Curriculum

The depth and breadth of Neuroscience disciplines are covered by core and elective courses.

Students enter the Neuroscience Program with diverse backgrounds, interests, and training. The Neuroscience laboratories that students may join cover a multitude of different disciplines. The Curriculum is designed to expose all students to the breadth of Neuroscience, but to also fit the needs of the individual student.  Courses are designed for students to have ample time to devote to their laboratory rotations.

School of Medicine Academic Calendar 2015 - 2016 Schedule of Courses 2015 – 2016

Required in the first year

ALL YEAR

Lab Rotations
Neuroscience Journal Club
Neuroscience Seminar Series

CORE COURSES

First Quarter
Neuroscience Cognition I (Dong, staff)
Science, Ethics and Society (O’Connor)

Second Quarter
Neuroscience Cognition I (Dong, staff)
Science, Ethics and Society (O’Connor

Third Quarter
Neuroscience Cognition II (Stuphorn)

Fourth Quarter
Neuroscience Cognition II (Stuphorn)        

Required in the second year

Begin thesis research
Neuroscience Journal Club
Neuroscience Seminar Series
Elective Courses – Total of 5 electives
Doctoral Board Oral Examination

Required in the third year

Thesis Proposal
Neuroscience Journal Club (required through year 4)

Required courses to be completed at any time prior to the Thesis Defense

Teaching in Neuroscience (Neuroscience faculty)
Additional teaching opportunities are available. Please see Graduate Program Directors for more information.

Statistics
It is required that all students complete their degree with an understanding of statistics. This requirement can be fulfilled by completing courses in statistics offered at the Medical Campus or at Homewood.

Neuroscience Career Skills (Kolodkin)
Taught third and fourth quarter, every other year. This course is intended for Neuroscience Program graduate students who are in their fourth year or beyond. There will be ten sessions, and each session we will include one or more invited discussion leaders. This is a pass/fail course and every participant is required to take it for credit. A grade of pass or fail will be decided based on attendance.

  • Core Courses


    Neuroscience and Cognition I (NeuroCogI)
    ME:440.811

    1st and 2nd quarters
    Course Directors:
    Xinzhong Dong PhD

    This is the first half of a 4-quarter course on the cellular and molecular basis of neural function and the neural basis of perception, cognition, and behavior. Topics covered in this half include (1) development and structure of the nervous system, (2) cellular neurophysiology, (3) neural signaling and coding, and (4) audition, vocalization, and language. Lectures will be presented by faculty in the Neuroscience, Neurology, Biomedical Engineering, Psychology, and Cognitive Science departments. The course will also include discussion sections based on current literature and several neurotechniques sessions designed to familiarize students with current experimental approaches in cellular, systems, and molecular neuroscience. This course is required of all students in the Neuroscience Graduate Program. Students outside the program may take this course independent of Neuroscience and Cognition II. Prerequisites: Basic Cell and Molecular biology (may be taken concurrently) or permission from Course Directors.

    Most recent syllabus

  • Neuroscience and Cognition II (NeuroCogII)
    ME:440.812

    3rd and 4th quarters
    Course Directors:
    Veit Stuphorn PhD

    This is the second half of a 4-quarter course on the cellular and molecular basis of neural function and the neural basis of perception, cognition, and behavior. Topics covered in this half include (1) perception of objects, space, and self, (2) movement and balance, (3) learning and memory, (4) neurological and psychiatric disorders, and (5) global function in the nervous system. Lectures will be presented by faculty in the Neuroscience, Neurology, Biomedical Engineering, Psychology, and Cognitive Science Departments. The course will also have a laboratory component. This course is required of all students in the Neuroscience Graduate Program. Students outside the program may take this course independent of Neuroscience and Cognition I with permission from Course Directors. Prerequisites: Basic Cell and Molecular biology (may be taken concurrently) or permission from Course Directors.

    Most recent syllabus

  • Science, Ethics and Society
    ME:440.712

    First and Second Quarter, every year
    Course Directors:
    Daniel O'Connor PhD

    Science as a profession has undergone radical changes in the last decade. Central issues include mentoring, misconduct in science, preparedness of graduate students and postdoctoral fellows for careers in science, and the career choices currently available. To this end, this course will focus on mentoring and issues of ethics and scientific misconduct. Preparedness for a career in science issues will be discussed in the context of funding currently available to scientists and preparation strategies involved in grant writing. In addition, methods of oral presentation and slide preparation will be discussed.

    Most recent announcement

  • Neuroscience Career Skills
    ME:440.724

    Third Quarter, every other year
    Course Directors:
    Alex Kolodkin PhD

    This course is intended to help graduate students in the Neuroscience Graduate Program obtain an appreciation of options, challenges, and steps towards careers in the field of neuroscience. This course is designed to complement the “Science, Ethics and Society” course offered to first year Neuroscience Graduate Program students. There will be one or two main topics covered at each class meeting, and one or more invited discussion leaders with expertise in the topic will participate in the class. Discussion leaders will include Johns Hopkins faculty members as well as outside experts.

    This is a pass/fail course and all participants are required to take it for credit. A grade of pass or fail will be assigned based on attendance.

  • Elective Courses

    In addition to the core courses and a statistics course, each student selects advanced electives offered by members of the Neuroscience Training Program or other departments at the Medical School. Students in the Neuroscience Training Program are required to complete five elective courses by the end of their second year. These may be a combination of small seminar-style elective courses in neuroscience, listed below, and advanced courses in other fields relevant to their research interests, such as molecular biology, genetics, immunology, biochemistry, biomedical engineering, biostatistics, pharmacology, physiology, anatomy and computer science.


    Neuropharmacology
    ME:440.709

    First quarter, every other year
    Course Directors:
    Jay Baraban MD, PhD
    Solomon Snyder MD, DSc, DPhil (Hon Causa)

    Classical studies elucidating the mechanisms of action of psychoactive substances led to seminal discoveries about how the brain works. Conversely, our ability to exploit modern advances in molecular neurobiology to treat neurological and psychiatric diseases will depend on successful development of new drugs based on these findings.
    The instructors present an overview of the mechanisms of action of several, widely used drug classes and the broad range of methods used to elucidate their effects on the brain. Furthermore, students present papers describing recent advances in this dynamic field of research.

    Most recent announcement

  • Trends in the Neurobiology of Aging
    ME:440.715

    First quarter, every other year
    Course Directors:
    Mark P. Mattson PhD

    As the average lifespan of humans increases, age-related dysfunction of the nervous system, and neurodegenerative disorders such as Alzheimer's and Parkinson's diseases, are becoming major concerns in our society. Recent advances in understanding the molecular and cellular underpinnings of nervous system aging and neurodegenerative disorders will be the focus of this course. Emerging findings of genetic and environmental factors that either promote successful brain aging or predispose to age-related neurological disorders, and elucidation of their underlying molecular and cellular mechanisms, will be emphasized. The course will consist of several introductory lectures and subsequent sessions in which hot topics in the field are discussed.

    Most recent announcement

  • Visual System
    ME:440.722

    First and Second Quarter, every year
    Course Directors:
    Stewart Hendry PhD

    From outer segments of photoreceptors to the Fusiform Face Area of the cerebral cortex we have come to understand how the visual system works at each of many fundamental levels. This course examines the basis for perception of visible objects at each of these levels. We will use the secondary literature (scientific reviews) to accent the hard-won truths about visual system functional organization and to highlight ongoing controversies. Students will be lead through carefully chosen reviews in a series of lectures and written summaries prepared by faculty. Three exams and a final exam will test students not on their memorization of minutiae but on their understanding of fundamental principles.

    Most recent announcement

  • Physiology of Sensory Transduction
    ME:440.808

    Second quarter, every other year
    Course Directors:
    King-Wai Yau PhD

    A seminar and reading course that covers current research in sensory transduction from a physiological perspective. Visual, chemical and auditory transductions will be covered.

    Most recent announcement

  • Writing About the Brain
    ME:440.723

    Third quarter, every other year
    Course Directors:
    David Linden PhD

    The goal of this course is to train neuroscientists to effectively and clearly communicate ideas about nervous system function to a general audience. Students shall read and analyze writings about neuroscience and shall interact with established science writers. More importantly, they shall develop, research and write both news and feature-length stories that shall be presented, critiqued and revised each week in a workshop format. Enrollment limited to 10 students.

    Prerequisites: Neuroscience and Cognition I and approval of instructor

    Most recent announcement

  • Theoretical and Computational Neuroscience
    AS.080.620

    One quarter course, offered all year
    Course Directors:
    Ernst Niebur PhD

    Topics of theoretical neuroscience and computational neuroscience will
    be discussed based on the original literature. Students are expected
    to actively participate in the discussion and also to present selected
    material to the class. Open to graduate students and postdocs and advanced undergraduates. Instructor's permission required.

    Most recent announcement

  • The Hypothalamus: The Brain's Master Homeostat
    ME:440.726

    Third quarter, every other year
    Course Directors:
    Seth Blackshaw PhD

    The hypothalamus is the central regulator of a broad range of homeostatic behaviors essential to survival, and plays a key role in controlling emotional and appetitive behaviors. This course offers an overview of both historical and recent work on this vital brain region. Topics covered will include the evolution and development of the hypothalamus, control of circadian rhythms and sleep, regulation of hunger and body temperature, as well as hypothalamic regulation of sexual, defensive, and affiliative behavior. Each class will include 10-15 minutes of introductory lecture, followed by in-class discussion of 2 relevant recent papers. The final grade will be based on class participation and one 6-page review article or mock grant proposal on any related topic. An optional lecture on good grant writing practices will also be offered. Students must have completed Neuroscience Cognition I and II or have permission of instructors. Maximum enrolement of 15 students.

    Most recent announcement

  • Current Issues in Systems and Cognitive Neuroscience
    ME:440.813

    Fourth quarter, every year
    Course Directors:
    Jeremiah Cohen PhD

    The brain is an information processing system without parallel. It excels at recognizing objects and substances, reconstructing space, analyzing sound environments, controlling complex behaviors, and storing a lifetime's worth of events and experiences. The neural mechanisms underlying these abilities are studied by a large community of systems and cognitive neuroscientists. This research has generated a rapidly evolving field of high-profile discoveries and lively debates between competing laboratories. This course aims to convey a clear sense of this field by focusing on current experimental and conceptual controversies regarding organization and function in the vertebrate nervous system. Each week will focus on a different topic represented by two or more recent papers (selected by an instructor) reflecting opposing points of view. Students will present the papers informally and direct a debate over the relative merits of the conflicting viewpoints. The quarter-long course will be divided into 2-3 week sections covering different sensory, motor, or cognitive systems, in addition to computational neuroscience. There will be one 2-hour debate each week, and participation in the 1-hour Systems Journal Club (Readings in Systems Neuroscience, ME440.810) will also be required.

    Most recent announcement

  • Mechanisms of Synaptic Transmission
    ME:440.707

    Fourth quarter, every other year
    Course Directors:
    Dwight Bergles PhD
    Elisabeth Glowatzki PhD
    Paul Worley MD

    A seminar and reading course devoted to the molecular mechanisms underlying synaptic transmission and the regulation of synaptic plasticity. The structure and function of neurotransmitter receptors, ion channels and synaptic vesicle proteins will be discussed. In addition, the molecular mechanisms involved in the control of synaptic transmission such as the trans-synaptic regulation of the function and expression of synaptic proteins will be examined.

    Most recent announcement

  • Brain diseases: Neurodevelopmental Diseases
    ME:440.727

    Fourth quarter, every other year
    Course Directors:
    Christopher Ross MD, PhD
    Daniel Weinberger MD

    The course will consider the emerging unity of approaches and concepts in understanding a range of brain diseases such as schizophrenia, bipolar disorder, autism and related disorders. Genetic mutations or risk factors for many of these diseases are beginning to illuminate pathogenesis, and genetic relationships among the diseases are beginning to change our thinking about diagnostic categories. Interactions among protein or RNA products of genes mutated in each disease may help establish pathogenic pathways. Environmental influences also appear to be important, including possible roles of infection and immunity. Schizophrenia and related adult onset disorders appear to be caused by mechanisms involving neurodevelopment, whose major consequences are most visible during adulthood. Cell and mouse models are increasingly central for understanding pathogenesis and developing novel therapeutics. For all the disorders, it is possible to conceive of a unified understanding ranging from molecular manifestations to systems neurobiology. Ultimately, the goal is to devise rationale disease-modifying treatments. Lectures by experts in each disease will be followed by student-led discussions critically reviewing current literature. Discussions will focus on strengths and limitations of current models, controversies about mechanisms, unresolved research questions, and potential paths to therapeutics. Student participation will include leading and participating in discussions of papers and writing a research proposal using an abbreviated NIH grant format on any topic related to the course.

  • Brain diseases: Neurodegenerative Diseases
    ME:440.728

    Fourth quarter, every other year
    Course Directors:
    Christopher Ross MD, PhD
    Jeffrey Rothstein MD, PhD

    The course will provide an in-depth examination of the biology of the classic neurodegenerative diseases such as Huntington's disease, Parkinson's disease, ALS and Alzheimer's disease, and other diseases may be considered depending on student and faculty interest. All involve toxicity or death of neurons. Rare genetic varients of many of the neurodegenerative diseases have greatly illuminated the more common, apparently sporadic, forms. Interactions among protein products of genes mutated in each disease are helping establish pathogenic pathways. Inflammation and metabolic stress are other common themes, and environmental contributions, possibly involving toxins, are important for some diseases. Cell and mouse models are increasingly central for understanding pathogensis and several diseases, though the exact mechanisms and relation to cell death are controversial. It is increasingly possible to conceive of a unified understanding ranging from molecular manifestations to systems neurobiology. Ultimately the goal is to devise rational disease-modifying treatments. Lectures by experts in each disease will be followed by student- led discussions critically reviewing current literature. Discussions will focus on strengths and limitations of current models, controversies about mechanisms, unresolved research questions, and potential paths to therapeutics. Student participation will include leading and participating in discussions of papers, and writing a research proposal, using an abbreviated NIH grant format, on any topic related to the course.

  • The Cellular and Molecular Basis of Neural Development
    ME:440.705 (Development II) & ME:440.711 (Development I) (alternating years)

    Fourth quarter, every year
    Course Directors:
    Alex Kolodkin PhD
    Shanthini Sockanathan PhD
    Christopher Potter PhD

    A seminar and reading course devoted to the discussion of the cellular and molecular processes underlying neuronal development. Topics to be covered include neural induction, cell differentiation, neurotrophic factors and their mechanism of action, mechanisms of axonal growth and guidance, target recognition and synapse formation, and the basis of synaptic specificity. Students must have completed Neuroscience Cognition I and II.

    Most Recent Development I Announcement

    Most Recent Development II Announcement

  • Elective Courses Preapproved as Neuroscience Electives


    Structure and Function of the Auditory and Vestibular Systems
    BME:580.626

    First and Second Quarter, even numbered years
    Course Directors:
    Xiaoqin Wang PhD

    Prereqs: an introduction to neuroscience. Recommended: familiarity with signal theory. Brain mechanisms and perception of sound and balance. This course is an accompaniment for 580.625, although the courses can be taken in either order. Topics include representation of sound and balance in neural discharge patterns, anatomy of the central auditory and vestibular systems, synaptic transmission and signal processing in central neurons, and complex sound perception and movement control. Aspects such as speech perception, sound localization, vestibular reflexes and vestibular compensation are discussed with an integrated perspective covering perceptual, physiological, and mechanistic data. Taught at the School of Medicine. Class size limited to 25.

    Most recent announcement

  • Structure and Function of the Auditory and Vestibular Periphery
    BME:580.625

    First and Second Quarter, odd-numbered years
    Course Directors:
    Paul Fuchs PhD
    Elisabeth Glowatzki PhD

    Prereqs: an introduction to neuroscience. This course will cover basic mechanisms and functions of the inner ear and brainstem. This is a companion course and alternates with 580.626, although these can be taken in either order. The focus is on transmission and transduction of sound and head movements by the auditory and vestibular periphery. Topics include: cellular and molecular mechanisms of mechanotransduction, synaptic signaling and development, primary afferents and the first-order brainstem nuclei, as well as clinical consequences of peripheral damage. Taught at the School of Medicine. Class size limited to 25.

    Most Recent Announcement

  • Cellular and Molecular Biology of Photoreceptors in Health and Disease
    ME:280.700

    Third quarter, every other year
    Course Directors:
    Don Zack MD, PhD

    The course will present a multidisciplinary approach to the biology and pathology of photoreceptor cells. The first block of lectures will discuss the develop¬ment, organization, cell biology and biochemistry of photoreceptor cells, and the metabolic bases of their susceptibility to injury; emphasis will be on vertebrate photoreceptors, but contributions from studies with invertebrates will also be included. The next block will be devoted to the photoreceptor microenvironment, including retinal pigment epithelial and Muller cells, the interphotoreceptor matrix, trophic factors and retinoids, light, oxygen and neuromodulators. The third block will be devoted to photoreceptor physiology, including the visual cycle, phototransduction, dark adaptation, spectral sensitivity and color mixture, electroreti¬nography, and rod and cone response dynamics. The next section, dealing with pathology of photoreceptors and related outer retinal struc¬tures, will cover some hereditary diseases of known genetic origin, such as retinitis pigmentosa, gyrate atrophy, and abnormalities of color vision, as well as hereditary photoreceptor dystrophies of unknown origin. One lecture will be devoted to strategies for the search for genetic defects responsible for these diseases. After a discussion of macular degeneration and retinal detachment, the last block of lectures will review recent progress in the search for preventive and therapeutic approaches for these diseases, including the development of animal models, gene therapy, transplantation techniques, possible uses of stem cell therapy, and growth factor administration.

    Most recent announcement

  • Statistical Connectomics
    EN:580.694

    Spring Semester, every other year
    Course Directors:
    Joshua Vogelstein PhD

    This course will cover the basics of an exciting emerging field of statistical connectomics (aka, brain-graphs). It is so new, that we are going to make some of it up in this class! The first week will be introductory lectures that I give. The rest of the semester will be run like a seminar; each week will focus on a different topic. On Tuesdays we will hear about a statistical method that operates on graphs, and on Thursdays we will read about some neuroscience data upon which one could apply these techniques. The final project will consist of implementing a statistical method devised for graphs on a brain-graph problem. Recommended background: coursework in probability, linear algebra, and numerical programming (eg, R, Python, Matlab).

  • Models of the Neuron
    EN:580.639

    Fall Semester, every year
    Course Directors:
    Sridevi Sarma

    This course discusses single neuron modeling, including molecular models of channels and channel gating, Hodgkin-Huxley style models of membrane currents, non-linear dynamics as a way of understanding membrane excitability, neural integration through cable theory, and network computation. The goals of the course are to understand how neurons work as biological computing elements and to give students experience with modeling techniques as applied to complex biological systems.

  • Quantitative Methods for Brain Sciences
    AS:200.318

    Spring Semester, every year
    Course Directors:
    Shreesh Mysore PhD

    The goal of this class is to train students in key quantitative methods that are commonly by brain scientists (neuroscientists,psychologists, cognitive scientists) to analyze data. It is designed to serve students who do not have a strong quantitative background. This is not a “stats” class. Rather, it serves as a guide to powerful quantitative techniques, along with some exposure to their underlying math. Topics covered will include dimensionality reduction, information theory, frequency domain analyses, curve fitting, and clustering, and will be applied to “brain activity” datasets (obtained with electrophysiology, imaging, and to some extent fMRI). Emphasis will be on gaining a conceptual understanding of techniques and their practical application, rather than on proofs. In order to develop expertise in the techniques and their use, students will work on problem sets, take short quizzes, and critique journal articles. Knowledge of MATLAB is a plus, but not necessary (we will go over MATLAB basics).

  • Learning Theory
    EN:580.691

    Spring Semester
    Course Directors:
    Reza Shadmehr PhD

    This course introduces the probabilistic foundations of learning theory. We will discuss topics in regression, estimation, optimal control, system identification, Bayesian learning, and classification. Our aim is to first derive some of the important mathematical results in these topics, and then apply the framework to problems in biology, particularly animal learning and control of action.