A5028639165- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Cancer Cells and Metastasis
- MicroRNA in disease regulation
- Cancer Immunotherapy and Biomarkers
- Cancer Genomics and Diagnostics
- Immune Cell Function and Interaction
- Cancer-related Molecular Pathways
- Genetic Mapping and Diversity in Plants and Animals
- Computational Drug Discovery Methods
- Cell Image Analysis Techniques
- Cancer-related molecular mechanisms research
- Gene Regulatory Network Analysis
- CAR-T cell therapy research
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Lung Cancer Research Studies
- Advanced Breast Cancer Therapies
- Genomics and Phylogenetic Studies
- Reproductive Biology and Fertility
- Cancer Research and Treatments
- CRISPR and Genetic Engineering
- PARP inhibition in cancer therapy
- Ubiquitin and proteasome pathways
- Immune cells in cancer
- Lung Cancer Treatments and Mutations
CHA University
2017-2025
Yonsei University
2011-2025
CHA Bundang Medical Center
2017-2025
The University of Texas at Austin
2014-2018
Catholic University of Daegu
2016
Seoul National University
2003
Abstract The success of clinical genomics using next generation sequencing (NGS) requires the accurate and consistent identification personal genome variants. Assorted variant calling methods have been developed, which show low concordance between their calls. Hence, a systematic comparison callers could give important guidance to NGS-based genomics. Recently, set high-confident calls for one individual (NA12878) has published by Genome in Bottle (GIAB) consortium, enabling performance...
Human gene networks have proven useful in many aspects of disease research, with numerous network-based strategies developed for generating hypotheses about gene-disease-drug associations. The ability to predict and organize genes most relevant a specific has especially important. We previously human functional network, HumanNet, by integrating diverse types omics data using Bayesian statistics framework demonstrated its retrieve genes. Here, we present HumanNet v2...
Abstract Immune checkpoint blockade is promising for treating non-small-cell lung cancer (NSCLC). We used multipanel markers to predict the response immune inhibitors (ICIs) by characterizing gene expression signatures or individual genes in patients who showed durable clinical benefit ICIs. Twenty-one with NSCLC treated single-agent anti-programmed cell death protein (PD)-1 antibody were analyzed and their clinicopathological characteristics ICIs characterized. Nine (43%) a (DCB), while...
Rice (Oryza sativa) is a staple food for more than half the world and model studies of monocotyledonous species, which include cereal crops candidate bioenergy grasses. A major limitation crop production imposed by suite abiotic biotic stresses resulting in 30%-60% yield losses globally each year. To elucidate stress response signaling networks, we constructed an interactome 100 proteins yeast two-hybrid (Y2H) assays around key regulators rice responses. We validated using protein-protein...
Arabidopsis thaliana is a reference plant that has been studied intensively for several decades. Recent advances in high-throughput experimental technology have enabled the generation of an unprecedented amount data from A. thaliana, which facilitated data-driven approaches to unravel genetic organization phenotypes. We previously published description genome-scale functional gene network AraNet, was constructed by integrating multiple co-functional networks inferred diverse types, and we...
Rice is a staple food for one-half the world's population and model other monocotyledonous species. Thus, efficient approaches identifying key genes controlling simple or complex traits in rice have important biological, agricultural, economic consequences. Here, we report on construction of RiceNet, an experimentally tested genome-scale gene network Many different datasets, derived from five organisms including plants, animals, yeast, humans, were evaluated, 24 most useful integrated into...
Breast cancer represents the number one global burden in women and hormone receptor (HR)-positive subtype comprises approximately 70% of breast cancers. Unfortunately, acquired resistance ultimately occurs almost all cases, even though cyclin-dependent kinase 4 6 (CDK4/6) inhibitors are a highly effective therapy for HR-positive/human epidermal growth factor 2-negative subtype. Here, we investigated mechanisms to CDK4/6 inhibitor potential therapeutic strategies using our...
The use of high-throughput array and sequencing technologies has produced unprecedented amounts gene expression data in central public depositories, including the Gene Expression Omnibus (GEO). immense amount GEO provides both vast research opportunities analysis challenges. Co-expression high-dimensional proven effective for study functions, several co-expression databases have been developed. Here, we present a new database, COEXPEDIA (www.coexpedia.org), which is distinctive from other...
Background: Exosomes are extracellular microvesicles that released by most cells and widely distributed in various body fluids.Malignant secrete large amounts of exosomes containing molecular constituents reflecting the originating tumor.We investigated difference microRNA (miRNA) expression serum from patients with benign, borderline malignant ovarian masses to assess diagnostic relevance exosomal miRNAs as biomarkers for preoperative diagnosis carcinoma.Methods: A total 68 cases were...
Rice is the most important staple food crop and a model grass for studies of bioenergy crops. We previously published genome-scale functional network server called RiceNet, constructed by integrating diverse genomics data demonstrated use in genetic dissection rice biotic stress responses its usefulness other species. Since initial construction network, there has been significant increase amount publicly available data. Here, we present an updated prioritization Oryza sativa ssp. japonica,...
Saccharomyces cerevisiae, i.e. baker's yeast, is a widely studied model organism in eukaryote genetics because of its simple protocols for genetic manipulation and phenotype profiling. The high abundance publicly available data that has been generated through diverse 'omics' approaches led to the use yeast many systems biology studies, including large-scale gene network modeling better understand molecular basis cellular phenotype. We have previously developed genome-scale YeastNet v2, which...
High-throughput experimental technologies gradually shift the paradigm of biological research from hypothesis-validation toward hypothesis-generation science. Translating diverse types large-scale data into testable hypotheses, however, remains a daunting task. We previously demonstrated that heterogeneous genomics can be integrated single genome-scale gene network with high prediction power for ribonucleic acid interference (RNAi) phenotypes in Caenorhabditis elegans, popular metazoan model...
Soybean (Glycine max) is a legume crop with substantial economic value, providing source of oil and protein for humans livestock. More than 50% edible oils consumed globally are derived from this crop. plants also important soil fertility, as they fix atmospheric nitrogen by symbiosis microorganisms. The latest soybean genome annotation (version 2.0) lists 56 044 coding genes, yet their functional contributions to traits remain mostly unknown. Co-functional networks have proven useful...
High-grade serous carcinoma (HGSCa) of the ovary is featured by TP53 gene mutation. Missense or nonsense mutation types accompany most cases HGSCa that correlate well with immunohistochemical (IHC) staining results-an all (missense) none (nonsense) pattern. However, some IHCs produce subclonal mosaic patterns from which types, including wild type gene, cannot be clearly deduced. We analyzed a total 236 ovarian and tumors other histology matching results p53 IHC targeted next-generation...
Ubiquitin-specific protease 7 (USP7) is one of the deubiquitinating enzymes (DUBs) in ubiquitin-specific (USP) family. It a key regulator numerous cellular functions including immune response, cell cycle, DNA damage and repair, epigenetics, several signaling pathways. USP7 acts by removing ubiquitin from substrate proteins. also binds to specific binding motif proteins having [P/A/E]-X-X-S or K-X-X-X-K protein sequences. To date, have been identified, but no studies conducted using that...
Laboratory mouse, Mus musculus, is one of the most important animal tools in biomedical research. Functional characterization mouse genes, hence, has been a long-standing goal mammalian and human genetics. Although large-scale knockout phenotyping under progress by international collaborative efforts, large portion genome still poorly characterized for cellular functions associations with disease phenotypes. A genome-scale functional network MouseNet, was previously developed context...
Abstract ZEB1 has intrinsic oncogenic functions that control the epithelial-to-mesenchymal transition (EMT) of cancer cells, impacting tumorigenesis from its earliest stages. By integrating microenvironment signals and being implicated in feedback regulatory loops, appears to be a central switch determines EMT metastasis cells. Here, we found collaborates with ELK3, ternary complex factor belonging ETS family, repress E-cadherin expression. as transcriptional activator ELK3. We first...
Abstract Pseudomonas aeruginosa is a Gram-negative bacterium of clinical significance. Although the genome PAO1, prototype strain P. , has been extensively studied, approximately one-third functional remains unknown. With emergence antibiotic-resistant strains there an urgent need to develop novel antibiotic and anti-virulence strategies, which may be facilitated by approach that explores gene function in systems-level models. Here, we present genome-wide network genes, PseudomonasNet,...
Triple-negative breast cancer (TNBC) refers to that does not have receptors for estrogen, progesterone, and HER2 protein. TNBC accounts 10–20% of all cases cancers is characterized by its metastatic aggressiveness, poor prognosis, limited treatment options. Here, we show the nature critically regulated a functional link between miR-200a transcription factor ELK3. We found expression levels ELK3 mRNA were negatively correlated in luminal subtypes cells. In vitro experiments revealed directly...
Abstract While mitochondria are known to be essential for intracellular energy production and overall function, emerging evidence highlights their role in influencing cell behavior through mitochondrial transfer. This phenomenon provides a potential basis the development of treatment strategies tissue damage degeneration. study aims evaluate whether isolated from osteoblasts can promote osteogenic differentiation mesenchymal stem cells (MSCs). Mitochondria MSCs, which primarily utilize...