Johns Hopkins School of Medicine

Curriculum

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

• 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

  Most recent announcement

• Neuroscience and Cognition II (NeuroCogII)
  ME:440.812

  3rd and 4th quarters
  Course Directors:
  James Knierim 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.

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• Rigor, Reproducibility, and Responsibility in Science
  ME:440.819

  First and Second Quarter, every year
  Course Directors:
  Hita Adwanikar, 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 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:
  Marshall Hussain Shuler 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 “Rigor, Reproducibility, and Responsibility in Science” 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.
  

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• 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 used 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).
  

• Circuits and Brain Disorders
  ME:440.820

  1st and 2nd quarters, every year
  Course Directors:
  Paul Worley MD
  Marilyn Albert PhD
  Barry Greenberg
  

  The course is designed to serve as an introduction to neurodegenerative disorders of the nervous system, and is intended to provide a balance of basic neurobiology, clinical presentation, biomarkers, genetics and therapeutic approaches. One of the goals would be to highlight the distinct circuitry that is most impacted in each disorder. The curriculum includes: (1) one lecture per week and (2) a coordinated journal club once per week.

• Quantitative Neurogenomics
  ME.440.825

  Fall
  Course Directors:
  Loyal Goff PhD
  

  Designed for students pursuing research in molecular or cellular neuroscience, this course provides a broad introduction to basic computational, statistical, and quantitative analysis tools, approaches, and methodologies for modern molecular neuroscience. Integrated lectures, programming labs, and homework sets will be used to teach such material as next generation sequencing algorithms; neurogenetics, neurogenomics, and RNA-seq; single cell analysis; exploratory data analysis across data types; quantitative imaging analysis; algorithms for data exploration and decomposition (PCA, NNMF, general decomposition; nonlinear dimension reduction); and an introduction to machine learning and neural networks. Class will meet twice/week for lectures and journal club presentations/discussions of problem sets, and labs.

• Elective Courses

  In addition to the core courses, a statistics course, a quantitative methods course, and a brain disease 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 three elective courses by the end of their second year (at least one of which must be a Neuroscience elective). 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 H. 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.

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• Computational Principles of Biological Vision
  ME:440.822

  First and Second Quarter, every year
  Course Directors:
  Ed Connor PhD
  Kristina Nielsen PhD
  

  Even though we rarely acknowledge it as such, vision is our superpower. It is so central to how we (or at least most of us) interact with the world, and it comes to us with such ease, that we underappreciate its complexity. To this date, there are no computer vision programs that can parallel the performance of the human visual system. Vision is also the topic that both of us actively research, and are passionately interested in. Lastly, the neural underpinnings of vision are amongst the most thoroughly studied. As such, vision provides a very useful framework for learning about general principles of Neuroscience.
  The goal of this class is to teach you the Neuroscience of vision, with topics ranging from a general overview of the visual system to highlighting ongoing research studies. We will also talk about state-of-the art computer vision efforts as a comparison. The class is designed to not only provide you with the relevant background knowledge, but also to teach you how to critically evaluate current research papers. As such, the class will be split into ‘classical’ lectures, in which we provide an overview over a particular topic, and discussion classes. Discussion classes will serve to discuss one or two original research papers in depth. Our intention is for the discussion classes to feel like a real journal club or lab meeting, with a very active discussion amongst all of the participants.
  To achieve the latter will require rigorous work by everybody. All of the reading for the discussion classes will be primary material, which might (at least initially) be challenging. However, if we all do our job right, you should be well able to easily read the primary literature by the end of the class. Nonetheless, be prepared to work hard, and set aside time for the reading. This is a small and very advanced seminar, and participation in the discussions will be a central part of it (including your grade). Talking (or not talking) about things you haven’t read will not go unnoticed (and make us annoyed), and will be reflected in your grade. Attendance at every session is required.
  

  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:
  

  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

  Semester class, only in Fall
  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.
  

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• 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 enrollment of 15 students.

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• 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.

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• 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.

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• 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 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.

  Most recent announcement

• 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.

  Most recent announcement

• 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

• Bioenergetics, Neuroplasticity and Brain Health
  ME:440.818

  2nd quarter, every other year
  Course Directors:
  Mark P. Mattson PhD
  

  Overindulgent sedentary lifestyles are increasingly common with adverse consequences for trajectories of brain health in current and future generations. This course reviews findings from studies of humans and animals that elucidate the cellular and molecular mechanisms by which energy intake and exercise affect structural and functional neuroplasticity. This topic is considered from a bioenergetics perspective with emphases on brain evolution, developmental neurobiology, adult neuroplasticity and disorders of mood and cognition. The course consists of a series of introductory lectures, and subsequent class meetings in which hot topics in the field are discussed.

• 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:
  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.

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• 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 development, 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, electroretinography, and rod and cone response dynamics. The next section, dealing with pathology of photoreceptors and related outer retinal structures, 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 PhD
  

  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.

• 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.