Advances in Single Cell Genomics to Study Brain Cell Types

SfN Member-Only Virtual Conference

June 4, 2018 | 9 a.m. – 5 p.m. EDT

A central goal of neuroscience is understanding the cellular components of neuronal circuits. New techniques have emerged that enable researchers to analyze the genomes and transcriptomes of individual cells and their relationships to cell morphology, connectivity, and function.

These techniques provide new avenues to define and catalogue neuronal cell types and to better understand brain circuit organization and development, function and dysfunction, and conservation and divergence across species.

In this day-long virtual conference for SfN members — organized by Z. Josh Huang and Ed Lein — experts will share recent technical and conceptual advances in single cell genomic analyses and how they are improving our understanding of the biological basis of neuronal cell type identity and diversity in the brain.

Advances you will hear about include:

  • Tools driving the discovery of molecularly-defined cell types across brain systems. These techniques include massively parallel single cell RNA and DNA sequencing, and corresponding multiplexed RNA in situ assays.
  • Quantitative and scalable single cell analysis approaches spanning multiple modalities — including gene expression, morphology, physiology, and connectivity — bringing us closer toward achieving a brain cell census.
  • A conceptual understanding of brain development and evolution made possible through these new tools and approaches.

All career stages are welcome to attend this virtual conference to hear from leading neuroscientists. This online event is a follow up to Short Course I from Neuroscience 2016, so sign up now to hear what has changed in this field over the past two years, and read this short introduction, Promises and Pitfalls of Single-Cell Analysis, to further familiarize yourself on this topic before this event.

Full agenda



Alex Pollen
Alex Pollen, PhD
Alex Pollen is an assistant professor of neurology at the University of California, San Francisco (UCSF). The Pollen lab studies human brain development from a genetic and evolutionary perspective using tools from single cell genomics and stem cell biology. Pollen earned his BA in biology from Harvard University, PhD in neuroscience from Stanford University, an completed his postdoctoral training on cortical development with Arnold Kriegstein at UCSF.
Andreas Tolias
Andreas Tolias, PhD
Andreas Tolias is an associate professor in the department of neuroscience at Baylor College of Medicine and the department of electrical and computer engineering at Rice University. He is also the founder and director of the Center for Neuroscience and Artificial Intelligence. Tolias is a Brown Foundation Endowed Chair of Neuroscience. He earned his BA and MA in natural sciences from Cambridge University, PhD in neuroscience at Massachusetts Institute of Technology (MIT), and completed his postdoctoral fellowship at the Max Planck Institute.
Bosiljka Tasic
Bosiljka Tasic, PhD
Bosiljka Tasic is an associate director of molecular genetics at the Allen Institute for Brain Science in Seattle. She is interested in molecularly guided cell classification in the mouse nervous system and its implications for mouse brain function in health and disease. She earned her PhD in biochemistry from Harvard University where she studied under Tom Maniatis and completed her postdoctoral training with Liqun Luo at Stanford University.
Chongyuan Luo
Chongyuan Luo, PhD
Chongyuan Luo is a postdoctoral research associate in the Joe Ecker lab at Howard Hughes Medical Institute and Salk Institute for Biological Studies. His current research focuses on cell type diversity of healthy brains and genetic as well as epigenetic causes of brain diseases. Chongyuan earned his BS in biology from China Agricultural University and his PhD from Rutgers University.
Ed Boyden
Ed Boyden, PhD
Ed Boyden is a professor of biological engineering and brain and cognitive sciences at the Massachusetts Institute of Technology (MIT) Media Lab and McGovern Institute. He leads the Synthetic Neurobiology Group, which develops tools for analyzing and repairing complex biological systems and applies them systematically to reveal principles of biological function as well as to repair these systems. He received his PhD in neuroscience as a Hertz Fellow at Stanford University, where he discovered the molecular mechanisms used to store a memory are determined by the content to be learned. Before that, he received three degrees in electrical engineering, computer science, and physics from MIT. He is an elected member of the American Academy of Arts and Sciences (2017), has contributed to more than 400 peer-reviewed papers and granted or pending patents, and has given over 400 invited talks on his group's work.
Ed Lein
Ed Lein, PhD
Ed Lein is an investigator at the Allen Institute for Brain Science and an affiliate professor in the department of neurological surgery at the University of Washington. His interests focus on using transcriptomics as a core phenotype to understand brain organization at the regional, cellular and functional brain level, to understand what is unique about human brain, and to understand what is disrupted in brain diseases. He currently leads the Human Cell Types program which aims to create a comprehensive understanding of human cortical cell types and circuits using quantitative single cell transcriptomic, anatomical and functional methods. Lein earned his BS in biochemistry from Purdue University, PhD in neurobiology from University of California, Berkeley, and completed his postdoctoral training at the Salk Institute for Biological Studies.
Evan Macosko
Evan Macosko, MD, PhD
Evan Macosko is an assistant professor of psychiatry at Harvard Medical School and a group leader in the Stanley Center at the Broad Institute. Macosko’s newly established lab focuses on developing new technologies in genomics to more deeply understand brain function and dysfunction. He earned his PhD in neuroscience from Rockefeller University and MD from Weill Cornell Medical College. He completed psychiatry residency at McLean and Massachusetts General Hospitals and postdoctoral training at Harvard Medical School.
Gioele La Manno
Giole La Manno
Gioele La Manno is a member of Linnarsson Lab at Karolinska Institute and is currently preparing to defend his PhD thesis. His work has focused on harnessing the wealth of information provided by single cell RNA sequencing to better understand brain development. In particular, he has been using machine learning and differential equation modelling to describe the sequence of states that neural progenitor cells undergo during their differentiation towards mature neurons. He earned his BS in biotechnology at University of Palermo and his MS in biomedicine at Karolinska Institute.
Giorgia Quadrato
Giorgia Quadrato, PhD
Giorgia Quadrato is an assistant professor in the Broad CIRM Center and Department of Stem Cell Biology and Regenerative Medicine at the University of Southern California (USC). She previously worked as a research associate in the Arlotta Laboratory at Harvard University and the Broad Institute of Massachusetts Institute of Technology and Harvard University. Quadrato's research focuses on modeling and investigating the molecular underpinnings behind human brain development and disease using 3D brain organoids derived from human pluripotent stem cells. Giorgia earned her BS, MS, and PhD in pharmacogenomic biotechnology from the University of Milano-Bicocca (Italy). She completed her postdoctoral training at the Hertie Institute for Clinical Brain Research in the Laboratory of Neuroregeneration and Repair, Tübingen Germany, where she investigated signaling pathways regulating adult neurogenesis and CNS axonal regeneration.
Jonathan Ting
Jonathan T. Ting, PhD
Jonathan T. Ting is an assistant investigator in the Human Cell Types group at the Allen Institute for Brain Science. His current work is focused on systematically exploring the diverse cell types of the human neocortex using an integrated electrophysiological, morphological, and molecular profiling approach. He earned his BS in biological sciences from the University of California at Davis, PhD in neurobiology and behavior from the University of Washington, and completed his postdoctoral training in the laboratory of Guoping Feng at the McGovern Institute for Brain Research at Massachusetts Institute of Technology (MIT) and Duke University Medical Center.
Z. Josh Huang
Z. Josh Huang, PhD
Josh Huang is an investigator and the Charles and Marie Robertson Professor of Neuroscience at the Cold Spring Harbor Laboratory. His research focuses on the organization, development, and function of neural circuits in the cerebral cortex. Huang earned his PhD in molecular biology from Brandeis University and completed his postdoctoral training at Massachusetts Institute of Technology (MIT).
Long Cai
Long Cai, PhD
Long Cai is a research professor in biology within the division of biology and biological engineering at California Institute of Technology (Caltech). His research focuses on single cell systems biology and his lab uses super-resolution and live cell microscopy to study gene regulatory networks in cells and organisms. Cai earned his undergraduate degree in physics and chemistry from Harvard College and his PhD from Harvard University working with Sunney Xie on single molecular detection of gene expression in living cells. He completed his postdoctoral training with Michael Elowitz at Caltech as a Beckman Fellow.
Maria Antonietta Tosches
Maria Antonietta Tosches, PhD
Maria Antonietta Tosches is a postdoc at the Max Planck Institute for Brain Research in Frankfurt, Germany. Her research focuses on the evolution of cell types and neural circuits in the vertebrate brain. She recently addressed the evolution of the cerebral cortex by applying single-cell genomics approaches to reptiles. Tosches studied biology in Pisa, Italy, and earned her PhD from the European Molecular Biology Laboratory in Heidelberg.
Mats Nilsson
Mats Nilsson, PhD
Mats Nilsson is professor of biochemistry and molecular diagnostics in the department of biochemistry and biophysics at Stockholm University. He is also visiting professor at the department of immunology and genetics and pathology at Uppsala University, and scientific director at the Science for Life Laboratory. He earned his PhD in medical genetics.
Naomi Habib
Naomi Habib, PhD
Naomi Habib is a postdoctoral fellow at the Broad Institute of Massachusetts Institute of Technology and Harvard University working with Dr. Feng Zhang and Dr. Aviv Regev. Habib's research focuses on understanding the cellular and molecular mechanisms of degeneration and regeneration in the adult and aging brain. She is a pioneer in single nucleus RNA-sequencing technologies and their applications to study cellular diversity and molecular processes in the brain. Habib earned her BS, MS, and PhD in computational biology from the Hebrew University of Jerusalem in Israel.
Sebastian Preissl
Sebastian Preissl, PhD
Sebastian Preissl is an associate director of single cell genomics at the Center for Epigenomics at University of California, San Diego. As a postdoctoral fellow in Dr. Bing Ren's laboratory at the Ludwig Institute for Cancer Research he studied brain development and cancer using single cell ATAC-seq and single cell RNA-seq approaches.
Tom Nowakowski
Tom Nowakowski, PhD
Tom Nowakowski is an assistant professor at University of California, San Francisco (UCSF). Nowakowski earned his PhD from the University of Edinburgh and completed his postdoctoral training in the laboratory of Arnold Kriegstein at UCSF in 2017 where he pioneered the use of single cell RNA sequencing to study the heterogeneity of cellular populations in the developing brain and discovered the biomarkers of outer radial glia.
Trygve Bakken
Trygve Bakken, MD, PhD
Trygve Bakken is a scientist at the Allen Institute for Brain Science and is helping build a quantitative census of cell types in the human brain. He builds computational tools to characterize the transcriptomic diversity of cell types with the aim to understand cell type evolution and role in neuropsychiatric disease. He earned his BA from Yale University, MS in physics and philosophy from the London School of Economics, and PhD in neuroscience and MD from the University of California, San Diego.

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