Our work
Publications
Discoveries, methods and collaborations. Explore selected work and our publication archive.
Featured
Selected papers
Bold = Donghoon Lee · Highlighted = lab members
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Single-cell atlas of transcriptomic vulnerability across brain disorders
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Plasticity of human microglia and brain perivascular macrophages in aging and Alzheimer’s disease
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Population-scale cross-disorder atlas of the human prefrontal cortex at single-cell resolution
Paper
doi:10.1038/s41597-025-04687-5 -
Single-nucleus transcriptome-wide association study of human brain disorders
Paper
doi:10.1038/s41586-026-10836-6 -
Lifespan single-cell transcriptomic atlas of the human prefrontal cortex
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Single-nucleus atlas of cell-type specific genetic regulation in the human brain
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AI-based characterization of Alzheimer’s disease phenotypes from population-scale single-cell data
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Efficient differential expression analysis of large-scale single-cell transcriptomics data using Dreamlet
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Genetic regulation of cell type–specific chromatin accessibility shapes brain disease etiology
Paper
doi:10.1126/science.adh4265 -
Multiomic single-cell profiling identifies critical regulators of postnatal brain
Paper
doi:10.1038/s41588-025-02083-8 -
Epigenome-based splicing prediction using a recurrent neural network
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STARRPeaker: uniform processing and accurate identification of STARR-seq active regions
Publication archive
All publications
2026
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Single-cell atlas of transcriptomic vulnerability across brain disorders
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Single-nucleus transcriptome-wide association study of human brain disorders
Paper
doi:10.1038/s41586-026-10836-6 -
Lifespan single-cell transcriptomic atlas of the human prefrontal cortex
-
Single-nucleus atlas of cell-type specific genetic regulation in the human brain
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AI-based characterization of Alzheimer’s disease phenotypes from population-scale single-cell data
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Efficient differential expression analysis of large-scale single-cell transcriptomics data using Dreamlet
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Personalized single-cell transcriptomics reveals molecular diversity in Alzheimer’s disease
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Plasticity of human microglia and brain perivascular macrophages in aging and Alzheimer’s disease
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SECmeres outperform extracellular vesicles as potential blood RNA biomarkers for Alzheimer’s disease
Paper
doi:10.1038/s41467-026-74541-8 -
Gene regulatory programs of cognitive resilience and pathogenesis in Alzheimer’s disease
Paper
doi:10.64898/2026.02.19.26346666
2025
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Alzheimer’s disease transcriptional landscape in ex vivo human microglia
Paper
doi:10.1038/s41593-025-02020-2 -
A Transcriptomic Roadmap of Parkinson’s Disease Progression at Single Cell Resolution
Paper
doi:10.1101/2025.07.30.25332436 -
A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
Paper
doi:10.1101/gr.279584.124 -
Population-scale cross-disorder atlas of the human prefrontal cortex at single-cell resolution
Paper
doi:10.1038/s41597-025-04687-5 -
Multiomic single-cell profiling identifies critical regulators of postnatal brain
Paper
doi:10.1038/s41588-025-02083-8 -
Cholesterol Dysregulation in APOE4 Astrocytes Promotes α-Synuclein Pathology in miBrains, a Human Brain Tissue Model
Paper
doi:10.1101/2025.02.09.637107
2024
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A multi-region single nucleus transcriptomic atlas of Parkinson’s disease
Paper
doi:10.1038/s41597-024-04117-y -
Myocardial infarction augments sleep to limit cardiac inflammation and damage
Paper
doi:10.1038/s41586-024-08100-w -
Beyond memory impairment: the complex phenotypic landscape of Alzheimer’s disease
Paper
doi:10.1016/j.molmed.2024.04.016 -
Genetic regulation of cell type–specific chromatin accessibility shapes brain disease etiology
Paper
doi:10.1126/science.adh4265 -
Evaluating performance and applications of sample-wise cell deconvolution methods on human brain transcriptomic data
Paper
doi:10.1126/sciadv.adh2588
2023
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Multi-omic profiling of the developing human cerebral cortex at the single-cell level
Paper
doi:10.1126/sciadv.adg3754 -
Interleukin-3 coordinates glial-peripheral immune crosstalk to incite multiple sclerosis
Paper
doi:10.1016/j.immuni.2023.04.013 -
Applications of artificial intelligence−machine learning for detection of stress: a critical overview
Paper
doi:10.1038/s41380-023-02047-6
2021
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Bayesian structural time series for biomedical sensor data: A flexible modeling framework for evaluating interventions
Paper
doi:10.1371/journal.pcbi.1009303 -
DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays
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SCAN-ATAC-Sim: a scalable and efficient method for simulating single-cell ATAC-seq data from bulk-tissue experiments
2020
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STARRPeaker: uniform processing and accurate identification of STARR-seq active regions
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NIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis
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RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins
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An integrative ENCODE resource for cancer genomics
Paper
doi:10.1038/s41467-020-14743-w -
TopicNet: a framework for measuring transcriptional regulatory network change
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DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring
Paper
doi:10.1186/s12859-020-03605-3 -
Epigenome-based splicing prediction using a recurrent neural network
2019
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Building a Hybrid Physical-Statistical Classifier for Predicting the Effect of Variants Related to Protein-Drug Interactions
Paper
doi:10.1016/j.str.2019.06.001 -
MicroRNA-dependent regulation of biomechanical genes establishes tissue stiffness homeostasis
Paper
doi:10.1038/s41556-019-0272-y
2018
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Network Analysis as a Grand Unifier in Biomedical Data Science
Paper
doi:10.1146/annurev-biodatasci-080917-013444
2017
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MicroRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos
Paper
doi:10.1016/j.devcel.2017.02.021
2016
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Oncogenic function and clinical implications of SLC3A2-NRG1 fusion in invasive mucinous adenocarcinoma of the lung
Paper
doi:10.18632/oncotarget.11913
2015
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Intron retention is a widespread mechanism of tumor-suppressor inactivation
Paper
doi:10.1038/ng.3414
2014
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Genetic Variations Associated with Postoperative Recurrence in Stage I Non–Small Cell Lung Cancer
Paper
doi:10.1158/1078-0432.ccr-13-2835
2013
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Pathway-Based Analysis Using Genome-wide Association Data from a Korean Non-Small Cell Lung Cancer Study
Paper
doi:10.1371/journal.pone.0065396
2012
Consortia Large consortium papers (27)
Collaborative work with PsychENCODE, PCAWG, ENCODE, the 1000 Genomes Project and others.
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Transcriptomic sex differences in postmortem brain samples from patients with psychiatric disorders
Paper
doi:10.1126/scitranslmed.adh9974 -
Single-cell genomics and regulatory networks for 388 human brains
Paper
doi:10.1126/science.adi5199 -
Single-cell multi-cohort dissection of the schizophrenia transcriptome
Paper
doi:10.1126/science.adg5136 -
Mapping genomic loci implicates genes and synaptic biology in schizophrenia
Paper
doi:10.1038/s41586-022-04434-5 -
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
Paper
doi:10.1038/s41467-020-18151-y -
Sex differences in oncogenic mutational processes
Paper
doi:10.1038/s41467-020-17359-2 -
Expanded encyclopaedias of DNA elements in the human and mouse genomes
Paper
doi:10.1038/s41586-020-2493-4 -
Perspectives on ENCODE
Paper
doi:10.1038/s41586-020-2449-8 -
A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
Paper
doi:10.1038/s41467-019-13825-8 -
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
Paper
doi:10.1038/s41586-020-1965-x -
Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
Paper
doi:10.1038/s42003-019-0741-7 -
Combined burden and functional impact tests for cancer driver discovery using DriverPower
Paper
doi:10.1038/s41467-019-13929-1 -
Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing
Paper
doi:10.1038/s41588-019-0576-7 -
Comprehensive molecular characterization of mitochondrial genomes in human cancers
Paper
doi:10.1038/s41588-019-0557-x -
Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer
Paper
doi:10.1038/s41588-019-0564-y -
Divergent mutational processes distinguish hypoxic and normoxic tumours
Paper
doi:10.1038/s41467-019-14052-x -
Genomic basis for RNA alterations in cancer
Paper
doi:10.1038/s41586-020-1970-0 -
Genomic footprints of activated telomere maintenance mechanisms in cancer
Paper
doi:10.1038/s41467-019-13824-9 -
High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations
Paper
doi:10.1038/s41467-019-13885-w -
Inferring structural variant cancer cell fraction
Paper
doi:10.1038/s41467-020-14351-8 -
Integrative pathway enrichment analysis of multivariate omics data
Paper
doi:10.1038/s41467-019-13983-9 -
Pan-cancer analysis of whole genomes
Paper
doi:10.1038/s41586-020-1969-6 -
Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition
Paper
doi:10.1038/s41588-019-0562-0 -
Pathway and network analysis of more than 2500 whole cancer genomes
Paper
doi:10.1038/s41467-020-14367-0 -
Patterns of somatic structural variation in human cancer genomes
Paper
doi:10.1038/s41586-019-1913-9 -
Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig
Paper
doi:10.1038/s41467-020-14352-7 -
A global reference for human genetic variation
Paper
doi:10.1038/nature15393