The Neuroscience Graduate Program is excited to announce Nanocourses: Advanced Topics in Neuroscience (Bio 5989) in 2021/2022!

Nanocourses are interactive 6-week courses (1.5 hours/week) that offer a deep exploration of an advanced topic through primary literature and guided discussions. 

Registration is open to WashU graduate students, post docs, staff, and faculty members. Participants ​who wish to take a nanocourse for credit should officially register and are expected to attend and complete assignments for at least 4 of 6 sessions.

Click here to register: WebSTAC/BIOL 5989 Advanced Topics in Neuroscience (WUSTL Key required)

General questions?  Contact Ilya Monosov.

For questions regarding registration contact Sally Vogt.

Fall 2021 Nanocourse

Advanced Topics in Neuroscience (Bio 5989)

Deadline to officially register: September 9

  • All other grad students, post docs, staff and faculty are welcome to audit, official registration is not necessary.

Advanced scientific computing: producing better code

Organizer: Timothy Holy

Select Mondays and Wednesdays
October 4 – November 3
10:00 – 11:30 am
Location: TBA

  • October 4*: Introduction to the course: “why Julia?” and brief tour
  • October 18: Git and GitHub
  • October 20: Testing & principles of design

*NOTE: This session is followed by two weeks for people to start learning the language for the remaining sessions.

  • October 25: Continuous integration, documentation, package versioning, and releases
  • October 27: High performance computing on your laptop I: understanding and measuring performance
  • November 3: High performance computing on your laptop II: algorithms, compilers, and inference

Course details

Many scientists are self-taught coders and struggle to learn the skills that best support collaboration, rigor and reproducibility, good design, extensibility, and wide community adoption.  Like so many other aspects of being a scientist, these are all skills that can be taught and learned via practice.

This nanocourse focuses primarily on tools and habits that make it easier to succeed in writing robust, flexible, and widely-adopted code.  Process-oriented topics include Git and GitHub, test-driven development, the workflow of continuous integration, and documentation and software releases.  More conceptual topics include principles of good design and the mechanisms for writing high-performance code.  Students will be introduced to all these issues via the Julia programming language, although some lessons will apply broadly.

This course is aimed at people who are comfortable in at least one programming language; it is not suitable for programming beginners.  Participants should plan to allocate several hours each week for homework assignments.

# Syllabus

  1. Introduction to the course: “why Julia?” and a brief tour
  2. Git and GitHub
  3. Testing & principles of design
  4. Continuous integration, documentation, package versioning, and releases
  5. High performance computing on your laptop I: understanding and measuring performance
  6. High performance computing on your laptop II: algorithms, compilers, and inference

Spring 2022 Nanocourses

Advanced Topics in Neuroscience (Bio 5989)

Stay tuned for registration information!

Antidepressant Mechanisms

Organizer: Joshua Siegel

January 7 – February 4
1:00 – 2:00 pm

  • January 7 (Siegel): The Neurotrophic Hypothesis
  • January 14: Ketamine + Psychedelics
  • January 21: Neurosteroids
  • January 28 (Siegel): Human Neuroimaging Studies
  • February 4 (Feng): Model organisms 

Course details

January 7: The Neurotrophic Hypothesis (Siegel)

  • A number of signal transduction pathways that center around BDNF and its receptor TrkB result in increased neuroplasticity (neurogenesis, neuritogensis, synaptogenesis). These pathways are suppressed in stress and are restored in antidepressant treatment. Blocking these pathways prevent antidepressants from working. Recent events suggest antidepressant drugs act directly on the TrkB receptor (Casarotto 2021). Recent human studies with SV2A suggest a means of measuring deficit in synapse formation in depression (Holmes 2019).

January 14: Rapid Antidepressants: Ketamine + NMDA Antagonist anesthetics 

  • Data began to emerge 20 years ago showing antidepressant benefits of ketamine, many speculated that the biological underpinnings of the dissociative experience were essential to the therapeutic mechanism. Over the next two decades, animal research discovered that sub-anesthetic ketamine induces rapid activation of the neurotrophic cascade and that this phenomenon was necessary and sufficient to produce antidepressant effects (Autry 2011, Adachi 2008, nosyrova 2013, duman). Human research suggest that cognitive and psychiatric benefits of ketamine could be seen under treatment conditions that obviated the subjective experience (Mortero et al., 2001; others). Yet, efforts to identify/test NMDA Antagonist antidepressants without dissociative properties have not been successful (e.g. Lanicemine)

January 21: Rapid Antidepressants: Psychedelics

  • “Classic psychedelics” are a class of compounds that producing unique acute effects on cognition and perception via 5-HT2A agonism. Under the right circumstances, these drugs can occasion a mystical experience with a fairly high reliability. But it is not the acute perceptual effect but rather the persisting effects that has gained substantial attention in recent years. After a long ‘sleep’, interest and ability to research these drugs for medical purposes has re-awakened. Recent clinical trials have shown impressive results. Laboratory research has shown that a single dose of a psychedelic drug can produce powerful stimulation of neurotrophic cascade that persists beyond that of ketamine.
    The link between the acute experience, neurotrophic stimulation, and the clinical benefits remains unclear. Can we design rapid antidepressants without acute hallucinogenic effects (Hesselgrave 2021, Cameron 2020)?

January 28: Neuroimaging Studies of the Neurotrophic Cascade (Siegel)

  • Human imaging approaches such as PET, MEG, EEG, fMRI are uniquely able answer important questions about acute and persisting effects of psychoplastogens. Human imaging studies of psychedelics have begun to explore how acute changes in brain circuitry might explain persisting clinical effects. Studies have reported a variety of acute changes in metabolic activity, brain blood flow, and electrical activity (Carhart-Harris et al., 2012; Robin L. Carhart-Harris et al., 2016; Tagliazucchi et al., 2016, 2014; Vollenweider et al., 1997). However, the complexity of drug effects on so many aspects of neurobiology also represent a mine field of confounds (e.g. neurovasculature, arousal, movement, attention) for human imaging research.

February 4: Model organisms (Yang-Yang Feng)

Introduction to Computational Neuroscience

Organizers: ShiNung Ching, Gaia Tavoni, Ilya Monosov

Wednesdays and Fridays
February 2 – 18
4:00-5:00 pm and 11:00 am-12:00 pm

  • February 2 (Ching, 4p): Normative approaches in neuroscience
  • February 4 (Ching, 4p): A pico-primer in stochastic control 
  • February 9 (Tavoni, 11a): Modeling neural networks
  • February 11 (Tavoni, 11a): Coding and information processing in neural networks 
  • February 18 (Monosov, 11a): Applications in psychiatry

Course details

February 2 (4p): Normative approaches in neuroscience (Ching)

  • Optimization-based frameworks for synthesizing and analyzing neural dynamics, including emerging connections with neural networks and machine learning.

February 4 (4p): A pico-primer in stochastic control (Ching)

  • Overview of basic concepts in Bellman dynamic programming, optimal decision policies for bandit problems, and model-based versus model-free control paradigms.

February 9 (11a): Modeling neural networks (Tavoni)

  • An introduction to different types of neural network models, including probabilistic graphical models to reconstruct and predict the statistics of neural activity patterns, and models of spiking neurons to simulate dynamical properties.

February 11 (11a): Coding and information processing in neural networks (Tavoni)

  • An introduction to information theory and the insights it brings to the problem of how information is encoded and transmitted in sensory systems.

February 18 (11a): Applications in psychiatry (Monosov)

  • Computational neuroscience has become an important tool in the clinic. This will be discussed in this concluding lecture.


Organizers: Steven Petersen, Benjamin Seitzman

February 8 – March 15
10:00-11:30 am

  • February 8: Imaging Brain Function
  • February 15: Imaging Brain Organization
  • February 22: Clinical Imaging (special emphasis on PET)
  • March 1: The Rise of Imaging Consortia: Large N Studies
  • March 8: Highly-Sampled Individuals: Small N Studies
  • March 15: Recent Studies

Course details

February 8: Imaging Brain Function

Main point for the week: The value and attributes of well-designed task fMRI studies

February 15: Imaging Brain Organization

Main point for the week: The value of taking a closer look at “noise” a.k.a. resting state functional “connectivity”

February 22: Clinical Imaging (special emphasis on PET)

Main point for the week: The value/potential of neuroimaging in the clinic

  • Paper TBD

March 1: The Rise of Imaging Consortia: Large N Studies

Main point for the week: stuff in = stuff out

  • Paper TBD

March 8: Highly-Sampled Individuals: Small N Studies

Main point for the week: The value of case studies and small, unique cohorts with lots of data

March 15 – Recent Studies

Main point for the week: The importance of basic science in neuroimaging

Glia: Neuroscience without Neurons

Organizers: Thomas Papouin, Erik Musiek

Select Wednesdays and Fridays
April 1-15
10:00-11:30 am

  • April 1 (Ulrich): Glial Genetics in Health and Disease
  • April 6 (Papouin): Glia Calcium Signaling and Ion Regulation
  • April 8 (Papouin): Gliotransmission and Neuromodulation
  • April 13 (Klein): Glia in Neuroinfectious Disease
  • April 15 (Musiek): Glia in Neurodegeneration

Course details

This course will focus on trending areas of research on glia. Through reading and discussing primary literature, students will debate emerging concepts involving the role of glia in development, brain health, and disease. Class sessions will include discussions guided by experts currently engaged in the topic of the week in order to provide students with a source of knowledge and perspective on the subject. Through attending the course, students will gain a broader appreciation for glia and will hopefully gather ideas for their own research.

Learning objectives

  • Participants will learn about the role of glia in development, health, and disease.
  • Participants will become more familiar with the different types of glial cells and how their functions change under various contexts.
  • Participants will connect with experts and other learners interested in research on glia.
  • Participants will critically evaluate historical perspectives and emerging trends in glia research.


Students will come to each session having read one review and one primary literature article to discuss during class. A short writing assignment (<1 single-spaced page) summarizing discussion points of interest will be required for each session.


  • Wednesday, April 1 (Jason Ulrich): Glial Genetics in Health and Disease
  • Monday, April 6 (Thomas Papouin): Glia in Calcium Signaling and Ion Regulation
  • Wednesday, April 8 (Thomas Papouin): Gliotransmission and Neuromodulation
  • Monday, April 13 (Robyn Klein): Glia in Neuroinfectious Disease
  • Wednesday, April 15 (Erik Musiek): Glia in Neurodegeneration

Maladaptive decision making: circuits and mechanisms

Organizers: Ilya Monosov and guests

Select Mondays and Fridays
March 7-25
9:00-10:00 am

  • March 7: Addiction
  • March 11: OCD
  • March 14: Risky decision making
  • March 21: Information seeking – the good and the bad
  • March 25: Computational psychiatry

Course details

Behavioral and neural differences across individuals measured during value-based decision-making tasks could be key for advancing computational-psychiatry and cognitive-neuroscience towards uncovering circuit-level mechanisms of behavior and designing novel modulation methods for the clinic. That is discovering the precise underlying behavioral underpinnings or features of psychiatric disorders will facilitate more precise identification of the neuronal mechanisms that underlie them. We will discuss the neural and behavioral underpinnings of maladaptive decision making and newly emerging approaches to biasing maladaptive behavior towards more adaptive strategies.


Organizer: Judith Golden

April 6 – May 11
1:00-2:30 pm

  • April 6: Introduction and Historical Theories of Pain Transmission
  • April 13: Anatomy of the Pain Neuraxis
  • April 20: Physiology of Pain Transduction

April 27: Supraspinal & Descending Mechanisms of Pain Modulation

May 4: Human Pain

May 11: Pain Research Methods (Evaluating pain in rodents)

Course details

The perception of pain serves the vital function of providing information about potential or actual injury. The International Association for the Study of Pain (IASP) defines pain as “An unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage.” Because pain is inherently aversive, it serves the function of limiting tissue damage when a noxious stimulus is encountered. In contrast, a number of chronic pain conditions involve pain which persists in the absence of injury.

It has been estimated that 100 million adults suffer from chronic pain in the United States, accounting for an expenditure of approximately 600 billion dollars in pain related patient care. Current pharmacological treatments for pain management are sub-optimal, and significant adverse effects limit their use. Consequently, there is significant motivation to develop new approaches to treat pain.

The objective of this nanocourse is to provide an understanding of the nervous system pathways that transmit and modulate pain and of the methodology used to study pain in rodents and humans. The course will cover the anatomy of peripheral and central pain pathways and the physiology of pain transmission, transduction and modulation. In addition, we will discuss human pain conditions and evaluation of pain in human subjects. Experimental approaches used to evaluate pain in rodents will also be discussed. We will include discussion of relevant literature (recent and classic papers) in each session.

  • Introduction and Historical Theories of Pain Transmission
    a. types of pain – definitions, examples
    b. history of pain and pain research
    c. outline of the goals of the course
  • Anatomy of the Pain Neuraxis
    a. Primary sensory neurons
    b. Spinal dorsal horn
    c. Ascending pain pathways
  • Physiology of Pain Transduction
    a. Peripheral Sensitization
    b. Central Sensitization
  • Supraspinal & Descending Mechanisms of Pain Modulation
    a. Affective Modulation of Pain
  • Human Pain
    a. Neuropathic pain
    b. Inflammatory pain
    c. Visceral Pain
    d. Headache
    e. Evaluating pain in human subjects
  • Pain Research Methods (Evaluating pain in rodents)
    a. Behavior
    b. Cell physiology