Michael Hawrylycz

Investigator, Sr. Informatics and Data Science

teams /

Allenite

Mike Hawrylycz joined the Allen Institute in 2003. He is responsible for the direction of the data analysis and annotation effort. Hawrylycz has worked in a variety of applied mathematics and computer science areas, addressing challenges in consumer and investment finance, electrical engineering and image processing, and computational biology and genomics. Hawrylycz received his Ph.D. in applied mathematics at the Massachusetts Institute of Technology. He subsequently was a post-doctoral researcher in the Computer Research and Applications Group at the Los Alamos National Laboratory.

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featured publications

publication / 2025

Accelerating biomedical discoveries in brain health through transformative neuropathology of aging and neurodegeneration

Neuron

publication / 2025

Connectivity of single neurons classifies cell subtypes in mouse brains

Nature Methods

publication / 2025

Integrating multimodal data to understand cortical circuit architecture and function

Nature Neuroscience

publication / 2024

Neuronal diversity and stereotypy at multiple scales through whole brain morphometry

Nature Communications

publication / 2024

Integrated multimodal cell atlas of Alzheimer's disease

Nature Neuroscience

publication / 2024

SEA-AD is a multimodal cellular atlas and resource for Alzheimer's disease

Nature Aging

publication / 2024

Hierarchical Bayesian inference to model continuous phenotypical progression in Alzheimer's Disease

bioRxiv

publication / 2023

Linking Neurogenetics and Functional Connectivity in Autism

Biological Psychiatry

publication / 2023

A guide to the BRAIN Initiative Cell Census Network data ecosystem

PLoS biology

publication / 2023

BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

Nature Methods

publication / 2023

A comparison of anatomic and cellular transcriptome structures across 40 human brain diseases

PLoS biology

publication / 2022

Petabyte-Scale Multi-Morphometry of Single Neurons for Whole Brains

Neuroinformatics

publication / 2022

Cross-modal coherent registration of whole mouse brains

Nature Methods

publication / 2021

Transcriptional network orchestrating regional patterning of cortical progenitors

Proceedings of the National Academy of Sciences of the United States of America

publication / 2021

A multimodal cell census and atlas of the mammalian primary motor cortex

Nature

publication / 2021

Cellular anatomy of the mouse primary motor cortex

Nature

publication / 2021

Comparative cellular analysis of motor cortex in human, marmoset and mouse

Nature

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 taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

Cell

publication / 2021

Integration of evidence across human and model organism studies: A meeting report

Genes, Brain, and Behavior

publication / 2021

Consistent cross-modal identification of cortical neurons with coupled autoencoders

Nature Computational Science

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

New light on cortical neuropeptides and synaptic network plasticity

Current Opinion in Neurobiology

publication / 2020

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas

Cell

publication / 2019

Single-cell transcriptomic evidence for dense intracortical neuropeptide networks

eLife

publication / 2019

Conserved cell types with divergent features in human versus mouse cortex

Nature

publication / 2019

TeraVR empowers precise reconstruction of complete 3-D neuronal morphology in the whole brain

Nature Communications

publication / 2019

Identification of genetic markers for cortical areas using a Random Forest classification routine and the Allen Mouse Brain Atlas

PloS One

publication / 2018

Shared and distinct transcriptomic cell types across neocortical areas

Nature

publication / 2018

Generalized leaky integrate-and-fire models classify multiple neuron types

Nature Communications

publication / 2017

SmartScope2: Simultaneous Imaging and Reconstruction of Neuronal Morphology

Scientific Reports

publication / 2017

Transcriptomic Perspectives on Neocortical Structure, Development, Evolution, and Disease

Annual Review of Neuroscience

publication / 2016

Reconstructing the brain: from image stacks to neuron synthesis

Brain Informatics

publication / 2016

Inferring cortical function in the mouse visual system through large-scale systems neuroscience

Proceedings of the National Academy of Sciences of the United States of America

publication / 2016

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

Nature Neuroscience

publication / 2015

Canonical genetic signatures of the adult human brain

Nature Neuroscience

publication / 2015

BlastNeuron for Automated Comparison, Retrieval and Clustering of 3D Neuron Morphologies

Neuroinformatics

publication / 2015

BigNeuron: Large-Scale 3D Neuron Reconstruction from Optical Microscopy Images

Neuron

publication / 2015

Adaptive Image Enhancement for Tracing 3D Morphologies of Neurons and Brain Vasculatures

Neuroinformatics

publication / 2015

Exploration and visualization of connectivity in the adult mouse brain

Methods (San Diego, Calif.)

publication / 2015

Neuroinformatics of the Allen Mouse Brain Connectivity Atlas

Methods (San Diego, Calif.)

publication / 2015

Cell-type-specific neuroanatomy of cliques of autism-related genes in the mouse brain

Frontiers in Computational Neuroscience

publication / 2014

Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis

Nature Communications

publication / 2014

Cell-type-based model explaining coexpression patterns of genes in the brain

Proceedings of the National Academy of Sciences of the United States of America

publication / 2014

Aerobic glycolysis in the human brain is associated with development and neotenous gene expression

Cell Metabolism

publication / 2013

Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system

Nucleic Acids Research

publication / 2010

Surface-based mapping of gene expression and probabilistic expression maps in the mouse cortex

Methods (San Diego, Calif.)

publication / 2010

Clustering of spatial gene expression patterns in the mouse brain and comparison with classical neuroanatomy

Methods (San Diego, Calif.)

publication / 2010

Molecular and anatomical signatures of sleep deprivation in the mouse brain

Frontiers in Neuroscience

publication / 2009

An anatomic gene expression atlas of the adult mouse brain

Nature Neuroscience

publication / 2009

A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale

PLoS computational biology

publication / 2008

Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data

Genome Biology

Michael Hawrylycz

Investigator, Sr. Informatics and Data Science

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