Publications

Choi, S., Kim, D. BIDpred: unraveling B cell Immunodominance hierarchical pattern using statistical feature discovery and deep learning prediction. Frontiers in Immunology, 16, 1646946. (2025). https://doi.org/10.3389/fimmu.2025.1646946

Choi, S., Kim, D. B cell epitope prediction by capturing spatial clustering property of the epitopes using graph attention network. Sci Rep 14, 27496 (2024). https://doi.org/10.1038/s41598-024-78506-z 

Ryu, B., Jeon, W. & Kim, D. Integrating genomic and molecular data to predict antimicrobial minimum inhibitory concentration in Klebsiella pneumoniae. Sci Rep 14, 25951 (2024). https://doi.org/10.1038/s41598-024-75973-2 

H. Y. Kim, S. Kim, W.-Y. Park, D. Kim, "TSpred: a robust prediction framework for TCR–epitope interactions using paired chain TCR sequence data," Bioinformatics, 2024, doi: https://doi.org/10.1093/bioinformatics/btae472. 

W. Jeon and D. Kim, "AbFlex: designing antibody complementarity determining regions with flexible CDR definition," Bioinformatics, 2024, doi: https://doi.org/10.1093/bioinformatics/btae122.

J. Son and D. Kim, "Applying network link prediction in drug discovery: an overview of the literature," Expert Opinion on Drug Discovery, 2024. doi: https://doi.org/10.1080/17460441.2023.2267020. 

H. Y. Kim, S. Kim, W.-Y. Park, D. Kim, "G-RANK: An equivariant graph neural network for the scoring of protein-protein docking models," Bioinformatics Advances, 2023, doi: https://doi.org/10.1093/bioadv/vbad011. 

C. Moon and D. Kim, "Prediction of drug–target interactions through multi-task learning," Scientific Reports, 2022, doi: https://doi.org/10.1038/s41598-022-23203-y. 

D. Yang, T. Chung, and D. Kim, "DeepLUCIA: predicting tissue-specific chromatin loops using Deep Learning-based Universal Chromatin Interaction Annotator," Bioinformatics, 2022, doi: https://doi.org/10.1093/bioinformatics/btac373. 

BJ Kim, HW Jeon, W Jeon, JH Han, J Oh, N Yi, MY Kim, M Kim, JN Kim, BH Kim, JY Hyon, D Kim, JW Koo, DY Oh, BY Choi, "Rising of LOXHD1 as a signature causative gene of down-sloping hearing loss in people in their teens and 20s," Journal of Medical Genetics, 2022, doi: http://dx.doi.org/10.1136/jmedgenet-2020-107594. 

Y Seo, S Bang, J Son, D Kim, Y Jeong, P Kim, J Yang, JH Eom, N Choi, HN Kim, "Brain physiome: A concept bridging in vitro 3D brain models and in silico models for predicting drug toxicity in the brain," Bioactive Materials, 2021, doi: https://doi.org/10.1016/j.bioactmat.2021.11.009. 

H. Y. Kim, W. Jeon, and D. Kim, "An enhanced variant effect predictor based on a deep generative model and the Born-Again Networks," Scientific Reports, 2021, doi: https://doi.org/10.1038/s41598-021-98693-3. 

J. Son and D. Kim, "Development of a graph convolutional neural network model for efficient prediction of protein-ligand binding affinities," PLOS ONE, 2021, doi: https://doi.org/10.1371/journal.pone.0249404. 

W. Jeon and D. Kim, "Autonomous Molecule Generation using reinforcement learning and docking to develop potential novel inhibitors," Scientific Reports, 2020, doi: https://doi.org/10.1038/s41598-020-78537-2. 

H. Y. Kim and D. Kim, "Prediction of mutation effects using a deep temporal convolutional network," Bioinformatics, 2020, doi: https://doi.org/10.1093/bioinformatics/btz873.

A. Lee and D. Kim, “CRDS: Consensus Reverse Docking System for target fishing,” Bioinformatics, 2019, doi: 10.1093/bioinformatics/btz656.

W. Jeon and D. Kim, “FP2VEC: a new molecular featurizer for learning molecular properties,” Bioinformatics, 2019, doi: 10.1093/bioinformatics/btz307.

K. Lee and D. Kim, “In-silico molecular binding prediction for human drug targets using deep neural multi-task learning,” Genes (Basel)., vol. 10, no. 11, Nov. 2019, doi: 10.3390/genes10110906.

I. Jung, A. Schmitt, Y. Diao, A. J. Lee, T. Liu, D. Yang, C. Tan, J. Eom, M. Chan, S. Chee, Z. Chiang, C. Kim, E. Masliah, C. L. Barr, B. Li, S. Kuan, D. Kim, and B. Ren, “A compendium of promoter-centered long-range chromatin interactions in the human genome,” Nat. Genet., 2019, doi: 10.1038/s41588-019-0494-8.

E. J. Lee, N. Kim, J. W. Park, K. H. Kang, W. il Kim, N. S. Sim, C. S. Jeong, S. Blackshaw, M. Vidal, S. O. Huh, D. Kim, J. H. Lee, and J. W. Kim, “Global Analysis of Intercellular Homeodomain Protein Transfer,” Cell Rep., 2019, doi: 10.1016/j.celrep.2019.06.056.

T. Chung and D. Kim, “Prediction of binding property of RNA-binding proteins using multi-sized filters and multi-modal deep convolutional neural network,” PLoS One, 2019, doi: 10.1371/journal.pone.0216257.

H. R. Chang, S. Y. Cho, J. H. Lee, E. Lee, J. Seo, H. R. Lee, D. P. Cavalcanti, O. Mäkitie, H. Valta, K. M. Girisha, C. Lee, K. Neethukrishna, G. S. Bhavani, A. Shukla, S. Nampoothiri, S. R. Phadke, M. J. Park, S. Ikegawa, Z. Wang, M. R. Higgs, G. S. Stewart, E. Jung, M. S. Lee, J. H. Park, E. A. Lee, H. Kim, K. Myung, W. Jeon, K. Lee, D. Kim, O. H. Kim, M. Choi, H. W. Lee, Y. Kim, and T. J. Cho, “Hypomorphic Mutations in TONSL Cause SPONASTRIME Dysplasia,” Am. J. Hum. Genet., vol. 104, no. 3, pp. 439–453, Mar. 2019, doi: 10.1016/j.ajhg.2019.01.009.

C. Cho, S. Hong, H. G. Moon, Y. S. Jang, D. Kim, and S. Y. Lee, “Engineering Clostridial Aldehyde/Alcohol Dehydrogenase for Selective Butanol Production,” MBio, 2019, doi: 10.1128/mBio.02683-18.

J. Min, D. Yang, M. Kim, K. Haam, A. Yoo, J. H. Choi, B. U. Schraml, Y. S. Kim, D. Kim, and S. J. Kang, “Inflammation induces two types of inflammatory dendritic cells in inflamed lymph nodes,” Exp. Mol. Med., 2018, doi: 10.1038/emm.2017.292.

A. Lee, S. Hong, and D. Kim, “KRDS: a web server for evaluating drug resistance mutations in kinases by molecular docking,” J. Cheminform., 2018, doi: 10.1186/s13321-018-0274-y.

D. Yang, I. Jang, J. Choi, M. S. Kim, A. J. Lee, H. Kim, J. Eom, D. Kim, I. Jung, and B. Lee, “3DIV: A 3D-genome Interaction Viewer and database,” Nucleic Acids Res., 2018, doi: 10.1093/nar/gkx1017.

J. S. Cho, S. H. Kim, H. Y. Kim, T. Chung, D. Kim, S. Jang, S. B. Lee, S. K. Yoo, J. Shin, J. il Kim, H. Kim, H. Hwang, J. H. Chae, J. Choi, K. J. Kim, and B. C. Lim, “FARS2 mutation and epilepsy: Possible link with early-onset epileptic encephalopathy,” Epilepsy Res., vol. 129, pp. 118–124, Jan. 2017, doi: 10.1016/j.eplepsyres.2016.11.022.

K. Lee, M. Lee, and D. Kim, “Utilizing random Forest QSAR models with optimized parameters for target identification and its application to target-fishing server,” BMC Bioinformatics, 2017, doi: 10.1186/s12859-017-1960-x.

M. H. Kim, D. Yang, M. Kim, S. Y. Kim, D. Kim, and S. J. Kang, “A late-lineage murine neutrophil precursor population exhibits dynamic changes during demand-adapted granulopoiesis,” Sci. Rep., 2017, doi: 10.1038/srep39804.

S. Hong and D. Kim, “Computational characterization of chromatin domain boundary-associated genomic elements,” Nucleic Acids Res., 2017, doi: 10.1093/nar/gkx738.

Y. Han and D. Kim, “Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction,” BMC Bioinformatics, 2017, doi: 10.1186/s12859-017-1997-x.

S. Hahn and D. Kim, “Relationship between spatial organization and biological function, analyzed using gene ontology and chromosome conformation capture of human and fission yeast genomes,” Genes and Genomics, 2016, doi: 10.1007/s13258-016-0413-7.

C. S. Jeong and D. Kim, “Inferring Crohn’s disease association from exome sequences by integrating biological knowledge,” BMC Med. Genomics, 2016, doi: 10.1186/s12920-016-0189-2.

C. S. Jeong and D. Kim, “Structure-based Markov random field model for representing evolutionary constraints on functional sites,” BMC Bioinformatics, 2016, doi: 10.1186/s12859-016-0948-2.

S. Hong and D. Kim, “Library of binding protein scaffolds (LibBP): A computational platform for selection of binding protein scaffolds,” Bioinformatics, 2016, doi: 10.1093/bioinformatics/btw032.

S. Hong and D. Kim, “Interaction between bound water molecules and local protein structures: A statistical analysis of the hydrogen bond structures around bound water molecules,” Proteins Struct. Funct. Bioinforma., 2016, doi: 10.1002/prot.24953.

A. Lee, K. Lee, and D. Kim, “Using reverse docking for target identification and its applications for drug discovery,” Expert Opinion on Drug Discovery. 2016, doi: 10.1080/17460441.2016.1190706.

I. Jung, J. Park, C. Choi, and D. Kim, “Identification of novel trans-crosstalk between histone modifications via genome-wide analysis of maximal deletion effect,” Genes and Genomics, vol. 37, no. 8, pp. 693–701, Aug. 2015, doi: 10.1007/s13258-015-0298-x.

M. Y. Chang, A. R. Kim, N. K. D. Kim, C. Lee, K. Y. Lee, W. S. Jeon, J. W. Koo, S. H. Oh, W. Y. Park, D. Kim, and B. Y. Choi, “Identification and clinical implications of novel MYO15A mutations in a non-consanguineous Korean family by targeted exome sequencing,” Mol. Cells, vol. 38, no. 9, pp. 781–788, 2015, doi: 10.14348/molcells.2015.0078.

N. K. D. Kim, T. Higashi, K. Y. Lee, A. R. Kim, S. Kitajiri, M. Y. Kim, M. Y. Chang, V. Kim, S. H. Oh, D. Kim, M. Furuse, W. Y. Park, and B. Y. Choi, “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, vol. 10, no. 2, Feb. 2015, doi: 10.1371/journal.pone.0116931.

I. Jung, J. Seo, H. S. Lee, L. W. Stanton, D. Kim, and J. K. Choi, “Global mapping of the regulatory interactions of histone residues,” FEBS Lett., 2015, doi: 10.1016/j.febslet.2015.11.016.

S. Hahn and D. Kim, “Identifying and reducing systematic errors in chromosome conformation capture data,” PLoS One, 2015, doi: 10.1371/journal.pone.0146007.

M. Nam, S. J. Lee, S. Han, D. Kim, M. Lee, E. J. Kang, H. O. Park, A. R. Lee, S. Lee, C. H. Kim, D. U. Kim, and K. L. Hoe, “Systematic targeted gene deletion using the gene-synthesis method in fission yeast,” J. Microbiol. Methods, vol. 106, pp. 72–77, 2014, doi: 10.1016/j.mimet.2014.08.005.

J. Chung, S. M. Park, S. O. Chang, T. Chung, K. Y. Lee, A. R. Kim, J. H. Park, V. Kim, W. Y. Park, S. H. Oh, D. Kim, W. J. Park, and B. Y. Choi, “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., vol. 92, no. 6, pp. 651–663, 2014, doi: 10.1007/s00109-014-1128-3.

Y. Lee, J. J. Lee, S. Kim, S. C. Lee, J. Han, W. Heu, K. Park, H. J. Kim, H. K. Cheong, D. Kim, H. S. Kim, and K. W. Lee, “Dissecting the critical factors for thermodynamic stability of modular proteins using molecular modeling approach,” PLoS One, 2014, doi: 10.1371/journal.pone.0098243.

J. J. Lee, H. J. Kim, C. S. Yang, H. H. Kyeong, J. M. Choi, D. E. Hwang, J. M. Yuk, K. Park, Y. J. Kim, S. G. Lee, D. Kim, E. K. Jo, H. K. Cheong, and H. S. Kim, “A high-affinity protein binder that blocks the IL-6/STAT3 signaling pathway effectively suppresses non-small cell lung cancer,” in Molecular Therapy, 2014, doi: 10.1038/mt.2014.59.

J. H. Ryou, K. Park, J. J. Lee, D. Kim, and H. S. Kim, “Soluble expression of human glycoprotein Ibα in Escherichia coli through replacement of the N-terminal capping domain,” Protein Expr. Purif., 2014, doi: 10.1016/j.pep.2014.06.001.

S. K. Kim, I. Jung, H. Lee, K. Kang, M. Kim, K. Jeong, C. S. Kwon, Y. M. Han, Y. S. Kim, D. Kim, and D. Lee, “Erratum: Human histone H3K79 methyltransferase DOT1L protein binds actively transcribing RNA polymerase II to regulate gene expression (Journal of Biological Chemistry (2012) 287 (39698-39709) DOI: 10.1074/jbc.A112.384057),” Journal of Biological Chemistry, vol. 288, no. 1. American Society for Biochemistry and Molecular Biology Inc., p. 295, 04-Jan-2013, doi: 10.1074/jbc.A112.384057.

B. Y. Choi, D. H. Kim, T. Chung, M. Chang, E. H. Kim, A. R. Kim, J. Seok, S. O. Chang, J. Bok, D. Kim, S. H. Oh, and W. Y. Park, “Destabilization and Mislocalization of POU3F4 by C-Terminal Frameshift Truncation and Extension Mutation,” Hum. Mutat., vol. 34, no. 2, pp. 309–316, Feb. 2013, doi: 10.1002/humu.22232.

S. Han, M. Lee, H. Chang, M. Nam, H. O. Park, Y. S. Kwak, H. jeong Ha, D. Kim, S. O. Hwang, K. L. Hoe, and D. U. Kim, “Construction of the first compendium of chemical-genetic profiles in the fission yeast Schizosaccharomyces pombe and comparative compendium approach,” Biochem. Biophys. Res. Commun., vol. 436, no. 4, pp. 613–618, Jul. 2013, doi: 10.1016/j.bbrc.2013.05.138.

M. Lee, S. Han, H. Chang, Y. S. Kwak, D. M. Weller, and D. Kim, “FitSearch: A robust way to interpret a yeast fitness profile in terms of drug’s mode-of-action,” BMC Genomics, 2013, doi: 10.1186/1471-2164-14-S1-S6.

K. Lee, S. C. Kim, I. Jung, K. Kim, J. Seo, H. S. Lee, G. K. Bogu, D. Kim, S. Lee, B. Lee, and J. K. Choi, “Genetic Landscape of Open Chromatin in Yeast,” PLoS Genet., 2013, doi: 10.1371/journal.pgen.1003229.

M. Lee, K. Park, and D. Kim, “Interaction network among functional drug groups,” BMC Syst. Biol., 2013, doi: 10.1186/1752-0509-7-S3-S4.

I. Jung and D. Kim, “LinkNMF: Identification of histone modification modules in the human genome using nonnegative matrix factorization,” Gene, 2013, doi: 10.1016/j.gene.2012.11.027.

S. Hahn and D. Kim, “Physical origin of the contact frequency in chromosome conformation capture data,” Biophys. J., 2013, doi: 10.1016/j.bpj.2013.08.043.

J. Lee, Y. Xia, M. Y. Son, G. Jin, B. Seol, M. J. Kim, M. J. Son, M. Do, M. Lee, D. Kim, K. Lee, and Y. S. Cho, “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. Chemie - Int. Ed., 2012, doi: 10.1002/anie.201206691.

J. Han, H. J. Kim, S. C. Lee, S. Hong, K. Park, Y. H. Jeon, D. Kim, H. K. Cheong, and H. S. Kim, “Structure-based rational design of a Toll-like receptor 4 (TLR4) decoy receptor with high binding affinity for a target protein,” PLoS One, 2012, doi: 10.1371/journal.pone.0030929.

S. C. Lee, K. Park, J. Han, J. J. Lee, H. J. Kim, S. Hong, W. Heu, Y. J. Kim, J. S. Ha, S. G. Lee, H. K. Cheong, Y. H. Jeon, D. Kim, and H. S. Kim, “Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering,” Proc. Natl. Acad. Sci. U. S. A., 2012, doi: 10.1073/pnas.1113193109.

C. Hong, M. Lee, D. Kim, D. Kim, K. H. Cho, and I. Shin, “A checkpoints capturing timing-robust Boolean model of the budding yeast cell cycle regulatory network,” BMC Syst. Biol., 2012, doi: 10.1186/1752-0509-6-129.

S. K. Kim, I. Jung, H. Lee, K. Kang, M. Kim, K. Jeong, C. S. Kwon, Y. M. Han, Y. S. Kim, D. Kim, and D. Lee, “Human histone H3K79 methyltransferase DOT1L methyltransferase binds actively transcribing RNA polymerase II to regulate gene expression,” J. Biol. Chem., 2012, doi: 10.1074/jbc.M112.384057.

I. Jung, S. K. Kim, M. Kim, Y. M. Han, Y. S. Kim, D. Kim, and D. Lee, “H2B monoubiquitylation is a 5′-enriched active transcription mark and correlates with exon-intron structure in human cells,” Genome Res., 2012, doi: 10.1101/gr.120634.111.

C. S. Jeong and D. Kim, “Coevolved residues and the functional association for intrinsically disordered proteins,” in Pacific Symposium on Biocomputing, 2012, doi: 10.1142/9789814366496_0014.

K. Park and D. Kim, “Structure-based rebuilding of coevolutionary information reveals functional modules in rhodopsin structure,” in Biochimica et Biophysica Acta - Proteins and Proteomics, 2012, doi: 10.1016/j.bbapap.2012.05.015.

I. Jung and D. Kim, “Histone modification profiles characterize function-specific gene regulation,” J. Theor. Biol., 2012, doi: 10.1016/j.jtbi.2012.06.009.

S. Hahn and D. Kim, “Transient protein-protein interaction of the SH3-peptide complex via closely located multiple binding sites,” PLoS One, 2012, doi: 10.1371/journal.pone.0032804.

C. S. Jeong and D. Kim, “Reliable and robust detection of coevolving protein residues,” in Protein Engineering, Design and Selection, 2012, doi: 10.1093/protein/gzs081.

M. Lee and D. Kim, “Large-scale reverse docking profiles and their applications.,” BMC Bioinformatics, 2012, doi: 10.1186/1471-2105-13-s17-s6.

B. J. Min, N. Kim, T. Chung, O. H. Kim, G. Nishimura, C. Y. Chung, H. R. Song, H. W. Kim, H. R. Lee, J. Kim, T. H. Kang, M. E. Seo, S. D. Yang, D. H. Kim, S. B. Lee, J. Il Kim, J. S. Seo, J. Y. Choi, D. Kang, D. Kim, W. Y. Park, and T. J. Cho, “Whole-exome sequencing identifies mutations of KIF22 in spondyloepimetaphyseal dysplasia with joint laxity, leptodactylic type,” Am. J. Hum. Genet., vol. 89, no. 6, pp. 760–766, Dec. 2011, doi: 10.1016/j.ajhg.2011.10.015.

Y. S. Kwak, S. Han, L. S. Thomashow, J. T. Rice, T. C. Paulitz, D. Kim, and D. M. Weller, “Saccharomyces cerevisiae genome-wide mutant screen for sensitivity to 2,4-diacetylphloroglucinol, an antibiotic produced by Pseudomonas fluorescens,” Appl. Environ. Microbiol., 2011, doi: 10.1128/AEM.02151-10.

K. Park and D. Kim, “Drug-drug relationship based on target information: application to drug target identification,” BMC Syst. Biol., 2011, doi: 10.1186/1752-0509-5-S2-S12.

N. Kim, H. Kim, I. Jung, Y. Kim, D. Kim, and Y. M. Han, “Expression profiles of miRNAs in human embryonic stem cells during hepatocyte differentiation,” Hepatol. Res., 2011, doi: 10.1111/j.1872-034X.2010.00752.x.

K. Park and D. Kim, “Modeling allosteric signal propagation using protein structure networks,” BMC Bioinformatics, 2011, doi: 10.1186/1471-2105-12-S1-S23.

T. Munesue, S. Yokoyama, K. Nakamura, A. Anitha, K. Yamada, K. Hayashi, T. Asaka, H. X. Liu, D. Jin, K. Koizumi, M. S. Islam, J. J. Huang, W. J. Ma, U. H. Kim, S. J. Kim, K. Park, D. Kim, M. Kikuchi, Y. Ono, H. Nakatani, S. Suda, T. Miyachi, H. Hirai, A. Salmina, Y. A. Pichugina, A. A. Soumarokov, N. Takei, N. Mori, M. Tsujii, T. Sugiyama, K. Yagi, M. Yamagishi, T. Sasaki, H. Yamasue, N. Kato, R. Hashimoto, M. Taniike, Y. Hayashi, J. Hamada, S. Suzuki, A. Ooi, M. Noda, Y. Kamiyama, M. A. Kido, O. Lopatina, M. Hashii, S. Amina, F. Malavasi, E. J. Huang, J. Zhang, N. Shimizu, T. Yoshikawa, A. Matsushima, Y. Minabe, and H. Higashida, “Two genetic variants of CD38 in subjects with autism spectrum disorder and controls,” Neurosci. Res., vol. 67, no. 2, pp. 181–191, Jun. 2010, doi: 10.1016/j.neures.2010.03.004.

D. U. Kim, J. Hayles, D. Kim, V. Wood, H. O. Park, M. Won, H. S. Yoo, T. Duhig, M. Nam, G. Palmer, S. Han, L. Jeffery, S. T. Baek, H. Lee, Y. S. Shim, M. Lee, L. Kim, K. S. Heo, E. J. Noh, A. R. Lee, Y. J. Jang, K. S. Chung, S. J. Choi, J. Y. Park, Y. Park, H. M. Kim, S. K. Park, H. J. Park, E. J. Kang, H. B. Kim, H. S. Kang, H. M. Park, K. Kim, K. Song, K. Bin Song, P. Nurse, and K. L. Hoe, “Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe,” Nat. Biotechnol., 2010, doi: 10.1038/nbt.1628.

S. Lee, K. Park, H. S. Ahn, and D. Kim, “Importance of structural information in predicting human acute toxicity from in vitro cytotoxicity data,” Toxicol. Appl. Pharmacol., 2010, doi: 10.1016/j.taap.2010.04.004.

I. Jung, A. Matsuyama, M. Yoshida, and D. Kim, “PostMod: Sequence based prediction of kinase-specific phosphorylation sites with indirect relationship,” BMC Bioinformatics, 2010, doi: 10.1186/1471-2105-11-S1-S10.

S. Lee and D. Kim, “Cytochrome P450 networks in chemical space,” Arch. Pharm. Res., 2010, doi: 10.1007/s12272-010-0910-1.

S. Hong, T. Chung, and D. Kim, “SH3 domain-peptide binding energy calculations based on structural ensemble and multiple peptide templates,” PLoS One, 2010, doi: 10.1371/journal.pone.0012654.

C. S. Jeong and D. Kim, “Linear predictive coding representation of correlated mutation for protein sequence alignment,” BMC Bioinformatics, 2010, doi: 10.1186/1471-2105-11-S2-S2.

K. Park, S. Lee, H. S. Ahn, and D. Kim, “Predicting the multi-modal binding propensity of small molecules: Towards an understanding of drug promiscuity,” Mol. Biosyst., 2009, doi: 10.1039/b901356c.

S. Lee, K. Park, and D. Kim, “Building a drugtarget network and its applications,” Expert Opinion on Drug Discovery. 2009, doi: 10.1517/17460440903322234.

I. Jung and D. Kim, “SIMPRO: Simple protein homology detection method by using indirect signals,” Bioinformatics, 2009, doi: 10.1093/bioinformatics/btp048.

K. Ii. Cho, D. Kim, and D. Lee, “A feature-based approach to modeling protein-protein interaction hot spots,” Nucleic Acids Res., 2009, doi: 10.1093/nar/gkp132.

K. Park and D. Kim, “Localized network centrality and essentiality in the yeast-protein interaction network,” Proteomics, 2009, doi: 10.1002/pmic.200900357.

B. C. Lee and D. Kim, “A new method for revealing correlated mutations under the structural and functional constraints in proteins,” Bioinformatics, 2009, doi: 10.1093/bioinformatics/btp455.

S. T. Baek, S. Han, M. Nam, Y. D. Kim, L. Kim, H. J. Lee, K. S. Heo, H. Lee, M. Lee, S. K. Park, P. J. Maeng, Y. Park, S. Lee, D. U. Kim, D. Kim, and K. L. Hoe, “Genome-wide identification of haploinsufficiency in fission yeast,” J. Microbiol. Biotechnol., vol. 18, no. 6, pp. 1059–1063, Jun. 2008.

S. T. Baek, D. U. Kim, S. Han, I. S. Woo, M. Nam, L. Kim, K. S. Heo, H. Lee, H. R. Hwang, S. J. Choi, M. Won, M. Lee, S. K. Park, S. Lee, H. J. Kwon, P. J. Maeng, H. M. Park, Y. Park, D. Kim, and K. L. Hoe, “Genome-wide drug-induced haploinsufficient screening of fission yeast for identification of hydrazinocurcumin targets,” J. Microbiol. Biotechnol., vol. 18, no. 2, pp. 263–269, Feb. 2008.

W. C. Lee, M. Lee, J. W. Woo, K. P. Pyo, and D. Kim, “SCUD: Saccharomyces cerevisiae ubiquitination database,” BMC Genomics, 2008, doi: 10.1186/1471-2164-9-440.

I. Jung, J. Lee, S. Y. Lee, and D. Kim, “Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection,” BMC Bioinformatics, 2008, doi: 10.1186/1471-2105-9-298.

B. C. Lee, K. Park, and D. Kim, “Analysis of the residue-residue coevolution network and the functionally important residues in proteins,” Proteins Struct. Funct. Genet., 2008, doi: 10.1002/prot.21972.

S. Han and D. Kim, “Inference of protein complex activities from chemical-genetic profile and its applications: Predicting drug-target pathways,” PLoS Comput. Biol., 2008, doi: 10.1371/journal.pcbi.1000162.

K. Park and D. Kim, “Binding similarity network of ligand,” Proteins Struct. Funct. Genet., 2008, doi: 10.1002/prot.21780.

C. Keum and D. Kim, “Protein function prediction via ligand interface residue match,” in IFMBE Proceedings, 2007, vol. 14, no. 1, pp. 191–192, doi: 10.1007/978-3-540-36841-0_56.

C. S. Jeong, M. Lee, and D. Kim, “Detecting remote homolog by protein similarity network,” in IFMBE Proceedings, 2007, vol. 14, no. 1, pp. 171–173, doi: 10.1007/978-3-540-36841-0_51.

W. Lee and D. Kim, “Prediction of Protein Kinase Specific Phosphorylation Sites with Multiple SVMs,” Interdiscip. Bio Cent., 2007, doi: 10.4051/ibce.2009.3.0024.

M. Lee, C. S. Jeong, and D. Kim, “Predicting and improving the protein sequence alignment quality by support vector regression,” BMC Bioinformatics, 2007, doi: 10.1186/1471-2105-8-471.

S. Lee and D. Kim, “Equation chapter 1 section 1A new method for predicting human hepatic clearance from in vitro experimental data using molecular descriptors,” Arch. Pharm. Res., 2007, doi: 10.1007/BF02977693.

D. Na, D. Kim, and D. Lee, “Mathematical modeling of humoral immune response suppression by passively administered antibodies in mice,” J. Theor. Biol., 2006, doi: 10.1016/j.jtbi.2006.01.019.

K. Il Cho, K. Y. Lee, K. H. Lee, D. Kim, and D. Lee, “Specificity of molecular interactions in transient protein-protein interaction interfaces,” Proteins Struct. Funct. Genet., 2006, doi: 10.1002/prot.21056.

K. Park and D. Kim, “A method to detect important residues using protein binding site comparison.,” Genome Inform., 2006, doi: 10.11234/gi1990.17.2_216.

S. Lee, B. C. Lee, and D. Kim, “Prediction of protein secondary structure content using amino acid composition and evolutionary information,” Proteins Struct. Funct. Genet., 2006, doi: 10.1002/prot.20821.

S. Han and D. Kim, “AtRTPrimer: Database for Arabidopsis genome-wide homogeneous and specific RT-PCR primer-pairs,” BMC Bioinformatics, 2006, doi: 10.1186/1471-2105-7-179.

S. Han, B. C. Lee, S. T. Yu, C. S. Jeong, S. Lee, and D. Kim, “Fold recognition by combining profile-profile alignment and support vector machine,” Bioinformatics, 2005, doi: 10.1093/bioinformatics/bti384.