SINTN– Stanford Institute for Neuro-Innovation & Translational Neurosciences

PhD Program courses

Core and other courses

Students are required to become familiar with current research in a broad range of neuroscience areas by taking five advanced courses, with at least one from each of the following core research areas:

1. Systems, Computational, Cognitive and Behavioral Neuroscience
2. Cellular, Molecular, and Developmental Neuroscience
3. Translational Neuroscience

Each of the courses in these categories is typically offered on alternate years so that the core course requirements can be completed within two years. These options may change, depending on which courses are offered during the next two years

1. Systems, Computational, Cognitive and Behavioral Neuroscience

Courses at this level focus on the computations performed by neural circuits and the role such computations play in behavior, perceptions, and plasticity.

Students can expect to learn how neurons:
• Organize circuits into larger functional units
• Represent and transform information
• Produce myriad movement
• Subserve higher-level processing related to perception, reasoning and learning

Predominant methods in this area include modeling single cells and circuits, design of behavioral paradigms, and statistical analysis of behavioral and electrophysiological data.

Affective Neuroscience (PSYCH 251) Focus is on theory and research in the field of affective neuroscience. Comparative and human research approaches map affective function to both neuroanatomical and neurochemical substrates. 3units. Next offered in the Spring quarter, 2009-10 academic year. (Knutson)

Central Mechanisms in Visual Cognition (NBIO 220) The course reviews the neural basis of visual perception and simple forms of visually based cognition such as attention, short-term memory, decision-making and motor planning. Emphasis is placed on topics of current interest in the visual neuroscience literature. 4units. Next offered in the Spring quarter, 2010-11 academic year. (Newsome & Moore)

Comparative Neuroanatomy (COMPMED 207) The structure and function of vertebrate brains. Focus is on laboratory animals commonly used in neuroscience research, and comparisons made with the human brain. Advantages and limitations of species chosen for neurobiological and biomedical research. Introduction to neuroanatomical methods and possible mechanisms of brain evolution. 4units. Next offered in the Autumn quarter, 2010-11 academic year. (Buckmaster & Darian-Smith)

Neural Systems and Behavior (BIO 163/263) 4units. Next offered in the Autumn quarter, 2009-10 academic year. (Fernald)

Computational Neuroscience: cells and circuits, from molecules to behavior (NENS 220) The course focuses on the application of computational approaches to understand the roles of individual molecules in the behavior of neurons, circuits, and organisms. The course begins with a discussion of the roles of various intrinsic excitability mechanisms (voltage-gated and leak ion channels, membrane transporters, ligand gated channels, etc.) in determining the overall resting state of neurons and their input/output relationships. The course then continues to explore microcircuit behavior and the development of emergent network behaviors. A final project will be developed based on the fundamentals and tools introduced in the course. 4units. Next offered in the Winter quarter, 2008-09 academic year. (Huguenard)

Large-Scale Neural Modeling (BIOE 332) Emphasis is on modeling neural systems at the circuit level, ranging from feature maps in neocortex to episodic memory in hippocampus. Simulation exercises to explore the roles of cellular properties, synaptic plasticity, spike synchrony, rhythmic activity, recurrent connectivity, and noise and heterogeneity; quantitative techniques to analyze and predict network behavior. Work in teams of two; run simulations in real-time on neuromorphic hardware developed for this purpose. 3units. Next offered in the Winter quarter, 2009-10 academic year. (Boahen)

The Neural Basis of Cognition: A PDP approach (PSYCH 209a) The neural basis of perception and attention; memory, learning, and semantic knowledge; language and reading; and action selection, planning, and problem solving. Findings from human behavioral experiments, neurophysiology, functional brain imaging, and the effects of brain disorders on performance and computational models that address these findings from the parallel distributed processing point of view will be covered 4units. Next offered in the Winter quarter, 2009-10 academic year. (McClelland)

Neural Basis of Behavior (NBIO 218) Advanced seminar on principles of information processing in the CNS of vertebrates, and the relationship of functional properties of neural systems with perception and behavior. Study of original papers, directed group discussion and student presentations. 4units. Next offered in the Spring quarter, 2009-10 academic year. (Knudsen & Raymond)

Human Neuroimaging Methods (PSYCH 204A) This course introduces the student to human neuroimaging using magnetic resonance scanners. The course is a mixture of lectures and hands-on software tutorials. The course begins by introducing basic MR principles. Then various MR measurement modalities are described, including several types of structural and functional imaging methods. Finally, algorithms for analyzing and visualizing the various types of neuroimaging data are explained, including anatomical images, functional data, diffusion imaging (e.g., DTI) and magnetization transfer. Emphasis is on explaining the software methods used for interpreting these types of data. 3units. Next offered in the Autumn quarter, 2009-10 academic year. (Wandell & Dougherty)

Computational Neuroimaging (PSYCH 204B) A course to develop skills in software and mathematical/statistical analysis of neuroimaging signals. Together with 204A will fulfill computational neuroscience core. 3units. Next offered in the Winter quarter, 2009-10 academic year. (Grill-Spector)

Systems: Information and Signaling Mechanisms in Neurons and Circuits (NBIO 258) How do synapses, cells and neural circuits process information relevant to a behaving organism? This course will examine how phenomena of information processing emerge at several levels of complexity in the nervous system, including sensory transduction in molecular cascades, information transmission through axons and synapses, plasticity and feedback in recurrent circuits, and encoding of sensory stimuli in neural circuits. 4units. Next offered in the Autumn quarter, 2009-10 academic year. (Baccus & Tsien)

High Level Vision (PSYCH 250) Seminar style course in which we read and review of theories and ongoing research of high level vision using a multidisciplinary approach including neuroscience, computational and behavioral studies. Topics include: visual recognition of faces and objects; categorization; invariances in recognition; the role of development and experience in shaping brain representations and behavior; Students will received 1 credit for in-class presentations and 3 credits if they will write an end-of-term paper. 1units. Next offered in the Spring quarter, 2008-09 academic year. (Grill-Spector)

Computational Neural Networks (BIOE 341) Distributed neural network implementations of algorithms for signal processing, function approximation, and control. Representation of information in networks of spiking neurons. Supervised and unsupervised learning algorithms. Radial basis functions, principal and independent components analysis, reinforcement learning, support-vector machines, self-organizing maps, auto-associative learning, hidden Markov models. Related methods from information theory, signal processing, Bayesian estimation, and stochastic systems. Final project in software or programmable hardware. Prerequisites: linear algebra, dynamic systems, and probability theory as in MATH103, EE102A, and EE178 or equivalent, and programming experience in C++ or Matlab. 3units. Next offered in the Autumn quarter, 2008-09 academic year. (Sanger)

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2. Cellular, Molecular, and Developmental Neuroscience

Courses in this area address fundamental mechanisms that enable cells of the nervous system to develop, function in adulthood, change during learning and memory, and/or malfunction in disease states.

Students can expect to learn core concepts in:
• Cell-cell communication
• Intracellular signal transduction
• Transcriptional and translational control
• mRNA and protein trafficking
• Membrane biophysics
• Cell motility

Dominant methods include molecular biology, genetics, cell biology, electrophysiology, and subcellular or multicellular imaging.

Developmental Neuroscience (BIO 258) This seminar course will consider recent findings about the mechanisms of neurogenesis, migration, axon outgrowth, synapse formation, and synaptic plasticity during the development of the nervous system. 4units. Next offered in the Spring quarter, 2010-11 academic year. (McConnell, Garner & Shen)

How Cells Works: Energetics, Compartments, and Coupling in Cell Biology (MCP 256) Examines dynamic aspects of cell function. Emphasis is on understanding the principles of how cellular functions are coupled 4units. Next offered in the Spring quarter, 2009-10 academic year. (Lewis, Maduke & Goodman)

Neuronal Biophysics (BIO 217) The goal of the course is to teach students the biophysical basis for neuronal dynamics and to allow students to use physical principles as tools for prediction of neuronal behavior. A few fundamental physical principles will be seen to give rise to a rich set of dynamical activities. Quantitative and computational techniques will be used to describe these physical principles and resulting models of neuronal dynamics. 3units. Next offered in the Winter quarter, 2009-10 academic year. (Schnitzer)

Synaptic Transmission (MCP 215) Anatomical, physiological and biochemical basis of synaptic function in the peripheral and central nervous system. Lectures by the faculty and intensive discussions of relevant research papers. 4units. Next offered in the Spring quarter, 2009-10 academic year. (Madison, Smith & Hestrin)

Molecular and Cellular Neurobiology (BIO 254) Cellular and molecular mechanisms in the organization and function of the nervous system. Topics: cell biology of the neuron, wiring of the neuronal network, synapse structure and synaptic transmission, signal transduction in the nervous system, the molecular basis of behavior including learning and memory, molecular pathogenesis of neurological diseases. 5units. Next offered in the Autumn quarter, 2010-11 academic year. (Luo, Shen & Clandinin)

Genetic Analysis of Behavior (NBIO 216) Advanced seminar on the findings and implications of behavioral genetics as applied to both invertebrate and vertebrate model systems. Topics will include, for example, studies of biological clocks, sensation and central pattern generators, and the course will provide both an introduction to the relevant genetic techniques as well as a historical perspective. Study of original papers, directed discussion, and student presentations. 4units. Next offered in the Spring quarter, 2010-11 academic year. (Goodman & Clandinin)

Mol/Cell: Information and Signaling Mechanisms in Neurons and Circuits (NBIO 258) How do synapses, cells and neural circuits process information relevant to a behaving organism? This course will examine how phenomena of information processing emerge at several levels of complexity in the nervous system, including sensory transduction in molecular cascades, information transmission through axons and synapses, plasticity and feedback in recurrent circuits, and encoding of sensory stimuli in neural circuits. 4units. Next offered in the Autumn quarter, 2009-10 academic year. (Baccus & Tsien)

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3. Translational Neuroscience

Courses in this area address fundamental concepts in studying disorders of the human brain and the peripheral nervous system and their treatment.

Students can expect to learn about basic themes in:
• Pathophysiological mechanisms
• Modeling of human diseases
• Approaches to designing diagnoses and treatments
• Implementing diagnoses and treatments

The courses highlight studies of human diseases that use genetics, molecular biology, psychological testing, and functional imaging.

Neurobiology of Disease (NENS 205) A series of case demonstrations of selected neurological disorders; discussion of the pathophysiological basis of the disorder; presentation of the basic principles underlying modern diagnostic and therapeutic management; and a discussion of recent advances for each disease entity. 3units. Next offered in the Winter quarter, 2008-09 academic year. (Reimer & Yang)

Molecular Mechanisms of neurodegenerative disease (BIO 267) 4units. Next offered in the Winter quarter, 2009-10 academic year. (Kopito, Reimer & Wyss-Coray, So, Bronte-Stewart, Greicius)

Brain and Immune System (Immunology 185/285) For advanced undergraduates, coterminal students, and graduate students. Molecular and cellular interactions between the nervous and immune systems. Focus is on the role of immune molecules in neural development, the bi-directional mechanisms by which the brain and immune system communicate with each other, and the role of the immune system in the diseased and infected brain. Topics include: molecular basis of fever, stress and inflammation, gender differences in autoimmune diseases, inflammation in neurodegenerative diseases, central nervous system infections, and the immune system in psychiatric disorders. Expert guest lectures, weekly discussion sections, and emphasis on science communication skills. This course is completely writing-based (no exams!). Students will have opportunities to develop science writing skills by writing NY Times style articles geared to a layperson audience. 3units. Next offered in the Winter quarter, 2009-10 academic year. (Steinman)

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