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Schedules & LinksSpring 2013.Note: All registration should be cleared with Mike Hawken. Click here for additional information regarding Ph.D. course requirements.
WS = Washington Square Campus Course DescriptionsCENTER FOR NEURAL SCIENCERegularly Offered Courses: In general, these courses are only open to doctoral students in neural science unless they are cross-listed with another department. Cellular Neuroscience NEURL-GA2201 Identical to BMSC-GA 2005 Semester: Fall 4 points Team-taught, intensive course. Lectures and readings cover basic biophysics and cellular, molecular, and developmental neuroscience. Sensory and Motor Systems NEURL-GA2202 Identical to BMSC-GA 4462 Semester: Spring 4 points Team-taught intensive course. Lectures and readings concentrate on neural regulation of sensory and motor systems. Laboratory in Neural Science I, II NEURL-GA2203, 2204 Corequisites: NEURL-GA 2201, NEURL-GA 2202 Semester: Fall, Spring 3 points Team-taught, state-of-the-art teaching laboratory in neural science. The first semester includes histology and cellular and molecular neuroscience. The second semester includes neuroanatomy, sensory neurophysiology, modern neuroanatomical tracer techniques, psychophysics, and computational neuroscience. Behavioral and Cognitive Neuroscience NEURL-GA2205 Identical to PSYCH-GA 2221 Semester: Spring 4 points Team-taught intensive course. Lectures, readings, and laboratory exercises cover neuroanatomy, cognitive neuroscience, learning, memory, and emotion. Mathematical Tools for Neuroscience NEURL-GA2207 Semester: Fall 4 points Team-taught intensive course. Lecture, readings, and homework exercises cover basic mathematical techniques for analysis and modeling of neural systems. Homework sets are based on the MATLAB software package. Introduction to Research in Neural Science I, II NEURL-GA2210, 2211 Semester: Fall, Spring 4 points Research component of the first-year core curriculum in neural science. Students participate in the research activities in several different laboratories to learn current questions and techniques in neuroscience. Performance is evaluated on the basis of learning the literature and proficiency in laboratory techniques, based on oral and/or written presentations with the laboratory group. Dissertation Research and Seminar NEURL-GA3301, 3302 May be repeated for credit 1-3 points Reading Course in Neural Science NEURL-GA3305, 3306 May be repeated for credit 1-3 points Research Problems in Neural Science NEURL-GA3321, 3322 May be repeated for credit 1-3 points Fellows' Seminar NEURL-GA3380, 3381 May be repeated for credit 1-3 points Seminar in Current Topics NEURL-GA3390, 3391 May be repeated for credit 1-3 points Seminar in Neuroeconomics NEURL-GA3410 Semester: Spring, every other year 3 points This seminar will survey the emerging field of neuroeconomics, the interdisciplinary study of the brain's mechanisms for decision evaluation and choice. We will approach these issues from multiple perspectives, drawing on theoretical, behavioral, and neural data from economics, psychology, and neurobiology. Major topics include: decision under risk and uncertainty; multiplayer interactions and social preferences; the role of learning in evaluating options; and choice mechanisms. Disorders of the Nervous system NEURL-GA4414 Instructor: Sanes, Scharfman, Rice, Lin Semester: Fall 3 points This course will cover key neurological and psychiatric diseases. Each week a different disorder will be addressed in a 2.5 hr-long class. Part of each class session will include an overview by a clinical expert, who will provide a clinical understanding of the disease, including signs and symptoms. A second part will be given by a scientist who does basic research in the field, who will discuss experimental strategies and current hypotheses about pathophysiological mechanisms at the cellular and genetic level. Readings will be provided from each of these experts for each topic. Topics may include post-traumatic stress disorder, Autism, Parkinson's disease, epilepsy, addiction, and schizophrenia. Special Topics Courses: These are advanced 3 point seminars led by the faculty to provide in-depth consideration of specific topic areas in neural science. Priority is given to doctoral students in neural science but others may be able to register if they meet the pre-requisites and there is room in the course. FALL SEMESTER Special Topics: Neuronal NetworksNEURL-GA 3041. Identical to MATH-GA 2855-002 Instructor: Rinzel Semester: Fall This course will involve the formulation and analysis of differential equation models for neuronal ensembles and neuronal computations. Spiking and firing rate mechanistic treatments of network dynamics as well as probabilistic behavioral descriptions will be covered. We will consider mechanisms of coupling, synaptic dynamics, rhythmogenesis, synchronization, bistability, adaptation,… Applications will likely include: central pattern generators and frequency control, perceptual bistability, working memory, decision-making and neuro-economics, feature detection in sensory systems, cortical dynamics (gamma and other oscillations, up-down states, balanced states,…). Students will undertake computing projects related to the course material: some in homework format and a term project with report and oral presentation. Neural Basis of Color Perception NEURL-GA3042 Instructor: Shapley Semester: Fall Lectures and readings on the major phenomena of color perception (colomixing, color induction and constancolor spaces) and on its retinal and ctical substrates. Readings are from research papers and some secondary sources. Students present critical reviews of one of the papers on the reading list. A paper is required by end of the course on a topic mutually agreeable to student and instructor. Mathematical Aspects of Neurophysiology NEURL-GA3042-001 Instructor: Rinzel Semester: Fall This course will focus on neurophysiology and biophysics at the cellular level; the mechanistic and mathematical descriptions of neuronal dynamics and input/output properties. Topics will include: ionic channels (current-voltage relations, gating kinetics, different types), Hodgkin-Huxley equations and reductions (the action potential, repetitive firing, bursting, propagation), dendrites (branching cable theory, passive and active membrane, spines), synapses (transmitter release, depression/facilitation, plasticity). Both analytical (perturbation and bifurcation methods) and numerical techniques will be described and used, serving as an applied introduction to these methodologies. Students will undertake computing projects related to the course material. Computational Neuroscience of Elemental Cognition NEURL-GA3042-003 Instructor: Wang Semester: Fall This is an advanced undergraduate / graduate course. It covers the basic ideas and methods of modeling single neurons, recurrent neural networks, synaptic plasticity and learning. The focus is on the neural circuit mechanisms of core cognitive functions such as decision-making and working memory, both in local neural networks and multi-regional large-scale brain systems. Special Topics: Bayesian Modeling of Behavior NEURL-GA3042-006 Instructor: Ma Semester: Fall This course will provide an intuitive yet mathematically rigorous introduction to Bayesian models of behavior in perception, memory, decision-making, and cognitive reasoning. This course is not about Bayesian data analysis, but about theories that the brain itself is a Bayesian decision-maker. Nevertheless, we will spend some time on model fitting and model comparison. The course will be taught at an introductory level, with many examples and basic exercises. Didactic principles will be strictly adhered to. If you wish to analyze your own data in a Bayesian framework, there will be an opportunity to do so in a final project. SPRING SEMESTER Special Topics: Experiment-based modeling of neurons and networksNEURL-GA3042 Instructor: Reyes Semester: Spring This course focuses on developing models that capture the salient features of neuron and network dynamics. Students will collect data using whole-cell recording, dynamic clamp, and optogenetic stimulation techniques in the in vitro slice or culture preparation. Several approaches to modeling the data will be discussed, including spiking (Hodgkin-Huxley, integrate-and-fire neurons and variants), rate, and mean field models. The goal is to choose the simplest model that will account for the intrinsic and statistical properties of individual neurons and networks. Special Topics: Neural Circuits NEURL-GA3042 Instructor: Carter Semester: Spring This reading course is focused on understanding the cellular and synaptic physiology of neural circuits in the mammalian brain. Each class consists of a short lecture covering the main cellular components of a particular circuit, followed by a round table discussion of key papers selected to highlight specific and distinguishing features of the circuit. Special Topics: Representation and Analysis of Visual Images NEURL-GA3042-005 Instructor: Simoncelli Semester: Spring (2014, 2009, 2003, 1998) A graduate-level lecture course on theory and tools for representing, manipulating and analyzing visual images. Topics include: imaging and optics, color, estimation and representation of position, alignment, displacement, and local orientation, Fourier and multi-scale image decompositions (wavelets), statistical image modeling and its use in compression, estimation, enhancement, synthesis and classification. Throughout, relationship of these computations to biological vision will be discsused. Special Topics: Perceptual Dynamics NEURL-GA3042 Instructor: Rinzel Semester: Spring This is a seminar course to develop familiarity with dynamics, behavioral and neuronal, associated with a range of perceptual phenomena. The format will be mixed: lectures, journal-club- like presentation of papers, and exploration with computer-driven stimuli. We will discuss neuronal mechanistic models and computational models to go with the behavior. Our approach will be case-study; relevant background will be presented. We will emphasize auditory perception (spatial hearing, pitch, auditory scene analysis) but we will likely include case studies from vision (e.g., binocular rivalry) and we may touch on time perception. Special Topics: Introduction to Computer Modeling of Neuronal Systems NEURL-GA3042 Instructor: Rinzel Semester: Spring We will use neural modeling software (and pre-written Matlab codes) to understand how neurons, synapses, and networks/systems work. We will simulate cellular neurophysiology experiments to explore resting and action potentials, firing properties, synaptic conductances and synaptic integration. Idealized models (firing rate and probability-based functional descriptions) will be used for system-level and network properties including receptive fields, perceptual and cognitive dynamics including decision-making, perceptual grouping and perceptual multistability. The software will include dynamic visualization and animation tools. The course will involve classroom lectures and interactive computing lab sessions, homework and a simulation project. No programming experience is necessary. Special Topics: Memory NEURL-GA 3042-002 Instructor: Alberini Semester: Spring Special Topics: Visual Neuroscience NEURL-GA 3042-003 Instructor: Movshon Semester: Spring The visual system is one of the most successful models for studies of higher brain function. This course will explore two aspects of visual neuroscience: First, the function of brain mechanisms that encode information about the form, color, motion, and structure of visual objects and scenes; and second, the mechanisms that decode this information to generate perceptual experience and visually-guided action. Students will be expected to prepare a term paper and a presentation. Some Previous Special Topics Courses: Computational Neuroscience Forum Instructor: Rinzel Lecture/seminar course on computational aspects of neural function at cellular/circuit/system levels. Case study approach with four- to six-week segments that focus on specific topic areas. Registered attendees are expected to complete a project and to present one or more journal articles on course related topics. Function and Dysfunction of Central Auditory Processing Instructor: Sanes Explores the relationship between cetral auditory physiology and psychocoustics and those elements of the ctral auditory system that may change with deafness. Information Processing and Visual Pathways Instructor: Shapley Seminar and lecture course in visual signal processing and visual pathways. The aim of the course is to reach an understanding of vision from a systems analysis point of view. Readings are from research papers and some secondary sources. Students present critical reviews of one of the papers on the reading list. A paper is required by the end of the course on a topic mutually agreeable to student and instructor. The Meaning of 'Understanding' in Brain Neural Science Instructor: Dudai Semester: Spring When you select a brain mechanism to study, what do you expect to 'understand' and how would you know that you have understood it? 'Understanding' as a cognitive accomplishment is intuitively understood but its meaning in science is debated. With the impressive advances in the armamentarium of neuroscience, the increasing pace of discovery at multiple levels of description, and the integration of such findings into models, discussion of what 'understanding' means in brain research becomes even more timely. This course will address 'understanding' from the point of view of practicing neuroscientists but also drawing on concepts and observations from a multitude of disciplines, including philosophy, history of science, and cognition. The course will combine frontal lectures and discussions, including guest presentations by members of the NYU faculty on what they consider as 'understanding' in their own research program. Simulation and Data Analysis Topics include numerical analysis, probability theory and mathematical statistics essential to developing and evaluating computer simulations of complex cognitive and neural processes. Synaptogenesis Prerequisites: NEURL-GA2201/PSYCH-GA2201 or another introductory course that covers topics of basic biophysics and cellular, molecular, and developmental neuroscience. Instructor: Aoki Lecture and discussions that explore the axonal, dendritic and intercellular mechanisms regulating the formation and stabilization of synapses. The discussions will also consider diseases associated with abnormalities in these mechanisms and resistance to mutations. Related DepartmentsDEPARTMENT OF BIOLOGYGenes and Animal Behavior BIOL-GA1082 Instructor: Blau 4 points Survey of principles and patterns of animal behavior. Covers classical ethological research of Lorenz and others and modern research on the molecular basis of behavior, especially in model systems. Behaviors studied include reproductive behavior, rhythmic behavior, learning and memory, and feeding behavior. Statistics in Biology BIOL-GA 2030 Instructor: Tranchina Semester: Fall 4 points This advanced course covers both classical and modern statistical methods. Areas covered include statistical inference, experimental design, parametric and non- parametric statistical tests, resampling, and permutation methods, Monte Carlo simulations, maximum likelihood methods, Bayesian methods, topics in bioinformatics such as microarray analysis and RNA-seq analysis. No previous background in statistics is required. This is a hands-on course held in a computer lab in which each student has his/her own computer. The course includes instruction in the public-domain statistical programming language/environment R, which is widely used in bioinformatics, genomics, and systems biology. Analyses are based on data from the textbook, simulated experimental data, and data from laboratories in the Biology Department. DEPARTMENT OF PSYCHOLOGYPerception PSYCH-GA 2223 Instructors: Heeger and Landy Semesters: Fall and Spring 3 points In-depth survey of psychophysical and modeling methodology, and vision and auditory research. Topic areas include linear systems theory, signal detection theory, optics, spatial vision, motion analysis, depth perception, color vision, auditory coding of intensity and frequency, sound localization, and speech perception. fMRI Lab PSYCH-GA 2245 Instructor: Heeger 3 points This course covers the major topics and issues in the field of fMRI. With this background, students will be able to design and implement their own fMRI experiments. SCHOOL OF MEDICINEFoundations of Cell and Molecular Biology I BMSC-GA 2001 Prerequisites: basic biochemistry and cell biology Lecture and conference Instructor: Borowiec and staff Semester: Fall 6 points This course provides a broad overview of gene expression, nuclear organization and nucleic acid metabolism. Part I (Basic Molecular Biology Boot Camp) consists of five weekly group discussions covering fundamental methodologies applicable to many areas of cell and molecular biology and introduces students to the art of reading of the primary scientific literature. Part II (Selected Topics in Molecular Biology) features nine weeks of intensive lectures and weekly discussion groups organized into timely themes such as control of gene transcription, chromatin structure and epigenetics, telomere biology, DNA replication and recombination, synthesis and folding of functional proteins, and RNA processing. The course emphasizes fundamental molecular processes that underlie almost all aspects of current research in molecular, cellular and developmental biology. Skills necessary for effective reading of primary research articles are heavily emphasized throughout. The course has a total of three exams. Activity dependent neuronal signaling BMSC-GA 4463 Instructors: Chao 1.5 points Brain function changes across a lifespan in response to experience, plasticity of neural circuits, homeostatic factors and the environment. A key component are activity-dependent proteins (Immediate early genes or IEGs) and their participation in synaptic function. Among the topics that will be covered are: Identification of IEGs, Transcriptional regulation, Role of Ca+2, Axonal vs dendritic targeting, Cytoskeletal regulation, Ion channels, Critical periods, Perineuronal nets, and Epigenetic modification. Assembly and Function of Circuits in the Central Nervous System BMSC-GA 4433 Instructors: Dasen and Salzer Semesters: Spring 4 points Through a combination of lectures and conferences, this course will cover the fundamental principles underlying nervous system development, from the early stages of neural induction through activity-dependent fine tuning of neuronal properties and synaptic connections at later phases of development. We will focus on how a variety of factors, including genetic and environmental factors, play dynamic roles in development and how functional neural circuits are established through these complex interactions to control behavior. We will address modern techniques to study neurodevelopment extensively, and students will attain a deep understanding of how and when to apply various approaches. Students will also become familiar with classic and current literature in the field, as primary research articles constitute the bulk of the required reading materials. Molecular Mechanisms of Neurodegeneration BMSC-GA 4461 Instructors: Sigurdsson and Ghiso Semesters: Spring 3 points This elective course for graduate students focuses on molecular and cellular mechanisms of neurodegeneration. Topics may include endoplasmic reticulum stress, endosomal dysfunction, parenchymal and vascular amyloid as well as cerebrovascular dysfunction, axonal degeneration, mitochondria and oxidative stress, viral infections, neuromuscular synapses, microglia and therapeutic approaches. Neuroanatomy Instructors: Lang Semesters: January 3 points This is an intensive three-week course focused on human neuroanatomy that includes lectures, conferences and laboratory sessions. All material will focus primarily on learning the structure of the human nervous system with related focus on function as well. Laboratory sessions will include sheep and human brain dissections. |
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