List of works by Choi Hyungwon

A Comparison of Methods for Meta-Analysis of Gene Expression Data

scientific article

A Mass-Action-Based Model for Gene Expression Regulation in Dynamic Systems

scientific article

A Web Resource for Improved Analysis of AP-MS Protein Interaction Data

scientific article published in May 2013

A double-layered mixture model for the joint analysis of DNA copy number and gene expression data

scientific article

A global protein kinase and phosphatase interaction network in yeast.

scientific article

A latent variable approach for meta-analysis of gene expression data from multiple microarray experiments

scientific article

A protein-centric approach for exome variant aggregation enables sensitive association analysis with clinical outcomes

scientific article published on 12 January 2020

A protein-centric approach for exome variant aggregation enables sensitive association analysis with clinical outcomes

scientific article

A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways

scientific article

A web-tool for visualizing quantitative protein-protein interaction data.

scientific article

Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics

scientific article published on 13 September 2008

Adjuvant-induced Human Monocyte Secretome Profiles Reveal Adjuvant- and Age-specific Protein Signatures

scientific article published on March 2016

Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data

scientific article

Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT

scientific article

Angiopoietin-like 4 Increases Pulmonary Tissue Leakiness and Damage during Influenza Pneumonia

scientific article

Cerebral transcriptome analysis reveals age-dependent progression of neuroinflammation in P301S mutant tau transgenic male mice

scientific article published on 11 April 2019

Combination therapy with hepatocyte growth factor and oseltamivir confers enhanced protection against influenza viral pneumonia.

scientific article published on January 2014

Comment

scientific article

Computational detection of protein complexes in AP-MS experiments.

scientific article published on May 2012

Computationally Tractable Multivariate HMM in Genome-Wide Mapping Studies

scientific article published on January 2017

Computationally scalable regression modeling for ultrahigh-dimensional omics data with ParProx

scientific article

Concentration-dependent protein loading of extracellular vesicles released by Histoplasma capsulatum after antibody treatment and its modulatory action upon macrophages.

scientific article

Context specific ubiquitin modification of ribosomes regulates translation under oxidative stress

Customized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow.

scientific article

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

scientific article

Data Independent Acquisition analysis in ProHits 4.0.

scientific article

Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress.

scientific article published on 20 January 2016

Differentiation of Club Cells to Alveolar Epithelial Cells In Vitro

scientific article published on 27 January 2017

EBprot: Statistical analysis of labeling-based quantitative proteomics data.

scientific article

EBprotV2: A Perseus Plugin for Differential Protein Abundance Analysis of Labeling-based Quantitative Proteomics Data

scientific article published on 19 November 2018

Environmental Effects of Nanoceria on Seed Production of Common Bean (Phaseolus vulgaris): A Proteomic Analysis

scientific article published on 21 October 2015

Evaluation of determinants of the serological response to the quadrivalent split‐inactivated influenza vaccine

Exploiting Interdata Relationships in Next-generation Proteomics Analysis

scientific article published on 24 May 2019

False discovery rates and related statistical concepts in mass spectrometry-based proteomics

scientific article published on 8 December 2007

Gene Essentiality Is a Quantitative Property Linked to Cellular Evolvability

scientific article published on 25 November 2015

Global analysis of protein palmitoylation in African trypanosomes.

scientific article

Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data

scientific article

Information loss from censoring in rank-based procedures

scientific article

Integration of large-scale multi-omic datasets: a protein-centric view

scientific article published on 08 September 2018

Label-free quantitative proteomics and SAINT analysis enable interactome mapping for the human Ser/Thr protein phosphatase 5

scientific article

Label-free quantitative proteomics reveals differentially regulated proteins in the latex of sticky diseased Carica papaya L. plants.

scientific article

Large-scale lipidomics identifies associations between plasma sphingolipids and T2DM incidence

scientific article published on 04 June 2019

Loss of hepatocyte cell division leads to liver inflammation and fibrosis

scientific article published on 04 November 2020

LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data.

scientific article

LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach

scientific article

MRMkit: automated data processing for large-scale targeted metabolomics analysis

scientific article published on 15 September 2020

MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines

scientific article

Mammographic Breast Density and Common Genetic Variants in Breast Cancer Risk Prediction

scientific article published on 24 September 2015

MetTailor: dynamic block summary and intensity normalization for robust analysis of mass spectrometry data in metabolomics.

scientific article

MetaboKit: a comprehensive data extraction tool for untargeted metabolomics

scientific article published on 10 June 2020

Metabolic signatures and risk of type 2 diabetes in a Chinese population: an untargeted metabolomics study using both LC-MS and GC-MS.

scientific article published on 11 August 2016

Metabolites of purine nucleoside phosphorylase (NP) in serum have the potential to delineate pancreatic adenocarcinoma

scientific article

Micro-RNAs in regenerating lungs: an integrative systems biology analysis of murine influenza pneumonia.

scientific article

Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome

scientific article published on 8 November 2011

Moving beyond P values: Everyday data analysis with estimation plots

New insights into the cellular temporal response to proteostatic stress

scientific article published on 12 October 2018

Non-genetic and genetic rewiring underlie adaptation to hypomorphic alleles of an essential gene

scientific article published on 15 September 2021

PECA: a novel statistical tool for deconvoluting time-dependent gene expression regulation

scientific article published on 26 November 2013

PECAplus: statistical analysis of time-dependent regulatory changes in dynamic single-omics and dual-omics experiments

scientific article published on 19 December 2017

PTMscape: an open source tool to predict generic post-translational modifications and map modification crosstalk in protein domains and biological processes

scientific article published on 01 June 2018

Phosphoprotein network analysis of white adipose tissues unveils deregulated pathways in response to high-fat diet.

scientific article published on 16 May 2016

Plasma Metabolome and Lipidome Associations with Type 2 Diabetes and Diabetic Nephropathy

scientific article

Plasma Metabonomic Profiling of Diabetic Retinopathy

scientific article published on 28 January 2016

Plasma Sphingolipids and Subclinical Atherosclerosis – Novel Associations Uncovered by a Large-scale Lipidomic Analysis (P18-129-19)

Plasma fatty acids, oxylipins, and risk of myocardial infarction: the Singapore Chinese Health Study

scientific article published on 24 May 2016

Plasma sphingolipids and risk of cardiovascular diseases: a large-scale lipidomic analysis

scientific article published on 20 August 2020

Plasma α-Linolenic and Long-Chain ω-3 Fatty Acids Are Associated with a Lower Risk of Acute Myocardial Infarction in Singapore Chinese Adults

scientific article

Prestroke proteomic changes in cerebral microvessels in stroke-prone, transgenic[hCETP]-Hyperlipidemic, Dahl salt-sensitive hypertensive rats

scientific article

Protein interaction network of the mammalian Hippo pathway reveals mechanisms of kinase-phosphatase interactions

scientific article

Proteomic analysis of Trypanosoma cruzi secretome: characterization of two populations of extracellular vesicles and soluble proteins.

scientific article published on 4 January 2013

QPROT: Statistical method for testing differential expression using protein-level intensity data in label-free quantitative proteomics.

scientific article

Reinvestigation of aminoacyl-tRNA synthetase core complex by affinity purification-mass spectrometry reveals TARSL2 as a potential member of the complex

scientific article

Remodelling of whole-body lipid metabolism and a diabetic-like phenotype caused by loss of CDK1 and hepatocyte division

scientific article published on 21 December 2020

SAINT-MS1: protein-protein interaction scoring using label-free intensity data in affinity purification-mass spectrometry experiments

scientific article

SAINT: probabilistic scoring of affinity purification-mass spectrometry data

scientific article

SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software

scientific article

SAINTq: Scoring protein-protein interactions in affinity purification - mass spectrometry experiments with fragment or peptide intensity data.

scientific article

SLIDE - a web-based tool for interactive visualization of large-scale - omics data

scientific article published on 01 January 2019

SUMOylation pathway in Trypanosoma cruzi: functional characterization and proteomic analysis of target proteins

scientific article published on 10 August 2011

Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics.

scientific article published on 27 December 2007

Significance analysis of spectral count data in label-free shotgun proteomics

scientific article

Sparsely correlated hidden Markov models with application to genome-wide location studies

scientific article published on 16 January 2013

Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling

scientific article

The CRAPome: a contaminant repository for affinity purification-mass spectrometry data

scientific article

Using ProHits to store, annotate, and analyze affinity purification-mass spectrometry (AP-MS) data

scientific article

Variability of the Plasma Lipidome and Subclinical Coronary Atherosclerosis

When one and one gives more than two: challenges and opportunities of integrative omics

scientific article published on January 2011

iOmicsPASS: network-based integration of multiomics data for predictive subnetwork discovery

scientific article published on 09 July 2019

mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry

scientific article

multiSLIDE: a web server for exploring connected elements of biological pathways in multi-omics data

scientific article

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