A5026578909- Single-cell and spatial transcriptomics
- Gene Regulatory Network Analysis
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- RNA Research and Splicing
- RNA modifications and cancer
- Cancer-related gene regulation
- Pancreatic function and diabetes
- Peptidase Inhibition and Analysis
- Genetics and Neurodevelopmental Disorders
- RNA and protein synthesis mechanisms
- Endoplasmic Reticulum Stress and Disease
- Histone Deacetylase Inhibitors Research
- Epigenetics and DNA Methylation
- Computational Drug Discovery Methods
- Advanced Cellulose Research Studies
- Noise Effects and Management
- Neuroinflammation and Neurodegeneration Mechanisms
- TGF-β signaling in diseases
- Electrospun Nanofibers in Biomedical Applications
- Cancer Genomics and Diagnostics
- CRISPR and Genetic Engineering
- Extracellular vesicles in disease
- Cell Image Analysis Techniques
- Digital Rights Management and Security
Electronics and Telecommunications Research Institute
2006-2025
Korea Institute of Science and Technology
2024-2025
Soongsil University
2020-2024
Inha University
2024
University of Copenhagen
2018-2023
Cedars-Sinai Medical Center
2023
Seoul National University
2004-2022
Chungbuk National University
2019-2022
Novo Nordisk Foundation
2018-2021
University of Pennsylvania
2012-2020
Abstract Single-cell omics technologies have revolutionized molecular profiling by providing high-resolution insights into cellular heterogeneity and complexity. Traditional bulk approaches average signals from heterogeneous cell populations, thereby obscuring important nuances. studies enable the analysis of individual cells reveal diverse types, dynamic states, rare populations. These techniques offer unprecedented resolution sensitivity, enabling researchers to unravel landscape cells....
Cellular behavior is determined not by a single molecule but many molecules that interact strongly with one another and form complex network. It unclear whether cellular can be controlled regulating certain molecular components in the By analyzing variety of biomolecular regulatory networks, we discovered only small fraction network need to regulated govern dynamics control behavior. We defined minimal set must make cell reach desired stable state as kernel developed general algorithm for...
To process large-scale single-cell RNA-sequencing (scRNA-seq) data effectively without excessive distortion during dimension reduction, we present SHARP, an ensemble random projection-based algorithm that is scalable to clustering 10 million cells. Comprehensive benchmarking tests on 17 public scRNA-seq sets show SHARP outperforms existing methods in terms of speed and accuracy. Particularly, for large-size (more than 40,000 cells), runs faster other competitors while maintaining high...
Abstract Understanding the specific survival of rare chronic myelogenous leukaemia (CML) stem cell population could provide a target for therapeutics aimed at eradicating these cells. However, little is known about how signalling regulated in CML In this study, we survey global metabolic differences between murine normal haematopoietic cells (HSCs) and using metabolomics techniques. Strikingly, show that accumulate significantly higher levels certain dipeptide species than HSCs. Once...
Recent advances in genome and transcriptome analysis have contributed to the identification of many potential cancer-related genes. Furthermore, biological clinical investigations candidate genes provide us with a better understanding carcinogenesis development cancer treatment. Here, we report novel role KIAA1324 as tumor suppressor gastric cancer. We observed that was downregulated most cancers from sequencing data found histone deacetylase involved suppression KIAA1324. Low levels were...
Triple-negative breast cancer (TNBC) is considered incurable with currently available treatments, highlighting the need for therapeutic targets and predictive biomarkers. Here, we report a unique role Bcl-2-associated athanogene 2 (BAG2), which significantly overexpressed in TNBC, regulating dual functions of cathepsin B as either pro- or anti-oncogenic enzyme. Silencing BAG2 suppresses tumorigenesis lung metastasis induces apoptosis by increasing intracellular mature form B, whereas...
Cells have evolved their communication methods to sense microenvironments and send biological signals. In addition using ligands receptors, cells use diverse channels including gap junctions communicate with immediate neighbors. Current approaches, however, cannot effectively capture the influence of various microenvironments. Here, we propose a novel approach investigate cell neighbor-dependent gene expression (CellNeighborEX) in spatial transcriptomics (ST) data. To categorize based on...
Development of multicellular organisms is orchestrated by persistent cell-cell communication between neighboring partners. Direct interaction different cell types can induce molecular signals that dictate lineage specification and fate decisions. Current single-cell RNA-seq technology cannot adequately analyze contact-dependent gene expression, mainly due to the loss spatial information. To overcome this obstacle resolve contact-specific expression during embryogenesis, we performed RNA...
An algorithmic approach enables the simplification of complex signaling networks and identifies potential therapeutic targets.
Constitutive heterochromatin undergoes a dynamic clustering and spatial reorganization during myogenic differentiation. However the detailed mechanisms its role in cell differentiation remain largely elusive. Here, we report identification of muscle-specific long non-coding RNA, ChRO1, involved constitutive reorganization. ChRO1 is induced terminal myoblasts, specifically localized to chromocenters myotubes. required for efficient differentiation, with global impacts on gene expression. It...
Abstract Accurate prediction of gene regulatory rules is important towards understanding cellular processes. Existing computational algorithms devised for bulk transcriptomics typically require a large number time points to infer networks (GRNs), are applicable small genes and fail detect potential causal relationships effectively. Here, we propose novel approach ‘TENET’ reconstruct GRNs from single cell RNA sequencing (scRNAseq) datasets. Employing transfer entropy (TE) measure the amount...
Abstract Bone undergoes a constant and continuous remodeling process that is tightly regulated by the coordinated sequential actions of bone-resorbing osteoclasts bone-forming osteoblasts. Recent studies have shown histone demethylases are implicated in osteoblastogenesis; however, little known about role osteoclast formation. Here, we identified KDM4B as an epigenetic regulator differentiation. Knockdown significantly blocked formation tartrate-resistant acid phosphatase-positive...
Abstract Although accumulating evidence indicates that alternative splicing is aberrantly altered in many cancers, the functional mechanism remains to be elucidated. Here, we show epithelial and mesenchymal isoform switches of leucine-rich repeat Fli-I-interacting protein 2 (LRRFIP2) regulated by regulatory 1 (ESRP1) correlate with metastatic potential gastric cancer cells. We found expression variants LRRFIP2 was closely correlated ESRP1 . Surprisingly, ectopic (variant 3) dramatically...
KIAA1324 is a transmembrane protein largely reported as tumor suppressor and favorable prognosis marker in various cancers, including gastric cancer. In this study, we report the role of N-linked glycosylation functional post-translational modification (PTM). Loss eliminated potential to suppress cancer cell proliferation migration. Furthermore, demonstrated that undergoes fucosylation, N-glycan mediated by fucosyltransferase, inhibition fucosylation also significantly suppressed...
Abstract More than half of tumor patients with high PD-L1 expression do not respond to anti-PD-1/PD-L1 therapy, and the underlying mechanisms are yet be clarified. Here we show that developmentally regulated GTP-binding protein 2 (DRG2) is required for response PD-L1-expressing tumors anti-PD-1 therapy. DRG2 depletion enhanced IFN-γ signaling increased level in melanoma cells. However, it inhibited recycling endosomal reduced surface levels, which led defects interaction PD-1. Anti-PD-1 did...
Biological pathways can provide key information on the organization of biological systems. ArrayXPath (http://www.snubi.org/software/ArrayXPath/) is a web-based service for mapping and visualizing microarray gene-expression data integrated pathway resources using Scalable Vector Graphics (SVG). By integrating major bio-databases searching resources, automatically maps different types identifiers from probes elements. When one inputs clusters, produces list best matching each cluster. We...
Abstract Transitional hypoglycemia in normal newborns occurs the first 3 days of life and has clinical features consistent with hyperinsulinism. We found a lower threshold for glucose-stimulated insulin secretion from freshly isolated embryonic day (E) 22 rat islets, which persisted into postnatal days. The reached adult level by (P) 14. Culturing P14 islets also decreased glucose threshold. Freshly P1 had response to 2-aminobicyclo-(2, 2, 1)-heptane-2-carboxylic acid, nonmetabolizable...
ArrayXPath (http://www.snubi.org/software/ArrayXPath/) is a web-based service for mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics (SVG). Deciphering the crosstalk among pathways integrating biomedical ontologies knowledge bases may help interpretation of data. empowered by gene-pathway, disease-pathway, drug-pathway pathway-pathway correlations Gene Ontology, Medical Subject Headings OMIM Morbid Map-based...
The co-regulation of transcription factors (TFs) has been widely observed in various species. Why is such a mechanism needed for transcriptional regulation? To answer this question, the following experiments and analyses were performed. First, examination human gene regulatory network (GRN) indicated that was significantly enriched GRN. Second, mathematical simulation an artificial showed related to biphasic dose-response patterns TFs. Third, relationship between pattern confirmed using...