Brown-NIH Neuroscience Graduate Partnership Program - Course Work


Required Coursework

First Year

In the first year of study, ALL entering students (GPP and NSGP students alike) enroll in a set of courses at Brown designed to provide fundamental knowledge in neuroscience. In the 2014-15 Academic Year, incoming students will enroll in the following courses:

NEUR2030           Advanced Molecular & Cellular Neurobiology I
This course focuses on molecular and cellular approaches used to study the CNS at the level of single molecules, individual cells and single synapses by concentrating on fundamental mechanisms of CNS information transfer, integration, and storage. Topics include biophysics of single channels, neural transmission and synaptic function.

NEUR2040           Advanced Molecular & Cellular Neurobiology II
This course continues the investigation of molecular and cellular approaches used to study the CNS from the level of individual genes to the control of behavior. Topics include patterning of the nervous system, generation of neuronal diversity, axonal guidance, synapse formation, the control of behavior by specific neural circuits and neurodegenerative diseases.

NEUR2050           Advanced Systems Neuroscience
This course focuses on systems approaches to study nervous system function. Lectures and discussions emphasizes neurophysiology, neuroimaging and lesion analysis in mammals, including humans. Computational approaches will become integrated into the material. Topics include the basic sensory, regulatory, and motor systems. Students will attend NEUR1650, "Structure of the Nervous System," as part of the curriculum.

NEUR2060          Advanced Cognitive Neuroscience
This course focuses on cognitive approaches to study nervous system function. Lectures and discussions emphasize neurophysiology, neuroimaging and lesion analysis in mammals, including humans. Computational approaches will become integrated into the material. Topics include the major cognitive systems, including perception, decisions, learning and memory, emotion and reward, language, and higher cortical function.

In addition, all first year students take an intensive laboratory course to gain practical experience in cellular and molecular neuroscience techniques. This 10 day course is held in January at the Marine Biological Laboratories in Woods Hole, MA.

Second Year

In the second year, while at NIH, GPP students must enroll in a graduate level statistics course or demonstrate core competence in statistics. Prior graduate level statistics may suffice. A placement exam will occur at the beginning of each semester. This exam will be administered by the Dep't of Biostatistics and focus on material in PHP2510. Otherwise, the following course at NIH, offered through the Foundation for Advanced Education in the Sciences (FAES), is recommended :

STAT500 - Statistics for Biomedical Scientists
The objective of this course is to provide an overview of statistics for biomedical research workers and clinicians who are interested in interpretation of the results of statistical analyses. A series of integrated lectures on analysis and interpretation of medical research data. Emphasis is on ideas and understanding rather than mechanics. Topics covered in the first semester include the foundation of statistical logic and the most commonly encountered statistical procedures in medical research. The second semester expands on the material covered in the first semester by looking at assumptions, extensions, and alternatives for common procedures. Those who will be routinely engaged in computing statistical procedures should consider STAT 200. STAT 500 is a full-year course. Material covered in the first semester is necessary to satisfactorily undertake the second semester. Registration is limited to 40 students.

In addition, it may be possible to fulfill the statistics requirement through distance learning by taking one of the following courses at Brown, with the professor's approval:

PHP2510 - Principles of Biostatistics and Data Analysis
Intensive first course in biostatistical methodology, focusing on problems arising in public health, life sciences, and biomedical disciplines. Summarizing and representing data; basic probability; fundamentals of inference; hypothesis testing; likelihood methods. Inference for means and proportions; linear regression and analysis of variance; basics of experimental design; nonparametrics; logistic regression.

APMA2610 - Recent Applications of Probability and Statistics
This topics course covers modern applications of probability and statistics in the computational, cognitive, engineering, and neural sciences. Topics include: Markov chains and their applications to MCMC computing and hidden Markov models; Dependency graphs and Bayesian networks; parameter estimation and the EM algorithm; Nonparametric statistics ("learning theory"), including consistency, bias/variance tradeoff, and regularization; Gibbs distributions, maximum entropy, and their connections to large deviations. Each topic will be introduced with several lectures on the mathematical underpinnings, and concluded with a computer project, carried out by each student individually, demonstrating the mathematics and utility of the approach.

Brown University Graduate School requires students to complete 24 course credits before graduation. Typically these credits are earned within the first three years of study. To satisfy any course requirement, students must earn a grade of B or higher. Students receiving grades of C or No-Credit (C and NC) must meet with their First Year Advisory or Thesis Committee to discuss remedial action.

Optional Courses

Students may also select from a large number of courses and seminars offered at NIH through the Foundation for Advanced Education in the Sciences (FAES) (For full catalog, click here) and by the major departments in the program at Brown including Neuroscience, Cognitive, Linguistic and Psychological Sciences, Applied Mathematics, Engineering, Molecular Biology, Cell Biology and Biochemistry, and Molecular Pharmacology, Physiology and Biotechnology. These courses are chosen to enhance students’ laboratory research experience. During the second year and beyond, it may be possible for GPP students to participate in Brown courses electronically at a distance, with approval of the professor and the department. Courses include:

Neuroscience

NEUR 1680 - Computational Neuroscience
A lecture and computing lab course providing an introduction to quantitative analysis of neural activity and encoding, as well as modeling of neurons and neural systems. Emphasizes Matlab-based computer simulation. Prerequisites: NEUR 0010, 1020 or 1030; APMA 0410 or 1650, or equivalent.

NEUR 2120 - Topics in Visual Physiology
Selected topics in visual physiology are examined through a close and critical reading of original research articles. Emphasizes the anatomical and physiological bases of visual function. Primarily for graduate students with a strong background in neuroscience and a working knowledge of the anatomy and physiology of the mammalian visual system. Offered in alternate years. Instructor permission required.

NEUR 1940G - Drugs and the Brain
This is a seminar course devoted to the reading and analyzing of original research articles dealing with the interaction between drugs and the brain. This will include drugs used to analyze normal brain function, as well as drugs of abuse and drugs used for therapeutic purposes. This course is intended for undergraduate and graduate students with a strong background in neuropharmacology. Sign-up sheet in Sidney Frank hall, Room 315 beginning November 1, 2011. Prerequisite: NEUR 0010, 1020, and 1030. Enrollment limited to 15. Instructor permission required.

NEUR 2120 - Topics in Visual Physiology
Selected topics in visual physiology are examined through a close and critical reading of original research articles. Emphasizes the anatomical and physiological bases of visual function. Primarily for graduate students with a strong background in neuroscience and a working knowledge of the anatomy and physiology of the mammalian visual system. Offered in alternate years. Instructor permission required.

NEUR 1930I - Neural Correlates of Consciousness
This couse will consider the neuroscience of consciousness from a variety of perspectives, using examples from behavior, neurophysiology, neuroimaging and neurology. The course content will focus on primary literature, using review articles for background. Students will lead discussions. Sign-up required by Google Docs. Strongly Recommended: NEUR 1030. Enrollment limited to 15. Instructor permission required.

NEUR 1930N - Region of Interest: An In-Depth Analyis of One Brain Area
In-depth exploration of one region of the brain. Topics will include: cell types and properties; synaptic properties; plasticity; connections to other brain areas; sub-divisions within the area; the region's role in sensation and perception; the region's role in action and behavior; the region's role in learning and memory; and diseases and disorders associated with the region. By studying one brain area closely, students will gain a deeper understanding of concepts and principles that apply throughout the brain. Students will gain experience with primary literature and learn about tools and techniques for studying the area. Enrollment limited to 15.

NEUR 1930G - Disease, Mechanism, Therapy: Harnessing Basic Biology for Therapeutic Development
The recent surge in understanding the cellular and molecular basis of neurological disease has opened the way for highly targeted drug discovery and development. In this course we will use several case studies to illuminate how mechanistic insights are being translated into novel therapeutic approaches. Instructors permission required. Enrollment limited to 15.

NEUR 2160 - Neurochemistry and Behavior
Examines behavior from a neurochemical perspective via readings and discussions based on original research articles. Intended primarily for graduate students with a strong background in neurochemistry and neuropharmacology and advanced undergraduates with an appropriate background. Offered alternate years.

NEUR 1940B - Neuroethology
Neuroethology is concerned with the neural systems serving such naturally occurring behaviors as orientation in the environment, finding food, predator detection, social communication, circadian and seasonal rhythms, and locomotion and tracking. This seminar will examine selected examples of the neuroethological approach to analysis of brain function, which sometime leads to conclusions different from those of laboratory-based experiments on traditional animal models.

NEUR 1740 - The Diseased Brain: Mechanisms of Neurological and Psychiatric Disorders
The goals of this course are to illustrate what basic science can teach us about neurological disorders and how these pathologies illuminate the functioning of the normal nervous system. Consideration will be given to monoallelic diseases (e.g. Fragile X Syndrome, Duchenne Muscular Dystrophy and Tuberous Sclerosis) as well as genetically complex disorders, such as Autism, Schizophrenia and Alzheimer's Disease. Emphasis will be on the cellular and molecular basis of these disorders and how insights at these levels might lead to the development of therapies.

NEUR 1670 - Neuropharmacology and Synaptic Transmission
Synaptic transmission will be studied from a biochemical and pharmacological point of view. We will explore the factors regulating neurotransmitter synthesis, storage, release, receptor interaction, and termination of action. Proposed mechanisms of psychoactive drugs and biochemical theories of psychiatric disorders will be examined.

Biology

BIOL 1150 - Stem Cell Engineering
Stem cell engineering focuses on using adult, embryonic, and induced stem cells to repair damaged or diseased tissues. This course will examine the role of stem cells in development, tissue homeostasis, and wound healing, as well as how they are being applied in regenerative medicine. The course will use a lecture and discussion format for major topic areas. Additionally, students will receive hands-on training in how to isolate, culture, and differentiate adult stem cells in a laboratory setting. Expected: CHEM 0330 and BIOL 0500 or an equivalent course in cell biology or physiology. Enrollment limited to 20. Instructor permission required.

BIOL 1190 - Synaptic Transmission and Plasticity
Synapses are the means by which the nervous system communicates. In this seminar-style course, we will explore the molecular and physiological underpinnings of synaptic transmission. We will then examine ways in which synapses can modulate their strength during development, learning, and other adaptive processes. Expected: BIOL 0800 or NEUR 1020. Enrollment limited to 20. Instructor's permission required.

BIOL 2290C - Neuronal Signaling Meets the RNA World
The concept of one gene, one protein is nowhere more violated than in protein encoding genes expressed in the nervous system. We will cover a variety of post-transcriptional processing events which serve to generate protein diversity in the nervous system including alternative splicing, trans-splicing, and RNA editing. We will also address non-coding RNAs and their roles, in particular, in regulating nervous system function. Since it is clear that nervous system complexity is not a function of gene number across large phylogenetic distances, the course will be aimed at instilling a greater understanding of how the regulation of shared "toolkit" genes results in organismal complexity.

BIOL 2320 - Genetic Control of Cell Fate Decisions
We will explore mechanisms underlying how neuronal cell fates are established during development and how the understanding of this process may provide insight into neurological disease and therapeutic intervention. Topics: Temporal identity in neuroblast and cerebral cortex cell fate specification, transcriptional control of lineage decisions in the spinal cord, the role of morphogen concentration and timing on cell fate decisions, micro RNA control of gene regulation, epigenetics, induced pluripotent stem cells, stem cell use in therapeutic approaches to intervene in neurological diseases. Primary literature will be discussed in lectures in the format of student-led, faculty-guided discussions. Enrollment limited to 20. Instructor permission required.

BIOL 2340 - Neurogenetics and Disease
Genetic mutations provides a powerful approach to dissect complex biologic problems. We will focus on fascinating discoveries from "forward genetic" studies ‚ moving from nervous system phenotype to genetic mutation discovery. There will be an emphasis of neurologic disease phenotypes and the use of novel genomic methods to elucidate the central molecular and cellular causes for these conditions. The course will emphasize the use of "reverse genetics", engineered mutations in model systems ‚ to dissect nervous system function and disease mechanisms. Disorders to be covered include autism, intellectual disability, schizophrenia, epilepsy. Enrollment limited to 20. Instructor permission required. .

Cognitive, Linguistic and Psychological Studies (CLPS)

CLPS1150 - Memory and the Brain
This class is for undergraduate and beginning graduate students of psychology, cognitive neuroscience, and biology interested in to biological research on memory. There are four parts: 1) how neurons are connected and communicate, 2) fundamental issues in the psychology of memory, 3) memory localization in the brain, and 4) consolidation of memory into a permanent store. The course is designed to be accessible to students in a variety of disciplines, but requires background in psychology, cognitive science, or neuroscience. The class will include lecture, writing assignments, and presentations of primary research articles.

CLPS 1291 - Computational Cognitive Science
Provides an introduction to computational modeling of cognition, summarizing traditional approaches and providing experience with state-of-the-art methods. Covers pattern recognition and connectionists networks as well as Bayesian probabilistic models, and illustrates how they have been applied in several key areas in cognitive science, including visual perception and attention, object and face recognition, learning and memory as well as decision-making and reasoning. Focuses on modeling simple laboratory tasks from cognitive psychology. Connections to contemporary research will be emphasized highlighting how computational models may motivate the development of new hypothesis for experiment design in cognitive psychology. Prerequisite: comfort with basic linear algebra and at least one introductory course in Computer Science or programming, or instructor permission.

CLPS 1400 - The Neural Bases of Cognition
Research using animal models has informed and guided many of the recent advances in our understanding of the brain mechanisms underlying cognition. This seminar course will address topics related to animal models of human cognition. Students learn about how different aspects of the neural bases of cognition are modeled in animals by reviewing the primary research literature. The course is divided into three sections, each addressing one animal model in one cognitive domain. Selected papers will emphasize learning, memory, and attention, but may also address other aspects of cognition, for example decision-making, or cognitive impairment associated with neuropathology or aging. Prerequisite: CLPS 0040 (COGS 0720), CLPS 0400 (PSYC 0470), or NEUR 0010; and CLPS 1190 (PSYC 1030), CLPS 1191 (PSYC 1450), CLPS 1192 (PSYC 1200), or NEUR 1600; or instructor permission. Enrollment limited to 20.

CLPS 1480B - Cognitive Aging and Dementia
This seminar examines the cognitive changes associated with normal aging and age-related dementia (e.g., Alzheimer's Disease). Topics covered will include changes in the neurocognitive systems mediating memory, perception, and attention. The course is primarily intended as an advanced seminar for junior and senior concentrators in Psychology, but is also intended for other students interested in aging and the neuropsychology of cognition. Recommended prerequisites: An introductory course in cognitive neuroscience (CLPS 0040 (COGS 0720), CLPS 0400 (PSYC 0470)) or permission of the instructor. Preference will be given to senior concentrators in Psychology and related areas. Enrollment limited to 20.

CLPS 1480C - Cognitive Control Functions of the Prefrontal Cortex
The prefrontal cortex has long been known to support higher cognitive functions, including working memory, planning, reasoning, and decision making. This seminar offers an in-depth review of recent empirical and theoretical approaches to understanding prefrontal cortex function. This year the course will focus on prefrontal contributions to the cognitive control of declarative memory. Enrollment limited to 20.

CLPS1490 - Functional Magnetic Resonance Imaging: Theory and Practice
This course will train students in the practice and use of functional magnetic resonance imaging (fMRI) as a cognitive neuroscience methodology. Topics covered include MRI physics, the physiological basis of the BOLD signal, experimental design, data collection, statistical analysis, and inference. A practical component of the course includes the opportunity to collect and analyze fMRI data at the Brown MRF.

CLPS 1491 - Neural Modeling Laboratory
Numerical simulations of cognitively oriented nervous system models. Discussion of parallel, distributed, associative models: construction, simulation, implications, and use. Prerequisites: MATH 0090, 0100, or equivalent; knowledge of a computer language; some background in neuroscience or cognitive science is helpful.

CLPS 1492 - Computational Cognitive Neuroscience
We explore neural network models that bridge the gap between biology and cognition. Begins with basic biological and computational properties of individual neurons and networks of neurons. Examines specialized functions of various brain systems (e.g., parietal cortex, frontal cortex, hippocampus, ganglia) and their involvement in various phenomena, including perception, attention, memory, language and higher-level cognition. Includes a lab component in which students get hands on experience with graphical neural network software, allowing deeper appreciation for how these systems work. Prerequisites: CLPS 0020 (COGS 0010) or CLPS 0200 (COGS 0420); and CLPS 0410 (PSYC 0750) or NEUR 0010.

CLPS 1520 - Computational Vision
A detailed introduction to computational models of biological and machine vision summarizing traditional approaches and providing experience with state-of-the-art methods. Topics include low-level vision (color, motion, depth and texture), segmentation, face, object and scene recognition. Connections to contemporary research in computer vision and computational neuroscience will be emphasized highlighting how computational models may motivate the development of new hypothesis for experiment design in cognitive psychology.

CLPS 1530 - 3D Shape Perception
Our ability to move in the environment, recognize and grasp objects, depends enormously on the capacity that the brain has in organizing the visual stimulation in the perceived 3D layout. 3D objects in the world project on the human retina flat images. How does the brain re- transform these flat images into a 3D representation? Enrollment limited to 40.

CLPS 1571 - Visual Consciouness
This course will focus on consciousness related to visual perception. The goal of this course is to understand the neural correlates of visual consciousness. 1) We will learn about basic neural mechanisms of visual processing and other brain functions. 2) We will discuss philosophical and neuroscientific models of visual consciousness. 3) We will examine the roles of attention, reward, and memory in visual consciousness. 4) We will evaluate recent neuroscientific experiments with animals and humans and their potential to advance the research of consciousness.

CLPS 1580B - Visual Attention
In daily life, most visual scenes are complex and crowded so that our visual system faces a daunting task of processing an enormous amount of information at a given movement. Thus, attentional mechanisms are crucial to select relevant objects /events and guide actions. In this seminar, we will understand behavioral and underlying neural mechanisms involved in visual attention and their interaction with visual cognition such as memory and learning and goal-directed actions. We will also study investigations of spared and impaired patterns of attention-based performances following brain injury.

CLPS 1620 - Developmental Cognitive Neuroscience
This course will examine fundamental topics in cognitive development from the point of view of the developing brain. Topics of interest will include developing abilities in perception, attention, action, object concepts, memory, learning, planning, language, and social cognition. Typical and atypical brain development will be considered. Prerequisite: One of CLPS 0600 (PSYC 0810), CLPS 0610 (COGS 0630), EDUC 0800, or permission of the instructor. Enrollment limited to 40.

CLPS 1621 - The Developing Brain
Analysis of brain development, focusing on neural substrates of psychological processes in both animals and humans. Prerequisites: CLPS 0010 (PSYC 0010) or NEUR 0010. Not open to first year students or sophomores. Instructor permission required.

CLPS 1820 - Language and the Brain
This course will examine the neural systems underlying language processing. Major focus will be on effects of brain injury on speaking and understanding in left hemisphere-damaged patients who have aphasia, right hemisphere-damaged patients, and split-brain patients. Behavioral, electrophysiological and neuroimaging evidence will be investigated.

CLPS 1821 - Neuroimaging and Language
Examines neuroimaging approaches to language processing including fMRI, PET, TMS, and ERP. Consideration of the neural systems underlying speaking and understanding. Topics include neural basis of speech, lexical/semantic, and syntactic processing, mirror neurons and language, multisensory integration, meanings of words, literacy, and special populations.

CLPS 2410 - Auditory Neuroscience
An in-depth analysis of the neural bases of audition. Topics include development, structure and function of the inner ear; ascending and descending neural circuitry for processing of complex sounds; and physiological correlates of auditory phenomena. Prerequisite: CLPS 2400 or NEUR 2050.

Computer Science

CSCI 1420 - Introduction to Machine Learning
How can artificial systems learn from examples, and discover information buried in massive datasets? We explore the theory and practice of statistical machine learning, focusing on computational methods for supervised and unsupervised data analysis. Specific topics include Bayesian and maximum likelihood parameter estimation, regularization and sparsity-promoting priors, kernel methods, the expectation maximization algorithm, and models for data with temporal or hierarchical structure. Applications to regression, categorization, clustering, and dimensionality reduction problems are illustrated by examples from vision, language, bioinformatics, and information retrieval. Prerequisites: CSCI 0040 or 0150 or 0180 or 0190; and CSCI 0450 or APMA 1650 or MATH 1610; and CSCI 0530 or MATH 0520 or 0540; or instructor permission.

CSCI 1430 - Introduction to Computer Vision
How can we program computers to understand the visual world? This course treats vision as inference from noisy and uncertain data and emphasizes probabilistic and statistical approaches. Topics may include perception of 3D scene structure from stereo, motion, and shading; segmentation and grouping; texture analysis; learning, object recognition; tracking and motion estimation. Strongly recommended: basic linear algebra, calculus, and probability.

Engineering

ENGN 1220 - Neuroengineering
Course Goals: To develop an advanced understanding of how signals are generated and propagated in neurons and neuronal circuits, and how this knowledge can be harnessed to design devices to assist people with neurologic disease or injury. Fundamental topics in neuronal and neural signal generation, recording methods, and stimulation methods. Clinical/Translational topics include multiple clinically available and emerging neurotechnologies. Prerequisites: NEUR 0010 and ENGN 0510; or instructor permission, which may be provided after discussion with course faculty.

ENGN 2560 - Computer Vision
An interdisciplinary exploration of the fundamentals of engineering computer vision systems (e.g., medical imaging, satellite photo interpretation, industrial inspection, robotics, etc.). Classical machine vision paradigms in relation to perceptual theories, physiology of the visual context, and mathematical frameworks. Selections from Gestalt psychology, Gibsonian approach primate visual pathways, edge-detection, segmentation, orientation-selectivity, relaxation-labeling, shading, texture, stereo, shape, object-recognition.