Results for BIOS

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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."