A5082966786- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- RNA and protein synthesis mechanisms
- Pancreatic and Hepatic Oncology Research
- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- Machine Learning in Bioinformatics
- RNA modifications and cancer
- Ferroptosis and cancer prognosis
- Logic, Reasoning, and Knowledge
- Advanced Text Analysis Techniques
- Cancer Cells and Metastasis
- Gene expression and cancer classification
- Semantic Web and Ontologies
- Molecular Biology Techniques and Applications
- Bayesian Modeling and Causal Inference
- Connexins and lens biology
- Cell Image Analysis Techniques
- Redox biology and oxidative stress
- Cancer Research and Treatments
- Single-cell and spatial transcriptomics
- Epigenetics and DNA Methylation
- Topic Modeling
- Glycosylation and Glycoproteins Research
Hanyang University
2014-2024
Government of the Republic of Korea
2015
University of Seoul
2004-2011
Seoul National University
1994-2011
Korea Institute of Science and Technology
2008-2010
Korean Association Of Science and Technology Studies
2008-2010
Seoul National University of Science and Technology
2010
Ewha Womans University
2008-2009
Yeungnam University
2009
Korea University
2008
Isoform-specific signaling of Akt, a major hub and prominent therapeutic target, remained poorly defined until recently. Subcellular distribution, tissue-specific expression, substrate specificity, posttranslational modifications are believed to underlie isoform-specific Akt. The studies reported here show inhibition Akt2 activity under physiologically relevant conditions oxidation created by PDGF-induced reactive oxygen species. Combined MS functional assays identified Cys124 located in the...
Post-translational modifications (PTMs) play key roles in the regulation of biological functions proteins. Although some progress has been made identifying several PTMs using existing approaches involving a combination affinity-based enrichment and mass spectrometric analysis, comprehensive identification remains challenging problem proteomics because dynamic complexities vivo their low abundance. We describe here strategy for rapid, efficient, occurring processes vivo. It involves...
Redox-active cysteine, a highly reactive sulfhydryl, is one of the major targets ROS. Formation disulfide bonds and other oxidative derivatives cysteine including sulfenic, sulfinic, sulfonic acids, regulates biological function various proteins. We identified novel low-abundant modifications in cellular GAPDH purified on 2-dimensional gel electrophoresis (2D-PAGE) by employing selectively excluded mass screening analysis for nano ultraperformance liquid...
Abstract The prognostic and therapeutic relevance of molecular subtypes for the most aggressive isocitrate dehydrogenase 1/2 ( IDH ) wild-type glioblastoma (GBM) is currently limited due to high heterogeneity tumors that impedes patient stratification. Here, we describe a distinct binary classification GBM derived from quantitative proteomic analysis 39 GBMs as well mutant low-grade glioma controls. Specifically, cluster 1 (GPC1) exhibit Warburg-like features, neural stem-cell markers,...
Identifying the sites of disulfide bonds in a protein is essential for thorough understanding protein's tertiary and quaternary structures its biological functions. Disulfide linked peptides are usually identified indirectly by labeling free sulfhydryl groups with alkylating agents, followed chemical reduction mass spectral comparison or detecting expected masses on scan level. However, these approaches determination become ambiguous when highly bridged modified. For accurate identification...
Various forms of protein (proteoforms) are generated by genetic variations, alternative splicing, translation initiation, co- or post-translational modification and proteolysis. Different proteoforms in part discovered characterizing their N-terminal sequences. Here, we introduce an N-terminal-peptide-enrichment method, Nrich. Filter-aided negative selection formed the basis for use two N-blocking reagents endoproteases this method. We identified 6,525 acetylated (or partially acetylated)...
Proteogenomics is a promising approach for various tasks ranging from gene annotation to cancer research. Databases proteogenomic searches are often constructed by adding peptide sequences inferred genomic or transcriptomic evidence reference protein sequences. Such inflation of databases has potential identifying novel peptides. However, it also raises concerns on sensitive and reliable identification. Spurious peptides included in target may result underestimated false discovery rate...
Automatic transliteration problem is to transcribe foreign words in one's own alphabet. Machine generated can be useful various applications such as indexing an information retrieval system and pronunciation synthesis a text-to-speech system. In this paper we present model for statistical English-to-Korean that generates candidates with probability. The designed utilize sources by extending conventional Markov window. Also, efficient accurate method alignment syllabification of units...
The assembly of the β-barrel proteins present in outer membrane (OM) Gram-negative bacteria is poorly characterized. After translocation across inner membrane, unfolded are escorted periplasm by chaperones that reside within this compartment. Two partially redundant chaperones, SurA and Skp, considered to transport bulk mass proteins. We found periplasmic disulfide isomerase DsbC cooperates with thiol oxidase DsbA folding essential protein LptD. LptD inserts lipopolysaccharides OM. It also...
Identification of post-translational modifications (PTMs) is important to understanding the biological functions proteins. MS/MS a useful tool identify PTMs. Most existing search tools are restricted take only few types PTMs as input. Here we describe new algorithm, called MOD(i) (pronounced "mod eye"), that rapidly searches for all known at once without limiting multitude modified sites in peptide. introduces notion tag chain, combination structure made from multiple sequence tags,...
Non-small cell lung cancer (NSCLC) is histologically classified into adenocarcinoma (LUAD) and squamous carcinoma (LSCC). However, some tumors are ambiguous other pathophysiological features or microenvironmental factors may be more prominent. Here we report integrative multiomics analyses using data for 229 patients from a Korean NSCLC cohort 462 previous studies. Histological examination reveals five molecular subtypes, one of which subtype with PI3K-Akt pathway upregulation, showing high...
MOD i ( http://modi.uos.ac.kr/modi/ ) is a powerful and convenient web service that facilitates the interpretation of tandem mass spectra for identifying post-translational modifications (PTMs) in peptide. It it can interpret spectrum even when hundreds modification types are considered number potential PTMs peptide large, contrast to most methods currently available limit PTM sites being used analysis. For example, using , one consider analysis both entire list published on unimod webpage...
A large proportion of MS/MS spectral analyses do not result in significant matches because their quality is too poor to produce meaningful identification. Throughput peptide identification can be greatly improved, if one filter out, advance, spectra that would lead wrong We introduce here an innovative approach assess utilizing a new feature called Xrea, based on cumulative intensity normalization.
In proteogenomic analysis, construction of a compact, customized database from mRNA-seq data and sensitive search both reference databases are essential to accurately determine protein abundances structural variations at the level. However, these tasks have not been systematically explored, but rather performed in an ad-hoc fashion. Here, we present effective method for constructing compact containing comprehensive sequences sample-specific variants--single nucleotide variants,...
Post-translational modifications regulate various cellular processes and are of great biological interest. Unrestrictive searches mass spectrometry data enable the detection any type modification. Here we propose MODplus, which makes practical unrestrictive possible by allowing (1) hundreds modifications, (2) multiple per peptide, (3) whole proteome database, (4) tolerant values in search parameters. The utility MODplus was demonstrated large human sets HEK293 cells TMT-labeled...
We propose to use cRFP (common Repository of FBS Proteins) in the MS (mass spectrometry) raw data search cell secretomes. is a small supplementary sequence list highly abundant fetal bovine serum proteins added reference database use. The aim behind using prevent contaminant from being misidentified as other database, just we would cRAP Adventitious present either by accident or through unavoidable contacts proteins. expect it be widely used experiments where are obtained serum-free media...
Predicting protein structures with high accuracy is a critical challenge for the broad community of life sciences and industry. Despite progress made by deep neural networks like AlphaFold2, there need further improvements in quality detailed structures, such as side-chains, along backbone structures.Building upon successes modifications we include changing losses side-chain torsion angles frame aligned point error, adding loss functions side chain confidence secondary structure prediction,...
Determining isotopic clusters and their monoisotopic masses is a first step in interpreting complex mass spectra generated by high-resolution spectrometers. We propose mathematical model for distributions of polypeptides an effective interpretation algorithm. Our uses two types ratios: intensity ratio adjacent peaks product three distribution. These ratios can be approximated as simple functions polypeptide mass, the values which fall within certain ranges, depending on mass. Given spectrum...
Planned digestion with missed cleavage identified disulfide bonds of RNase A.
Abstract Background Protein quantification is an essential step in many proteomics experiments. A number of labeling approaches have been proposed and adopted mass spectrometry (MS) based relative quantification. The mTRAQ, one the stable isotope methods, amine-specific available triplex format, so that sample throughput could be doubled when compared with duplex reagents. Methods results Here we propose a novel data analysis algorithm for peptide mTRAQ It improved accuracy two features....