Showcase Symposium 2021

2021 Showcase Symposium

Thank you for joining us for our annual Showcase Symposium to learn about research being done at the Allen Institute for Brain Science through innovative, team science approaches.

The 2021 Showcase featured presentations by scientists from the Allen Institute for Brain Science and MindScope Program, as well as our 2021 Next Generation Leaders, distinguished early-career scientists from institutions across the world.

Tuesday, December 7 - Wednesday, December 8, 2021 

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Event Overview

Allen Institute Team Talks 

  • Cell Type Cards: Creation of 'Cell Types Explorer' for presenting multimodal features of cell types

  • Genomics: Defining cell types in health and disease by single cell genomics in mouse and human

  • RA Relay (MET): A Human Neuron’s Journey Through the MET Pipeline

  • MindScope mFISH: Connecting functional and transcriptomic neuronal types

  • MindScope Tiny Blue Dot: Seeking the neural correlates of consciousness

Allen Institute Showcase Committee

Next Generation Leaders

  • Emilia Favuzzi, Ph.D.

  • Arif Hamid, Ph.D.

  • Lucas Pinto, Ph.D.

  • Cindy Poo, Ph.D.

  • Kanaka Rajan, Ph.D.

  • Jessica Tsai, Ph.D.

  • Yan Wang, Ph.D.


Featured Speakers

Emilia Favuzzi

Harvard Medical School

"GABA-Receptive Microglia Selectively Sculpt Developing Inhibitory Circuits"

Abstract: Microglia, the primary brain macrophages, regulate a plethora of processes that impact the organization of neural circuits, including synapse pruning. Whether microglia are generic effectors of synapse pruning or if specialized microglia are able to discriminate between distinct synapse types is unknown. We found that GABA-receptive microglia selectively interact with inhibitory cortical synapses during a critical window of mouse postnatal development. Single cell RNA-seq and MERFISH profiling showed that ablation of microglial GABAB receptors cell-autonomously alters a transcriptional synapse remodeling program. As a result, loss of GABAB receptors within microglia affects inhibitory connectivity without impacting excitatory synapses and leads to behavioral abnormalities. The overarching implication of these findings is that specialized microglia differentially engage with specific synapse types during development.

Bio: Emilia Favuzzi is a postdoctoral fellow in Gord Fishell’s laboratory at Harvard Medical School and the Broad Institute. She grew up in Italy and received a B.S. in Biology and a M.S. in Neurobiology from Sapienza University of Rome. She did her doctoral training in the lab of Beatriz Rico at the Institute of Neuroscience in Alicante (Spain) and at the Centre for Developmental Neurobiology at King’s College London. Her graduate research focused on the cellular and molecular mechanisms of inhibitory circuit development and plasticity in the cerebral cortex. In her postdoctoral work, Emilia focused on microglia-inhibitory synapse interactions during development and discovered that specialized microglia differentially engage with specific synapse types. In particular, she found that GABA-receptive microglia selectively sculpt cortical inhibitory – but not excitatory – circuits during development. Over the years, Emilia was awarded numerous prizes such as the Beddington Medal from the British Society for Developmental Biology and the Krieg Cortical Kudos Scholar Award from the Cajal Club. In the future as an independent investigator, she will study how the selective communication between neuronal and glial cell types influences brain wiring.

Arif Hamid

Brown University

"Dopaminergic specialization for flexible behaviors"

Abstract: Dopamine potently regulates forebrain physiology that underlies reward learning and behavioral flexibility. A detailed accounting of how cellular and circuit interactions come to impact reinforcement learning continues to be refined at multiple levels of analysis. In this talk, I will provide a summary of our current understanding of quantitative decision variables relayed by dopamine dynamics in striatal targets, circuit substrates that support specific dopaminergic computations, and how different behavioral task-demands leverage these specializations to afford adaptive behaviors. Moreover, I will motivate the revision of a longstanding hypothesis for globally broadcast dopamine prediction error signals, and instead, make the case for regionally specialized forebrain dopamine dynamics tailored to local computational needs that arrive as wave-like spatiotemporal patterns.

Bio: Arif Hamid is a Hannah Gray Fellow at HHMI and Assistant Professor of Neuroscience at the University of Minnesota Medical School. His research program is focused on deeply understanding brain substrates for flexible behavioral control and reinforcement learning (RL). With extensive training in behavioral, systems, and computational neuroscience, Arif’s research group will combine interdisciplinary approaches to study  (i) the functional properties of key brain decision-circuits and, (ii) link identified circuit mechanisms to specific computational operations within normative theoretical frameworks, (iii) to ultimately understand how these circuit and computational specialization become leveraged during various behavioral demands. To this end, Arif’s previous scientific contributions have reported novel empirical findings (including dopamine midbrain-forebrain dissociation, and striatal dopamine waves) that have significantly (re)shaped formalizations of dopamine’s role in RL. The lab seeks to build on this trajectory to make deep contributions that integrate experimental findings into multilevel neurocomputational models for tandem and cyclical advances in the simulated and empirical understanding of brain mechanisms for valuation, selection, planning, and execution of behavioral goals.

Lucas Pinto

Northwestern University

"Large-scale mechanisms of flexible decision making"

Abstract: The ability to make decisions that meet different behavioral demands is essential for survival. However, how local and large-scale circuits across the brain interact flexibly to support different decision-making computations is poorly understood. To investigate this, the Pinto lab combines navigational decisions in mouse virtual reality, optical tools to record and perturb neural dynamics at multiple spatiotemporal scales, and computational modeling. In my talk, I will present my recent postdoctoral work in which I asked how distributed cortical activity supporting decision making is. I will argue that the answer depends crucially on the cognitive demands of the task. Specifically, I will discuss experiments involving systematic optogenetic mapping and widefield calcium imaging across the dorsal cortex, performed during navigational-decision tasks in virtual reality requiring different underlying computations. Our findings suggest that tasks with higher cognitive demands engage more distributed cortical circuits. Further, they suggest that widespread cortical areas contribute to the gradual accumulation of sensory evidence accrual on different timescales. Taken together, our results show that changing the computations underlying a decision results in a reorganization of whole-cortical dynamics. I will briefly discuss how my lab is working to reveal the circuit mechanisms and behavioral logic behind this reorganization.

Bio: Lucas Pinto is an Assistant Professor in the Department of Neuroscience at Northwestern University. He is broadly interested in neural mechanisms underlying cognition, both at the local circuit level and in terms of large-scale interactions between different brain areas. In particular, his lab seeks to understand which circuit mechanisms allow for such interactions between different areas to change according to different cognitive demands during decision making. To do so, they use a combination of optical tools to record and perturb neural activity at cellular or mesoscale resolution, genetic circuit dissection tools, high-throughput virtual-reality mouse behavior, and computational modeling. Lucas obtained his MD from the Federal University of Minas Gerais, Brazil, in 2006. He then did an MS in physiology at the same university, where he studied visual processing in owls with Jerome Baron. Lucas earned his PhD in neuroscience from the University of California, Berkeley in 2014, working in in Yang Dan's laboratory. He investigated how circuits downstream of the sensory cortex participate in perceptual decision-making. He moved to Princeton University in 2015 for his post-doctoral research in the laboratories of David Tank and Carlos Brody, where he studied how large-scale cortical dynamics change as a function of task complexity. Lucas started his lab at Northwestern in 2021.

Cindy Poo

Champalimaud Research

"Cortical circuits for olfactory behavior"

Abstract: Olfaction is essential for the survival of living beings from unicellular organisms to mammals and is used for a wide range of natural behaviors. Rodents use odors in their environment to forage and navigate. To support these olfactory behaviors, the brain seamlessly and dynamically integrates odor information with an internal model of the spatial environment. I am interested in how hierarchical circuits in the brain for olfaction and spatial cognition interact to generate such behaviors. Neural circuits in primary olfactory (piriform) cortex (PCx) are highly recurrent and plastic with abundant connections to spatial memory centers, making it an excellent site to investigate associative olfactory processes. Using neural ensemble recordings in an odor-cued spatial choice task for freely-moving rats, we discovered that individual PCx neurons were not only odor-selective, but also fired differentially to the same odor sampled at different locations, forming an “odor-place map”. PCx spatial maps were maintained across behavioral contexts and coupled to the hippocampus. This joint olfactory and spatial representation in primary olfactory cortex allows incoming sensory evidence to directly update an internal model of the world, and provides a unique opportunity to address the general question of how sensory and memory systems interact to generate flexible behavior.

Bio: Cindy Poo is a postdoctoral researcher at Champalimaud Research in Lisbon, Portugal, in the lab of Dr. Zachary Mainen. Cindy grew up in Taipei, Taiwan and has lived and worked across multiple continents. She received her undergraduate degree in neuroscience from Brown University. She completed her doctoral training in the laboratory of Dr. Jeffry Isaacson at the University of California, San Diego, where she used in vitro and in vivo patch-clamp recordings to understand synaptic mechanisms contributing to odor-evoked activity in olfactory cortex. As a postdoctoral researcher, Cindy was supported by postdoctoral fellowships from the Helen Hay Whitney Foundation and Human Frontiers Science Programme. Her current research uses freely-moving and head-fixed rodent behavioral paradigms combined with contemporary electrophysiological recording, perturbation, and data analysis methods to further understand the olfactory system in the context of spatial navigation. Cindy’s long-term research goal is to understand the neural dynamics and mechanisms for olfactory perception, cognition, and behavior in distributed circuits across the brain.

Kanaka Rajan

Icahn School of Medicine at Mount Sinai

"How Brain Circuits Function in Health and Disease: Understanding Brain-Wide Current Flow"

Abstract: Dr. Rajan and her lab design neural network models based on experimental data, and reverse-engineer them to figure out how brain circuits function in health and disease. They recently developed a powerful framework for tracing neural paths across multiple brain regions— called Current-Based Decomposition (CURBD). This new approach enables the computation of excitatory and inhibitory input currents that drive a given neuron, aiding in the discovery of how entire populations of neurons behave across multiple interacting brain regions. Dr. Rajan’s team has applied this method to studying the neural underpinnings of behavior. As an example, when CURBD was applied to data gathered from an animal model often used to study depression- and anxiety-like behaviors (i.e., learned helplessness) the underlying biology driving adaptive and maladaptive behaviors in the face of stress was revealed. With this framework Dr. Rajan's team probes for mechanisms at work across brain regions that support both healthy and disease states - as well as identify key divergences from multiple different nervous systems, including zebrafish, mice, non-human primates, and humans.

Bio: Kanaka Rajan, Ph.D. is a Computational Neuroscientist and Assistant Professor at the Friedman Brain Institute at the Icahn School of Medicine at Mount Sinai in New York. Her research seeks to understand how important cognitive functions — such as learning, remembering, and deciding — emerge from the cooperative activity of multi-scale neural processes. Using data from neuroscience experiments, Kanaka applies computational frameworks derived from machine learning and statistical physics to uncover integrative theories about the brain that bridge neurobiology and artificial intelligence. Leveraging her unique expertise in the fields of engineering, biophysics, and neuroscience, Kanaka has pioneered computational approaches for understanding how the brain processes information, and how these processes become disrupted by neuropsychiatric diseases.

Dr. Rajan’s work has been recognized with several awards, including: The Lamport Basic Science Research Award, Young Investigator Award from the Brain and Behavior Foundation, Understanding Human Cognition Scholar Award from the James S McDonnell Foundation, Research Scholars Awards from the Di Sabato Foundation and the Dyal Foundation, and a Sloan Research Fellowship. Her work is supported by R01 funding from the National Institutes of Health (NIH) through the BRAIN Initiative, and FOUNDATIONS and CAREER awards from the National Science Foundation (NSF).

Prior to joining the faculty at Mount Sinai, Kanaka completed her postdoctoral work at Princeton University where she made significant contributions to the modeling of important neural processes, including feature selectivity and recurrent neural networks (RNNs). She received her Ph.D. at Columbia University.

For more information about Dr. Rajan, please visit

Jessica Tsai

Dana-Farber Cancer Institute / Boston Children's Hospital

"Transcription factor hijacking in pediatric gliomas"

Abstract: Transcription factors are known to be frequently altered in pediatric cancers. Amongst childhood cancers, pediatric brain tumors are associated with the highest rates of morbidity and mortality. Diffuse intrinsic pontine gliomas (DIPGs), fatal pediatric brainstem tumors with a median survival of less than one year, pose particular challenges for treatment. How do transcription factors mediate oncogenesis? We initially identified the transcription factor FOXR2 as an oncogene in DIPG, then subsequently found that FOXR2 is aberrantly upregulated in 70% of all tumor types, across adult and pediatric cancers. We have delineated genetic and novel epigenetic mechanisms that induce expression of FOXR2, and further uncovered a previously unknown interaction between FOXR2 and ETS transcription factors across cancers. My research leverages functional, genomic, transcriptomic, epigenomic, and large scale screening approaches to determine precisely how developmental pathways are hijacked in pediatric cancers. As a physician-scientist, my ultimate goal is to work at the intersection of neuroscience and pediatric oncology, providing rational, mechanistic-based approaches for disease-altering therapy.

Bio: Jessica Tsai is a post-doctoral scholar in the Department of Pediatric Oncology at Dana-Farber Cancer Institute, in the laboratory of Pratiti Bandopadhayay. She is also an attending physician in Pediatric Hematology, Oncology, and Stem Cell Transplant at the Dana-Farber/Boston Children’s Hospital Cancer and Blood Disorders Center. As a graduate student with Tom Clandinin at Stanford, she identified a novel transcriptional feedback pathway critical for synapse maintenance, revealing a critical role for the interaction of presynaptic proteins and phospholipids to maintain neuronal networks. Jess completed her MD/PhD in the Medical Scientist Training Program at Stanford University School of Medicine, then subsequently completed her residency in Pediatrics at Boston Children’s Hospital and her fellowship in Pediatric Oncology at Dana-Farber Cancer Institute. She is dedicated to a career as a physician-scientist, with an interest specifically in pediatric brain and solid tumors. Jess now utilizes single cell approaches, epigenetics, and genome-scale functional modifier screens to identify drivers of pediatric high grade gliomas and novel dependencies. Her long-term research interest is to determine precisely how developmental pathways are hijacked in pediatric brain cancers. She is also Director of Research for the STEM Advocacy Institute (SAi), a non-profit incubator that provides support to accelerate the building of novel STEM programs and tools and envisions a future where STEM is more accessible and inclusive. Jess is a recipient of a St. Baldrick’s Foundation Fellowship with support from Griffin’s Guardians, a Young Investigator Award from Alex’s Lemonade Stand, and a Helen Gurley Brown Presidential Initiative Fellowship.

Yan Wang

Princeton University

"Boom and Bust Brains: invertebrate brains in developmental and evolutionary time"

Abstract: The global population is aging at an unprecedented rate, and it is imperative to take multidisciplinary approaches to accelerate our understanding of healthy aging processes. My research examines the neurobiological mechanisms that underlie aging, senescence, and death. I am particularly interested in uncovering the evolutionary origins and social dimensions of aging by investigating the nervous systems of two emerging invertebrate models—the bumblebee and the octopus. In this talk, I share two tales of “boom and bust” in these animals: the first on the neuroendocrine control of death in octopuses, and the second on the social and neurogenomic factors that shape development of adult behaviors in bumblebees. My future research will apply evolutionary and developmental perspectives, in conjunction with multiple high-dimensional omics, behavioral, and molecular approaches, to understand how nervous systems organize, encode, and mediate natural end-of-life transitions and death and uncover fundamental rules of aging in the brain.

Bio: Z Yan Wang, PhD. is an incoming Assistant Professor of Psychology and Biology at the University of Washington, Seattle. She is a neuroscientist interested in the evolutionary and social dimensions of aging. She uses emerging invertebrate model systems, such as the bee and the octopus, to investigate how the nervous system organizes, encodes, and mediates end-of-life transitions and death. Her work uses multiple high-dimensional omics, behavioral, and molecular approaches to uncover fundamental rules about the aging nervous system. As a postdoctoral researcher at Princeton University, she studies the impacts of social isolation on nervous system development and behavioral expression of bumblebees. She holds a PhD in neurobiology from the University of Chicago, where she characterized the neuroendocrine mechanisms of maternal behaviors and death in octopuses. To learn more about her lab, please visit