Microbial Genomics and Bioinformatics Laboratory
Research Field
I am a professor at the Graduate Institute of Biomedical Informatics, Taipei Medical University, Taiwan. I am interested in problems broadly related to deciphering bacteria and microbiomes using computational methods. I am also interested in designing algorithms and applying machine learning techniques in solving biological problems.
Our lab is focused on developing machine learning methods for predicting antimicrobial resistant pathogens and extracting potential antimicrobial resistance genes.
We are working on developing machine learning methods for predicting antimicrobial resistant pathogens and extracting potential antimicrobial resistance genes. Here are some of our published papers related to this topic.
1. Duyen Thi Do, Ming-Ren Yang, Tran Nam Son Vo, Nguyen Quoc Khanh Le, Yu-Wei Wu*, “Unitig-Centered Pan-Genome Machine Learning Approach for Predicting Antibiotic Resistance and Discovering Novel Resistance Genes in Bacterial Strains”, Computational and Structural Biotechnology Journal, 23:1864-1876, 2024.
2. Ming-Ren Yang, Shun-Feng Su, and Yu-Wei Wu*, “Using bacterial pan-genome-based feature selection approach to improve the prediction of minimum inhibitory concentration (MIC)”, Frontiers in Genetics, 14:1054032, 2023.
3. Ming-Ren Yang and Yu-Wei Wu*, “A Cross-Validated Feature Selection approach for extracting the most parsimonious feature sets and discovering potential antimicrobial resistance (AMR) biomarkers”, Computational and Structural Biotechnology Journal, 21:769-779, 2023.
4. Ming-Ren Yang and Yu-Wei Wu*, “Enhancing predictions of antimicrobial resistance of pathogens by expanding the potential resistance gene repertoire using a pan-genome-based feature selection approach”, BMC Bioinformatics, 23:131, 2022.
5. Hsuan-Lin Her and Yu-Wei Wu*, "A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains", Bioinformatics, 34(13): i89-i95, 2018.
Ranked as top 2% scientists from 2021-2024.
Best Oral Presentation Award, 20th Asia Pacific Bioinformatics Conference, 2022.
Best Teaching Award, Graduate Institute of Biomedical Informatics, Taipei Medical University, 2021.
MoST Exceptional Young Scientist Grant, 2019.
Fine Creation Award, 4th SPINTECH Technology Thesis Award (co-advisor; advised with Dr. Po-Ting Lin), 2018.
Best Paper Award (Gold), The 16th International Conference on Bioinformatics (InCoB), 2017.
MoST Special Talent Recruitment, 2017.
MoST Special Talent Recruitment, 2016.
Outstanding Research Contribution Award, Joint BioEnergy Institute, 2016.
Young Scientist Travel Grant, 6th Soil Metagenomics Annual Meeting, 2014.
Travel Fellowship, 11th European Conference on Computational Biology, 2012.
Travel Grant, Taiwan Ministry of Education, 2010
Ph.D. in Bioinformatics (09/2007—08/2012), Indiana University, Bloomington IN, USA
M.S. in Computer Science (09/1998—06/2000), National Tsing Hua University, Taiwan
B.S. in Computer Science (09-1994—06/1998), Tunghai University, Taiwan