Results for BIOS

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.

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.

Autumn quarter enrollment limited to ADVANCE students; instructor consent required for enrollment. 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.

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 minutenpresentation 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.

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.

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.

Focuses on application of two-photon imaging to modern neuroscience. Topics include microscopy and imaging.

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.

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.

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.

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.

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.

After a brief introduction to drug discovery and development process in pharmaceutical industry, we discuss integrative computational approaches to drug discovery, development, and marketing. Illustrative case studies and examples explain how applications are used at various stages, including bioinformatics, data mining, high-throughput screening, predicting human response to drugs, and adverse drug event monitoring.

Focuses on the immune defenses that the human body uses to prevent and control infectious diseases. Covers both innate and adaptive immune defenses against bacterial, fungal, and viral pathogens will be covered. This course is targeted primarily at graduate students and postdocs whose primary focus is not in immunology, but whose research and interests intersect with the host response to infectious diseases. Motivated undergraduates may also participate.

Meta-analysis is the quantitative synthesis and analysis of a collection of independent studies. It provides a more objective and powerful way of summarizing evidence across studies than descriptive reviews. The importance and utility of this quantitative method for answering new questions and synthesizing existing results in different fields of scientific research is demonstrated by the dramatic increase in the number of studies using meta-analysis in the last ten years. Focuses on the basics of meta-analysis. The emphasis of the course is both on the conceptual understanding and practical use of this method, as applied to biological questions.

One-week intensive course is specifically dedicated to graduate students and postdocs in Biology and Environmental Science eager to be introduced to, and get proficient in, scientific computing. Focus is on acquiring the necessary skills to boost their productivity by learning state-of-the-art and cutting-edge techniques to retrieve and process big data. Course introduces Unix/Linux, R, ggplot2 graphic package, regular expressions and version control, dynamic reporting generation through hands-on and interactive learning opportunities both during lectures and in extensive lab sessions based on real world case studies extracted from published papers.

Focus is on phototactic behavior of single celled organisms and the biophysical principles of feedback control and hydrodynamics underlying it. Enables real biology experimentation in the cloud, and is ultimately intended to illustrate and teach the scientific method (free exploration, hypothesis formation, measurement, data analysis, modeling, conclusions).

Focuses on decision making in science, with particular attention to skills for identifying when to solicit interdisciplinary input, and how to guide such discussions to productive endpoints. Uses case studies based on Novartis projects to teach ways to leverage interdisciplinary knowledge, effectively communicate across disciplines, and drive teams to decision points. Two-day workshop presented by Novartis scientists who lead participants through these real life examples of interactive teams within pharma solving problems through collaborative decision making. Participants develop collaborative decision making skills highlighted through group exercises.