printer friendly pageBIOE 36Q: The Biophysics of Innate Immunity
The innate immune system provides our first line of defense against disease--both infections, and cancer. Innate immune effectors such as host defense peptides are deployed by numerous cell types (for instance neutrophils, macrophages, NK cells, epithelial cells and keratinocytes) and work by biophysical mechanisms of action. The ourse draws from the primary literature and covers the evolution, structures, mechanisms,and physiological functions of important "innate immune effectors" (components of the innate immune system that can attack pathogens, and infected or host cells, and kill or incapacitate them directly). The course is aimed at students who have an interest in biochemistry, molecular/cellular biology, biophysics, and/or bioengineering.
Terms: Aut
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Units: 3
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Grading: Letter or Credit/No Credit
Instructors:
Barron, A. (PI)
BIOE 44: Fundamentals for Engineering Biology Lab
Introduction to next-generation techniques in genetic, molecular, biochemical, and cellular engineering. Lab modules build upon current research including: gene and genome engineering via decoupled design and construction of genetic material; component engineering focusing on molecular design and quantitative analysis of experiments; device and system engineering using abstracted genetically encoded objects; and product development based on useful applications of biological technologies.
Terms: Aut, Spr
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Units: 4
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Grading: Letter (ABCD/NP)
Instructors:
Endy, A. (PI)
;
Shih, J. (PI)
BIOE 101: Systems Biology (BIOE 210)
Complex biological behaviors through the integration of computational modeling and molecular biology. Topics: reconstructing biological networks from high-throughput data and knowledge bases. Network properties. Computational modeling of network behaviors at the small and large scale. Using model predictions to guide an experimental program. Robustness, noise, and cellular variation. Prerequisites:
CME 102;
BIO 41,
BIO 42; or consent of instructor.
Terms: Aut
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Units: 4
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Grading: Letter (ABCD/NP)
Instructors:
Covert, M. (PI)
BIOE 141A: Biodesign Project I
First of a two quarter series. Team-based experience in biological and biomedical technology design including need validation, design, initial prototyping, analysis and quantitative testing. This course is open only to students in the undergraduate Bioengineering program.
Terms: Aut
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Units: 4
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Grading: Letter (ABCD/NP)
Instructors:
Camarillo, D. (PI)
;
Sanchez, G. (PI)
;
Shih, J. (PI)
;
Smolke, C. (PI)
...
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Instructors:
Camarillo, D. (PI)
;
Sanchez, G. (PI)
;
Shih, J. (PI)
;
Smolke, C. (PI)
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
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Units: 1-5
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Repeatable for credit
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Grading: Letter or Credit/No Credit
Instructors:
Altman, R. (PI)
;
Bammer, R. (PI)
;
Barron, A. (PI)
;
Batzoglou, S. (PI)
...
more instructors for BIOE 191 »
Instructors:
Altman, R. (PI)
;
Bammer, R. (PI)
;
Barron, A. (PI)
;
Batzoglou, S. (PI)
;
Boahen, K. (PI)
;
Bryant, Z. (PI)
;
Butte, A. (PI)
;
Camarillo, D. (PI)
;
Carter, D. (PI)
;
Cochran, J. (PI)
;
Covert, M. (PI)
;
Deisseroth, K. (PI)
;
Delp, S. (PI)
;
Endy, A. (PI)
;
Fahrig, R. (PI)
;
Feinstein, J. (PI)
;
Fisher, D. (PI)
;
Gambhir, S. (PI)
;
Gold, G. (PI)
;
Goodman, S. (PI)
;
Heilshorn, S. (PI)
;
Huang, K. (PI)
;
Jacobs, C. (PI)
;
Kovacs, G. (PI)
;
Krummel, T. (PI)
;
Kuhl, E. (PI)
;
Levenston, M. (PI)
;
Levin, C. (PI)
;
Lin, M. (PI)
;
Longaker, M. (PI)
;
Pauly, K. (PI)
;
Pelc, N. (PI)
;
Plevritis, S. (PI)
;
Prakash, M. (PI)
;
Quake, S. (PI)
;
Riedel-Kruse, H. (PI)
;
Sanger, T. (PI)
;
Schnitzer, M. (PI)
;
Scott, M. (PI)
;
Shenoy, K. (PI)
;
Smolke, C. (PI)
;
Spielman, D. (PI)
;
Swartz, J. (PI)
;
Taylor, C. (PI)
;
Yang, F. (PI)
;
Yock, P. (PI)
;
Zenios, S. (PI)
Gold, G. (PI)
;
Goodman, S. (PI)
;
Heilshorn, S. (PI)
;
Huang, K. (PI)
;
Jacobs, C. (PI)
;
Kovacs, G. (PI)
;
Krummel, T. (PI)
;
Kuhl, E. (PI)
;
Levenston, M. (PI)
;
Levin, C. (PI)
;
Lin, M. (PI)
;
Longaker, M. (PI)
;
Pauly, K. (PI)
;
Pelc, N. (PI)
;
Plevritis, S. (PI)
;
Prakash, M. (PI)
;
Quake, S. (PI)
;
Riedel-Kruse, H. (PI)
;
Sanger, T. (PI)
;
Schnitzer, M. (PI)
;
Scott, M. (PI)
;
Shenoy, K. (PI)
;
Smolke, C. (PI)
;
Spielman, D. (PI)
;
Swartz, J. (PI)
;
Taylor, C. (PI)
;
Yang, F. (PI)
;
Yock, P. (PI)
;
Zenios, S. (PI)
BIOE 191X: Out-of-Department Advanced Research Laboratory in Bioengineering
Individual research by arrangement with out-of-department instructors. Credit for 191X is restricted to declared Bioengineering majors pursuing honors and requires department approval. See
https://bioengineering.stanford.edu/education/undergraduate.html for additional information. May be repeated for credit.
Terms: Aut, Win, Spr, Sum
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Units: 1-15
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Repeatable for credit
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Grading: Letter (ABCD/NP)
Instructors:
Barres, B. (PI)
;
Elias, J. (PI)
BIOE 210: Systems Biology (BIOE 101)
Complex biological behaviors through the integration of computational modeling and molecular biology. Topics: reconstructing biological networks from high-throughput data and knowledge bases. Network properties. Computational modeling of network behaviors at the small and large scale. Using model predictions to guide an experimental program. Robustness, noise, and cellular variation. Prerequisites:
CME 102;
BIO 41,
BIO 42; or consent of instructor.
Terms: Aut
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Units: 4
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Grading: Letter (ABCD/NP)
Instructors:
Covert, M. (PI)
BIOE 214: Representations and Algorithms for Computational Molecular Biology (BIOMEDIN 214, CS 274, GENE 214)
Topics: introduction to bioinformatics and computational biology, algorithms for alignment of biological sequences and structures, computing with strings, phylogenetic tree construction, hidden Markov models, Gibbs Sampling, basic structural computations on proteins, protein structure prediction, protein threading techniques, homology modeling, 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, machine learning (clustering and classification), and natural language text processing. Prerequisites: programming skills; consent of instructor for 3 units.
Terms: Aut
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Units: 3-4
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Grading: Medical Option (Med-Ltr-CR/NC)
Instructors:
Altman, R. (PI)
BIOE 222A: Multimodality Molecular Imaging in Living Subjects I (RAD 222A)
Focuses on instruments and chemistries for imaging of cellular and molecular processes in vivo. Basics of instrumentation physics, chemistry of molecular imaging probes, and an introduction to preclinical and clinical molecular imaging modalities.
Terms: Aut
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Units: 4
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Grading: Medical Option (Med-Ltr-CR/NC)
Instructors:
Levin, C. (PI)
;
Moseley, M. (PI)
BIOE 224: Ultrasound Imaging and Therapeutic Applications (RAD 225)
Covers the basic concepts of ultrasound imaging including acoustic properties of biological tissues, transducer hardware, beam formation, and clinical imaging. Also includes the therapeutic applications of ultrasound including thermal and mechanical effects, visualization of the temperature and radiation force with MRI, tissue assessment with MRI and ultrasound, and ultrasound-enhanced drug delivery.
Terms: Aut
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Units: 3
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Grading: Letter or Credit/No Credit
Instructors:
Pauly, K. (PI)
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