A5075624025- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Advanced Proteomics Techniques and Applications
- Genomics and Phylogenetic Studies
- Genetic Associations and Epidemiology
- Cancer Genomics and Diagnostics
- Computational Drug Discovery Methods
- Biomedical Text Mining and Ontologies
- Microbial Metabolic Engineering and Bioproduction
- Data Mining Algorithms and Applications
- Dermatologic Treatments and Research
- Genetic Mapping and Diversity in Plants and Animals
- Plant Pathogenic Bacteria Studies
- Genomics and Chromatin Dynamics
- Cancer Mechanisms and Therapy
- Antimicrobial Peptides and Activities
- Fungal Infections and Studies
- Nail Diseases and Treatments
- Scientific Computing and Data Management
- Metabolomics and Mass Spectrometry Studies
- Fungal and yeast genetics research
- Antifungal resistance and susceptibility
- Wound Healing and Treatments
- Laser Applications in Dentistry and Medicine
- Systemic Sclerosis and Related Diseases
Yonsei University
2010-2024
Network "guilt by association" (GBA) is a proven approach for identifying novel disease genes based on the observation that similar mutational phenotypes arise from functionally related genes. In principle, this could account even nonadditive genetic interactions, which underlie synergistic combinations of mutations often linked to complex diseases. Here, we analyze large-scale, human gene functional interaction network (dubbed HumanNet). We show candidate can be effectively identified GBA...
Abstract The reconstruction of transcriptional regulatory networks (TRNs) is a long-standing challenge in human genetics. Numerous computational methods have been developed to infer interactions between factors (TFs) and target genes from high-throughput data their performance evaluation requires gold-standard interactions. Here we present database literature-curated TF-target interactions, TRRUST ( t ranscriptional r egulatory elationships u nravelled by s entence-based ext-mining,...
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...
A major challenge for distinguishing cancer-causing driver mutations from inconsequential passenger is the long-tail of infrequently mutated genes in cancer genomes. Here, we present and evaluate a method prioritizing accounting not only individual but also their neighbors functional networks, MUFFINN (MUtations For Functional Impact on Network Neighbors). This pathway-centric shows high sensitivity compared with gene-centric analyses mutation data. Notably, marginal decrease performance...
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...
During the past several decades, Escherichia coli has been a treasure chest for molecular biology. The mechanisms of many fundamental cellular processes have discovered through research on this bacterium. Although much basic now focuses more complex model organisms, E. still remains important in metabolic engineering and synthetic Despite its long history as subject investigation, than one-third genome no pathway annotation supported by either experimental evidence or manual curation....
During the last decade, genome-wide association studies (GWAS) have represented a major approach to dissect complex human genetic diseases. Due in part limited statistical power, most identify only small numbers of candidate genes that pass conventional significance thresholds (e.g. P ≤ 5 × 10-8). This limitation can be partly overcome by increasing sample size, but this comes at higher cost. Alternatively, weak signals boosted incorporating independent data. Previously, we demonstrated...
Abstract Cryptococcus neoformans is an opportunistic human pathogenic fungus that causes meningoencephalitis. Due to the increasing global risk of cryptococcosis and emergence drug-resistant strains, development predictive genetics platforms for rapid identification novel genes governing pathogenicity drug resistance C. imperative. The analysis functional genomics data genome-scale mutant libraries may facilitate genetic dissection such complex phenotypes but with limited efficiency. Here,...
The goal of our study was to demonstrate the spectrum genomic alterations present in residual disease patients with advanced high-grade serous ovarian cancer (HGSOC) after neoadjuvant chemotherapy (NAC), including matched pretreatment biopsies. During period between 2006 and 2017, we collected pre-NAC post-NAC tumor tissue samples from HGSOC. We performed combined next-generation sequencing immunohistochemistry identify actionable targets pathway activation tumors. also examined whether...
We describe an integrated proteome database, termed Yonsei Proteome Research Center Database (YPRC-PDB) which can store, retrieve and analyze various information including two-dimensional electrophoresis (2-DE) images associated spot that were obtained during studies of hepatocellular carcinoma (HCC). YPRC-PDB is also designed to perform as a laboratory management system manages sample information, clinical background, conditions both preparation 2-DE, entire sets experimental results. It...
Drosophila melanogaster (fruit fly) has been a popular model organism in animal genetics due to the high accessibility of reverse-genetics tools. In addition, close relationship between and human genomes rationalizes use as an invertebrate for neurobiology disease research. A platform technology predicting candidate genes or functions would further enhance usefulness this long-established gene-to-phenotype mapping. Recently, power network prioritization mapping demonstrated many organisms....
Functional protein-protein interaction (PPI) networks elucidate molecular pathways underlying complex phenotypes, including those of human diseases. Extrapolation domain-domain interactions (DDIs) from known PPIs is a major domain-based method for inferring functional PPI networks. However, the protein domain unit protein. Therefore, we should be able to effectively infer between proteins based on co-occurrence domains.Here, present accurate similarity composition by weighted mutual...
A network-based approach has proven useful for the identification of novel genes associated with complex phenotypes, including human diseases. Because gene prioritization algorithms are based on propagating information known phenotype-associated through networks, pathway structure each phenotype might significantly affect effectiveness algorithms. We systematically compared two popular network distinct mechanisms – direct neighborhood which propagates to only neighbors, and diffusion...
ABSTRACT Since the 1980s, development of new drug classes for treatment multidrug-resistant Klebsiella pneumoniae has become limited, highlighting urgent need novel antibiotics. To address this challenge, study aimed to explore synergistic interactions between chemical compounds and representative antibiotics, such as carbapenem colistin. The primary objective was not only mitigate adverse impact K. on public health but also establish a sustainable balance among humans, animals, environment....
Multiple genes and their interactions are involved in most human diseases. This pathway-centric view of pathology is beginning to guide our approaches disease research. Analytical algorithms describing gene networks have been developed for three major tasks research: (i) prioritization, (ii) module discovery, (iii) stratification complex To understand the underlying biology diseases, identification pathways crucial. The functional interdependence between progression has identified by...
Protein domains are basic functional units of proteins. Many protein pervasive among diverse biological processes, yet some associated with specific pathways. Human complex diseases generally viewed as pathway-level disorders. Therefore, we hypothesized that pathway-specific could be highly informative for human diseases. To test the hypothesis, developed a network-based scoring scheme to quantify specificity domain-pathway associations. We first generated domain profiles proteins, then...
Abstract Background Failure to respond treatment in epithelial ovarian cancer can often be attributed platinum‐based chemotherapy resistance. However, the possible mechanisms or candidate biomarkers associated with platinum resistance are yet elucidated, even though many researchers have performed related studies. Methods We RNA sequencing of clinical specimens obtained from patients platinum‐sensitive resistant (EOC). Furthermore, various bioinformatics approaches, including spatial...