A5090632282- Plant Molecular Biology Research
- Bioinformatics and Genomic Networks
- Plant Gene Expression Analysis
- Gene expression and cancer classification
- Plant Genetic and Mutation Studies
- Photosynthetic Processes and Mechanisms
- Metabolomics and Mass Spectrometry Studies
- Silicon Effects in Agriculture
- Genetic Mapping and Diversity in Plants and Animals
- CRISPR and Genetic Engineering
- Plant biochemistry and biosynthesis
- RNA Research and Splicing
- Cancer-related molecular mechanisms research
- Plant nutrient uptake and metabolism
- Time Series Analysis and Forecasting
- Artificial Intelligence in Healthcare
- Plant-Microbe Interactions and Immunity
- Connective Tissue Growth Factor Research
- Bone health and osteoporosis research
- Neuroinflammation and Neurodegeneration Mechanisms
- Agriculture and Farm Safety
- Developmental Biology and Gene Regulation
- RNA modifications and cancer
- Tryptophan and brain disorders
- Wnt/β-catenin signaling in development and cancer
University of Suwon
2020-2025
Green Cross (South Korea)
2023
Seoul National University
2013-2020
Allen Institute for Brain Science
2015
Icahn School of Medicine at Mount Sinai
2011-2015
Depression and anxiety disorders are more prevalent in females, but the majority of research animal models, first step finding new treatments, has focused predominantly on males. Here we report that exposure to subchronic variable stress (SCVS) induces depression-associated behaviors female mice, whereas males resilient as they do not develop these behavioral abnormalities. In concert with different responses, transcriptional analysis nucleus accumbens (NAc), a major brain reward region, by...
The neurobiological underpinnings of mood and anxiety disorders have been linked to the nucleus accumbens (NAc), a region important in processing rewarding emotional salience stimuli. Using chronic social defeat stress, an animal model disorders, we investigated whether alterations synaptic plasticity are responsible for long-lasting behavioral symptoms induced by this form stress. We hypothesized that stress alters strength or connectivity medium spiny neurons (MSNs) NAc induce avoidance....
Background/Objectives: Vitamin D deficiency (VDD) is a global health concern associated with metabolic disease and immune dysfunction. Despite known risk factors like limited sun exposure, diet, lifestyle, few studies have explored these comprehensively on large scale. This cross-sectional study aimed to identify VDD-associated in South Korea via an integrative approach of machine learning statistical analyses using National Health Nutrition Examination Survey (KNHANES) IX-1 data. Methods:...
This study is to investigate at the molecular level how a transgenic version of Nipponbare obtained drought resistance phenotype. Using multi-omics sequencing data, we compared wild-type rice (WT) and (erf71) that obtains drought-resistance phenotype by overexpressing OsERF71, one AP2/ERF transcription factor families. A comprehensive bioinformatics analysis pipeline, including networks cascade tree, was developed for data. The results showed presence OsERF71 source network controlled global...
Abstract Background In cancer, mutations of DNA methylation modification genes have crucial roles for epigenetic modifications genome-wide, which lead to the activation or suppression important including tumor suppressor genes. Mutations on modifiers could affect enzyme activity, would result in difference genome-wide profiles and, downstream Therefore, we investigated effect such as DNMT1, DNMT3A, MBD1, MBD4, TET1, TET2 and TET3 through a pan-cancer analysis. Methods First, profiles. We...
Abstract Motivation Identifying biologically meaningful gene expression patterns from time series data is important to understand the underlying biological mechanisms. To identify significantly perturbed sets between different phenotypes, analysis of transcriptome requires consideration and sample dimensions. Thus, such seeks search that exhibit similar or two more conditions, constituting three-dimensional data, i.e. gene-time-condition. Computational complexity for analyzing very high,...
Abstract Human pluripotent stem cells (hPSCs) have promising therapeutic applications due to their infinite capacity for self-renewal and pluripotency. Genomic stability is imperative the clinical use of hPSCs; however, copy number variation (CNV), especially recurrent CNV at 20q11.21, may contribute genomic instability hPSCs. Furthermore, effects CNVs in hPSCs whole-transcriptome scale are poorly understood. This study aimed examine functional vivo vitro frequently detected 20q11.21 during...
Drought tolerance is an important trait related to growth and yield in crop. Until now, drought research has focused on coding genes. However, non-coding RNAs also respond significantly environmental stimuli such as stress. Unfortunately, characterizing the role of siRNAs under stress difficult since a large number heterogenous siRNA species are expressed have very weak evolutionary conservation. Thus, characterize siRNAs, we need well designed biological bioinformatics strategy. In this...
MicroRNAs, small noncoding RNAs, are conserved in many species, and they key regulators that mediate post-transcriptional gene silencing. Since biologists cannot perform experiments for each of target genes thousands microRNAs numerous specific conditions, prediction on microRNA has been extensively investigated. A general framework is a two-step process selecting candidates based sequence binding energy features then predicting targets negative correlation their targets. However, there few...
Transcription factor (TF) has a significant influence on the state of cell by regulating multiple down-stream genes. Thus, experimental and computational biologists have made great efforts to construct TF gene networks for regulatory interactions between TFs their target Now, an important research question is how utilize investigate response plant stress at transcription control level using time-series transcriptome data. In this article, we present new network, PropaNet, dynamics from data...
Multifunctional transcription factor (TF) gene EWS/EWSR1 is involved in various cellular processes such as regulation, noncoding RNA splicing genotoxic stress response, and cancer generation. Role of a TF can be effectively studied by measuring genome-wide expression, i.e., transcriptome, an animal model Ews/Ewsr1 knockout (KO). However, when has complex multi-functions, conventional approaches differentially expressed genes (DEGs) analysis are not successful to characterize the role EWS...
Understanding the factors contributing to depression in farmers is crucial for ensuring their well-being and productivity. To address this issue, our study delves into among farmers, employing advanced tree-based machine learning (ML) algorithms, specifically focusing on Category Boosting (CatB) algorithm. Applying Patient Health Questionnaire-9 (PHQ-9) criteria, 2,446 individuals 14,810 repondents were classified including mild symptoms. In classification, CatB achieved an impressive 79.7%...
Abstract Background Integrated analysis that uses multiple sample gene expression data measured under the same stress can detect response genes more accurately than of individual data. However, integrated is challenging since experimental conditions (strength and number time points) are heterogeneous across samples. Results HTRgene a computational method to perform time-series condition. The goal identify “response order preserving DEGs” defined as not only which differentially expressed but...
Recently, a number of studies have been conducted to investigate how plants respond stress at the cellular molecular level by measuring gene expression profiles over time. As result, set time-series data for response are available in databases. With data, an integrated analysis multiple stresses is possible, which identifies stress-responsive genes with higher specificity because considering can capture effect interference between stresses. To analyze such machine learning model needs be...
To investigate how plant responds to various types of stress, measuring gene expression profiles in several time points is a common practice. Analyzing such series transcriptome data can be useful understand biological mechanisms responding stress. One important question which genes are related stress types. This hardly answered by analyzing from single experiments since too many affected i.e., false positives. Performing integrated analysis multiple certainly improve the situation. However,...
Electronic Health Records (EHRs) are a significant source of big data used to track health variables over time. The analysis EHR can uncover medical markers or risk factors, aiding in the diagnosis and monitoring diseases. We introduce novel method for identifying with various temporal trend patterns, including monotonic fluctuating trends, using machine learning models such as Long Short-Term Memory (LSTM). By applying our pneumonia patients intensive care unit MIMIC-III dataset, we...
Recently developed highly parallelized sequencing technologies allow now even small research groups to conduct multi-time point analysis in affordable time and cost, thus available time-series gene expression data sets are rapidly increasing. However, when the series generated from different considered, meta-properties of such as points age samples become heterogeneous bunch data. Thus, we propose a novel three-step algorithm integrate set. The key ideas convert incomparable multi-time-point...
Time-series gene expression datasets measured under the same stress are increasing, and they available for an integrated analysis to investigate response signaling genes. However, requires well-established strategic methods because meta-properties (the number of time points phenotype) heterogeneous across multiple samples. We present algorithm, HTRgene, that performs time-series condition. HTRgene identifies differentially expressed genes (DEGs) consistently samples, clusters based on...
Abstract Cambium drives lateral growth of stems and roots, contributing to diverse plant forms. Root crop is one outstanding example the cambium-driven growth. To understand its molecular basis, we used radish generate a compendium root tissue- stage-specific transcriptomes from two contrasting inbred lines in Expression patterns key cambium regulators hormone signaling components were validated. Clustering GO enrichment analyses datasets followed by comparative analysis against newly...
Genetic interactions (GIs), such as the synthetic lethal interaction, are promising therapeutic targets in precision medicine. However, despite extensive efforts to characterize GIs by large-scale perturbation screening, considerable false positives have been reported multiple studies. We propose a new computational approach for improved GI identification applying constraints that consider actual biological phenomena. In this study, were characterized assessing mutation, loss of function,...
The cholinergic synapse pathway related with significantly down-regulated genes by ClueGO. Selected DEGs are highlighted in colors chosen KEGG mapper. Blue genes, and red up-regulated Ews/Ewsr1 KO mice compared to WT mice. Green color not changed. (DOCX 53 kb)