Sun Kim - RankMe

206 papers A* 10A 1B 6C 2Misc 4Journal 127Unranked 51

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	General Theta function identities. J. Comb. Theory, Ser. A Sun Kim
2025	J	`jnl`	ADME-drug-likeness: enriching molecular foundation models via pharmacokinetics-guided multi-task learning for drug-likeness prediction. Bioinform. Dongmin Bang, Juyeon Kim, Haerin Song, Sun Kim
2025	J	`jnl`	AI-driven Automation of End-to-end Assessment of Suturing Expertise. CoRR Atharva Deo, Nicholas Matsumoto, Sun Kim, Peter Wager, Randy G. Tsai, Aaron Denmark, Cherine Yang, Xi Li, Jay Moran, Miguel E. Hernandez, Andrew J. Hung
2025	A*	`conf`	BounDr.E: Predicting Drug-likeness via Biomedical Knowledge Alignment and EM-like One-Class Boundary Optimization. ICML Dongmin Bang, Inyoung Sung, Yinhua Piao, Sangseon Lee, Sun Kim
2025	A*	`conf`	CheapNet: Cross-attention on Hierarchical representations for Efficient protein-ligand binding Affinity Prediction. ICLR Hyukjun Lim, Sun Kim, Sangseon Lee
2025	A*	`conf`	CombiMOTS: Combinatorial Multi-Objective Tree Search for Dual-Target Molecule Generation. ICML Thibaud Southiratn, Bonil Koo, Yijingxiu Lu, Sun Kim
2025	J	`jnl`	Dual Representation Learning for Predicting Drug-Side Effect Frequency Using Protein Target Information. IEEE J. Biomed. Health Informatics Sungjoon Park, Sangseon Lee, Minwoo Pak, Sun Kim
2025	J	`jnl`	Fate-tox: fragment attention transformer for E(3)-equivariant multi-organ toxicity prediction. J. Cheminformatics Sumin Ha, Dongmin Bang, Sun Kim
2025	J	`jnl`	GraphT5: Unified Molecular Graph-Language Modeling via Multi-Modal Cross-Token Attention. CoRR Sangyeup Kim, Nayeon Kim, Yinhua Piao, Sun Kim
2025	J	`jnl`	Identification of severity related mutation hotspots in SARS-CoV-2 using a density-based clustering approach. BioData Min. Sohyun Youn, Dabin Jeong, Hwijun Kwon, Eonyong Han, Sun Kim, Inuk Jung
2025	J	`jnl`	Improving Reaction Yield Prediction with Chemical Atom-Level Reaction Learning. J. Chem. Inf. Model. Yijingxiu Lu, Yinhua Piao, Ming Shen, Sun Kim
2025	—	`conf`	MV-CLAM: Multi-View Molecular Interpretation with Cross-Modal Projection via Language Model. EMNLP (Findings) Sumin Ha, Jun Hyeong Kim, Yinhua Piao, Changyun Cho, Sun Kim
2025	J	`jnl`	MV-CLAM: Multi-View Molecular Interpretation with Cross-Modal Projection via Language Model. CoRR Sumin Ha, Jun Hyeong Kim, Yinhua Piao, Sun Kim
2025	J	`jnl`	MixingDTA: improved drug-target affinity prediction by extending mixup with guilt-by-association. Bioinform. Youngoh Kim, Dongmin Bang, Bonil Koo, Jungseob Yi, Changyun Cho, Jeonguk Choi, Sun Kim
2025	J	`jnl`	Residue-Level Multiview Deep Learning for ATP Binding Site Prediction and Applications in Kinase Inhibitors. J. Chem. Inf. Model. Jaechan Lee, Dongmin Bang, Sun Kim
2025	J	`jnl`	SubDyve: Subgraph-Driven Dynamic Propagation for Virtual Screening Enhancement Controlling False Positive. CoRR Jungseob Yi, Seoyoung Choi, Sun Kim, Sangseon Lee
2025	J	`jnl`	Survey on AI-Drug Discovery with Knowledge Graphs: Data, Algorithm, and Application. J. Comput. Sci. Eng. Daeun Kong, Yoojin Ha, Haeun Yoo, Dongmin Bang, Sun Kim
2025	—	`conf`	Taxonomy and Analysis of Sensitive User Queries in Generative AI Search System. NAACL (Findings) Hwiyeol Jo, Taiwoo Park, Hyunwoo Lee, Nayoung Choi, Changbong Kim, Ohjoon Kwon, Donghyeon Jeon, Eui-Hyeon Lee, Kyoungho Shin, Sun Suk Lim, Kyungmi Kim, Jihye Lee, Sun Kim
2025	J	`jnl`	Transcriptome Transformer: improving patient survival prediction via multitask learning of transcriptomic and clinical features. Briefings Bioinform. Bonil Koo, Inyoung Sung, Sangseon Lee, Sun Kim
2024	A*	`conf`	DiSCO: Diffusion Schrödinger Bridge for Molecular Conformer Optimization. AAAI Danyeong Lee, Dohoon Lee, Dongmin Bang, Sun Kim
2024	—	`conf`	Enhancing Drug-Drug Interaction Prediction with Context-Aware Architecture. Tiny Papers @ ICLR Yijingxiu Lu, Yinhua Piao, Sun Kim
2024	J	`jnl`	Finding Highly Similar Regions of Genomic Sequences Through Homomorphic Encryption. J. Comput. Biol. Magsarjav Bataa, Siwoo Song, Kunsoo Park, Miran Kim, Jung Hee Cheon, Sun Kim
2024	A*	`conf`	Improving Out-of-Distribution Generalization in Graphs via Hierarchical Semantic Environments. CVPR Yinhua Piao, Sangseon Lee, Yijingxiu Lu, Sun Kim
2024	J	`jnl`	Improving out-of-distribution generalization in graphs via hierarchical semantic environments. CoRR Yinhua Piao, Sangseon Lee, Yijingxiu Lu, Sun Kim
2024	J	`jnl`	PONYTA: prioritization of phenotype-related genes from mouse KO events using PU learning on a biological network. Bioinform. Jun Hyeong Kim, Bonil Koo, Sun Kim
2024	—	`conf`	SLM as Guardian: Pioneering AI Safety with Small Language Model. EMNLP (Industry Track) Ohjoon Kwon, Donghyeon Jeon, Nayoung Choi, Gyu-Hwung Cho, Hwiyeol Jo, Changbong Kim, Hyunwoo Lee, Inho Kang, Sun Kim, Taiwoo Park
2024	J	`jnl`	SLM as Guardian: Pioneering AI Safety with Small Language Models. CoRR Ohjoon Kwon, Donghyeon Jeon, Nayoung Choi, Gyu-Hwung Cho, Changbong Kim, Hyunwoo Lee, Inho Kang, Sun Kim, Taiwoo Park
2024	J	`jnl`	Taxonomy and Analysis of Sensitive User Queries in Generative AI Search. CoRR Hwiyeol Jo, Taiwoo Park, Nayoung Choi, Changbong Kim, Ohjoon Kwon, Donghyeon Jeon, Hyunwoo Lee, Eui-Hyeon Lee, Kyoungho Shin, Sun Suk Lim, Kyungmi Kim, Jihye Lee, Sun Kim
2024	J	`jnl`	Transfer learning of condition-specific perturbation in gene interactions improves drug response prediction. Bioinform. Dongmin Bang, Bonil Koo, Sun Kim
2023	J	`jnl`	A model-agnostic framework to enhance knowledge graph-based drug combination prediction with drug-drug interaction data and supervised contrastive learning. Briefings Bioinform. Jeonghyeon Gu, Dongmin Bang, Jungseob Yi, Sangseon Lee, Dong Kyu Kim, Sun Kim
2023	—	`conf`	Clinical Note Owns its Hierarchy: Multi-Level Hypergraph Neural Networks for Patient-Level Representation Learning. ACL (1) Nayeon Kim, Yinhua Piao, Sun Kim
2023	J	`jnl`	Clinical Note Owns its Hierarchy: Multi-Level Hypergraph Neural Networks for Patient-Level Representation Learning. CoRR Nayeon Kim, Yinhua Piao, Sun Kim
2023	—	`conf`	Deep learning-based survival prediction using DNA methylation-derived 3D genomic information. BCB Jeewon Yang, Dohoon Lee, Bonil Koo, Dabin Jeong, Sun Kim
2023	J	`jnl`	GOAT: Gene-level biomarker discovery from multi-Omics data using graph ATtention neural network for eosinophilic asthma subtype. Bioinform. Dabin Jeong, Bonil Koo, Minsik Oh, Tae-Bum Kim, Sun Kim
2023	J	`jnl`	Improved drug response prediction by drug target data integration via network-based profiling. Briefings Bioinform. Minwoo Pak, Sangseon Lee, Inyoung Sung, Bonil Koo, Sun Kim
2023	J	`jnl`	Metheor: Ultrafast DNA methylation heterogeneity calculation from bisulfite read alignments. PLoS Comput. Biol. Dohoon Lee, Bonil Koo, Jeewon Yang, Sun Kim
2022	J	`jnl`	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. BMC Bioinform. Inyoung Sung, Sangseon Lee, Minwoo Pak, Yunyol Shin, Sun Kim
2022	—	`conf`	Embedding of FDA Approved Drugs in Chemical Space Using Cascade Autoencoder with Metric Learning. BigComp Jungwoo Kim, Sangsoo Lim, Sangseon Lee, Changyun Cho, Sun Kim
2022	J	`jnl`	Generative Modeling to Predict Multiple Suitable Conditions for Chemical Reactions. J. Chem. Inf. Model. Youngchun Kwon, Sun Kim, Youn-Suk Choi, Seokho Kang
2022	J	`jnl`	MLDEG: A Machine Learning Approach to Identify Differentially Expressed Genes Using Network Property and Network Propagation. IEEE ACM Trans. Comput. Biol. Bioinform. Ji Hwan Moon, Sangseon Lee, Minwoo Pak, Benjamin Hur, Sun Kim
2022	J	`jnl`	SPGP: Structure Prototype Guided Graph Pooling. CoRR Sangseon Lee, Dohoon Lee, Yinhua Piao, Sun Kim
2022	A*	`conf`	Sparse Structure Learning via Graph Neural Networks for Inductive Document Classification. AAAI Yinhua Piao, Sangseon Lee, Dohoon Lee, Sun Kim
2022	J	`jnl`	Triangular Contrastive Learning on Molecular Graphs. CoRR MinGyu Choi, Wonseok Shin, Yijingxiu Lu, Sun Kim
2021	J	`jnl`	A generalization of the modular equations of higher degrees. J. Comb. Theory A Sun Kim
2021	—	`conf`	A probabilistic model for pathway-guided gene set selection. BIBM Inyoung Kim, Sangseon Lee, Youngkuk Kim, Hugh Namkoong, Sun Kim
2021	J	`jnl`	BioVLAB-Cancer-Pharmacogenomics: tumor heterogeneity and pharmacogenomics analysis of multi-omics data from tumor on the cloud. Bioinform. Sungjoon Park, Dohoon Lee, Youngkuk Kim, Sangsoo Lim, Heejoon Chae, Sun Kim
2021	J	`jnl`	Erratum to: Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations. Briefings Bioinform. Minsik Oh, Sungjoon Park, Sun Kim, Heejoon Chae
2021	J	`jnl`	Handling Long-Tail Queries with Slice-Aware Conversational Systems. CoRR Cheng Wang, Sun Kim, Taiwoo Park, Sajal Choudhary, Sunghyun Park, Young-Bum Kim, Ruhi Sarikaya, Sungjin Lee
2021	—	`conf`	IDEA: Integrating Divisive and Ensemble-Agglomerate hierarchical clustering framework for arbitrary shape data. IEEE BigData Hongryul Ahn, Inuk Jung, Heejoon Chae, Minsik Oh, Inyoung Kim, Sun Kim
2021	J	`jnl`	Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations. Briefings Bioinform. Minsik Oh, Sungjoon Park, Sun Kim, Heejoon Chae
2021	J	`jnl`	Ranked k-Spectrum Kernel for Comparative and Evolutionary Comparison of Exons, Introns, and CpG Islands. IEEE ACM Trans. Comput. Biol. Bioinform. Sangseon Lee, Taeheon Lee, Yung-Kyun Noh, Sun Kim
2021	J	`jnl`	Sparse Structure Learning via Graph Neural Networks for Inductive Document Classification. CoRR Yinhua Piao, Sangseon Lee, Dohoon Lee, Sun Kim
2021	Misc	`conf`	TeamTat: A Collaborative Text Annotation Tool for Creating Gold-Standard Corpora. AMIA Rezarta Islamaj, Dongseop Kwon, Sun Kim, Zhiyong Lu
2021	J	`jnl`	Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches. Briefings Bioinform. Dohoon Lee, Youngjune Park, Sun Kim
2021	J	`jnl`	mirTime: identifying condition-specific targets of microRNA in time-series transcript data using Gaussian process model and spherical vector clustering. Bioinform. Hyejin Kang, Hongryul Ahn, Kyuri Jo, Minsik Oh, Sun Kim
2020	J	`jnl`	Better synonyms for enriching biomedical search. J. Am. Medical Informatics Assoc. Lana Yeganova, Sun Kim, Qingyu Chen, Grigory Balasanov, W. John Wilbur, Zhiyong Lu
2020	J	`jnl`	BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale. PLoS Comput. Biol. Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu
2020	J	`jnl`	Cancer subtype classification and modeling by pathway attention and propagation. Bioinform. Sangseon Lee, Sangsoo Lim, Taeheon Lee, Inyoung Sung, Sun Kim
2020	J	`jnl`	Comprehensive and critical evaluation of individualized pathway activity measurement tools on pan-cancer data. Briefings Bioinform. Sangsoo Lim, Sangseon Lee, Inuk Jung, SungMin Rhee, Sun Kim
2020	J	`jnl`	Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records. BMC Medical Informatics Decis. Mak. Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu
2020	—	`conf`	Homomorphic Computation of Local Alignment. BIBM Magsarjav Bataa, Siwoo Song, Kunsoo Park, Miran Kim, Jung Hee Cheon, Sun Kim
2020	J	`jnl`	TeamTat: a collaborative text annotation tool. CoRR Rezarta Islamaj Dogan, Dongseop Kwon, Sun Kim, Zhiyong Lu
2020	J	`jnl`	TeamTat: a collaborative text annotation tool. Nucleic Acids Res. Rezarta Islamaj Dogan, Dongseop Kwon, Sun Kim, Zhiyong Lu
2019	J	`jnl`	A secure SNP panel scheme using homomorphically encrypted K-mers without SNP calling on the user side. BMC Genom. Sungjoon Park, Minsu Kim, Seokjun Seo, Seungwan Hong, Kyoohyung Han, Keewoo Lee, Jung Hee Cheon, Sun Kim
2019	J	`jnl`	BioConceptVec: creating and evaluating literature-based biomedical concept embeddings on a large scale. CoRR Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu
2019	J	`jnl`	CaPSSA: visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data. Bioinform. Yeongjun Jang, Jihae Seo, Insu Jang, Byungwook Lee, Sun Kim, Sanghyuk Lee
2019	J	`jnl`	Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records. CoRR Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu
2019	—	`conf`	DeepFunNet: Deep Learning for Gene Functional Similarity Network Construction. BigComp Hongryul Ahn, SeungHyun Son, Sun Kim
2019	—	`conf`	Evaluation of Five Sentence Similarity Models on Electronic Medical Records. BCB Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu
2019	J	`jnl`	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. BMC Bioinform. Hongryul Ahn, Inuk Jung, Heejoon Chae, Dongwon Kang, Woosuk Jung, Sun Kim
2019	J	`jnl`	LitSense: making sense of biomedical literature at sentence level. Nucleic Acids Res. Alexis Allot, Qingyu Chen, Sun Kim, Roberto Vera Alvarez, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2019	J	`jnl`	Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database J. Biol. Databases Curation Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C. Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C. Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altinel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, Tung Tran, Ramakanth Kavuluru, Ling Luo, Albert Steppi, Jinfeng Zhang, Jinchan Qu, Zhiyong Lu
2019	J	`jnl`	PRISM: methylation pattern-based, reference-free inference of subclonal makeup. Bioinform. Do-Hoon Lee, Sangseon Lee, Sun Kim
2019	J	`jnl`	Venn-diaNet : venn diagram based network propagation analysis framework for comparing multiple biological experiments. BMC Bioinform. Benjamin Hur, Dongwon Kang, Sangseon Lee, Ji Hwan Moon, Gung Lee, Sun Kim
2018	A*	`conf`	A Fast Deep Learning Model for Textual Relevance in Biomedical Information Retrieval. WWW Sunil Mohan, Nicolas Fiorini, Sun Kim, Zhiyong Lu
2018	J	`jnl`	A Fast Deep Learning Model for Textual Relevance in Biomedical Information Retrieval. CoRR Sunil Mohan, Nicolas Fiorini, Sun Kim, Zhiyong Lu
2018	J	`jnl`	BRCA-Pathway: a structural integration and visualization system of TCGA breast cancer data on KEGG pathways. BMC Bioinform. Inyoung Kim, Saemi Choi, Sun Kim
2018	J	`jnl`	Cloud-BS: A MapReduce-based bisulfite sequencing aligner on cloud. J. Bioinform. Comput. Biol. Joungmin Choi, Yoonjae Park, Sun Kim, Heejoon Chae
2018	J	`jnl`	DeepFam: deep learning based alignment-free method for protein family modeling and prediction. Bioinform. Seokjun Seo, Minsik Oh, Youngjune Park, Sun Kim
2018	J	`jnl`	Discovering themes in biomedical literature using a projection-based algorithm. BMC Bioinform. Lana Yeganova, Sun Kim, Grigory Balasanov, W. John Wilbur
2018	J	`jnl`	Editorial for Selected Papers of a Joint Conferences, Genome Informatics Workshop/International Conference on Bioinformatics (GIW/InCoB) 2015. IEEE ACM Trans. Comput. Biol. Bioinform. Sun Kim
2018	—	`conf`	HTRgene: Integrating Multiple Heterogeneous Time-series Data to Investigate Cold and Heat Stress Response Signaling Genes in Arabidopsis. BIBM Hongryul Ahn, Inuk Jung, Heejoon Chae, Dongwon Kang, Woosuk Jung, Sun Kim
2018	A*	`conf`	Hybrid Approach of Relation Network and Localized Graph Convolutional Filtering for Breast Cancer Subtype Classification. IJCAI SungMin Rhee, Seokjun Seo, Sun Kim
2018	—	`conf`	Identifying stress-related genes and predicting stress types in Arabidopsis using logical correlation layer and CMCL loss through time-series data. BIBM Dongwon Kang, Hongryul Ahn, Sangseon Lee, Chai-Jin Lee, Jihye Hur, Woosuk Jung, Sun Kim
2018	—	`conf`	Sentence Similarity Measures Revisited: Ranking Sentences in PubMed Documents. BCB Qingyu Chen, Sun Kim, W. John Wilbur, Zhiyong Lu
2018	J	`jnl`	The Circle Problem of Gauss and the Divisor Problem of Dirichlet - Still Unsolved. Am. Math. Mon. Bruce C. Berndt, Sun Kim, Alexandru Zaharescu
2018	J	`jnl`	The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature. BMC Syst. Biol. Inuk Jung, Hyejin Kang, Jang Uk Kim, Hyeonsook Chang, Sun Kim, Woosuk Jung
2018	J	`jnl`	ezTag: tagging biomedical concepts via interactive learning. Nucleic Acids Res. Dongseop Kwon, Sun Kim, Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
2017	—	`conf`	BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations. BioNLP Rezarta Islamaj Dogan, Andrew Chatr-aryamontri, Sun Kim, Chih-Hsuan Wei, Yifan Peng, Donald C. Comeau, Zhiyong Lu
2017	J	`jnl`	Bridging the gap: Incorporating a semantic similarity measure for effectively mapping PubMed queries to documents. J. Biomed. Informatics Sun Kim, Nicolas Fiorini, W. John Wilbur, Zhiyong Lu
2017	—	`conf`	Deep Learning for Biomedical Information Retrieval: Learning Textual Relevance from Click Logs. BioNLP Sunil Mohan, Nicolas Fiorini, Sun Kim, Zhiyong Lu
2017	—	`conf`	Flow maximization analysis of cell cycle pathway activation status in breast cancer subtypes. BigComp Sangseon Lee, Ji Hwan Moon, Youngjune Park, Sun Kim
2017	J	`jnl`	Hybrid Approach of Relation Network and Localized Graph Convolutional Filtering for Breast Cancer Subtype Classification. CoRR SungMin Rhee, Seokjun Seo, Sun Kim
2017	—	`conf`	Integration of heterogeneous time series gene expression data by clustering on time dimension. BigComp Hongryul Ahn, Heejoon Chae, Woosuk Jung, Sun Kim
2017	J	`jnl`	Iterative segmented least square method for functional microRNA-mRNA module discovery in breast cancer. Int. J. Data Min. Bioinform. SungMin Rhee, Sangsoo Lim, Sun Kim
2017	J	`jnl`	PINTnet: construction of condition-specific pathway interaction network by computing shortest paths on weighted PPI. BMC Syst. Biol. Ji Hwan Moon, Sangsoo Lim, Kyuri Jo, Sangseon Lee, Seokjun Seo, Sun Kim
2017	J	`jnl`	The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions. Database J. Biol. Databases Curation Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-aryamontri, Christie S. Chang, Rose Oughtred, Jennifer M. Rust, W. John Wilbur, Donald C. Comeau, Kara Dolinski, Mike Tyers
2017	J	`jnl`	TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes. Bioinform. Inuk Jung, Kyuri Jo, Hyejin Kang, Hongryul Ahn, Youngjae Yu, Sun Kim
2016	J	`jnl`	BioC viewer: a web-based tool for displaying and merging annotations in BioC. Database J. Biol. Databases Curation Soo-Yong Shin, Sun Kim, W. John Wilbur, Dongseop Kwon
2016	—	`conf`	BioCconvert: A Conversion Tool Between BioC and PubAnnotation. ICBO/BioCreative Donald C. Comeau, Rezarta Islamaj Dogan, Sun Kim, Chih-Hsuan Wei, W. John Wilbur, Zhiyong Lu
2016	J	`jnl`	BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database J. Biol. Databases Curation Sun Kim, Rezarta Islamaj Dogan, Andrew Chatr-aryamontri, Christie S. Chang, Rose Oughtred, Jennifer M. Rust, Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou, Sérgio Matos, André Santos, David Campos, José Luís Oliveira, Onkar Singh, Jitendra Jonnagaddala, Hong-Jie Dai, Emily Chia-Yu Su, Yung-Chun Chang, Yu-Chen Su, Chun-Han Chu, Chien Chin Chen, Wen-Lian Hsu, Yifan Peng, Cecilia N. Arighi, Cathy H. Wu, K. Vijay-Shanker, Ferhat Aydin, Zehra Melce Hüsünbeyi, Arzucan Özgür, Soo-Yong Shin, Dongseop Kwon, Kara Dolinski, Mike Tyers, W. John Wilbur, Donald C. Comeau
2016	J	`jnl`	Bridging the Gap: a Semantic Similarity Measure between Queries and Documents. CoRR Sun Kim, W. John Wilbur, Zhiyong Lu
2016	J	`jnl`	Clustering and evolutionary analysis of small RNAs identify regulatory siRNA clusters induced under drought stress in rice. BMC Syst. Biol. Inuk Jung, Hongryul Ahn, Seon-Ju Shin, Jukon Kim, Hawk-Bin Kwon, Woosuk Jung, Sun Kim
2016	J	`jnl`	Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways. Bioinform. Kyuri Jo, Inuk Jung, Ji Hwan Moon, Sun Kim
2016	J	`jnl`	Information theoretic sub-network mining characterizes breast cancer subtypes in terms of cancer core mechanisms. J. Bioinform. Comput. Biol. Jinwoo Park, Benjamin Hur, SungMin Rhee, Sangsoo Lim, Min-Su Kim, Kwangsoo Kim, Wonshik Han, Sun Kim
2016	—	`conf`	Iterative segmented least square method for functional microRNA-mRNA module discovery in breast cancer. BIBM SungMin Rhee, Sangsoo Lim, Sun Kim
2016	—	`conf`	Networks and models for the integrated analysis of multi omics data. BIBM Sun Kim
2016	J	`jnl`	Prioritizing biological pathways by recognizing context in time-series gene expression data. BMC Bioinform. Jusang Lee, Kyuri Jo, Sunwon Lee, Jaewoo Kang, Sun Kim
2016	—	`conf`	PubTermVariants: biomedical term variants and their use for PubMed search. BioNLP@ACL Lana Yeganova, Won Kim, Sun Kim, Rezarta Islamaj Dogan, Wanli Liu, Donald C. Comeau, Zhiyong Lu, W. John Wilbur
2016	J	`jnl`	RDDpred: a condition-specific RNA-editing prediction model from RNA-seq data. BMC Genom. Min-Su Kim, Benjamin Hur, Sun Kim
2016	J	`jnl`	Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines. BMC Syst. Biol. Heejoon Chae, Sangseon Lee, Kenneth P. Nephew, Sun Kim
2015	J	`jnl`	BioVLAB-MMIA-NGS: microRNA-mRNA integrated analysis using high-throughput sequencing data. Bioinform. Heejoon Chae, SungMin Rhee, Kenneth P. Nephew, Sun Kim
2015	J	`jnl`	Extracting drug-drug interactions from literature using a rich feature-based linear kernel approach. J. Biomed. Informatics Sun Kim, Haibin Liu, Lana Yeganova, W. John Wilbur
2015	J	`jnl`	Identifying named entities from PubMed®; for enriching semantic categories. BMC Bioinform. Sun Kim, Zhiyong Lu, W. John Wilbur
2015	A*	`conf`	Summarizing Topical Contents from PubMed Documents Using a Thematic Analysis. EMNLP Sun Kim, Lana Yeganova, W. John Wilbur
2015	J	`jnl`	Weighted divisor sums and Bessel function series, V. J. Approx. Theory Bruce C. Berndt, Sun Kim, Alexandru Zaharescu
2014	—	`conf`	An algorithm for identifying differentially expressed genes in multiclass RNA-seq samples. BigComp Jaehyun An, Kwangsoo Kim, Sun Kim
2014	J	`jnl`	Assisting manual literature curation for protein-protein interactions using BioQRator. Database J. Biol. Databases Curation Dongseop Kwon, Sun Kim, Soo-Yong Shin, Andrew Chatr-aryamontri, W. John Wilbur
2014	J	`jnl`	Author name disambiguation for PubMed. J. Assoc. Inf. Sci. Technol. Wanli Liu, Rezarta Islamaj Dogan, Sun Kim, Donald C. Comeau, Won Kim, Lana Yeganova, Zhiyong Lu, W. John Wilbur
2014	Misc	`conf`	Extracting drug-drug interactions from literature using a rich feature-based linear kernel approach. AMIA Sun Kim, Haibin Liu, Lana Yeganova, W. John Wilbur
2014	J	`jnl`	Partitions with part difference conditions and Bressoud's conjecture. J. Comb. Theory A Sun Kim, Ae Ja Yee
2014	J	`jnl`	Retro: concept-based clustering of biomedical topical sets. Bioinform. Lana Yeganova, Won Kim, Sun Kim, W. John Wilbur
2014	J	`jnl`	piClust: A density based piRNA clustering algorithm. Comput. Biol. Chem. Inuk Jung, Jong Chan Park, Sun Kim
2013	J	`jnl`	Bio and health informatics meets cloud : BioVLab as an example. Health Inf. Sci. Syst. Heejoon Chae, Inuk Jung, Hyungro Lee, Suresh Marru, Seong-Whan Lee, Sun Kim
2013	J	`jnl`	Designing discriminative spatial filter vectors in motor imagery brain-computer interface. Int. J. Imaging Syst. Technol. Kyeong-Yeon Lee, Sun Kim
2013	J	`jnl`	Genome-Wide Analysis and Modeling of DNA methylation susceptibility in 30 Breast Cancer Cell Lines by using CPG Flanking Sequences. J. Bioinform. Comput. Biol. Jaehyun An, Kwangsoo Kim, SungMin Rhee, Heejoon Chae, Kenneth P. Nephew, Sun Kim
2013	J	`jnl`	Integrated profiling of three dimensional cell culture models and 3D microscopy. Bioinform. Cemal Çagatay Bilgin, Sun Kim, Elle Leung, Hang Chang, Bahram Parvin
2013	J	`jnl`	The Rogers-Ramanujan-Gordon identities, the generalized Göllnitz-Gordon identities, and parity questions. J. Comb. Theory A Sun Kim, Ae Ja Yee
2013	—	`conf`	Towards simultaneous clustering and motif-modeling for a large number of protein family. BIBM Young Joon Yoo, Tushar Sandhan, Jin Young Choi, Sun Kim
2012	J	`jnl`	A novel k-mer mixture logistic regression for methylation susceptibility modeling of CpG dinucleotides in human gene promoters. BMC Bioinform. Youngik Yang, Kenneth P. Nephew, Sun Kim
2012	—	`conf`	Classifying Gene Sentences in Biomedical Literature by Combining High-Precision Gene Identifiers. BioNLP@HLT-NAACL Sun Kim, Won Kim, Donald C. Comeau, W. John Wilbur
2012	B	`conf`	Discriminative spatial pattern vectors selection for motor imagery classification. SMC Kyeong-Yeon Lee, Sun Kim
2012	J	`jnl`	GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis. Bioinform. Vikas Rao Pejaver, Jaehyun An, SungMin Rhee, Ankita Bhan, Jeong-Hyeon Choi, Boshu Liu, Heewook Lee, Pamela J. Brown, David Kysela, Yves V. Brun, Sun Kim
2012	J	`jnl`	Introduction. J. Bioinform. Comput. Biol. Sun Kim, Wei Wang
2012	J	`jnl`	PIE Bioinform. Sun Kim, Dongseop Kwon, Soo-Yong Shin, W. John Wilbur
2012	J	`jnl`	Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information. Database J. Biol. Databases Curation Sun Kim, Won Kim, Chih-Hsuan Wei, Zhiyong Lu, W. John Wilbur
2012	J	`jnl`	Thematic clustering of text documents using an EM-based approach. J. Biomed. Semant. Sun Kim, W. John Wilbur
2011	—	`ed.`	ACM International Conference on Bioinformatics, Computational Biology and Biomedicine, BCB' 11, Chicago, IL, USA - July 31 - August 03, 2011 BCB Robert Grossman, Andrey Rzhetsky, Sun Kim, Wei Wang
2011	—	`conf`	An EM Clustering Algorithm which Produces a Dual Representation. ICMLA (2) Sun Kim, W. John Wilbur
2011	—	`conf`	BioVLAB-MMIA: A Reconfigurable Cloud Computing Environment for microRNA and mRNA Integrated Analysis. BIBM Hyungro Lee, Youngik Yang, Heejoon Chae, Seungyoon Nam, Donghoon Choi, Patanachai Tangchaisin, Chathura Herath, Suresh Marru, Kenneth P. Nephew, Sun Kim
2011	J	`jnl`	Classifying protein-protein interaction articles using word and syntactic features. BMC Bioinform. Sun Kim, W. John Wilbur
2011	J	`jnl`	Göllnitz-Gordon identities and parity questions. Eur. J. Comb. Sun Kim, Ae Ja Yee
2011	—	`conf`	Sequence-Based Enzyme Catalytic Domain Prediction Using Clustering and Aggregated Mutual Information Content. HISB Kwangmin Choi, Sun Kim
2011	J	`jnl`	Sequence-Based enzyme catalytic Domain Prediction Using Clustering and Aggregated Mutual Information Content. J. Bioinform. Comput. Biol. Kwangmin Choi, Sun Kim
2011	J	`jnl`	The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinform. Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew G. Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers, Gerold Schneider, Fabio Rinaldi, Robert Leaman, Graciela Gonzalez, Sérgio Matos, Sun Kim, W. John Wilbur, Luis M. Rocha, Hagit Shatkay, Ashish V. Tendulkar, Shashank Agarwal, Feifan Liu, Xinglong Wang, Rafal Rak, Keith Noto, Charles Elkan, Zhiyong Lu
2011	—	`conf`	Transitioning BioVLab cloud workbench to a science gateway. TG Suresh Marru, Heejoon Chae, Patanachai Tangchaisin, Sun Kim, Marlon E. Pierce, Kenneth P. Nephew
2010	J	`jnl`	Annotation confidence score for genome annotation: a genome comparison approach. Bioinform. Youngik Yang, Donald Gilbert, Sun Kim
2010	J	`jnl`	Data mining for the study of disease genes and proteins. Artif. Intell. Medicine Sun Kim
2010	—	`conf`	EGGSlicer: predicting biologically meaningful gene sets from gene clusters using gene ontology information. BCB Heejoon Chae, Kwangmin Choi, Sun Kim, Haleh Ashki
2010	—	`conf`	Gene cluster profile vectors: A novel method to infer functional coupling using both gene proximity and co-occurrence profiles. BIBM Vikas Rao Pejaver, Sun Kim
2009	J	`jnl`	Bijective proofs of partition identities arising from modular equations. J. Comb. Theory A Sun Kim
2009	J	`jnl`	Computational analysis of microRNA profiles and their target genes suggests significant involvement in breast cancer antiestrogen resistance. Bioinform. Fuxiao Xin, Meng Li, Curtis Balch, Michael Thomson, Meiyun Fan, Yunlong Liu, Scott M. Hammond, Sun Kim, Kenneth P. Nephew
2009	J	`jnl`	Ensembled support vector machines for human papillomavirus risk type prediction from protein secondary structures. Comput. Biol. Medicine Sun Kim, Jeongmi Kim, Byoung-Tak Zhang
2009	A	`conf`	Evolutionary hypernetwork classifiers for protein-proteininteraction sentence filtering. GECCO Jakramate Bootkrajang, Sun Kim, Byoung-Tak Zhang
2009	B	`conf`	Evolving hypernetwork models of binary time series for forecasting price movements on stock markets. IEEE Congress on Evolutionary Computation Elena Bautu, Sun Kim, Andrei Bautu, Henri Luchian, Byoung-Tak Zhang
2009	—	`conf`	Experience report: issues in comparing gene function annotation in text. SIGDOC Youngik Yang, Sun Kim
2009	J	`jnl`	MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. Nucleic Acids Res. Seungyoon Nam, Meng Li, Kwangmin Choi, Curtis Balch, Sun Kim, Kenneth P. Nephew
2008	—	`ed.`	2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008, Philadephia, Pennsylvania, USA, November 3-5, 2008 BIBM Xue-wen Chen, Xiaohua Hu, Sun Kim
2008	J	`jnl`	A gene pattern mining algorithm using interchangeable gene sets for prokaryotes. BMC Bioinform. Meng Hu, Kwangmin Choi, Wei Su, Sun Kim, Jiong Yang
2008	J	`jnl`	A machine-learning approach to combined evidence validation of genome assemblies. Bioinform. Jeong-Hyeon Choi, Sun Kim, Haixu Tang, Justen Andrews, Don G. Gilbert, John Colbourne
2008	—	`conf`	BioVLAB-Microarray: Microarray Data Analysis in Virtual Environment. eScience Youngik Yang, Jong Youl Choi, Kwangmin Choi, Marlon E. Pierce, Dennis Gannon, Sun Kim
2008	J	`jnl`	ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts. BMC Bioinform. Kwangmin Choi, Sun Kim
2008	J	`jnl`	Enriched transcription factor binding sites in hypermethylated gene promoters in drug resistant cancer cells. Bioinform. Meng Li, Hyun-il Henry Paik, Curtis Balch, Yoosung Kim, Lang Li, Tim Hui-Ming Huang, Kenneth P. Nephew, Sun Kim
2008	J	`jnl`	PIE: an online prediction system for protein-protein interactions from text. Nucleic Acids Res. Sun Kim, Soo-Yong Shin, In-Hee Lee, Soo-Jin Kim, Ram Sriram, Byoung-Tak Zhang
2008	Misc	`conf`	Predicting DNA Methylation Susceptibility Using CpG Flanking Sequences. Pacific Symposium on Biocomputing Sun Kim, Meng Li, Hyun-il Henry Paik, Kenneth P. Nephew, Huidong Shi, Robin Kramer, Dong Xu, Tim Hui-Ming Huang
2007	J	`jnl`	A Study of Residue Correlation within Protein Sequences and Its Application to Sequence Classification. EURASIP J. Bioinform. Syst. Biol. Christopher Michael Hemmerich, Sun Kim
2007	—	`ch.`	Bioinformatics: Mining the Massive Data from High Throughput Genomics Experiments. Analysis of Biological Data: A Soft Computing Approach Haixu Tang, Sun Kim
2007	C	`conf`	CLASSEQ: Classification of Sequences via Comparative Analysis of Multiple Genomes. ICMLA Kwangmin Choi, Youngik Yang, Sun Kim
2007	—	`conf`	EGGS: Extraction of Gene Clusters Using Genome Context Based Sequence Matching Techniques. BIBM Sun Kim, Ankita Bhan, Bharath K. Maryada, Kwangmin Choi, Yves V. Brun
2007	B	`conf`	Evolving hypernetwork classifiers for microRNA expression profile analysis. IEEE Congress on Evolutionary Computation Sun Kim, Soo-Jin Kim, Byoung-Tak Zhang
2007	C	`conf`	Finding Cancer-Related Gene Combinations Using a Molecular Evolutionary Algorithm. BIBE Chan-Hoon Park, Soo-Jin Kim, Sun Kim, Dong-Yeon Cho, Byoung-Tak Zhang
2007	J	`jnl`	dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis. Bioinform. Seung-Hee Bae, Haixu Tang, Jing Wu, Jun Xie, Sun Kim
2006	—	`conf`	A Tree Kernel-Based Method for Protein-Protein Interaction Mining from Biomedical Literature. KDLL Jae-Hong Eom, Sun Kim, Seong-Hwan Kim, Byoung-Tak Zhang
2006	J	`jnl`	A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha. Bioinform. Lang Li, Alfred S. L. Cheng, Victor X. Jin, Henry H. Paik, Meiyun Fan, Xiaoman Li, Wei Zhang, Jason Robarge, Curtis Balch, Ramana V. Davuluri, Sun Kim, Tim Hui-Ming Huang, Kenneth P. Nephew
2006	J	`jnl`	ARCS: an aggregated related column scoring scheme for aligned sequences. Bioinform. Bin Song, Jeong-Hyeon Choi, Guangyu Chen, Jacek Szymanski, Guo-Qiang Zhang, Anthony K. H. Tung, Jaewoo Kang, Sun Kim, Jiong Yang
2006	J	`jnl`	Advanced Signal Processing Techniques for Bioinformatics. EURASIP J. Adv. Signal Process. Xue-wen Chen, Sun Kim, Vladimir I. Pavlovic, David P. Casasent
2006	—	`conf`	An Approximate de Bruijn Graph Approach to Multiple Local Alignment and Motif Discovery in Protein Sequences. VDMB Rupali Patwardhan, Haixu Tang, Sun Kim, Mehmet M. Dalkilic
2006	J	`jnl`	BAG: a graph theoretic sequence clustering algorithm. Int. J. Data Min. Bioinform. Sun Kim, Jason Lee
2006	J	`jnl`	COMPAM : visualization of combining pairwise alignments for multiple genomes. Bioinform. Do-Hoon Lee, Jeong-Hyeon Choi, Mehmet M. Dalkilic, Sun Kim
2006	—	`ed.`	Data Mining and Bioinformatics, First International Workshop, VDMB 2006, Seoul, Korea, September 11, 2006, Revised Selected Papers VDMB Mehmet M. Dalkilic, Sun Kim, Jiong Yang
2006	—	`conf`	Genome Data Type: a Vehicle to Deliver a Genome Comparison System on the Web. ICDM Workshops Kwangmin Choi, Amit Saple, Sun Kim
2006	—	`conf`	Human Papillomavirus Risk Type Classification from Protein Sequences Using Support Vector Machines. EvoWorkshops Sun Kim, Byoung-Tak Zhang
2006	—	`conf`	Prediction of the Human Papillomavirus Risk Types Using Gap-Spectrum Kernels. ISNN (2) Sun Kim, Jae-Hong Eom
2006	J	`jnl`	REFINEMENT: A search framework for the identification of interferon-responsive elements in DNA sequences - a case study with ISRE and GAS. Comput. Biol. Chem. Takuma Tsukahara, Sun Kim, Milton W. Taylor
2006	B	`conf`	Text Classifiers Evolved on a Simulated DNA Computer. IEEE Congress on Evolutionary Computation Sun Kim, Min-Oh Heo, Byoung-Tak Zhang
2005	—	`conf`	An Application of Support Vector Machines for Customer Churn Analysis: Credit Card Case. ICNC (2) Sun Kim, Kyung-shik Shin, Kyungdo Park
2005	—	`conf`	Cluster Utility: A New Metric for Clustering Biological Sequences. CSB Workshops Jason Lee, Sun Kim
2005	J	`jnl`	GAME: A simple and efficient whole genome alignment method using maximal exact match filtering. Comput. Biol. Chem. Jeong-Hyeon Choi, Hwan-Gue Cho, Sun Kim
2005	—	`conf`	Gene Teams with Relaxed Proximity Constraint. CSB Sun Kim, Jeong-Hyeon Choi, Jiong Yang
2005	—	`conf`	Motif discovery for proteins using subsequence clustering. BIOKDD Hardik A. Sheth, Sun Kim
2005	—	`conf`	PLATCOM: Current Status and Plan for the Next Stages. DILS Kwangmin Choi, Jeong-Hyeon Choi, Amit Saple, Zhiping Wang, Jason Lee, Sun Kim
2005	—	`conf`	PLATCOM: a Platform for Computational Comparative Genomics on the Web. CSB Workshops Kwangmin Choi, Jeong-Hyeon Choi, Amit Saple, Zhiping Wang, Jason Lee, Sun Kim
2005	J	`jnl`	PLATCOM: a Platform for Computational Comparative Genomics. Bioinform. Kwangmin Choi, Yu Ma, Jeong-Hyeon Choi, Sun Kim
2004	Misc	`conf`	Guiding motif discovery by iterative pattern refinement. SAC Zhiping Wang, Mehmet M. Dalkilic, Sun Kim
2004	B	`conf`	Multi-objective Evolutionary Probe Design Based on Thermodynamic Criteria for HPV Detection. PRICAI In-Hee Lee, Sun Kim, Byoung-Tak Zhang
2004	—	`conf`	Multiple Genome Alignment by Clustering Pairwise Matches. Comparative Genomics Jeong-Hyeon Choi, Kwangmin Choi, Hwan-Gue Cho, Sun Kim
2003	J	`jnl`	Genetic Mining of HTML Structures for Effective Web-Document Retrieval. Appl. Intell. Sun Kim, Byoung-Tak Zhang
2003	—	`ch.`	Graph Theoretic Sequence Clustering Algorithms and Their Applications to Genome Comparison. Computational Biology and Genome Informatics Sun Kim
2003	—	`conf`	Motif Discovery from Large Number of Sequences: A Case Study with Disease Resistance Genes in Arabidopsos thaliana. METMBS Irfan Gunduz, Sihui Zhao, Mehmet M. Dalkilic, Sun Kim
2001	—	`conf`	A probabilistic approach to sequence assembly validation. BIOKDD Sun Kim, Li Liao, Jean-François Tomb
2001	B	`conf`	Evolutionary learning of Web-document structure for information retrieval. CEC Sun Kim, Byoung-Tak Zhang
2000	—	`conf`	Web-Document Retrieval by Genetic Learning of Importance Factors for HTML Tags. PRICAI Workshop on Text and Web Mining Sun Kim, Byoung-Tak Zhang
1999	J	`jnl`	A New String-Pattern Matching Algorithm Using Partitioning and Hashing Efficiently. ACM J. Exp. Algorithmics Sun Kim
1999	J	`jnl`	AMASS: A Structured Pattern Matching Approach to Shotgun Sequence Assembly. J. Comput. Biol. Sun Kim, Alberto Maria Segre
1999	—	`conf`	SCAI TREC-8 Experiments. TREC Dong-Ho Shin, Yu-Hwan Kim, Sun Kim, Jae-Hong Eom, Hyung-Joo Shin, Byoung-Tak Zhang
1994	A*	`conf`	ModGen: Theorem Proving by Model Generation. AAAI Sun Kim, Hantao Zhang