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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 201: Next Generation Sequencing and Applications

Usher in the golden age of biological discovery with next generation sequencing (NGS) through its wide spectrum of applications. Modules include general introduction of Next Generation Sequencing (NGS) technologies, applications of these sequencing technologies, caveats and comparisons with previous approaches, analysis and interpretation of sequencing data, principles of tools and resources and practical ways to utilize them, and features and pitfalls. Prerequisite: background in molecular biology.
Terms: Win | Units: 2 | Grading: Medical Option (Med-Ltr-CR/NC)
Instructors: ; Li, J. (PI)

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 | Units: 1-3 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOS 225: Diversity and Inclusion in Science

Introduction to the social science literature on factors contributing to gender disparities in the scientific workplace (e.g. implicit bias and stereotype threat). Discussions focus on steps that individuals and institutions can take to promote the advancement of women and other underrepresented groups in science, and thus promote the advancement of science.
Terms: Spr | Units: 1 | Grading: Medical Satisfactory/No Credit

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 256: Sculptural Data Illustrations

Mini-course. Students will use learn make and print 3D models of their data to use as a focal point when describing their project. We will teach the students how to use Autocad and Blender to process existing data sets and students are encouraged to bring their own data. We strive to make wearable models to enable instant mini-lectures any place and anytime.
Terms: Spr | Units: 1 | Grading: Medical Option (Med-Ltr-CR/NC)
Instructors: ; Schneider, D. (PI)

BIOS 257: HIV: The Virus, the Disease, the Research

Mini-Course. Medical students, graduate students in biological sciences, undergraduate students with strong biological background. Topics: Immunopathogenesis, immune deficits, opportunistic infections including TB, and malignancies; Genomics viral genetic analyses that have traced the origin of HIV-1 and HIV-2 to primates, dated the spread of infection in humans, and characterized theevolution of virus within infected individuals; Antiretroviral drug development identification of drug targets, structure-based drug design, overcoming drug resistance; Challenges of vaccine development; Public health strategies.
Terms: Sum | Units: 1 | Grading: Medical Satisfactory/No Credit
Instructors: ; Shafer, R. (PI)

BIOS 263: Applied Grant-Writing Skills for Fellowships

Graduate students in the Biosciences PhD Programs develop a fellowship proposal (e.g. NIH F31) focusing on required documents: 1-page specific aims as well as research and career development plans. Students establish a writing practice and learn fundamental grant writing skills through guided exercises, including in-class review and focused faculty feedback.
Terms: Spr | Units: 2 | Repeatable for credit | Grading: Medical Satisfactory/No Credit

BIOS 265: Introduction to Quantitative Reasoning in Biology

Mini-course. Focus on development of basic skills for quantitative reasoning in biology, including order-of-magnitude estimation and use of the broad spectrum of time scales to enable understanding. Primary examples include going from molecular size and energy scales to functions of single cells and going from mutational and selective processes acting on organisms to evolution of populations on laboratory global scales.
Terms: Win | Units: 2 | Grading: Medical Satisfactory/No Credit

BIOS 266: Mini Proposal Bootcamp

In an intensive 1-day format, students learn the fundamentals for writing competitive fellowships, i.e. NIH NRSA fellowships (F30, F31, F32). Topics include developing specific aims; outlining research and career development plans; and using the review criteria to inform writing. Students develop early drafts of the 1-page specific aims, NIH biosketch, and training plan, and receive feedback from instructor. Students are expected to be in the early stages of writing a fellowship proposal.
Terms: Spr | Units: 1 | Grading: Medical Satisfactory/No Credit
Instructors: ; Botham, C. (PI)

BIOS 270: Planetary Health: Socioeconomic & Ecological Links Between Human Health & Earth's Natural Ecosystems

Two of the biggest challenges humanity has to face - promoting human health and halting environmental degradation are are strongly connected and too big to be addressed in an incremental, sector-specific way. Breakthroughs can be achieved through a creative, interdisciplinary approach that fully recognizes the complex nature of links between human health and healthy, functioning ecosystems. Through a series of lectures and case-study discussions with experts from multiple Schools and Departments, students will develop an in-depth understanding of the "Planetary Health" concept, its foundation, goals, priority areas of action and methods of investigation, and the most relevant immediate and long-term challenges.
Terms: Win | Units: 2 | Grading: Medical Satisfactory/No Credit

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 279: Applied Grant-Writing Skills for Science and Engineering Students

Participants develop proposals in the non-medical fields of science and engineering (e.g. for the National Science Foundation) focusing on required documents such as the 1-page Project Summary, Broader Impacts, Intellectual Merit, and Research Plan. Students establish a writing practice and learn fundamental grant writing skills through guided exercises, including in-class review and focused faculty feedback.
Terms: Spr | Units: 2 | Repeatable for credit | Grading: Medical Option (Med-Ltr-CR/NC)

BIOS 280: Apico-basolateral Epithelial Cell Polarity

Cells must polarize, localizing unique macromolecules along distinct axes, to function correctly. This lecture/lab mini-course will provide students with a broad overview of cell polarity, using recent literature to guide understanding of the shared and divergent mechanisms underlying polarity establishment in different tissues and organisms. Additionally, students will engage in hands-on research using C. elegans and a large particle flow cytometer (BIOSORTER) to perform high throughput forward genetic screens to discover novel pathways involved in epithelial polarity establishment. This course is geared toward STEM graduate students, postdocs, and advanced undergraduates interested in topics and applications in cell and developmental biology.
Terms: Win | Units: 2 | Grading: Medical Satisfactory/No Credit

BIOS 281: Career Explorations Opportunities: Transitioning to your Career Choice

The Career Exploration Opportunities (CEO) program highlights the skills necessary to make significant contributions to scientific research, business, policy, communication, and more. This course offers tools and exercises to help late-stage trainees clarify academic and professional priorities. Trainees will be empowered to take charge of their chosen career of choice options through hands-on experiences, which fit their skills, interests, and values.Throughout this course, trainees will receive ongoing support from mentors and employers in their desired field as they develop a job search plan, create tailored resumes/cvs, and cover letters, become more confident in their networking, interviewing, and negotiation skills, and choose the experiential learning options necessary to transition to the next phase of their professional development.
Terms: Win | Units: 1 | Grading: Medical Satisfactory/No Credit

BIOS 282: Clarifying Career Choices: Your Self-Reflective Research Project

Using the ADAPT Integrated Development Model, this course will focus on the areas of Development and Awareness. It is designed for students who aspire to gain clarity and insights about themselves their career choices and options. It is designed to encourage self-knowledge and increased awareness of roles and job opportunities inside and outside of academia, where an in-depth Science background is desired. The course requires students to complete up to 3 assessments, short writing assignments, and participate in small group discussions. All students will have the opportunity to have a 1:1 follow-up session with the Instructor to discuss the insights gained from the course as well as opportunities to network with alumni and future employers from various fields.
Terms: Win | Units: 1 | Grading: Medical Satisfactory/No Credit
Instructors: ; Eberle, S. (PI)

BIOS 283: Dendritic Cells and Other Myeloid Cells: function and analytical tools

Dendritic cells and other myeloid cells are capable of activating and modulating a broad range of immune responses. This course focuses on understanding myeloid cell diversity, plasticity and functions in host physiology, disease states (i.e., cancer, inflammatory and infectious diseases) and during therapeutic interventions. Students are exposed to a combination of lectures (including field-expert talks) and dry lab workshops with the goal of acquiring tools for dissecting human and mouse myeloid cell function experimentally. This course is intended for biosciences graduate students and postdocs with basic immunology knowledge (enrollment limited to 20).
Terms: Sum | Units: 2 | 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 288: Quantitative Methods in Marine Conservation and Ocean Science

The goal of this two-week mini-course will be to quantitatively characterize marine fishery populations and how these populations change as a consequence of environmental drivers, anthropogenic pressures, and, ultimately, climate change. We will objectively assess the status or health of fishery populations by applying ecological theory and statistical and mathematical models to real data collected on marine species. We will learn how to effectively communicate quantitative scientific information and learn what it takes to wisely manage these resources.
Terms: Win | Units: 3 | Grading: Medical Satisfactory/No Credit

BIOS 289: Preparation & Practice: Biotechnology Business and Finance

This course combines guest lectures with case study and hands-on projects to examine the necessary skills and practical steps necessary to create a business from biotechnology invention. Students will interface with current CEOs, expert practitioners, and investment professionals to gain practical insight into the mechanics and practices of the biotechnology industry, and the variety of roles and responsibilities available to them.
Terms: Win | Units: 1 | Grading: Medical Satisfactory/No Credit
Instructors: ; Eberle, S. (PI)

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 291: Preparation & Practice: Management Consulting

This course is designed for students who are interested in learning about consulting including tools and techniques to gain a consulting mindset. The course requires students to complete short assignments, participate in classroom discussions, and a team project. Students will have the opportunity to understand the consulting process right from sourcing and starting engagements to closure and follow up engagements. Further, with the help of some practical execution in the classroom, students will also learn how to manage client needs and situations, articulating client needs in a succinct proposal, planning and executing consulting assignments, managing client interactions and in the process, learn to leverage some common frameworks for consulting.
Terms: Spr | Units: 1 | Grading: Medical Satisfactory/No Credit

BIOS 292: Preparation & Practice: Science Communication & Media

Through tailored lecture, case study, and a practical final project, academic and professional leaders will help you gain insight into the science communications and media industry. This course assists students in developing the communication skills necessary for post-training and internship success in a science communications/media field and it provides an understanding of the scope of career opportunities within the science communications sector, focusing on the development, organization, and management issues specific to it. Through connections with alumni, faculty, and other practitioners from a variety of fields and organizations, as well as hands-on experience with the techniques and methodologies most useful on the job market, students will define their own professional goals, increase their awareness of industry terminology and theories, and hone expertise in the areas of: publishing, editing, workflow, ethics, trends, principles of effective scholarly/news writing, interviewing techniques, and media/website management.
Terms: Sum | Units: 1 | Grading: Medical Satisfactory/No Credit

BIOS 293: Preparation & Practice: Science Policy

Through tailored lecture, case study, and a practical final project, academic and professional leaders will help you gain insight into the science policy industry and the skills necessary to succeed within the various positions and levels available within it. This course aims to demystify the U.S. science policy process and teach both how policy affects scientific funding and administration, and how science is used to create and influence the creation of law and policy in the U.S. This course will be taught in two parts. The first part outlines the basic structure of the US government, and fundamental issues in US political system, and refreshes students who haven't encountered basic civics since high school, this introductory material will cover the structure of the US government, the governance of key agencies, broad concepts of federalism and shared federal and power, the political party system, and a brief and general modern history of the role of science in policy making. The second part will review four key concepts: 1) who's who and how they work. 2) The policy making process and the role of science in creating policy. 3) Government funding science. 4) Issues, theories and trends in science and policy. This final section will review a variety of cross-cutting issues in science policy development, including innovation theory, the role of uncertainty, and a discussion of the government's role as a developer and repository of science data, and other current topics in the relationship between science and government.
Terms: Spr | 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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