General Theta function identities. - Kim, Sun (J. Comb. Theory, Ser. A, 2026)

Fate-tox: fragment attention transformer for E(3)-equivariant multi-organ toxicity prediction. - Ha, Sumin; Bang, Dongmin; Kim, Sun (J. Cheminformatics, 2025)

Residue-Level Multiview Deep Learning for ATP Binding Site Prediction and Applications in Kinase Inhibitors. - Lee, Jaechan; Bang, Dongmin; Kim, Sun (J. Chem. Inf. Model., 2025)

Dual Representation Learning for Predicting Drug-Side Effect Frequency Using Protein Target Information. - Park, Sungjoon; Lee, Sangseon; Pak, Minwoo; Kim, Sun (IEEE J. Biomed. Health Informatics, 2025)

CheapNet: Cross-attention on Hierarchical representations for Efficient protein-ligand binding Affinity Prediction. - Lim, Hyukjun; Kim, Sun; Lee, Sangseon (2025)

Taxonomy and Analysis of Sensitive User Queries in Generative AI Search System. - Jo, Hwiyeol; Park, Taiwoo; Lee, Hyunwoo; Choi, Nayoung; Kim, Changbong; Kwon, Ohjoon; Jeon, Donghyeon; Lee, Eui-Hyeon; Shin, Kyoungho; Lim, Sun Suk; Kim, Kyungmi; Lee, Jihye; et al. (2025)

MV-CLAM: Multi-View Molecular Interpretation with Cross-Modal Projection via Language Model. - Ha, Sumin; Kim, Jun Hyeong; Piao, Yinhua; Kim, Sun (CoRR, 2025)

GraphT5: Unified Molecular Graph-Language Modeling via Multi-Modal Cross-Token Attention. - Kim, Sangyeup; Kim, Nayeon; Piao, Yinhua; Kim, Sun (CoRR, 2025)

AI-driven Automation of End-to-end Assessment of Suturing Expertise. - Deo, Atharva; Matsumoto, Nicholas; Kim, Sun; Wager, Peter; Tsai, Randy G.; Denmark, Aaron; Yang, Cherine; Li, Xi; Moran, Jay; Hernandez, Miguel; Hung, Andrew J. (CoRR, 2025)

Transfer learning of condition-specific perturbation in gene interactions improves drug response prediction. - Bang, Dongmin; Koo, Bonil; Kim, Sun (Bioinform., 2024)

Finding Highly Similar Regions of Genomic Sequences Through Homomorphic Encryption. - Bataa, Magsarjav; Song, Siwoo; Park, Kunsoo; Kim, Miran; Cheon, Jung Hee; Kim, Sun (J. Comput. Biol., 2024)

DiSCO: Diffusion Schrödinger Bridge for Molecular Conformer Optimization. - Lee, Danyeong; Lee, Dohoon; Bang, Dongmin; Kim, Sun (2024)

Improving Out-of-Distribution Generalization in Graphs via Hierarchical Semantic Environments. - Piao, Yinhua; Lee, Sangseon; Lu, Yijingxiu; Kim, Sun (2024)

SLM as Guardian: Pioneering AI Safety with Small Language Model. - Kwon, Ohjoon; Jeon, Donghyeon; Choi, Nayoung; Cho, Gyu-Hwung; Jo, Hwiyeol; Kim, Changbong; Lee, Hyunwoo; Kang, Inho; Kim, Sun; Park, Taiwoo (2024)

Enhancing Drug-Drug Interaction Prediction with Context-Aware Architecture. - Lu, Yijingxiu; Piao, Yinhua; Kim, Sun (2024)

Improving out-of-distribution generalization in graphs via hierarchical semantic environments. - Piao, Yinhua; Lee, Sangseon; Lu, Yijingxiu; Kim, Sun (CoRR, 2024)

Taxonomy and Analysis of Sensitive User Queries in Generative AI Search. - Jo, Hwiyeol; Park, Taiwoo; Choi, Nayoung; Kim, Changbong; Kwon, Ohjoon; Jeon, Donghyeon; Lee, Hyunwoo; Lee, Eui-Hyeon; Shin, Kyoungho; Lim, Sun Suk; Kim, Kyungmi; Lee, Jihye; et al. (CoRR, 2024)

SLM as Guardian: Pioneering AI Safety with Small Language Models. - Kwon, Ohjoon; Jeon, Donghyeon; Choi, Nayoung; Cho, Gyu-Hwung; Kim, Changbong; Lee, Hyunwoo; Kang, Inho; Kim, Sun; Park, Taiwoo (CoRR, 2024)

Improved drug response prediction by drug target data integration via network-based profiling. - Pak, Minwoo; Lee, Sangseon; Sung, Inyoung; Koo, Bonil; Kim, Sun (Briefings Bioinform., 2023)

A model-agnostic framework to enhance knowledge graph-based drug combination prediction with drug-drug interaction data and supervised contrastive learning. - Gu, Jeonghyeon; Bang, Dongmin; Yi, Jungseob; Lee, Sangseon; Kim, Dong Kyu; Kim, Sun (Briefings Bioinform., 2023)

GOAT: Gene-level biomarker discovery from multi-Omics data using graph ATtention neural network for eosinophilic asthma subtype. - Jeong, Dabin; Koo, Bonil; Oh, Minsik; Kim, Tae-Bum; Kim, Sun (Bioinform., 2023)

Metheor: Ultrafast DNA methylation heterogeneity calculation from bisulfite read alignments. - Lee, Dohoon; Koo, Bonil; Yang, Jeewon; Kim, Sun (PLoS Comput. Biol., 2023)

Clinical Note Owns its Hierarchy: Multi-Level Hypergraph Neural Networks for Patient-Level Representation Learning. - Kim, Nayeon; Piao, Yinhua; Kim, Sun (2023)

Deep learning-based survival prediction using DNA methylation-derived 3D genomic information. - Yang, Jeewon; Lee, Dohoon; Koo, Bonil; Jeong, Dabin; Kim, Sun (2023)

Clinical Note Owns its Hierarchy: Multi-Level Hypergraph Neural Networks for Patient-Level Representation Learning. - Kim, Nayeon; Piao, Yinhua; Kim, Sun (CoRR, 2023)

AutoCoV: tracking the early spread of COVID-19 in terms of the spatial and temporal patterns from embedding space by K-mer based deep learning. - Sung, Inyoung; Lee, Sangseon; Pak, Minwoo; Shin, Yunyol; Kim, Sun (BMC Bioinform., 2022)

Generative Modeling to Predict Multiple Suitable Conditions for Chemical Reactions. - Kwon, Youngchun; Kim, Sun; Choi, Youn-Suk; Kang, Seokho (J. Chem. Inf. Model., 2022)

MLDEG: A Machine Learning Approach to Identify Differentially Expressed Genes Using Network Property and Network Propagation. - Moon, Ji Hwan; Lee, Sangseon; Pak, Minwoo; Hur, Benjamin; Kim, Sun (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Sparse Structure Learning via Graph Neural Networks for Inductive Document Classification. - Piao, Yinhua; Lee, Sangseon; Lee, Dohoon; Kim, Sun (2022)

Embedding of FDA Approved Drugs in Chemical Space Using Cascade Autoencoder with Metric Learning. - Kim, Jungwoo; Lim, Sangsoo; Lee, Sangseon; Cho, Changyun; Kim, Sun (2022)

Triangular Contrastive Learning on Molecular Graphs. - Choi, MinGyu; Shin, Wonseok; Lu, Yijingxiu; Kim, Sun (CoRR, 2022)

SPGP: Structure Prototype Guided Graph Pooling. - Lee, Sangseon; Lee, Dohoon; Piao, Yinhua; Kim, Sun (CoRR, 2022)

Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations. - Oh, Minsik; Park, Sungjoon; Kim, Sun; Chae, Heejoon (Briefings Bioinform., 2021)

Erratum to: Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations. - Oh, Minsik; Park, Sungjoon; Kim, Sun; Chae, Heejoon (Briefings Bioinform., 2021)

Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches. - Lee, Dohoon; Park, Youngjune; Kim, Sun (Briefings Bioinform., 2021)

mirTime: identifying condition-specific targets of microRNA in time-series transcript data using Gaussian process model and spherical vector clustering. - Kang, Hyejin; Ahn, Hongryul; Jo, Kyuri; Oh, Minsik; Kim, Sun (Bioinform., 2021)

BioVLAB-Cancer-Pharmacogenomics: tumor heterogeneity and pharmacogenomics analysis of multi-omics data from tumor on the cloud. - Park, Sungjoon; Lee, Dohoon; Kim, Youngkuk; Lim, Sangsoo; Chae, Heejoon; Kim, Sun (Bioinform., 2021)

A generalization of the modular equations of higher degrees. - Kim, Sun (J. Comb. Theory A, 2021)

Ranked k-Spectrum Kernel for Comparative and Evolutionary Comparison of Exons, Introns, and CpG Islands. - Lee, Sangseon; Lee, Taeheon; Noh, Yung-Kyun; Kim, Sun (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

TeamTat: A Collaborative Text Annotation Tool for Creating Gold-Standard Corpora. - Islamaj, Rezarta; Kwon, Dongseop; Kim, Sun; Lu, Zhiyong (2021)

A probabilistic model for pathway-guided gene set selection. - Kim, Inyoung; Lee, Sangseon; Kim, Youngkuk; Namkoong, Hugh; Kim, Sun (2021)

IDEA: Integrating Divisive and Ensemble-Agglomerate hierarchical clustering framework for arbitrary shape data. - Ahn, Hongryul; Jung, Inuk; Chae, Heejoon; Oh, Minsik; Kim, Inyoung; Kim, Sun (2021)

Handling Long-Tail Queries with Slice-Aware Conversational Systems. - Wang, Cheng; Kim, Sun; Park, Taiwoo; Choudhary, Sajal; Park, Sunghyun; Kim, Young-Bum; Sarikaya, Ruhi; Lee, Sungjin (CoRR, 2021)

Sparse Structure Learning via Graph Neural Networks for Inductive Document Classification. - Piao, Yinhua; Lee, Sangseon; Lee, Dohoon; Kim, Sun (CoRR, 2021)

Comprehensive and critical evaluation of individualized pathway activity measurement tools on pan-cancer data. - Lim, Sangsoo; Lee, Sangseon; Jung, Inuk; Rhee, SungMin; Kim, Sun (Briefings Bioinform., 2020)

Cancer subtype classification and modeling by pathway attention and propagation. - Lee, Sangseon; Lim, Sangsoo; Lee, Taeheon; Sung, Inyoung; Kim, Sun (Bioinform., 2020)

Better synonyms for enriching biomedical search. - Yeganova, Lana; Kim, Sun; Chen, Qingyu; Balasanov, Grigory; Wilbur, W. John; Lu, Zhiyong (J. Am. Medical Informatics Assoc., 2020)

Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records. - Chen, Qingyu; Du, Jingcheng; Kim, Sun; Wilbur, W. John; Lu, Zhiyong (BMC Medical Informatics Decis. Mak., 2020)

TeamTat: a collaborative text annotation tool. - Dogan, Rezarta Islamaj; Kwon, Dongseop; Kim, Sun; Lu, Zhiyong (Nucleic Acids Res., 2020)

BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale. - Chen, Qingyu; Lee, Kyubum; Yan, Shankai; Kim, Sun; Wei, Chih-Hsuan; Lu, Zhiyong (PLoS Comput. Biol., 2020)

Homomorphic Computation of Local Alignment. - Bataa, Magsarjav; Song, Siwoo; Park, Kunsoo; Kim, Miran; Cheon, Jung Hee; Kim, Sun (2020)

TeamTat: a collaborative text annotation tool. - Dogan, Rezarta Islamaj; Kwon, Dongseop; Kim, Sun; Lu, Zhiyong (CoRR, 2020)

Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. - Dogan, Rezarta Islamaj; Kim, Sun; Chatr-aryamontri, Andrew; Wei, Chih-Hsuan; Comeau, Donald C.; Antunes, Rui; Matos, Sérgio; Chen, Qingyu; Elangovan, Aparna; Panyam, Nagesh C.; Verspoor, Karin; Liu, Hongfang; et al. (Database J. Biol. Databases Curation, 2019)

PRISM: methylation pattern-based, reference-free inference of subclonal makeup. - Lee, Do-Hoon; Lee, Sangseon; Kim, Sun (Bioinform., 2019)

CaPSSA: visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data. - Jang, Yeongjun; Seo, Jihae; Jang, Insu; Lee, Byungwook; Kim, Sun; Lee, Sanghyuk (Bioinform., 2019)

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. - Ahn, Hongryul; Jung, Inuk; Chae, Heejoon; Kang, Dongwon; Jung, Woosuk; Kim, Sun (BMC Bioinform., 2019)

Venn-diaNet : venn diagram based network propagation analysis framework for comparing multiple biological experiments. - Hur, Benjamin; Kang, Dongwon; Lee, Sangseon; Moon, Ji Hwan; Lee, Gung; Kim, Sun (BMC Bioinform., 2019)

A secure SNP panel scheme using homomorphically encrypted K-mers without SNP calling on the user side. - Park, Sungjoon; Kim, Minsu; Seo, Seokjun; Hong, Seungwan; Han, Kyoohyung; Lee, Keewoo; Cheon, Jung Hee; Kim, Sun (BMC Genom., 2019)

LitSense: making sense of biomedical literature at sentence level. - Allot, Alexis; Chen, Qingyu; Kim, Sun; Alvarez, Roberto Vera; Comeau, Donald C.; Wilbur, W. John; Lu, Zhiyong (Nucleic Acids Res., 2019)

Evaluation of Five Sentence Similarity Models on Electronic Medical Records. - Chen, Qingyu; Du, Jingcheng; Kim, Sun; Wilbur, W. John; Lu, Zhiyong (2019)

DeepFunNet: Deep Learning for Gene Functional Similarity Network Construction. - Ahn, Hongryul; Son, Seunghyun; Kim, Sun (2019)

Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records. - Chen, Qingyu; Du, Jingcheng; Kim, Sun; Wilbur, W. John; Lu, Zhiyong (CoRR, 2019)

BioConceptVec: creating and evaluating literature-based biomedical concept embeddings on a large scale. - Chen, Qingyu; Lee, Kyubum; Yan, Shankai; Kim, Sun; Wei, Chih-Hsuan; Lu, Zhiyong (CoRR, 2019)

DeepFam: deep learning based alignment-free method for protein family modeling and prediction. - Seo, Seokjun; Oh, Minsik; Park, Youngjune; Kim, Sun (Bioinform., 2018)

BRCA-Pathway: a structural integration and visualization system of TCGA breast cancer data on KEGG pathways. - Kim, Inyoung; Choi, Saemi; Kim, Sun (BMC Bioinform., 2018)

Discovering themes in biomedical literature using a projection-based algorithm. - Yeganova, Lana; Kim, Sun; Balasanov, Grigory; Wilbur, W. John (BMC Bioinform., 2018)

The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature. - Jung, Inuk; Kang, Hyejin; Kim, Jang Uk; Chang, Hyeonsook; Kim, Sun; Jung, Woosuk (BMC Syst. Biol., 2018)

Cloud-BS: A MapReduce-based bisulfite sequencing aligner on cloud. - Choi, Joungmin; Park, Yoonjae; Kim, Sun; Chae, Heejoon (J. Bioinform. Comput. Biol., 2018)

ezTag: tagging biomedical concepts via interactive learning. - Kwon, Dongseop; Kim, Sun; Wei, Chih-Hsuan; Leaman, Robert; Lu, Zhiyong (Nucleic Acids Res., 2018)

The Circle Problem of Gauss and the Divisor Problem of Dirichlet - Still Unsolved. - Berndt, Bruce C.; Kim, Sun; Zaharescu, Alexandru (Am. Math. Mon., 2018)

Editorial for Selected Papers of a Joint Conferences, Genome Informatics Workshop/International Conference on Bioinformatics (GIW/InCoB) 2015. - Kim, Sun (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Sentence Similarity Measures Revisited: Ranking Sentences in PubMed Documents. - Chen, Qingyu; Kim, Sun; Wilbur, W. John; Lu, Zhiyong (2018)

HTRgene: Integrating Multiple Heterogeneous Time-series Data to Investigate Cold and Heat Stress Response Signaling Genes in Arabidopsis. - Ahn, Hongryul; Jung, Inuk; Chae, Heejoon; Kang, Dongwon; Jung, Woosuk; Kim, Sun (2018)

Identifying stress-related genes and predicting stress types in Arabidopsis using logical correlation layer and CMCL loss through time-series data. - Kang, Dongwon; Ahn, Hongryul; Lee, Sangseon; Lee, Chai-Jin; Hur, Jihye; Jung, Woosuk; Kim, Sun (2018)

Hybrid Approach of Relation Network and Localized Graph Convolutional Filtering for Breast Cancer Subtype Classification. - Rhee, SungMin; Seo, Seokjun; Kim, Sun (2018)

A Fast Deep Learning Model for Textual Relevance in Biomedical Information Retrieval. - Mohan, Sunil; Fiorini, Nicolas; Kim, Sun; Lu, Zhiyong (2018)

A Fast Deep Learning Model for Textual Relevance in Biomedical Information Retrieval. - Mohan, Sunil; Fiorini, Nicolas; Kim, Sun; Lu, Zhiyong (CoRR, 2018)

The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions. - Dogan, Rezarta Islamaj; Kim, Sun; Chatr-aryamontri, Andrew; Chang, Christie S.; Oughtred, Rose; Rust, Jennifer M.; Wilbur, W. John; Comeau, Donald C.; Dolinski, Kara; Tyers, Mike (Database J. Biol. Databases Curation, 2017)

TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes. - Jung, Inuk; Jo, Kyuri; Kang, Hyejin; Ahn, Hongryul; Yu, Youngjae; Kim, Sun (Bioinform., 2017)

PINTnet: construction of condition-specific pathway interaction network by computing shortest paths on weighted PPI. - Moon, Ji Hwan; Lim, Sangsoo; Jo, Kyuri; Lee, Sangseon; Seo, Seokjun; Kim, Sun (BMC Syst. Biol., 2017)

Iterative segmented least square method for functional microRNA-mRNA module discovery in breast cancer. - Rhee, SungMin; Lim, Sangsoo; Kim, Sun (Int. J. Data Min. Bioinform., 2017)

Bridging the gap: Incorporating a semantic similarity measure for effectively mapping PubMed queries to documents. - Kim, Sun; Fiorini, Nicolas; Wilbur, W. John; Lu, Zhiyong (J. Biomed. Informatics, 2017)

Flow maximization analysis of cell cycle pathway activation status in breast cancer subtypes. - Lee, Sangseon; Moon, Ji Hwan; Park, Youngjune; Kim, Sun (2017)

Integration of heterogeneous time series gene expression data by clustering on time dimension. - Ahn, Hongryul; Chae, Heejoon; Jung, Woosuk; Kim, Sun (2017)

BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations. - Dogan, Rezarta Islamaj; Chatr-aryamontri, Andrew; Kim, Sun; Wei, Chih-Hsuan; Peng, Yifan; Comeau, Donald C.; Lu, Zhiyong (2017)

Deep Learning for Biomedical Information Retrieval: Learning Textual Relevance from Click Logs. - Mohan, Sunil; Fiorini, Nicolas; Kim, Sun; Lu, Zhiyong (2017)

Hybrid Approach of Relation Network and Localized Graph Convolutional Filtering for Breast Cancer Subtype Classification. - Rhee, SungMin; Seo, Seokjun; Kim, Sun (CoRR, 2017)

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. - Kim, Sun; Dogan, Rezarta Islamaj; Chatr-aryamontri, Andrew; Chang, Christie S.; Oughtred, Rose; Rust, Jennifer M.; Batista-Navarro, Riza; Carter, Jacob; Ananiadou, Sophia; Matos, Sérgio; Santos, André; Campos, David; et al. (Database J. Biol. Databases Curation, 2016)

BioC viewer: a web-based tool for displaying and merging annotations in BioC. - Shin, Soo-Yong; Kim, Sun; Wilbur, W. John; Kwon, Dongseop (Database J. Biol. Databases Curation, 2016)

Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways. - Jo, Kyuri; Jung, Inuk; Moon, Ji Hwan; Kim, Sun (Bioinform., 2016)

Meshable: searching PubMed abstracts by utilizing MeSH and MeSH-derived topical terms. - Kim, Sun; Yeganova, Lana; Wilbur, W. John (Bioinform., 2016)

Prioritizing biological pathways by recognizing context in time-series gene expression data. - Lee, Jusang; Jo, Kyuri; Lee, Sunwon; Kang, Jaewoo; Kim, Sun (BMC Bioinform., 2016)

RDDpred: a condition-specific RNA-editing prediction model from RNA-seq data. - Kim, Min-Su; Hur, Benjamin; Kim, Sun (BMC Genom., 2016)

Clustering and evolutionary analysis of small RNAs identify regulatory siRNA clusters induced under drought stress in rice. - Jung, Inuk; Ahn, Hongryul; Shin, Seon-Ju; Kim, Jukon; Kwon, Hawk-Bin; Jung, Woosuk; Kim, Sun (BMC Syst. Biol., 2016)

Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines. - Chae, Heejoon; Lee, Sangseon; Nephew, Kenneth P.; Kim, Sun (BMC Syst. Biol., 2016)

Information theoretic sub-network mining characterizes breast cancer subtypes in terms of cancer core mechanisms. - Park, Jinwoo; Hur, Benjamin; Rhee, SungMin; Lim, Sangsoo; Kim, Min-Su; Kim, Kwangsoo; Han, Wonshik; Kim, Sun (J. Bioinform. Comput. Biol., 2016)

Networks and models for the integrated analysis of multi omics data. - Kim, Sun (2016)

Iterative segmented least square method for functional microRNA-mRNA module discovery in breast cancer. - Rhee, SungMin; Lim, Sangsoo; Kim, Sun (2016)

PubTermVariants: biomedical term variants and their use for PubMed search. - Yeganova, Lana; Kim, Won; Kim, Sun; Dogan, Rezarta Islamaj; Liu, Wanli; Comeau, Donald C.; Lu, Zhiyong; Wilbur, W. John (2016)

BioCconvert: A Conversion Tool Between BioC and PubAnnotation. - Comeau, Donald C.; Dogan, Rezarta Islamaj; Kim, Sun; Wei, Chih-Hsuan; Wilbur, W. John; Lu, Zhiyong (2016)

Bridging the Gap: a Semantic Similarity Measure between Queries and Documents. - Kim, Sun; Wilbur, W. John; Lu, Zhiyong (CoRR, 2016)

BioVLAB-MMIA-NGS: microRNA-mRNA integrated analysis using high-throughput sequencing data. - Chae, Heejoon; Rhee, SungMin; Nephew, Kenneth P.; Kim, Sun (Bioinform., 2015)

Identifying named entities from PubMed®; for enriching semantic categories. - Kim, Sun; Lu, Zhiyong; Wilbur, W. John (BMC Bioinform., 2015)

Weighted divisor sums and Bessel function series, V. - Berndt, Bruce C.; Kim, Sun; Zaharescu, Alexandru (J. Approx. Theory, 2015)

Extracting drug-drug interactions from literature using a rich feature-based linear kernel approach. - Kim, Sun; Liu, Haibin; Yeganova, Lana; Wilbur, W. John (J. Biomed. Informatics, 2015)

Summarizing Topical Contents from PubMed Documents Using a Thematic Analysis. - Kim, Sun; Yeganova, Lana; Wilbur, W. John (2015)

Assisting manual literature curation for protein-protein interactions using BioQRator. - Kwon, Dongseop; Kim, Sun; Shin, Soo-Yong; Chatr-aryamontri, Andrew; Wilbur, W. John (Database J. Biol. Databases Curation, 2014)

Retro: concept-based clustering of biomedical topical sets. - Yeganova, Lana; Kim, Won; Kim, Sun; Wilbur, W. John (Bioinform., 2014)

piClust: A density based piRNA clustering algorithm. - Jung, Inuk; Park, Jong Chan; Kim, Sun (Comput. Biol. Chem., 2014)

Author name disambiguation for PubMed. - Liu, Wanli; Dogan, Rezarta Islamaj; Kim, Sun; Comeau, Donald C.; Kim, Won; Yeganova, Lana; Lu, Zhiyong; Wilbur, W. John (J. Assoc. Inf. Sci. Technol., 2014)

Partitions with part difference conditions and Bressoud's conjecture. - Kim, Sun; Yee, Ae Ja (J. Comb. Theory A, 2014)

Extracting drug-drug interactions from literature using a rich feature-based linear kernel approach. - Kim, Sun; Liu, Haibin; Yeganova, Lana; Wilbur, W. John (2014)

An algorithm for identifying differentially expressed genes in multiclass RNA-seq samples. - An, Jaehyun; Kim, Kwangsoo; Kim, Sun (2014)

Integrated profiling of three dimensional cell culture models and 3D microscopy. - Bilgin, Cemal Çagatay; Kim, Sun; Leung, Elle; Chang, Hang; Parvin, Bahram (Bioinform., 2013)

Bio and health informatics meets cloud : BioVLab as an example. - Chae, Heejoon; Jung, Inuk; Lee, Hyungro; Marru, Suresh; Lee, Seong-Whan; Kim, Sun (Health Inf. Sci. Syst., 2013)

Designing discriminative spatial filter vectors in motor imagery brain-computer interface. - Lee, Kyeong-Yeon; Kim, Sun (Int. J. Imaging Syst. Technol., 2013)

Genome-Wide Analysis and Modeling of DNA methylation susceptibility in 30 Breast Cancer Cell Lines by using CPG Flanking Sequences. - An, Jaehyun; Kim, Kwangsoo; Rhee, SungMin; Chae, Heejoon; Nephew, Kenneth P.; Kim, Sun (J. Bioinform. Comput. Biol., 2013)

The Rogers-Ramanujan-Gordon identities, the generalized Göllnitz-Gordon identities, and parity questions. - Kim, Sun; Yee, Ae Ja (J. Comb. Theory A, 2013)

Towards simultaneous clustering and motif-modeling for a large number of protein family. - Yoo, Young Joon; Sandhan, Tushar; Choi, Jin Young; Kim, Sun (2013)

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information. - Kim, Sun; Kim, Won; Wei, Chih-Hsuan; Lu, Zhiyong; Wilbur, W. John (Database J. Biol. Databases Curation, 2012)

PIE the search: searching PubMed literature for protein interaction information. - Kim, Sun; Kwon, Dongseop; Shin, Soo-Yong; Wilbur, W. John (Bioinform., 2012)

GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis. - Pejaver, Vikas Rao; An, Jaehyun; Rhee, SungMin; Bhan, Ankita; Choi, Jeong-Hyeon; Liu, Boshu; Lee, Heewook; Brown, Pamela J.; Kysela, David; Brun, Yves V.; Kim, Sun (Bioinform., 2012)

Thematic clustering of text documents using an EM-based approach. - Kim, Sun; Wilbur, W. John (J. Biomed. Semant., 2012)

A novel k-mer mixture logistic regression for methylation susceptibility modeling of CpG dinucleotides in human gene promoters. - Yang, Youngik; Nephew, Kenneth P.; Kim, Sun (BMC Bioinform., 2012)

Introduction. - Kim, Sun; Wang, Wei (J. Bioinform. Comput. Biol., 2012)

Classifying Gene Sentences in Biomedical Literature by Combining High-Precision Gene Identifiers. - Kim, Sun; Kim, Won; Comeau, Donald C.; Wilbur, W. John (2012)

Discriminative spatial pattern vectors selection for motor imagery classification. - Lee, Kyeong-Yeon; Kim, Sun (2012)

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. - Krallinger, Martin; Vazquez, Miguel; Leitner, Florian; Salgado, David; Chatr-aryamontri, Andrew; Winter, Andrew G.; Perfetto, Livia; Briganti, Leonardo; Licata, Luana; Iannuccelli, Marta; Castagnoli, Luisa; Cesareni, Gianni; et al. (BMC Bioinform., 2011)

Classifying protein-protein interaction articles using word and syntactic features. - Kim, Sun; Wilbur, W. John (BMC Bioinform., 2011)

Göllnitz-Gordon identities and parity questions. - Kim, Sun; Yee, Ae Ja (Eur. J. Comb., 2011)

Sequence-Based enzyme catalytic Domain Prediction Using Clustering and Aggregated Mutual Information Content. - Choi, Kwangmin; Kim, Sun (J. Bioinform. Comput. Biol., 2011)

BioVLAB-MMIA: A Reconfigurable Cloud Computing Environment for microRNA and mRNA Integrated Analysis. - Lee, Hyungro; Yang, Youngik; Chae, Heejoon; Nam, Seungyoon; Choi, Donghoon; Tangchaisin, Patanachai; Herath, Chathura; Marru, Suresh; Nephew, Kenneth P.; Kim, Sun (2011)

Sequence-Based Enzyme Catalytic Domain Prediction Using Clustering and Aggregated Mutual Information Content. - Choi, Kwangmin; Kim, Sun (2011)

An EM Clustering Algorithm which Produces a Dual Representation. - Kim, Sun; Wilbur, W. John (2011)

Transitioning BioVLab cloud workbench to a science gateway. - Marru, Suresh; Chae, Heejoon; Tangchaisin, Patanachai; Kim, Sun; Pierce, Marlon E.; Nephew, Kenneth P. (2011)

ACM International Conference on Bioinformatics, Computational Biology and Biomedicine, BCB' 11, Chicago, IL, USA - July 31 - August 03, 2011 (ACM, 2011)

Data mining for the study of disease genes and proteins. - Kim, Sun (Artif. Intell. Medicine, 2010)

Annotation confidence score for genome annotation: a genome comparison approach. - Yang, Youngik; Gilbert, Donald; Kim, Sun (Bioinform., 2010)

EGGSlicer: predicting biologically meaningful gene sets from gene clusters using gene ontology information. - Chae, Heejoon; Choi, Kwangmin; Kim, Sun; Ashki, Haleh (2010)

Gene cluster profile vectors: A novel method to infer functional coupling using both gene proximity and co-occurrence profiles. - Pejaver, Vikas Rao; Kim, Sun (2010)

Computational analysis of microRNA profiles and their target genes suggests significant involvement in breast cancer antiestrogen resistance. - Xin, Fuxiao; Li, Meng; Balch, Curtis; Thomson, Michael; Fan, Meiyun; Liu, Yunlong; Hammond, Scott M.; Kim, Sun; Nephew, Kenneth P. (Bioinform., 2009)

Ensembled support vector machines for human papillomavirus risk type prediction from protein secondary structures. - Kim, Sun; Kim, Jeongmi; Zhang, Byoung-Tak (Comput. Biol. Medicine, 2009)

Bijective proofs of partition identities arising from modular equations. - Kim, Sun (J. Comb. Theory A, 2009)

MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. - Nam, Seungyoon; Li, Meng; Choi, Kwangmin; Balch, Curtis; Kim, Sun; Nephew, Kenneth P. (Nucleic Acids Res., 2009)

Evolving hypernetwork models of binary time series for forecasting price movements on stock markets. - Bautu, Elena; Kim, Sun; Bautu, Andrei; Luchian, Henri; Zhang, Byoung-Tak (2009)

Evolutionary hypernetwork classifiers for protein-proteininteraction sentence filtering. - Bootkrajang, Jakramate; Kim, Sun; Zhang, Byoung-Tak (2009)

Experience report: issues in comparing gene function annotation in text. - Yang, Youngik; Kim, Sun (2009)

A machine-learning approach to combined evidence validation of genome assemblies. - Choi, Jeong-Hyeon; Kim, Sun; Tang, Haixu; Andrews, Justen; Gilbert, Don G.; Colbourne, John (Bioinform., 2008)

Enriched transcription factor binding sites in hypermethylated gene promoters in drug resistant cancer cells. - Li, Meng; Paik, Hyun-il Henry; Balch, Curtis; Kim, Yoosung; Li, Lang; Huang, Tim Hui-Ming; Nephew, Kenneth P.; Kim, Sun (Bioinform., 2008)

ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts. - Choi, Kwangmin; Kim, Sun (BMC Bioinform., 2008)

A gene pattern mining algorithm using interchangeable gene sets for prokaryotes. - Hu, Meng; Choi, Kwangmin; Su, Wei; Kim, Sun; Yang, Jiong (BMC Bioinform., 2008)

PIE: an online prediction system for protein-protein interactions from text. - Kim, Sun; Shin, Soo-Yong; Lee, In-Hee; Kim, Soo-Jin; Sriram, Ram; Zhang, Byoung-Tak (Nucleic Acids Res., 2008)

BioVLAB-Microarray: Microarray Data Analysis in Virtual Environment. - Yang, Youngik; Choi, Jong Youl; Choi, Kwangmin; Pierce, Marlon E.; Gannon, Dennis; Kim, Sun (2008)

Predicting DNA Methylation Susceptibility Using CpG Flanking Sequences. - Kim, Sun; Li, Meng; Paik, Hyun-il Henry; Nephew, Kenneth P.; Shi, Huidong; Kramer, Robin; Xu, Dong; Huang, Tim Hui-Ming (2008)

2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008, Philadephia, Pennsylvania, USA, November 3-5, 2008 (IEEE Computer Society, 2008)

dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis. - Bae, Seung-Hee; Tang, Haixu; Wu, Jing; Xie, Jun; Kim, Sun (Bioinform., 2007)

A Study of Residue Correlation within Protein Sequences and Its Application to Sequence Classification. - Hemmerich, Christopher Michael; Kim, Sun (EURASIP J. Bioinform. Syst. Biol., 2007)

Finding Cancer-Related Gene Combinations Using a Molecular Evolutionary Algorithm. - Park, Chan-Hoon; Kim, Soo-Jin; Kim, Sun; Cho, Dong-Yeon; Zhang, Byoung-Tak (2007)

EGGS: Extraction of Gene Clusters Using Genome Context Based Sequence Matching Techniques. - Kim, Sun; Bhan, Ankita; Maryada, Bharath K.; Choi, Kwangmin; Brun, Yves V. (2007)

Evolving hypernetwork classifiers for microRNA expression profile analysis. - Kim, Sun; Kim, Soo-Jin; Zhang, Byoung-Tak (2007)

CLASSEQ: Classification of Sequences via Comparative Analysis of Multiple Genomes. - Choi, Kwangmin; Yang, Youngik; Kim, Sun (2007)

Bioinformatics: Mining the Massive Data from High Throughput Genomics Experiments. - Tang, Haixu; Kim, Sun (2007)

COMPAM : visualization of combining pairwise alignments for multiple genomes. - Lee, Do-Hoon; Choi, Jeong-Hyeon; Dalkilic, Mehmet M.; Kim, Sun (Bioinform., 2006)

A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha. - Li, Lang; Cheng, Alfred S. L.; Jin, Victor X.; Paik, Henry H.; Fan, Meiyun; Li, Xiaoman; Zhang, Wei; Robarge, Jason; Balch, Curtis; Davuluri, Ramana V.; Kim, Sun; Huang, Tim Hui-Ming; et al. (Bioinform., 2006)

ARCS: an aggregated related column scoring scheme for aligned sequences. - Song, Bin; Choi, Jeong-Hyeon; Chen, Guangyu; Szymanski, Jacek; Zhang, Guo-Qiang; Tung, Anthony K. H.; Kang, Jaewoo; Kim, Sun; Yang, Jiong (Bioinform., 2006)

REFINEMENT: A search framework for the identification of interferon-responsive elements in DNA sequences - a case study with ISRE and GAS. - Tsukahara, Takuma; Kim, Sun; Taylor, Milton W. (Comput. Biol. Chem., 2006)

Advanced Signal Processing Techniques for Bioinformatics. - Chen, Xue-wen; Kim, Sun; Pavlovic, Vladimir I.; Casasent, David P. (EURASIP J. Adv. Signal Process., 2006)

BAG: a graph theoretic sequence clustering algorithm. - Kim, Sun; Lee, Jason (Int. J. Data Min. Bioinform., 2006)

Text Classifiers Evolved on a Simulated DNA Computer. - Kim, Sun; Heo, Min-Oh; Zhang, Byoung-Tak (2006)

Human Papillomavirus Risk Type Classification from Protein Sequences Using Support Vector Machines. - Kim, Sun; Zhang, Byoung-Tak (2006)

Genome Data Type: a Vehicle to Deliver a Genome Comparison System on the Web. - Choi, Kwangmin; Saple, Amit; Kim, Sun (2006)

Prediction of the Human Papillomavirus Risk Types Using Gap-Spectrum Kernels. - Kim, Sun; Eom, Jae-Hong (2006)

A Tree Kernel-Based Method for Protein-Protein Interaction Mining from Biomedical Literature. - Eom, Jae-Hong; Kim, Sun; Kim, Seong-Hwan; Zhang, Byoung-Tak (2006)

An Approximate de Bruijn Graph Approach to Multiple Local Alignment and Motif Discovery in Protein Sequences. - Patwardhan, Rupali; Tang, Haixu; Kim, Sun; Dalkilic, Mehmet M. (2006)

Data Mining and Bioinformatics, First International Workshop, VDMB 2006, Seoul, Korea, September 11, 2006, Revised Selected Papers (Springer, 2006)

PLATCOM: a Platform for Computational Comparative Genomics. - Choi, Kwangmin; Ma, Yu; Choi, Jeong-Hyeon; Kim, Sun (Bioinform., 2005)

GAME: A simple and efficient whole genome alignment method using maximal exact match filtering. - Choi, Jeong-Hyeon; Cho, Hwan-Gue; Kim, Sun (Comput. Biol. Chem., 2005)

PLATCOM: a Platform for Computational Comparative Genomics on the Web. - Choi, Kwangmin; Choi, Jeong-Hyeon; Saple, Amit; Wang, Zhiping; Lee, Jason; Kim, Sun (2005)

Gene Teams with Relaxed Proximity Constraint. - Kim, Sun; Choi, Jeong-Hyeon; Yang, Jiong (2005)

Cluster Utility: A New Metric for Clustering Biological Sequences. - Lee, Jason; Kim, Sun (2005)

PLATCOM: Current Status and Plan for the Next Stages. - Choi, Kwangmin; Choi, Jeong-Hyeon; Saple, Amit; Wang, Zhiping; Lee, Jason; Kim, Sun (2005)

An Application of Support Vector Machines for Customer Churn Analysis: Credit Card Case. - Kim, Sun; Shin, Kyung-shik; Park, Kyungdo (2005)

Motif discovery for proteins using subsequence clustering. - Sheth, Hardik A.; Kim, Sun (2005)

Multi-objective Evolutionary Probe Design Based on Thermodynamic Criteria for HPV Detection. - Lee, In-Hee; Kim, Sun; Zhang, Byoung-Tak (2004)

Multiple Genome Alignment by Clustering Pairwise Matches. - Choi, Jeong-Hyeon; Choi, Kwangmin; Cho, Hwan-Gue; Kim, Sun (2004)

Guiding motif discovery by iterative pattern refinement. - Wang, Zhiping; Dalkilic, Mehmet M.; Kim, Sun (2004)

Genetic Mining of HTML Structures for Effective Web-Document Retrieval. - Kim, Sun; Zhang, Byoung-Tak (Appl. Intell., 2003)

Motif Discovery from Large Number of Sequences: A Case Study with Disease Resistance Genes in Arabidopsos thaliana. - Gunduz, Irfan; Zhao, Sihui; Dalkilic, Mehmet M.; Kim, Sun (2003)

Graph Theoretic Sequence Clustering Algorithms and Their Applications to Genome Comparison. - Kim, Sun (2003)

Evolutionary learning of Web-document structure for information retrieval. - Kim, Sun; Zhang, Byoung-Tak (2001)

A probabilistic approach to sequence assembly validation. - Kim, Sun; Liao, Li; Tomb, Jean-François (2001)

Web-Document Retrieval by Genetic Learning of Importance Factors for HTML Tags. - Kim, Sun; Zhang, Byoung-Tak (2000)

AMASS: A Structured Pattern Matching Approach to Shotgun Sequence Assembly. - Kim, Sun; Segre, Alberto Maria (J. Comput. Biol., 1999)

A New String-Pattern Matching Algorithm Using Partitioning and Hashing Efficiently. - Kim, Sun (ACM J. Exp. Algorithmics, 1999)

SCAI TREC-8 Experiments. - Shin, Dong-Ho; Kim, Yu-Hwan; Kim, Sun; Eom, Jae-Hong; Shin, Hyung-Joo; Zhang, Byoung-Tak (1999)

ModGen: Theorem Proving by Model Generation. - Kim, Sun; Zhang, Hantao (1994)