A5002474894- Bioinformatics and Genomic Networks
- Cancer Cells and Metastasis
- Single-cell and spatial transcriptomics
- Genetic factors in colorectal cancer
- Wnt/β-catenin signaling in development and cancer
- CRISPR and Genetic Engineering
- Ferroptosis and cancer prognosis
- RNA and protein synthesis mechanisms
- Fungal and yeast genetics research
- Microbial Metabolic Engineering and Bioproduction
- Cancer Genomics and Diagnostics
- Protein Structure and Dynamics
- Neonatal Respiratory Health Research
- Cancer-related gene regulation
- Aging and Gerontology Research
- Colorectal Cancer Treatments and Studies
- Traditional Chinese Medicine Studies
- RNA modifications and cancer
- Genetics, Aging, and Longevity in Model Organisms
- Galectins and Cancer Biology
- 14-3-3 protein interactions
- Pluripotent Stem Cells Research
- Insurance, Mortality, Demography, Risk Management
- Advanced biosensing and bioanalysis techniques
- Cancer, Lipids, and Metabolism
Institute for Basic Science
2023-2024
Institute of Molecular Biotechnology
2021-2023
Austrian Academy of Sciences
2021-2023
Vienna Biocenter
2022-2023
Seoul National University Bundang Hospital
2023
Pohang University of Science and Technology
2014-2020
// Seong Kyu Han 1 , Dongyeop Lee Heetak Donghyo Kim Heehwa G. Son Jae-Seong Yang 4 Seung-Jae V. 1,2,3 and Sanguk Department of Life Sciences, Pohang University Science Technology, Pohang, Korea 2 IT Convergence Engineering, 3 School Interdisciplinary Bioscience Bioengineering, EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain Correspondence to: Lee, email: Kim, Keywords : web-service, statistics, survival, maximum lifespan, healthspan Received...
Abstract Cancer patient classification using predictive biomarkers for anti-cancer drug responses is essential improving therapeutic outcomes. However, current machine-learning-based predictions of response often fail to identify robust translational from preclinical models. Here, we present a machine-learning framework by taking advantage network-based analyses pharmacogenomic data derived three-dimensional organoid culture The identified our approach accurately predict the 114 colorectal...
Adult stem cells constantly react to local changes ensure tissue homeostasis. In the main body of stomach, chief produce digestive enzymes; however, upon injury, they undergo rapid proliferation for prompt regeneration. Here, we identified p57Kip2 (p57) as a molecular switch reserve cell state in mice. During homeostasis, p57 is expressed but rapidly diminishes after followed by robust proliferation. Both single-cell RNA sequencing and dox-induced lineage tracing confirmed sequential loss...
Abstract Background Previous investigations of transcriptomic signatures cancer patient survival and post-therapy relapse have focused on tumor tissue. In contrast, here we show that in colorectal (CRC) transcriptomes derived from n ormal tissues a djacent to t umors (NATs) are better predictors relapse. Results Using the paired NAT specimens 80 Korean CRC patients retrospectively determined be recurrence or nonrecurrence states, found that, when comparing recurrent with nonrecurrent...
Mice have been widely used as a model organism to investigate human gene–phenotype relationships based on conjecture that orthologous genes generally perform similar functions and are associated with phenotypes. However, phenotypes often turn out be quite different between mouse. Herein, we devised method quantitatively compare annotations mouse models human. Using semantic similarity comparisons, identified phenotype annotations, of which the score is par random gene pairs. Analysis...
The modular architecture of protein-protein interaction (PPI) networks is evident in diverse species with a wide range complexity. However, the molecular components that lead to evolution modularity PPI have not been clearly identified. Here, we show weak domain-linear motif interactions (DLIs) are more likely connect different biological modules than strong domain-domain (DDIs). This division labor essential for complex eukaryotic species. In particular, DLIs may compensate reduction module...
The mammalian intestine is one of the most rapidly self-renewing tissues, driven by stem cells residing at crypt bottom. Paneth form a major element niche microenvironment providing various growth factors to orchestrate intestinal cell homeostasis, such as Wnt3. Different Wnt ligands can selectively activate β-catenin-dependent (canonical) or -independent (noncanonical) signaling. Here, we report that Dishevelled-associated activator morphogenesis 1 (Daam1) and its paralogue Daam2...
Traditional Korean Sasang constitutional (SC) medicine categorizes individuals into four types [Tae-eum (TE), So-eum (SE), Tae-yang (TY), or So-yang (SY)] based on biological and physiological characteristics. As these characteristics are closely related to the bioenergetics of human body, we assessed correlation between SC type energy metabolism features.Forty healthy, young (22.3 ± 1.4 years) males volunteered participate in this study. Participants answered an questionnaire, their face...
Abstract Recent studies have shed light on the signaling pathways required for gastric tissue maintenance and how aberrations in these key lead to cancer development. Although it has been shown that WNT pathway is important epithelial homeostasis, identity source of responsible canonical ligands remain unknown. Furthermore, unclear acquires niche independence - an early step tumorigenesis. Using human mouse organoids vivo models, we found mesenchymal WNT2B WNT7B maintain epithelium...
Abstract Within a protein family, proteins with the same domain often exhibit different cellular functions, despite shared evolutionary history and molecular function of domain. We hypothesized that domain-mediated interactions (DMIs) may categorize family into subfamilies because diversified functions single depend on interacting partners domains. Here we systematically identified DMI subfamilies, in which share domains partners, as well various functional physical interaction networks...
Abstract The generation of conditional alleles using CRISPR technology is still challenging. Here, we introduce a Short Conditional intrON (SCON, 189 bp) that enables the rapid via one-step zygote injection. In this study, total 13 SCON mouse lines were successfully generated by 2 different laboratories. has intronic functions in various vertebrate species, and its target insertion as simple CRISPR/Cas9-mediated gene tagging.
Abstract Image-based lineage tracing enables tissue turnover kinetics and potentials of different adult cell populations to be investigated. Previously, we reported a genetic mouse model system, Red2Onco , which ectopically expressed mutated oncogenes together with red fluorescent proteins (RFP). This system enabled the expansion neighboring effects oncogenic clones dissected. We now report Red2Flpe-SCON: mosaic knockout that uses multicolor reporters label both mutant wild-type cells....
To develop in vitro respiratory models, it is crucial to identify the factors involved epithelial cell differentiation. In this study, we comprehensively analyzed effects of air-liquid interface (ALI) culture on differentiation using single-cell RNA sequencing (scRNA-seq). ALI induced a pronounced shift composition, marked by fivefold increase ciliated cells and reduction more than half basal cells. Transcriptional signatures associated with differentiation, iPathwayGuide software, revealed...
Recent studies have shown that many essential genes (EGs) change their essentiality across various contexts. Finding contextual EGs in pathogenic conditions may facilitate the identification of therapeutic targets. We propose link clustering as an indicator are non-central protein-protein interaction (PPI) networks. In human and yeast PPI networks, we found 29-47% were better characterized by than centrality. Importantly, prone to different cell lines between species. Compared with central...
Abstract The generation of conditional alleles using CRISPR technology is still challenging. Here, we introduce a Short Conditional intrON (SCON, 189 bp) that enables rapid via one-step zygote injection. SCON has intronic function in various vertebrate species and its target insertion as simple CRISPR/Cas9-mediated gene tagging.
Abstract Image-based lineage tracing enables tissue turnover kinetics and potentials of different adult cell populations to be investigated. Previously, we reported a genetic mouse model system, Red2Onco , which ectopically expressed mutated oncogenes together with red fluorescent proteins (RFP). This system enabled the expansion neighboring effects oncogenic clones dissected. We now report Red2Flpe-SCON: new mosaic knockout that uses multicolor reporters label both mutant wild-type cells....
Abstract The mammalian intestine is one of the most rapidly self-renewing tissues, driven by actively cycling stem cells residing at crypt bottom 1,2 . Together with stromal cells, Paneth form a major element niche microenvironment that provides various growth factors to orchestrate intestinal cell homeostasis, such as Wnt3 3 With 19 family members, different Wnt ligands can selectively activate β-catenin dependent (canonical) or independent (non-canonical) signaling 4,5 Here, we report...
Essential genes (EGs) often form central nodes in protein-protein interaction (PPI) networks. However, many reports have shown that numerous EGs are non-central, suggesting another principle governs gene essentiality. We propose link clustering as a distinct indicator of the essentiality for non-central nodes. Specifically, various human and yeast PPI networks, we found 29 to 47% were better characterized by than centrality. Such with clustered links significant impacts on communities at...
Abstract Identifying cancer type-specific driver mutations is crucial for illuminating distinct pathologic mechanisms across various tumors and providing opportunities of patient-specific treatment. However, although many computational methods were developed to predict in a manner, the still have room improve. Here, we devise novel feature based on sequence co-evolution analysis identify construct machine learning (ML) model with state-of-the-art performance. Specifically, relying 28 000...