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BIOS 200: Foundations in Experimental Biology

This course is divided into three 3-week cycles and is focused on the broad themes of Evolution, Energy and Information. During each cycle, students work in small teams and will be coached by faculty to develop an original research project and compose a brief written proposal explaining the research. 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. Peer assessment and workshops; substantial face-to-face discussion with faculty drawn from across the Biosciences programs.
Terms: Aut | Units: 6
Instructors: ; Clandinin, T. (PI); Schneider, D. (PI); Sherlock, G. (PI); Prieto, J. (GP)

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: Spr | Units: 2
Instructors: ; Greenleaf, W. (PI); Li, J. (PI); Montgomery, S. (PI); Urban, A. (PI); Prieto, J. (GP)

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: Spr | Units: 2
Instructors: ; Ferrell, J. (PI); Prieto, J. (GP)

BIOS 205: Introductory Data Analysis in R for Biomedical Students

Topics include: basics of R (widely used, open-source programming and data analysis environment) programming language and data structures, reading/writing files, graphics tools for figure generation, basic statistical and regression operations, survey of relevant R library packages. Interactive format combining lectures and computer lab. For course and enrollment information, see http://bios205.stanford.edu.
Terms: Aut, Win, Spr | Units: 1
Instructors: ; Bagley, S. (PI); Prieto, J. (GP)

BIOS 208: Computational Macromolecule Structure Modeling

Concepts, workflow, and methodology of protein structure modeling presented through short lectures followed by hands-on exercises with the Rosetta software package. Several problem types demonstrate how to formulate and test well-defined hypotheses, in addition to the design and engineering of structure, function, and interactions.
Terms: Spr | Units: 2

BIOS 211: Histology for Biosciences

Fundamentals of tissue organization as seen by light microscopy. Includes: epithelium, connective tissue, muscle, bone, cartilage, blood cells, nerve, and quick overview of several major organs. Each session has interactive 30 minutennpresentation followed by 1.5 hours viewing glass histology slides using individual microscopes and a multi-­headed microscope. Slide sessions interspersed with interactive exercises to stimulate discussions. Supporting materials include select readings from histology atlas, electron micrographs, and virtual (whole-slide) images provided online.
Terms: Spr | Units: 1
Instructors: ; Connolly, A. (PI); Prieto, J. (GP)

BIOS 213: Scientific Illustration and Animation

Techniques of presenting big picture ideas and detailed experiments as simple cartoons. Mixed lecture/lab course culminates with students producing figures and animations for an introduction/conclusion of a research presentation. Covers basic design principles to help produce figures useful for broad and focused audiences. Includes static illustrations, Flash style, and stop motion animation.
Terms: Spr | Units: 1
Instructors: ; Schneider, D. (PI); Prieto, J. (GP)

BIOS 218: Molecular basis of membrane traffic

Transport of proteins through the secretory and endocytic pathways is essential for life; dysregulation causes disease and pathogens hijack these pathways to their best advantage. 5 international experts present didactic lectures and engage with students. Topics include: history of genetic and biochemical experiments to identify key components; reconstitution approaches; coated vesicle formation and cargo selection; control of membrane traffic by Rab GTPases; siRNA screens; high throughput microscopy analysis and systems biology approaches. Students devise and present research proposals based on the research of the guest speakers.
Terms: Win | Units: 2
Instructors: ; Pfeffer, S. (PI); Prieto, J. (GP)

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. Instructor consent.
Terms: Sum | Units: 3
Instructors: ; Holmes, S. (PI)

BIOS 222: Authentic Courage for Constructive Change: Skills and Practice for Leadership

Explores concepts in decision making and constructive conflict as a mechanism for desired change via purposeful actions. Students assess personal conflict comfort zones and use case studies and class activities to develop skills with authenticity, active and intentional decision making, and other related topics.
Terms: Spr | Units: 1
Instructors: ; Thadaney Israni, S. (PI); Herschlag, D. (SI); Prieto, J. (GP)

BIOS 229: Drug Discovery and Development Project Simulation

Two-day short course. Focus is on the progression of a drug discovery project from target identification through pre-clinical research, early and late clinical development, and registration with the health authorities. Presented by Novartis. Enrollment limited to postdoctoral students and graduate students with research experience.
Terms: Win | Units: 2
Instructors: ; Herschlag, D. (PI); Prieto, J. (GP)

BIOS 230: Biomedical Data Analysis in MATLAB

Focuses on empowering biomedical scientists and engineers with MATLAB tools that are directly useful in their research. Topics include linear- and non-linear-parameter estimation, ordinary- and partial-differential equations, Simulink, GUI design and image processing. Weekly hands-on tutorials accompany lectures and help students code more efficiently and elegantly. Weekly problems sets use MATLAB to interrogate a biomedical phenomenon. Pre-requisites: permission of instructor required.
Terms: Spr | Units: 2
Instructors: ; Jain, N. (PI); Covert, M. (SI); Prieto, J. (GP)

BIOS 232: Two-photon Imaging of Neural Circuits

Focuses on application of two-photon imaging to modern neuroscience. Topics include microscopy and imaging.
Terms: Win | Units: 2
Instructors: ; Ding, J. (PI); Prieto, J. (GP)

BIOS 234: Personalized Genomic Medicine

Focuses on next-generation sequencing and its implications for personalized genomic medicine. Students gain hands-on experience with popular DNA sequence analysis tools as well as a practical understanding of the underlying algorithms and biomedicine.
Terms: Win | Units: 1
Instructors: ; Goldfeder, R. (PI); Wall, D. (PI); Prieto, J. (GP)

BIOS 235: Metabolism and Metabolic Ecology: Microbes, Gut and Cancer

Preference to graduate students. Focuses on modern aspects of metabolism and metabolic biochemistry as it affects fitness and ecology of cells and organisms on a systems level. Students obtain a broad understanding of the governing principles and logic of metabolic pathways and their networks as well as an intuition of metabolism in context of natural selection and fitness acting on the cell or host. Emphasis is primarily on microorganisms and their habitats in nature and the human gut, but topics also include metabolism of cancer cells and of engineered microbes.
Terms: Spr | Units: 2
Instructors: ; Spormann, A. (PI); Prieto, J. (GP)

BIOS 236: Developmental Biology in the Ocean: Comparative Embryology and Larval Development

Three-week course at Hopkins Marine Station. Focuses on the embryology and larval development of a broad range of marine invertebrate phyla. The goal of the course is to give students an appreciation of the range of developmental strategies and larval forms in the ocean and why this is critical for constructing hypotheses of EvoDevo and animal evolution. Includes observation and documentation of the development of embryos and larvae by scientific illustration and photo/video microscopy. Pre-requisite: Developmental Biology coursework and instructor consent.
Terms: Spr | Units: 4
Instructors: ; Lowe, C. (PI); Prieto, J. (GP)

BIOS 237: Investigating Biology with Fluorescent Proteins

Focuses on fluorescent proteins, a proven research tool for imaging a wide range of biological phenomena and continuously uncover exciting discoveries in many areas. Students gain practical expertise in concepts, methodology, and data analysis through lectures, literature discussion, and hands-on computer exercises with "real world" data.
Terms: Win | Units: 1
Instructors: ; Cochran, V. (PI); Lin, M. (PI); Prieto, J. (GP)

BIOS 238: Quantitative single cell analysis of live cell images

Terms: Aut | Units: 1
Instructors: ; Meyer, T. (PI)

BIOS 239: Synapse Development

Focuses on the mechanisms of synapse development, including the role of adhesion molecules in establishing neuronal contacts, the function of synapse-inducing molecules, how pre- and postsynaptic material is transported to nascent synapses, synapse maturation, synapse elimination as well as how synaptic dysfunction may lead to neurological disorders. Readings from primary literature.
Terms: Win | Units: 3
Instructors: ; Kurshan, P. (PI); Shen, K. (PI); Prieto, J. (GP)

BIOS 240: Cellular Metabolism: An Emerging Hallmark of Cancer and Aging

Introduction to cellular metabolism, including changes in metabolic flux that drive diverse disease states from cancer to aging. Topics covered include cancer metabolism, cellular nutrient sensing, metabolism in aging, and the influence of metabolism on stem cell fate. This course uses discussion of recent advances in the field to place an emphasis on practical applications, including the integration of metabolomics into the era of ¿Big Data¿. This mini-course culminates with a lab section allowing the students to conduct an extracellular flux experiment using the Seahorse analyzer to study changes in mitochondrial respiration and glycolysis in cancer cells.
Terms: Win | Units: 1
Instructors: ; Giaccia, A. (PI); LaGory, E. (PI); Prieto, J. (GP)

BIOS 241: Dissecting algorithms for RNA Sequencing

Class focuses on a few popular and commonly used algorithms for RNA-Seq analysis. The course dissects the algorithmic assumptions, statistical methods they use to test hypotheses about RNA expression and evaluates properties such as robustness, sensitivity and specificity, highlighting some large "blind spots" in many algorithms.
Terms: Win | Units: 2
Instructors: ; Salzman, J. (PI); Prieto, J. (GP)

BIOS 242: Writing Successful NIH Fellowships and K Awards

An overview of principles and fundamentals for writing competitive NIH Kirschstein NRSA fellowships (F31, F32) and career-development awards (K). Topics include: developing specific aims and career development plans; using the review criteria to inform writing; timelines and resources. Participants develop F or K proposals through guided exercises with an emphasis on in-class peer review and focused faculty feedback.
Terms: Aut | Units: 2
Instructors: ; Botham, C. (PI); Herschlag, D. (PI); Kleppner, S. (PI); Mayes, T. (PI)

BIOS 243: Grant Writing Academy Mini Course: Specific Aims

Concise overview of the fundamentals for writing competitive NIH Kirschtein NRSA fellowships (F31, F32) and K Awards. Topics include developing specific aims; outlining research and career development plans; and using the review criteria to inform writing. Participants develop their one-page NIH-Specific Aims document with an emphasis on in-class peer review and protected daily proposal writing. Students enroll for units in one small-group section, and also attend two mandatory lectures as noted in class schedule.
Terms: Win | Units: 1
Instructors: ; Botham, C. (PI); Herschlag, D. (PI)

BIOS 202: Hippocampal Field Potentials, an Introduction to CNS in Vitro Electrophysiology

Enrollment limited to graduate students in the School of Medicine; undergraduates may enroll with instructor consent. Introduces students to theory and practice of in vitro CNS electrophysiology. Lectures cover basic electrical and electrode theory, hippocampal anatomy, interpretation of these potentials, common pitfalls and misinterpretations, design of experiments using field potentials and other related topics. Practicum is hands on training in obtaining, recording and interpreting field potentials from in vitro hippocampal slices. Students develop skills in data collection, analysis and evaluation, art and design of electrophysiological studies of the brain.
| Units: 1-3

BIOS 203: Introduction to Atomistic Simulations for Biochemical Applications

Theory and application of atomistic simulations needed to model and understand systems of biological relevance (proteins, DNA, small molecule therapeutic drug properties) for beginners. Topics: molecular interactions and classical force fields, first principles energy approaches, molecular dynamics, rare event and transition-state finding techniques, protein folding, and solvation methods. Hands-on tutorials based on key topics in biochemical simulation that use variety of state-of-the-art software packages on both standard and new, advanced graphical processing unit hardware for simulation and analysis ofnnbiochemical properties. Prerequisites: Some knowledge of quantum mechanics, biochemistry, and shell scripting (BASH or python) preferred.
| Units: 3

BIOS 206: Stem Cells and Regeneration: Transitioning from Basic Research to Clinical Therapies

Presents emerging therapies based on stem cell by the scientists leading these pioneering efforts, including academic and industry-based groups. Provides hands-on instruction in laboratory methods valuable in development of stem cell therapies.
| Units: 1-2

BIOS 207: Interdisciplinary Approaches to Biochemistry: Single Molecule Biophysics to Clinical Outcomes

Interdisciplinary analysis from basic biochemistry and biophysics to clinical outcomes of disease states and potential therapeutic interventions. Focus on cardiac system. Single molecule biophysics and classical enzyme kinetics and use of induced pluripotent stem (iPS) cells and single cell studies lay foundation for discussions of effects of cardiomyopathy mutations on heart function. Analytical approaches discussed include genetic analysis, reconstitution of functional assemblies, x-ray diffraction, 3D reconstruction of electron microscope images, spectroscopic methods, computational approaches, single molecule biophysics, use of induced pluripotent stem cells in research.
| Units: 1

BIOS 209: Practical Protein NMR Structure Determination

Work toward solving a high-resolution 3D structure from unprocessed NMR data acquired on a small well-characterized protein. Short lectures followed by hands-on computer exercises demonstrate best practices for data processing, spectra interpretation, and structure calculation with attention to troubleshooting and validation methods. Students should be familiar with fundamental concepts of protein structure and NMR spectroscopy and comfortable with the command-line environment. Prerequisite: SBIO242/BIOPHYS 242 strongly recommended, but not required.
| Units: 2

BIOS 210: Axonal Transport and Neurodegenerative Diseases

Introduction to mechanisms underlying axonal transport, significance of proper regulation in maintaining neuronal activities, and its implication in disease pathology. Lab section: visualize axonal transport of various axonal organelles such as mitochondria, synaptic vesicles and dense core vesicles in live cells and tissues.
| Units: 1

BIOS 214: Molecules & Math

Introduction to molecular systems and their behavior as well as fundamental mathematical and computational tools for modeling molecular systems. Application of tools to critical medical areas: modeling of cardiovascular physiology; simulation of protein interactions; modeling of cellular differentiation; extraction of useful information from anatomic, functional and molecular images. Weekly lectures, group discussions, and individual project work.
| Units: 1

BIOS 215: Transplantation Immunology and Tolerance

Extensive literature review of experimental strategies to promote tolerance, including limitations involved in translating tolerance-promoting strategies to the clinic and targets of Immunosuppression. State of art approaches and limitations of current approaches. Discussions with prominent scientists and clinicians in field of transplantation. Student presentations on novel concepts and approaches in basic science, translational and clinical transplant.
| Units: 2

BIOS 216: Structural Biology and Vaccine Design

Structural biology is playing an increasing role in the development and analysis of vaccines and deepening understanding of challenging vaccine targets. Structural studies of target antigens have allowed mapping of neutralizing antibody epitopes and antigenic variation. Studies of antibody:antigen complexes have clarified how rare antibodies can confer broad neutralization to highly variant viruses, such as influenza virus and HIV. Course explores current structure-based efforts to improve vaccines to highly potent neutralizing epitopes, utilizing protein fragments, carbohydrate engineering and epitope scaffolding. Research from current literature on viruses including HIV, influenza virus, RSV and others examined.
| Units: 1

BIOS 217: The Ultimate Face Book: Understanding Normal and Abnormal Craniofacial Development

How the face is assembled during embryonic development to gain insights into facial birth defects and new "regenerative medicine" approaches to reconstruct the face following disease or injury. Learn how "a man finds room in the few square inches of the face for the traits of all his ancestors; for the expression of all his history, and his wants."
| Units: 1

BIOS 219: Human Gene Regulation: Genomic Thinking and Genomic Tools for Experimentalists

Focused look at the promoter/enhancer and related landscape of the human genome. Genomics and epigenomics of human gene regulation - truth, myths and mysteries. Genomic tools for the interpretation of vertebrate gene regulation experiments and predictions, and the insights behind them. Genomic thinking: purity vs. comprehensiveness, genome-wide vs. single locus. Prerequisites: undergraduate Biology or equivalent. Programming skills not required or taught.
| Units: 1

BIOS 220: Adventures in the Human Virosphere

Structure and function of viruses focusing on viruses that infect humans. Explore the interaction of humans and viruses from diverse perspectives: historical, cultural, political, demographic, organismal, molecular biological, biochemical, immunological, taxonomic. Emphasis on general principles of biology and matters of decision-making and policy. Selected case studies illustrate course material. Full-time immersive format of lectures, discussions, videos and model building. Recommended for non-virology students.
| Units: 3

BIOS 223: 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.
| Units: 1

BIOS 224: Big Topics in Stem Cell Ethics

Mini-course. Focuses on framing the major ethical issues, legal issues, normative ethical guidelines and oversight in stem cell research. Includes discussion of religious and ethical debates around the moral status of the human embryo.
| Units: 2

BIOS 225: Gender 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.
| Units: 1

BIOS 226: Introduction to Force Spectroscopy

Mini-course. Covers the fundamentals of major single-molecule manipulation methods (optical tweezers, magnetic tweezers, and atomic force microscopy), principles of force measurement signal and noise, and applications to studies of folding, binding, measurement signal and noise, and applications to studies of folding, binding, polymer elasticity, and structural transitions in proteins and nucleic acids. Intended for students with no previous exposure to single-molecule manipulation or for beginning practitioners. Lectures and discussion of current literature.
| Units: 1

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.
| Units: 2

BIOS 228: Understanding Chemistry in Biology and Biological Experiments

Chemical transformations are central to biology and function and chemical methods provide some of the most powerful tools for everyday experimental biology. Focuses on the concepts and principles underlying biological chemical transformations, allowing students to generalize and understand cell metabolism and regulation. Topics include basic principles and procedures to evaluate and utilize in practice chemical approaches in biological experiments. In-class problems and evaluation of literature. Three-week mini-course.
| Units: 2

BIOS 231: Neuroimaging Genomics

Preference to graduate students and medical students. Emphasis is on introducing students to the field of neuroimaging genomics, characterizing large-scale genomic and imaging datasets to uncover relationships between imaging features, molecular genomic profiles, and phenotype.
| Units: 3

BIOS 233: Experimental Metagenomics: Nectar Microbes as a Model System

Preference to graduate students and post-docs; open to upper-level undergraduates with instructor consent. Emphasis on developing a practical understanding of how to conduct metagenomic research by combining cutting-edge molecular sequencing with experimental ecological approaches. Focuses on the community ecology of the bacterial and yeast species that colonize floral nectar via pollinators and the implications for plant-pollinator interactions within an agriculturally relevant framework. Ecological, evolutionary, and phylogenetic principles and microbiological and molecular techniques that will be taught are broadly applicable in many biological fields, including the medical ecology of hte human microbiome. Inquiry-based with individual student-led projects.
| Units: 3
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