ModGen: Theorem Proving by Model Generation. - Sun Kim; Hantao Zhang 001 (AAAI, 1994)

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

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

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

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

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

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

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

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

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

Multi-objective Evolutionary Probe Design Based on Thermodynamic Criteria for HPV Detection. - In-Hee Lee 001; Sun Kim; Byoung-Tak Zhang (PRICAI, 2004)

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

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

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

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

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

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

An Application of Support Vector Machines for Customer Churn Analysis: Credit Card Case. - Sun Kim; Kyung-shik Shin; Kyungdo Park (ICNC (2), 2005)

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

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

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

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

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

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

Prediction of the Human Papillomavirus Risk Types Using Gap-Spectrum Kernels. - Sun Kim; Jae-Hong Eom (ISNN (2), 2006)

A Tree Kernel-Based Method for Protein-Protein Interaction Mining from Biomedical Literature. - Jae-Hong Eom; Sun Kim; Seong-Hwan Kim 006; Byoung-Tak Zhang (KDLL, 2006)

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

COMPAM : visualization of combining pairwise alignments for multiple genomes. - Do-Hoon Lee; Jeong-Hyeon Choi; Mehmet M. Dalkilic; Sun Kim (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. - Lang Li 001; 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; et al. (Bioinform., 2006)

ARCS: an aggregated related column scoring scheme for aligned sequences. - Bin Song; Jeong-Hyeon Choi; Guangyu Chen; Jacek Szymanski; Guo-Qiang Zhang 001; Anthony K. H. Tung; Jaewoo Kang; Sun Kim; Jiong Yang 001 (Bioinform., 2006)

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

Advanced Signal Processing Techniques for Bioinformatics. - Xue-wen Chen 001; Sun Kim; Vladimir I. Pavlovic; David P. Casasent (EURASIP J. Adv. Signal Process., 2006)

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

Bioinformatics: Mining the Massive Data from High Throughput Genomics Experiments. - Haixu Tang; Sun Kim (Analysis of Biological Data: A Soft Computing Approach, 2007)

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

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

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

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

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

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

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

Predicting DNA Methylation Susceptibility Using CpG Flanking Sequences. - Sun Kim; Meng Li 013; Hyun-il Henry Paik; Kenneth P. Nephew; Huidong Shi; Robin Kramer; Dong Xu; Tim Hui-Ming Huang (Pacific Symposium on Biocomputing, 2008)

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

Enriched transcription factor binding sites in hypermethylated gene promoters in drug resistant cancer cells. - Meng Li 013; Hyun-il Henry Paik; Curtis Balch; Yoosung Kim; Lang Li 001; Tim Hui-Ming Huang; Kenneth P. Nephew; Sun Kim (Bioinform., 2008)

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

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

PIE: an online prediction system for protein-protein interactions from text. - Sun Kim; Soo-Yong Shin; In-Hee Lee 001; Soo-Jin Kim; Ram Sriram; Byoung-Tak Zhang (Nucleic Acids Res., 2008)

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

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

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

Computational analysis of microRNA profiles and their target genes suggests significant involvement in breast cancer antiestrogen resistance. - Fuxiao Xin; Meng Li 013; Curtis Balch; Michael Thomson; Meiyun Fan; Yunlong Liu; Scott M. Hammond; Sun Kim; Kenneth P. Nephew (Bioinform., 2009)

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

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

MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. - Seungyoon Nam; Meng Li 013; Kwangmin Choi; Curtis Balch; Sun Kim; Kenneth P. Nephew (Nucleic Acids Res., 2009)

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

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

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

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

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

An EM Clustering Algorithm which Produces a Dual Representation. - Sun Kim; W. John Wilbur (ICMLA (2), 2011)

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

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

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. - 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; et al. (BMC Bioinform., 2011)

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

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

Classifying Gene Sentences in Biomedical Literature by Combining High-Precision Gene Identifiers. - Sun Kim; Won Kim 003; Donald C. Comeau; W. John Wilbur (BioNLP@HLT-NAACL, 2012)

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

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information. - Sun Kim; Won Kim 003; Chih-Hsuan Wei; Zhiyong Lu; W. John Wilbur (Database J. Biol. Databases Curation, 2012)

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

GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis. - 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 (Bioinform., 2012)

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

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

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

Towards simultaneous clustering and motif-modeling for a large number of protein family. - Young Joon Yoo; Tushar Sandhan; Jin Young Choi 002; Sun Kim (BIBM, 2013)

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

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

Designing discriminative spatial filter vectors in motor imagery brain-computer interface. - Kyeong-Yeon Lee; Sun Kim (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. - Jaehyun An; Kwangsoo Kim; SungMin Rhee; Heejoon Chae; Kenneth P. Nephew; Sun Kim (J. Bioinform. Comput. Biol., 2013)

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

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

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

Retro: concept-based clustering of biomedical topical sets. - Lana Yeganova; Won Kim 003; Sun Kim; W. John Wilbur (Bioinform., 2014)

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

Author name disambiguation for PubMed. - Wanli Liu; Rezarta Islamaj Dogan; Sun Kim; Donald C. Comeau; Won Kim 003; Lana Yeganova; Zhiyong Lu; W. John Wilbur (J. Assoc. Inf. Sci. Technol., 2014)

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

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

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

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

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

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

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

PubTermVariants: biomedical term variants and their use for PubMed search. - Lana Yeganova; Won Kim 003; Sun Kim; Rezarta Islamaj Dogan; Wanli Liu; Donald C. Comeau; Zhiyong Lu; W. John Wilbur (BioNLP@ACL, 2016)

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

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. - 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 001; et al. (Database J. Biol. Databases Curation, 2016)

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

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

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

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

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

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

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

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

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

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

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

BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations. - Rezarta Islamaj Dogan; Andrew Chatr-aryamontri; Sun Kim; Chih-Hsuan Wei; Yifan Peng 002; Donald C. Comeau; Zhiyong Lu (BioNLP, 2017)

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

The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions. - 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 (Database J. Biol. Databases Curation, 2017)

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

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

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

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

Sentence Similarity Measures Revisited: Ranking Sentences in PubMed Documents. - Qingyu Chen 001; Sun Kim; W. John Wilbur; Zhiyong Lu (BCB, 2018)

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

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

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

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

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

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

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

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

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

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

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

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

Evaluation of Five Sentence Similarity Models on Electronic Medical Records. - Qingyu Chen 001; Jingcheng Du; Sun Kim; W. John Wilbur; Zhiyong Lu (BCB, 2019)

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

Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. - Rezarta Islamaj Dogan; Sun Kim; Andrew Chatr-aryamontri; Chih-Hsuan Wei; Donald C. Comeau; Rui Antunes 002; Sérgio Matos; Qingyu Chen 001; Aparna Elangovan; Nagesh C. Panyam; Karin Verspoor; Hongfang Liu; et al. (Database J. Biol. Databases Curation, 2019)

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

PRISM: methylation pattern-based, reference-free inference of subclonal makeup. - Do-Hoon Lee; Sangseon Lee; Sun Kim (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. - Hongryul Ahn; Inuk Jung; Heejoon Chae; Dongwon Kang; Woosuk Jung; Sun Kim (BMC Bioinform., 2019)

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

A secure SNP panel scheme using homomorphically encrypted K-mers without SNP calling on the user side. - Sungjoon Park; Minsu Kim; Seokjun Seo; Seungwan Hong 001; Kyoohyung Han; Keewoo Lee; Jung Hee Cheon; Sun Kim (BMC Genom., 2019)

LitSense: making sense of biomedical literature at sentence level. - Alexis Allot; Qingyu Chen 001; Sun Kim; Roberto Vera Alvarez; Donald C. Comeau; W. John Wilbur; Zhiyong Lu (Nucleic Acids Res., 2019)

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

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

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

Better synonyms for enriching biomedical search. - Lana Yeganova; Sun Kim; Qingyu Chen 001; Grigory Balasanov; W. John Wilbur; Zhiyong Lu (J. Am. Medical Informatics Assoc., 2020)

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

BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale. - Qingyu Chen 001; Kyubum Lee; Shankai Yan; Sun Kim; Chih-Hsuan Wei; Zhiyong Lu (PLoS Comput. Biol., 2020)

Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records. - Qingyu Chen 001; Jingcheng Du; Sun Kim; W. John Wilbur; Zhiyong Lu (BMC Medical Informatics Decis. Mak., 2020)

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

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

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

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

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

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

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

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

Handling Long-Tail Queries with Slice-Aware Conversational Systems. - Cheng Wang 002; Sun Kim; Taiwoo Park; Sajal Choudhary; Sunghyun Park; Young-Bum Kim; Ruhi Sarikaya; Sungjin Lee (CoRR, 2021)

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

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

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

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

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. - Inyoung Sung; Sangseon Lee; Minwoo Pak; Yunyol Shin; Sun Kim (BMC Bioinform., 2022)

Triangular Contrastive Learning on Molecular Graphs. - MinGyu Choi; Wonseok Shin 002; Yijingxiu Lu; Sun Kim (CoRR, 2022)

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

Generative Modeling to Predict Multiple Suitable Conditions for Chemical Reactions. - Youngchun Kwon; Sun Kim; Youn-Suk Choi; Seokho Kang 001 (J. Chem. Inf. Model., 2022)

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

Clinical Note Owns its Hierarchy: Multi-Level Hypergraph Neural Networks for Patient-Level Representation Learning. - Nayeon Kim 008; Yinhua Piao; Sun Kim (ACL (1), 2023)

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

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

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

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

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

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

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

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

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

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

Taxonomy and Analysis of Sensitive User Queries in Generative AI Search. - 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; et al. (CoRR, 2024)

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

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

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

Taxonomy and Analysis of Sensitive User Queries in Generative AI Search System. - 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; et al. (NAACL (Findings), 2025)

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

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

GraphT5: Unified Molecular Graph-Language Modeling via Multi-Modal Cross-Token Attention. - Sangyeup Kim; Nayeon Kim 008; Yinhua Piao; Sun Kim (CoRR, 2025)

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

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

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

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