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
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.
Last offered: Winter 2020
BIOS 202: Understanding Kinetics for Biologists and Biology
Students in the biological and chemical sciences are typically exposed to the kinetic and thermodynamic formalisms that describe rate and equilibrium processes, but rarely develop an intuition that allows them to use the material creatively in their own research. This Mini-course is designed to help each student begin to develop this intuition and an ability to evaluate the literature and their own data in terms of kinetic and thermodynamic models. This will be achieved through a combination of interactive lectures, in-class problem-solving, and a tutorial problem set that can be completed individually or in groups.
Terms: Sum
| Units: 3
Instructors:
Herschlag, D. (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
Instructors:
Ferrell, J. (PI)
BIOS 212: Analytical Methods in Biotechnology (EE 235, RAD 236)
This course provides fundamental principles underlying important analytical techniques used in modern biotechnology. The course comprises of lectures and hands-on laboratory experiments. Students will learn the core principles for designing, implementing and analyzing central experimental methods including polymerase chain reaction (PCR), electrophoresis, immunoassays, and high-throughput sequencing. The overall goal of the course is to enable engineering students with little or no background in molecular biology to transition into research in the field of biomedicine.
Terms: Spr
| Units: 3
BIOS 216: The Practice of Reproducible Research
This course will cover the basic principles and practices underlying rigorous and reproducible biomedical research, both in the clinic and the lab. Approximately 40% of the course will cover the basic scientific and statistical principles, with an emphasis on elements of design and analysis that pose threats to reproducibility; e.g. multiplicity, selective reporting, design effects, non-random assignment, pseudo-replication and handling of outliers. The remainder of the course will focus on computational approaches to ensure that all data, code, and analyses can be captured in a reproducible workflow, to be confirmed and replicated by you in the future, by other members of your team, and by reviewers and other researchers. We will cover how to satisfy FAIR principles, version control, how to create a git repository, utilize Github and how to create a reproducible dataset. Prerequisites: Basic knowledge of R. Recommended (not required):
EPI 202 or 261/262,
STATS 60, or MS&E 125
Terms: Sum
| Units: 2
BIOS 217: Foundations of statistics and reproducible research
Introduction to foundations of rigorous, reproducible research in experimental biology and clinical research. Provides conceptual framework for linking hypotheses to experimental design, quantitative measurement, statistical analysis and assessment of uncertainty. Course combines lecture presentation and discussion of core concepts from statistics and reproducibility with hands-on exposure to best practices for reproducible workflows spanning design, data collection, annotation, analysis and presentation of results. Brief discussion of social, legal, and ethical issues with reproducibility in scientific practice, along with NIH grant requirements. Course provides foundations for future learning in these areas. Examples drawn from multiple areas of experimental biology and clinical research. Target audience: Students in
BIOS 200 (Foundations in Experimental Biology), in Biosciences graduate programs or T32 training programs. Prerequisites: None
Terms: Aut
| Units: 2
Instructors:
Baiocchi, M. (PI)
;
Goodman, S. (PI)
BIOS 221: Modern Statistics for Modern Biology (STATS 155, STATS 256, 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: Working knowledge of R and two core Biology courses. Note that the 155 offering is a writing intensive course for undergraduates only and requires instructor consent. (WIM). See
https://web.stanford.edu/class/bios221/index.html
Terms: Spr
| Units: 3
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
Instructors:
Goodman, M. (PI)
BIOS 227: Mass Spectrometry and Proteomics: Opening the Black Box
Focus on designing and analyzing effective proteomics experiments using mass spectrometry and critically evaluating published mass spectrometry-based studies and datasets. Introduces students to the instrumentation, experimental strategies, and computational methods used for identifying and quantifying proteins and protein post-translational modifications using mass spectrometry. Topics include comparative evaluation of mass spectrometer instrument configurations, tandem mass spectrum interpretation, relative and absolute quantitation, and proteome-scale data set analysis. Laboratory time will focus on sample preparation methods, real-time data acquisition, and data analysis software and techniques.
Terms: Win
| Units: 2
Instructors:
Mallick, P. (PI)
;
Pitteri, S. (PI)
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