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Program Guidelines


The NIH Training Grant in Biotechnology Traineeships are awarded to Ph.D. degree seeking graduate students. Traineeships cover nine units of graduate level tuition and a partial stipend, are for two years or eight quarters, and run consecutively, including summer quarter, unless an internship is taken during the training period. In this case, the remaining quarter(s) of the award will be held, and training resumed by the trainee at the conclusion of the internship. It is expected that trainees will have broad interests in the area of biotechnology. The Program Director and Faculty Affiliates actively seek to provide an exposure to the broad scope of "Biotechnology" that goes beyond what a single department offers.

The key aspects of the program are:

Coursework

Each Trainee is expected to attend the ongoing quarterly seminar series Frontiers in Interdisciplinary Biosciences and to complete a one-quarter graduate-level course in Responsible Conduct of Research (course descriptions listed below)

CHEMENG 459. Frontiers in Interdisciplinary Biosciences-(Same as BIOSCHI 459, CHEM 459, PSYCH 459, BIOC 459, BIOE 459.) For specialists and non-specialists. Sponsored by the Stanford BioX Program . Three seminars per quarter address scientific and technical themes related to interdisciplinary approaches in bioengineering, medicine, and the chemical, physical, and biological sciences. Leading investigators from Stanford and the world present breakthroughs and endeavors that cut accros core disciplines. Pre-seminars introduce basic concepts and background for non-experts. Registered students must attend all-pre-seminars: others welcome. See BioX Courses. Recommended prerequisite: basic mathematics, biology, chemistry, and physics.
1 unit, Autumn, Winter, and Spring (Robertson)

MED 255. The Responsible Conduct of Research-Forum. How to identify and approach ethical dilemmas that commonly arise in biomedical research. Issues in the practice of research such as in publication and interpretation of data, and issues raised by academic/industrial interactions. Contemporary debates at the interface of biomedical science and society regarding research on stem cells, bioweapons, genetic testing, human subjects, and vertebrate animals. Completion fulfills NIH/ADAMHA requirement for instruction in the ethical conduct of research. Recommended prerequisite: research experience.
1 unit, Autumn, Winter, and Spring (Staff)

In addition each trainee is expected to complete three of the following courses: (However, related courses may be substituted with the approval of the Program Director). These must be courses outside of your degree department..

BIOC 202. Metabolic Biochemistry: Structure, Metabolism, and Energetics - Structure and function of biological molecules, enzyme kinetics and mechanisms, bioenergetics, pathways of intermediary metabolism and their control, and membrane structure and functions. Course offerred via online lectures and problem sets, with weekly small-group review sessions.
1-3 units, Autumn (Brutlag)
.

BIOC 214. Physical and Chemical Principles of Enzyme Function - Enzymatic mechanisms, with emphasis on the fundamental behavior of biochemical systems and the properties that emerge due to the complex nature of these systems. Student presentations on specific enzymes based on classic and current literature, developed in consultation with the instructor. Prerequisites: BIOC/SBIO241 and a course in organic chemistry.
3-5 units, not given 2005-2006 (Herschlag)

BIOC 218. Computational Molecular Biology - Online course; see Biochem 218. For molecular biologists and computer scientists. Major issues, existing methods, and future directions concerning biological sequences, rapid similarity searching, phylogenics, automated pattern learning, representing protein structure, gene expression profiling, clustering expressed genes, and discovering transcription factor binding sites. Lecture/lab. Final project. Enrollment limited to 40. Prerequisite: BIOSCI 52 or equivalent, or consent of instructor.
3 units, not given 2005-2006 (Brutlag)

BIOC 220. Chemistry of Biological Processes - (Same as MPHA 220) The principles of organic and physical chemistry as applied to biomolecules. Goal is a working knowledge of chemical principles that underlie biological processes and of chemical tools used to study and manipulate biological systems. Prerequisite: Organic Chemistry and Biochemistry or equivalent, or consent of instructor.
4 units, Autumn (Therlot, Harbury)

BIOC 241. Biological Macromolecules - (Enroll in SBIO 241) Introduction to the physical and chemical basis of macromolecular functions. The forces that stabilize biopolymers with three-dimensional structure and their functional implications. Thermodynamics, molecular forces, and kinetics of enzymatic and diffusion processes, and relationship to their practical application in experimental design and interpretation. Biological function at the level of individual molecular interactions and at the level of complex processes.
5 units, Autumn (Puglisi, Block, Herschlag, Kirkegaard, McKay, Pande, Gracia)

BIOE 200A. Molecular and Cellular Engineering - Preference to Bioengineering graduate students. The molecular and cellular bases of life from an engineering perspective. Metabolism, information flow and feedback, signal transduction, and means for engineering these processes. Clinical motivations and practical applications.
3 units, Autumn (Cochran, Staff)

BIOE 200B. Systems Biology and Tissue Engineering - Preference to Bioengineering graduate students. The interaction, communication, and disorders of organ systems. Major organ systems and engineering means of probing them. Relevant developmental biology and tissue engineering from cells to complex organs
3 units, Winter (Deisseroth, Staff)

BIOE 200C. Medical Devices, Diagnostics, and Pharmaceuticals, Technologies, Regulation, and Applications - Preference to Bioengineering graduate students. Major classes of technologies including imaging techniques, chemical diagnostics, drug design and delivery. Topics include pacemakers, fMRI, PCR, stents, and biomaterials. Principles, practical limitations, and features trade-offs in clinical settings.
3 units, Spring (Ku, Sorger)

BIOE 214. Representations & Algorithms for Computational Molecular Biology - (Enroll in BIOMEDIN 214, CS 274). Algorithms for alignment of biological sequences and structures, computing with strings, phylogenetic tree construction, hidden Markov models, computing with networks of genes, 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 terminology for molecular biology, graphical display of biological data, and genetics algorithms and programming applied to biological problems.
3-4 units, Spring (Altman)

BIOE 331. Biomolecular Engineering - This course will explore design and engineering of optimized biomolecules, with a special emphasis on proteins.  Course will include fundamentals of protein structure and function, combinatorial methodologies, and biophysical analyses of modified biomolecules. Clinically relevant examples from the literature and biotechnology industry will be used.
2-3 units, Spr (Cochran)

BIOE 360A. Tissue Engineering Lab - (Enroll in ME 385). Tissue engineering is an expanding discipline that applies biological and engineering principles to create substitutes or replacements for defective tissues or organs. The principles of cell biology as a foundation for using engineering approaches to generate tissue structure and function. Emphasis is on how scaffolds, smart polymers, and mechanical forces can be used to reproduce the physical environment that acts, at the whole organ system level, to maintain specialized cellular function through molecular and genetic mechanisms.
1-2 units, Winter (Jacob)

CHEMENG 355. Advanced Biochemical Engineering - (Same as BIOE 355). Quantitative biological concepts and the technological tools used to exploit the power of modern biology. How a cell interacts with and influences its environmental, and how a production organism is produced and optimized. Concepts for large-scale bioproduct production, isolation, and purification. How proteins are manufactured without living cells, how biopharmaceuticals are formulated and delivered, and the regulatory requirements for drug approval and sale. Prerequisite: BIOSCI 41 or equivalent.
3 units, Spring (Swartz)

CHEMENG 450. Introduction to Biotechnology Faculty from the schools of Medicine, Humanities and Sciences, and Engineering, and industrial speakers review the interrelated elements of modern biotechnology. Topics: life-cycle of a biotechnology company, therapeutic proteins, small molecule therapeutic, non-therapeutics protein products, small molecule products from biotechnology, manufacturing and formulation of therapeutic products from biotechnology, manufacturing and formulation of therapeutic products, drug delivery systems, medical devices, diagnostics, intellectual property in biotechnology. Prerequisite: graduate student of upper-division undergraduate in science or engineering.
3 units, Spring (Khosla)

CHEMENG 454. Metabolic Engineering Methods and Applications - The analysis and optimization of industrial organisms. Applications illustrate the basic principles of metabolic pathway regulations, metabolic flux analysis, and traditional and new methods for genetic engineering. Examples: production of amino acids, protein synthesis and post-translational modification, and the production of isoprenoids, peptides, and polyketides. Prerequisites: CHEMENG 250, 355 or equivalent.
3 units, Spring(Swartz)

Trainee Bi-Weekly Journal Club Meetings

Trainees must attend the Trainees Meetings held approximately twice each month for one hour.

Biotechnology Symposium

Trainees must participate in the NIH Training Grant in Biotechnology Industrial Biotechnology Symposium and Poster Session held annually.

Reading Committee

Trainees must establish a Reading Committee and meet with committees at least once each year.

Internships

Trainees must set aside one quarter for their industrial internship, usually in the San Francisco Bay Area; there are approximately 35 industrial affiliates associated with this training grant. Internships are to be arranged with the approval of the trainee's advisor with regards to timing. The NIH grant Program Director will assist with the arrangements. During their internship, trainees take a one-quarter or 3-months leave of absence from the university, and the Industrial Affiliate Biotechnology Company that provide the internship pays trainee's normal quarterly stipend.


To contact us:
Roosmery Yang - NIH Grant Administrator
Department of Chemical Engineering
Stauffer III, Mail Code 5025
Stanford University
Stanford, CA 94305-5025
Tel: (650) 736-1807
Fax: (650) 725-7294
rwyang@stanford.edu

Link to Stanford University's Site

Professor James Swartz - Project DIrector
Department of Chemical Engineering
Stauffer III, Mail Code 5025
Stanford University
Stanford, CA 94305-5025
Tel: (650) 723-5398
Fax: (650) 725-7294
jswartz@stanford.edu