Hojung Nam, Ph.D.

Assistant Professor
Computational Systems Biology Lab.
School of Information & Communications
Gwangju Institute of Science and Technology (GIST)
(Email) hjnam{at}gist{dot}ac{dot}kr
 
  
Office: +82-62-715-2641

RESEARCH AREAS

    
Bioinformatics, Systems Biology, Gene expression analysis, Genomic sequence analysis,Data Mining, Metabolic profile analysis, Cancer Markers Discovery

EDUCATION

  • Ph.D. in Bio and Brain Engineering, KAIST, Daejeon, Korea. 
Dissertation: Combined analysis of transcriptome and metabolome
Advisor: Prof. Doheon Lee
  • M.S. in Computer Science, KAIST, Daejeon, Korea.                
Thesis: An Efficient Clustering Algorithm for Categorical Data Sets
Advisor: Prof. Yoon Jun Lee
  • B.S. in Computer Science (Cum Laude), Sogang Univ., Seoul, Korea .    

ACADEMIC EXPERIENCES 

  • Assistant Professor, School of Information and Communications, 
    Gwangju Institute of Science and Technology (GIST)
                Feb. 2013 - Present.
  • Systems Biology Research Group, Dept. of Bioengineering, 
    University of California, San Diego, CA USA
              
Aug. 2009 - Feb. 2013.        
Postdoctoral Researcher
  • Dept. of Bio and Brain Engineering, KAIST, Daejeon, Korea
              Mar. 2009 - July 2009.     Postdoctoral Researcher
              Mar. 2004 - Jan. 2009.    Graduate Researcher
              Mar. 2004 - Jan. 2008.    Teaching Assistant
  • German Cancer Research Center, Heidelberg, Germany
              June 2005 - July 2005.     Visiting Researcher
           

PUBLICATIONS

 JOURNAL (Peer Reviewed)  [Link to the Google Scholar page]

  1. Eunyoung Kim, Hojung Nam*, "Prediction models for drug-induced hepatotoxicity by using weighted molecular fingerprints", Accepted.
  2. 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, In press.
  3. Soobok Joe, Hojung Nam*, "Prognostic Factor Analysis for Breast Cancer Using Gene Expression Profiles", BMC Medical Informatics and Decision Making, 2016 16(Suppl 1):56.
  4. 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.
  5. 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
  6. 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.
  7. 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.
  8. 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 (accepted for publication) / Software available at http://sourceforge.net/projects/virmid/
  9. 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, 2012337(6098):1101-1104, DOI: 10.1126/science.1216861
  10. 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.
  11. 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.
  12. 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.
  13. 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.  
  14. 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. 
  15. 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. 
  16. 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.
  17. 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.


  CONFERENCE
  1. Soobok Joe, Hojung Nam*, "Prognostic Factor Analysis for Breast Cancer Using Gene Expression Profiles", BMC Medical Informatics and Decision Making, 2016 16(Suppl 1):56.
  2. 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)
  3. 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
  4. Hojung Nam, Doheon Lee, "Qualitative Cellular Dynamics Analysis with Gene Regulatory Information and Metabolic Pathways", The International Symposium on Optimization and Systems Biology, Beijing (China) August 8-10, , 2007, ORSC & APORC, pp. 143-150
  5. 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)
  6. 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) 
  7. 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 
  8. 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

PATENTS

  1. Doheon Lee, Bong Chul Chung, Hojung Nam, "Marker for diagnosis of papillary thyroid cancer comprising 3-indoleacetonitrile", Application No.1020090059270 (Korea)(2009.06.30)
  2. Doheon Lee, Bong Chul Chung, Hojung Nam, "Marker for diagnosis of papillary thyroid cancer comprising 3-indoleacetonitrile", International Application No.PCT/KR2010/003048No.1020090059270


INVITED TALKS

  • National Cancer Center (NCC, 국립암센터), "Enzyme specificity analysis & Prediction of oncometabolites in cancer", July 2013
  • Korea Institute of Science & Technology Information (KISTI, 한국과학기술정보연구원), "Systematic Approaches for Exploring Cellular Metabolism", June 2013
  • Korea Research Institute of Bioscience & Biotechnology (KRIBB, 한국생명공학연구원), "Systematic Approaches for Exploring Cellular Metabolism", June 2013

SKILLS

Omics- data analysis experiences:
Gene expression (Affymatrix, NimbleGen tiling array), ChIP-chip, Illumina sequencing data, GC-MS,
KEGG pathway, Gene Ontology

Programming languages: 
C, Java, Python, MATLAB, R



ACTIVITY & AWARDS

        




Last Update: July 22, 2013