Principal Investigator
Alumni
HUNGOO LEE
Assistant Professor at Johns Hopkins School of Medicine (from Sep. 2024)
He has been studying molecular mechanisms of epigenetic abnormalities by the expanded long tandem repeats in Fragile X syndrome. During his Postdoc in Dr. Jeannie Lee’s lab at Harvard Medical School, he identified the molecular mechanisms that can induce the shortening of the pathogenic long tandem repeats in Fragile X patient cells. Before his postdoc, he earned his Ph.D. in epigenetics and molecular biology in the laboratory of Dr. Vincenzo Pirrotta, where his dissertation work focused on the genome-wide epigenetic regulatory roles of Polycomb group proteins and Trithorax group proteins especially at the intergenic regions. Before his Ph.D., he worked as a computational biologist at Dong-a Seetech IT company and studied a condition-specific transcriptional regulatory network in yeast. By combining his diverse background in computational biology, epigenetics, and molecular biology, he plans to tackle the diverse repeat expansion diseases including Huntington's, Myotonic Dystrophy, Friedreich's ataxia, ALS, and other autism spectrum disorders by understanding why the patients show increased repeat instability.
Contact: hlee308 at jh dot edu
Miller Research Building Room 449
RUOYAN PU
Research Technologist
M.Sc. Biomedical Engineering, Johns Hopkins University
B.S. Neuroscience, Simmons University
She is interested in the epigenetic changes associated with neurological disorders, including Autism spectrum disorders (ASD) and Alzheimer’s disease (AD). Her research also focuses on the use of induced pluripotent stem cells (iPSCs), and explores their applications in disease modeling. Previously, she investigated the correlation between COVID-19 infection and Alzheimer’s disease pathology using the iPSC model. She joined H. Lee lab to study repeat expansion disorders (REDs) and explore potential therapeutic methods for these diseases.
SHREYAN URHEKAR
Research Assistant
M.Sc. Biotechnology, Johns Hopkins University
Bachelor of Technology in Biotechnology, D. Y. Patil University
He is interested in understanding the molecular basis of CGG repeat expansion disorders, particularly in fragile X syndrome, by applying a diverse combination of technologies from immunology, biophysical characterization, and iPSCs. Previously, he worked on biophysical characterizations of proteins in the ubiquitin-proteasome pathway and studied the molecular dynamics of pioneer factors in histone methylation patterns. He joined the H. Lee lab to further explore repeat expansion disorders (REDs) and contribute to developing potential therapeutic strategies
DENA SAGHAI MAROOF
PhD Student (Human Genetics and Genomics)
B.S Biology, University of Virginia
She is interested in identifying RNA-mediated epigenetic mechanisms driven by repeat expansions in neurological disease with a focus on amyotrophic lateral sclerosis (ALS). Her work examines the interplay between R-loops, G-quadruplex structures, and epigenetic modifications using computational and experimental approaches. Previously, she sought to unravel the genetic architecture of type 1 diabetes and molecular mechanisms of cystic fibrosis.
She joined the H. Lee laboratory to study repeat expansion-mediated pathology in ALS and to integrate insights across repeat expansion disorders for therapeutic development.
YUXIN JIN
Master Student (Biochemistry and Molecular Biology)
B.Sc. in Biomedical Sciences, The Chinese University of Hong Kong
She is interested in applying genome-editing approaches to understand the molecular mechanisms underlying repeat expansion disorders and to develop potential therapeutic strategies. Previously, she developed in vitro models of neurodevelopmental disorders by applying CRISPR base editing and prime editing to introduce monoallelic, disease-associated DHX9 variants in human embryonic stem cells. She joined the H. Lee Lab to investigate base-editing strategies targeting pathogenic repeats in amyotrophic lateral sclerosis and fragile X syndrome, and to understand the molecular mechanisms that shape editing outcomes. Using patient-derived iPSCs and neuronal models, she evaluates repeat remodeling, editing mechanisms, and transcriptional outcomes following genome editing with different delivery approaches.
ISSAC LOCK
PhD Student (Human Genetics and Genomics)
B.S. Biological Engineering and Philosophy, Massachusetts Institute of Technology
Isaac is interested in the mechanisms of repeat instability and pathogenesis across repeat expansion disorders. His work focuses on X-Linked Dystonia Parkinsonism (XDP), where he is trying to understand the role of a repeat expansion, and explore mitigation strategies using CRISPR-based technologies. Previously, he used an engineered CRISPRi system to investigate gene regulatory networks related to key genes on the X and Y chromosomes. Alongside his lab work, Isaac also works with Debra Mathews, a bioethicist at the Johns Hopkins Berman Institute of Bioethics to explore ethical issues in translating CRISPR-based systems into clinical treatment options.
HongLi Liu
Master’s Student (Biochemistry and Molecular Biology)
B.S. Biological Science, South China Agricultural University & University College Dublin
He is interested in understanding how genetic and genomic variation influences gene regulation during human brain development and contributes to neurodevelopmental disorders. His work combines computational genomics and functional experiments to interrogate repetitive DNA elements across both disease discovery and mechanistic validation. Currently, he is developing a computational pipeline to identify autism-associated transposable element variations using family-based whole-genome sequencing cohorts, while experimentally investigating targeted dCas9-mediated R-loop induction to drive repeat contraction and epigenetic rescue in Fragile X syndrome. Previously, he analyzed single-cell transcriptomic atlases of cortical circuitry in the Anterior Cingulate Cortex region. He joined the H. Lee laboratory to bridge computational and molecular approaches in unraveling repeat-associated genomic mechanisms in neurodevelopment.
SOOJI PARK
Postdoctoral Fellow
Ph.D. Biomedical Sciences, Korea University
B.S. Life Science, Kyonggi University
She has developed a strong foundation in molecular biology and genome engineering, with a particular focus on advancing CRISPR-based technologies. During her doctoral training, she designed CMP-PE-V1 and eCas12f1, enabling more efficient and versatile manipulation of genomic targets. She applied these CRISPR tools across diverse biological contexts, including genome editing, transcriptional regulation, targeted cancer therapy, and mouse disease models.
She joined the H. Lee lab as a postdoctoral fellow to extend her research into the biology of DNA repeat expansion disorders (REDs). Her current work leverages CRISPR-based genome engineering to generate diverse cellular models for systematically analyzing repeat expansion and contraction. Through these models, she aims to identify key genetic and epigenetic factors that drive repeat instability and to elucidate the underlying molecular mechanisms.
With a particular interest in REDs associated with autism spectrum disorders (ASD), her long-term research goal is to integrate genome engineering, epigenetics, and stem cell biology to uncover fundamental principles of repeat instability and to translate these insights into precise and effective therapeutic strategies for currently incurable disorders.