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BIOS 200: Foundations in Experimental Biology

This course is divided into two 3-week cycles. During the first cycle, students will be developing a 2-page original research proposal, which may be used for NSF or other fellowship applications. In the second cycle, students will work in small teams and will be mentored by faculty to develop an original research project for oral presentation. Skills emphasized include: 1) reading for breadth and depth; 2) developing compelling, creative arguments; 3) communicating with the spoken and written word; 4) working in teams. Important features of the course include peer assessment, interactive joint classes, and substantial face-to-face discussion with faculty drawn from across the Biosciences programs. Shortened autumn quarter class; class meets during weeks 1 through 8 of the quarter.
Terms: Aut | Units: 5 | Grading: Medical Satisfactory/No Credit

BIOS 204: Practical Tutorial on the Modeling of Signal Transduction Motifs

Basics of ordinary differential equation modeling of signal transduction motifs, small circuits of regulatory proteins and genes that serve as building blocks of complex regulatory circuits. Morning session covers numerical modeling experiments. Afternoon session explores theory underpinning that day's modeling session. Modeling done using Mathematica, Standard Edition provided to enrolled students.
Terms: Aut | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOS 221: Modern Statistics for Modern Biology (STATS 366)

Application based course in nonparametric statistics. Modern toolbox of visualization and statistical methods for the analysis of data, examples drawn from immunology, microbiology, cancer research and ecology. Methods covered include multivariate methods (PCA and extensions), sparse representations (trees, networks, contingency tables) as well as nonparametric testing (Bootstrap, permutation and Monte Carlo methods). Hands on, use R and cover many Bioconductor packages. Prerequisite: Minimal familiarity with computers.
Terms: Aut, Sum | Units: 1-3 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOS 242: Writing Compelling Fellowships and Career Development Awards

An overview of principles and fundamentals for writing competitive fellowships (e.g. NIH F31, F32) and career development awards (e.g. NIH K Awards). Topics include: developing specific aims and career development plans; using the review criteria to inform writing; timelines and resources. Participants develop proposals through guided exercises with an emphasis on in-class peer review and focused faculty feedback.
Terms: Aut | Units: 2 | Grading: Satisfactory/No Credit
Instructors: ; Botham, C. (PI)

BIOS 254: DataLucence::Images

Increasingly, research in the biosciences involves data in digital formats and scientists spend a significant fraction of their time building and using software to harvest insight from digital data. A central goal of this course is to expose students to concepts adopted from computer science and data science regarding data management, data curation, and analytical workflows for analyzing digital data. We will focus on digital images since this image type is used in diverse sub-fields in the biosciences. The course will consist of a two-day workshop/lab¿SoftwareCarpentry¿and six DataLucence::Images+Hackathon class meetings.
Terms: Aut | Units: 2 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOS 271: Writing Graduate Research Fellowships

Initial sessions focus on the basics of grantsmanship, review criteria (i.e. intellectual merit and broader impact), and required materials, with particular focus on the National Science Foundation (NSF) Graduate Research Fellowship Program (GRFP). Students draft a 2-page research proposal and 3-page personal, relevant background and future goals statement. During small group peer review sessions, students receive detailed feedback to improve the clarity of their writing.
Terms: Aut | Units: 1 | Grading: Medical Satisfactory/No Credit

BIOS 274: Introductory Python Programming for Genomics

An inherent part of genomics research is the creation and then analysis of large quantities of data. A variety of useful tools are available for data analysis; however, research often requires the skill to create software scripts to extend the analysis. You will learn the basics of the Python programming language. Lectures will foster developing the basics through the process of writing code. Discussion sections will build on the skills from lectures by applying them to complete assigned problem sets. Problem sets are designed to learn good coding style, logic, and the use Python libraries. No programming experience is required.
Terms: Aut | Units: 3 | Grading: Medical Satisfactory/No Credit
Instructors: ; Cherry, J. (PI)

BIOS 277: Prions in Health & Disease

Prions consist of misfolded, polymerized proteins and are agents of transmissible neurodegenerative diseases such as bovine spongiform encephalopathy and Creutzfeldt-Jakob disease of man. However, "prion-like" polymerization of proteins is a more general phenomenon involved in a long-term memory, innate immunity and most likely other important functions. In microbes, prions are non0Mendelian genetic elements. The course will emphasize that "prion-like" polymerization is part of a more general allosteric regulation of gene expression that can sometimes go wrong, as in Alzheimer's and Parkinson's diseases, and only exceptionally may cause transmissible infectious disease that spread in the population.
Terms: Aut | Units: 1 | Grading: Medical Satisfactory/No Credit

BIOS 284: Diversifying Graduate Admissions

Admissions processes are inherently biased, but can we make them better? In four workshops, we will aim to: (1) examine literature on diversity and predictors of success in science/academia; (2) design and propose a holistic admissions rubric; and (3) discuss how to negotiate with program/department administrators. Topics will include bias (unconscious bias, performance bias, bias in publishing and funding), the myth of meritocracy, and ambient belonging.
Terms: Aut | Units: 1 | Grading: Satisfactory/No Credit

BIOS 285: Rodent Animal Models: Selection, Detection, Dissection, Inspection

This 2-week mini-course will discuss pragmatic approaches to rodent utilization with the aim of empowering graduate students across multiple disciplines to maximize rodent-derived data and minimize the redundant use of animals in biomedical research. Topics will include an introduction to clinical models, practical aspects of rodent blood collection and interpretation, algorithmic approaches to tissue collection for research applications, and an introduction to rodent histopathology, immunohistochemistry, and immunofluorescence. Course instructors include board-certified laboratory animal medicine clinicians and comparative pathologists that are expert h these topics. This course is open to graduate students with or without prior rodent experience.
Terms: Aut | Units: 1 | Grading: Medical Satisfactory/No Credit

BIOS 286: Single Cell Immunogenomics

Preference is for graduate students and undergraduates with background in biology and genetics. The emphasis of the course will be on learning the essential principles of single cell genomics as applied to research questions in immunology. The topics will include understanding the fundamental principles of the technology, experimental methods, types of single cell sequencing assays available and data analysis. The emphasis will be on how these methods are used to delineate immunologic cell types, their interactions with other cells in the local microenvironment and determining differential gene expression patterns and signatures. Specialized topics will include the analysis of single cell T-cell and B-cell receptor characteristics as well as joining antibody staining information at single cell resolution. Guest speakers will include thought leaders in the field who are demonstrating how single cell immunogenomics are being applied to immunotherapy development. Enrollment is limited.
Terms: Aut | Units: 1 | Grading: Medical Satisfactory/No Credit

BIOS 287: Proteostatis: guarding the proteome in health and disease

The control of cellular protein homeostasis, also called Proteostasis, is emerging as the central cellular process controlling the stability, function and quality control of the proteome and central to our understanding of a vast range of diseases. The proteostasis machinery maintains the function of destabilized and mutant proteins; assists the degradation of damaged and aggregated proteins and monitors the health of the proteome, adjusting it in response to environmental or metabolic stresses. This class will introduce students to the exciting cutting edge discoveries in this field, and will relate them to medical and biotechnology applications, as well as how a better understanding of proteostasis can be leveraged to understand fundamental biological processes, such as evolution and aging and to ameliorate a wide range of diseases. Given the increasingly close links between aging, protein misfolding, and neurodegenerative disease, understanding proteostasis networksis of critical fundamental and practical importance. These insights are particularly relevant in view of the increased prevalence of late-onset neurodegenerative aggregation diseases caused by an increasingly elderly population.
Terms: Aut | Units: 3 | Grading: Medical Satisfactory/No Credit

BIOS 290: Preparation & Practice: Law

Through tailored lecture, case study and a practical final project, Biosciences and interdisciplinary sciences students and trainees will learn how to apply the skills they acquired in their academic training to a career in Patent Prosecution and related fields. Taught by field and faculty experts, this is your opportunity to network with IP law representatives and to gain hands-on experience in a new career of choice option. Topics include: applying for positions, the importance of IP protection, licensing, overview of the patent process, drafting applications and litigation.
Terms: Aut | Units: 1 | Grading: Medical Satisfactory/No Credit

BIOS 294: Chemistry for Biologists and Others

Chemical transformations are central to biology and function, and chemical methods provide some of the most powerful tools for everyday experimental biology. Yet, most practitioners of biology have learned chemistry through memorization and do not use chemical principles or intuition in their research, even though chemistry underlies most processes and experiments carried out in biology and by biologists. Fortunately, a basic understanding and working knowledge can be gained in a short time, through a small set of simple concepts and limited number of memorized ¿facts¿. These concepts and facts will be introduced and then mastered through use in highly interactive, in-class problems and evaluation of selected literature. At the end of the three-week course students will have an ability to understand the chemistry underlying cellular processes and to better discuss and evaluate chemical tools and approaches. Prerequisites: High school or college introductory chemistry recommended but not required.
Terms: Aut | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOS 301: Graduate Environment of Support

Psychosocial, financial, and career issues in adapting graduate students to Stanford; how these issues relate to diversity, resources, policies, and procedures. Discussions among faculty, advanced graduate students, campus resource people, and the dean's office. (Thomas)
Terms: Aut | Units: 1 | Grading: Satisfactory/No Credit
Instructors: ; Thomas, A. (PI)
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