Hai C. T. Nguyen†, Bukyung Baik†, Sora Yoon, Taesung Park, Dougu Nam*, Benchmarking integration of single-cell differential expression, 14: 1570, Nature Communications (2023)
Woobeen Jo, Min Kim, Jiyoung Oh, Chu-Sook Kim, Chanho Park, Sora Yoon, Changhu Lee, Sahee Kim, Dougu Nam, Jiyoung Park*, MicroRNA-29 Ameliorates Fibro-Inflammation and Insulin Resistance in HIF1α-Deficient Obese Adipose Tissue by Inhibiting Endotrophin Generation, Diabetes (2022)
Yo Han Lee†, Hyun-Jun Jang†, Sounkou Kim†, Sun Sil Choi, Keon Woo Khim, Hye-Jin Eom, Jimin Hyun, Kyeong Jin Shin, Young Chan Chae, Hongtae Kim, Jiyoung Park, Neung Hwa Park, Chang-Yun Woo, Chung Hwan Hong, Eun Hee Koh, Dougu Nam*, Jang Hyun Choi*, Hepatic MIR20B promotes nonalcoholic fatty liver disease by suppressing PPARA, 10:e70472, eLife (2021)
Sora Yoon†, Bukyung Baik†, Taesung Park & Dougu Nam*, Powerful p-value combination methods to detect incomplete association, 11: 6980, Scientific Reports (2021)
Mohammed Dwidar*, Hyochan Jang, Naseer Sangwan, Wonsik Mun, Hansol Im, Sora Yoon, Sooin Choi, Dougu Nam*, Robert J. Mitchell*, Diffusible Signaling Factor, a Quorum-Sensing Molecule, Interferes with and Is Toxic Towards Bdellovibrio bacteriovorus 109J, accepted, Microbial Ecology (2020)
Bukyung Baik, Sora Yoon, Dougu Nam*, Benchmarking RNA-seq differential expression analysis methods using spike-in and simulation data, 15(4): e0232271, Plos One (2020)
Ji-hyung Kim, Yoonhee Ki, Hoyeon Lee, Moon Seong Hur, Bukyung Baik, Jin-Hoe Hur, Dougu Nam, Chunghun Lim*, The voltage-gated potassium channel Shaker promotes sleep via thermosensitive GABA transmission, Communications Biology, 3:174 (2020)
Gunhwan Ko, Pan-Gyu Kim, Youngbum Cho, Seongmun Jeong, Jae-Yoon Kim, Kyoung Hyoun Kim, Ho-Yeon Lee, Jiyeon Han, Namhee Yu, Seokjin Ham, Insoon Jang, Byunghee Kang, Sunguk Shin, Lian Kim, Seung-Won Lee, Dougu Nam, Jihyun F. Kim, Namshin Kim, Seon-Young Kim, Sanghyuk Lee, Tae-Young Roh, and Byungwook Lee* Bioinformatics services for analyzing massive genomic datasets, Genomics & Informatics, Mar; 18(1): e8 (2020)
Yu Geon Lee, Yeji Nam, Kyeong Jin Shin, Sora Yoon, Weon Seo Park, Jae Young Joung, Jeong Kon Seo, Jinho Jang, Semin Lee, Dougu Nam, M. Cecilia Caino, Pann-Ghill Suh, Young Chan Chae∗, Androgen-induced expression of DRP1 regulates mitochondrial metabolic reprogramming in prostate cancer, Cancer Letters, 471, 72 - 87 (2020)
Hye-Kyung Park, Nam Gu Yoon, Ji-Eun Lee, Sung Hu , Sora Yoon, So Yeon Kim , Jun-Hee Hong, Dougu Nam, Young Chan Chae , Jong Bae Park and Byoung Heon Kang*, Unleashing the full potential of Hsp90 inhibitors as cancer therapeutics through simultaneous inactivation of Hsp90, Grp94, and TRAP1, Experimental & Molecular Medicine, 52:79–91 (2020)
Keon Woo Khim , Sun Sil Choi, Hyun-Jun Jang, Yo Han Lee, Eujin Lee, Ji-Min Hyun, Hye-Jin Eom, Sora Yoon, Jeong-Won Choi, Tae-Eun Park, Dougu Nam and Jang Hyun Choi *, PPM1A Controls Diabetic Gene Programming through Directly Dephosphorylating PPAR at Ser273, Cells, 9, 343 (2020)
Hyun-Jun Jang, Seyoung Lim, Jung-Min Kim, Sora Yoon, Chae Young Lee, Hyeon-Jeong Hwang, Jeong Woo Shin, Kyeong Jin Shin, Hye Yun Kim, Kwang Il Park, Dougu Nam, Ja Yil Lee, Kyungmoo Yea, Yoshio Hirabayashi, Yu Jin Lee, Young Chan Chae, Pann-Ghill Suh*, Jang Hyun Choi*, Glucosylceramide synthase regulates adipo-osteogenic differentiation through synergistic activation of PPARγ with GlcCer, FASEB J. 4:1270–1287 (2020)
Jinhwan Kim, Sora Yoon, Dougu Nam*, netGO: R-Shiny package for network-integrated pathway enrichment analysis, doi: 10.1093/bioinformatics/btaa077, Bioinformatics (2020)
Eun Jin Yoo, Sun Woo Lim, Hyun Je Kang, Hyun Park, Sora Yoon, Dougu Nam, Satoru Sanada, Mi Jin Kwon, Whaseon Lee-Kwon, Soo Youn Choi,* and Hyug Moo Kwon*, Transcriptional Regulator TonEBP Mediates Oxidative Damages in Ischemic Kidney Injury, Cells, 8, 1284 (2019)
Sora Yoon†, Jinhwan Kim†, Seonkyu Kim†, Bukyung Baik, Sang-Mun Chi, Seon-Young Kim*, Dougu Nam*, GScluster: network-weighted gene-set clustering analysis, 20:352, BMC Genomics (2019)
Sora Yoon, Hai C. T. Nguyen, Woobeen Jo, Jinhwan Kim, Sang-Mun Chi, Jiyoung Park, Seon-Young Kim, Dougu Nam*, Biclustering analysis of transcriptome big data identifies condition-specific microRNA targets, 47(9), e53, Nucleic Acids Research (2019)
Jae Min Lee, Sun Sil Choi, Yo Han Lee, Keon Woo Khim, Sora Yoon, Byung-gyu Kim, Dougu Nam, Pann-Ghill Suh, Kyungjae Myung, Jang Hyun Choi*, The E3 ubiquitin ligase TRIM25 regulates adipocyte differentiation via proteasome-mediated degradation of PPARγ, Experimental & Molecular Medicine, 50, Article number: 135 (2018)
Sora Yoon†, Hai C. T. Nguyen†, Yun Joo Yoo, Jinhwan Kim, Bukyung Baik, Sounkou Kim, Jin Kim, Sangsoo Kim and Dougu Nam*, Efficient pathway enrichment and network analysis of GWAS summary data using GSA-SNP2. Nucleic Acids Research, 46(10), e60 (2018)
Hyeonseong Jeon, Suh-Ryung Kim, Dougu Nam, and Yun Joo Yoo, Analysis of triangular motifs in protein interaction networks and their implications to protein ages and cancer genes, Int. J. Data Mining and Bioinformatics, accepted (2018)
Sora Yoon, Dougu Nam*, Gene dispersion is the key determinant of the read count bias in differential expression analysis of RNA-seq data, BMC Genomics 18:408 (2017)
YR Yang, S Song, H Hwang, JH Jung, SJ Kim, S Yoon, JH Hur, JI Park, C Lee, D Nam, YK Seo, JH Kim, H Rhim, PG Suh, Memory and synaptic plasticity are impaired by dysregulated hippocampal O-GlcNAcylation, Scientific Reports 7:44921 (2017).
Sora Yoon, Seon-Young Kim, Dougu Nam*, Improving Gene-Set Enrichment Analysis of RNA-Seq Data with Small Replicates, PLoS ONE 11(11): e0165919 (2016)
Dougu Nam*, Effect of the absolute statistic on gene-sampling gene-set analysis methods, Statistical Methods in Medical Research, (4%, Statistics & Probability) (2015)
YR Yang, H-J Jang, S Yoon, YH Lee, D Nam, IS Kim, H Lee, H Kim, JH Choi, BH Kang, SH Ryu and P-G Suh, OGA heterozygosity suppresses intestinal tumorigenesis in Apcmin/þ mice, Oncogenesis, 3: e109 (2014)
Sang-Mun Chi, Young-Kyo Seo, Young-Kyu Park, Sora Yoon, Chan Young Park, Yong Sung Kim, Seon-Young Kim*, Dougu Nam*, REGNET: Mining context-specific human transcription networks using composite genomic i information, BMC Genomics, 15:450-459 (2014).
Mohammed Dwidar, Dougu Nam*, Robert J. Mitchell*, Indole negatively impacts predation byBdellovibrio bacteriovorus and its release from the bdelloplast, Environmental Microbiology, published online: 28 APR (2014).
Vinuselvi Parisutham, Sang-Kyu Jung, Dougu Nam, and Sung KuK Lee*, Transcriptome-driven synthetic re-modeling of Escherichia coli to enhance cellobiose utilization, Chemical Engineering Science, 103: 50-57 (2013).
Ji-sun Kwon, Jihye Kim, Dougu Nam, and Sangsoo Kim*, Performance Comparison of Two Gene Set Analysis Methods for Genome-wide Association Study Results: GSA-SNP vs i-GSEA4GWAS,Genomics and Informatics, 10: 123-127 (2012).
Siseon Lee, Dougu Nam, Joon Young Jung, Min-Kyu Oh, Byoung-In Sang*, and Robert J. Mitchell*, Identification of Escherichia coli biomarkers responsive to various lignin-hydrolysate compounds, Bioresource Technology, 114: 450-456 (2012).
Sang-Mun Chi*, Dougu Nam*, WegoLoc: accurate prediction of protein subcellular localization using weighted Gene Ontology terms, Bioinformatics, 28: 1028-1030 (2012).
Sang-Mun Chi, Jin Kim, Seon-Young Kim* and Dougu Nam*, ADGO 2.0: Interpreting microarray data and list of genes using composite annotations, Nucleic Acids Research (Web Server Issue), W302-W306 (2011).
Dougu Nam*, De-correlating expression in gene-set analysis, Bioinformatics, 26 ECCB 2010 issue, i511–i516 (2010).
Dougu Nam+, Jin Kim+, Seon-Young Kim and Sangsoo Kim*, GSA-SNP: a general approach for gene set analysis of polymorphisms, Nucleic Acids Research (Web Server Issue), W749-W754 (2010).
Dougu Nam, Seon-Young Kim, Gene set and pathway-based analysis for cancer omics, Cancer Systems Biology, edited by Edwin Wang, Chapman & Hall/CRC Mathematical and Computational Biology Series (Book chapter) (2010).
Before 2010
Eun-Youn Kim, Seon-Young Kim, Daniel Ashlock, Dougu Nam*, MULTI-K: Accurate classification of microarray subtypes using ensemble k-means clustering, BMC Bioinformatics, 10, 260-271 (2009).
Dougu Nam, Seon-Young Kim*, Gene-set approach for expression pattern analysis, Briefings in Bioinformatics, 9 (3), 189-197 (2008).
Dougu Nam*, Sung Ho Yoon, Jihyun F. Kim*, Ensemble learning of genetic networks from time-series expression data, Bioinformatics, 23, 3225-3231 (2007).
Dougu Nam, Sang-Bae Kim, Sun-Kyu Kim, Sungjin Yang, Seon-Young Kim and In-Sun Chu*, ADGO: analysis of differentially expressed gene sets using composite GO annotation, Bioinformatics, 22, 2249-2253 (2006).
Dougu Nam*, Seunghyun Seo and Sangsoo Kim, An efficient top-down search algorithm for learning Boolean networks of gene expression, Machine Learning 65, 229-245 (2006).
Sung-Ho Goh, Tae-Hyung Kim, Jee-Hyub Kim, Dougu Nam, Doil Choi, and Cheol-Goo Hur*, Computational Analysis of Neighboring Genes on Arabidopsis thaliana Chromosomes 4 and 5: Their Genomic Association as Functional Subunits, Genomics and Informatics, 1, no. 1, 40-49 (2003).
Probability & Stochastic Processes
Hyung Geun Kim and Dougu Nam*, Optimal estimation of diffusion processes hidden by general obstacles, Journal of applied probability, 38, 1067-1073 (2001)
Changsun Choi and Dougu Nam*, Some boundary crossing results for linear diffusion processes,Statistics and probability letters, 62, 281-291 (2003)
Changsun Choi and Dougu Nam*, Interpolation for partly hidden diffusion processes, Stochastic processes and their applications, 113, 199-216 (2004)
Dougu Nam*, On exact convergence rate of strong numerical schemes for stochastic differential equations, Bull. Korean Mathematical Society , 44. 125-130 (2007)