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BMC Bioinformatics, Volume 17 - Supplements
Volume 17, Number S-1, January 2016
- Suvir Jain, Kashyap R., Tsung-Ting Kuo
, Shitij Bhargava, Gordon Lin, Chun-Nan Hsu:
Weakly supervised learning of biomedical information extraction from curated data. 1 - Chien-Hung Huang, Peter Mu-Hsin Chang, Chia-Wei Hsu, Chi-Ying F. Huang
, Ka-Lok Ng:
Drug repositioning for non-small cell lung cancer by using machine learning algorithms and topological graph theory. 2 - Shih-Wei Lee, Lawrence Shih-Hsin Wu, Guan-Mau Huang, Kai-Yao Huang, Tzong-Yi Lee, Julia Tzu-Ya Weng:
Gene expression profiling identifies candidate biomarkers for active and latent tuberculosis. 3 - Sunil Kumar, Philipp Bucher:
Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features. 4 - Yafei Lyu, Qunhua Li:
A semi-parametric statistical model for integrating gene expression profiles across different platforms. 5 - Moraima Pagan, Richard T. Kloos, Chu-Fang Lin, Kevin J. Travers, Hajime Matsuzaki, Ed Y. Tom, Su Yeon Kim, Mei G. Wong, Andrew C. Stewart, Jing Huang, P. Sean Walsh, Robert J. Monroe, Giulia C. Kennedy:
The diagnostic application of RNA sequencing in patients with thyroid cancer: an analysis of 851 variants and 133 fusions in 524 genes. 6 - Henan Wang, Chong He, Garima Kushwaha, Dong Xu, Jing Qiu:
A full Bayesian partition model for identifying hypo- and hyper-methylated loci from single nucleotide resolution sequencing data. 7 - Chao Fan, Diwei Liu, Rui Huang, Zhigang Chen, Lei Deng:
PredRSA: a gradient boosted regression trees approach for predicting protein solvent accessibility. 8 - Lujia Chen, Chunhui Cai, Vicky Chen, Xinghua Lu:
Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model. 9 - Yang Yang, Zhuangdi Xu, Dandan Song:
Missing value imputation for microRNA expression data by using a GO-based similarity measure. 10
Volume 17, Number S-2, January 2016
- Said el Bouhaddani
, Jeanine J. Houwing-Duistermaat
, Perttu Salo, Markus Perola, Geurt Jongbloed, Hae-Won Uh
:
Evaluation of O2PLS in Omics data integration. 11 - Séverine Affeldt
, Louis Verny, Hervé Isambert:
3off2: A network reconstruction algorithm based on 2-point and 3-point information statistics. 12 - Yasaman Karami
, Elodie Laine, Alessandra Carbone
:
Dissecting protein architecture with communication blocks and communicating segment pairs. 13 - Marcella Vacca
, Kumar Parijat Tripathi, Luisa Speranza, Riccardo Aiese Cigliano
, Francesco Scalabrì
, Federico Marracino
, Michele Madonna
, Walter Sanseverino
, Carla Perrone-Capano
, Mario Rosario Guarracino
, Maurizio D'Esposito:
Effects of Mecp2 loss of function in embryonic cortical neurons: a bioinformatics strategy to sort out non-neuronal cells variability from transcriptome profiling. 14 - Matteo Bersanelli
, Ettore Mosca
, Daniel Remondini
, Enrico Giampieri, Claudia Sala
, Gastone C. Castellani, Luciano Milanesi
:
Methods for the integration of multi-omics data: mathematical aspects. 15 - Claudia Sala
, Silvia Vitali
, Enrico Giampieri, Ìtalo Faria do Valle
, Daniel Remondini
, Paolo Garagnani, Matteo Bersanelli
, Ettore Mosca
, Luciano Milanesi
, Gastone C. Castellani:
Stochastic neutral modelling of the Gut Microbiota's relative species abundance from next generation sequencing data. 16
Volume 17, Number S-3, February 2016
Volume 17, Number S-4, March 2016
- Arnaud Céol
, Lisette G. G. C. Verhoef, Mark Wade
, Heiko Müller
:
Genome and network visualization facilitates the analyses of the effects of drugs and mutations on protein-protein and drug-protein networks. 54 - Federica Chiappori
, Luca Mattiazzi, Luciano Milanesi
, Ivan Merelli:
A novel molecular dynamics approach to evaluate the effect of phosphorylation on multimeric protein interface: the αB-Crystallin case study. 57 - Paolo Romano
, Aldo Profumo
, Mattia Rocco
, Rosa Mangerini, Fabio Ferri
, Angelo M. Facchiano
:
Geena 2, improved automated analysis of MALDI/TOF mass spectra. 61 - Paolo Romano
, Francesca Cordero
:
NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology. 62 - Nicola Prezza, Francesco Vezzi, Max Käller, Alberto Policriti:
Fast, accurate, and lightweight analysis of BS-treated reads with ERNE 2. 69 - Claudio Angione
, Maxwell Conway, Pietro Liò
:
Multiplex methods provide effective integration of multi-omic data in genome-scale models. 83
Volume 17, Number S-5, June 2016
- Ioannis Kavakiotis, Aliki Xochelli, Andreas Agathangelidis
, Grigorios Tsoumakas
, Nicos Maglaveras
, Kostas Stamatopoulos
, Anastasia Hadzidimitriou, Ioannis P. Vlahavas
, Ioanna Chouvarda
:
Integrating multiple immunogenetic data sources for feature extraction and mining somatic hypermutation patterns: the case of "towards analysis" in chronic lymphocytic leukaemia. 173 - Sebastián Moschen
, Janet Higgins, Julio A. Di Rienzo, Ruth A. Heinz, Norma Paniego
, Paula Fernandez:
Network and biosignature analysis for the integration of transcriptomic and metabolomic data to characterize leaf senescence process in sunflower. 174 - Andrew J. Sedgewick, Ivy Shi, Rory M. Donovan
, Panayiotis V. Benos
:
Learning mixed graphical models with separate sparsity parameters and stability-based model selection. S175 - Animesh Acharjee
, Bjorn Kloosterman, Richard G. F. Visser, Chris Maliepaard:
Integration of multi-omics data for prediction of phenotypic traits using random forest. 180 - Panagiotis Chouvardas
, George Kollias
, Christoforos Nikolaou
:
Inferring active regulatory networks from gene expression data using a combination of prior knowledge and enrichment analysis. 181 - Nikolas Papanikolaou, Georgios A. Pavlopoulos
, Theodosios Theodosiou
, Ioannis S. Vizirianakis
, Ioannis Iliopoulos:
DrugQuest - a text mining workflow for drug association discovery. 182 - Costas Bouyioukos
, Mohamed Elati
, François Képès:
Analysis tools for the interplay between genome layout and regulation. 191 - Vincenzo Lagani, Argyro D. Karozou, David Gomez-Cabrero
, Gilad Silberberg
, Ioannis Tsamardinos:
A comparative evaluation of data-merging and meta-analysis methods for reconstructing gene-gene interactions. S194 - Frans M. van der Kloet
, Patricia Sebastián-León
, Ana Conesa
, Age K. Smilde
, Johan A. Westerhuis:
Separating common from distinctive variation. S195 - Esteban Vegas
, Josep M. Oller, Ferran Reverter
:
Inferring differentially expressed pathways using kernel maximum mean discrepancy-based test. 205 - Francesco Strino, Michael Lappe:
Identifying peaks in *-seq data using shape information. S206
Volume 17, Number S-6, July 2016
- Jongsoo Keum, Sunyong Yoo
, Doheon Lee
, Hojung Nam
:
Prediction of compound-target interactions of natural products using large-scale drug and protein information. 219 - Kimin Oh, Gwan-Su Yi:
Prediction of scaffold proteins based on protein interaction and domain architectures. 220 - Woochang Hwang, Jaejoon Choi, Mijin Kwon, Doheon Lee
:
Context-specific functional module based drug efficacy prediction. 275
Volume 17, Number S-7, July 2016
- Yijia Zhang, Hongfei Lin, Zhihao Yang, Jian Wang, Yiwei Liu, Shengtian Sang:
A method for predicting protein complex in dynamic PPI networks. 229 - Ahmed AbdoAziz Ahmed Abdulla, Hongfei Lin, Bo Xu
, Santosh Kumar Banbhrani:
Improving biomedical information retrieval by linear combinations of different query expansion techniques. 238 - Mark T. W. Ebbert, Mark E. Wadsworth, Lyndsay A. Staley, Kaitlyn L. Hoyt, Brandon D. Pickett
, Justin Miller, John Duce, John S. K. Kauwe, Perry G. Ridge:
Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches. 239 - Wenpin Hou
, Yushan Qiu, Nobuyuki Hashimoto, Wai-Ki Ching, Kiyoko F. Aoki-Kinoshita:
A systematic framework to derive N-glycan biosynthesis process and the automated construction of glycosylation networks. 240 - Aaron R. Sharp, Joshua Udall:
OMWare: a tool for efficient assembly of genome-wide physical maps. 241 - Arman Sargolzaei, Mohamed N. Abdelghani, Kang K. Yen, Saman Sargolzaei:
Sensorimotor control: computing the immediate future from the delayed present. 245 - Thi Thanh Thuy Phan, Takenao Ohkawa:
Protein-protein interaction extraction with feature selection by evaluating contribution levels of groups consisting of related features. 246 - Paul M. Bodily, M. Stanley Fujimoto, Justin T. Page, Mark J. Clement, Mark T. W. Ebbert, Perry G. Ridge:
A novel approach for multi-SNP GWAS and its application in Alzheimer's disease. 268 - Emad Ramadan
, Ahmed Naef, Moataz A. Ahmed:
Protein complexes predictions within protein interaction networks using genetic algorithms. 269 - Emad Ramadan
, Sadiq Al-Insaif
, Md. Rafiul Hassan:
Network topology measures for identifying disease-gene association in breast cancer. 274
Volume 17, Number S-8, August 2016
- Leonid Zaslavsky, Stacy Ciufo, Boris Fedorov, Tatiana A. Tatusova:
Clustering analysis of proteins from microbial genomes at multiple levels of resolution. 276 - Sefa Kiliç, Ivan Erill
:
Assessment of transfer methods for comparative genomics of regulatory networks in bacteria. 277 - ChenHsiang Shen, Xiaxia Yu, Robert W. Harrison
, Irene T. Weber:
Automated prediction of HIV drug resistance from genotype data. 278 - Gaoshi Li, Min Li, Jianxin Wang, Jingli Wu, Fang-Xiang Wu
, Yi Pan
:
Predicting essential proteins based on subcellular localization, orthology and PPI networks. 279 - Xiaojun Xu, Hong Thai, Kathryn M. Kitrinos, Guo-liang Xia, Anuj Gaggar, Matthew Paulson, Lilia Ganova-Raeva, Yury Khudyakov, James Lara:
Modeling the functional state of the reverse transcriptase of hepatitis B virus and its application to probing drug-protein interaction. 280 - Ashraf Yaseen, Mais Nijim, Brandon Williams, Lei Qian, Min Li, Jianxin Wang, Yaohang Li:
FLEXc: protein flexibility prediction using context-based statistics, predicted structural features, and sequence information. 281 - Jianyu Shi
, Jia-Xin Li, Hui-Meng Lu
:
Predicting existing targets for new drugs base on strategies for missing interactions. 282 - Cuncong Zhong, Youngik Yang, Shibu Yooseph
:
GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly. 283 - Stéphane Chrétien, Christophe Guyeux
, Bastien Conesa, Régis Delage-Mouroux, Michèle Jouvenot, Philippe Huetz, Françoise Descôtes:
A Bregman-proximal point algorithm for robust non-negative matrix factorization with possible missing values and outliers - application to gene expression analysis. 284 - Yongtao Ye
, Tak Wah Lam
, Hing-Fung Ting:
PnpProbs: a better multiple sequence alignment tool by better handling of guide trees. 285
Volume 17, Number S-9, July 2016
- Yanqing Ji, Hao Ying, John Tran, Peter Dews, R. Michael Massanari:
Integrating unified medical language system and association mining techniques into relevance feedback for biomedical literature search. 264 - Tian Bai, Leiguang Gong, Ye Wang, Yan Wang, Casimir A. Kulikowski, Lan Huang:
A method for exploring implicit concept relatedness in biomedical knowledge network. 265 - Qiang Yu, Hongwei Huo, Ruixing Zhao, Dazheng Feng, Jeffrey Scott Vitter, Jun Huan:
RefSelect: a reference sequence selection algorithm for planted (l, d) motif search. 266 - Haidong Lan, Yuandong Chan, Kai Xu, Bertil Schmidt, Shaoliang Peng
, Weiguo Liu:
Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters. 267 - Dan He, Laxmi Parida:
Does encoding matter? A novel view on the quantitative genetic trait prediction problem. 272
Volume 17, Number S-10, August 2016
Volume 17, Number S-11, September 2016
- Hongjian Li, Kwong-Sak Leung, Man Hon Wong, Pedro J. Ballester
:
Correcting the impact of docking pose generation error on binding affinity prediction. 308 - Danilo Pellin, Clelia Di Serio:
A novel scan statistics approach for clustering identification and comparison in binary genomic data. 320 - Antonino Fiannaca, Massimo La Rosa, Laura La Paglia, Riccardo Rizzo, Alfonso Urso:
MiRNATIP: a SOM-based miRNA-target interactions predictor. 321 - Andrea Bracciali, Marco Aldinucci
, Murray Patterson, Tobias Marschall, Nadia Pisanti, Ivan Merelli, Massimo Torquati
:
PWHATSHAP: efficient haplotyping for future generation sequencing. 342 - Daniela Evangelista
, Kumar Parijat Tripathi, Mario Rosario Guarracino
:
An Atlas of annotations of Hydra vulgaris transcriptome. 360
Volume 17, Number S-12, October 2016
- Luciano Milanesi
, Alessandro Guffanti, Giancarlo Mauri
, Marco Masseroli:
BITS 2015: the annual meeting of the Italian Society of Bioinformatics. 1-4 - Angelo Nuzzo, Giovanni Carapezza, Sebastiano Di Bella
, Alfredo Pulvirenti, Antonella Isacchi, Roberta Bosotti:
KAOS: a new automated computational method for the identification of overexpressed genes. 5-14 - Susanna Zucca
, Margherita Villaraggia, Stella Gagliardi, Gaetano Salvatore Grieco, Marialuisa Valente, Cristina Cereda
, Paolo Magni:
Analysis of amplicon-based NGS data from neurological disease gene panels: a new method for allele drop-out management. 15-26 - Ìtalo Faria do Valle, Enrico Giampieri, Giorgia Simonetti
, Antonella Padella
, Marco Manfrini
, Anna Ferrari
, Cristina Papayannidis
, Isabella Zironi
, Marianna Garonzi, Simona Bernardi
, Massimo Delledonne
, Giovanni Martinelli
, Daniel Remondini
, Gastone C. Castellani:
Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data. 27-35 - Marco Pellegrini
, Miriam Baglioni
, Filippo Geraci
:
Protein complex prediction for large protein protein interaction networks with the Core&Peel method. 37-58 - Andrea Manconi, Marco Moscatelli, Giuliano Armano, Matteo Gnocchi, Alessandro Orro, Luciano Milanesi
:
Removing duplicate reads using graphics processing units. 59-71 - Maria Angela Diroma
, Paolo Lubisco, Marcella Attimonelli:
A comprehensive collection of annotations to interpret sequence variation in human mitochondrial transfer RNAs. 73-82 - Davide Cangelosi
, Simone Pelassa
, Martina Morini
, Massimo Conte
, Maria Bosco, Alessandra Eva
, Angela Rita Sementa, Luigi Varesio:
Artificial neural network classifier predicts neuroblastoma patients' outcome. 83-93 - Arianna Consiglio, Corrado Mencar, Giorgio Grillo, Flaviana Marzano
, Mariano Francesco Caratozzolo
, Sabino Liuni:
A fuzzy method for RNA-Seq differential expression analysis in presence of multireads. 95-110 - Claudia Cava
, Antonio Colaprico
, Gloria Bertoli
, Gianluca Bontempi
, Giancarlo Mauri
, Isabella Castiglioni
:
How interacting pathways are regulated by miRNAs in breast cancer subtypes. 111-133 - Ilaria Granata
, Mara Sangiovanni
, Francesco Maiorano, Marco Miele
, Mario Rosario Guarracino
:
Var2GO: a web-based tool for gene variants selection. 135-140
Volume 17, Number S-13, October 2016
- Inimary T. Toby, Mikhail K. Levin, Edward Salinas, Scott Christley, Sanchita Bhattacharya, Felix Breden, Adam Buntzman
, Brian Corrie, John M. Fonner, Namita T. Gupta
, Uri Hershberg
, Nishanth Marthandan, Aaron M. Rosenfeld
, William Rounds, Florian Rubelt
, Walter Scarborough, Jamie K. Scott, Mohamed Uduman, Jason A. Vander Heiden, Richard H. Scheuermann, Nancy Monson, Steven H. Kleinstein, Lindsay G. Cowell:
VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. 333 - Edmund R. Glass, Mikhail G. Dozmorov
:
Improving sensitivity of linear regression-based cell type-specific differential expression deconvolution with per-gene vs. global significance threshold. 334 - Ryan Eshleman, Rahul Singh:
Leveraging graph topology and semantic context for pharmacovigilance through twitter-streams. 335 - Yongsheng Bai, Lizhong Ding, Steve Baker, Jenny M. Bai, Ethan Rath, Feng Jiang, Jianghong Wu, Hui Jiang
, Gary W. Stuart:
Dissecting the biological relationship between TCGA miRNA and mRNA sequencing data using MMiRNA-Viewer. 336 - Yang Liu, Saad M. Khan
, Juexin Wang, Mats Rynge
, Yuanxun Zhang, Shuai Zeng, Shiyuan Chen, João V. Maldonado dos Santos, Babu Valliyodan
, Prasad Calyam, Nirav C. Merchant
, Henry T. Nguyen, Dong Xu, Trupti Joshi
:
PGen: large-scale genomic variations analysis workflow and browser in SoyKB. 337 - Quang Tran, Shanshan Gao, Vinhthuy Phan:
Analysis of optimal alignments unfolds aligners' bias in existing variant profiles. 349 - Sujoy Roy
, Brandon C. Curry, Behrouz Madahian, Ramin Homayouni:
Prioritization, clustering and functional annotation of MicroRNAs using latent semantic indexing of MEDLINE abstracts. 350 - Navadon Khunlertgit
, Byung-Jun Yoon:
Incorporating topological information for predicting robust cancer subnetwork markers in human protein-protein interaction network. 351 - Jonathan D. Wren
, Inimary T. Toby, Huxiao Hong, Bindu Nanduri, Rakesh Kaundal, Mikhail G. Dozmorov
, Shraddha Thakkar:
Proceedings of the 2016 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. 356 - Mutlu Mete, Ünal Sakoglu
, Jeffrey S. Spence, Michael Devous, Thomas S. Harris, Bryon Adinoff:
Successful classification of cocaine dependence using brain imaging: a generalizable machine learning approach. 357 - Sertan Kaya, Mustafa Bayraktar, Sinan Kockara, Mutlu Mete, Tansel Halic, Halle E. Field, Henry K. Wong
:
Abrupt skin lesion border cutoff measurement for malignancy detection in dermoscopy images. 367 - Mikyung Lee, Zhichao Liu, Ruili Huang, Weida Tong:
Application of dynamic topic models to toxicogenomics data. 368 - Si Chen, Lih-Yuan Deng, Dale Bowman, Jyh-Jen Horng Shiau, Tit-Yee Wong
, Behrouz Madahian, Henry Horng-Shing Lu:
Phylogenetic tree construction using trinucleotide usage profile (TUP). 381 - Xueyuan Cao, Kristine R. Crews, James R. Downing, Jatinder Lamba, Stanley Pounds:
CC-PROMISE effectively integrates two forms of molecular data with multiple biologically related endpoints. 382 - Hyundoo Jeong, Xiaoning Qian, Byung-Jun Yoon:
Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model. 395
Volume 17, Number S-14, November 2016
- Pedro Feijão, Eloi Araujo:
Fast ancestral gene order reconstruction of genomes with unequal gene content. 187-200 - Ashok Rajaraman, Jian Ma:
Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction. 201-212 - Nikita Alexeev
, Pavel Avdeyev
, Max A. Alekseyev
:
Comparative genomics meets topology: a novel view on genome median and halving problems. 213-223 - Laurent Bulteau
, Guillaume Fertin
, Eric Tannier:
Genome rearrangements with indels in intergenes restrict the scenario space. 225-231 - Zhe Yu, David Sankoff:
A continuous analog of run length distributions reflecting accumulated fractionation events. 233-240 - Lawrence H. Uricchio, Tandy J. Warnow, Noah A. Rosenberg
:
An analytical upper bound on the number of loci required for all splits of a species tree to appear in a set of gene trees. 241-250 - Mark Jones, Christophe Paul
, Céline Scornavacca:
On the consistency of orthology relationships. 251-262 - Mehmood Alam Khan, Owais Mahmudi, Ikram Ullah, Lars Arvestad
, Jens Lagergren
:
Probabilistic inference of lateral gene transfer events. 263-270 - Jiafan Zhu, Yun Yu, Luay Nakhleh:
In the light of deep coalescence: revisiting trees within networks. 271-282
Volume 17, Number S-15, November 2016
- Pedro Furió-Tarí, Ana Conesa
, Sonia Tarazona:
RGmatch: matching genomic regions to proximal genes in omics data integration. 1-10 - Sara Aibar
, María Abáigar
, Francisco J. Campos-Laborie
, Jose Manuel Sánchez-Santos, Jesus M. Hernandez-Rivas
, Javier De Las Rivas
:
Identification of expression patterns in the progression of disease stages by integration of transcriptomic data. 11-21 - David Gomez-Cabrero
, Jörg Menche
, Claudia Vargas, Isaac Cano
, Dieter Maier, Albert-László Barabási, Jesper Tegnér, Josep Roca
:
From comorbidities of chronic obstructive pulmonary disease to identification of shared molecular mechanisms by data integration. 23-35 - Animesh Acharjee
, Zsuzsanna Ament, James A. West, Elizabeth Stanley, Julian L. Griffin:
Integration of metabolomics, lipidomics and clinical data using a machine learning method. 37-49
Volume 17, Number S-16, December 2016
- Aalt D. J. van Dijk, Harri Lähdesmäki, Dick de Ridder, Juho Rousu:
Selected proceedings of Machine Learning in Systems Biology: MLSB 2016. 51-52 - Saulius Lukauskas
, Roberto Visintainer
, Guido Sanguinetti, Gabriele Beate Schweikert:
DGW: an exploratory data analysis tool for clustering and visualisation of epigenomic marks. 53-63 - Sung Hee Park, Sunmin Lee
, Young-Joon Kim, Sangsoo Kim:
ChARM: Discovery of combinatorial chromatin modification patterns in hepatitis B virus X-transformed mouse liver cancer using association rule mining. 65-83 - Séverine Affeldt
, Nataliya Sokolovska, Edi Prifti
, Jean-Daniel Zucker
:
Spectral consensus strategy for accurate reconstruction of large biological networks. 85-97 - André Veríssimo
, Arlindo Limede Oliveira
, Marie-France Sagot, Susana Vinga
:
DegreeCox - a network-based regularization method for survival analysis. 109-121 - Mehmet Gönen
:
Integrating gene set analysis and nonlinear predictive modeling of disease phenotypes using a Bayesian multitask formulation. 123-135
Volume 17, Number S-17, December 2016
- Guangyong Zheng, Yaochen Xu, Xiujun Zhang
, Zhi-Ping Liu, Zhuo Wang, Luonan Chen, Xin-Guang Zhu:
CMIP: a software package capable of reconstructing genome-wide regulatory networks using gene expression data. 137-144 - Mengmeng Wu, Ting Chen, Rui Jiang
:
Global inference of disease-causing single nucleotide variants from exome sequencing data. 145-157 - Jihyeob Mun, Dong-Uk Kim, Kwang-Lae Hoe