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Systems Neuroscience

Our research in Systems Neuroscience is highly diverse, ranging from more circuit-oriented analyses of brain networks to studies of neural activity involved in motor planning and execution ,and includes functional imaging studies in humans. Many of the studies are inherently translational, with significant ongoing studies for spinal injury, amyotrophic lateral sclerosis, cerebral stroke, Parkinson's disease, Huntington’s disease, pain and more.

Labs in This Research Area

 Apkar Apkarian Lab

Spearheading the joint NIH, NIDA and NINDS flagship initiative in pain research for brain imaging data sharing

Research Description

For lab information and more, see Dr. Apkarian’s faculty profile or lab site.


See Dr. Apkarian's publications on Pub


See Dr. Apkarian's publications on PubMed.


Research Faculty: Lejian HuangRami Jabakhanji

Research Study Coordinator: Jennifer Perez

Research Data Analyst: Maria Centeno

Graduate Student: Andrew Vigotsky

Visiting Scholar: Bo Wu

 James Baker Lab

Focusing on neuron activity that processes vestibular sensory signals and on oculomotor and electromyographic recordings

Research Description

Jim Baker's interests are in systems neurophysiology and neuroanatomy. Dr. Baker’s laboratory focused on neuron activity that processes vestibular sensory signals and on oculomotor and electromyographic recordings. The laboratory is no longer active as of 2013. Dr. Baker maintains active collaborations with the laboratories of Drs. Disterhoft, Heckman, Miller, and others. His areas of expertise are neuron recordings from conscious animals, general neuroanatomy, and technical aspects of neuroscience experimentation across a wide range of approaches. Faculty, staff, and students in any area of neuroscience, especially systems neuroscience, are welcome to come to Jim Baker to discuss their ideas and technical situations.

For publication information and more, see Dr. Baker's faculty profile.


See Dr. Baker's publications on PubMed.


 Mark Bevan Lab

Defining the principles underlying the normal and abnormal operation of the basal ganglia

Research Description

Our research focuses on the basal ganglia, a group of subcortical brain nuclei that are critical for voluntary movement, learning and motivation, and the primary site of dysfunction in psychomotor disorders such as Parkinson's disease, Huntington's disease, obsessive-compulsive disorder and addiction. Our objectives are to define the principles underlying the normal and abnormal operation of the basal ganglia. Our hope is that this information will provide the foundation for the rational development of therapies that more effectively treat the symptoms or underlying causes of these disorders.

We utilize multiple experimental approaches including electrophysiology, 2-photon imaging, anatomical and molecular profiling, and viral vector-based techniques including optogenetics, pharmacogenetics and knockdown of synaptic receptors and ion channels. Our research is supported by the National Institute for Neurological Disorders and Stroke and the Cure Huntington's Disease Initiative.

For lab information and more, see Dr. Bevan's faculty profile and lab website.


See Dr. Bevan's publications on PubMed.


Contact Dr. Bevan at 312-503-4828.

Research Faculty: Jeremy AthertonJoshua Callahan, Timothy Searl

Postdoctoral Fellows: Flavia Aluisi, Maia Datunashvili, Esther Lara-Gonzalez

Graduate Students: Andrew Hunter, YueJun Liu

Undergraduate Student: Brandon Ozobu

Technical Staff: Mazen Mohamed

 C Savio Chan Lab

Understanding the cellular and molecular building blocks of basal ganglia macrocircuit

Research Description

Neurodegenerative diseases: To date, millions of people in the US suffer from neurodegenerative diseases. Current therapeutic strategies are limited, short-lived, and ineffective. Our research seeks to provide the mechanisms that underlie the pathogenesis of Alzheimer's Disease, Parkinson’s disease, and Huntington’s Disease. We hope to translate our insights into developing novel treatments for these neurological disorders.

Alzheimer's disease is the most common neurodegenerative disease and it is the most common underlying cause of dementia. It affects primarily the cortex and hippocampus. Severe synapse loss and inclusions can be observed. Our research seek to delineate the cellular processes that lead to the network dysfunction and the endogenous clearing mechanism of oligomers.

Parkinson’s disease and Huntington’s disease are the two major neurodegenerative diseases that affect the motor function. Our research interests center on better understanding the cellular and molecular building blocks that make up the basal ganglia macrocircuit as well as their implications in both health and disease.

Inter-cell communications: An effective communication in the brain involves proper controls of how signals are generated, how they are terminated, and how they are spatiotemporally distributed. This process involves a complex architecture of ion channels, receptors, synapse, release and clearance machinery, etc. Our lab studies how this is achieved and how it is altered in disease conditions. The main focus is on intrinsic excitability, neurotransmission, and their regulation by astrocytes.

Multidisciplinary approach: Using cell-population transcriptomic analysis as a guide, a more effective and targeted electrophysiological analyses can be devised. The combination cell-specific Cre-driver lines, Cre-responsive transgenic mice and viral constructs forms a very powerful research tool that will allow us to tackle difficult research question that would not be otherwise possible. 

Our research is currently funded by the NINDS, NIA/CNADC, DoD, PDF, NMF, APDA and CHDI.

For lab information and more, see Dr. Chan's faculty profile and lab website.


See Dr. Chan's publications on PubMed.


Contact Dr. Chan at 312-503-1146 or the lab at 312-503-1146.

Research Faculty: Qiaoling Cui, Harry Xenias

Lab Manager: Alexandria Granados

Graduate Student: Arin Pamukcu

Technical Staff: Brianna Berceau, Nicole Curtis

 John Disterhoft Lab

We study the neurobiology of associative learning in the mammalian brain at the molecular, cellular and systems levels using both in vivo and in vitro techniques. Our laboratory focuses on characterizing how neurons store new information during associative learning. An important component of our research program is identifying mechanisms for altered learning in aging. We use a combination of behavioral, biophysical and molecular biological approaches to address these questions.

Research Description

Eyeblink conditioning is our primary model paradigm to assess associative learning. This Pavlovian task offers excellent stimulus control, ease of precise behavioral measurement, robust associative learning, and can be used to test both human and non-human animal subjects. We study rabbits, rats, mice, or humans depending upon the question being asked. We also use a broad set of additional techniques, including fear conditioning, spatial navigation in the Morris water maze and others, to assess other types of behavior to evaluate the specificity of experimental manipulations on mechanisms of associative learning.

Our program focuses on characterizing the ways in which neurons store new information during associative learning at the cellular and subcellular levels. Experiments focus on the hippocampus, a paleocortical region involved in transferring information during learning from the short- to long-term memory store. We make biophysical measurements from hippocampal brain slices taken from eyeblink-trained animals to define what ionic mechanisms underlie the changes in neuronal excitability recorded in the intact animal. An important focus of our research is on cellular mechanisms for altered learning in aging. Recently, we have incorporated calcium-imaging techniques using both a charge-coupled device (CCD) camera system and a two-photon laser scanning microscopy (2P-LSM) system to investigate learning- and aging-related changes in calcium properties in CA1 pyramidal neurons.

Our laboratory conducts multiple-single neuron recording experiments using chronically implantable microdrives in rabbits as they perform eye blink conditioning, an associative memory task. We take advantage of an integrated approach combining several techniques such as paired recordings from anatomically identified neurons, optogenetic, immunohistochemistry, light and electron microscopy applied to wild-type and transgenic animals. We use these techniques to test hypotheses about the neurophysiological properties and the functional role of neurons from brain regions that are involved in associative memory such as the prefrontal cortex, hippocampus, thalamus, and the basal ganglia.

Magnetic resonance imaging permits examination of the entire brain simultaneously and observation of changes in brain activity in the same individual over time. Functional magnetic resonance imaging is being done in rabbits with our collaborators Daniel Procissi and Lei Wang.

For lab information and more, see Dr. Disterhoft's faculty profile and lab website.


See Dr. Disterhoft's publications on PubMed.


Contact Dr. Disterhoft at 312-503-7982 or the lab at 312-503-3112.

Research Faculty: Craig Weiss

Postdoctoral Fellow: Hannah Wirtshafter

Graduate Student: Birsu Bac

Undergraduate Student: Gabi Angeles Camacho

 Charles Heckman Lab

Investigating the mechanisms of motor output the spinal cord in both normal and disease states

Research Description

Neurons in the spinal cord provide the neural interface for sensation and movement. Our lab focuses on the mechanisms of motor output in both normal and disease states (spinal injury, amyotrophic lateral sclerosis). We use a broad range of techniques including intracellular recordings, array recordings of firing patterns, 2-photon imaging, pharmacological manipulations, and behavioral testing. These techniques are applied in in vitro and in vivo animal preparations. In addition we have extensive collaborations with colleagues who study motor output in human subjects.

For lab information and more, see Dr. Heckman's faculty profile.


See Dr. Heckman's publications on PubMed.


Contact Dr. Heckman at 312-503-2164.

Research Faculty: Matthieu Chardon, Mingchen Jiang, Michael JohnsonThomas Sandercock

Postdoctoral Fellows: Amr Mahrous, Jack Miller, Gregory Pearcey

Graduate Students: Seoan Huh, Edward KimEmily Reedich, Theeradej Thaweerattanasinp, Jessica Wilson

Technical Staff: Rebecca Cranmer

 Ann Kennedy Lab
Studying the structure of animal behavior and the neural mechanisms of flexible and adaptive behavior control, using tools from dynamical systems, statistical modeling, and machine learning

Research Description

The three core goals of our research are:

  1. To develop new theories for the distributed control of behavior by multiple recurrently connected neural populations.
  2. To understand computation in heterogeneous neural populations with diverse cell types and signaling molecules, by building and training biologically constrained neural population models, and
  3. To construct richer descriptions of animal behavior and movement by creating novel pose estimation and supervised/unsupervised machine learning techniques.

By collaborating broadly with experimental labs working in diverse model organisms and neural systems, we aim to develop new theories and models to better understand how neural structure governs function and shapes behavior across the animal kingdom.

For lab information and more, see Dr. Kennedy’s faculty profile and lab website.


See Dr. Kennedy's publications on Google Scholar.


Contact Dr. Kennedy.

Postdoctoral Fellows: Richard Gast, Amadeus MaesArin Pamukcu

Graduate Students: Ryan LuSebastian Malagon PerezAndrew Ulmer, Ruize Yang

Technical Staff: Kevin Bodkin, Venus Sherathiya

 Talia Lerner Lab

Exploring the synaptic- and circuit-level mechanisms underlying the generation and dissemination of neuromodulatory information in the brain

Research Description

Early studies into the neuromodulatory information encoded by midbrain dopamine neurons suggested that a key function of dopamine is to transmit reward prediction error signals - a measure of whether events were better or worse than expected based on previous experience. However, not all midbrain dopamine neurons appear to encode similar information in their activity patterns. For example, our research has shown that substantia nigra dopamine neurons differ in their responses to aversive stimuli depending on their projection target, a finding that comports with previous literature on heterogeneous dopamine firing patterns and further suggests that diversity in the dopamine system can be best understood in the context of specific circuits and behaviors. Building on this investigative framework, we are now working to correlate individual variability in dopamine-related behaviors with detailed structural and functional connectivity observations within the midbrain dopamine system. By using natural sources of variability in mouse behavior, we gain access to study the potentially large yet unexplored natural range of individual variation in the circuit organization of the midbrain dopamine system. By simultaneously obtaining whole-brain anatomical and functional neural circuitry datasets, we hope to build a comprehensive theory of how specific individual differences in the circuitry of the heterogeneous midbrain dopamine system support a diverse set of behaviors, including reinforcement learning, motivation, risk preference and addiction.

For lab information and more, see Dr. Lerner's faculty profile and lab website.


See Dr. Lerner's publications on PubMed.


Contact Dr. Lerner.

Lab Manager: Louis Van Camp

Postdoctoral Fellows: Ryan Kovaleski, Michael Schaid, Jillian SeilerManHua Zhu

Graduate Students: Gabriela Lopez, Nkatha Mwenda, Jacob Nadel

Post-Baccalaureate Research Fellow: Naeliz Lopez

Undergraduate Students: Baran Demir, Irene Son, Andrew Hou

Technical Staff: Venus Sherathiya

 Marco Martina Lab

Researching mechanisms of neuronal excitability and organization of brain microcircuits

Research Description

The lab has two main research lines: mechanisms of neuronal excitability and organization of brain microcircuits.

We pursue these two wide basic science interests by investigating scientific questions with immediate potential for bench to bed translation. In particular, altered neuronal excitability is involved in important pathologies such as epilepsy, neurodegenerative diseases and neuropathic pain. Similarly, understanding the local brainstem networks that underlie the generation and regulation of breathing is a necessary step to understanding the mechanisms of SIDS (Sudden Infant Death Syndrome). Finally, we are interested in the identification of the role of unipolar brush cells, a recently discovered cell type of the cerebellar cortex, in cerebellar microcircuits.

To investigate these questions we use multiple techniques such as electrophysiological recordings from neurons and dendrites in brain slices and cultures, PCR analysis of gene expression, histochemical analysis of protein expression and optogenetic manipulations.

For lab information and more, see Dr. Martina's faculty profile.


See Dr. Martina's publications on PubMed.


Contact Dr. Martina at 312-503-4654.

Research Faculty: Gabriella Sekerkova 

Postdoctoral Fellows: Soumil DeyJeehaeh Do, Rafiq Huda, Haram Kim

Graduate Students: Crystle Ashford, Taylor Jefferson

Technical Staff: Yen-Hsin Cheng

 Donald R. McCrimmon Lab

Studying neural and reflex control of breathing and respiratory rhythm generation

For lab information and more, see Dr. McCrimmon’s faculty profile.


Contact Dr. McCrimmon at 312-503-1220 or the lab at 312-503-0188.

Lab Staff

Postdoctoral Fellow

Anthony Kowal

Graduate Student

Jeehaeh Do

 Lee E. Miller Lab

Understanding the nature of the somatosensory and motor signals within the brain that are used to control arm movements

Research Description

The primary goal of the research in my lab is to understand the nature of the somatosensory and motor signals within the brain that are used to control arm movements. Most of the experiments in my laboratory rely on multi-electrode arrays that are surgically implanted in the brains of monkeys. These “neural interfaces” allow us to record simultaneously from roughly 100 individual neurons in the somatosensory and motor cortices and thereby study the brain’s own control signals as the monkey makes reaching and grasping movements. We can also pass tiny electrical currents through the electrodes to manipulate the natural neural activity and study their effect on neural activity and the monkey’s behavior.

Current projects seek to understand:

  1. How motor cortical activity leads to the complex patterns of muscle contractions needed to produce movement
  2. How movement of the limb and forces exerted by the hand are “encoded” in the activity of neurons in the somatosensory cortex

We also study how these relations are affected by behavioral context: the magnitude and dynamics of exerted forces, the varied requirements for sensory discrimination, and the quality of the visual feedback that is provided to the monkey to guide its movements.

Along with this basic research, we can use these neural interfaces to bypass the peripheral nervous system, in order to connect the monkey’s brain directly to the outside world. We are developing neural interfaces that ultimately will use signals recorded from the brain to allow patients who have lost a limb to operate a prosthetic limb. The interface may also be used to bypass a patient’s injured spinal cord in order to restore voluntary control of their paralyzed muscles. Conversely, electrical stimulation of the brain will restore the sense of touch and limb movement to patients with limb amputation or spinal cord injury. This highly interdisciplinary work is enabled by numerous collaborations at Northwestern University and other institutions.

For lab information and more, see Dr. Miller's faculty profile and lab website.


See. Dr. Miller's publications on PubMed.


Contact Dr. Miller at 312-503-8677.

Postdoctoral Fellows: Xuan Ma, Fabio Rizzoglio

Technical Staff: Kevin BodkinHenry Powell

 Jones Parker Lab

Targeting neural substrates to improve treatment outcomes for neuropsychiatric diseases

Research Description

We use imaging approaches to acquire large-scale recordings of neural activity during behavior, focusing on deep-brain areas implicated in neurological and psychiatric diseases, such as striatum. We use these tools to delineate the functional contribution of neuronal sub-populations in these brain areas to normal behavior in control subjects and pathological behavior in models for brain diseases. Our aim is to target these neural substrates to improve treatment outcomes for neuropsychiatric diseases.

For lab information and more, see Dr. Parker's faculty profile and lab website.


See Dr. Parker's publications on PubMed.


Contact Dr. Parker at 312-503-3165.

Postdoctoral Fellows: Ben Yang, Seongsik Yun

Graduate Students: Justin Anair, Niki Moya, Xunhui Wu

Undergraduate Students: Allison Kane

Technical Staff: Stefan Fleps

 Lucas Pinto Lab

Large-scale networks underlying decision making

Research Description

We want to understand how neural circuits across many brain areas interact to support decision making. In particular, how are these interactions flexibly reconfigured when animals make decisions that use different underlying computations? To do this we combine high-throughput mouse behavior in virtual reality, optical and genetic tools to measure and manipulate the dynamics of single neurons and neuronal populations, and computational approaches to understand both the behavior and its relationship to neural activity.

  • Decision-making and its different underlying computations: There is much evidence to suggest that decision-making computations happen across widespread brain areas, including many in the cerebral cortex. But how do these areas interact to make a single decision? And how can the brain perform different computations using the same pool of neural circuits? Decisions that require different combinations of underlying computations appear to be associated with distinct patterns of large-scale activity across the cerebral cortex. We want to understand how neuromodulatory mechanisms potentially control these different dynamic configurations of neural activity, and how they map onto different cognitive operations.
  • Neuromodulatory mechanisms of the reorganization of large-scale cortical dynamics: We study the brain circuits that switch between, and maintain, the different dynamic configurations of large-scale cortical activity that support different types of decisions. A particular focus is on the role of neuromodulators such as acetylcholine. This line of inquiry is also of potential clinical interest, as it may help us understand how neurodegenerative diseases such as Alzheimer’s lead to decision-making deficits.
  • Functional organization of large-scale cortical dynamics: Another crucial question is whether there is actually a logic to the way large-scale cortical dynamics change according to the behaviors they support. To put it another way, are there core computations performed by each cortical area that explain why activity across the cortex looks the way it does during different tasks? We believe answering this will help us provide parsimonious explanations of cortical function using general computational principles.

For lab information and more, see Dr. Pinto's faculty profile and laboratory website.


See Dr. Pinto's publications on PubMed.


Contact Dr. Pinto at 312-503-7928.

Research Faculty: Julia Cox

Postdoctoral Fellows: Jose Ernesto Canton-Josh, Renan Costa, Jiaqi Keith Luo, Matthew Rynes

Graduate Students: Lyn Ackert-Smith, Junhua Tan

Technical Staff: Camey Calzolano, Erin Myhre

 Gordon MG Shepherd Lab

Applying multiple tools of quantitative synaptic circuit analysis to elucidate the functional ‘wiring diagrams’ of neocortical neurons in the mouse motor cortex

Research Description

Synaptic circuits in motor areas of neocortex engage in neural operations underlying many aspects of cognition and behavior – motor control, executive functions, working memory, and more – yet circuit organization at the synaptic, cellular, and molecular levels remains poorly understood in agranular cortex. What is the functional organization of these synaptic pathways? What cellular and circuit-level operations do neurons in these perform? How do these local circuits communicate with each other and how do they interact with subcortical systems in the basal ganglia and thalamus? The focus of our laboratory is to apply multiple tools of quantitative synaptic circuit analysis to elucidate the functional ‘wiring diagrams’ of neocortical neurons in motor cortex. We use laser scanning photostimulation (LSPS) microscopy, based on glutamate uncaging and channelrhodopsin-2 excitation, for rapid functional mapping of synaptic pathways onto single neurons in brain slices of motor cortex. We are also applying a variety of circuit analysis tools in efforts to identify circuit-level mechanisms in mouse models of disease, including autism, Rett syndrome, epilepsy, and motor neuron diseases.

For lab information and more, see Dr. Shepherd’s faculty profile and lab website.


See Dr. Shepherd's publications on PubMed.


Contact Dr. Shepherd at 312-503-1342 or the lab at 312-503-0753.

Research Faculty: John Barrett

Postdoctoral Fellows: Mang Gao, Daniela Pina Novo, Louis Richevaux

Undergraduate Student: Tanya Kukreja

Technical Staff: Miraya Baid

Research Data Analyst: Adam Forrest

 D. James Surmeier Lab

Understanding the principles of neuronal dysfunction in disease states

Research Description

Our group has five research topics. The first topic area is what drives Parkinson’s disease (PD). Using a combination of optical, electrophysiological and molecular approaches, we are examining the factors governing neurodegeneration in PD and its network consequences, primarily in the striatum. This work has led to a Phase III neuroprotection clinical trial for early stage PD and a drug development program targeting a sub-class of calcium channels. The second topic area is network dysfunction in Huntington’s disease (HD). Using the same set of approaches, we are exploring striatal and pallidal dysfunction in genetic models of HD, again with the aim of identifying novel drug targets. The third topic area is striatal dysfunction in schizophrenia, with a particular interest in striatal adaptations to neuroleptic treatment. The fourth topic area is post-traumatic stress disorder and the role played by neurons in the locus ceruleus in its manifestations. The last topic area is chronic pain states and the impact these have on the circuitry of the ventral striatum.

For lab information and more, see Dr. Surmeier's faculty profile.


See Dr. Surmeier's publications on PubMed.


Contact Dr. Surmeier at 312-503-4904.

Lab Manager and Research Associate: Sasha Ulrich

Research Faculty: Vernon Clarke, Qiaoling CuiMichelle Day, Jaime Guzman-Lucero, Ema IlijicDavid Wokosin, Weixing Shen, Tatiana Tkatch, Jun UedaZhong Xie, Enrico Zampese, Shenyu Zhai

Postdoctoral Fellows: Marziyeh BelalMartin HenrichJames MoranDeNard SimmonsYichen Wu, Enrico Zampese, Shenyu Zhai

Research Staff: Tamara Perez-Rosello

Technical Staff: Marisha Alicea, Kang Chen, Yu Chen, Bonnie Erjavec, Daniel Galtieri, Christine KamideDanielle SchowalterMarisol Serrano

Visiting Scholar: Fanni Geibl

 Matthew Tresch Lab

Examining the neural control of movement, focusing on the role of spinal circuitry

Research Description

We use an interdisciplinary approach in this research, using a combination of behavioral, biomechanical, and neurophysiological techniques.  Our current research examines the neural control of internal joint variables, evaluating the hypothesis that the nervous system actively regulates the stresses and strains within joints in order to minimize injury. We examine this issue using biomechanics, characterizing how muscles affect the stresses and strains within joints; using behavioral studies, characterizing how the CNS adapts kinematics and muscle activations to compensate for alterations in joint structures; and using electrophysiological studies, examining the neural systems involved in regulating joint stresses and strains.

We are also developing neuroprostheses for restoring functional movements following spinal cord injury. This is collaborative work with Dr. Lee Miller.  Previous work from his lab has shown the potential of cortically controlled FES: using cortical predictions of muscle activation to drive stimulation of paralyzed muscles, thereby restoring natural control of a paralyzed animals’ own limb.  We are developing these procedures in a rodent model, examining whether this approach can be used to restore the hindlimb movements underlying locomotion in animals paralyzed by spinal cord injury.

For lab information and more, see Dr. Tresch's faculty profile.


See Dr. Tresch's publications on PubMed.


Contact Dr. Tresch at 312-503-1373.

Postdoctoral Fellow: Zhong Wang

Technical Staff: Diya BasraiSam Tran

Temporary Staff: Alex Benedetto

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