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Recent Journal Publications

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 [2011]

-           Hyojung Paik, Eunjung Lee, Inho Park, Junho Kim, Doheon Lee, "Prediction of cancer prognosis with the genetic basis of transcriptional variations," Genomics 2011 [PDF] *Cover Article

-           Hyojung Paik, Taewoo Ryu, Hyoung-Sam Heo, Seung-Won Seo, Doheon Lee, and Cheol-Goo Hur, "Predicting tissue-specific expressions based on sequence characteristics," BMB Reports 2011 [PDF]

-           Dokyun Na, Sunjae Lee, Gwansu Yi, Doheon Lee, "Synthetic inter-species cooperation of host and virus for targeted genetic evolution," Journal of Biotechnology 2011 [PDF]

-           Sejoon Lee, Kwang H. Lee, Min Song, Doheon Lee, "Building the process-drug-side effect network to discover the relationship between biological processes and side effects," BMC Bioinformatics 2011 [PDF] *Best Paper in ACM DTMBIO 2011

-           Sejoon Lee, Eunjung Lee, Kwang H. Lee, Doheon Lee, "Predicting disease phenotypes based on the molecular networks with condition-responsive correlation," Int'l Jour. of Data Mining and Bioinformatics 2011 [PDF]

-           Sohyun Hwang, Sangwoo Kim, Heesung Shin, Doheon Lee, "Context-dependent transcriptional regulations between signal transduction pathways," BMC Bioinformatics 2011 [PDF]

 

[2010]

-           Hyojung Paik, Eunjung Lee, Doheon Lee, "Relationships between genetic polymorphisms and transcriptional profiles for the outcome prediction in the treatment of anticancer agents," BMB Reports 2010 [PDF]

-           Thai Quang Tung, Doheon Lee, “PSExplorer: Whole parameter space exploration for molecular signaling pathway dynamics,” Bioinformatics 2010 [PDF]

-           Hyojin Kang, Eunkyoo Oh, Giltsu Choi, Doheon Lee, “Genome-wide DNA-binding specificity of PIL5, a Arabidopsis basic helix-loop-helix (bHLH) transcription factor,”Int'l Jour. Of Data Mining and Bioinformatics 2010 [PDF]

-           Dokyuna Na, Doheon Lee, "RBSDesigner: software for designing synthetic ribosome binding sites that yield a desired level of protein expression," Bioinformatics 2010 [PDF]

-           Hyun-Sik Kim, Doheon Lee, "Intelligent PSR Estimator for Feature Extraction of a Passive Sonar Target,"International Journal of Control, Automation, and Systems 2010 [PDF]

-           Dokyun Na, Sunjae Lee and Doheon Lee, "Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with a desired expression level in prokaryotes," BMC Systems Biology 2010 [PDF]

-           Inho Park, Kwang H. Lee, Doheon Lee, "Inference of Combinatorial Boolean Rules of Synergistic Gene Sets from Cancer Microarray Datasets," Bioinformatics 2010 [PDF]

-           Younghoon Kim, Imhoi Koo, Byung Hwa Jung, Bong Chul Chung, Doheon Lee, "Multivariate classification of urine metabolome profiles for breast cancer diagnosis," BMC Bioinformatics 2010 [PDF]

-           Ali Z. Ijaz, Min Song, Doheon Lee, "MKEM: A Multi-level Knowledge Emergence Model for Mining Undiscovered Public Knowledge," BMC Bioinformatics 2010 [PDF]

-           Juhyun Jeong, Taewoo Ryu, Yongdeuk Hwang, Eunjung Lee, Doheon Lee, "Prediction of extracellular matrix proteins based on distinctive sequence and domain characteristics," Journal of Computational Biology 2010 [PDF]

-           Sungwon Jung, Yoonkey Nam, Doheon Lee, "Inference of Combinatorial Neuronal Synchrony with Bayesian Networks," Journal of Neuroscience Methods 2010 [PDF]

 

[2009]

-           Taewoo Ryu, Sejun Lee, Cheol-Goo Hur, Doheon Lee, "CONVIRT: a web-based tool for transcriptional regulatory site identification using a conserved virtual chromosome," BMB Reports 2009 [PDF]

-           Byoungwook Lee, Doheon Lee, "Protein comparison at the domain architecture level," BMC Bioinformatics 2009 [PDF]

-           Hojung Nam, Bongchul Chung, Younghoon Kim, KiYoung Lee, Doheon Lee, "Combining Tissue Transcriptomics and Urine Metabolomics for Breast Cancer Biomarker Identification," Bioinformatics 2009 [PDF]

-           Hyunchul Jung, Eunjung Lee, Jong-Won Kim, Doheon Lee, "Pathway level analysis by augmenting activities of transcription factor target genes," IET Systems Biology 2009 [PDF]

-           Eunjung Lee, Hyunchul Jung, Predrag Radivojac, Jong-Won Kim, Doheon Lee, "Analysis of AML Genes in Dysregulated Molecular Networks," BMC Bioinformatics 2009 [PDF]

-           Kyu-il Cho, Dongsup Kim, Doheon Lee, "A feature-based approach to modelling protein-protein interaction hot spots," Nucleic Acids Research 2009 [PDF]

-           Jieun Shin, Keunhwa Kim, Hyojin Kang, Ismayil S. Zulfugarov, Gabyong Bae, Choon-Hwan Lee, Doheon Lee, Giltsu Choi, "Phytochromes promote seedling light responses by inhibiting four negatively acting phytochrome-interacting factors," PNAS 2009 [PDF]

-           Hojung Nam, Jinwon Lee, Doheon Lee, "Computational Identification of Altered Metabolism using Gene Expression and Metabolic Pathways," Biotechnology and Bioengineering 2009 [PDF]

-           Hojung Nam, KiYoung Lee, Doheon Lee, "Identification of Temporal Association Rules from Time-Series Microarray Data Set," BMC Bioinformatics 2009 [PDF]

-           Sangwoo Kim, Doheon Lee, "Mining metastasis related genes by primary-secondary tumor comparisons from large-scale database," BMC Bioinformatics 2009 [PDF]

-           Eunkyoo Oh, Hyojin Kang, Shinjiro Yamaguchi, Jeongmoo Park, Doheon Lee, Yuji Kamiya, Giltsu Choi, "Genome-wide analysis of genes targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during seed germination in Arabidopsis," Plant Cell 2009 [PDF]

-           Thai Quang Tung, Doheon Lee, "A method to improve protein subcellular localization prediction by integrating various biological data sources," BMC Bioinformatics 2009 [PDF]

-           Hong-Hee Won, Inho Park, Eunjung Lee, Jong-Won Kim and Doheon Lee, "Comparative analysis of the JAK/STAT signaling through erythropoietin receptor and thrombopoietin receptor using a systems approach," BMC Bioinformatics 2009 [PDF]

 

[2008]

-           Eunjung Lee, Han-Yu Chuang, Jong-Won Kim, Trey Ideker, Doheon Lee, "Inferring pathway activity toward precise disease classification," PLoS Computational Biology 2008 [PDF] *Highlighted in ISMB 2009

-           Hojung Nam, Taewoo Ryu, KiYoung Lee, Sangwoo Kim, Doheon Lee, "Computational Identification of Significantly Regulated Metabolic Reactions by Integration of Data on Enzyme Activity and Gene Expression," BMB Reports 2008 [PDF]

-           Sohyun Hwang, Seung-Woo Son, Sang Cheol Kim, Young Joo Kim, Hawoong Jeong, Doheon Lee, "A protein interaction network associated with asthma," Journal of Theoretical Biology 2008 [PDF]

-           Young-Kyu Park, Seong-Min Park, Young-Chul Choi, Doheon Lee, Misun Won, Young Joo Kim," AsiDesigner: exon-based siRNA design server considering alternative splicing," Nucleic Acids Research 2008 [PDF]

-           Byungwook Lee, Doheon Lee, "DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture," Nucleic Acids Research 2008 [PDF]

 

[2007]

-           Doheon Lee, Sangwoo Kim, YoungHoon Kim, "BioCAD: An Information Fusion Platform for Bio-Network Inference and Analysis," BMC Bioinformatics 2007 [PDF]

-           Han-Yu Chuang, Eunjung Lee, Yu-Tsueng Liu, Doheon Lee, Trey Ideker, "Network-based classification of breast cancer metastasis ," Molecular Systems Biology 2007 [PDF] *Highlighted in ISMB 2008

-           Taewoo Ryu, Younghoon Kim, Dae-Won Kim, Doheon Lee, "Computational identification of combinatorial regulation and transcription factor binding sites," Biotechnology and Bioengineering 2007 [PDF]

-           Sungwon Jung, Kwang H. Lee, Doheon Lee, "H-CORE: Enabling Genome-Scale Bayesian Analysis of Biological Systems Without Prior Knowledge," Biosystems (Elsevier) 2007 [PDF]

-           Sungwon Jung, Kwang H. Lee, Doheon Lee, "Enabling Large-scale Bayesian Network Learning by Preserving Intercluster Directionality ," IEICE Transactions on Information and Systems 2007 [PDF]

-           Taewoo Ryu, Juhyun Jung, Sunjae Lee, Ho Jung Nam, Sun Woo Hong, Jae Wook Yoo, Dong-ki Lee, Doheon Lee, "bZIPDB: A database of regulatory information for human bZIP transcription factors," BMC Genomics 2007 [PDF]

-           Jungsun Park, Sohyun Hwang, Yong Seok Lee, Sang-Cheol Kim, Doheon Lee, "SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms," Nucleic Acids Research 2007 [PDF]

-           Dae-Won Kim, Ki-Young Lee, Kwang H. Lee, Doheon Lee, "Towards clustering of incomplete microarray data without the use of imputation," Bioinformatics 2007 [PDF]

-           Byongwook Lee, Taehyung Kim, Seon-Kyu Kim, Kwang H. Lee, Doheon Lee, "Patome: a database server for biological sequence annotation and analysis in issued patents and published patent applications," Nucleic Acids Research 2007 [PDF]

-           KiYoung Lee, Dae-Won Kim, Kwang H. Lee, Doheon Lee, "Density-Induced Support Vector Data Description," IEEE Trans. on Neural Networks 2007 [PDF]

 

[2006]

-           Kyu-il Cho, KiYoung Lee, Kwang-Hyung Lee, Dongsup Kim, Doheon Lee, "Specificity of molecular interactions in transient protein-protein interaction interfaces," PROTEINS: Structure, Function, and Bioinformatics 2006 [PDF]

-           KiYoung Lee, Daewon Kim, Dokyun Na, Kwang H. Lee, Doheon Lee, "PLPD: Reliable Protein Localization Prediction from Imbalanced and Overlapped Data Sets," Nucleic Acids Research 2006 [PDF]

-           Dokyun Na, Dongsup Kim, Doheon Lee, "Mathematical Modeling of Humoral Immune Response Suppression by Passively Administered Antibodies in Mice," Journal of Theoretical Biology 2006 [PDF]

 

[2005]

-           Doheon Lee, "Component-Based Software Architecture for Biosystem Reverse Engineering," Biotechnology and Bioprocess Engineering 2005 [PDF]

-           KiYoung Lee, Dae-Won Kim, Doheon Lee, Kwang H. Lee, "Improving support vector data description using local density degree," Pattern Recognition 2005 [PDF]

-           KiYoung Lee, Dae-Won Kim, Doheon Lee, Kwang H. Lee, "Possibilistic Support Vector Machines," Pattern Recognition 2005 [PDF]

-           Dae-Won Kim, KiYoung Lee, Doheon Lee, Kwang H. Lee, "A k-Populations Algorithm for Clustering Categorical Data," Pattern Recognition 2005 [PDF]

-           Phil Hyoun Lee, Doheon Lee, "Modularized Learning of Genetic Interaction Networks from Biological Annotations and mRNA Expression Data," Bioinformatics 2005 [PDF]

-           Dae-Won Kim, Kwang Hyung Lee, Doheon Lee, "Detecting Clusters of Different Geometrical Shapes in Microarray Gene Expression Data," Bioinformatics 2005 [PDF]

-           Dae-Won Kim, KiYoung Lee, Doheon Lee, Kwang Hyung Lee, "A Kernel-Based Substractive Clustering Method," Pattern Recognition Letters 2005 [PDF]

-           Hyun S. Moon, Jonghwa Bhak, Kwang H. Lee, Doheon Lee, "Architecture of Basic Building Blocks in Protein and Domain Structural Interaction Networks," Bioinformatics 2005 [PDF]

-           Dae-Won Kim, KiYoung Lee, Doheon Lee, Kwang-Hyung Lee, "Evaluation of the [PDF]Performance of Clustering Algorithms in Kernel-Induced Feature Space," Pattern Recognition 2005 [PDF]

-           Dae-Won Kim, Young-il Kim, Doheon Lee, Kwang H. Lee, "Assessing the Quality of Fuzzy Partitions using Relative Intersection," IEICE Transactions on Information and Systems 2005 [PDF]

-           Jong Hwa Jin, Ui Sub Jung, Jae Wook Nam, Yong Ho In, Sang Yup Lee, Doheon Lee, Jinwon Lee, "Construction of Comprehensive Metabolic Network for Glycolysis with Regulation Mechanisms and Effectors," Journal of Microbiology and Biotechnology 2005 [PDF]

 

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