Lee A, Kim D, "CRDS: Consensus Reverse Docking System for Target Fishing", Bioinformatics. 2019 Aug 20. pii: btz656. doi: 10.1093/bioinformatics/btz656.
Lee EJ, Kim N, Park JW, Kang KH, Kim WI, Sim NS, Jeong CS, Blackshaw S, Vidal M, Huh SO, Kim D, Lee JH, Kim JW, "Global Analysis of Intercellular Homeodomain Protein Transfer", 2019 Jul 16;28(3):712-722.e3.
Jeon W, Kim D., "FP2VEC: a new molecular featurizer for learning molecular properties", Bioinformatics. 2019 May 9. pii: btz307.
Chung T, Kim D. "Prediction of binding property of RNA-binding proteins using multi-sized filters and multi-modal deep convolutional neural network", PLoS One. 2019 Apr 26;14(4):e0216257.
Chang HR, et al. "Hypomorphic Mutations in TONSL Cause SPONASTRIME Dysplasia", Am J Hum Genet. 2019 Mar 7;104(3):439-453.
Cho C, Hong S, Moon HG, Jang YS, Kim D, Lee SY., "Engineering Clostridial Aldehyde/Alcohol Dehydrogenase for Selective Butanol Production", MBio. 2019 Jan 22;10(1). pii: e02683-18.
Lee M, Choi SJ, Han S, Nam M, Kim D, Kim DU, Hoe KL, "Mutation Analysis of Synthetic DNA Barcodes in a Fission Yeast Gene Deletion Library by Sanger Sequencing", Genomics Inform. 2018 Jun;16(2):22-29.
Lee A, Hong S, Kim D., "KRDS: a web server for evaluating drug resistance mutations in kinases by molecular docking", J Cheminform. 2018 Apr 10;10(1):20
Min J, et al., "Inflammation induces two types of inflammatory dendritic cells in inflamed lymph nodes", Exp Mol Med. 2018 Mar 16;50(3):e458.
Lee K, Lee M, Kim D., "Utilizing random Forest QSAR models with optimized parameters for target identification and its application to target-fishing server", BMC Bioinformatics. 2017 Dec 28;18(Suppl 16):567.
Han Y, Kim D. "Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction". BMC bioinformatics. 2017 Dec;18(1):585.
Yang D, Jang I, Choi J, Kim MS, Lee AJ, Kim H, Eom J, Kim D, Jung I, Lee B., "3DIV: A 3D-genome Interaction Viewer and database", Nucleic Acids Res., 2017 Nov 2.
Hong S, Kim D, "Computational characterization of chromatin domain boundary-associated genomic elements.", Nucleic Acids Res. 2017 Oct 13;45(18):10403-10414.
Kim MH, Yang D, Kim M, Kim SY, Kim D, Kang SJ, "A late-lineage murine neutrophil precursor population exhibits dynamic changes during demand-adapted granulopoiesis.", Sci Rep. 2017 Jan 6;7:39804.
Cho JS, et al., "FARS2 mutation and epilepsy: Possible link with early-onset epileptic encephalopathy", Epilepsy Res. 2017 Jan;129:118-124.
Jeong CS, Kim D, "Inferring Crohn's disease association from exome sequences by integrating biological knowledge", BMC Med Genomics. 2016 Aug 12;9 Suppl 1:35.
Cho SY, et al., "BGN Mutations in X-Linked Spondyloepimetaphyseal Dysplasia", Am J Hum Genet. 2016 Jun 2;98(6).
Lee A, Lee K, Kim D, "Using reverse docking for target identification and its applications for drug discovery", Expert Opin Drug Discov. 2016 Jun 1:1-9.
Jeong CS, Kim D, "Structure-based Markov random field model for representing evolutionary constraints on functional sites", BMC Bioinformatics. 2016 Feb 24;17:99.
Hong S, Kim D, "Library of binding protein scaffolds (LibBP): a computational platform for selection of binding protein scaffolds", Bioinformatics. 2016 Jun 1;32(11):1709-15.
Hong S, Kim D, "Interaction between bound water molecules and local protein structures: A statistical analysis of the hydrogen bond structures around bound water molecules", Proteins. 2016 Jan;84(1):43-51.
Hahn S, Kim D, "Identifying and Reducing Systematic Errors in Chromosome Conformation Capture Data", PLoS One. 2015 Dec 30;10(12):e0146007.
Jung I, Seo J, Lee HS, Stanton LW, Kim D, Choi JK, "Global mapping of the regulatory interactions of histone residues", FEBS Lett. 2015 Dec 21;589(24 Pt B):4061-70.
Chang MY, et al., "Identification and Clinical Implications of Novel MYO15A Mutations in a Non-consanguineous Korean Family by Targeted Exome Sequencing", Mol Cells. 2015 Sep;38(9):781-8.
Kim NK, et al., "Downsloping high-frequency hearing loss due to inner ear tricellular tight junction disruption by a novel ILDR1 mutation in the Ig-like domain", PLoS One. 2015 Feb 10;10(2):e0116931.
Nam M., et al., "Systematic targeted gene deletion using the gene-synthesis method in fission yeast", J Microbiol Methods. 2014 Nov;106:72-7.
Ryou JH, Park K, Lee JJ, Kim D, Kim HS., "Soluble expression of human glycoprotein Ibα in Escherichia coli through replacement of the N-terminal capping domain", Protein Expr Purif. 2014 Sep;101:21-7.
Lee Y, et al., "Dissecting the critical factors for thermodynamic stability of modular proteins using molecular modeling approach", PLoS One. 2014 May 21;9(5):e98243.
Lee JJ, et al., "A high-affinity protein binder that blocks the IL-6/STAT3 signaling pathway effectively suppresses non-small cell lung cancer", Mol Ther. 2014 Jul;22(7):1254-65.
Chung J, et al., "A novel mutation of TMPRSS3 related to milder auditory phenotype in Korean postlingual deafness: a possible future implication for a personalized auditory rehabilitation", J Mol Med (Berl). 2014 Jun;92(6):651-63.
Lee M. Park K. Kim D* , "Interaction network among functional drug groups", BMC Systems Biology, 2013 Sep 21.
Hahn S, Kim D, "Physical origin of the contact frequency in chromosome conformation capture data", Biophys J. 2013 Oct 15;105(8):1786-95.
Han S., et al., "Construction of the first compendium of chemical-genetic profiles in the fission yeast Schizosaccharomyces pombe and comparative compendium approach", Biochem Biophys Res Commun. 2013 Jul 12;436(4):613-8.
Lee K, et al., "Genetic landscape of open chromatin in yeast", PLoS Genet. 2013;9(2):e1003229.
Lee M,Kim D*, "FitSearch: a robust way to interpret a yeast fitness profile in terms of drug's mode-of-action", BMC Genomics. 2013 Jan 21.
Lee M, Kim D*, "Large-scale reverse docking profiles and their applications", BMC Bioinformatics. 2012;13
Lee M,Kim D*, "A novel small molecule facilitates the reprogramming of human somatic cells into a pluripotent state and supports the maintenance of an undifferentiated state of human pluripotent stem cells.", Angew Chem Int Ed Engl. 2012 Dec 7;51(50):12509-13.
Jeong CS, Kim D*, "Reliable and robust detection of coevolving protein residues", Protein Engineering, 2012 Nov;25(11):705-13.
Hong C, Lee M, Kim D, Kim D, Cho KH, Shin I*, "A checkpoints capturing timing-robust Boolean model of the budding yeast cell cycle regulatory network", BMC Systems Biology, 2012 Sep 28;6(1):129.
Kim SK, Jung I, Lee H, Kang K, Kim M, Jeong K, Kwon CS, Han YM, Kim YS, Kim D, Lee D*, "Human histone H3K79 methyltransferase DOT1L binds actively transcribing RNA polymerase II to regulate gene expression", J. Biol. Chem. 2012 Sep 25.
Jung I, Kim D*, "Histone modification profiles characterize function-specific gene regulation", J. Theo. Biol. 2012 Oct 7;310:132-42.
Park K, Kim D*, "Structure-based rebuilding of coevolutionary information reveals functional modules in rhodopsin structure", Biochim Biophys Acta. 2012 Jun 8.
Hahn S. Kim D*, "Transient protein-protein interaction of the SH3-peptide complex via closely located multiple binding sites", PLoS One 2012;7(3):e32804.
Jung I, Kim SK, Kim M, Han YM, Kim YS, Kim D*, Lee D*, "H2B monoubiquitylation is a 5'-enriched active transcription mark and correlates with exon-intron structure in human cells", Genome Res. 2012 Jun;22(6):1026-35.
Han J, Kim HJ, Lee SC, Hong S, Park K, Jeon YH, Kim D, Cheong HK, Kim HS*, "Structure-based rational design of a Toll-like receptor 4 (TLR4) decoy receptor with high binding affinity for a target protein", PLoS One. 2012;7(2):e30929.
Lee SC, Park K, Han J, Lee JJ, Kim HJ, Hong S, Heu W, Kim YJ, Ha JS, Lee SG, Cheong HK, Jeon YH, Kim D*, Kim HS*, "Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering", PNAS. 2012 Feb 28;109(9):3299-304.
Jeong CS, Kim D, "Coevolved residues and the functional association for intrinsically disordered proteins", Pac Symp Biocompt. 2012:140-51.
Park K, Kim D*, "Drug-drug relationship based on target information: application to drug target identification", BMC Systems Biology, 2011;14;5 Suppl 2:S12.
Min BJ, et al., "Whole-exome sequencing identifies mutations of KIF22 in spondyloepimetaphyseal dysplasia with joint laxity, leptodactylic type", Am J Hum Genet. 2011 Dec 9;89(6):760-6.
Park K, Kim D*, "Modeling allosteric signal propagation using protein structure networks", BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S23.
Kim N, Kim H, Jung I, Kim Y, Kim D, Han YM*, "Expression profiles of miRNAs in human embryonic stem cells during hepatocyte differentiation", Hepatol Res. 2011 Feb;41(2):170-83.
Kwak YS, Han S, Thomashow LS, Rice JT, Paulitz TC, Kim D, Weller DM*, "Expression profiles of miRNAs in human embryonic stem cells during hepatocyte differentiation", Appl Environ Microbiol. 2011 Mar;77(5):1770-6.
Jung I, Lee J, Choi C, Kim D*, " Inferring Relative Activity between Pathway and Downstream Genes to Classify Melanoma Cancer Progression", IBC. 2011; 3(5).
Lee S, Kim D*, "Cytochrome P450 networks in chemical space", Arch Pharm Res. 2010 Sep;33(9):1361-74.
Hong S, Chung T, Kim D*, "SH3 domain-peptide binding energy calculations based on structural ensemble and multiple peptide templates", PLoS One. 2010 Sep 15;5(9):e12654.
KIM DU, et al, "Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe", Nat Biotechnol. 2010 Jun;28(6):617-23.
Jeong CS, Kim D*, "Linear predictive coding representation of correlated mutation for protein sequence alignment", BMC Bioinformatics. 2010 Apr 16;11 Suppl 2:S2.
Munesue T, et al., "Two genetic variants of CD38 in subjects with autism spectrum disorder and controls", Neurosci Res. 2010 Jun;67(2):181-91.
Lee S, Park K, Ahn HS, Kim D*, "Importance of structural information in predicting human acute toxicity from in vitro cytotoxicity data", Toxicol Appl Pharmacol. 2010 Jul;246(1-2):38-48.
Jung I, Matsuyama A, Yoshida M, Kim D*, "PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship", BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S10.
Lee S, Kim D*, "Utility of structural information to predict drug clearance from in vitro data", IBC 2010;2:3.
Park K, Kim D*, "Localized network centrality and essentiality in the yeast-protein interaction network", Proteomics. 2009 Nov;9(22):5143-54.
Lee BC, Kim D*, "A new method for revealing correlated mutations under the structural and functional constraints in proteins", Bioinformatics. 2009 Oct 1;25(19):2506-13.
Park K, Lee S, Ahn HS, Kim D*, "Predicting the multi-modal binding propensity of small molecules: towards an understanding of drug promiscuity", Mol Biosyst. 2009 Aug;5(8):844-53.
Cho KI, Kim D*, Lee D*, "A feature-based approach to modeling protein-protein interaction hot spots", Nucleic Acids Res. 2009 May;37(8):2672-87.
Jung I, Kim D*, "SIMPRO: simple protein homology detection method by using indirect signals", Bioinformatics. 2009 Mar 15;25(6):729-35.
Lee S, Park K, Kim D*, "Building a drug-target network and its applications", Expert Opinion on Drug Discovery 2009;4(11):1177-1189.
Jung I, Kim D*, "Regulatory patterns of histone modifications to control the DNA methylation status at CpG islands", IBC 2009;1:4.
Lee WC, Lee M, Jung JW, Kim KP*, Kim D*, "SCUD: Saccharomyces cerevisiae ubiquitination database", BMC Genomics. 2008 Sep 24;9:440.
Han S, Kim D*, "Inference of protein complex activities from chemical-genetic profile and its applications: predicting drug-target pathways", PLoS Comput Biol. 2008 Aug 29;4(8):e1000162.
Baek ST, et al., "Genome-wide identification of haploinsufficiency in fission yeast", J Microbiol Biotechnol. 2008 Jun;18(6):1059-63.
Jung I, Lee J, Lee SY, Kim D*, "Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection", BMC Bioinformatics. 2008 Jul 1;9:298.
Baek ST, et al, "Genome-wide drug-induced haploinsufficient screening of fission yeast for identification of hydrazinocurcumin targets", J Microbiol Biotechnol. 2008 Feb;18(2):263-9.
Lee BC, Park K, Kim D*, "Analysis of the residue-residue coevolution network and the functionally important residues in proteins", Proteins. 2008 Aug 15;72(3):863-72.
Lee M, Jeong CS, Kim D*, "Predicting and improving the protein sequence alignment quality by support vector regression", BMC Bioinformatics. 2007 Dec 3;8:471.
Park K, Kim D*, "Binding similarity network of ligand", Proteins. 2008 May 1;71(2):960-71.
Park K, Kim D*, "A method to detect important residues using protein binding site comparison", Genome Inform. 2006;17(2):216-25.
Lee S, Kim D*, "A New method for predicting human hepatic clearance from in vitro experimental data using molecular descriptors", Arch Pharm Res. 2007 Feb;30(2):182-90.
Cho KI, Lee K, Lee KH, Kim D*, Lee D*, "Specificity of molecular interactions in transient protein-protein interaction interfaces", Proteins. 2006 Nov 15;65(3):593-606.
Han S, Kim D*, "AtRTPrimer: database for Arabidopsis genome-wide homogeneous and specific RT-PCR primer-pairs", BMC Bioinformatics. 2006 Mar 30;7:179.
Na D, Kim D, Lee D*, "Mathematical modeling of humoral immune response suppression by passively administered antibodies in mice", J Theor Biol. 2006 Aug 21;241(4):830-51.
Lee S, Lee BC, Kim D*, "Prediction of protein secondary structure content using amino acid composition and evolutionary information", Proteins. 2006 Mar 1;62(4):1107-14.
Han S, Lee BC, Yu ST, Jeong CS, Lee S, Kim D*, "Fold recognition by combining profile-profile alignment and support vector machine", Bioinformatics. 2005 Jun 1;21(11):2667-73.
Lee A, Kim D, "CRDS: Consensus Reverse Docking System for Target Fishing", Bioinformatics. 2019 Aug 20. pii: btz656. doi: 10.1093/bioinformatics/btz656.
Lee EJ, Kim N, Park JW, Kang KH, Kim WI, Sim NS, Jeong CS, Blackshaw S, Vidal M, Huh SO, Kim D, Lee JH, Kim JW, "Global Analysis of Intercellular Homeodomain Protein Transfer", 2019 Jul 16;28(3):712-722.e3.
Jeon W, Kim D., "FP2VEC: a new molecular featurizer for learning molecular properties", Bioinformatics. 2019 May 9. pii: btz307.
Chung T, Kim D. "Prediction of binding property of RNA-binding proteins using multi-sized filters and multi-modal deep convolutional neural network", PLoS One. 2019 Apr 26;14(4):e0216257.
Chang HR, et al. "Hypomorphic Mutations in TONSL Cause SPONASTRIME Dysplasia", Am J Hum Genet. 2019 Mar 7;104(3):439-453.
Cho C, Hong S, Moon HG, Jang YS, Kim D, Lee SY., "Engineering Clostridial Aldehyde/Alcohol Dehydrogenase for Selective Butanol Production", MBio. 2019 Jan 22;10(1). pii: e02683-18.
Lee M, Choi SJ, Han S, Nam M, Kim D, Kim DU, Hoe KL, "Mutation Analysis of Synthetic DNA Barcodes in a Fission Yeast Gene Deletion Library by Sanger Sequencing", Genomics Inform. 2018 Jun;16(2):22-29.
Lee A, Hong S, Kim D., "KRDS: a web server for evaluating drug resistance mutations in kinases by molecular docking", J Cheminform. 2018 Apr 10;10(1):20
Min J, et al., "Inflammation induces two types of inflammatory dendritic cells in inflamed lymph nodes", Exp Mol Med. 2018 Mar 16;50(3):e458.
Lee K, Lee M, Kim D., "Utilizing random Forest QSAR models with optimized parameters for target identification and its application to target-fishing server", BMC Bioinformatics. 2017 Dec 28;18(Suppl 16):567.
Han Y, Kim D. "Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction". BMC bioinformatics. 2017 Dec;18(1):585.
Yang D, Jang I, Choi J, Kim MS, Lee AJ, Kim H, Eom J, Kim D, Jung I, Lee B., "3DIV: A 3D-genome Interaction Viewer and database", Nucleic Acids Res., 2017 Nov 2.
Hong S, Kim D, "Computational characterization of chromatin domain boundary-associated genomic elements.", Nucleic Acids Res. 2017 Oct 13;45(18):10403-10414.
Kim MH, Yang D, Kim M, Kim SY, Kim D, Kang SJ, "A late-lineage murine neutrophil precursor population exhibits dynamic changes during demand-adapted granulopoiesis.", Sci Rep. 2017 Jan 6;7:39804.
Cho JS, et al., "FARS2 mutation and epilepsy: Possible link with early-onset epileptic encephalopathy", Epilepsy Res. 2017 Jan;129:118-124.
Jeong CS, Kim D, "Inferring Crohn's disease association from exome sequences by integrating biological knowledge", BMC Med Genomics. 2016 Aug 12;9 Suppl 1:35.
Cho SY, et al., "BGN Mutations in X-Linked Spondyloepimetaphyseal Dysplasia", Am J Hum Genet. 2016 Jun 2;98(6).
Lee A, Lee K, Kim D, "Using reverse docking for target identification and its applications for drug discovery", Expert Opin Drug Discov. 2016 Jun 1:1-9.
Jeong CS, Kim D, "Structure-based Markov random field model for representing evolutionary constraints on functional sites", BMC Bioinformatics. 2016 Feb 24;17:99.
Hong S, Kim D, "Library of binding protein scaffolds (LibBP): a computational platform for selection of binding protein scaffolds", Bioinformatics. 2016 Jun 1;32(11):1709-15.
Hong S, Kim D, "Interaction between bound water molecules and local protein structures: A statistical analysis of the hydrogen bond structures around bound water molecules", Proteins. 2016 Jan;84(1):43-51.
Hahn S, Kim D, "Identifying and Reducing Systematic Errors in Chromosome Conformation Capture Data", PLoS One. 2015 Dec 30;10(12):e0146007.
Jung I, Seo J, Lee HS, Stanton LW, Kim D, Choi JK, "Global mapping of the regulatory interactions of histone residues", FEBS Lett. 2015 Dec 21;589(24 Pt B):4061-70.
Chang MY, et al., "Identification and Clinical Implications of Novel MYO15A Mutations in a Non-consanguineous Korean Family by Targeted Exome Sequencing", Mol Cells. 2015 Sep;38(9):781-8.
Kim NK, et al., "Downsloping high-frequency hearing loss due to inner ear tricellular tight junction disruption by a novel ILDR1 mutation in the Ig-like domain", PLoS One. 2015 Feb 10;10(2):e0116931.
Nam M., et al., "Systematic targeted gene deletion using the gene-synthesis method in fission yeast", J Microbiol Methods. 2014 Nov;106:72-7.
Ryou JH, Park K, Lee JJ, Kim D, Kim HS., "Soluble expression of human glycoprotein Ibα in Escherichia coli through replacement of the N-terminal capping domain", Protein Expr Purif. 2014 Sep;101:21-7.
Lee Y, et al., "Dissecting the critical factors for thermodynamic stability of modular proteins using molecular modeling approach", PLoS One. 2014 May 21;9(5):e98243.
Lee JJ, et al., "A high-affinity protein binder that blocks the IL-6/STAT3 signaling pathway effectively suppresses non-small cell lung cancer", Mol Ther. 2014 Jul;22(7):1254-65.
Chung J, et al., "A novel mutation of TMPRSS3 related to milder auditory phenotype in Korean postlingual deafness: a possible future implication for a personalized auditory rehabilitation", J Mol Med (Berl). 2014 Jun;92(6):651-63.
Lee M. Park K. Kim D* , "Interaction network among functional drug groups", BMC Systems Biology, 2013 Sep 21.
Hahn S, Kim D, "Physical origin of the contact frequency in chromosome conformation capture data", Biophys J. 2013 Oct 15;105(8):1786-95.
Han S., et al., "Construction of the first compendium of chemical-genetic profiles in the fission yeast Schizosaccharomyces pombe and comparative compendium approach", Biochem Biophys Res Commun. 2013 Jul 12;436(4):613-8.
Lee K, et al., "Genetic landscape of open chromatin in yeast", PLoS Genet. 2013;9(2):e1003229.
Lee M,Kim D*, "FitSearch: a robust way to interpret a yeast fitness profile in terms of drug's mode-of-action", BMC Genomics. 2013 Jan 21.
Lee M, Kim D*, "Large-scale reverse docking profiles and their applications", BMC Bioinformatics. 2012;13
Lee M,Kim D*, "A novel small molecule facilitates the reprogramming of human somatic cells into a pluripotent state and supports the maintenance of an undifferentiated state of human pluripotent stem cells.", Angew Chem Int Ed Engl. 2012 Dec 7;51(50):12509-13.
Jeong CS, Kim D*, "Reliable and robust detection of coevolving protein residues", Protein Engineering, 2012 Nov;25(11):705-13.
Hong C, Lee M, Kim D, Kim D, Cho KH, Shin I*, "A checkpoints capturing timing-robust Boolean model of the budding yeast cell cycle regulatory network", BMC Systems Biology, 2012 Sep 28;6(1):129.
Kim SK, Jung I, Lee H, Kang K, Kim M, Jeong K, Kwon CS, Han YM, Kim YS, Kim D, Lee D*, "Human histone H3K79 methyltransferase DOT1L binds actively transcribing RNA polymerase II to regulate gene expression", J. Biol. Chem. 2012 Sep 25.
Jung I, Kim D*, "Histone modification profiles characterize function-specific gene regulation", J. Theo. Biol. 2012 Oct 7;310:132-42.
Park K, Kim D*, "Structure-based rebuilding of coevolutionary information reveals functional modules in rhodopsin structure", Biochim Biophys Acta. 2012 Jun 8.
Hahn S. Kim D*, "Transient protein-protein interaction of the SH3-peptide complex via closely located multiple binding sites", PLoS One 2012;7(3):e32804.
Jung I, Kim SK, Kim M, Han YM, Kim YS, Kim D*, Lee D*, "H2B monoubiquitylation is a 5'-enriched active transcription mark and correlates with exon-intron structure in human cells", Genome Res. 2012 Jun;22(6):1026-35.
Han J, Kim HJ, Lee SC, Hong S, Park K, Jeon YH, Kim D, Cheong HK, Kim HS*, "Structure-based rational design of a Toll-like receptor 4 (TLR4) decoy receptor with high binding affinity for a target protein", PLoS One. 2012;7(2):e30929.
Lee SC, Park K, Han J, Lee JJ, Kim HJ, Hong S, Heu W, Kim YJ, Ha JS, Lee SG, Cheong HK, Jeon YH, Kim D*, Kim HS*, "Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering", PNAS. 2012 Feb 28;109(9):3299-304.
Jeong CS, Kim D, "Coevolved residues and the functional association for intrinsically disordered proteins", Pac Symp Biocompt. 2012:140-51.
Park K, Kim D*, "Drug-drug relationship based on target information: application to drug target identification", BMC Systems Biology, 2011;14;5 Suppl 2:S12.
Min BJ, et al., "Whole-exome sequencing identifies mutations of KIF22 in spondyloepimetaphyseal dysplasia with joint laxity, leptodactylic type", Am J Hum Genet. 2011 Dec 9;89(6):760-6.
Park K, Kim D*, "Modeling allosteric signal propagation using protein structure networks", BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S23.
Kim N, Kim H, Jung I, Kim Y, Kim D, Han YM*, "Expression profiles of miRNAs in human embryonic stem cells during hepatocyte differentiation", Hepatol Res. 2011 Feb;41(2):170-83.
Kwak YS, Han S, Thomashow LS, Rice JT, Paulitz TC, Kim D, Weller DM*, "Expression profiles of miRNAs in human embryonic stem cells during hepatocyte differentiation", Appl Environ Microbiol. 2011 Mar;77(5):1770-6.
Jung I, Lee J, Choi C, Kim D*, " Inferring Relative Activity between Pathway and Downstream Genes to Classify Melanoma Cancer Progression", IBC. 2011; 3(5).
Lee S, Kim D*, "Cytochrome P450 networks in chemical space", Arch Pharm Res. 2010 Sep;33(9):1361-74.
Hong S, Chung T, Kim D*, "SH3 domain-peptide binding energy calculations based on structural ensemble and multiple peptide templates", PLoS One. 2010 Sep 15;5(9):e12654.
KIM DU, et al, "Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe", Nat Biotechnol. 2010 Jun;28(6):617-23.
Jeong CS, Kim D*, "Linear predictive coding representation of correlated mutation for protein sequence alignment", BMC Bioinformatics. 2010 Apr 16;11 Suppl 2:S2.
Munesue T, et al., "Two genetic variants of CD38 in subjects with autism spectrum disorder and controls", Neurosci Res. 2010 Jun;67(2):181-91.
Lee S, Park K, Ahn HS, Kim D*, "Importance of structural information in predicting human acute toxicity from in vitro cytotoxicity data", Toxicol Appl Pharmacol. 2010 Jul;246(1-2):38-48.
Jung I, Matsuyama A, Yoshida M, Kim D*, "PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship", BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S10.
Lee S, Kim D*, "Utility of structural information to predict drug clearance from in vitro data", IBC 2010;2:3.
Park K, Kim D*, "Localized network centrality and essentiality in the yeast-protein interaction network", Proteomics. 2009 Nov;9(22):5143-54.
Lee BC, Kim D*, "A new method for revealing correlated mutations under the structural and functional constraints in proteins", Bioinformatics. 2009 Oct 1;25(19):2506-13.
Park K, Lee S, Ahn HS, Kim D*, "Predicting the multi-modal binding propensity of small molecules: towards an understanding of drug promiscuity", Mol Biosyst. 2009 Aug;5(8):844-53.
Cho KI, Kim D*, Lee D*, "A feature-based approach to modeling protein-protein interaction hot spots", Nucleic Acids Res. 2009 May;37(8):2672-87.
Jung I, Kim D*, "SIMPRO: simple protein homology detection method by using indirect signals", Bioinformatics. 2009 Mar 15;25(6):729-35.
Lee S, Park K, Kim D*, "Building a drug-target network and its applications", Expert Opinion on Drug Discovery 2009;4(11):1177-1189.
Jung I, Kim D*, "Regulatory patterns of histone modifications to control the DNA methylation status at CpG islands", IBC 2009;1:4.
Lee WC, Lee M, Jung JW, Kim KP*, Kim D*, "SCUD: Saccharomyces cerevisiae ubiquitination database", BMC Genomics. 2008 Sep 24;9:440.
Han S, Kim D*, "Inference of protein complex activities from chemical-genetic profile and its applications: predicting drug-target pathways", PLoS Comput Biol. 2008 Aug 29;4(8):e1000162.
Baek ST, et al., "Genome-wide identification of haploinsufficiency in fission yeast", J Microbiol Biotechnol. 2008 Jun;18(6):1059-63.
Jung I, Lee J, Lee SY, Kim D*, "Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection", BMC Bioinformatics. 2008 Jul 1;9:298.
Baek ST, et al, "Genome-wide drug-induced haploinsufficient screening of fission yeast for identification of hydrazinocurcumin targets", J Microbiol Biotechnol. 2008 Feb;18(2):263-9.
Lee BC, Park K, Kim D*, "Analysis of the residue-residue coevolution network and the functionally important residues in proteins", Proteins. 2008 Aug 15;72(3):863-72.
Lee M, Jeong CS, Kim D*, "Predicting and improving the protein sequence alignment quality by support vector regression", BMC Bioinformatics. 2007 Dec 3;8:471.
Park K, Kim D*, "Binding similarity network of ligand", Proteins. 2008 May 1;71(2):960-71.
Park K, Kim D*, "A method to detect important residues using protein binding site comparison", Genome Inform. 2006;17(2):216-25.
Lee S, Kim D*, "A New method for predicting human hepatic clearance from in vitro experimental data using molecular descriptors", Arch Pharm Res. 2007 Feb;30(2):182-90.
Cho KI, Lee K, Lee KH, Kim D*, Lee D*, "Specificity of molecular interactions in transient protein-protein interaction interfaces", Proteins. 2006 Nov 15;65(3):593-606.
Han S, Kim D*, "AtRTPrimer: database for Arabidopsis genome-wide homogeneous and specific RT-PCR primer-pairs", BMC Bioinformatics. 2006 Mar 30;7:179.
Na D, Kim D, Lee D*, "Mathematical modeling of humoral immune response suppression by passively administered antibodies in mice", J Theor Biol. 2006 Aug 21;241(4):830-51.
Lee S, Lee BC, Kim D*, "Prediction of protein secondary structure content using amino acid composition and evolutionary information", Proteins. 2006 Mar 1;62(4):1107-14.
Han S, Lee BC, Yu ST, Jeong CS, Lee S, Kim D*, "Fold recognition by combining profile-profile alignment and support vector machine", Bioinformatics. 2005 Jun 1;21(11):2667-73.