Young-Rae Cho

  Professor
  Department of Software
  Department of Digital Healthcare
  Department of Applied Artificial Intelligence
  Yonsei University - Mirae Campus
  youngcho (at) yonsei (dot) ac (dot) kr
 
  [Papers]  [Talks]  [Teaching]  [Biography]

 
                Research

  • Bioinformatics:  Bio-Networks, Bio-Ontologies, Functional Genomics, Systems Biology, AI Drug Discovery, Drug Repositioning
  • Data Mining:  Pattern Mining, Clustering, Classification, Deep Learning, Data Integration

              Publications

Journal Articles (SCI-indexed)
Journal Articles (KCI-indexed)
Conference / Workshop Papers
Book Chapters
  • Young-Rae Cho. "Filtering Protein-Protein Interactions by Integration of Ontology Data". In Mourad Elloumi and Albert Y Zomaya (eds.), Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, Wiley, 2013.
  • Young-Rae Cho and Aidong Zhang. "Functional Influence Based Approach to Identify Overlapping Modules in Biological Networks". In Philip S Yu, Christos Faloutsos, and Jiawei Han (eds.), Link Mining: Models, Algorithms, and Applications, Springer, 2010.
  • Young-Rae Cho and Aidong Zhang. "Integration of Gene Ontology into the Analysis of Protein Interaction Networks". In Aidong Zhang, Protein Interaction Networks: Computational Approaches, Cambridge University Press, 2009.
  • Chuan Lin, Young-Rae Cho, Woochang Hwang, Pengjun Pei and Aidong Zhang. "Clustering Methods In Protein-Protein Interaction Network". In Xiaohua Hu and Yi Pan (eds.), Knowledge Discovery in Bioinformatics: Techniques, Methods and Application, Wiley, 2007.
Patents
  • Aidong Zhang, Murali Ramanathan, Woochang Hwang and Young-Rae Cho. "Bridging Centrality: a concept and formula to identify bridging nodes in scale-free networks". US 7,808,921. October 5, 2010.
  • Young-Rae Cho, Wook-yeol Ryu and Sang-kyun Lee. ">Method for manufacturing semiconductor package containing cylindrical type Bump Grid Array". US 6,352,915. March 5, 2002.
  • Sam-Il Kim and Young-Rae Cho. "Chip-size packages assembled using mass production techniques at the wafer-level". US 6,004,867. December 21, 1999.

             Presentations
Invited Talks
  • Drug Repositioning and Drug Development Using Network-Based AI Models (Digital Healthcare Workshop at Yonsei University, Wonju, 2023)
  • Network-Based Computational Approaches for Drug Repositioning (Digital Healthcare R&D Kick-off Seminar at Yonsei University, Wonju, 2023)
  • Network-Based Computational Approaches in Bioinformatics and Biomedicine (Special Lecture on Cooperative Program of Bioinformatics at Seoul National University, 2021)
  • Bioinformatics: Past, Present, and Future (Special Lecture at National Health Insurance Service, Wonju, 2020)
  • Functional Pattern Mining from Genome-Scale Protein-Protein Interaction Networks (Colloquium Series on Department of Mathematics at University of North Texas, 2013)
  • Systematic analysis of Interactome: a new trend in Bioinformatics (KOCSEA Technical Symposium at Vienna, 2010)
  • Surfing on complex biological networks: the next generation of bioinformatics research (BEARS: Baylor Engineering and Research Seminar at Baylor University, 2009)
Conference / Workshop Talks
  • LePrimAlign: local entropy-based alignment of PPI networks to predict conserved modules, APBioNet International Conference on Bioinformatics (InCoB 2019), Jarkarta, Indonesia, September 10-12, 2019.
  • An integrative measure of graph- and vector-based semantic similarity using information content distance, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2015), Washington DC, November 10-12, 2015.
  • P-Finder: Reconstruction of signaling networks from protein-protein interactions and GO annotations, ISCA International Conference on Bioinformatics and Computational Biology (BICoB 2015), Honolulu, HI, March 9-11, 2015.
  • Signaling pathway prediction approaches on protein-protein interaction networks, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2013), Shanghai, China, December 19-21, 2013.
  • M-Finder: Functional association mining from protein interaction networks weighted by semantic similarity, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012), Philadelphia, PA, October 5-7, 2012.
  • Entropy-based graph clustering: application to biological and social networks, IEEE International Conference on Data Mining (ICDM 2011), Vancouver, Canada, December 11-14, 2011.
  • Evaluating functional module detection from PPI networks, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta, GA, November 12-15, 2011.
  • Decomposing protein interactome networks by graph entropy, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2010), Hong Kong, China, December 18-21, 2010.
  • flowNet: Flow-based approach for efficient analysis of complex biological networks, IEEE International Conference on Data Mining (ICDM 2009), Miami, FL, December 6-9, 2009.
  • Restructuring protein interaction networks to reveal structural hubs and functional organizations, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2009), Washington DC, November 1-4, 2009.
  • Discovering frequent patterns of functional associations in protein interaction networks for function prediction, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2008), Philadelphia, PA, November 3-5, 2008.
  • Feature extraction from microarray expression data by integration of semantic knowledge, IEEE International Conference on Machine Learning and Application (ICMLA 2007), Cincinnati, OH, December 13-15, 2007.
  • Information flow-based modularization in protein interaction networks, IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2007), Boston, MA, October 14-17, 2007.
  • Efficient modularization of weighted protein interaction networks using k-hop graph reduction, IEEE Symposium on Bioinformatics and Bioengineering (BIBE 2006), Washington DC, October 16-18, 2006.

                Activities
Journal Editorial Board
  • Yonsei Medical Journal (YMJ)
  • International Journal of Data Mining and Bioinformatics (IJDMB), Inderscience Publishers
Conference Chair / Program Committee
  • Workshop Chair in IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2024)
  • Program Chair in IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2020)
  • Workshop Chair in IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2019)
  • Poster Chair in IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2013)
  • PC in IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2024)
  • PC in International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2018, 2019)
  • PC in International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2017)
  • PC in IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2013)
  • PC in IEEE International Symposium on Computer-Based Medical Systems (CBMS 2012)
  • PC in ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2010, 2011)
Workshop Organizer
  • 1st International Workshop on Artificial Intelligence in Drug Discovery and Drug Repositioning (AI-DDDR), in conjunction with BIBM 2024 at Lisbon
  • 14th International Workshop on Biological Network Analysis and Integrative Graph-Based Approaches (IWBNA), in conjunction with BIBM 2021 online
  • 13th International Workshop on Biological Network Analysis and Integrative Graph-Based Approaches (IWBNA), in conjunction with BIBM 2020 at Seoul
  • 12th International Workshop on Biological Network Analysis and Integrative Graph-Based Approaches (IWBNA), in conjunction with BIBM 2019 at San Diego
  • 11th International Workshop on Biological Network Analysis and Integrative Graph-Based Approaches (IWBNA), in conjunction with BIBM 2018 at Madrid
  • 10th International Workshop on Biological Network Analysis and Integrative Graph-Based Approaches (IWBNA), in conjunction with BIBM 2017 at Kansas City
  • 9th International Workshop on Biological Network Analysis and Integrative Graph-Based Approaches (IWBNA), in conjunction with BIBM 2016 at Shenzhen
  • 8th International Workshop on Biomolecular Interaction Network Analysis and Interactomics (IWBNA), in conjunction with BIBM 2015 at Washington DC
  • 7th International Workshop on Biomolecular Network Analysis (IWBNA), in conjunction with BIBM 2013 at Shanghai
  • 6th International Workshop on Biomolecular Network Analysis (IWBNA), in conjunction with BCB 2013 at Washington DC
  • 5th International Workshop on Biomolecular Network Analysis (IWBNA), in conjunction with BIBM 2012 at Philadelphia
  • 4th International Workshop on Biomolecular Network Analysis (IWBNA), in conjunction with BIBM 2011 at Atlanta
  • 3rd International Workshop on Biomolecular Network Analysis (IWBNA), in conjunction with BCB 2011 at Chicago
  • 2nd International Workshop on Graph Theoretic Analysis of Biological Networks (IWBNA), in conjunction with BIBM 2010 at Hong Kong
  • 1st International Workshop on Graph Theoretic Approaches for Biological Network Analysis (IWBNA), in conjunction with BCB 2010 at Niagara Falls

                Teaching
  • Data Mining
    • At Baylor University
      1. Introduction to Data Mining: Fall 2009, Fall 2010, Fall 2011, Fall 2012, Fall 2013, Fall 2014, Fall 2015, Fall 2016, Fall 2017, Fall 2018, Fall 2019
      2. Advanced Data Mining (Graduate-level): Spring 2019
    • At Yonsei University
      1. Data Mining: 2020 2nd Term, 2021 2nd Term, 2022 2nd Term, 2023 2nd Term, 2024 2nd Term
  • Bioinformatics
    • At Baylor University
      1. Introduction to Computational Biology: Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, Spring 2018, Spring 2019
      2. Advanced Computational Biology (Graduate-level): Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2015, Fall 2016, Fall 2017
      3. Genomics and Bioinformatics: Fall 2010, Fall 2011, Fall 2012, Fall 2013, Fall 2014, Fall 2015
      4. Bioinformatics Senior Capstone Project: Fall 2018, Fall 2019
    • At Yonsei University
      1. Bio-Computing: 2021 2nd Term, 2022 2nd Term, 2023 1st Term, 2024 1st Term
      2. Bio-Data Mining (Graduate-level): 2020 2nd Term, 2021 1st Term, 2022 1st Term, 2023 2nd Term, 2024 1st Term
      3. AI-Driven Drug Discovery (Graduate-level): 2024 2nd Term
  • Digital Healthcare
    • At Yonsei University
      1. Introduction to Digital Healthcare: 2023 2nd Term, 2024 2nd Term
      2. Digital Healthcare Capstone Project (RIS): 2024 1st Term
  • Programming & Methematics
    • At Baylor University
      1. Java Programming: Spring 2016, Fall 2016, Spring 2017, Fall 2017
      2. Discrete Structures: Spring 2018
    • At Yonsei University
      1. Computational Thinking: 2020 1st-2nd Terms, 2021 1st Term, 2022 1st Term
      2. Object-Oriented Programming in C++: 2020 1st Term
      3. Computer Programming in C: 2021 1st Term

               Biography

Last Updated 7/12/2024