Publications

Chang, Y. C., Yang, S. H., Hsieh, T. T., Wu, C. Y., Lee, K. H., Lai, H. C., Lin, S. S., Chang, P. H., Wen, C. T., Chen, L. C., Su, Y. L., Chen, H. L., Chou, M. H., Liu, C. W., Hsieh, P. H., & Hsieh, J. C. H. (2026). Pre-analytical Stability-Driven Circulating miRNA Biomarkers and Multi-center LDCT Integration for Robust Lung Cancer Early Detection. Manuscript submitted.

Hsieh, P. H., Wu, C. Y., Hsieh, T. T., Lai, H. C., Lin, S. S., Lee, K. H., Yang, S. H., Chian, C. F., Wen, C. T., Chen, L. C., Chang, P. H., Su, Y. L., Kuo, Y. L., Chou, P. C., Hung, J. Y., Lu, Y. J., Chen, H. L., Chou, M. H., Liu, C. W., Chang, Y. C., & Hsieh, J. C. H. (2026). Multi-Institutional Integration of Circulating miRNAs and Protein Tumor Markers for Early Lung Cancer Detection. JTO Clinical and Research Reports, 7, 101051. https://doi.org/10.1016/j.jtocrr.2026.101051

Pop, R. T., Hsieh, P. H., Belova, T., Mathelier, A., & Kuijjer, M. L. (2025). Gene regulatory network integration with multi-omics data enhances survival predictions in cancer. Briefings in Bioinformatics, 26(4), bbaf315. https://doi.org/10.1093/bib/bbaf315

Struck, E. C., Belova, T., Hsieh, P. H., Odeberg, J. O., Kuijjer, M. L., Dusart, P. J., & Butler, L. M. (2024). Global transcriptome analysis reveals distinct phases of the endothelial response to TNF. The Journal of Immunology, 212(1), 117-129. https://doi.org/10.4049/jimmunol.2300351

Hsieh, P. H., Lopes-Ramos, C. M., Zucknick, M., Sandve, G. K., Glass, K., & Kuijjer, M. L. (2023). Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data. Bioinformatics, 39(10), btad610. https://doi.org/10.1093/bioinformatics/btad610

Belova, T., Biondi, N., Hsieh, P. H., Lutsik, P., Chudasama, P., & Kuijjer, M. L. (2023). Heterogeneity in the gene regulatory landscape of leiomyosarcoma. NAR Cancer, 5(3), zcad037. https://doi.org/10.1093/narcan/zcad037

Pavlović, M., Scheffer, L., Motwani, K., Kanduri, C., Kompova, R., Vazov, N., Waagan, K., Bernal, F. L. M., Costa, A. A., Corrie, B., Akbar, R., Al Hajj, G. S., Balaban, G., Brusko, T. M., Chernigovskaya, M., Christley, S., Cowell, L. G., Frank, R., Grytten, I., Gundersen, S., Haff, I. H., Hovig, E., Hsieh, P. H., Klambauer, G., Kuijjer, M. L., Lund-Andersen, C., Martini, A., Minotto, T., Pensar, J., Rand, K., Riccardi, E., Robert, P. A., Rocha, A., Slabodkin, A., Snapkov, I., Sollid, L. M., Titov, D., Weber, C. R., Widrich, M., Yaari, G., Greiff, V., & Sandve, G. K. (2021). The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires. Nature Machine Intelligence, 3(11), 936-944. https://doi.org/10.1038/s42256-021-00413-z

Chang, Y. C., Wu, J. T., Hong, M. Y., Tung, Y. A., Hsieh, P. H., Yee, S. W., Kathleen, M. G., Oyang, Y. J., Chen, C. Y., & Alzheimer’s Disease Neuroimaging Initiative. (2020). GenEpi: gene-based epistasis discovery using machine learning. BMC Bioinformatics, 21(1), 68. https://doi.org/10.1186/s12859-020-3368-2

Kuijjer, M. L., Hsieh, P. H., Quackenbush, J., & Glass, K. (2019). lionessR: single sample network inference in R. BMC Cancer, 19(1), 1003. https://doi.org/10.1186/s12885-019-6235-2

Hsieh, P. H., Oyang, Y. J., & Chen, C. Y. (2019). Effect of de novo transcriptome assembly on quality of read mapping and transcript quantification. Scientific Reports, 9(1), 8304. https://doi.org/10.1038/s41598-019-44499-3

Lee, C. Y., Hsieh, P. H., Chiang, L. M., Chattopadhyay, A., Li, K. Y., Lee, Y. F., Lu, T. P., Lai, L. C., Lin, E. C., Lee, H. Y., Ding, S. T., Tsai, M. H., Chen, C. Y., & Chuang, E. Y. (2018). Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant. GigaScience, 7(5), giy044. https://doi.org/10.1093/gigascience/giy044

Keller, A., Gerkin, R. C., Guan, Y., Dhurandhar, A., Turu, G., Szalai, B., Mainland, J. D., Ihara, Y., Yu, C. W., Wolfinger, R., Vens, C., Schietgat, L., Grave, K. D., Norel, R., Dream Olfaction Prediction Consortium, Stolovitzky, G., Cecchi, G. A., Vosshall, L. B., & Meyer, P. (2017). Predicting human olfactory perception from chemical features of odor molecules. Science, 355(6327), 820-826. https://doi.org/10.1126/science.aal2014

Palomino-Echeverria, S., Junquera, A., Falco, M. M., Elomaa, H., Belova, T., Pajanoja, C., Chen, W., Dai, J., Hsieh, P. H., Vähärautio, A., Färkkilä, A., & Kuijjer, M. L. (2026). Hierarchical integration of spatial transcriptomics and proteomics reveals tumor clusters in HGSC. Poster presentation. ECCB 2026. Geneva, Switzerland.

Pajanoja, C., Hsieh, P. H., Belova, T., & Kuijjer, M. L. (2026). Towards stable clustering in hierarchical variational autoencoder models for multi-omics cancer data integration. Poster presentation. ECCB 2026. Geneva, Switzerland.

Belova, T., Hsieh, P. H., Hovan, L., Osorio, D., & Kuijjer, M. L. (2026). Large-scale single-sample regulatory network inference across 9778 tumors uncovers clinically relevant heterogeneity. Poster presentation ECCB 2026. Geneva, Switzerland.

Hsieh, P. H., Hsiao, R. X., Belova, T., Ference, K., Mathelier, A., Burkholz, R., Chen, C. Y., Sandve, G. K., & Kuijjer, M. L. (2022, November). Using hierarchical variational autoencoders to incorporate conditional independent priors for paired single-cell multi-omics data integration Poster/Paper presentation. NeurIPS 2022 Workshop on Learning Meaningful Representations of Life, New Orleans, LA, United States.

Hsieh, P. H., Lopes-Ramos, C. M., Glass, K., & Kuijjer, M. L. (2019). Correlation adjustment to improve the modeling of association-based networks. Poster presentation. 2019 EMBL Partnership Conference. Heidelberg, Germany.

Lin, K. T., Lee, C. Y., Hsieh, P. H., Lu, T. P., Lai, L. C., Ding, S. T., Chen, C. Y., Chuang, E. Y., & Tsai, M. H. (2018). Whole-genome de novo assembly and adaptive evolution of the Swinhoe’s pheasant. Poster presentation. ICIBM 2018. Los Angeles, California, USA.

Hsieh, P. H., Oyang, Y. J., & Chen, C. Y. (2017). Effects of de novo transcriptome assembly on quality of read mapping and transcript quantification. Poster presentation. ISMB/ECCB 2017. Prague, Czech Republic.

Hsieh, P. H., Wang, W. T., Wang, H., Huang, W. J., Oyang, Y. J., & Chen, C. Y. (2016). Investigating the effect of similar subsequences present in assembled transcripts on RNA-seq quantification for non-model organisms. Poster presentation. ECCB 2016. The Hague, Netherlands.

Hsieh, P. H., Cherng, B. W., Chang, Y. C., Hong, M. Y., Tung, Y. A., Oyang, Y. J., & Chen, C. Y. (2016). A two-layer predictor for DREAM 9.5 olfaction prediction. Poster presentation. RECOMB 2016. Santa Monica, California, USA.