Sun Kim

发表

MIDAS: Mining differentially activated subpaths of KEGG pathways from multi-class RNA-seq data.

Sangseon Lee, Sun Kim, Youngjune Park, 2017, Methods.

Measuring intratumor heterogeneity by network entropy using RNA-seq data

Jin-Wu Nam, Youngjune Park, Sun Kim, 2016, Scientific Reports.

Transcriptional Network Analysis Reveals Drought Resistance Mechanisms of AP2/ERF Transgenic Rice

Jukon Kim, Sun Kim, H. Kwon, 2017, Front. Plant Sci..

Identification of conserved gene regulatory networks that integrate environmental sensing and growth in the root cambium

Z. Fei, Yi Zheng, Ji-Young Lee, 2019, bioRxiv.

Graph pyramids for protein function prediction

J. Choi, Sun Kim, T. Sandhan, 2015, BMC Medical Genomics.

CLIP-GENE: a web service of the condition specific context-laid integrative analysis for gene prioritization in mouse TF knockout experiments

Jaewoo Kang, Heejoon Chae, Seokjun Seo, 2016, Biology Direct.

Computational regulatory network construction from microRNA and transcription factor perspectives

Sun Kim, Jinwoo Park, SungMin Rhee, 2013, SIGBIO.

Development of genetic quality tests for good manufacturing practice-compliant induced pluripotent stem cells and their derivatives

Jung-Hyun Kim, Sun Kim, Hyo-Won Han, 2020, Scientific Reports.

StressGenePred: a twin prediction model architecture for classifying the stress types of samples and discovering stress-related genes in arabidopsis

Sangseon Lee, Sun Kim, Hongryul Ahn, 2019, BMC Genomics.

PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network Propagation

Sun Kim, Minwoo Pak, Hongryul Ahn, 2019, Front. Plant Sci..

Logic-based Analysis of Gene Expression Data Predicts Pathway Crosstalk between TNF, TGFB1 and EGF in Basal-like Breast Cancer

C. Talcott, Sun Kim, Minsu Kim, 2019, bioRxiv.

Epstein–Barr virus and microsatellite instability in gastric carcinogenesis

H. Lee, Sun Kim, W. Kim, 2003, The Journal of pathology.

Logic-based Analysis of Gene Expression Data Predicts Association Between TNF, TGFB1 and EGF Pathways in Basal-like Breast Cancer.

C. Talcott, Sun Kim, Minsu Kim, 2020, Methods.

BioVLAB-mCpG-SNP-EXPRESS: A system for multi-level and multi-perspective analysis and exploration of DNA methylation, sequence variation (SNPs), and gene expression from multi-omics data.

K. Nephew, Sangseon Lee, Sun Kim, 2016, Methods.

Learning Cell-Type-Specific Gene Regulation Mechanisms by Multi-Attention Based Deep Learning With Regulatory Latent Space

Sangseon Lee, Sun Kim, Minji Kang, 2020, Frontiers in Genetics.

Network-Based Metric Space for Phenotypic Stratification of Samples Using Transcriptome Profiles

Sangseon Lee, Sun Kim, Inyoung Sung, 2021 .

Metheor: Ultrafast DNA methylation heterogeneity calculation from bisulfite read alignments

Sun Kim, Dohoon Lee, Bonil Koo, 2022, bioRxiv.

Combined analysis of gene regulatory network and SNV information enhances identification of potential gene markers in mouse knockout studies with small number of samples

Sun Kim, B. Hur, H. Chae, 2015, BMC Medical Genomics.

IDEA: Integrating Divisive and Ensemble-Agglomerate hierarchical clustering framework for arbitrary shape data

Sun Kim, Hongryul Ahn, Inuk Jung, 2021, 2021 IEEE International Conference on Big Data (Big Data).

A Survey on Computational Methods for Investigation on ncRNA-Disease Association through the Mode of Action Perspective

Sun Kim, Inuk Jung, Joonhyeong Park, 2022, International journal of molecular sciences.

BioVLAB-Cancer-Pharmacogenomics: tumor heterogeneity and pharmacogenomics analysis of multi-omics data from tumor on the cloud

Heejoon Chae, Sungjoon Park, Sun Kim, 2021, Bioinform..

DRIM: A Web-Based System for Investigating Drug Response at the Molecular Level by Condition-Specific Multi-Omics Data Integration

Kyuri Jo, Inuk Jung, Sangseon Lee, 2020, Frontiers in Genetics.

Inferring transcriptomic cell states and transitions only from time series transcriptome data

Sun Kim, Inyoung Sung, Kyuri Jo, 2021, Scientific Reports.

Deep hierarchical embedding for simultaneous modeling of GPCR proteins in a unified metric space

Sangseon Lee, Sun Kim, Taeheon Lee, 2021, Scientific Reports.

TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes

Hyejin Kang, Youngjae Yu, Sun Kim, 2017, Bioinform..

Time-series RNA-seq analysis package (TRAP) and its application to the analysis of rice, Oryza sativa L. ssp. Japonica, upon drought stress.

Kyuri Jo, Sun Kim, Hawk-Bin Kwon, 2014, Methods.

piClust: A density based piRNA clustering algorithm

Sun Kim, Inuk Jung, Jong Chan Park, 2014, Comput. Biol. Chem..

Hybrid Approach of Relation Network and Localized Graph Convolutional Filtering for Breast Cancer Subtype Classification

Seokjun Seo, Sun Kim, SungMin Rhee, 2017, IJCAI.

MONTI: A Multi-Omics Non-negative Tensor Decomposition Framework for Gene-Level Integrative Analysis

Sun Kim, Minsu Kim, Sangsoo Lim, 2021, Frontiers in Genetics.

A review on compound-protein interaction prediction methods: Data, format, representation and model

Sun Kim, Youngkuk Kim, Inyoung Sung, 2021, Computational and structural biotechnology journal.

GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis

Sun Kim, Jaehyun An, Jeong-Hyeon Choi, 2012, Bioinform..

SpliceHetero: An information theoretic approach for measuring spliceomic intratumor heterogeneity from bulk tumor RNA-seq

Sangseon Lee, Sun Kim, Minsu Kim, 2019, PloS one.

Genome-Wide Analysis and Modeling of DNA methylation susceptibility in 30 Breast Cancer Cell Lines by using CPG Flanking Sequences

Kenneth P. Nephew, Heejoon Chae, Sun Kim, 2013, J. Bioinform. Comput. Biol..

RDDpred: a condition-specific RNA-editing prediction model from RNA-seq data

Sun Kim, Minsu Kim, B. Hur, 2016, BMC Genomics.

Functional in vivo and in vitro effects of 20q11.21 genetic aberrations on hPSC differentiation

Jung-Hyun Kim, Sun Kim, Hongryul Ahn, 2020, Scientific Reports.

Determining the effect of DNA methylation on gene expression in cancer cells.

Sun Kim, Kwangsoo Kim, H. Chae, 2014, Methods in molecular biology.

Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches

Sun Kim, Youngjune Park, Dohoon Lee, 2020, Briefings Bioinform..

An integrative analysis of cellular contexts, miRNAs and mRNAs reveals network clusters associated with antiestrogen-resistant breast cancer cells

K. Nephew, Sun Kim, S. Nam, 2012, BMC Genomics.

Development of genetic quality tests for good manufacturing practice-compliant induced pluripotent stem cells and their derivatives

Jung-Hyun Kim, Sun Kim, Hyo-Won Han, 2020, Scientific Reports.

PRISM: methylation pattern-based, reference-free inference of subclonal makeup

Sangseon Lee, Dohoon Lee, Sun Kim, 2019, Bioinform..

A novel k-mer mixture logistic regression for methylation susceptibility modeling of CpG dinucleotides in human gene promoters

Kenneth P. Nephew, Youngik Yang, Sun Kim, 2011, BCB '11.

Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines

Kenneth P. Nephew, Heejoon Chae, Sun Kim, 2016, BMC Systems Biology.

Comprehensive and critical evaluation of individualized pathway activity measurement tools on pan-cancer data

Sun Kim, Inuk Jung, Sangseon Lee, 2018, Briefings Bioinform..

Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways

Sun Kim, Kyuri Jo, Inuk Jung, 2016, Bioinform..

Information theoretic sub-network mining characterizes breast cancer subtypes in terms of cancer core mechanisms

Jinwoo Park, Kwangsoo Kim, Min-Su Kim, 2016, J. Bioinform. Comput. Biol..

MONGKIE: an integrated tool for network analysis and visualization for multi-omics data

Sun Kim, Namhee Yu, Yeongjun Jang, 2016, Biology Direct.

Towards simultaneous clustering and motif-modeling for a large number of protein family

Tushar Sandhan, Jin Young Choi, Sun Kim, 2013, 2013 IEEE International Conference on Bioinformatics and Biomedicine.

Cloud-BS: A MapReduce-based bisulfite sequencing aligner on cloud

Heejoon Chae, Sun Kim, Yoonjae Park, 2018, J. Bioinform. Comput. Biol..

Cancer subtype classification and modeling by pathway attention and propagation

Sangseon Lee, Sun Kim, Sangsoo Lim, 2020, Bioinform..

DeepFam: deep learning based alignment-free method for protein family modeling and prediction

Seokjun Seo, Sun Kim, Minsik Oh, 2018, Bioinform..

Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations

Heejoon Chae, Minsik Oh, Sungjoon Park, 2020, Briefings Bioinform..

Flow maximization analysis of cell cycle pathway activation status in breast cancer subtypes

Sun Kim, Ji Hwan Moon, Sangseon Lee, 2017, 2017 IEEE International Conference on Big Data and Smart Computing (BigComp).

Novel drought-responsive regulatory coding and non-coding transcripts from Oryza Sativa L.

Sun Kim, H. Kwon, Hongryul Ahn, 2016, Genes & Genomics.

Literature-based condition-specific miRNA-mRNA target prediction

Jaewoo Kang, Heejoon Chae, Sunwon Lee, 2017, PloS one.

Impact of mutations in DNA methylation modification genes on genome-wide methylation landscapes and downstream gene activations in pan-cancer

Hongryul Ahn, Chai-Jin Lee, Dabin Jeong, 2020, BMC Medical Genomics.

Clustering and evolutionary analysis of small RNAs identify regulatory siRNA clusters induced under drought stress in rice

Sun Kim, Inuk Jung, Hongryul Ahn, 2016, BMC Systems Biology.

PINTnet: construction of condition-specific pathway interaction network by computing shortest paths on weighted PPI

Seokjun Seo, Sun Kim, Kyuri Jo, 2017, BMC Systems Biology.

BioVLAB-MMIA: A Reconfigurable Cloud Computing Environment for microRNA and mRNA Integrated Analysis

Kenneth P. Nephew, Suresh Marru, Chathura Herath, 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine.

Bio and health informatics meets cloud : BioVLab as an example

Suresh Marru, Seong-Whan Lee, Hyungro Lee, 2013, Health Inf. Sci. Syst..

Ranked k-Spectrum Kernel for Comparative and Evolutionary Comparison of Exons, Introns, and CpG Islands

Yung-Kyun Noh, Sangseon Lee, Sun Kim, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Integration of heterogeneous time series gene expression data by clustering on time dimension

Heejoon Chae, Sun Kim, Hongryul Ahn, 2017, 2017 IEEE International Conference on Big Data and Smart Computing (BigComp).

BRCA-Pathway: a structural integration and visualization system of TCGA breast cancer data on KEGG pathways

Sun Kim, Inyoung Kim, Saemi Choi, 2018, BMC Bioinformatics.

Suppression of ribosomal protein synthesis and protein translation factors by Peg-interferon alpha/ribavirin in HCV patients blood mononuclear cells (PBMC)

Milton W. Taylor, Sun Kim, Rahul Gupta, 2012, Journal of Translational Medicine.

Bioinformatic analysis of peripheral blood RNA-sequencing sensitively detects the cause of late graft loss following overt hyperglycemia in pig-to-nonhuman primate islet xenotransplantation

Sun Kim, Jung‐Sik Kim, Chung-Gyu Park, 2019, Scientific Reports.

HTRgene: a computational method to perform the integrated analysis of multiple heterogeneous time-series data: case analysis of cold and heat stress response signaling genes in Arabidopsis

Heejoon Chae, Dongwon Kang, Hongryul Ahn, 2019, BMC Bioinformatics.

mirTime: identifying condition-specific targets of microRNA in time-series transcript data using Gaussian process model and spherical vector clustering

Hyejin Kang, Kyuri Jo, Hongryul Ahn, 2019, Bioinform..

CLIP-GENE: a web service of the condition specific context-laid integrative analysis for gene prioritization in mouse TF knockout experiments

Jaewoo Kang, Sun Kim, Seokjun Seo, 2016, Biology Direct.

In silico experiment system for testing hypothesis on gene functions using three condition specific biological networks.

Jaewoo Kang, Sun Kim, Sunwon Lee, 2018, Methods.

Construction of Condition-Specific Gene Regulatory Network Using Kernel Canonical Correlation Analysis

Sangseon Lee, Sun Kim, Sangsoo Lim, 2021, Frontiers in Genetics.

Abstract 5013: CpG island shore methylation regulates caveolin-1 expression in breast cancer

Yunlong Liu, K. Nephew, T. Huang, 2012 .

Learning the histone codes of gene regulation with large genomic windows and three-dimensional chromatin interactions using transformer

Sun Kim, Dohoon Lee, Jeewon Yang, 2021, bioRxiv.

HTRgene: Integrating Multiple Heterogeneous Time-series Data to Investigate Cold and Heat Stress Response Signaling Genes in Arabidopsis

Heejoon Chae, Sun Kim, Dongwon Kang, 2018, 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Venn-diaNet : venn diagram based network propagation analysis framework for comparing multiple biological experiments

Sun Kim, Dongwon Kang, Gung Lee, 2019, BMC Bioinformatics.

DegPack: a web package using a non-parametric and information theoretic algorithm to identify differentially expressed genes in multiclass RNA-seq samples.

Kwangsoo Kim, Heejoon Chae, Sun Kim, 2014, Methods.

An algorithm for identifying differentially expressed genes in multiclass RNA-seq samples

Kwangsoo Kim, Sun Kim, Jaehyun An, 2014, 2014 International Conference on Big Data and Smart Computing (BIGCOMP).

The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature

Hyejin Kang, Sun Kim, Inuk Jung, 2018, BMC Systems Biology.

Efficiency of methylated DNA immunoprecipitation bisulphite sequencing for whole-genome DNA methylation analysis.

Y. Shin, Sangseon Lee, Sun Kim, 2016, Epigenomics.

DeepFunNet: Deep Learning for Gene Functional Similarity Network Construction

Sun Kim, Hongryul Ahn, Seunghyun Son, 2019, 2019 IEEE International Conference on Big Data and Smart Computing (BigComp).

Suppression of ribosomal protein synthesis and protein translation factors by Peg-interferon alpha/ribavirin in HCV patients blood mononuclear cells (PBMC)

Milton W. Taylor, Sun Kim, Rahul Gupta, 2012, Journal of Translational Medicine.

RDDpred: a condition-specific RNA-editing prediction model from RNA-seq data

Min-Su Kim, Sun Kim, Benjamin Hur, 2016, BMC Genomics.

Prioritizing biological pathways by recognizing context in time-series gene expression data

Jusang Lee, Jaewoo Kang, Sunwon Lee, 2016, BMC Bioinformatics.

BioVLAB-mCpG-SNP-EXPRESS: A system for multi-level and multi-perspective analysis and exploration of DNA methylation, sequence variation (SNPs), and gene expression from multi-omics data.

K. Nephew, Sangseon Lee, Sun Kim, 2016, Methods.