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people

Ed Lein

Executive Vice President and Director, Brain Health

Leadership
Allenite
/
Brain Health

biography

Ed Lein leads the Brain Health accelerator’s research and global collaboration efforts aimed at advancing foundational insights into the human brain and neurodegenerative disease. Prior to this, Ed led the Human Cell Types Department in the Brain Science accelerator.  His research has aimed to create comprehensive cell atlases of the human and non-human primate brain, understand what is disrupted in Alzheimer’s disease, and create tools for precision genetic targeting of brain cell types as transformative tools for basic neuroscience and gene therapy. This work is now expanding to encompass a much wider range of neurodegenerative diseases including Alzheimer’s, Parkinson’s, Huntington’s, and ALS, combining large-scale discovery science, AI and disease modeling, and development of cell- and circuit-based genetic therapies. Ed’s areas of expertise include developmental neurobiology, structural and cellular neuroanatomy, transcriptomics and epigenomics, comparative neurobiology, and Alzheimer’s disease. He is a member of the BRAIN Initiative Cell Atlas Network (BICAN), a member of the organizing committee of the Human Cell Atlas (HCA), and a Canadian Institute for Advanced Research (CIFAR) fellow. Ed is also an affiliate professor in the Departments of Neurological Surgery and Laboratory Medicine and Pathology (DLMP) at the University of Washington in Seattle. He received a BS in Biochemistry from Purdue University, a PhD in Neurobiology from UC Berkeley, and performed postdoctoral work at the Salk Institute for Biological Studies.

Since joining the Allen Institute in 2004, Ed has provided scientific leadership for the creation of large-scale anatomical, cellular and gene expression atlases of the adult and developing mammalian brain as catalytic community resources, including the inaugural Allen Mouse Brain Atlas and a range of developmental and adult human and non-human primate brain atlases.

‍

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featured contributions
featured media
featured stories
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featured publications

featured events

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featured stories

news
BioCentury Grand Rounds conference highlights importance of big data
The conference hosted Nobel Laureates, researchers, and biotech leaders in Seattle looking to advance better treatments in medicine
news
Brain Health accelerator to transform our understanding of brain disorders and develop new treatments
The global collaborative research initiative will initially target Alzheimer’s, Parkinson’s, Huntington’s disease, ALS, and Lewy body dementia
news
Mapping the brain to improve lives
A collaborative effort between UW and the Allen Institute is creating a first-of-its-kind brain atlas, paving the way for breakthroughs in brain...

featured media

media / KIRO Radio
‘It’s going to come quicker than we think’: Parkinson’s advocate shares hope for treatment as Allen Institute launches AI-powered initiative
The institute has launched the Brain Health Accelerator, an international collaboration involving about 30 research organizations that will use artificial intelligence, human brain tissue and advanced cellular mapping to better understand diseases including Parkinson’s, Alzheimer’s disease, ALS, Huntington’s disease and Lewy body dementia.
media / Endpoints News
Allen Institute launches $400M effort to turn brain atlas lessons into medicines
A Seattle-based nonprofit is launching an initiative to translate its knowledge into drug development for neurodegenerative diseases, including Alzheimer’s.
media / TheScientist
The Brain Health Accelerator Seeks to Revolutionize Neuroscience Research
The Allen Institute launched a new project to accelerate the mechanistic understanding of neurodegenerative diseases and develop potential therapies.

featured publications

publication / 2008
Genomic anatomy of the hippocampus
Neuron
publication / 2009
Shifting the paradigm: new approaches for characterizing and classifying neurons
Current Opinion in Neurobiology
publication / 2009
An anatomic gene expression atlas of the adult mouse brain
Nature Neuroscience
publication / 2010
A robust and high-throughput Cre reporting and characterization system for the whole mouse brain
Nature Neuroscience
publication / 2010
Surface-based mapping of gene expression and probabilistic expression maps in the mouse cortex
Methods (San Diego, Calif.)
publication / 2010
Areal and laminar differentiation in the mouse neocortex using large scale gene expression data
Methods (San Diego, Calif.)
publication / 2011
Differential connectivity and response dynamics of excitatory and inhibitory neurons in visual cortex
Nature Neuroscience
publication / 2010
Divergent and nonuniform gene expression patterns in mouse brain
Proceedings of the National Academy of Sciences of the United States of America
publication / 2011
Multi-scale correlation structure of gene expression in the brain
Neural Networks: The Official Journal of the International Neural Network Society
publication / 2011
Cell-type-specific consequences of Reelin deficiency in the mouse neocortex, hippocampus, and amygdala
The Journal of Comparative Neurology
publication / 2012
Transcriptional architecture of the primate neocortex
Neuron
publication / 2012
Large-scale cellular-resolution gene profiling in human neocortex reveals species-specific molecular signatures
Cell
publication / 2012
An anatomically comprehensive atlas of the adult human brain transcriptome
Nature
publication / 2014
Evolution and development of the mammalian cerebral cortex
Brain, Behavior and Evolution
publication / 2013
Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism
Cell
publication / 2013
Conserved molecular signatures of neurogenesis in the hippocampal subgranular zone of rodents and primates
Development (Cambridge, England)
publication / 2014
Patches of disorganization in the neocortex of children with autism
The New England Journal of Medicine
publication / 2014
Improving reliability and absolute quantification of human brain microarray data by filtering and scaling probes using RNA-Seq
BMC genomics
publication / 2014
Transcriptional landscape of the prenatal human brain
Nature
publication / 2014
Disruptive CHD8 mutations define a subtype of autism early in development
Cell
publication / 2014
Functional organization of the hippocampal longitudinal axis
Nature Reviews. Neuroscience
publication / 2014
Convergent transcriptional specializations in the brains of humans and song-learning birds
Science (New York, N.Y.)
publication / 2015
Spatial mapping of structural and connectional imaging data for the developing human brain with diffusion tensor imaging
Methods (San Diego, Calif.)
publication / 2015
Correlated gene expression and target specificity demonstrate excitatory projection neuron diversity
Cerebral Cortex (New York, N.Y.: 1991)
publication / 2015
Cortical fast-spiking parvalbumin interneurons enwrapped in the perineuronal net express the metallopeptidases Adamts8, Adamts15 and Neprilysin
Molecular Psychiatry
publication / 2015
Spatiotemporal dynamics of the postnatal developing primate brain transcriptome
Human Molecular Genetics
publication / 2015
Canonical genetic signatures of the adult human brain
Nature Neuroscience
publication / 2016
Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons
Nature Protocols
publication / 2016
A comprehensive transcriptional map of primate brain development
Nature
publication / 2016
Comprehensive cellular-resolution atlas of the adult human brain
The Journal of Comparative Neurology
publication / 2017
PRODUCTION OF A PRELIMINARY QUALITY CONTROL PIPELINE FOR SINGLE NUCLEI RNA-SEQ AND ITS APPLICATION IN THE ANALYSIS OF CELL TYPE DIVERSITY OF POST-MORTEM HUMAN BRAIN NEOCORTEX
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
publication / 2017
Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation
Neuron
publication / 2017
Transcriptomic Perspectives on Neocortical Structure, Development, Evolution, and Disease
Annual Review of Neuroscience
publication / 2017
Fast assembling of neuron fragments in serial 3D sections
Brain Informatics
publication / 2017
SmartScope2: Simultaneous Imaging and Reconstruction of Neuronal Morphology
Scientific Reports
publication / 2017
The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing
Science (New York, N.Y.)
publication / 2017
Neuropathological and transcriptomic characteristics of the aged brain
eLife
publication / 2017
STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array
Scientific Reports
publication / 2017
Cell type discovery and representation in the era of high-content single cell phenotyping
BMC bioinformatics
publication / 2017
The Human Cell Atlas
eLife
publication / 2018
Single-nucleus and single-cell transcriptomes compared in matched cortical cell types
PloS One
publication / 2018
Preparation of Acute Brain Slices Using an Optimized N-Methyl-D-glucamine Protective Recovery Method
Journal of Visualized Experiments: JoVE
publication / 2018
An anatomic transcriptional atlas of human glioblastoma
Science (New York, N.Y.)
publication / 2018
Cell type discovery using single-cell transcriptomics: implications for ontological representation
Human Molecular Genetics
publication / 2018
A robust ex vivo experimental platform for molecular-genetic dissection of adult human neocortical cell types and circuits
Scientific Reports
publication / 2018
Genetic identification of brain cell types underlying schizophrenia
Nature Genetics
publication / 2018
Distinctive Structural and Molecular Features of Myelinated Inhibitory Axons in Human Neocortex
eNeuro
publication / 2018
Sparse recurrent excitatory connectivity in the microcircuit of the adult mouse and human cortex
eLife
publication / 2018
Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type
Nature Neuroscience
publication / 2018
Shared and distinct transcriptomic cell types across neocortical areas
Nature
publication / 2018
h-Channels Contribute to Divergent Intrinsic Membrane Properties of Supragranular Pyramidal Neurons in Human versus Mouse Cerebral Cortex
Neuron
publication / 2019
Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity
Nature Genetics
publication / 2019
Classification of electrophysiological and morphological neuron types in the mouse visual cortex
Nature Neuroscience
publication / 2019
Conserved cell types with divergent features in human versus mouse cortex
Nature
publication / 2019
Single-cell transcriptomic evidence for dense intracortical neuropeptide networks
eLife
publication / 2020
Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons
Nature Communications
publication / 2020
Distinct Transcriptomic Cell Types and Neural Circuits of the Subiculum and Prosubiculum along the Dorsal-Ventral Axis
Cell Reports
publication / 2020
Parallel RNA and DNA analysis after deep sequencing (PRDD-seq) reveals cell type-specific lineage patterns in human brain
Proceedings of the National Academy of Sciences of the United States of America
publication / 2020
Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue
Nucleic Acids Research
publication / 2020
Common cell type nomenclature for the mammalian brain
eLife
publication / 2020
A community-based transcriptomics classification and nomenclature of neocortical cell types
Nature Neuroscience
publication / 2020
Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells
Cell
publication / 2021
Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex
Cell Reports
publication / 2021
FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman-Rafsky non-parametric test
Briefings in Bioinformatics
publication / 2021
Enhancer viruses for combinatorial cell-subclass-specific labeling
Neuron
publication / 2021
Comprehensive in situ mapping of human cortical transcriptomic cell types
Communications Biology
publication / 2021
Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization
eLife
publication / 2021
Signature morpho-electric, transcriptomic, and dendritic properties of human layer 5 neocortical pyramidal neurons
Neuron
publication / 2021
Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans
eLife
publication / 2021
A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing
Genome Research
publication / 2021
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Nature
publication / 2021
Human neocortical expansion involves glutamatergic neuron diversification
Nature
publication / 2021
Cell type ontologies of the Human Cell Atlas
Nature Cell Biology
publication / 2022
Cellular resolution anatomical and molecular atlases for prenatal human brains
The Journal of Comparative Neurology
publication / 2022
Local connectivity and synaptic dynamics in mouse and human neocortex
Science (New York, N.Y.)
publication / 2022
Single nucleus multi-omics identifies human cortical cell regulatory genome diversity
Cell Genomics
publication / 2022
Verbal and General IQ Associate with Supragranular Layer Thickness and Cell Properties of the Left Temporal Cortex
Cerebral Cortex (New York, N.Y.: 1991)
publication / 2007
Neuroinformatics for genome-wide 3D gene expression mapping in the mouse brain
IEEE/ACM transactions on computational biology and bioinformatics
publication / 2007
Genome-wide atlas of gene expression in the adult mouse brain
Nature
publication / 2008
Sleep deprivation effects on circadian clock gene expression in the cerebral cortex parallel electroencephalographic differences among mouse strains
The Journal of Neuroscience: The Official Journal of the Society for Neuroscience
publication / 2008
Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data
Genome Biology
publication / 2008
New developments in sleep research: molecular genetics, gene expression, and systems neurobiology
The Journal of Neuroscience: The Official Journal of the Society for Neuroscience
publication / 2022
Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH
Science (New York, N.Y.)
publication / 2022
Strong and reliable synaptic communication between pyramidal neurons in adult human cerebral cortex
Cerebral Cortex (New York, N.Y.: 1991)
publication / 2022
Scalable in situ single-cell profiling by electrophoretic capture of mRNA using EEL FISH
Nature Biotechnology
publication / 2022
A scalable and modular automated pipeline for stitching of large electron microscopy datasets
eLife
publication / 2022
Single-neuron models linking electrophysiology, morphology, and transcriptomics across cortical cell types
Cell Reports
publication / 2022
Oligodendrocyte precursor cells ingest axons in the mouse neocortex
Proceedings of the National Academy of Sciences of the United States of America
publication / 2022
Multi-modal characterization and simulation of human epileptic circuitry
Cell Reports
publication / 2023
Brain Data Standards - A method for building data-driven cell-type ontologies
Scientific Data
publication / 2021
A multimodal cell census and atlas of the mammalian primary motor cortex
Nature
publication / 2023
A comparison of anatomic and cellular transcriptome structures across 40 human brain diseases
PLoS biology
publication / 2023
Functional gene delivery to and across brain vasculature of systemic AAVs with endothelial-specific tropism in rodents and broad tropism in primates
Nature Communications
publication / 2023
Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain
Scientific Reports
publication / 2023
Target cell-specific synaptic dynamics of excitatory to inhibitory neuron connections in supragranular layers of human neocortex
eLife
publication / 2023
A guide to the BRAIN Initiative Cell Census Network data ecosystem
PLoS biology
publication / 2023
Genes associated with cognitive ability and HAR show overlapping expression patterns in human cortical neuron types
Nature Communications
publication / 2023
Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex
Science (New York, N.Y.)
publication / 2023
Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution
Nature Ecology & Evolution
publication / 2023
Transcriptomic cytoarchitecture reveals principles of human neocortex organization
Science (New York, N.Y.)
publication / 2023
Interindividual variation in human cortical cell type abundance and expression
Science (New York, N.Y.)
publication / 2023
A comparative atlas of single-cell chromatin accessibility in the human brain
Science (New York, N.Y.)
publication / 2023
Comparative transcriptomics reveals human-specific cortical features
Science (New York, N.Y.)
publication / 2023
Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex
Science (New York, N.Y.)
publication / 2023
Single-cell DNA methylation and 3D genome architecture in the human brain
Science (New York, N.Y.)
publication / 2023
Transcriptomic diversity of cell types across the adult human brain
Science (New York, N.Y.)
publication / 2023
Single-cell genomics reveals region-specific developmental trajectories underlying neuronal diversity in the human hypothalamus
Science Advances
publication / 2023
Conserved and divergent gene regulatory programs of the mammalian neocortex
Nature
publication / 2024
Morpho-electric diversity of human hippocampal CA1 pyramidal neurons
Cell Reports
publication / 2024
Integrated multimodal cell atlas of Alzheimer's disease
Nature Neuroscience
publication / 2024
Areal specializations in the morpho-electric and transcriptomic properties of primate layer 5 extratelencephalic projection neurons
Cell Reports
publication / 2024
SEA-AD is a multimodal cellular atlas and resource for Alzheimer's disease
Nature Aging
publication / 2024
Distinctive physiology of molecularly identified medium spiny neurons in the macaque putamen
Cell Reports
publication / 2025
A versatile cell line for establishing potency of cell type-specific AAV transgenes
Molecular Therapy. Methods & Clinical Development
publication / 2025
Integrating multimodal data to understand cortical circuit architecture and function
Nature Neuroscience
publication / 2025
Interneuron-specific dual-AAV SCN1A gene replacement corrects epileptic phenotypes in mouse models of Dravet syndrome
Science Translational Medicine
publication / 2025
AAV delivery of full-length SYNGAP1 rescues epileptic and behavioral phenotypes in a mouse model of SYNGAP1-related disorders
Molecular Therapy: The Journal of the American Society of Gene Therapy
publication / 2025
Accelerating biomedical discoveries in brain health through transformative neuropathology of aging and neurodegeneration
Neuron
publication / 2025
A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types
Cell
publication / 2025
Enhancer AAV toolbox for accessing and perturbing striatal cell types and circuits
Neuron
publication / 2025
Enhancer AAVs for targeting spinal motor neurons and descending motor pathways in rodents and macaque
Cell Reports
publication / 2025
Evaluating methods for the prediction of cell-type-specific enhancers in the mammalian cortex
Cell Genomics
publication / 2026
Connecting single-cell transcriptomes to projectomes in the mouse visual cortex
Nature
publication / 2026
Somatic cancer variants enriched in Alzheimer's disease microglia-like cells drive inflammatory and proliferative states
Cell
publication / 2025
AAV-PHP.eB achieves superior neuronal transduction over AAV9 in pigtail macaques following intracerebroventricular administration
Molecular Therapy. Methods & Clinical Development
publication / 2026
Single-cell multiomic human brain atlas reveals regulatory drivers of cortical regionality
Nature Communications
publication / 2026
Technical and biological sources of noise confound multiplexed enhancer AAV screening
Nature Communications
publication / 2026
HCN channels reveal conserved and divergent physiology in supragranular pyramidal neurons in primate species
Communications Biology
view all publications
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