Dongsup Kim

发表

Analysis of the residue–residue coevolution network and the functionally important residues in proteins

Byung-chul Lee, Keunwan Park, Dongsup Kim, 2008, Proteins.

Binding similarity network of ligand

Keunwan Park, Dongsup Kim, 2008, Proteins.

Improving the performance of DomainParser for structural domain partition using neural network.

Dong Xu, Dongsup Kim, Jun-tao Guo, 2003, Nucleic acids research.

Raptor: Optimal Protein Threading by Linear Programming

Ying Xu, Ming Li, Dongsup Kim, 2003, J. Bioinform. Comput. Biol..

A feature-based approach to modeling protein–protein interaction hot spots

Doheon Lee, Dongsup Kim, Kyu-il Cho, 2009, Nucleic acids research.

Building a drug–target network and its applications

Soyoung Lee, Keunwan Park, Dongsup Kim, 2009, Expert opinion on drug discovery.

Specificity of molecular interactions in transient protein–protein interaction interfaces

Doheon Lee, Dongsup Kim, Doheon Lee, 2006, Proteins.

Prediction of protein secondary structure content using amino acid composition and evolutionary information

Dongsup Kim, Soyoung Lee, Byung-chul Lee, 2005, Proteins.

H2B monoubiquitylation is a 5′-enriched active transcription mark and correlates with exon–intron structure in human cells

Inkyung Jung, Dongsup Kim, Daeyoup Lee, 2012, Genome research.

Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe

Dongsup Kim, V. Wood, J. Hayles, 2010, Nature Biotechnology.

Engineering Clostridial Aldehyde/Alcohol Dehydrogenase for Selective Butanol Production

Dongsup Kim, Y. Jang, S. Lee, 2019, mBio.

Structure-based rebuilding of coevolutionary information reveals functional modules in rhodopsin structure.

Keunwan Park, Dongsup Kim, Keunwan Park, 2012, Biochimica et biophysica acta.

Localized network centrality and essentiality in the yeast–protein interaction network

Keunwan Park, Dongsup Kim, Keunwan Park, 2009, Proteomics.

Discovering cis-regulatory motifs by combining multiple predictors

Dongsup Kim, Hyeshik Chang, ksbsb ibc, 2007 .

Inferring Crohn’s disease association from exome sequences by integrating biological knowledge

Dongsup Kim, Chan-seok Jeong, 2016, BMC Medical Genomics.

A high-affinity protein binder that blocks the IL-6/STAT3 signaling pathway effectively suppresses non-small cell lung cancer.

Keunwan Park, Dongsup Kim, Hak-Sung Kim, 2014, Molecular therapy : the journal of the American Society of Gene Therapy.

Importance of structural information in predicting human acute toxicity from in vitro cytotoxicity data.

Keunwan Park, Dongsup Kim, Soyoung Lee, 2010, Toxicology and applied pharmacology.

Mathematical modeling of humoral immune response suppression by passively administered antibodies in mice.

Doheon Lee, Dongsup Kim, D. Na, 2006, Journal of theoretical biology.

Relationship between spatial organization and biological function, analyzed using gene ontology and chromosome conformation capture of human and fission yeast genomes

Dongsup Kim, Seungsoo Hahn, 2016, Genes & Genomics.

Prediction of Protein Kinase Specific Phosphorylation Sites with Multiple SVMs

Dongsup Kim, ksbsb ibc, Won-Chul Lee, 2007 .

SH3 Domain-Peptide Binding Energy Calculations Based on Structural Ensemble and Multiple Peptide Templates

Dongsup Kim, Seungpyo Hong, Taesu Chung, 2010, PloS one.

Construction of the first compendium of chemical-genetic profiles in the fission yeast Schizosaccharomyces pombe and comparative compendium approach.

Dongsup Kim, K. Hoe, Dong-Uk Kim, 2013, Biochemical and biophysical research communications.

A novel mutation of TMPRSS3 related to milder auditory phenotype in Korean postlingual deafness: a possible future implication for a personalized auditory rehabilitation

Dongsup Kim, W. Park, B. Choi, 2014, Journal of Molecular Medicine.

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.

Dongsup Kim, Misol Do, M. Son, 2012, Angewandte Chemie.

Interaction network among functional drug groups

Minho Lee, Dongsup Kim, Keunwan Park, 2013, BMC Systems Biology.

Linear predictive coding representation of correlated mutation for protein sequence alignment

Dongsup Kim, Chan-seok Jeong, 2010, BMC Bioinform..

Detecting remote homolog by protein similarity network

Dongsup Kim, Minho Lee, Chan-seok Jeong, 2007 .

Global mapping of the regulatory interactions of histone residues

Dongsup Kim, J. Choi, L. Stanton, 2015, FEBS letters.

Identification of novel trans-crosstalk between histone modifications via genome-wide analysis of maximal deletion effect

Dongsup Kim, Chulhee Choi, Inkyung Jung, 2015, Genes & Genomics.

Prediction of binding property of RNA-binding proteins using multi-sized filters and multi-modal deep convolutional neural network

Dongsup Kim, Taesu Chung, 2019, PloS one.

Prediction of drug–target interactions through multi-task learning

Dongsup Kim, Chaeyoung Moon, 2022, Scientific Reports.

Characterization of protein structure and function at genome scale with a computational prediction pipeline.

Dong Xu, Dongsup Kim, Ying Xu, 2003, Genetic engineering.

BGN Mutations in X-Linked Spondyloepimetaphyseal Dysplasia.

Dongsup Kim, W. Park, K. Girisha, 2016, American journal of human genetics.

Transient Protein-Protein Interaction of the SH3-Peptide Complex via Closely Located Multiple Binding Sites

Dongsup Kim, Seungsoo Hahn, 2012, PloS one.

FARS2 mutation and epilepsy: Possible link with early-onset epileptic encephalopathy

Ha Young Kim, Dongsup Kim, Jong-il Kim, 2017, Epilepsy Research.

Genetic Landscape of Open Chromatin in Yeast

Inkyung Jung, Gireesh K. Bogu, Jung Kyoon Choi, 2013, PLoS genetics.

A Compendium of Promoter-Centered Long-Range Chromatin Interactions in the Human Genome

Bing Ren, Inkyung Jung, Zachary Chiang, 2019, Nature Genetics.

Physical origin of the contact frequency in chromosome conformation capture data.

Dongsup Kim, Seungsoo Hahn, 2013, Biophysical journal.

A checkpoints capturing timing-robust Boolean model of the budding yeast cell cycle regulatory network

Minho Lee, Kwang-Hyun Cho, Insik Shin, 2012, BMC Systems Biology.

Brain physiome: A concept bridging in vitro 3D brain models and in silico models for predicting drug toxicity in the brain

Dongsup Kim, P. Kim, H. Kim, 2021, Bioactive materials.

Expression profiles of miRNAs in human embryonic stem cells during hepatocyte differentiation

Dongsup Kim, Inkyung Jung, Nury Kim, 2011, Hepatology research : the official journal of the Japan Society of Hepatology.

Identification and Clinical Implications of Novel MYO15A Mutations in a Non-consanguineous Korean Family by Targeted Exome Sequencing

Dongsup Kim, W. Park, B. Choi, 2015, Molecules and cells.

Structure-Based Rational Design of a Toll-like Receptor 4 (TLR4) Decoy Receptor with High Binding Affinity for a Target Protein

Keunwan Park, Dongsup Kim, Seungpyo Hong, 2012, PloS one.

Library of binding protein scaffolds (LibBP): a computational platform for selection of binding protein scaffolds

Dongsup Kim, Seungpyo Hong, Dongsup Kim, 2016, Bioinform..

Hypomorphic Mutations in TONSL Cause SPONASTRIME Dysplasia.

O. Mäkitie, Dongsup Kim, G. Stewart, 2019, American journal of human genetics.

University of Birmingham Hypomorphic Mutations in TONSL Cause SPONASTRIME Dysplasia

O. Mäkitie, Dongsup Kim, G. Stewart, 2019 .

Regulatory Patterns of Histone Modifications to Control the DNA Methylation Status at CpG Islands

Inkyung Jung, Dongsup Kim, Dongsup Kim, 2009 .

KRDS: a web server for evaluating drug resistance mutations in kinases by molecular docking

Dongsup Kim, Seungpyo Hong, Aeri Lee, 2018, Journal of Cheminformatics.

Human histone H3K79 methyltransferase DOT1L protein binds actively transcribing RNA polymerase II to regulate gene expression.

Dongsup Kim, Mirang Kim, Y. S. Kim, 2013, The Journal of Biological Chemistry.

Human Histone H3K79 Methyltransferase DOT1L Methyltransferase Binds Actively Transcribing RNA Polymerase II to Regulate Gene Expression*

Dongsup Kim, Mirang Kim, Y. S. Kim, 2012, The Journal of Biological Chemistry.

Fold recognition by combining profile-profile alignment and support vector machine

Chan-seok Jeong, Dongsup Kim, Sangjo Han, 2005, Bioinform..

A method to detect important residues using protein binding site comparison.

Keunwan Park, Dongsup Kim, Keunwan Park, 2006, Genome informatics. International Conference on Genome Informatics.

A novel mutation of TMPRSS3 related to milder auditory phenotype in Korean postlingual deafness: a possible future implication for a personalized auditory rehabilitation

Dongsup Kim, B. Choi, Juyong Chung, 2014, Journal of Molecular Medicine.

Histone modification profiles characterize function-specific gene regulation.

Dongsup Kim, Inkyung Jung, 2012, Journal of theoretical biology.

A late-lineage murine neutrophil precursor population exhibits dynamic changes during demand-adapted granulopoiesis

Dongsup Kim, Mirang Kim, Seon-Young Kim, 2017, Scientific Reports.

Predicting the multi-modal binding propensity of small molecules: towards an understanding of drug promiscuity.

Keunwan Park, Dongsup Kim, Soyoung Lee, 2009, Molecular bioSystems.

Computational characterization of chromatin domain boundary-associated genomic elements

Seungpyo Hong, Dongsup Kim, Dongsup Kim, 2017, Nucleic acids research.

FitSearch: a robust way to interpret a yeast fitness profile in terms of drug's mode-of-action

Minho Lee, Dongsup Kim, Sangjo Han, 2013, BMC Genomics.

Saccharomyces cerevisiae Genome-Wide Mutant Screen for Sensitivity to 2,4-Diacetylphloroglucinol, an Antibiotic Produced by Pseudomonas fluorescens

Sangjo Han, Dongsup Kim, Linda S. Thomashow, 2010, Applied and Environmental Microbiology.

Inference of Protein Complex Activities from Chemical-Genetic Profile and Its Applications: Predicting Drug-Target Pathways

Dongsup Kim, Sangjo Han, Dongsup Kim, 2008, PLoS Comput. Biol..

G-RANK: an equivariant graph neural network for the scoring of protein–protein docking models

Dongsup Kim, Woong-Yang Park, Sungsik Kim, 2023, Bioinformatics advances.

AtRTPrimer: database for Arabidopsis genome-wide homogeneous and specific RT-PCR primer-pairs

Dongsup Kim, Sangjo Han, Dongsup Kim, 2006, BMC Bioinformatics.

Inference of Gene Regulatory Networks Using Time Sliding Comparison and Transcriptional Lagging Time from Time Series Gene Expression Profiles

Dongsup Kim, Sheehyun Kim, Dongsup Kim, 2007, 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering.

Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction

Dongsup Kim, Youngmahn Han, 2017, BMC Bioinformatics.

SCUD: Saccharomyces Cerevisiae Ubiquitination Database

Dongsup Kim, Dongsup Kim, Minho Lee, 2008, BMC Genomics.

Cytochrome P450 networks in chemical space

Soyoung Lee, Dongsup Kim, 2010, Archives of pharmacal research.

3DIV: A 3D-genome Interaction Viewer and database

Byungwook Lee, Jinhyuk Choi, Dongsup Kim, 2017, Nucleic Acids Res..

Two genetic variants of CD38 in subjects with autism spectrum disorder and controls

H. Yamasue, N. Kato, E. Huang, 2010, Neuroscience Research.

Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering

Seungpyo Hong, Keunwan Park, Dongsup Kim, 2012, Proceedings of the National Academy of Sciences.

Systematic targeted gene deletion using the gene-synthesis method in fission yeast.

Cheol‐Hee Kim, Dongsup Kim, K. Hoe, 2014, Journal of microbiological methods.

Reliable and robust detection of coevolving protein residues.

Dongsup Kim, Chan-Seok Jeong, Dongsup Kim, 2012, Protein engineering, design & selection : PEDS.

A new method for revealing correlated mutations under the structural and functional constraints in proteins

Dongsup Kim, Byung-chul Lee, Byung-chul Lee, 2009, Bioinform..

CRDS: Consensus Reverse Docking System for target fishing

Dongsup Kim, Aeri Lee, Dongsup Kim, 2019, Bioinform..

Global Analysis of Intercellular Homeodomain Protein Transfer

M. Vidal, Dongsup Kim, S. Blackshaw, 2019, Cell reports.

Utilizing random Forest QSAR models with optimized parameters for target identification and its application to target-fishing server

Dongsup Kim, Minho Lee, Kyoungyeul Lee, 2017, BMC Bioinformatics.

Development of a graph convolutional neural network model for efficient prediction of protein-ligand binding affinities

Dongsup Kim, Jeongtae Son, 2021, PloS one.

Autonomous molecule generation using reinforcement learning and docking to develop potential novel inhibitors

Dongsup Kim, Woosung Jeon, Dongsup Kim, 2020, Scientific Reports.

Downsloping High-Frequency Hearing Loss Due to Inner Ear Tricellular Tight Junction Disruption by a Novel ILDR1 Mutation in the Ig-Like Domain

Dongsup Kim, W. Park, B. Choi, 2015, PloS one.

Whole-exome sequencing identifies mutations of KIF22 in spondyloepimetaphyseal dysplasia with joint laxity, leptodactylic type.

Dongsup Kim, D. Kang, W. Park, 2011, American journal of human genetics.

PROSPECT II: protein structure prediction program for genome-scale applications.

Dong Xu, Ying Xu, Kyle Ellrott, 2003, Protein engineering.

FP2VEC: a new molecular featurizer for learning molecular properties

Dongsup Kim, Woosung Jeon, Dongsup Kim, 2019, Bioinform..

Soluble expression of human glycoprotein Ibα in Escherichia coli through replacement of the N-terminal capping domain.

Keunwan Park, Dongsup Kim, Hak-Sung Kim, 2014, Protein expression and purification.

An enhanced variant effect predictor based on a deep generative model and the Born-Again Networks

Ha Young Kim, Dongsup Kim, Woosung Jeon, 2021, Scientific Reports.

Prediction of mutation effects using a deep temporal convolutional network

Ha Young Kim, Dongsup Kim, Ha Young Kim, 2019, Bioinform..

DeepLUCIA: predicting tissue-specific chromatin loops using Deep Learning-based Universal Chromatin Interaction Annotator

Dongsup Kim, Taesu Chung, Dongchan Yang, 2022, Bioinform..

MTBAN: An Enhanced Variant Effect Predictor Based on a Deep Generative Model

Dongsup Kim, Woosung Jeon, Ha Young Kim, 2021 .

Utilizing random Forest QSAR models with optimized parameters for target identification and its application to target-fishing server

Minho Lee, Dongsup Kim, Kyoungyeul Lee, 2017, BMC Bioinformatics.

Large-scale reverse docking profiles and their applications

Minho Lee, Dongsup Kim, Dongsup Kim, 2012, BMC Bioinformatics.

LinkNMF: identification of histone modification modules in the human genome using nonnegative matrix factorization.

Dongsup Kim, Inkyung Jung, 2013, Gene.

Structure-based Markov random field model for representing evolutionary constraints on functional sites

Dongsup Kim, Chan-seok Jeong, 2016, BMC Bioinformatics.

Inferring Relative Activity between Pathway and Downstream Genes to Classify Melanoma Cancer Progression

Dongsup Kim, Chulhee Choi, Inkyung Jung, 2011 .

Optimization of a microarray for fission yeast

Dongsup Kim, K. Hoe, Dong-Uk Kim, 2019, Genomics & informatics.

Using reverse docking for target identification and its applications for drug discovery

Dongsup Kim, Aeri Lee, Kyoungyeul Lee, 2016, Expert opinion on drug discovery.

In-Silico Molecular Binding Prediction for Human Drug Targets Using Deep Neural Multi-Task Learning

Dongsup Kim, Kyoungyeul Lee, Dongsup Kim, 2019, Genes.

Relationship between spatial organization and biological function, analyzed using gene ontology and chromosome conformation capture of human and fission yeast genomes

Dongsup Kim, Seungsoo Hahn, 2016, Genes & Genomics.

Identifying and Reducing Systematic Errors in Chromosome Conformation Capture Data

Dongsup Kim, Seungsoo Hahn, 2015, PloS one.

gkx 1017 3 DIV : A 3 D-genome Interaction Viewer and database

Dongsup Kim, Inkyung Jung, Andrew J. Lee, 2017 .

Rising of LOXHD1 as a signature causative gene of down-sloping hearing loss in people in their teens and 20s

Dongsup Kim, B. Choi, J. Koo, 2021, Journal of Medical Genetics.

SIMPRO: simple protein homology detection method by using indirect signals

Dongsup Kim, Inkyung Jung, Dongsup Kim, 2009, Bioinform..

Global Analysis of Intercel lular Homeodomain Protein Transfer Graphical

M. Vidal, Dongsup Kim, S. Blackshaw, 2019 .

Mutation Analysis of Synthetic DNA Barcodes in a Fission Yeast Gene Deletion Library by Sanger Sequencing

Dongsup Kim, K. Hoe, Dong-Uk Kim, 2018, Genomics & informatics.

Structure-based Markov random field model for representing evolutionary constraints on functional sites

Chan-seok Jeong, Dongsup Kim, Dongsup Kim, 2016, BMC Bioinformatics.

Identification of novel trans-crosstalk between histone modifications via genome-wide analysis of maximal deletion effect

Dongsup Kim, Chulhee Choi, Inkyung Jung, 2015, Genes & Genomics.

Predicting and improving the protein sequence alignment quality by support vector regression

Dongsup Kim, Minho Lee, Chan-seok Jeong, 2007, BMC Bioinformatics.

A high-affinity protein binder that blocks the IL-6/STAT3 signaling pathway effectively suppresses non-small cell lung cancer.

Keunwan Park, Dongsup Kim, Joong-jae Lee, 2014, Molecular therapy : the journal of the American Society of Gene Therapy.

PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship

Dongsup Kim, Minoru Yoshida, Inkyung Jung, 2010, BMC Bioinformatics.

SCUD: Saccharomyces Cerevisiae Ubiquitination Database

Dongsup Kim, Minho Lee, Jin Woo Jung, 2008, BMC Genomics.

Dissecting the Critical Factors for Thermodynamic Stability of Modular Proteins Using Molecular Modeling Approach

Keunwan Park, Dongsup Kim, Keun Woo Lee, 2014, PloS one.

Human Histone H3K79 Methyltransferase DOT1L Methyltransferase Binds Actively Transcribing RNA Polymerase II to Regulate Gene Expression*

Dongsup Kim, Mirang Kim, Y. S. Kim, 2012, The Journal of Biological Chemistry.

Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction

Dongsup Kim, Youngmahn Han, Dongsup Kim, 2017, BMC Bioinformatics.

Linear predictive coding representation of correlated mutation for protein sequence alignment

Chan-seok Jeong, Dongsup Kim, Dongsup Kim, 2009, BMC Bioinformatics.

Automated assignment of backbone NMR peaks using constrained bipartite matching

Tao Jiang, Ying Xu, Dong Xu, 2002, Comput. Sci. Eng..

Drug-drug relationship based on target information: application to drug target identification

Keunwan Park, Dongsup Kim, 2011, BMC Systems Biology.

Predicting and improving the protein sequence alignment quality by support vector regression

Minho Lee, Chan-seok Jeong, Dongsup Kim, 2007, BMC Bioinformatics.

Histone modification profiles characterize function-specific gene regulation.

Dongsup Kim, Inkyung Jung, 2012, Journal of theoretical biology.