Office of Postdoctoral Affairs

Nam Phan

Postdoctoral Research Fellow

Computational biologist with expertise in bioinformatics, AI-driven biomedical research, and multi-omics data analysis. Seeking a postdoctoral position to apply machine learning and deep learning techniques to cancer research, spatial transcriptomics, and biomedical image analysis.

  • Professional Background

    Education

    • 2022 - PhD - National Taiwan University
    • 2014 - Master of Science - Chinese Culture University, Taiwan
    • 2012 - Bachelor in Biotechnology - International University- National Vietnam University

    Honors

    • 2023 - The 20th Taiwan National Innovation Award
    • 2022 - Nominated by Information Science Center, Academia Sinica, Taiwan and selected to participate the Global Young Scientist Summit, Singapore
  • Research

    My research integrates multiple data modalities such as next-generation sequencing, biomedical imaging, and FISH-based sequencing data to gain a holistic understanding of cancer biology. We also develop machine learning and deep learning models to predict patient outcomes, cancer subtypes, and gene expression profiles demonstrating the power of computational approaches in biomedical research.

    Furthermore, the prediction of mRNA expression and copy number variation using pathological images with deep learning models has been particularly innovative in recent years. By combining pathological embedding features with functional expression data, we aim to improve data representation for outcome predictions, which could have significant implications for personalized medicine and treatment strategies.

    Moreover, my team also explores spatial single-cell transcriptomics in order to decode the tumor microenvironment. By leveraging morphological and transcriptome data, we aim to better predict cellular identity within the tumor microenvironment, which could provide valuable insights into cancer progression and potential therapeutic targets.

    Overall, my research highlights the importance of interdisciplinary approaches and advanced technologies in advancing our understanding of cancer biology and improving patient outcomes.

  • Publications

     

    1. Tsai MH, Hwa HL, Chuang Eric Y, and Phan NN. A Method for Identifying Individual Gene and Its Deep Learning Model. Patent No. I783699. Taiwan Intellectual Property Office. 11/2022.

    2. Tseng, W.H.S., Chattopadhyay, A., Phan, N.N., Chuang, E.Y. and Lee, O.K., 2024. Utilizing multimodal approach to identify candidate pathways and biomarkers and predicting frailty syndrome in individuals from UK Biobank. GeroScience, 46(1), pp.1211-1228.

    3. Phan N.N, Chattopadhyay A., Lee T.T, Yin H.I , Lu T.P, Lai  L.C, Chuang EY, Hwa HL, Tsai M.H. High-Performance Deep Learning Pipeline Predicts Individuals in Mixtures of DNA Using Sequencing Data. Briefings in Bioinformatics. DOI: 10.1093/bib/bbab283. 

    4. Phan N.N, CY Hsu, CC Huang, LM Tseng, EY Chuang. Prediction of breast cancer recurrence using a deep convolutional neural network without region-of-interest labeling. Frontiers in Oncology. p.4274.

    5. Phan, N.N., Huang, C.C., Tseng, L.M. and Chuang, E.Y., 2021. Predicting Breast Cancer Gene Expression Signature by Applying Deep Convolutional Neural Networks from Unannotated Pathological Images. Frontiers in Oncology, 11, pp.769447-769447. 

    6. Phan, N.N., Chattopadhyay, A. and Chuang, E.Y., 2019. Role of artificial intelligence in integrated analysis of multi-omics and imaging data in cancer research. Translational Cancer Research, 8(8), p.E7.

    7. Phan, N.N., Chattopadhyay, A., Lu, T.P. and Tsai, M.H., 2020. Leveraging well-annotated databases for deep learning in biomedical research. Translational Cancer Research, 9(12), pp.7682-7684.

    8. Phan, N.N., Wang, C.Y., Chen, C.F., Sun, Z., Lai, M.D. and Lin, Y.C., 2017. Voltage-gated calcium channels: Novel targets for cancer therapy. Oncology letters, 14(2), pp.2059-2074.

    9. Phan, N.N., Wang, C.Y., Li, K.L., Chen, C.F., Chiao, C.C., Yu, H.G., Huang, P.L. and Lin, Y.C., 2018. Distinct expression of CDCA3, CDCA5, and CDCA8 leads to shorter relapse free survival in breast cancer patient. Oncotarget, 9(6), p.6977.

    10. Phan N.N, Tung T. Huynh, Yen-Chang Lin. Hyperpolarization-activated cyclic nucleotide-gated gene signatures and poor clinical outcome of cancer patient. Transl Can Res. 6(4), 698-708, 2017 

    11. Phan, N.N., Liu, S., Wang, C.Y., Hsu, H.P., Lai, M.D., Li, C.Y., Chen, C.F., Chiao, C.C., Yen, M.C., Sun, Z. and Jiang, J.Z., 2020. Overexpressed gene signature of EPH receptor A/B family in cancer patients-comprehensive analyses from the public high-throughput database. IJCEP, 13(5), p.1220.

    12. Phan, N.N., Moreno, C.S. and Lai, Y.H., 2020. Overexpression of SOX4 induces up-regulation of miR-126 and miR-195 in LNCaP prostate cancer cell line. Cytotechnology, pp.1-11.

    13. Phan, N.N., Li, K.L. and Lin, Y.C., 2018. Arsenic induces cardiac rhythm dysfunction and acylcarnitines metabolism perturbation in rats. Toxicol. Mech. Methods, 28(6), pp.423-431.

    14. Phan N.N, Lin YC. Arsenic Induced Adverse Effects on Cardiac Function in Sprague Dawley Rats. Asia-Pacific International Congress on Engineering and Natural Sciences. Taiwan. 2013 

    15. Phan N.N , C.-Y. Wang, and Y.-C. Lin, "The novel regulations of MEF2A, CAMKK2, CALM3, and TNNI3 in ventricular hypertrophy induced by arsenic exposure in rats," Toxicology, vol. 324, pp. 123-135, 2014.

    16. Huang, C.C., Tsai, Y.F., Liu, C.Y., Lien, P.J., Lin, Y.S., Chao, T.C., Feng, C.J., Chen, Y.J., Lai, J.I., Phan, N.N. and Hsu, C.Y., 2022. Prevalence of tumor genomic alterations in homologous recombination repair genes among Taiwanese breast cancers. Annals of Surgical Oncology, 29(6), pp.3578-3590.

    17. Do, D.T., Phan, N.N. (equal contribution), Wang, C.Y., Sun, Z. and Lin, Y.C., 2016. Novel regulations of MEF2-A, MEF2-D, and CACNA1S in the functional incompetence of adipose-derived mesenchymal stem cells by induced indoxyl sulfate in chronic kidney disease. Cytotechnology, 68(6), pp.2589-2604.

    18. Thuy, T.D., Phan, N.N.(equal contribution), Wang, C.Y., Yu, H.G., Wang, S.Y., Huang, P.L., Do, Y.Y. and Lin, Y.C., 2017. Novel therapeutic effects of sesamin on diabetes-induced cardiac dysfunction. Mol. Med. Rep., 15(5), pp.2949-2956.

    19. Wisesty, U.N., Purwarianti, A., Pancoro, A., Chattopadhyay, A., Phan, N.N., Chuang, E.Y. and Mengko, T.R., 2022. Join Classifier of Type and Index Mutation on Lung Cancer DNA using Sequential Labeling Model. IEEE Access.

    20. Chen, Y.J., Huang, C.S., Phan, N.N., Lu, T.P., Liu, C.Y., Huang, C.J., Chiu, J.H., Tseng, L.M. and Huang, C.C., 2021. Molecular subtyping of breast cancer intrinsic taxonomy with oligonucleotide microarray and NanoString nCounter. Bioscience reports, 41(8).

    21. C.-Y. Wang, M.-D. Lai, Phan N. N., Z. Sun, and Y.-C. Lin, "Meta-Analysis of Public Microarray Datasets Reveals Voltage-Gated Calcium Gene Signatures in Clinical Cancer Patients," PloS one, vol. 10, p. e0125766, 2015.

    22. Choy, T.K., Wang, C.Y., Phan, N.N., Khoa Ta, H.D., Anuraga, G., Liu, Y.H., Wu, Y.F., Lee, K.H., Chuang, J.Y. and Kao, T.J., 2021. Identification of Dipeptidyl Peptidase (DPP) family genes in clinical breast cancer patients via an integrated bioinformatics approach. Diagnostics, 11(7), p.1204.

    23. Anuraga, G., Tang, W.C., Phan, N.N., Ta, H.D.K., Liu, Y.H., Wu, Y.F., Lee, K.H. and Wang, C.Y., 2021. Comprehensive Analysis of Prognostic and Genetic Signatures for General Transcription Factor III (GTF3) in clinical colorectal cancer patients using bioinformatics approaches. Current Issues in Molecular Biology, 43(1), pp.2-20.

    24. Khoa Ta, H.D., Tang, W.C., Phan, N.N., Anuraga, G., Hou, S.Y., Chiao, C.C., Liu, Y.H., Wu, Y.F., Lee, K.H. and Wang, C.Y., 2021. Analysis of LAGEs family gene signature and prognostic relevance in breast cancer. Diagnostics, 11(4), p.726.

    25. Ta, H.D.K., Wang, W.J., Phan, N.N., An Ton, N.T., Anuraga, G., Ku, S.C., Wu, Y.F., Wang, C.Y. and Lee, K.H., 2021. Potential therapeutic and prognostic values of lsm family genes in breast cancer. Cancers, 13(19), p.4902.

    26. Anuraga, G., Wang, W.J., Phan, N.N., An Ton, N.T., Ta, H.D.K., Berenice Prayugo, F., Minh Xuan, D.T., Ku, S.C., Wu, Y.F., Andriani, V. and Athoillah, M., 2021. Potential prognostic biomarkers of nima (Never in mitosis, gene a)-related kinase (nek) family members in breast cancer. Journal of personalized medicine, 11(11), p.1089.

    27. Chiao, C.C., Liu, Y.H., Phan, N.N., An Ton, N.T., Ta, H.D.K., Anuraga, G., Minh Xuan, D.T., Fitriani, F., Putri Hermanto, E.M., Athoillah, M. and Andriani, V., 2021. Prognostic and genomic analysis of proteasome 20s subunit alpha (PSMA) family members in breast cancer. Diagnostics, 11(12), p.2220.

    28. Wang, C.Y., Shahi, P., Huang, J.T.W., Phan, N.N., Sun, Z., Lin, Y.C., Lai, M.D. and Werb, Z., 2017. Systematic analysis of the achaete-scute complex-like gene signature in clinical cancer patients. Molecular and clinical oncology, 6(1), pp.7-18.

    29. Yeh, C.C., Luo, J.L., Phan, N.N., Cheng, Y.C., Chow, L.P., Tsai, M.H., Chuang, E.Y. and Lai, L.C., 2018. Different effects of long noncoding RNA NDRG1-OT1 fragments on NDRG1 transcription in breast cancer cells under hypoxia. RNA biology, 15(12), pp.1487-1498.

    30. Wang, C.Y., Chang, Y.C., Kuo, Y.L., Lee, K.T., Chen, P.S., Cheung, C.H.A., Chang, C.P., Phan, N.N., Shen, M.R. and Hsu, H.P., 2019. Mutation of the PTCH1 gene predicts recurrence of breast cancer. Sci. Rep., 9(1), pp.1-14.

    31. Wu, Y.H., Yeh, I.J., Phan, N.N., Yen, M.C., Hung, J.H., Chiao, C.C., Chen, C.F., Sun, Z., Hsu, H.P., Wang, C.Y. and Lai, M.D., 2021. Gene signatures and potential therapeutic targets of Middle East respiratory syndrome coronavirus (MERS-CoV)-infected human lung adenocarcinoma epithelial cells. Journal of Microbiology, Immunology and Infection, 54(5), pp.845-857.

    32. Wang, C.Y., Chiao, C.C., Phan, N.N., Li, C.Y., Sun, Z.D., Jiang, J.Z., Hung, J.H., Chen, Y.L., Yen, M.C., Weng, T.Y. and Chen, W.C., 2020. Gene signatures and potential therapeutic targets of amino acid metabolism in estrogen receptor-positive breast cancer. American journal of cancer research, 10(1), p.95.

    33. Lin, Y.Y., Wang, C.Y., Phan, N.N., Chiao, C.C., Li, C.Y., Sun, Z., Hung, J.H., Chen, Y.L., Yen, M.C., Weng, T.Y. and Hsu, H.P., 2020. PODXL2 maintains cellular stemness and promotes breast cancer development through the Rac1/Akt pathway. Int. J. Med. Sci., 17(11), p.1639.

    34. Cheng, L.C., Chao, Y.J., Overman, M.J., Wang, C.Y., Phan, N.N., Chen, Y.L., Wang, T.W., Hsu, H.P., Shan, Y.S. and Lai, M.D., 2020. Increased expression of secreted frizzled related protein 1 (SFRP1) predicts ampullary adenocarcinoma recurrence. Sci. Rep., 10(1), pp.1-16.

    35. P.-A. Hwang, Y.-L. Hung, N. N. Phan, P.-M. Chang, K.-L. Li, and Y.-C. Lin, "The in vitro and in vivo effects of the low molecular weight fucoidan on the bone osteogenic differentiation properties," Cytotechnology, pp. 1-11, 2015. 

    36. Kao, T.J., Wu, C.C., Phan, N.N., Liu, Y.H., Ta, H.D.K., Anuraga, G., Wu, Y.F., Lee, K.H., Chuang, J.Y. and Wang, C.Y., 2021. Prognoses and genomic analyses of proteasome 26S subunit, ATPase (PSMC) family genes in clinical breast cancer. Aging (Albany NY), 13(14), p.17970.

    37. Wang, C.Y., Chao, Y.J., Chen, Y.L., Wang, T.W., Phan, N.N., Hsu, H.P., Shan, Y.S. and Lai, M.D., 2021. Upregulation of peroxisome proliferator-activated receptor-α and the lipid metabolism pathway promotes carcinogenesis of ampullary cancer. International journal of medical sciences, 18(1), p.256.

    38. Wu, C.C., Ekanem, T.I., Phan, N.N., Loan, D.T.T., Hou, S.Y., Lee, K.H. and Wang, C.Y., 2020. Gene signatures and prognostic analyses of the Tob/BTG pituitary tumor-transforming gene (PTTG) family in clinical breast cancer patients. International journal of medical sciences, 17(18), p.3112.

    39. Lin, Y.Y., Wang, C.Y., Phan, N.N., Chiao, C.C., Li, C.Y., Sun, Z., Hung, J.H., Chen, Y.L., Yen, M.C., Weng, T.Y. and Hsu, H.P., 2020. PODXL2 maintains cellular stemness and promotes breast cancer development through the Rac1/Akt pathway. International journal of medical sciences, 17(11), p.1639.

    40. Wu, Y.H., Yeh, I.J., Phan, N.N., Yen, M.C., Liu, H.L., Wang, C.Y. and Hsu, H.P., 2021. Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infection induces dysregulation of immunity: In silico gene expression analysis. International journal of medical sciences, 18(5), p.1143.

    41. Chen, P.S., Hsu, H.P., Phan, N.N., Yen, M.C., Chen, F.W., Liu, Y.W., Lin, F.P., Feng, S.Y., Cheng, T.L., Yeh, P.H. and Omar, H.A., 2021. CCDC167 as a potential therapeutic target and regulator of cell cycle-related networks in breast cancer. Aging (Albany NY), 13(3), p.4157.

    42. Xie, Q., Shen, K.N., Hao, X., Phan N.N., Ngoc Hieu, B.T., Chen, C.H., Zhu, C., Lin, Y.C. and Hsiao, C.D., 2017. The complete chloroplast genome of Tianshan snow lotus (Saussurea involucrata), a famous traditional Chinese medicinal plant of the family Asteraceae. Mitochondrial DNA, 28(2), pp.294-295.

    43. Q.T Dang and N.N. Phan, “Optimization of supercritical CO2 extraction of oleoresin from black pepper (Piper nigrum L.) and antioxidant capacity of the oleoresin,” Int. Food Res. J., vol 21(4), pp. 1489-1493, 2014.

    44. Hwang, P.A., Phan, N.N., Lu, W.J., Hieu, B.T.N. and Lin, Y.C., 2016. Low-molecular-weight fucoidan and high-stability fucoxanthin from brown seaweed exert prebiotics and anti-inflammatory activities in Caco-2 cells. J. Food Nutr. Res, 60(1), p.32033.

    45. Hwang, P.A., Yan, M.D., Kuo, K.L., Phan, N.N. and Lin, Y.C., 2017. A mechanism of low molecular weight fucoidans degraded by enzymatic and acidic hydrolysis for the prevention of UVB damage. J. Appl. Phycol, 29(1), pp.521-529.

    46. Jiang, J. H., Ho, J., Phan, N. N., Tian, D. T., Do, T. D., Chang, H., & Lin, Y. C. (2013). “Inhibition of Src kinase activity reduces heart rate with slight alteration of heart rate variability”. The FASEB Journal, 27(1_MeetingAbstracts), 706-1.

    47. CH Tsai, Phan N.N and Yen -Chang Lin, 2017. Fucoidan and Fucoxanthin Ameliorate Cardiac Function of Aging Canine. Asian J Anim Vet Adv, 12: 294-301.

    48. Cheng, L.C., Kao, T.J., Phan, N.N., Chiao, C.C., Yen, M.C., Chen, C.F., Hung, J.H., Jiang, J.Z., Sun, Z., Wang, C.Y. and Hsu, H.P., 2021. Novel signaling pathways regulate SARS-CoV and SARS-CoV-2 infectious disease. Medicine, 100(7).

    49. Wu, S.Y., Phan, N.N., Ho, S.H., Lai, Y.H., Tsai, C.H., Yang, C.H., Yu, H.G., Wang, J.C., Huang, P.L. and Lin, Y.C., 2018. Metabolomic assessment of arsenite toxicity and novel biomarker discovery in early development of zebrafish embryos. Toxicol. Lett., 290, pp.116-122.

    50. Dang QT, P.N.N. Optimization of supercritical CO2 extraction   of oleoresin from black pepper (Piper nigrum L.) and antioxidant capacity of the oleoresin. 13th ASEAN Food Conference, Meeting Future Food Demands: Security & Sustainability. Singapore. 2013