Eunjung Alice Lee

Hybrid transcriptome assembly and annotation of Japanese macaque prefrontal cortex

The paper presents a hybrid transcriptome assembly and annotation of Japanese macaque prefrontal cortex using short- and long-read RNA sequencing data.

Recurrent patterns of TOP1-mediated neuronal genomic damage shared by major neurodegenerative disorders

The paper identifies a shared TOP1-mediated mutagenic mechanism in ALS, FTD, and AD through single-cell genomic analysis and experimental validation.

Inverted Alu repeats in loop-out exon skipping across hominoid evolution

The paper identifies inverted Alu pairs that promote exon skipping through RNA stem-loop structures and shows their evolutionary significance in hominoid genomes.

STRUMP-I: Structure-based machine learning approach to pMHC-I binding prediction using force field energy features

STRUMP-I improves pMHC-I binding prediction by using force-field energy features, outperforming sequence-based methods on underrepresented MHC alleles and showing synergy with them.

Activating Ras-MAPK pathway variants drive hippocampal clonal competition in human epilepsy

This study identifies somatic Ras-MAPK pathway variants in hippocampal tissue from patients with drug-resistant epilepsy, showing their association with clonal competition and worse surgical outcomes.

Benchmarking of duplex sequencing approaches to reveal somatic mutation landscapes

This study benchmarks six duplex sequencing technologies to evaluate their performance in detecting somatic mutations across different genomic contexts and tissue types.

Diverse somatic genomic alterations in single neurons in chronic traumatic encephalopathy

The paper identifies somatic genomic alterations in neurons from CTE patients, finding patterns similar to Alzheimer's disease and suggesting mechanisms beyond repetitive head impacts.

Image-based DNA Sequencing Encoding for Detecting Low-Mosaicism Somatic Mobile Element Insertions

RetroNet detects low-mosaicism somatic mobile element insertions using deep learning on sequencing read images, achieving high precision and recall with minimal reads.

Multi-platform framework for mapping somatic retrotransposition in human tissues

The paper develops a framework to detect and trace somatic retrotransposition events in human tissues, identifying rare L1 insertions and improving detection accuracy.

VEGFR2 blockade overcomes acquired KRAS G12D inhibitor resistance driven by PI3Kγ activation

This paper identifies VEGFA-VEGFR2 signaling driven by PI3Kγ activation as a mechanism of acquired resistance to KRAS G12D inhibitors and shows that blocking this pathway restores drug sensitivity in resistant cancer models.

High resolution kinematic approach for quantifying impaired mobility of dystrophic zebrafish larvae

This paper develops a high-resolution kinematic method to quantify impaired mobility in dystrophic zebrafish larvae, finding significant differences in swimming performance between mutants and wild-types.

Cell-type-specific patterns and consequences of somatic mutation in development and aging brain

The paper introduces Duplex-Multiome, a method to identify cell-type-specific somatic mutations in brain tissue, revealing age-related mutation patterns and developmental lineage relationships.

Clonal Hematopoiesis Mutations Increase Risk of Alzheimer's Disease with APOE ϵ3/ϵ3 Genotype

This study finds that Alzheimer's disease patients have more clonal hematopoiesis mutations than controls, especially those with APOE ε3/ε3 genotype, suggesting a risk factor independent of APOE ε4.

Maternal obesity and offspring neurodevelopment are associated with hypoxic gene expression in term human placenta

The paper links maternal obesity to hypoxia gene expression in term placenta and its association with offspring neurodevelopmental outcomes.

Metabolomic and transcriptomic signature in Kabuki syndrome

This study identifies metabolomic and transcriptomic signatures in Kabuki syndrome patients, revealing altered metabolites and pathways that could serve as biomarkers for early detection.

Multi-omic analysis of the ciliogenic transcription factor RFX3 reveals a role in promoting activity-dependent responses via enhancing CREB binding in human neurons

This study investigates RFX3's role in human neurons, showing that monoallelic loss disrupts synaptic gene expression and activity-dependent responses by impairing CREB binding.

Chromosomal rearrangements and instability caused by the LINE-1 retrotransposon

This study uses whole-genome sequencing to show that LINE-1 retrotransposition directly causes chromosomal rearrangements and instability in cancer genomes.

A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders

The paper develops a cell type-aware framework to identify non-coding variants in Mendelian disorders by integrating single-cell multi-omic data and applying it to congenital cranial dysinnervation disorders.

Somatic cancer driver mutations are enriched and associated with inflammatory states in Alzheimer's disease microglia

The paper identifies somatic driver mutations in microglia of Alzheimer's disease brains, showing increased clonal expansion and inflammatory signatures.

ATM-deficiency induced microglial activation promotes neurodegeneration in Ataxia-Telangiectasia

This study shows that ATM deficiency causes microglial activation, which contributes to neurodegeneration in Ataxia-Telangiectasia by inducing cytotoxicity in neurons.

Somatic mosaicism in amyotrophic lateral sclerosis and frontotemporal dementia identifies focal mutations associated with widespread degeneration

The paper identifies rare somatic mutations in sporadic ALS and FTD cases, suggesting they contribute to disease and widespread neurodegeneration.

Characterizing the molecular impact of KMT2D variants on the epigenetic and transcriptional landscapes in Kabuki Syndrome

This study examines how KMT2D mutations affect histone modifications and gene expression in PBMCs from KS patients, identifying altered enhancer activity and transcriptional changes linked to immune and metabolic gene dysregulation.

Enrichment of somatic mutations in schizophrenia brain targets prenatally active transcription factor bindings sites

The paper identifies prenatal mutational processes in schizophrenia brains linked to transcription factor binding sites and proposes a new term 'skiagenesis' for these mutations.

Whole-genome analysis of de novo and polymorphic retrotransposon insertions in Autism Spectrum Disorder

This study identifies de novo and polymorphic retrotransposon insertions in ASD families, finding increased exonic and intronic insertions in ASD cases compared to controls.

HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data

HiTea uses Hi-C data to detect non-reference transposable element insertions, outperforming whole genome sequencing-based methods in human cell lines.

Parallel RNA and DNA analysis after Deep-sequencing (PRDD-seq) reveals cell type-specific lineage patterns in human brain

PRDD-seq simultaneously reconstructs cell type, lineage, and birthdate in human brain tissue by analyzing RNA and DNA mutations in single cells.

Genomic footprints of activated telomere maintenance mechanisms in cancer

The paper analyzes whole-genome sequencing data from cancer samples to identify genomic footprints of telomere maintenance mechanisms, finding specific telomere variant repeat patterns associated with ATRX/DAXX mutations.

Spatial Genome Organization as a Framework for Somatic Alterations in Human Cancer

The paper examines how somatic structural variations affect TAD boundaries and gene regulation in human cancers using whole genome sequencing data.

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

This study analyzes chromothripsis in 2,658 cancers using whole-genome sequencing, finding it prevalent across multiple cancer types with complex structural alterations.

Evidence that APP gene copy number changes reflect recombinant vector contamination

The paper reanalyzes data from a study claiming somatic APP gene copy number gains in AD neurons, finding evidence of contamination by recombinant vectors instead of true somatic retrotransposition.