Publications
Peer-reviewed articles and conference proceedings, newest first. Starred entries are selected work; colored chips mark the domains each contribution serves. Invited talks and posters follow.
Also on Google Scholar, and in the CV (PDF).
2025
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Functional connectomics spanning multiple areas of mouse visual cortex ★
2024
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Toward a Framework for Providing Equitable Opportunities to Activate STEM Talent
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EM and XRM Connectomics Imaging and Experimental Metadata Standards
2023
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A SwarmAI Testbed for Workforce Development and Collaborative, Interdisciplinary Research
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Empowering trailblazers toward scalable, systematized, research-based workforce development
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Using machine learning on clinical data to identify unexpected patterns in groups of COVID-19 patients ★
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An Immersive Curriculum to Develop Computational Science and Research Skills in a Cohort-Based Internship Program ★
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Utilizing Technical Competitions to Enhance Diverse Workforce Recruitment and Retention
2022
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A framework for rigorous evaluation of human performance in human and machine learning comparison studies ★
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The Brain Observatory Storage Service and Database (BossDB): A Cloud-Native Approach for Petascale Neuroscience Discovery ★
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Scalable graph analysis tools for the connectomics community
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Online learning for orientation estimation during translation in an insect ring attractor network
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Connectomics Annotation Metadata Standardization for Increased Accessibility and Queryability
2021
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Mine your own view: Self-supervised learning through across-sample prediction
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Multi-Scale Modeling of Neural Structure in X-Ray Imagery
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CONFIRMS: a toolkit for scalable, black box connectome assessment and investigation
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Eliminating accidental deviations to minimize generalization error and maximize replicability: Applications in connectomics and genomics
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A low-resource reliable pipeline to democratize multi-modal connectome estimation and analysis
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DotMotif: an open-source tool for connectome subgraph isomorphism search and graph queries ★
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An Integrated toolkit for extensible and reproducible neuroscience
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Circuit motifs and graph properties of connectome development in C. elegans
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Benchmarking Human Performance for Visual Search of Aerial Images ★
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Online learning for orientation estimation during translation in an insect ring attractor network
2020
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Leveraging Tools from Autonomous Navigation for Rapid, Robust Neuron Connectivity
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Connectome subgraph isomorphisms and graph queries with DotMotif
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A three-dimensional thalamocortical dataset for characterizing brain heterogeneity
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STEM Leadership and Training for Trailblazing Students in an Immersive Research Environment
2019
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An Accessible, Distributed, Technology-Based Approach for Student and Mentor Engagement
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Transfer Learning Analysis of Image Processing Workflows for Electron Microscopy Datasets
2018
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CIRCUIT summer program: A computational neuroscience outreach experience for high-achieving undergraduates via sponsored research
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The college prep program at APL: An experiential model to help high-achieving, underserved students trailblaze and achieve success
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A High-Throughput Pipeline Identifies Robust Connectomes But Troublesome Variability
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A community-developed open-source computational ecosystem for big neuro data ★
2017
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Quantifying mesoscale neuroanatomy using X-ray microtomography ★
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Science in the cloud (SIC): A use case in MRI connectomics.
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A substrate for modular, extensible data-visualization
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Neural Reconstruction Integrity: A metric for assessing the connectivity of reconstructed neural networks
2016
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SANTIAGO : Spine Association for Neuron Topology Improvement
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From sample to knowledge : Towards an integrated approach for neuroscience discovery
2015
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An Automated Images-to-Graphs Framework for High Resolution Connectomics
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VESICLE : Volumetric Evaluation of Synaptic Interfaces using Computer vision at Large Scale
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Saturated Reconstruction of a Volume of Neocortex ★
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Gradient-Domain Fusion for Color Correction in Large EM Image Stacks
2013
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The Open Connectome Project Data Cluster: Scalable Analysis and Vision for High-Throughput Neuroscience
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MIGRAINE: MRI Graph Reliability Analysis and Inference for Connectomics
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Computing Scalable Multivariate Glocal Invariants of Large (Brain-) Graphs
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Graph classification using signal-subgraphs: applications in statistical connectomics. ★
2012
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Magnetic resonance connectome automated pipeline: an overview.
2026
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Learning Engineering for Next-Generation Systems: A New Concentration at Johns Hopkins
2024
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Scalably and Systematically Empowering Trailblazing (STEM) Students
2022
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Invited panel
2021
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NeuroAI Engines: Revolutionary Function through Biological Form
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Enhanced Learning Environment for Accelerating Training and Engagement
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Accelerating the Pipeline of Trailblazing STEM Students Workshop
2020
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Toward Petascale and Exascale Connectomics
2019
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STEM Workforce Development Workshop
2018
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Invited participant
2017
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BigNeuro 2017: Analyzing brain data from nano to macroscale
2016
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Enabling Scalable Neurocartography: Images to Graphs for Discovery
2015
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Images to Graphs for Inference
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Images to Graphs: Techniques and Strategies for Mapping the Brain
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Machine Intelligence from Cortical Networks (MICRONS) IRAD
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Volumetric Evaluation of Synaptic Interfaces using Computer Vision at Large Scale
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BigNeuro 2015: Making sense of big neural data workshop
2014
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Graph Inference for Connectomics
2013
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Connectome Annotation for Joint Analysis of Large 3-Dimensional Data: Research Progress
2012
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Towards A Fully Automatic Pipeline for Connectome Estimation from High-Resolution EM Data
2011
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Predicting Human Performance from Brain Connectivity
2017
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RETINA: Real -time evaluation tools for integrated neuroscience analysis
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Toward a Common, Extensible Cloud Architecture for Images to Graphs
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CONFIRMS: Creating Optimized Networks for Informing Reconstruction Metrics and Science
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Cloud-Native Infrastructure and Accessible Interfaces to Enable Petascale Neuroscience
2016
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ndparse: Tools and Interfaces for Scalable Neuroscience Discovery
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ndio: Neuroscience Discovery Input and Output
2015
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Web Visualization of Massive Neuroscience Datasets using the Open Connectome Project
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Scalable automated (synapse) detection using the Open Connectome Project
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Community Connectomics via Cloud Computing Utilizing m2g - a Reference Pipeline
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Computational statistics for whole brain CLARITY analysis using the Open Connectome Project
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Open Connectome Project and NeuroData: Enabling Data-Driven Neuroscience at Scale
2014
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A Semantic Framework to Guide Computer Vision in (EM) Connectomics
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Automated Neuronal Graph Creation Using the Open Connectome Project RAMON Data Open Connectome Project ( OCP ) Services
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Automatic Annotation of 3D Axoplasmic Reticula for Neuron Segmentation
2013
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Towards a Fully Automatic Pipeline for Connectome Estimation from High-Resolution EM Data
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Large-Scale Synapse Detection Using CAJAL3D
2012
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Towards a Fully Automatic Pipeline for Connectome Estimation from High-Resolution EM Data
2011
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Magnetic resonance connectome automated pipeline and repeatability analysis
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Connectome Classification using statistical graph theory and machine learning
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Connectome Classification: Statistical Graph Theoretic Methods for Analysis of MR-Connectome Data