Eric Kenji Lee

Publications

Papers, talks & trajectory

A timeline of my scholarly output, 2016–2026, grouped into research streams: stars are first-author work, dots are co-authored papers and talks. Full lists follow below.

View everything on Google Scholar →

First author Co-author Invited talk Contributed talk Cell types & methods Primate cortex & decisions Mouse visual cortex · Allen Early / other Conference talks WaveMAP — cell type diversity via nonlinear dimensionality reduction of waveforms. eLife, 2021. First author. Published. WaveMAP for identifying putative cell types from extracellular electrophysiology. STAR Protocols, 2023. First author. Published. In vivo cell-type and brain region classification via multimodal contrastive learning. ICLR Spotlight, 2025. Co-author. Published. PhysMAP — multi-modal visualization & identification of electrophysiological cell types. Nature Communications, 2026. First author. Published. WaveMAP Protocol PhysMAP A cortical information bottleneck during decision-making. eLife, 2023. Co-author. Published. Neuropixels reveal laminar microcircuit organization in monkey V1 in vivo (Carr et al.). PNAS, 2026. Co-author. Published. Aberrant cortical activity in GCaMP6 transgenic lines. eNeuro, 2017. Co-author. Published. Biological variation in the sizes, shapes and locations of visual cortical areas in the mouse. PLOS ONE, 2019. Second author. Published. Allen Brain Observatory — large-scale physiological survey of mouse visual cortex. Nature Neuroscience, 2020. Co-author — 44th of 72, alphabetical. Citation heavyweight. Published. VIP interneurons enhance responses to weak stimuli in mouse V1. eLife, 2020. Co-author. Published. A standardized behavioral event equally impacts cortical visual areas and layers (Ramadan et al.). eNeuro, 2022. Second author. Published. Measuring stimulus-evoked neurophysiological differentiation in mouse V1. eNeuro, 2022. Co-author. Published. Whole-brain monosynaptic input connectome to neuron classes in mouse V1. Nature Neuroscience, 2023. Co-author. Published. Somata / apical dendrite responses in mouse V1 over days (dataset). Scientific Data, 2023. Co-author. Published. Pattern-violating visual stimuli in somata vs distal dendrites over days. J. Neuroscience, 2024. Co-author. Published. Brain Observatory Bisphenol A alters GnRH3 neuron development in medaka. NeuroToxicology, 2016. Co-author (undergraduate). Published. Neuropathological / transcriptomic characteristics of the aged brain. eLife, 2017. Co-author. Published. IN PREP: Multimodal characterization of pan-inhibitory enhancers for assessing inhibitory neuron function in macaque monkeys (Medalla et al.). Co-author. Cell types & methods. PREPRINT: Distinct neural dynamics in prefrontal and premotor cortex underlie flexible perceptual decisions (Wang, Lee, Carr, Chandrasekaran). bioRxiv 2026. Second author. IN PREP: The computational geometry of flexible decision making in prefrontal cortex. First author. (Co-first with T. Wang on earlier posters.) IN PREP: Prefrontal neural dynamics underlying abstract perceptual decisions. First author. IN PREP: Population dynamics during mnemonic working memory are structured by a single inhibitory cell type. First author. CONTRIBUTED talk: "Multi-modal composition of physiological signals to delineate neuronal cell types." NSF AI Planning Institute, CMU, Pittsburgh. Jan 2023. CONTRIBUTED talk: "Multi-modal composition of physiological signals to delineate neuronal cell types." CCN Junior Theoretical Neuroscientist Workshop, Flatiron Institute, NYC. June 2023. INVITED talk: "Manifolds for identification of cell types and neural computation geometry." Rutgers CMBN, Newark. May 2024. CONTRIBUTED: "Bridging cell types and spike trains" — workshop co-organizer (with Josh Siegle). COSYNE, Lisbon. March 2026. INVITED panel: "Impacting our communities at every training stage" (panelist). COSYNE Mentorship Panel, Lisbon. March 2026. Service / outreach. UPCOMING (in prep): "Cell type-informed dynamical systems uncover mechanisms of cortical computation." Gordon Research Seminar: Neurobiology of Cognition. Bridges cell-type methods + primate decisions — first talk to unite both. 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025 2026 in pipeline First author Co-author Invited talk Contributed in pipeline 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025 2026 Cell types Primate Mouse VC Early Talks In vivo cell-type and brain region classification via multimodal contrastive learning. ICLR Spotlight, 2025. Co-author. Published. A cortical information bottleneck during decision-making. eLife, 2023. Co-author. Published. Neuropixels reveal laminar microcircuit organization in monkey V1 in vivo (Carr et al.). PNAS, 2026. Co-author. Published. Aberrant cortical activity in GCaMP6 transgenic lines. eNeuro, 2017. Co-author. Published. Biological variation in the sizes, shapes and locations of visual cortical areas in the mouse. PLOS ONE, 2019. Second author. Published. Allen Brain Observatory — large-scale physiological survey of mouse visual cortex. Nature Neuroscience, 2020. Co-author — 44th of 72, alphabetical. Citation heavyweight. Published. VIP interneurons enhance responses to weak stimuli in mouse V1. eLife, 2020. Co-author. Published. A standardized behavioral event equally impacts cortical visual areas and layers (Ramadan et al.). eNeuro, 2022. Second author. Published. Measuring stimulus-evoked neurophysiological differentiation in mouse V1. eNeuro, 2022. Co-author. Published. Whole-brain monosynaptic input connectome to neuron classes in mouse V1. Nature Neuroscience, 2023. Co-author. Published. Somata / apical dendrite responses in mouse V1 over days (dataset). Scientific Data, 2023. Co-author. Published. Pattern-violating visual stimuli in somata vs distal dendrites over days. J. Neuroscience, 2024. Co-author. Published. Bisphenol A alters GnRH3 neuron development in medaka. NeuroToxicology, 2016. Co-author (undergraduate). Published. Neuropathological / transcriptomic characteristics of the aged brain. eLife, 2017. Co-author. Published. IN PREP: Multimodal characterization of pan-inhibitory enhancers for assessing inhibitory neuron function in macaque monkeys (Medalla et al.). Co-author. Cell types & methods. PREPRINT: Distinct neural dynamics in prefrontal and premotor cortex underlie flexible perceptual decisions (Wang, Lee, Carr, Chandrasekaran). bioRxiv 2026. Second author. CONTRIBUTED talk: "Multi-modal composition of physiological signals to delineate neuronal cell types." NSF AI Planning Institute, CMU, Pittsburgh. Jan 2023. CONTRIBUTED talk: "Multi-modal composition of physiological signals to delineate neuronal cell types." CCN Junior Theoretical Neuroscientist Workshop, Flatiron Institute, NYC. June 2023. INVITED talk: "Manifolds for identification of cell types and neural computation geometry." Rutgers CMBN, Newark. May 2024. CONTRIBUTED: "Bridging cell types and spike trains" — workshop co-organizer (with Josh Siegle). COSYNE, Lisbon. March 2026. INVITED panel: "Impacting our communities at every training stage" (panelist). COSYNE Mentorship Panel, Lisbon. March 2026. Service / outreach. UPCOMING (in prep): "Cell type-informed dynamical systems uncover mechanisms of cortical computation." Gordon Research Seminar: Neurobiology of Cognition. Bridges cell-type methods + primate decisions — first talk to unite both. WaveMAP — cell type diversity via nonlinear dimensionality reduction of waveforms. eLife, 2021. First author. Published. WaveMAP for identifying putative cell types from extracellular electrophysiology. STAR Protocols, 2023. First author. Published. PhysMAP — multi-modal visualization & identification of electrophysiological cell types. Nature Communications, 2026. First author. Published. IN PREP: The computational geometry of flexible decision making in prefrontal cortex. First author. (Co-first with T. Wang on earlier posters.) IN PREP: Prefrontal neural dynamics underlying abstract perceptual decisions. First author. IN PREP: Population dynamics during mnemonic working memory are structured by a single inhibitory cell type. First author.

Publications

Year / statusPaperVenueRoleStream
in prepPopulation dynamics during mnemonic working memory are structured by a single inhibitory cell type.—FirstCell types × Primate
in prepThe computational geometry of flexible decision-making in prefrontal cortex.—FirstPrimate
in prepPrefrontal neural dynamics underlying abstract perceptual decisions.—FirstPrimate
in prepMultimodal characterization of pan-inhibitory enhancers for assessing inhibitory neuron function in macaque monkeys.—Co-authorCell types × Primate
2026 preDistinct neural dynamics in prefrontal and premotor cortex during flexible perceptual decisions.bioRxivSecondPrimate
2026A multimodal approach for visualizing and identifying electrophysiological cell types in vivo.Nature CommunicationsFirstCell types × Mouse VC
2026Neuropixels reveal laminar microcircuit organization in monkey V1 in vivo.PNASCo-authorPrimate
2025In vivo cell-type and brain region classification via multimodal contrastive learning.ICLR (Spotlight)Co-authorCell types
2024Responses to pattern-violating visual stimuli evolve differently over days in somata and distal apical dendrites.J. NeuroscienceCo-authorMouse VC
2023 preDifferential encoding of temporal context and expectation under representational drift across hierarchically connected areas.bioRxivCo-authorMouse VC
2023WaveMAP for identifying putative cell types from in vivo electrophysiology.STAR ProtocolsFirstCell types
2023A cortical information bottleneck during decision-making.eLifeCo-authorPrimate
2023A whole-brain monosynaptic input connectome to neuron classes in mouse visual cortex.Nature NeuroscienceCo-authorMouse VC
2023Responses of pyramidal cell somata and apical dendrites in mouse visual cortex over multiple days.Scientific DataCo-authorMouse VC
2022A standardized nonvisual behavioral event is broadcasted homogeneously across cortical visual areas without modulating visual responses.eNeuroSecondMouse VC
2022Measuring stimulus-evoked neurophysiological differentiation in distinct populations of neurons in mouse visual cortex.eNeuroCo-authorMouse VC
2021Non-linear dimensionality reduction on extracellular waveforms reveals cell type diversity in premotor cortex.eLifeFirstCell types
2020A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex.Nature NeuroscienceCo-authorMouse VC
2020VIP interneurons in mouse primary visual cortex selectively enhance responses to weak but specific stimuli.eLifeCo-authorMouse VC
2019Biological variation in the sizes, shapes and locations of visual cortical areas in the mouse.PLOS ONESecondMouse VC
2017Aberrant cortical activity in multiple GCaMP6-expressing transgenic mouse lines.eNeuroCo-authorMouse VC
2017Neuropathological and transcriptomic characteristics of the aged brain.eLifeCo-authorOther
2016Low-dose exposure to Bisphenol A alters development of gonadotropin-releasing hormone 3 neurons and larval locomotor behavior in Japanese Medaka.NeuroToxicologyCo-authorOther

Invited talks & seminars

YearHostFormat
2026Gordon Research Seminar
Neurobiology of Cognition
Upcoming
2026Steinmetz Lab
University of Washington
In person
2026Sainsbury Wellcome Centre
University College London
In person
2026Rutishauser Lab
Caltech & Cedars-Sinai
Virtual
2024Center for Molecular & Behavioral Neuroscience
Rutgers University
In person
2024Varol Lab
New York University
Virtual
2021Svoboda Lab
Janelia Research Campus
Virtual
2021Valiante Lab
University of Toronto
Virtual
2021Brain Observatory Group
Allen Institute for Brain Science
Virtual

Conference talks & panels

YearTitleVenueTypeStream
2026Impacting our communities at every training stage (panelist)COSYNE Mentorship Panel, LisbonInvitedService
2026"Bridging cell types and spike trains" — workshop co-organizer (w/ J. Siegle)COSYNE Workshop, LisbonContribCell types
2023Multi-modal composition of physiological signals to delineate neuronal cell typesCCN Jr. Theo. Neuro Workshop, Flatiron, NYCContribCell types
2023Multi-modal composition of physiological signals to delineate neuronal cell typesNSF AI Planning Institute, CMU, PittsburghContribCell types

Honors

  • NIH NINDS F31 NRSA — awarded at the 8th percentile
  • Computational Properties of Prefrontal Cortex (CPPC) Conference Travel Award
  • ETC Excellence in Mentorship Award
  • Puget Sound Research Travel Grant