The goal for the CoB-KIBM Program is to provide undergraduates from historically underrepresented backgrounds a positive and fruitful research experience to demonstrate how a career in science is not only possible, but also highly rewarding. Therefore, the Colors of the Brain graduate mentors have curated a list of potential Faculty Mentors for the CoB-KIBM scholars to select from. Selection of Faculty Mentors is based on their demonstrable commitment to train historically underrepresented students in neuroscience.
Systems/Molecular
One approach to studying our brain is to identify how we detect relevant information in our environment and use that to drive behaviors. This task is difficult in our brains with all of its stunning complexity. Fortunately, neural circuit motifs are conserved allowing us to analyze simpler nervous systems and define basic circuit principles that underlie complex brain functions. We use two small nervous system models- the nematode, Caenorhabditis elegans and the vertebrate, Danio rerio. The C. elegans nervous system consists of just 302 neurons that are connected by identified chemical and electrical synapses. Despite its simplicity, this animal displays a number of sophisticated behaviors providing us an ideal model to study neural circuit properties.
Molecular
Dr. Coufal is a physician scientist with training in pediatric critical care and a research interest in neuroimmunology. The goal of her lab is to understand the contribution of innate immunity to neurodevelopmental and pediatric neurodegenerative diseases. By understanding the interaction between the brain environment and cellular ontogeny on macrophage function, the lab strives to understand the molecular and cellular mechanisms underlying innate immune dysfunction to ultimately identify novel therapeutic targets in untreatable pediatric diseases. Her lab utilizes a combination of translational, patient-specific pluripotent stem cell modeling, genome-wide approaches, and organoid cocultures and a murine xenotransplantation model to identify cellular mechanisms by which microglia contribute to common neurodevelopmental and rare pediatric neurodegenerative disorders.
Systems/Cognitive
Dr. Gremel’s lab focuses on understanding how the brain does decision-making. This requires an understanding of both the behavioral and neural mechanisms involved. We take an integrative approach using mice, in which we can combine both simple and sophisticated quantitative behavioral measurements, with powerful molecular and genetic tools and monitoring techniques to delineate molecular mechanisms within specific cell-types in identified circuits that control decision-making processes.
Computational
His lab focuses on the development of deep learning-based computational methods for recognition and modeling of complex biological systems, with applications ranging from neuroscience to cancer and plant biology. His recent work has demonstrated how advances in deep learning and computer vision can enable quantitative phenotyping of complex behaviors through the development and application of approaches for markerless motion capture (sleap.ai).
Cognitive/Developmental
From our first moments, humans live in a near-constant stream of social information. My lab studies the cognitive processes that allow children to understand other people, and the social meaning of things people create, such as tools, art, music, and technology. For example, we’re studying how children understand video chat, and how video chat impacts children’s perspective-taking and social reasoning. We also explore the origins of musicality, asking why human musicality is so early developing and socially impactful from early in life.
Systems/Molecular
Epigenetic processes which modulate gene expression are critical for the development, plasticity, and degeneration of neural circuits throughout the lifespan. However, the normal development of methylation patterns and their effect on gene expression in brain cells is largely unknown. In the 15 years since completing the human genome project, many individual labs and large-scale consortia have focused on mapping the epigenomic landscape of coding and non-coding DNA elements. Our lab seeks to exploit the full potential of these resources for elucidating developmental and regulatory processes, by creating computational analysis tools and theoretical models which are tailored to the scope and resolution of the data.
Systems/Computational
Kay M. Tye is a Professor and Wylie Vale Chair of the Systems Neuroscience Laboratory at the Salk Institute for Biological Sciences, and an adjunct faculty member at the University of California, San Diego (UCSD). Her research program is focused on understanding the neurobiological mechanisms underlying social and emotional processes at the circuit, cellular and synaptic levels, particularly those relevant to psychiatric disease.
Systems/Cognitive/Computational
Our laboratory aims to understand the mechanisms through which dynamic engagement between neural networks is achieved. This selective engagement is critically necessary for filtering information from multitudinous afferents and coordinating processing between regions that must communicate for successful computation. The ability to selectively coordinate information processing across regions enables an organism to attend to information relevant to behavioral circumstances. Neural oscillations can reflect the recruitment of cells into functional circuits and the successful coordination of neural network activity. Studying network oscillations during behavior can thus provide insight into the flexible participation of cells in local and cross-regional circuit processes. Our projects combine computational and statistical models with in vivo electrophysiology to 1) identify elements within neural networks that give rise to rhythmically identifiable processing states and 2) test the impact of rhythmic coordination upon successful network engagement in rodent models.
Cognitive/Computational
His research lab combines large-scale data science and machine learning to study how brain regions communicate with one another, and how that communication changes with aging and disease. He is an advocate for promoting science to the public and speaks extensively with students at all grade levels about the joys of scientific research and discovery.
Systems/Molecular
The Jin lab research focuses on the molecular genetic mechanisms underlying the development and function of the nervous system using the nematode Caenorhabditis elegans. The transparency, defined anatomy, and rapid life cycle of this organism greatly facilitate our studies at the subcellular resolution. Moreover, the entire cell lineage and connectome are known, enabling functional understanding at deep levels. Through forward genetic screening in combination with multi-layered molecular and cellular manipulations, we are discovering key molecules that play conserved roles in synapse formation, maintenance, and function, as well as those underlying adult axon regeneration. Our ultimate goal is to connect the studies of basic mechanisms to the understanding of human neurological disorders and neuronal repair.
Dr. Dhananjay (DJ) Bambah-Mukku
Cognitive/Systems/Molecular
How does the enormous cellular diversity of the brain give rise to complex behaviors? How do emotional states influence behavior and how are they generated by the brain? Social behaviors provide an accessible entry point to answer these questions due to their close association with emotions and strong genetic underpinnings. The Bambah-Mukku lab studies cell-type and circuit specific mechanisms governing ethologically meaningful social behaviors. We are particularly interested in how neural circuits are modulated by the sex, age and physiological state of the animal.
Computational/Cognitive
Our research focuses on understanding how behavioral goals influence perception, decision making, and memory. Perception is thought to be based on the activity of sensory neurons that receive input from the world around us (in the form of light, sound, etc.). However, sensory neurons are very noisy and unreliable, so small groups of these neurons must work together to support stable perceptual representations. In addition, a combination of factors such as prior experiences, current expectations, and behavioral goals influence the activity of sensory neurons to bias perception in favor of the most important objects in the environment. What we experience is therefore not merely a product of the raw sensory input, but instead reflects the combined influence of sensory factors and the internal state of the observer. To investigate the influence of behavioral goals and previous experiences on perception and cognition, we employ a combination of psychophysics, computational modeling, and neuroimaging techniques.
Systems/Molecular
Our work investigates how neuronal synapses are regulated throughout life by asking how non-neuronal glial cells, specifically astrocytes, regulate synapse number and synaptic function. This has led to identification of proteins secreted by developing astrocytes that are sufficient to induce immature synapses to form, and additional signals secreted by adult astrocytes that induce synapse maturation and limit synaptic plasticity. We have further identified altered protein secretion from astrocytes in genetic neurodevelopmental disorders, and determined which of these alterations is responsible for negatively impacting neuronal development. We are now asking if manipulation of synapse-regulating factors in astrocytes is sufficient to delay progression of synaptic dysfunction in aging and neurodegeneration.
Systems/Molecular
We are studying the organization and function of neural circuits in the visual cortex to better understand how specific neural components contribute to the computations that give rise to visual perception and to elucidate the basic neural mechanisms that underlie cortical function. We employ anatomical and physiological methods both in vivo and in vitro to reveal neuronal circuitry and to identify the emergent functional properties of the component neurons. Present studies focus on: identifying the roles of specific cell types in cortical function by mapping their connections, and monitoring and manipulating their activity using genetic and viral tools; understanding the contributions of cortical and subcortical structures and cell types to functional interactions between visual cortical areas; understanding the neural mechanisms that underlie changes in behavioral performance with attention and that regulate shifts in attention.
Systems/Molecular
Our brains are in constant flux — leading us to behave differently if we are alert or sleepy, hungry or sated, alone or in a group. What biological mechanisms allow nervous systems to be so flexible? We address this problem by studying the brains of zebrafish (Danio rerio) and glassfish (Danionella translucida) as they adjust their behavior to different circumstances. The brains of these vertebrates share much with mammals, but are small and transparent — allowing us to observe the entire brain in action.
Cognitive/Developmental
Human infants’ worlds are intensely social. They spend much of their lives interacting with or observing their caregivers, as well as other adults and children, and use these experiences to establish social bonds and gain information about the world. Our lab studies how early cognitive and brain development shapes and is shaped by infants’ social experiences. In particular, we study the neural systems that support infants’ attention to friendly or informative social partners, and their engagement in prosocial behavior. We’re also interested in the development of specialized neural substrates for perceiving elements of the social world, including faces, bodies, and interacting social partners.
Systems/Molecular
Our goal is to understand the molecular mechanisms that regulate blood-brain barrier (BBB) function during health and disease. The BBB is a specialized structure formed by the blood vessels in the central nervous system (CNS) that is critical for proper brain function as well as protecting the brain from injury and disease. Breakdown of the BBB occurs during stroke, edema, brain trauma, and multiple sclerosis and is a major component of the symptoms and progression of these diseases. Furthermore, the BBB not only impedes the movement of toxins and pathogens, but also inhibits the delivery of potential therapeutic agents to the CNS.
Systems/Cognitive
Memories can be retained as briefly as a few seconds or as long as a lifetime. What is the biological foundation for memory over such diverse time scales? What endows the brain with the capacity to not just generate an exact recollection of past events but store information in a way that can be flexibly and creatively used? What are the critical changes in brain circuits that limit these capabilities in brain diseases, such as depression, epilepsy, and Alzheimer’s diseases, and how can we restore brain function in disease? Our laboratories study these questions with an emphasis on one of the core systems for memory, which includes the hippocampus and entorhinal cortex. In humans, these brain regions are known to be the basis for declarative memory – the form of memory that we are aware of and can recollect when being asked. In addition, the hippocampus and associated brain regions are also critically important for perceiving space and for navigating in familiar and new environments.
Cognitive/Developmental/Computational
Our lab studies brain network organization, how this organization supports cognitive and sensorimotor development, and how it goes awry in neurodevelopmental disorders (specifically Tourette syndrome and related conditions – ADHD, OCD). We use multimodal MRI techniques in humans, including resting state functional connectivity (RSFC), task-based fMRI, and structural MRI, and we apply quantitative analytic methods, such as network analysis and machine learning. We study typically and atypically developing populations, and we use group- level approaches (averaging groups of people) as well as individual-level approaches to deeply characterize individual people with the goal of arriving at more precise inferences than have been previously possible.
Cognitive/Computational
I am an Assistant Professor in the Cognitive Science and Design Lab, and the director of the Creativity Lab at the University of California, San Diego. My research area is Human-Computer Interaction. I specialize in developing highly interactive systems that seamlessly interface human cognition with computation for a variety of tasks, including sensemaking, design, computer-supported cooperative work, information visualization, and more. The core thread of my work is to investigate how graphical user interfaces should be revamped to enable truly fluid and enjoyable human-computer interaction. I approach this from three levels: underlying information representation, activity-level information management, and intent-level human-AI collaboration.
Systems/Molecular
Our goal is to understand molecular mechanisms that drive experience dependent circuit plasticity. from the moment an animal is born, its brain is working to extract information from its surroundings and initiate appropriate behavioral responses. This is done through the activity of excitatory and inhibitory neurons that are organized into synaptically connected circuits. Our lab is interested in understanding how experience, via the execution of activity-dependent gene expression, regulates the connectivity of inhibitory and excitatory neurons and how these processes relate to animal behavior and disease states.
Systems/Molecular
Research in the lab is centered around understanding how cognitive processes influence pain perception by recruiting endogenous opioid signaling throughout the brain. Although functional imaging studies in humans implicate multiple brain structures in expectation-driven pain relief, due to a lack of mechanistic studies in model organisms, current models of top-down pain modulation are based almost entirely on correlative data. Currently, our primary goals are to delineate the neural pathways that support placebo analgesia, decipher their computational roles, and uncover the function of opioid neuropeptide signaling in the underlying circuits. Ultimately, we hope to leverage this information to develop novel behavioral and pharmacological therapies for pain.
Computational/Cognitive
Our research interests include the basal forebrain’s role in spatial attention and associative learning, as well as amygdaloid representations of affect.
Systems/Molecular
A major focus of our lab is to understand how gene expression is controlled at the RNA level to maintain proper functioning of cells during development and aging. Over the past decade, there has been a dramatic increase in the recognition that members of a broad class of proteins termed RNA binding proteins (RBPs) are crucial for maintaining molecular and cellular homeostasis. RBPs regulate processes such as cell survival, pluripotency of embryonic stem cells, and neuronal function, as well as aid in the transition between cellular states in response to stimuli, such as during neural specification of stem cells, cellular stresses, or viral infections.
Cognitive/Systems
In our cognitive neuroscience lab, we study how the brain maintains transient mental representations for goal-directed behavior. This function is typically called ‘working memory’ and humans use it for many purposes: to follow a conversation, to solve problems, to guide attention in a visual scene, and so much more. Sometimes this working memory can be impaired by ongoing demands (i.e., you forget the security code you’re trying to mentally rehearse), and at other times working memory content can inadvertently drive our actions or attention in the environment (i.e., you accidentally type out the wrong word because it was going through your mind). We use a combination of behavioral, neuroimaging (fMRI; EEG), and brain stimulation (transcranial magnetic stimulation, TMS) methods to examine how humans prioritize moment-to-moment goals in the face of competing demands. We welcome curious, kind, and collaborative new team members to join us.
UC San Diego Organization 