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people

Jeremy Miller

Scientist, Sr.

Allenite
/
Brain Health

biography

Dr. Miller joined the Allen Institute in 2011 to help with computational data analysis of the Allen Human Brain Atlas project. He is first author on several major manuscripts describing the Allen Institute’s large-scale transcriptomic resources on the adult and developing human and non-human primate brain, including the Aging, Dementia, and Traumatic Brain Injury Study. Miller received his Ph.D. in neuroscience from UCLA, where he studied gene expression changes in the brain in Alzheimer’s disease and normal aging in the lab of Dr. Daniel Geschwind.

research focus

Miller's current work focuses in three general areas: (1) characterizing cell types of the mammalian brain and their underlying features, including molecular pathways unique to human; (2) understanding how features of these cell types change with disease in human; and (3) developing tools for standardizing cell type taxonomies and for communicating cell type findings to the general scientific community.

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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

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featured publications

publication / 2012
An anatomically comprehensive atlas of the adult human brain transcriptome
Nature
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
Aerobic glycolysis in the human brain is associated with development and neotenous gene expression
Cell Metabolism
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
A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain
Neuron
publication / 2015
Correlated gene expression and target specificity demonstrate excitatory projection neuron diversity
Cerebral Cortex (New York, N.Y.: 1991)
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 / 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
Neuropathological and transcriptomic characteristics of the aged brain
eLife
publication / 2017
Cell type discovery and representation in the era of high-content single cell phenotyping
BMC bioinformatics
publication / 2018
Single-nucleus and single-cell transcriptomes compared in matched cortical cell types
PloS One
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
Genetic identification of brain cell types underlying schizophrenia
Nature Genetics
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
A Microglial Signature Directing Human Aging and Neurodegeneration-Related Gene Networks
Frontiers in Neuroscience
publication / 2019
An Inflammatory Landscape for Preoperative Neurologic Deficits in Glioblastoma
Frontiers in Genetics
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
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
Common cell type nomenclature for the mammalian brain
eLife
publication / 2021
The Delayed Neuropathological Consequences of Traumatic Brain Injury in a Community-Based Sample
Frontiers in Neurology
publication / 2021
Consistent cross-modal identification of cortical neurons with coupled autoencoders
Nature Computational Science
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
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
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 / 2022
Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH
Science (New York, N.Y.)
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 / 2023
A comparison of anatomic and cellular transcriptome structures across 40 human brain diseases
PLoS biology
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
A guide to the BRAIN Initiative Cell Census Network data ecosystem
PLoS biology
publication / 2023
Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex
Science (New York, N.Y.)
publication / 2023
Interindividual variation in human cortical cell type abundance and expression
Science (New York, N.Y.)
publication / 2023
Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex
Science (New York, N.Y.)
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 / 2025
Evaluating methods for the prediction of cell-type-specific enhancers in the mammalian cortex
Cell Genomics
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