Publications

 

      Click: Google Scholar Citation Page 

   * Corresponding Author(s)

    Names in bold letters: CSBL members

 

Ongoing papers

  1. Sangwoo Kim, Hojung Nam*, "Systematic identification of the role of loss-of-function variants in ethnic specific metabolism", In prep.

  2. Soobok Joe , Hojung Nam*, "Prediction model construction of stem cell pluripotency using CpG and non-CpG DNA methylation markers", Submitted.

 

Peer Reviewed Journals (2019)

  1. Hyunho Kim, Hojung Nam*, "hERG-Att: Self-Attention-Based Deep Neural Network for Predicting hERG Blockers", Accepted.​​​

  2. Heeyeon Choi, Soobok Joe, Hojung Nam*, "Development of Tissue-Specific Age Predictors Using DNA Methylation Data", Genes 2019, 10(11), 888.

  3. Ka-Kyung Kim†, Byung-Joon Seung†, Dohyun Kim†, Hee-Myung Park, Sejoon Lee, Doo-Won Song, Gunho Lee, Jae-Ho Cheong, Hojung Nam*, Jung-Hyang Sur*, Sangwoo Kim*, "Whole-exome and whole-transcriptome sequencing of canine mammary gland tumors", Scientific Data volume 6, Article number: 147 (2019)

  4. Ingoo Lee, Jongsoo Keum, Hojung Nam*, "DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences", PLoS Computational Biology 15(6): e1007129. https://doi.org/10.1371/journal.pcbi.1007129

  5. Eunyoung Kim, A-sol Choi, Hojung Nam*, "Drug repositioning of herbal compounds via a machine-learning approach", BMC Bioinformatics, 2019 20 (Suppl 10) :247. 

  6. Junho Kim, Dachan Kim, Jae Seok Lim, Ju Heon Maeng, Hyeonju Son, Hoon-Chul Kang, Hojung Nam, Jeong Ho Lee* and Sangwoo Kim*, "The use of technical replication for detection of low-level somatic mutations in next-generation sequencing", Nature Communications 10: 1047 (2019)

  7. Wan-Su Choi, Gyuseok Lee, Won-Hyun Song, Jeong-Tae Koh, Jiye Yang, Ji-Sun Kwak, Hyo-Eun Kim, Seul Ki Kim, Young-Ok Son, Hojung Nam, Iljung Jin, Zee-Yong Park, Jiyeon Kim, In Young Park, Jeong-Im Hong, Hyun Ah Kim, Churl-Hong Chun, Je-Hwang Ryu & Jang-Soo Chun, "The CH25H–CYP7B1–RORα axis of cholesterol metabolism regulates osteoarthritis", Nature 2019.

 

 

Peer Reviewed Journals (2018)

  1. Sunyong Yoo, Suhyun Ha, Moonshik Shin, Kyungrin Noh, Hojung Nam* and Doheon Lee*,"A Data-Driven Approach for Identifying Medicinal Combinations of Natural Products", IEEE Access, Vol.6, 58106 - 58118.

  2. Sunyong Yoo, Kwansoo Kim, Hojung Nam*, Doheon Lee*,"Discovering Health Benefits of Phytochemicals with Integrated Analysis of the Molecular Network, Chemical Properties and Ethnopharmacological Evidence ", Nutrients 2018, 10(8), 1042; https://doi.org/10.3390/nu10081042.

  3. Sunyong Yoo, Hojung Nam* and Doheon Lee*, "Phenotype-oriented network analysis for discovering pharmacological effects of natural compounds", Scientific Reports, 2018 Aug 3;8(1):11667. doi: 10.1038/s41598-018-30138-w.

  4. Ingoo Lee, Hojung Nam*, "Identification of drug-target interaction by a random walk with restart method on an interactome network ", BMC Bioinformatics, 2018 19(Suppl 8):208.

  5. Donghyuk Kim, Sang Woo Seo, Ye` Gao, Hojung Nam, Gabriela Guzman, Byung-Kwan Cho, Bernhard Palsson, "Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP", Nucleic Acids Research, 2018 Jan 31. doi: 10.1093/nar/gky069.

  6. Sunyong Yoo, Kyungrin Noh, Moonshik Shin, Junseok Park, Kwang Hyung Lee*, Hojung Nam*, and Doheon Lee*, "In silico profiling of systemic effects of drugs to predict unexpected interactions", Scientific Reports, 8 (1), 1612 (2018).

 

 

Peer Reviewed Journals (2017)

  1. Jongsoo KeumHojung Nam*, "SELF-BLM: Prediction of drug-target interactions via self-training SVM", PLoS One, 2017, 12(2): e0171839.

  2. Eunyoung KimHojung Nam*, "Prediction models for drug-induced hepatotoxicity by using weighted molecular fingerprints", BMC Bioinformatics, 2017, 18(Suppl 7):227.

  3. Geunho Lee, Hyun Beom Lee, Byung Hwa Jung* and Hojung Nam*, "MVP: an open-source preprocessor for cleaning duplicate records and missing values in mass spectrometry data", FEBS Open Bio., 2017, doi:10.1002/2211-5463.12247.

  4. Sangwoo Kim and Hojung Nam*, "In Silico Simulation of Signal Cascades in Biomedical Networks Based on the Production Rule System", Lecture Notes in Computer Science,  vol 10330. Springer, Cham.

 

 

Peer Reviewed Journals (2016)

  1. Moonshik Shin, Donjin Jang, Hojung Nam, Kwang Hyung Lee, Doheon Lee, "Predicting the Absorption Potential of Chemical Compounds through Deep-learning Approach", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 15, No. 2, March/April 2018. Online published Feb. 26, 2016

  2. Soobok JoeHojung Nam*, "Prognostic Factor Analysis for Breast Cancer Using Gene Expression Profiles", BMC Medical Informatics and Decision Making, 2016 16(Suppl 1):56.

  3. Jongsoo Keum, Sunyong Yoo, Doheon Lee, Hojung Nam*, "Prediction of Compound-Target Interactions of Natural Products Using Large-scale Drug and Protein Information", BMC Bioinformatics, 2016 17(Suppl 6):219.

 

 

Peer Reviewed Journals  (2015)

  1. Junho Kim, Sanghyeon Kim, Hojung Nam, Sangwoo Kim, Doheon Lee, "SoloDel: A probabilistic model for detecting low-frequent somatic deletions from unmatched sequencing data", Bioinformaitcs, 2015 31(19): 3105-3113; doi: 10.1093/bioinformatics/btv358

  2. Seunghwan Jung, Sejoon Lee, Sangwoo Kim, Hojung Nam*, "Identification of Genomic Features in the Classification of Loss- and Gain-of-Function Mutation", BMC Medical Informatics and Decision Making 2015, 15(Suppl 1):S6  doi:10.1186/1472-6947-15-S1-S6.

 

 

Peer Reviewed Journals & Conferences (2014)
  1. Soobok JoeHojung Nam*, "Identification of a Specific Base Sequence of Pathogenic E. coli through a Genomic Analysis", Proceedings of the ACM 8th International Workshop on Data and Text Mining in Bioinformatics, Shanghai, China, Sep. 7, 2014. pp. 25~28.

  2. Hojung Nam*, Miguel Campodonico, Aarash Bordbar, Daniel R. Hyduke, Sangwoo Kim, Bernhard O. Palsson* (*co-corresponding), "A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks", PLoS Comput Biol, 10(9): e1003837. doi:10.1371/journal.pcbi.1003837.

    • Media covered:  연합뉴스(10/7/2014), 뉴스1(10/7/2014), 전자신문(10/7/2014), 디지털타임즈(10/7/2014), 대덕넷(10/7/2014), 데일리한국(10/7/2014), etc

 

 

Peer Reviewed Journals & Conferences (2013)
  1. Seunghwan Jung, Soobok Joe, Hojung Nam*, "Analysis of Functional Impacts on Massive Cancer Mutation Data", The 3rd Annual Translational Bioinformatics Conference (TBC 2013) / ISCB-Asia 2013, JW Marriott, Seoul, Korea, Oct. 2nd ~ 4th, 2013 (poster)

  2. Sangwoo Kim, Kyowon Jeong, Kunal Bhutani, Jeong Ho Lee, Eric Scott, Hojung Nam, Hayan Lee, Joseph G. Gleeson and Vineet Bafna, "Virmid: Virtual Microdissection of sample mixtures for accurate somatic mutation profiling", Genome Biology, 29 August 2013, 14:R90 | doi:10.1186/gb-2013-14-8-r90 / Software available at http://sourceforge.net/projects/virmid/

    • Media coverd: 한국을빛내는사람들 (09/05/2013)

 

PeerReviewed Journals (~ 2012)
  1. Hojung Nam†, Nathan E. Lewis†, Joshua A. Lerman, DaeHee Lee, Roger L. Chang, Donghyuk Kim, Bernhard O. Palsson* (†equal contribution) , "Network context and selection in the evolution to enzyme specificity", Science, 2012, 337(6098):1101-1104, DOI: 10.1126/science.1216861

    • Media covered: UCSD news center (08/30/2012), ScienceDaily (08/30/2012) , ScienceNews (08/30/2012). Phys.org (08/30/2012), 한국을빛내는사람들(09/01/2012), 연합뉴스 (09/11/2012), 매일경제 (09/11/2012), 한국경제 (09/11/2012) and in other 11 Korean daily newspapers.

  2. Jeffrey D. Orth, Tom M. Conrad, Jessica Na, Joshua A. Lerman, Hojung Nam, Adam M. Feist, Bernhard Ø. Palsson, "A comprehensive genome-scale reconstruction of Escherichia coli metabolism - 2011", Molecular Systems Biology, 2011, 7:535, doi:10.1038/msb.2011.65.

  3. Sangwoo Kim, Hojung Nam, Doheon Lee, "Exploring molecular links between lymph node invasion and cancer prognosis in human breast cancer", BMC Systems Biology, 2011, 5(Suppl 2):S4.

  4. Hojung Nam†, Tom Conrad, and Nathan E. Lewis† (†equal contribution), "The role of cellular objectives and selective pressures in metabolic pathway evolution", Current Opinion in Biotechnology, 2011, 22(4):595–600; doi:10.1016/j.copbio.2011.03.006.

  5. Hojung Nam, Bong Chul Chung, Younghoon Kim, KiYoung Lee, Doheon Lee, "Combining Tissue Transcriptomics and Urine Metabolomics for Breast Cancer Biomarker Identification", Bioinformatics 2009 25(23):3151-3157; doi:10.1093/bioinformatics/btp558.

  6. Hojung Nam, Jinwon Lee, Doheon Lee, "Computational Identification of Altered Metabolism using Gene Expression and Metabolic Pathways", Biotechnology and Bioengineering, 2009, 103(4):835-843.

  7. Hojung Nam, KiYoung Lee, Doheon Lee, "Identification of Temporal Association Rules from Time-series Microarray Data Set", Special Issue, BMC Bioinformatics, 2009, 10(Suppl 3):S6.

  8. Hojung Nam, Taewoo Ryu, KiYoung Lee, Sangwoo Kim, Doheon Lee, "Computational Identification of Significantly Regulated Metabolic Reactions by Integration of Data on Enzyme Activity and Gene Expression", BMB Rep., 2008.08.31; 41(8):609~614.

  9. Taewoo Ryu, Juhyun Jung, Sunjae Lee, Ho Jung Nam, Sun Woo Hong, Jae Wook Yoo, Dong-ki Lee and Doheon Lee, "A database of regulatory information for human bZIP transcription factors", BMC Genomics, 2007, 8:136.

 
Conferences
  1. IlJung Jin, Hojung Nam*, “Genome-wide transcriptome analysis of osteoarthritis with protein-protein interaction network”, ISMB 2018, Chicago, Illinois, USA, July 6-10, 2018 (poster)

  2. Ingoo Lee, Jongsoo Keum, Hojung Nam*, “Identification of drug-target interaction via deep learning approach”, ISMB 2018, Chicago, Illinois, USA, July 6-10, 2018 (poster)

  3. Heeyeon Choi, Hojung Nam*,"Identification of tissue-specific aging-related epigenetic marker using age prediction model", RECOMB 2018, Paris, France, April 19~24, 2018 (poster)

  4. Eunyoung Kim, A-sol Choi, Hojung Nam*, "Drug repositioning for natural products using machine learning approaches", RECOMB 2018, Paris, France, April 19~24, 2018 (poster)

  5. Soobok Joe, Hojung Nam*, "Prediction of stem cell pluripotency using parallel single-cell transcriptome and methylome sequencing data", ISMB/ECCB 2017, Prague Congress Center, Czech Republic, July 21~25, 2017 (poster)

  6. Eunyoung Kim, Hojung Nam*, "Prediction of drug-drug interactions using molecular structure information and link prediction approaches", ISMB/ECCB 2017, Prague Congress Center, Czech Republic, July 21~25, 2017 (poster)

  7. Ingoo Lee, Hojung Nam* , "Identification of drug-target interactions using weighted interactome network", RECOMB 2017, Hong Kong, China, May 3~7, 2017 (poster)

  8. Jongsoo Keum, Hojung Nam*, "Prediction of drug-target interaction model using deep neural networks approach", RECOMB 2017, HongKong, May, 3~7, 2017 (poster)

  9. Soobok Joe, Hojung Nam*, "Prediction of Stem Cell Pluripotency using Transcriptome and Methylome Sequencing Data", The 13th KOGO Winter Symposium 2017, Hongcheon, Korea, Feb 8~10, 2017 (poster)

  10. Jongsoo Keum, Hojung Nam*, "SELF-BLM: Prediction of drug-target interactions via self-training SVM", The 13th KOGO Winter Symposium 2017, Hongcheon, Korea, Feb 8~10, 2017 (poster)

  11. Eunyoung Kim, Hojung Nam*, "Prediction models for drug-induced liver injury using substructure information", The 13th KOGO Winter Symposium 2017, Hongcheon, Korea, Feb 8~10, 2017 (poster)

  12. Soobok Joe, Hojung Nam*, "Identification of epigenetic control markers for predicting stem cell pluripotency", KSMCB 2016, Hongcheon, Korea, Dec 14~16, 2016 (poster)

  13. Jongsoo Keum, Hojung Nam*, "Prediction of compound-protein interactions using deep neural networks approach" BIOINFO 2016, Incheon, Korea, Aug, 17~19, 2016 (poster)

  14. Eunyoung Kim, Hojung Nam*, "Developing prediction model for drug-induced liver injury by using substructure information" BIOINFO 2016, Incheon, Korea, Aug, 17~19, 2016 (poster)

  15. Jusung Lee, Hojung Nam*, ''Mutation in TET genes induce microsatellite instability by epigenetic silencing of MLH1.", ISMB 2016, Orlando, Florida, USA, July 8~12, 20 (poster)

  16. Jongsoo Keum, Hojung Nam*, ''Prediction of compound-target interactions by using deep-learning networks", ISMB 2016, Orlando, Florida, USA, July 8~12, 20 (poster)

  17. Geunho Lee, Hyun Beom Lee, Byung Hwa Jung*, Hojung Nam*, "MVP: Duplicate Records and Missing Values Preprocessor of Mass spectrometry Data", ISMB 2016, Orlando, Florida, USA, July 8~12, 2016 (poster)

  18. A-sol Choi, Hojung Nam*, "Statistical analysis of cancer mutation enrichments in chromosomes", The 12th KOGO Winter Symposium 2016, Hongcheon, Korea, Feb 1~3, 2016 (poster)

  19. Geunho Lee, Hojung Nam*, "Breast Cancer Subtype Classification using Deep Learning Approach", The 12th KOGO Winter Symposium 2016, Hongcheon, Korea, Feb 1~3, 2016 (poster)

  20. Eunyoung Kim, Sangwoo Kim, Suhyun Ha, Hojung Nam*, "Developing compound toxicity classification models using physicochemical properties and structure information", San Francisco Bay Area, United States, Jan 11-13, 2016 (poster)

  21. Eunyoung Kim, Sangwoo Kim, Suhyun Ha, Hojung Nam*, "Toxicity Predictions using Compound Descriptions", the ACM 9th International Workshop on Data and Text Mining in Bioinformatics, Melbourne, Australia, Oct. 23, 2015 (poster)

  22. Jongmin Lee, Hojung Nam*, "Comparing similarity measures for drug-target interactions prediction model", BIOINFO 2015, Seoul, Korea, Oct, 21~23, 2015 (poster)

  23. Hojung Nam, Asian Regional Conference on Systems Biology/TriSys Workshop, 8-9 September 2015, Bangi, Selangor, Malaysia, Invited Talk.

  24. Seunghwan Jung, Soobok Joe, Hojung Nam*, "Analysis of Functional Impacts on Massive Cancer Mutation Data", The 3rd Annual Translational Bioinformatics Conference (TBC 2013) / ISCB-Asia 2013, JW Marriott, Seoul, Korea,  Oct. 2nd ~ 4th, 2013 (poster)

  25. Hojung Nam, Steve Federowicz, Bernhard Ø. Palsson, and Byung-Kwan Cho, "Oxygen and Nitrate-dependent Regulons of Broad-acting Transcription Factors in Escherichia coli K-12 MG1655", American Society for Microbiology 2010, San Diego, May 23-27, 2010 (poster)

  26. Hojung Nam, KiYoung Lee, Doheon Lee, "Identification of Temporal Association Rules from Time-series Microarray Data Set", ACM Second International Workshop on Data and Text Mining in Bioinformatics in conjunction with CIKM, Napa Valley Marriott Hotel, Napa Valley, California, October 26-30, 2008, pp. 21~27

  27. Hojung Nam, Doheon Lee, "Analyzing active metabolic reactions in perturbations by integrating regulation information", The International Symposium on Optimization and Systems Biology, Beijing (China) August 8-10, , 2007, ORSC & APORC, pp. 143-150

  28. Ho Jung Nam, Hyojin Kang, Sejun Lee, Doheon Lee, "Finding co-effects between genes and metabolites by integrating genetic regulatory network and metabolic pathway", The 3rd International E.coli Alliance Conference on Systems Biology (IECA'2006), Oct.30-Nov.3, International Convention Center Jeju, Jeju, Korea, 2006 (poster)

  29. Ho Jung Nam, Hyojin Kang, Sejun Lee, Doheon Lee, "Finding perturbation corresponding global regulation path by integrating genetic regulatory network and metabolic pathway", The 7th International Conference on Systems Biology (ICSB'2006), Pacifico Yokohama, Yokohama, Japan, October, 2006 (poster)

  30. Ho Jung Nam, Doheon Lee, "Finding temporal association rules from time-series microarray data", The 6th International Symposium on Advanced Intelligent Systems (ISIS'2005), Yousu University, Yousu, Korea, September 2005

  31. Ho Jung Nam, Doheon Lee, "Finding association between genes from microarray sequential pattern analysis", The 2005 International Joint Conference of InCoB, AASBi and KSBI, BEXCO, Busan Korea, September 22-24, 2005

Computational Systems Biology Lab.

School of Electrical Engineering and Computer Science (EECS),

Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea