorn, S. (PI) ; Huang, K. (PI) ; Huang, P. (PI) ; Jarosz, D. (PI) ; Konermann, S. (PI) ; Kovacs, G. (PI) ; Krummel, T. (PI) ; Kuhl, E. (PI) ; Lee, J. (PI) ; Leskovec, J. (PI) ; Levenston, M. (PI) ; Levin, C. (PI) ; Lin, M. (PI) ; Liphardt, J. (PI) ; Longaker, M. (PI) ; Marsden, A. (PI) ; Melosh, N. (PI) ; Moore, T. (PI) ; Nishimura, D. (PI) ; Nolan, G. (PI) ; Pauly, K. (PI) ; Pelc, N. (PI) ; Plevritis, S. (PI) ; Poldrack, R. (PI) ; Prakash, M. (PI) ; Qi, S. (PI) ; Quake, S. (PI) ; Rogers, K. (PI) ; Sapolsky, R. (PI) ; Sattely, E. (PI) ; Schnitzer, M. (PI) ; Scott, M. (PI) ; Shenoy, K. (PI) ; Skylar-Scott, M. (PI) ; Smolke, C. (PI) ; Soltesz, I. (PI) ; Spielman, D. (PI) ; Swartz, J. (PI) ; Taylor, C. (PI) ; Theriot, J. (PI) ; Ting, A. (PI) ; Vasanawala, S. (PI) ; Venook, R. (PI) ; Wall, D. (PI) ; Wall, J. (PI) ; Wang, S. (PI) ; Woo, J. (PI) ; Wu, J. (PI) ; Yang, F. (PI) ; Yock, P. (PI) ; Zeineh, M. (PI) ; Zenios, S. (PI)

BIOE 392: Directed Investigation

For Bioengineering graduate students. Previous work in 391 may be required for background; faculty sponsor required. May be repeated for credit.
Terms: Aut, Win, Spr, Sum | Units: 1-10 | Repeatable for credit
Instructors: Airan, R. (PI) ; Alizadeh, A. (PI) ; Altman, R. (PI) ; Andriacchi, T. (PI) ; Annes, J. (PI) ; Appel, E. (PI) ; Baker, J. (PI) ; Bammer, R. (PI) ; Bao, Z. (PI) ; Barron, A. (PI) ; Batzoglou, S. (PI) ; Bertozzi, C. (PI) ; Bintu, L. (PI) ; Boahen, K. (PI) ; Bowden, A. (PI) ; Brophy, J. (PI) ; Bryant, Z. (PI) ; Butte, A. (PI) ; Camarillo, D. (PI) ; Carter, D. (PI) ; Chang, H. (PI) ; Chaudhuri, O. (PI) ; Chen, X. (PI) ; Cheng, C. (PI) ; Chichilnisky, E. (PI) ; Chiu, W. (PI) ; Cochran, J. (PI) ; Coleman, T. (PI) ; Contag, C. (PI) ; Covert, M. (PI) ; Criddle, C. (PI) ; Curtis, C. (PI) ; Dabiri, J. (PI) ; Dahl, J. (PI) ; Das, R. (PI) ; De Leo, G. (PI) ; DeSimone, J. (PI) ; Deisseroth, K. (PI) ; Delp, S. (PI) ; Demirci, U. (PI) ; Dionne, J. (PI) ; Elias, J. (PI) ; Endy, D. (PI) ; Engleman, E. (PI) ; Ennis, D. (PI) ; Etkin, A. (PI) ; Fahrig, R. (PI) ; Feinstein, J. (PI) ; Feng, L. (PI) ; Ferrara, K. (PI) ; Fire, A. (PI) ; Fischbach, M. (PI) ; Fordyce, P. (PI) ; Fuller, G. (PI) ; Gambhir, S. (PI) ; Ganguli, S. (PI) ; Gao, X. (PI) ; Garcia, C. (PI) ; Giaccia, A. (PI) ; Glenn, J. (PI) ; Glover, G. (PI) ; Gold, G. (PI) ; Goodman, S. (PI) ; Graves, E. (PI) ; Greenleaf, W. (PI) ; Gurtner, G. (PI) ; Hargreaves, B. (PI) ; Heilshorn, S. (PI) ; Heller, S. (PI) ; Herschlag, D. (PI) ; Huang, K. (PI) ; Huang, P. (PI) ; Idoyaga, J. (PI) ; Ingelsson, E. (PI) ; James, M. (PI) ; Jarosz, D. (PI) ; Jonikas, M. (PI) ; Khuri-Yakub, B. (PI) ; Kim, P. (PI) ; Konermann, S. (PI) ; Kovacs, G. (PI) ; Krasnow, M. (PI) ; Krummel, T. (PI) ; Kuhl, E. (PI) ; Kuo, C. (PI) ; Lee, J. (PI) ; Leskovec, J. (PI) ; Levenston, M. (PI) ; Levin, C. (PI) ; Lin, M. (PI) ; Liphardt, J. (PI) ; Longaker, M. (PI) ; Malenka, R. (PI) ; Marsden, A. (PI) ; Melosh, N. (PI) ; Monje-Deisseroth, M. (PI) ; Montgomery, S. (PI) ; Moore, T. (PI) ; Nishimura, D. (PI) ; Nolan, G. (PI) ; Nuyujukian, P. (PI) ; O'Brien, L. (PI) ; Okamura, A. (PI) ; Pauly, J. (PI) ; Pauly, K. (PI) ; Pelc, N. (PI) ; Petrov, D. (PI) ; Plevritis, S. (PI) ; Prakash, M. (PI) ; Qi, S. (PI) ; Quake, S. (PI) ; Rando, T. (PI) ; Raymond, J. (PI) ; Red-Horse, K. (PI) ; Reddy, S. (PI) ; Reijo Pera, R. (PI) ; Relman, D. (PI) ; Rose, J. (PI) ; Rutt, B. (PI) ; Saggar, M. (PI) ; Sanger, T. (PI) ; Santa Maria, P. (PI) ; Sapolsky, R. (PI) ; Satpathy, A. (PI) ; Sattely, E. (PI) ; Schnitzer, M. (PI) ; Scott, M. (PI) ; Shenoy, K. (PI) ; Skotheim, J. (PI) ; Skylar-Scott, M. (PI) ; Smolke, C. (PI) ; Snyder, M. (PI) ; Soh, H. (PI) ; Soltesz, I. (PI) ; Sonnenburg, J. (PI) ; Spielman, D. (PI) ; Sunwoo, J. (PI) ; Swartz, J. (PI) ; Taylor, C. (PI) ; Theriot, J. (PI) ; Walbot, V. (PI) ; Wall, D. (PI) ; Wang, B. (PI) ; Wang, P. (PI) ; Wang, S. (PI) ; Weissman, I. (PI) ; Wernig, M. (PI) ; Woo, J. (PI) ; Wu, J. (PI) ; Wu, S. (PI) ; Wyss-Coray, T. (PI) ; Xing, L. (PI) ; Yang, F. (PI) ; Yang, Y. (PI) ; Yock, P. (PI) ; Zeineh, M. (PI) ; Zenios, S. (PI)

BIOE 500: Thesis (Ph.D.)

(Staff)
Terms: Aut, Win, Spr, Sum | Units: 1-15 | Repeatable for credit
Instructors: Alizadeh, A. (PI) ; Altman, R. (PI) ; Andriacchi, T. (PI) ; Appel, E. (PI) ; Baker, J. (PI) ; Bammer, R. (PI) ; Bao, Z. (PI) ; Barron, A. (PI) ; Batzoglou, S. (PI) ; Bertozzi, C. (PI) ; Bintu, L. (PI) ; Boahen, K. (PI) ; Bryant, Z. (PI) ; Butte, A. (PI) ; Camarillo, D. (PI) ; Carter, D. (PI) ; Chang, H. (PI) ; Chaudhuri, O. (PI) ; Cheng, C. (PI) ; Chichilnisky, E. (PI) ; Cochran, J. (PI) ; Contag, C. (PI) ; Covert, M. (PI) ; Dabiri, J. (PI) ; Dahl, J. (PI) ; Deisseroth, K. (PI) ; Delp, S. (PI) ; Demirci, U. (PI) ; Elias, J. (PI) ; Endy, D. (PI) ; Engleman, E. (PI) ; Etkin, A. (PI) ; Fahrig, R. (PI) ; Feinstein, J. (PI) ; Feng, L. (PI) ; Fire, A. (PI) ; Fischbach, M. (PI) ; Fordyce, P. (PI) ; Gambhir, S. (PI) ; Ganguli, S. (PI) ; Garcia, C. (PI) ; Glenn, J. (PI) ; Glover, G. (PI) ; Gold, G. (PI) ; Goodman, S. (PI) ; Graves, E. (PI) ; Greenleaf, W. (PI) ; Hargreaves, B. (PI) ; Heilshorn, S. (PI) ; Huang, K. (PI) ; Huang, P. (PI) ; Khuri-Yakub, B. (PI) ; Kim, P. (PI) ; Kovacs, G. (PI) ; Krummel, T. (PI) ; Kuhl, E. (PI) ; Lee, J. (PI) ; Levenston, M. (PI) ; Levin, C. (PI) ; Lin, M. (PI) ; Liphardt, J. (PI) ; Longaker, M. (PI) ; Montgomery, S. (PI) ; Moore, T. (PI) ; Nishimura, D. (PI) ; Nuyujukian, P. (PI) ; Okamura, A. (PI) ; Pauly, J. (PI) ; Pauly, K. (PI) ; Pelc, N. (PI) ; Plevritis, S. (PI) ; Prakash, M. (PI) ; Qi, S. (PI) ; Quake, S. (PI) ; Rando, T. (PI) ; Raymond, J. (PI) ; Reijo Pera, R. (PI) ; Relman, D. (PI) ; Rose, J. (PI) ; Sanger, T. (PI) ; Sapolsky, R. (PI) ; Sattely, E. (PI) ; Schnitzer, M. (PI) ; Scott, M. (PI) ; Shenoy, K. (PI) ; Smolke, C. (PI) ; Soh, H. (PI) ; Spielman, D. (PI) ; Swartz, J. (PI) ; Taylor, C. (PI) ; Theriot, J. (PI) ; Wang, B. (PI) ; Wang, P. (PI) ; Weissman, I. (PI) ; Wernig, M. (PI) ; Woo, J. (PI) ; Wu, J. (PI) ; Xing, L. (PI) ; Yang, F. (PI) ; Yock, P. (PI) ; Zenios, S. (PI)