Showcase Symposium 2020

Showcase Symposium 2020

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

The 2020 Showcase featured presentations by scientists from the Allen Institute for Brain Science and MindScope Program, as well as our Next Generation Leaders, distinguished early-career scientists from institutions across the world.

Allen Institute project talks covered:

  • Transcriptomics and transgenics: Our work to uncover the genomic diversity of cell types in the mouse brain
  • Patch-seq: Our pipeline to link cell types across transcriptomic, electrophysiological, and morphological modalities
  • Human cell types: Efforts to uncover conserved and divergent cell types across mammalian species, specifically human
  • Electron microscopy: Our imaging and analysis efforts of the connections within a cubic millimeter of mouse neocortex
  • Synaptic physiology: The latest insights from our in vitro electrophysiology pipeline investigating connectivity, synaptic strength, and short-term plasticity of cortical circuits in mouse and human
  • Visual Coding (2-photon): The latest insights from our analysis of in vivo imaging in the mouse visual cortex
  • Visual Coding (Neuropixels): the latest insights from our in vivo electrophysiology pipeline, recording with Neuropixels probes in the mouse visual cortex and related areas
  • Visual Behavior: The latest insights from our active behavior pipeline with in vivo imaging in the mouse visual cortex while mice perform a change detection task
  • Technology & Knowledge Integration: Our latest data releases and the analysis, visualization, and modeling tools to make them accessible

MONDAY, 12/14/2020 - WEDNESDAY, 12/16/2020
9:00am-12:00pm Pacific Time daily


Watch Recordings

View Agenda


Please contact with any questions. 



Event Overview (All Times Pacific)

Monday, December 14:

  • Sign in, 8:30-9:00am
  • Welcome and introduction, 9:00am
  • Presentations, 9:00am-12:00pm
  • Project Talk Q&A (internal & NGLs only), 12:00-12:30pm
  • Roundtable discussions (internal & NGLs only), 12:30-1:30pm

Tuesday, December 15:

  • Sign in, 8:30-9:00am
  • Welcome and introduction, 9:00am
  • Presentations, 9:00am-12:00pm
  • Project Talk Q&A (internal & NGLs only), 12:00-12:30pm
  • Roundtable discussions (internal & NGLs only), 12:30-1:30pm

Wednesday, December 16:

  • Sign in, 8:30-9:00am
  • Welcome remarks by Christof Koch, 9:00am
  • Presentations, 9:00-11:15am
  • Closing remarks by Hongkui Zeng, 11:15-11:45am
  • Project Talk Q&A (internal & NGLs only), 11:45am-12:30pm
  • Roundtable discussions (internal & NGLs only), 12:30-1:30pm

Allen Institute for Brain Science - Showcase Committee

  • Chair: Jennie Close, Ph.D., Senior Scientist
  • Saskia de Vries, Ph.D., Assistant Investigator
  • Sarah Naylor, Ph.D., Scientific Program Manager
  • Kate Roll, Research Associate III
  • Stephanie Seeman, Ph.D., Scientist II
  • Kaitlyn Casimo, Ph.D., Training & Outreach Specialist II

2020 Next Generation Leaders

  • Clint Cave, Ph.D, Middlebury College
  • Lucas Cheadle, Ph.D, Cold Spring Harbor Laboratory
  • Yvette Fisher, Ph.D, Harvard Medical School
  • Bianca Jones Marlin, Ph.D, Columbia University
  • Fenna Krienen, Ph.D, Harvard Medical School
  • *Cindy Poo, Ph.D, Champalimaud Research

*Will present at a future Showcase Symposium.


View Agenda

Clinton Cave

Middlebury College

"GDE Signaling in Development and Disease"

Abstract: Over the past decade, members of the Glycerophosphodiester Phosphodiesterase (GDE) family have been identified as integral proteins in the context of cell proliferation and differentiation during neurodevelopment. These proteins have a shared topology of six transmembrane domains with intracellular N- and C-termini and an extracellular enzymatic domain. Expressed on the cell surface, GDE proteins regulate the release of glycosylphosphatidylinositol-anchored proteins (GPI-APs). GPI-anchorage is a common post-translational modification that tethers proteins to the cell surface with a lipid anchor. GDEs can cleave within the GPI-anchor, releasing the protein into the extracellular space. The release of GPI-APs can produce cell autonomous effects (due to the loss of a surface protein) and non-cell autonomous effects (via the conditioning of the extracellular matrix with cleaved GPI-APs). Here, I will summarize the role of GDE2 signaling in the embryonic differentiation and postnatal survival of spinal motor neurons and share the approaches used to study GDE6 in my laboratory at Middlebury College.

Bio: Clinton Cave is an Assistant Professor of Neuroscience at Middlebury College. Clinton holds a B.A. in Psychology from Yale University, and he completed his Ph.D. in Neuroscience and postdoctoral fellowship at Johns Hopkins University in the laboratory of Shanthini Sockanathan. Clinton’s doctoral work expanded the known roles of a small family of cell surface enzymes—the 6-transmembrane GDE proteins. These proteins are unique in their ability to enzymatically sever the lipid anchor of GPI-anchored proteins on the cell surface. During embryonic neurogenesis, this signaling axis is critical for the successful differentiation of spinal and cortical neurons. Using functional genetic approaches in mice, Clinton’s work demonstrated that GDE2 also plays a crucial role for neuronal survival in the postnatal nervous system. These efforts heralded a new line of research investigating how GDE2 dysfunction integrates into neurodegenerative diseases such as Amyotrophic Lateral Sclerosis. Clinton began his professorship at Middlebury in the fall of 2018. He teaches courses on Cellular and Molecular Neuroscience, Behavioral Neuroscience, Neurodevelopment, and the History of Neuroscience. He runs a research laboratory with undergraduate students examining the molecular mechanisms regulating progenitor patterning, neurogenesis, and cell fate decisions in the vertebrate neural tube through the lens of GDE-GPI signaling. As a Next Generation Leader, Clinton is interested in developing tools and approaches at the intersection of neuroscience research and education.

Lucas Cheadle

Cold Spring Harbor Laboratory

"Non-neuronal plasticity and function in the stimulated brain"

Abstract: Sensory experience is critical for the development of neural circuits early in postnatal life, yet the cellular and molecular mechanisms through which experience shapes the developing brain remain incompletely defined. In recent work, we discovered that experience induces robust programs of gene expression in neurons of the mouse visual system, and that these genes encode critical molecular regulators of brain development. We further found that experience-dependent gene programs are not restricted to neurons but are also induced in microglia, the resident immune cells of the brain, which we have shown to remodel synapses in response to sensory experience. The discovery that non-neuronal brain cells mount robust transcriptional responses to experience through which they regulate synaptic connectivity directed my research focus toward a more holistic framework that takes into account the remarkable cellular heterogeneity of the brain. Taking advantage of recent advances in single-cell RNA-sequencing, we have now performed an unbiased whole-transcriptome analysis of sensory-dependent gene expression in the mouse visual cortex, identifying diverse and largely unique stimulus-dependent gene programs in all non-neuronal cell types. These data reveal a functional relationship between experience-dependent gene expression in non-neuronal cells and sensory-driven circuit plasticity, and identify a large number of cell-cell signaling pathways that are likely to enable non-neuronal cells to control circuit wiring and function in the stimulated brain.

Bio: Dr. Lucas Cheadle is an assistant professor of neuroscience at Cold Spring Harbor Laboratory. Originally from the Chickasaw Nation in rural Oklahoma, Dr. Cheadle developed a passion for biomedical research as an undergraduate at Smith College. He later earned a PhD in neuroscience working with Dr. Thomas Biederer at Yale University and completed a postdoctoral fellowship in the laboratory of Dr. Michael Greenberg at Harvard Medical School. Throughout his training, Dr. Cheadle’s work has focused on understanding how neurons in the brain form precise connections with one another. Currently, Dr. Cheadle’s team merges large-scale genomic and transcriptomic approaches such as single-cell RNA-sequencing with functional assays such as high-resolution imaging of neuronal connections in the brains of living mice. Using these approaches, the Cheadle Lab characterizes the contributions of non-neuronal brain cells to the sensory experience-dependent remodeling of neural circuits during postnatal brain development. In the future, they hope to turn these insights into novel therapeutic strategies for treating neurodevelopmental disorders.

Yvette Fisher

Harvard Medical School

"Flexibility of visual input to the Drosophila compass network "

Abstract: We can maintain some sense of direction in the dark by keeping track of our own movements, but when visual landmarks are available, our sense of direction is more accurate and stable. Moreover, we can learn new landmarks in new environments. What mechanisms reconcile self-movement information with ever-changing landmarks to generate a coherent sense of direction? In the Drosophila brain, compass neurons form an attractor network whose activity tracks the angular position of the fly using both self-movement and visual inputs. Using whole-cell recordings and calcium imaging from Drosophila compass neurons, we show that each compass neuron is inhibited by visual cues in specific horizontal positions, with different visual maps in different individuals. Inhibition arises from GABAergic axons that form an all-to-all matrix of synaptic connections onto compass neurons. We show that visual input to the compass network can reorganize over minutes when visuo-motor correlations change in virtual reality. This reorganization causes persistent changes in the reference frame of the compass network and can depress or potentiate visually-evoked inhibition in a manner that depends on visual-heading correlations. Plasticity of sensory inputs, when combined with network attractor dynamics, should allow the brain’s spatial maps to incorporate sensory cues in new environments.

Bio: Yvette Fisher is currently a Hanna Gray Postdoctoral Fellow in Rachel Wilson’s lab at Harvard Medical School. In 2021 she will start her own lab as an Assistant Professor at UC Berkeley in the department of Molecular & Cell Biology and the Helen Wills Neuroscience Institute. Her research uses spatial navigation in fruit flies to understand how nervous systems flexibly process information. During her Ph.D. with Tom Clandinin at Stanford University, Yvette identified critical neurons and algorithms that allow the fly brain to perceive visual motion. She also built a generalizable genetic toolkit that allows target genes to be conditionally turned on or off in any cell type of interest. As a postdoc, Yvette solved the problem of how visual scenes map onto head direction cells (compass neurons) in the fly brain, creating a sense of direction. Her ongoing work combines advanced genetic manipulations, quantitative behavioral analysis, in vivo whole-cell electrophysiology, and calcium imaging to understand how the sense of direction can switch its mode of operation rapidly when contexts change, while also functioning stably across a lifetime.

Bianca Jones Marlin

Columbia University

"Bridging the gap between innate and learned behaviors: A parent’s role in promoting survival"

Abstract: My research investigates the relationship between the innate and the learned. I have examined how an organism unlocks an innate behavior at the appropriate time i.e.-maternal instinct, and how a traumatic experience is passed to subsequent generations via paternal lineage. Changes in gene expression, and consequent behavior, of a parent may permit offspring to exhibit an inherited adaptation to the environment. This process, known as transgenerational epigenetic inheritance of environmental information remains a complex mystery. Novel experiments performed by myself and others have demonstrated that odors in the environment of a mouse associated with aversive consequences result in compensatory alterations in the olfactory system of their offspring. I combine neural imaging, behavior, and molecular genetics to understand the transfer of information inherent in neurons of the parent, through the gamete, to neurons of their offspring. Our goal is to uncover the process through which learning and emotion in one generation can be transmitted not culturally, but rather biologically through DNA. We believe understanding how a learned behavior in the parent can essentially become an innate behavior in the offspring will have profound implications in societal health and well-being.

Bio: Bianca Jones Marlin is an incoming Assistant Professor of Psychology and Neuroscience at Columbia University’s Zuckerman Institute, 2021. She is a neuroscientist and postdoctoral researcher at Columbia University in the laboratory of Richard Axel, where she investigates transgenerational epigenetic inheritance, or how traumatic experiences in parents affect the brain structure of their offspring. She holds a PhD in neuroscience from New York University, and dual bachelor degrees from St. John’s University, in biology and adolescent education. As a graduate student, her research focused on the vital bond between parent and child, and studied the use of neurochemicals, such as the “love drug” oxytocin, as a treatment to strengthen fragile and broken parent-child relationships. Bianca aims to utilize neurobiology and the science of learning to better inform both the scientific and educational community on how positive experiences dictate brain health, social well being.

Fenna Krienen

Harvard Medical School

"Innovations present in the primate interneuron repertoire"

Abstract: Primates possess cognitive capabilities and other specialized functions that have a little-known basis in cells and molecules. I will describe what we have learned from comparing RNA expression in brain cell types across distinct brain regions and from various mammalian species. Homologous interneuron types – which were readily identified from their RNA-expression patterns – varied significantly in abundance and expression among ferrets, mice and primates, but varied much more modestly among primates. Markers identified in one species did not always generalize to the same interneuron populations in the others. In the primate neocortex, dozens of genes exhibited spatial expression gradients among interneurons of the same type, suggesting that adult neocortical interneurons encode details of their local cortical context. An interneuron type previously associated with the mouse hippocampus has become abundant across the primate neocortex. The most striking innovation, however, was subcortical: an abundant striatal interneuron type in primates that had no molecularly homologous counterpart in mouse or ferret. I’ll share some other delights we’ve learned about primate transcriptomic cell types, and our efforts to generate new genetic tools to study them.

Bio: Fenna Krienen is a postdoctoral fellow in Steve McCarroll's lab in the department of Genetics at Harvard Medical School. She received her B.A. in Cognitive Science from University of California, Berkeley, and did her doctoral work at Harvard University with Randy Buckner using noninvasive neuroimaging in large human cohorts to infer functional connectivity in the cerebral cortex and cerebellum. She was a Brain-Mind Fellow at the Center for Advanced Study of Human Paleobiology at The George Washington University with Chet Sherwood, where she developed an analytic approach for jointly analyzing human neuroimaging and microarray data to reveal transcriptional correlates of large-scale connectivity, before joining the McCarroll lab. Fenna uses single nucleus DNA and RNA sequencing across species (focusing on primates) to understand how brain cell types have evolved, and as a way to build better links between human genetics and animal models. She is a recipient of a Simons Foundation for Autism Research (SFARI) Bridge to Independence Award.