Publication

Publications (My Google Scholar page)

(*: Papers I served as corresponding author; &: equally contributed co-first author)

1. Po-Ting Lin and Yu-Wei Wu*, “Highly-accurate prediction of colorectal cancer through low abundance uncultivated genomes recovered using metagenomic co-assembly and binning approach”, BMC Cancer, 25:1418, 2025.

2. Yu-En Lin, Chung-Shien Wu, Yu-Wei Wu, Shu-Miaw Chaw, “Phylogenomic inference suggests differential deep time phylogenetic signals from nuclear and organellar genomes in gymnosperms”, Plants, 14(9):1335, 2025.

3. Tzi-Yuan Wang&, Yu-Wei Wu&, Hao-Jun Lu&, Te-Yu Liao, Jui-Hung Tai, Shih-Pin Huang, Feng-Yu Wang, Tsung-Han Yu, Chau-Ti Ting, Shu-Miaw Chaw, Hurng-Yi Wang, “Chromosome-Level Genome Assembly of the Loach Goby Rhyacichthys aspro Offers Insights Into Gobioidei Evolution”, Molecular Ecology Resources, 25(7):e14100, 2025.

4. Herdiantri Sufriyana, Fariska Zata Amani, Aufar Zimamuz Zaman Al Hajiri, Yu-Wei Wu, Emily Chia-Yu Su, "Widely accessible prognostication using medical history for fetal growth restriction and small for gestational age in nationwide insured women", Scientific Reports, 15:8340, 2025.

5. Buyandelger Batsaikhan, Pei-Chun Lin, Katsumi Shigemura, Yu-Wei Wu, Reo Onishi, Pei-Ru Chang, Hung-Yen Cheng, Shiuh-Bin Fang, "Comparison of global transcriptomes for nontyphoidal Salmonella clinical isolates from pediatric patients with and without bacteremia after their interaction with human intestinal epithelial cells in vitro", Journal of Microbiology, Immunology, and Infection, 58(1):38-47, 2025.

6. 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.

7. Herdiantri Sufriyana, Fariska Zata Amani, Aufar Zimamuz Zaman Al Hajiri, Yu-Wei Wu, Emily Chia-Yu Su, "Prognosticating Fetal Growth Restriction and Small for Gestational Age by Medical History", Studies in Health Technology and Informatics, 310:740-744, 2024.

8. Szu-Ju Chen, Yu-Jun Wu, Chieh-Chang Chen, Yu-Wei Wu, Jyh-Ming Liou, Ming-Shiang Wu, Ching-Hua Kuo and Chin-Hsien Lin, “Plasma metabolites of aromatic amino acids associate with clinical severity and gut microbiota of Parkinson’s disease”, npj Parkison’s disease, 9:165, 2023.

9. Zheng-Jie Huang, Brijesh Patel, Wei-Hao Lu, Tz-Yu Yang, Wei-Cheng Tung, Vytautas Bučinskas, Modris Greitans, Yu-Wei Wu*, and Po Ting Lin*, “Yeast cell detection using fuzzy automatic contrast enhancement (FACE) and you only look once (YOLO)”, Scientific Reports, 13:16222, 2023.

10. 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.

11. Tzi-Yuan Wang, King-Siang Goh, Liang-Jong Wang, Li-Ling Wu, Feng-Yu Wang*, and Yu-Wei Wu*, “Long-Read Genome Sequencing of Abscondita cerata (Coleoptera: Lampyridae), the Endemic Firefly of Taiwan”, Zoological Studies, 62:25, 2023.

12. Herdiantri Sufriyana, Yu-Wei Wu, Emily Chia-Yu Su, “Human-guided deep learning with ante-hoc explainability by convolutional network from non-image data for pregnancy prognostication”, Neural Networks, 162:99-116, 2023.

13. Yung-Hsien Shao, Yu-Wei Wu, Muhammad Naufal, and Jer-Horng Wu, “Genome-centered metagenomics illuminates adaptations of core members to a partial Nitritation–Anammox bioreactor under periodic microaeration”, Frontiers in Microbiology, 14:1046769, 2023.

14. Bo-Siyuan Jian, Shao-Lun Chiou, Chun-Chia Hsu, Josh Ho, Yu-Wei Wu*, and John Chu*, “Bioinformatic Analysis Reveals both Oversampled and Underexplored Biosynthetic Diversity in Nonribosomal Peptides”, ACS Chemical Biology, 18(3):476-483, 2023.

15. Sathishkumar Subburaj, Chih-Ho Yeh, Brijesh Patel, Tsung-Han Huang, Wei-Song Hung, Ching-Yuan Chang, Yu-Wei Wu*, and Po Ting Lin*, “K-mer-Based Human Gesture Recognition (KHGR) Using Curved Piezoelectric Sensor”, Electronics, 12(1):210, 2023.

16. 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.

17. Lauren M. Tom, Martina Aulitto, Yu-Wei Wu, Kai Deng, …, and Steven W. Singer, “Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction”, Microbiome, 10:183, 2022.

18. Herdiantri Sufriyana, Hotimah Masdan Salim, Akbar Reza Muhammad, Yu-Wei Wu, and Emily Chia-Yu Su, “Blood biomarkers representing maternal-fetal interface tissues used to predict early-and late-onset preeclampsia but not COVID-19 infection”, Computational and Structural Biotechnology Journal, 20:4206-4224, 2022.

19. Duyen Thi Do, Ming-Ren Yang, Luu Ho Thanh Lam, Nguyen Quoc Khanh Le*, and Yu-Wei Wu*, “Improving MGMT methylation status prediction of glioblastoma through optimizing radiomics features using genetic algorithm-based machine learning approach”, Scientific Reports, 12:13412, 2022. 

20. 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.

21. Po-Hsiang Wang, Yi-Lung Chen, Tien-Yu Wu, Yu-Wei Wu, Tzi-Yuan Wang, Chao-Jen Shih, Sean Ting-Shyang Wei, Yi-Li Lai, Cheng-Xuan Liu, Yin-Ru Chiang, “Omics and mechanistic insights into di-(2-ethylhexyl) phthalate degradation in the O2-fluctuating estuarine sediments”, Chemosphere, 299:134406, 2022.

22. Szu-Ju Chen, Chieh-Chang Chen, Hsin-Yu Liao, Ya-Ting Lin, Yu-Wei Wu, Jyh-Ming Liou, Ming-Shiang Wu, Ching-Hua Kuo, Chin-Hsien Lin, “Association of Fecal and Plasma Levels of Short-Chain Fatty Acids With Gut Microbiota and Clinical Severity in Parkinson Disease Patients”, Neurology, 98(8):e848-e858, 2022.

23. Hsuan-Lin Her, Po-Ting Lin*, and Yu-Wei Wu*, “PangenomeNet: a pan-genome-based network reveals functional modules on antimicrobial resistome for Escherichia coli strains”, BMC Bioinformatics, 22:548, 2021.

24. Luis B. Gómez-Luciano, Yu-Wei Wu, Chien-Min Chiang, Te-Sheng Chang, Jiumn-Yih Wu, Tzi-Yuan Wang, “Complete Genome Sequence of the Soil-Isolated Psychrobacillus sp. Strain AK 1817, Capable of Biotransforming the Ergostane Triterpenoid Antcin K”, Microbiology Resource Annnouncements, 10(40):e0124220, 2021.

25. Chun-Chao Chen, Cheng-Hsin Lin, Wen-Rui Hao, Jong-Shiuan Yeh, Kuang-Hsing Chiang, Yu-Ann Fang, Chun-Chih Chiu*, Tsung Yeh Yang*, Yu-Wei Wu*, Ju-Chi Liu*, “Influenza vaccination and the risk of ventricular arrhythmias in patients with chronic obstructive pulmonary disease: a population-based longitudinal study”, Frontiers in Cardiovascular Medicine, 8:731844, 2021.

26. Liang-Jong Wang, Yu-Wei Wu, and Tzi-Yuan Wang, “Characterization of the complete mitochondrial genome of Abscondita cerata (Olivier, 1911) (Coleoptera: Lampyridae) and its phylogenetic implications”, Mitochondrial DNA Part B, 6(9): 2528-2530, 2021.

27. Sean Ting-Shyang Wei, Yi-Lung Chen, Yu-Wei Wu, Tien-Yu Wu, Yi-Li Lai, Po-Hsiang Wang, Wael Ismail, Tzong-Huei Lee, and Yin-Ru Chiang, “Integrated Multi-omics Investigations Reveal the Key Role of Synergistic Microbial Networks in Removing Plasticizer Di-(2-Ethylhexyl) Phthalate from Estuarine Sediments”, mSystems, 6(3): e00358-21, 2021. 

28. Yu-Wei Wu* and Steven Singer, “Recovering Individual Genomes from Metagenomes Using MaxBin 2.0”, Current Protocols, 1(5):e128, 2021.

29. Te-Sheng Chang, Chien-Min Chiang, Tzi-Yuan Wang, Yu-Li Tsai, Yu-Wei Wu, Huei-Ju Ting, Jiumn-Yih Wu, “One-Pot Bi-Enzymatic Cascade Synthesis of Novel Ganoderma Triterpenoid Saponins”, Catalysis, 11(5):580, 2021.

30. Te-Sheng Chang, Tzi-Yuan Wang, Chien-Min Chiang, Yu-Ju Lin, Hui-Lien Chen, Yu-Wei Wu, Huei-Ju Ting, Jiumn-Yih Wu, “Biotransformation of celastrol to a novel, well-soluble, low-toxic and anti-oxidative celastrol-29-O-β-glucoside by Bacillus glycosyltransferases”, Journal of bioscience and bioengineering, 131(2):176-182, 2021.

31. Nai-Fang Chi, Tzu-Hao Chang, Chen-Yang Lee, Yu-Wei Wu, Ting-An Shen, Lung Chan, Yih-Ru Chen, Hung-Yi Chiou, Chung Y. Hsu, Chaur-Jong Hu, “Untargeted metabolomics predicts the functional outcome of ischemic stroke”, Journal of the Formosan Medical Association, 120(1): 234-241, 2021.

32. Wei-Kai Wu, Suraphan Panyod, Po-Yu Liu, …, Yu-Wei Wu, …, Ming-Shiang Wu, “Characterization of TMAO productivity from carnitine challenge facilitates personalized nutrition and microbiome signatures discovery”, Microbiome 8:162, 2020.

33. Herdiantri Sufriyana, Atina Husnayain, Ya-Lin Chen, Chao-Yang Kuo, Onkar Singh, Tso-Yang Yeh, Yu-Wei Wu, and Emily Chia-Yu Su, “Comparison of Multivariable Logistic Regression and Other Machine Learning Algorithms for Prognostic Prediction Studies in Pregnancy Care: Systematic Review and Meta-Analysis”, JMIR Medical Informatics, 8(11):e16503, 2020.

34. Yi-Han Huang, Yu-Wei Wu, Jian-Ying Chuang, Yung-Chiao Chang, Hsiao-Fu Chang, Pao-Luh Tao, Horace H. Loh, Shiu-Hwa Yeh, “Morphine produces potent antinociception, sedation, and hypothermia in humanized mice expressing human mu-opioid receptor splice variants”, PAIN, 161(6):1177-1190, 2020.

35. Herdiantri Sufriyana, Yu-Wei Wu, and Emily Chia-Yu Su, “Artificial intelligence-assisted prediction of preeclampsia: Development and external validation of a nationwide health insurance dataset of the BPJS Kesehatan in Indonesia”, EBioMedicine, in press, 2020.

36. Herdiantri Sufriyana, Yu-Wei Wu, and Emily Chia-Yu Su, “Prediction of Preeclampsia and Intrauterine Growth Restriction: Development of Machine Learning Models on a Prospective Cohort”, JMIR Medical Informatics, 8(5):e15411, 2020.

37. Te-Sheng Chang, Tzi-Yuan Wang, Tzu-Yu Hsueh, Yu-Wen Lee, Jiumn-Yih Wu, Chien-Min Chiang, Hsin-Mei Chuang, Wen-Xuan Cai, and Yu-Wei Wu*, "A Genome-Centric Approach Reveals a Novel Glycosyltransferase from the GA A07 Strain of Bacillus thuringiensis Responsible for Catalyzing 15-O-Glycosylation of Ganoderic Acid A", International Journal of Molecular Sciences, 20(20): 5192, 2019.

38. Te-Sheng Chang, Chien-Min Chiang, Yu-Han Kao, Jiumn-Yih Wu, Yu-Wei Wu, and Tzi-Yuan Wang, "A New Triterpenoid Glucoside from a Novel Acidic Glycosylation of Ganoderic Acid A via Recombinant Glycosyltransferase of Bacillus subtilis", Molecules, 24(19): 3457, 2019.

39. Yu-Wei Wu*, Shih-Hung Yang, Myung Hwangbo, and Kung-Hui Chu*, "Analysis of Zobellella denitrificans ZD1 draft genome: Genes and gene clusters responsible for high polyhydroxybutyrate (PHB) production from glycerol under saline conditions and its CRISPR-Cas system", PLoS ONE, 14(9): e0222143, 2019.

40. Ankita Kothari, Yu-Wei Wu, John-Marc Chandonia, Marimikel Charrier, Lara Rajeev, Andrea Rocha, Dominique Joyner, Terry Hazen, Steven Singer, and Aindrila Mukhopadhyay, "Large circular plasmids from groundwater plasmidomes span multiple incompatibility groups and are enriched in multi-metal resistance genes", mBio, 10(1):e02899-18, 2019.  (featured by ScienceDaily and EurekaAlert)

41. Shan-Hua Yang, Kshitij Tandon, Chih-Ying Lu, Naohisa Wada, Chao-Jen Shih, Silver Sung-Yun Hsiao, Wann-Neng Jane, Tzan-Chain Lee, Chi-Ming Yang, Chi-Te Liu, Vianney Denis, Yu-Ting Wu, Li-Ting Wang, Lina Huang, Der-Chuen Lee, Yu-Wei Wu, Hideyuki Yamashiro, and Sen-Lin Tang, "Metagenomic, phylogenetic and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera", Microbiome, 7:3, 2019. (featured by Nature Microbiology Research Community)

42. Shu-Miaw Chaw, Yu-Ching Liu, Yu-Wei Wu, Han-Yu Wang, Chan-Yi Lin, Chung-Shien Wu, Huei-Mien Ke, Lo-Yu Chang, Chih-Yao Hsu, Hui-Ting Yang, Edi Sudianto, Ming-Hung Hsu, Kun-Pin Wu, Ling-Ni Wang, James Leebens-Mack, and Isheng Tsai, "Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution", Nature Plants, 5:63-73, 2019. (featured by Nature News and Views and Academia Sinica News Center [Chinese version] [English version])

43. Sean Wei, Yu-Wei Wu, Tzong-Huei Lee, Yi-Shiang Huang, Cheng-Yu Yang, Yi-Lung Chen, and Yin-Ru Chiang, "Microbial functional responses to cholesterol catabolism in denitrifying sludge", mSystems, 3:e00113-18, 2018.

44. Xiaoyu Liang, Jason M. Whitham, Evert K. Holwerda, Xiongjun Shao, Liang Tian, Yu-Wei Wu, Vincent Lombard, Bernard Henrissat, Dawn M. Klingeman, Zamin K. Yang, Mircea Podar, Tom L. Richard, James G. Elkins, Steven D. Brown, and Lee R. Lynd, "Development and Characterization of Stable Anaerobic Thermophilic Methanogenic Microbiomes Fermenting Switchgrass at Decreasing Residence Times", Biotechnology for Biofuels, 11:243, 2018.

45. Yu-Wei Wu* and Yu-Chuan Jack Li, "Development and implementation of computational models provides solutions for biomedical community", Computer Methods and Programs in Biomedicine, 159: A1, 2018.

46. Jefferey Kimbrel, Nicholas Ballor, Yu-Wei Wu, Maude David, Terry C Hazen, Blake Simmons, Steven Singer, and Janet Jansson, "Microbial community structure and functional potential along a hypersaline gradient", Frontiers in Microbiology, 9:1492, 2018.

47. Hsuan-Lin Her and Yu-Wei Wu*, "A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains", Selected paper in the 26th Conference on Intelligent System for Molecular Biology (ISMB 2018); Bioinformatics, 34(13): i89-i95, 2018.

48. Harry R. Beller, Andria V. Rodrigues, Kamrun Zargar, Yu-Wei Wu, Avneesh K. Saini, Renee M. Saville, Jose H. Pereira, Paul D. Adams, Susannah G. Tringe, Christopher J. Petzold, and Jay D. Keasling, "Enzyme discovery for toluene synthesis in anoxic microbial communities", Nature Chemical Biology, 14:451-457, 2018. (featured by Berkeley Lab News Center, Science, EurekaAlert, and ScienceDaily)

49. Yu-Wei Wu*, “ezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes”, BMC Genomics, 19(Supp 1): 921, 2018. (Software download) (InCoB 2017 Best Paper Gold Award)

50. Sebastian Kolinko, Yu-Wei Wu, Firehiwot Tachea, Evelyn Denzel, Jennifer Hiras, Raphael Gabriel, Nora Baecker, Leanne Jade Chan, Stephanie Eichorst, Dario Frey, Qiushi Chen, Parastoo Azadi, Paul Adams, Todd Pray, Deepti Tanjore, Christopher Petzold, John Gladden, Blake Simmons, and Steven Singer, “A Bacterial Pioneer Produces Cellulase Complexes that Persist through Community Succession”, Nature Microbiology, 3:99-107, 2018. (featured by Berkeley Lab News Center and ScienceDaily)

51. Alexander Sczyrba, Peter Hofmann, …, Yu-Wei Wu, …, Alice C McHardy, “Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software”, Nature Methods, 14(11): 1063-1071, 2017. (featured by GEN)

52. Yu-Wei Wu, Yiru Shao, Kamil Khanipov, George Golovko, Maria Pimenova, Yuriy Fofanov, and Kung-Hui Chu, “Draft Genome Sequence of Zobellella denitrificans ZD1 (JCM 13380), a salt-tolerant denitrifying bacterium capable of producing poly(3-hydroxybutyrate)”, Genome Announcements, 5(36): e00948-17, 2017.

53. Yu-Wei Wu, Brendan Higgins, Chaowei Yu, Amitha P. Reddy, Shannon Ceballos, Larry D. Joh, Blake A. Simmons, Steven W. Singer, and Jean S. VanderGheynst, “Ionic liquids impact the bioenergy feedstock degrading microbiome and transcription of enzymes relevant to polysaccharide hydrolysis”, mSystems, 1(6): e00120-16, 2016.

54. Ankita Kothari, Marimikel Charrier, Yu-Wei Wu, Stephanie Malfatti, Carol E. Zhou, Steven W. Singer, Larry Dugan, and Aindrila Mukhopadhyay, “Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization”, FEMS Microbiology Letter, 363(20): fnw224, 2016.

55. Jennifer Hiras, Yu-Wei Wu&, Kai Deng, Carrie D. Nicora, Joshua T. Aldrich, Dario Frey, Sebastian Kolinko, Errol R. Robinson, Jon M. Jacobs, Paul Adams, Trent Northen, Blake A. Simmons, and Steven W. Singer, “Comparative community proteomics demonstrates the unexpected importance of an actinobacterial glycoside hydrolase family 12 for crystalline cellulose hydrolysis”, mBIO, 7(4): e01106-16, 2016. (featured by Phys.org and U.S. Department of Energy Science Highlights)

56. Jennifer Hiras, Yu-Wei Wu&, Stephanie A Eichorst, Blake A Simmons, and Steven W Singer, “Refining the Phylum Chlorobi by Resolving the Phylogeny and Metabolic Potential of the Representative of a Deeply Branching, Uncultivated Lineage”, ISME, 10:833-845, 2016.

57. Yu-Wei Wu*, Blake A Simmons, and Steven W Singer, "MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets", Bioinformatics, 32(4): 605-607, 2016. (Software download)

58. William Nelson, Yukari Maezato, Yu-Wei Wu, Margaret Romine, and Stephen Lindemann, “Identification and resolution of microdiversity through metagenomic sequencing of parallel consortia”, Applied and Environmental Microbiolgy, 82(1): 255-267, 2016. (featured by PNNL Science News and Highlights and declara.com)

59. Kuei-Han Lin, Ben-Yang Liao, Hao-Wei Chang, Shiao-Wei Huang, Ting-Yan Chang, Cheng-Yu Yang, Yu-Bin Wang, Yu-Teh Kirk Lin, Yu-Wei Wu, Sen-Lin Tang, Hon-Tsen Yu, “Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics”, BMC Genomics, 16:1029, 2015.

60. Yu-Wei Wu, Chijioke Joshua, Stephanie A. Eichorst, John M. Gladden, Blake A. Simmons, and Steven W. Singer, “Genomic Analysis of Xylose Metabolism in Members of the Deinoccocus-Thermus Phylum from Thermophilic Biomass-Deconstructing Bacterial Consortia”, BioEnergy Research, 8(3): 1031-1035, 2015.

61. Yu-Wei Wu*, Yung-Hsu Tang, Susannah G. Tringe, Blake A. Simmons, and Steven Singer, "MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm", Microbiome, 2:26, 2014. (Software download) (Featured by Berkeley Lab News Center, ScienceDaily, and Biomass magazine)

62. Yu-Wei Wu, Thomas G. Doak, and Yuzhen Ye, "The gain and loss of chromosomal integron systems in the Treponema species", BMC Evolutionary Biology, 13:16, 2013.

63. Yu-Wei Wu, Mina Rho, Thomas G. Doak, and Yuzhen Ye, "Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics", Selected paper in the 12th European Conferences on Computational Biology (ECCB 2012); Bioinformatics, 28 (18): i363-i369, 2012.

64. Yu-Wei Wu, Mina Rho, Thomas G. Doak, and Yuzhen Ye "Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes", Applied and Environmental Microbiology, 78(15): 5288-5296, 2012.

65. Mina Rho, Yu-Wei Wu, Haixu Tang, Thomas G. Doak, and Yuzhen Ye "Diverse CRISPRs evolving in human microbiomes", PLoS Genetics, 8(6): e1002441, 2012.

66. Yu-Wei Wu and Yuzhen Ye, "A novel abundance-based algorithm for binning metagenomic sequences using l-tuples", Lecture Notes in Computer Science, 6044: 535-549, RECOMB 2010, 2010. (Note that this paper also appeared in Journal of Computational Biology 18(3): 523-534 in 2011 as an invited submission for accepted RECOMB 2010 conference paper. Several new features, including the integration of AbundanceBin and other binning tools, are investigated in the journal version.) (Software download)

67. Michael Lee Salmans, Shu-Miaw Chaw, Ching-Ping Lin, Arthur Chun-Chieh Shih, Yu-Wei Wu and Michael R. Mulligan, "Editing site analysis in a gymnosperm mitochondrial genome reveals similarities with angiosperm mitochondrial genomes", Current Genetics, 56(5): 439-446, 2010.

68. Shu-Miaw Chaw, Arthur Chun-Chieh Shih, Daryi Wang, Yu-Wei Wu, Shu-Mei Liu and The-Yuan Chou, "The Mitochondrial Genome of the Gymnosperm Cycas taitungensis Contains a Novel Family of Short Interspersed Elements, Bpu sequences, and Abundant RNA Editing Sites", Molecular Biology and Evolution, 25(3): 603-615, 2008.

69. Daryi Wang, Yu-Wei Wu, Arthur Chun-Chieh Shih, Chung-Shien Wu, Ya-Nan Wang, Shu-Miaw Chaw, "Transfer of chloroplast genomic DNA to mitochondrial genome occurred at least 300 million years ago," Molecular Biology and Evolution 24(9): 2040-2048, 2007.

70. Arthur Chun-Chieh Shih, D.T. Lee, Chin-Lin Peng, and Yu-Wei Wu, "Phylo-mLogo: An interactive multiple-logo visualization tool for large-number sequence alignments", BMC Bioinformatics 8: 63, 10 pages, 2007.

71. Arthur C-C Shih, D T Lee, Laurent Lin, Chin-Lin Peng, Shiang-Heng Chen, Yu-Wei Wu, Chun-Yi Wong, Meng-Yuan Chou, Tze-Chang Shiao and Mu-Fen Hsieh. "SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools", BMC Bioinformatics, 7: 103, 15 pages, 2006.

Conference Presentations

(*: presenter)

1. Yu-Cheng Chen, Ming-Ren Yang, and Yu-Wei Wu, "CVFS 2.0: A Novel Machine Learning-Driven Algorithm for Precision Feature Selection in Antimicrobial Resistance Prediction", 15th National Clinical Medicine Joint Conference, Taipei Medical University, Taipei, Taiwan, 2025. (poster)

2. Ming-Ren Yang, Yu-Cheng Chen, and Yu-Wei Wu, "Modeling Antimicrobial Resistance as a Regression Problem via Cross-Validated Pan-Genome-Informed Feature Selection", 15th National Clinical Medicine Joint Conference, Taipei Medical University, Taipei, Taiwan, 2025. (oral)

3. Duyen Thi Do, Ming-Ren Yang, and Yu-Wei Wu, "Enhancing Antimicrobial Resistance Prediction through a Combined Pan-genome Approach with both Gene Cluster and SNP Information using Machine Learning Feature Selection Methods", Great Lakes Bioinformatics Conference (GLBIO 2025), Minneapolis, Minnesota, USA, 2025. (poster)

4. Ming-Ren Yang, Yu-Cheng Chen, Fei-Hung Hung, Yu-Wei Wu, "Enhancing MIC prediction of bacterial antimicrobial resistance through a pan-genome-based feature selection strategy incorporating cross-validated feature selection (CVFS)", International Symposium on Evolutionary Genomics and Bioinformatics (ISEGB 2025), National Cheng Kung University, Tainan, Taiwan, 2025. (poster)

5. Yu-Wei Wu*, "Mining Antimicrobial Resistance Pathogens and Resistance Gene Distribution using Machine Learning Algorithms", Interdisciplinary Technologies in Next Generation Marine Biomolecular Research Forum, Academia Sinica, Taipei, Taiwan, 2025. (oral)

6. Yu-Wei Wu*, "Mining potential oceanic microbes and their environmental relationships using machine learning techniques", Taiwan Ocean Union Annual Conference, National Taiwan University, Taipei, Taiwan, 2024. (oral)

7. Thi Phuong Nguyen*, Hsuan-Chia Yang, and Yu-Wei Wu, “Pangenome-based Feature Selection to Predict Antimicrobial Resistance in Klebsiella pneumoniae”, Multiomics and Precision Medicine Joint Conference (MOPM 2024), National Taiwan University, Taipei, Taiwan, 2024. (poster)

8. Yu-Cheng Chen*, Ming-Ren Yang, and Yu-Wei Wu, “CVFS 2.0: A Novel Machine Learning-Driven Algorithm for Precision Feature Selection in Antimicrobial Resistance Prediction”, Multiomics and Precision Medicine Joint Conference (MOPM 2024), National Taiwan University, Taipei, Taiwan, 2024. (poster)

9. Duyen Thi Do, Ming-Ren Yang, and Yu-Wei Wu*, “A Unitig-Centered Pan-Genome Approach for Predicting Antibiotic Resistance and Discovering Novel Resistance Genes in Bacterial Strains”, The 1st Asia and Pacific Bioinformatics Joint Conference (APBJC 2024), Naha Cultural Arts Theater NAHArt, Okinawa, Japan. (poster)

10. Yu-Cheng Chen*, Chao-Yang Kuo, Ming-Ren Yang, and Yu-Wei Wu, “A Pan-genome-based Feature Selection and Regression Method for Predicting Bacterial Minimum Inhibitory Concentration (MIC)”, The 1st Asia and Pacific Bioinformatics Joint Conference (APBJC 2024), Naha Cultural Arts Theater NAHArt, Okinawa, Japan. (poster)

11. Hong-Ren Huang* and Yu-Wei Wu, “Data balancing does not affect prediction performances in pan-genome-based antimicrobial resistance classification tasks”, The 1st Asia and Pacific Bioinformatics Joint Conference (APBJC 2024), Naha Cultural Arts Theater NAHArt, Okinawa, Japan. (poster)

12. Duyen Thi Do*, Ming-Ren Yang, and Yu-Wei Wu, “Enhancing Antimicrobial Resistance Prediction through a Combined Pan-genome Approach with both Gene Cluster and SNP Information using Machine Learning Feature Selection Methods”, The 32nd Conference on Intelligent Systems for Molecular Biology, Palais des Congrés de Montréal, Montreal, Quebec, Canada. (poster)

13. Duyen Thi Do, Ming-Ren Yang, and Yu-Wei Wu*, “A Unitig-Centered Pan-Genome Approach for Predicting Antibiotic Resistance and Discovering Novel Resistance Genes in Bacterial Strains”, The 32nd Conference on Intelligent Systems for Molecular Biology, Palais des Congrés de Montréal, Montreal, Quebec, Canada. (poster)

14. Duyen Thi Do, Ming-Ren Yang, and Yu-Wei Wu*, “A Unitig-Centered Pan-Genome Approach for Predicting Antibiotic Resistance and Discovering Novel Resistance Genes in Bacterial Strains”, The 14th RECOMB (Research in Computational Molecular Biology) Satellite Conference on Biological Sequence Analysis, Massachusetts Institute of Technology (MIT), Boston, U.S.A. (poster)

15. Ming-Ren Yang and  Yu-Wei Wu*, “CVFS: A Cross-Validated Feature Selection approach for extracting potential biomarkers for predicting antimicrobial resistance”, MiTalk Mini Symposium and Workshop, Tzu Chi University, Hua Lien, Taiwan, 2024. (poster)

16. Herdiantri Sufriyana*, Yu-Wei Wu, and Emily Chia-Yu Su, "Low- and high-level information analyses of transcriptome connecting endometrial-decidua-placental origin of preeclampsia subtypes: A preliminary study", 2024 Pacific Symposium on Biocomputing (PSB 2024), Hawaii, U.S.A., 2024; Accepted paper is available at Pacific Symposium on Biocomputing 2024, pp. 549-563.

17. Ming-Ren Yang*, Chao-Yang Kuo, Yu-Cheng Chen, Yu-Wei Wu, “A new method uses XGBoost analysis to screen important drug resistance genes”, MiTalk Mini Symposium and Workshop, Tzu Chi University, Hua Lien, Taiwan, 2024. (poster)

18. Duyen Thi Do*, Ming-Ren Yang, and Yu-Wei Wu, “Unitig-Centered Pan-Genome Machine Learning for Predicting Antibiotic Resistance and Discovering Novel Resistance Genes in Bacterial Strains”, International Conference on Bioinformatics (InCoB 2023), Translational Research Institute (TRI), Brisbane, Australia, 2023. (oral)

19. Ming-Ren Yang*, Chao-Yang Kuo, Zne-Jung Lee, Shun-Feng Su, and Yu-Wei Wu, “Unveiling Crucial Drug-Resistance Genes : Leveraging the Power of XGBoost and mRMR Analysis”, International Conference on Bioinformatics (InCoB 2023), Translational Research Institute (TRI), Brisbane, Australia, 2023. (poster)

20. Szu-Yu Lee* and Yu-Wei Wu, “Using Pan-Genome-Based Machine Learning Approach for Predicting Antibiotic Resistances and Extracting Potential Resistance Genes for Neisseria gonorrhoeae”, Multiomics and Precision Medicine Joint Conference (MOPM 2023), National Taiwan University, Taipei, Taiwan, 2023. (poster)

21. Yu-Wei Wu*, “Workshop: Brief Introduction of Genomics and Metagenomics Assembly and Analysis”, Annual Meeting of Taiwan Society of Microbial Ecology (TSME 2023), I-Shou University, Kaohsiung, Taiwan, 2023. (oral)

22. Yu-Wei Wu*, “Microbiota state-of-the-art bioinformatics advances”, 2023 Taiwan Digestive Disease Week, National Sun Yat-sen University, Kaohsiung, Taiwan, 2023. (oral)

23. Ming-Ren Yang*, Duyen Thi Do, Bin-Yu Peng, Yu-Wei Wu, “A Pan-Genome-Based Feature Selection Approach Enhances Minimum Inhibitory Concentration (MIC) Prediction of Bacterial Antimicrobial Resistance”, MiTalk Workshop, National Taiwan Ocean University, Keelung, Taiwan, 2023. (poster)

24. Po-Ting Lin and Yu-Wei Wu*, “Highly-accurate prediction of colorectal cancer through low abundance uncultivated genomes recovered using metagenomic co-assembly and binning approach”, International Conference on Genome Informatics (GIW 2022), National Cheng Kung University, Tainan, Taiwan, 2022. (oral)

25. Duyen Thi Do*, Ming-Ren Yang, and Yu-Wei Wu, “Single nucleotide polymorphism (SNP) scanned through unsupervised SNP identification approach serve as better indicators for classifying antimicrobial resistance pathogens than gene cluster presence/absence patterns”, International Conference on Genome Informatics (GIW 2022), National Cheng Kung University, Tainan, Taiwan, 2022. (poster)

26. Ming-Ren Yang*, Duyen Thi Do, Shun-Feng Su, Bin-Yu Peng, Yu-Wei Wu, “Using bacterial pan-genome-based feature selection approach to improve the prediction of minimum inhibitory concentration (MIC)”, International Conference on Genome Informatics (GIW 2022), National Cheng Kung University, Tainan, Taiwan, 2022. (poster)

27. Ming-Ren Yang and Yu-Wei Wu*, “Using bacterial pan-genome-based feature selection approach to improve the prediction of minimum inhibitory concentration (MIC)”, International Conference on Bioinformatics (InCoB 2022), King Abdullah University of Science and Technology, Saudi Arabia, 2022. (oral; online conference)

28. Ming-Ren Yang and Yu-Wei Wu*, “From feature selection to biomarker discovery: using an ensembled Cross-Validated Feature Selection (CVFS) approach to identify key genes as bacterial antimicrobial resistance biomarkers”, Multiomics and Precision Medicine Joint Conference, Taipei, Taiwan, 2022. (oral)

29. Ming-Ren Yang and Yu-Wei Wu*, “From feature selection to biomarker discovery: using an ensembled machine learning approach to identify key genes as bacterial antimicrobial resistance biomarkers”, Engineering Bioscience Symposium, National Yang-Ming Chao-Tung University, Hsinchu, Taiwan, 2022. (oral)

30. Yu-Wei Wu*, “Using bacterial pan-genome to discover novel antimicrobial resistance genes and enhance antimicobial resistance pathogen prediction”, Annual Meeting of Taiwan Microbiota Consortium, National Taiwan University Hospital, Taipei, Taiwan, 2022. (oral; hybrid conference)

31. Yu-Wei Wu*, “Using explainable machine learning algorithm to identify gene biomarkers for better predicting antimicrobial resistance pathogens”, Annual Meeting of Taiwan Society of Microbial Ecology (TSME 2022), Fujen University, Taiwan. (oral; online conference)

32. Ming-Ren Yang and Yu-Wei Wu*, “A Cross-Validated Feature Selection (CVFS) Approach for Selecting Potential Biomarker Genes related to Antimicrobial Resistances from Salmonella enterica Pan-genome”, Asia Pacific Bioinformatics Conference (APBC 2022), Malaysia, 2022. (oral; online hybrid conference) 

33. Duyen Thi Do*, Ming-Ren Yang, Nguyen Quoc Khanh Le, and Yu-Wei Wu, “Improved prediction of the MGMT Methylation status of Glioblastoma using Genetic algorithm-based machine learning”, International Symposium on Evolutionary Genomics and Bioinformatics (ISEGB 2022), National Yang Ming Chiao Tung University, Taipei, Taiwan, 2022. (poster)

34. Ming-Ren Yang* and Yu-Wei Wu, “A Cross-Validated Feature Selection (CVFS) Approach for Selecting Potential Biomarker Genes related to Antimicrobial Resistances from Salmonella enterica pan-genome”, International Symposium on Evolutionary Genomics and Bioinformatics (ISEGB 2022), National Yang Ming Chiao Tung University, Taipei, Taiwan, 2022. (poster)

35. Yu-Wei Wu*, “Network construction and interpretation”, MiTalk Workshop, Tunghai University, Taichung, Taiwan, 2022. (oral) 

36. 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”, 20th International Conference on Bioinformatics (InCoB 2021), Kunming, China, 2021. (oral; online hybrid conference)

37. Ming-Ren Yang and Yu-Wei Wu*, “Mining Antimicrobial Resistance Genes from a Salmonella enterica pan-genome using A Cross-Validated Feature Selection (CVFS) Approach”, 29th Conference on Intelligent Systems for Molecular Biology And the 20th European Conference on Computational Biology (ISMB/ECCB 2021), Lyon, France, 2021. (poster; online virtual conference)

38. Yu-Ta Yao*, Yu-Wei Wu, and Po-Ting Lin, “A Two-Stage Multi-Fidelity Design Optimization for K-mer-Based Pattern Recognition (KPR) in Image Processing”, International Design Engineering Technical Conferences & Computers and Information in Engineering Conference (IDETC/CIE), Paper no. DETC2020-22263, Seoul, South Korea, 2020. (oral)

39. Ming-Ren Yang, Hsuan-Lin Her, and Yu-Wei Wu*, “Predicting antimicrobial resistance (AMR) activities from the bacterial pan-genomes using machine learning algorithms”, Multiomics and Precision Medicine Joint Conference, Chang Gung University, Taipei, Taiwan, 2020. (oral)

40. Hsuan-Lin Her, Ming-Ren Yang, and Yu-Wei Wu*, “Using bacterial pan-genome information to predict antimicrobial resistance activities via machine learning algorithms”, The annual meeting of Taiwan Society of Microbial Ecology (TSME), National Taiwan University, Taipei, Taiwan, 2020. (poster)

41. Yu-Wei Wu*, “The roles of metagenome-assembled genomes (MAG) in disease-related microbiomes”, MiTalk Workshop, National Taiwan University, Taiwan, 2020. (oral)

42. Yu-Wei Wu*, “The roles of metagenome-assembled genomes (MAG) in disease-related microbiomes”, 4th Asia Microbiome Conference, Academia Sinica, Taipei, Taiwan, 2020. (oral)

43. Yu-Wei Wu*, “Machine Learning Algorithms and Where to Use Them on Microbiome Problems”, Medical AI workshop, National Taiwan University, Taipei, Taiwan, 2019. (oral)

44. Yu-Wei Wu*, “Using multi-omics to decipher microbial functional potentials for different environmental factors”, Taiwan Biogenome Annual Retreat Seminar, Academia Sinica, Taipei, Taiwan, 2019. (oral)

45. Yu-Wei Wu*, “A genome-based multi-omics approach for elucidating the microbial functional potential for different environmental factors”, Microbiota NGS Bioinformatics Workshop, National Yang-Ming University, Taipei, Taiwan, 2019. (oral)

46. Yu-Wei Wu*, “Utilizing genome-resolved metagenome approach for analyzing individual species for environmental and clinical microbiome”, 3rd Asia Microbiome Conference, Academia Sinica, Taipei, Taiwan, 2019. (oral)

47. Yu-Wei Wu* and Kung-Hui Chu, “Identification of a glycerol-to-polyhydroxybutyrate (PHB) pathway and a marine-specific PHB gene cluster from the Zobellella denitrificans ZD1 draft genome”, The International Symposium on Evolutionary Genomics and Bioinformatics (ISEGB 2018), National Taiwan University Hospital, Taipei, Taiwan, 2018. (poster)

48. Hsuan-Lin Her* and Yu-Wei Wu, “A Pan-genome Based Co-inheritance Network to Predict Antibiotic-Resistance Potential of Hypothetical Proteins”, The International Symposium on Evolutionary Genomics and Bioinformatics (ISEGB 2018), National Taiwan University Hospital, Taipei, Taiwan, 2018. (poster)

49. Yu-Wei Wu*, “Recovering novel bacterial genomes from environmental and clinical samples”, Taiwan Biogenome Annual Retreat, Academia Sinica, Taipei, Taiwan, 2018. (oral)

50. Yu-Wei Wu*, “Resolving the environmental microbiome through genomics and multi-omics perspectives”, Russia-Taiwan Bilateral Symposium, Academia Sinica, Taipei, Taiwan, 2018. (oral)

51. Yu-Wei Wu*, “Binning as a tool for multi-omics analysis of microbiome studies”, MiTalk Workshop, Academia Sinica, Taipei, Taiwan, 2018. (oral)

52. Yu-Wei Wu*, “Genome recovery and multi-omics analysis for meta-omics datasets”, Microbiome Metagenome and Cancer Genomic Data Analysis Workshop, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, 2018. (oral)

53. Hsuan-Lin Her and Yu-Wei Wu*, "A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains", 26th conference on Intelligent Systems for Molecular Biology (ISMB 2018), Chicago, USA, 2018. (oral)

54. Hsuan-Lin Her and Yu-Wei Wu, “A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains”, The annual meeting of Taiwan Society of Microbial Ecology (TSME), National Yang-Ming University, Taipei, Taiwan, 2018. (poster)

55. Yu-Wei Wu*, “Interdisciplinary science: a computer scientist’s perspective on microbiology and microbiome”, MiTalk Mini Symposium and Workshop, Tzu Chi University, Hualien, Taiwan, 2018. (oral)

56. Hsuan-Lin Her* and Yu-Wei Wu, “Using Pan-Genome to Identify and Classify the Antimicrobial Resistant Escherichia Coli Strains”, Symposium on Engineering, Medicine, and Biology Applications, Taipei Medical University, Taipei, Taiwan, 2018. (Full Paper accepted for oral presentation)

57. Yu-Wei Wu*, “Resolving and analyzing uncultivated microbial populations from metagenomes”, The International Symposium on Evolutionary Genomics and Bioinformatics (ISEGB 2017), Tzu Chi University, Hualien, Taiwan, 2017. (oral)

58. Yu-Wei Wu*, “ezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes”, The 16th International Conference on Bioinformatics (InCoB 2017), Tsinghua University, Shenzhen, China, 2017. (oral)

59. Yu-Wei Wu*, "Genome-resolved metagenome: exploring the individual microbes, their identities, and their functional profiles", The annual meeting of Taiwan Society of Microbial Ecology (TSME), Taichung, Taiwan, 2017. (poster + three minute oral presentation)

60. Yu-Wei Wu*, “Establishing benchmark data sets for further development of unsupervised binning tools”, Evaluation Workshop of the first CAMI Challenge, Cambridge, UK, 2016. (oral)

61. Ankita Kothari*, Yu-Wei Wu, Marimikel Charrier, Lara Rajeev, Andrea M. Rocha, Terry C. Hazen, Paramvir S. Dehal, Dylan Chivian, Sarah J. Spencer, Eric J. Alm, Steven Singer, Aindrila Mukhopadhyay, “Plasmidome studies reveal a variety of horizontally transferred functions within the microbial communities at the Oak Ridge Field Research sites,” International Symposium for Microbial Ecology, Montreal, Canada, 2016. (oral)

62. Ankita Kothari*, Yu-Wei Wu, Marimikel Charrier, Lara Rajeev, Andrea M. Rocha, Terry C. Hazen, Paramvir S. Dehal, Dylan Chivian, Sarah J. Spencer, Eric J. Alm, Steven Singer, Aindrila Mukhopadhyay, Adam P. Arkin, and Paul D. Adams, “Extrachromosomal Plasmid DNA Project,” USDA‐DOE Plant Feedstock Genomics for Bioenergy Meeting, 2016. (poster)

63. Yu-Wei Wu*, “Extracting genomes from metagenomes and comparing the microbial contents among different environments: a computational point of view”, UCB-NTU Junior Scientist Symposium on Microbial Ecology, Genomics, and Metagenomics, 2015. (oral)

64. Yu-Wei Wu*, Blake A Simmons, and Steven Singer, “MaxBin 2.0: Integrating multiple metagenomes to recover more high quality individual genomes from the environmental data”, DOE JGI Annual User Meeting, Joint Genome Institute, 2015. (poster)

65. Yu-Wei Wu*, Blake A Simmons, and Steven W Singer, “Improving the assembly qualities of draft genomes extracted from metagenomes”, the Great Lakes Bioinformatics Conference, 2015. (Full Paper accepted for oral presentation)

66. Yu-Wei Wu*, Blake A Simmons, and Steven W Singer, “MaxBin 2.0: Integrating Multiple Metagenomes to Recover More High Quality Individual Genomes from the Environmental Data”, the Great Lakes Bioinformatics Conference, 2015. (poster)

67. Jennifer Hiras*, Yu-Wei Wu, Susannah G Tringe, Carrie Nicora, Joshua Aldrich, Errol Robinson, Jon Jacobs, Blake A Simmons and Steven W Singer, “The unexpected importance of actinobacterial GH12 in hydrolysis of crystalline cellulose”, the Symposium on Biotechnology for Fuels and Chemicals, 2015. (oral)

68. Steven W Singer* and Yu-Wei Wu, “The Promise and Perils of Automating Metagenomic Binning”, The 17th Genomic Standards Consortium meeting, 2015 (oral)

69. Yu-Wei Wu*, Stephanie A Eichorst, Susannah G Tringe, Blake A Simmons, and Steven W Singer, "MaxBin: recovering individual genomes from complex metagenomes using an expectation-maximization algorithm", the 6th Soil Metagenomics Annual Meeting, Argonne National Laboratory, 2014. (poster)

70. Yu-Wei Wu*, Stephanie A Eichorst, Susannah G Tringe, Blake A Simmons, Steven W Singer, "Recovering individual genomes from a compost metagenome using MaxBin, a novel binning algorithm," the 6th Soil Metagenomics Annual Meeting, St. Charles, Illinois, USA, 2014. (oral)

71. Yu-Wei Wu*, Yung-Hsu Tang, Susannah G Tringe, Blake A Simmons, and Steven W Singer, "MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm" DOE JGI Annual User Meeting, Joint Genome Institute, 2014. (poster)

72. Yu-Wei Wu* and Yuzhen Ye, "A novel abundance-based algorithm for binning metagenomic sequences using l-tuples" Industry Collaboration Workshop on Life Sciences Informatics, Indiana University, 2010. (poster)

73. Yu-Wei Wu* and Yuzhen Ye, “A novel abundance-based algorithm for binning metagenomic sequences using l-tuples”, International Conference on Research in Computational Molecular Biology, 2010. (oral)

74. Arthur Chun-Chieh Shih*, D.T. Lee, Chin-Lin Peng, and Yu-Wei Wu, "Phylo-mLogo: An interactive multiple-logo visualization tool for large-number sequence alignments," IEEE Computational Systems Bioinformatics Conference, Stanford University, 2006. (poster)