A5037879375- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- Biomedical Text Mining and Ontologies
- Gene expression and cancer classification
- Gene Regulatory Network Analysis
- Machine Learning in Bioinformatics
- Microbial Metabolic Engineering and Bioproduction
- Semantic Web and Ontologies
- Data Mining Algorithms and Applications
- Metabolomics and Mass Spectrometry Studies
- RNA and protein synthesis mechanisms
- Genetics, Bioinformatics, and Biomedical Research
- Data Management and Algorithms
- Advanced Database Systems and Queries
- Rough Sets and Fuzzy Logic
- Genomics and Phylogenetic Studies
- Advanced Text Analysis Techniques
- Artificial Immune Systems Applications
- RNA modifications and cancer
- Protein Structure and Dynamics
- Advanced Clustering Algorithms Research
- Gut microbiota and health
- Genomics and Chromatin Dynamics
- Face and Expression Recognition
- Genetic Associations and Epidemiology
Korea Advanced Institute of Science and Technology
2016-2025
Korea Institute of Brain Science
2015-2024
Mando Corporation (South Korea)
2023
Park University
2022
Aix-Marseille Université
2021
The London College
2021
King's College London
2021
KTH Royal Institute of Technology
2021
Karolinska Institutet
2021
Science for Life Laboratory
2021
Mapping the pathways that give rise to metastasis is one of key challenges breast cancer research. Recently, several large-scale studies have shed light on this problem through analysis gene expression profiles identify markers correlated with metastasis. Here, we apply a protein-network-based approach identifies not as individual genes but subnetworks extracted from protein interaction databases. The resulting provide novel hypotheses for involved in tumor progression. Although known...
The advent of microarray technology has made it possible to classify disease states based on gene expression profiles patients. Typically, marker genes are selected by measuring the power their discriminate among patients different states. However, expression-based classification can be challenging in complex diseases due factors such as cellular heterogeneity within a tissue sample and genetic across A promising technique for coping with these challenges is incorporate pathway information...
PIF3 is a phytochrome-interacting basic helix-loop-helix transcription factor that negatively regulates light responses, including hypocotyl elongation, cotyledon opening, and negative gravitropism. However, the role of in chlorophyll biosynthesis has not been clearly defined. Here, we show also by repressing biosynthetic genes dark. Consistent with gene expression patterns, etiolated pif3 mutant accumulated higher amount protochlorophyllide was bleached severely when transferred into light....
Abstract Gut mucosal microbes evolved closest to the host, developing specialized local communities. There is, however, insufficient knowledge of these communities as most studies have employed sequencing technologies investigate faecal microbiota only. This work used shotgun metagenomics biopsies explore microbial communities’ compositions terminal ileum and large intestine in 5 healthy individuals. Functional annotations genome-scale metabolic modelling selected species were then identify...
Abstract PHYTOCHROME INTERACTING FACTOR 3-LIKE5 (PIL5) is a basic helix-loop-helix transcription factor that inhibits seed germination by regulating the expression of gibberellin (GA)- and abscisic acid (ABA)-related genes either directly or indirectly. It not yet known, however, whether PIL5 regulates solely through GA ABA. Here, we used Chromatin immunoprecipitation-chip (ChIP-chip) analysis to identify 748 novel binding sites in Arabidopsis thaliana genome. Consistent with molecular...
Whole-genome expression profiling in postmortem brain tissue has recently provided insight into the pathophysiology of schizophrenia. Previous microarray and RNA-Seq studies identified several biological processes including synaptic function, mitochondrial function immune/inflammation response as altered cortex subjects with Now using data from hippocampus, we have 144 differentially expressed genes schizophrenia cases compared unaffected controls. Immune/inflammation was main process...
Identifying features that effectively represent the energetic contribution of an individual interface residue to interactions between proteins remains problematic. Here, we present several new and show they are more effective than conventional features. By combining proposed with features, develop a predictive model for interaction hot spots. Initially, 54 multifaceted composed different levels information including structure, sequence molecular information, quantified. Then, identify best...
Abstract Motivation: RBSDesigner predicts the translation efficiency of existing mRNA sequences and designs synthetic ribosome binding sites (RBSs) for a given coding sequence (CDS) to yield desired level protein expression. The program implements mathematical model initiation described in Na et al. (Mathematical modeling estimation its computationally design with expression prokaryotes. BMC Syst. Biol., 4, 71). additionally incorporates effect on spacer length between Shine–Dalgarno (SD) an...
Activation of dopamine receptors in forebrain regions, for minutes or longer, is known to be sufficient positive reinforcement stimuli and actions. However, the firing rate neurons increased only about 200 milliseconds following natural reward events that are better than expected, a response which has been described as "reward prediction error" (RPE). Although RPE drives learning (RL) computational models, it not possible directly test whether transient signal actually RL. Here we have...
Abstract Motivation: For the early detection of cancer, highly sensitive and specific biomarkers are needed. Particularly, in bio-fluids relatively more useful because those can be used for non-biopsy tests. Although altered metabolic activities cancer cells have been observed many studies, little is known about screening. In this study, a systematic method proposed identifying urine samples by selecting candidate from genome-wide gene expression signatures cells. Biomarkers identified...
The FALC-Loop web server provides an online interface for protein loop modeling by employing ab initio method called FALC (fragment assembly and analytical closure). may be used to construct regions in homology modeling, refine unreliable experimental structures or model segments of designed sequences. is computationally less expensive than typical methods because the conformational search space effectively reduced use fragments derived from a structure database. closure algorithm allows...
DNA methylation and hydroxymethylation have been implicated in normal development differentiation, but our knowledge is limited about the genome-wide distribution of 5-methylcytosine (5 mC) 5-hydroxymethylcytosine hmC) during cellular differentiation. Using an vitro model system gradual differentiation human embryonic stem (hES) cells into ventral midbrain-type neural precursor terminally dopamine neurons, we observed dramatic changes 5 mC hmC patterns lineage commitment. The pattern was...
Abstract Background Within the emerging field of synthetic biology, engineering paradigms have recently been used to design biological systems with novel functionalities. One essential challenges hampering construction such is need precisely optimize protein expression levels for robust operation. However, it difficult mRNA sequences at targeted levels, since even a few nucleotide modifications around start codon may alter translational efficiency and dramatically (up 250-fold) change...
As pharmacodynamic drug-drug interactions (PD DDIs) could lead to severe adverse effects in patients, it is important identify potential PD DDIs drug development. The signaling starting from targets propagated through protein-protein interaction (PPI) networks. occur by close interference on the same or within pathways as well distant cross-talking pathways. However, most of previous approaches have considered only measuring distances between comparing target neighbors. We applied a random...
Identifying the health benefits of phytochemicals is an essential step in drug and functional food development. While many vitro screening methods have been developed to identify effects phytochemicals, there still room for improvement because high cost low productivity. Therefore, researchers alternatively proposed silico methods, primarily based on three types approaches; utilizing molecular, chemical or ethnopharmacological information. Although each approach has its own strength...