USC.edu

Tsu-Pei Chiu

Assistant Professor (Teaching) of Quantitative and Computational Biology
Tsu-Pei Chiu
Email tsupeich@usc.edu Office RRI 413J

Biography

My teaching centers on the intersection of Artificial Intelligence (AI) and Machine Learning (ML) with Biology and Medicine through both foundational and advanced concepts. From classic neural networks to the latest in attention mechanisms, transformers, and generative AI, my courses offer a comprehensive exploration of how these technologies can be applied to solve complex biological and medical problems. I also teach essential topics in data structures, algorithms, and computational structural biology.

In my research, I focus on unraveling gene regulatory mechanisms, particularly how transcription factors recognize their DNA binding sites. To bridge the gap between genomics and structural biology, I’ve developed multiple computational tools, detailed in my publications. These tools are instrumental in enhancing our ability to analyze sequencing data, contributing to a deeper understanding of disease mechanisms and potential therapeutic approaches.

  • Summary Statement of Research Interests

    Computational structural biology; statistical machine learning; AI and deep learning; high-throughput prediction of DNA shape; genome-wide analysis of sequence and structure

    • (Spring 2024) QBIO 401. Introduction to Computational Analysis of Biological Data, TTh, 09:30am – 10:50am, RRI 421
    • (Spring 2024) QBIO 499. Special Topics – AI and Machine Learning in Biology and Medicine, TTh, 12:30pm – 01:50pm, RRI 421
    • (Fall 2024) QBIO 460. Introduction to Machine Learning in Biology, MW, 02:00pm – 03:20pm, RRI301
    • (Fall 2024) QBIO 481. Structural Bioinformatics: From Atoms to Cells, TTh, 11:00am – 12:20pm, RRI101
    • (Fall 2024) QBIO 570. Data Structures and Algorithms for the Sciences, MW, 10:00am – 11:20am, RRI301

  • Journal Article

    • Mitra, R., Li, J., Sagendorf, J. M., Jiang, Y., Cohen, A. S., Chiu, T. P., Glasscock, C. J., Rohs, R. (2024). Geometric deep learning of protein-DNA binding specificity. Nature methods. PubMed Web Address
    • Bonnell, V. A., Zhang, Y., Brown, A. S., Horton, J., Josling, G. A., Chiu, T. P., Rohs, R., Mahony, S., Gordân, R., Llinás, M. (2024). DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum. Nucleic acids research. PubMed Web Address
    • Li, J., Chiu, T. P., Rohs, R. (2024). Predicting DNA structure using a deep learning method. Nature communications. Vol. 15 (1), pp. 1243. PubMed Web Address
    • Jiang, Y., Chiu, T. P., Mitra, R., Rohs, R. (2024). Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox-DNA binding. Biophysical journal. Vol. 123 (2), pp. 248-259. PubMed Web Address
    • Chiu, T. P., Rao, S., Rohs, R. (2023). Physicochemical models of protein-DNA binding with standard and modified base pairs. Proceedings of the National Academy of Sciences of the United States of America. Vol. 120 (4), pp. e2205796120. PubMed Web Address
    • Cooper, B. H., Chiu, T. P., Rohs, R. (2022). Top-Down Crawl: a method for the ultra-rapid and motif-free alignment of sequences with associated binding metrics. Bioinformatics (Oxford, England). Vol. 38 (22), pp. 5121-5123. PubMed Web Address
    • Chiu, T. P., Li, J., Jiang, Y., Rohs, R. (2022). It is in the flanks: Conformational flexibility of transcription factor binding sites. Biophysical journal. Vol. 121 (20), pp. 3765-3767. PubMed Web Address
    • Li, Y., Zhu, Y., Feng, S., Ishida, Y., Chiu, T. P., Saito, T., Wang, S., Ann, D. K., Ou, J. J. (2022). Macrophages activated by hepatitis B virus have distinct metabolic profiles and suppress the virus via IL-1β to downregulate PPARα and FOXO3. Cell reports. Vol. 40 (1), pp. 111068. PubMed Web Address
    • Wu, X., Cao, B., Aquino, P., Chiu, T. P., Chen, C., Jiang, S., Deng, Z., Chen, S., Rohs, R., Wang, L., Galagan, J. E., Dedon, P. C. (2020). Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria. Proceedings of the National Academy of Sciences of the United States of America. Vol. 117 (25), pp. 14322-14330. PubMed Web Address
    • Chiu, T. P., Xin, B., Markarian, N., Wang, Y., Rohs, R. (2020). TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites. Nucleic acids research. Vol. 48 (D1), pp. D246-D255. PubMed Web Address
    • Azad, R. N., Zafiropoulos, D., Ober, D., Jiang, Y., Chiu, T. P., Sagendorf, J. M., Rohs, R., Tullius, T. D. (2018). Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations. Nucleic acids research. Vol. 46 (5), pp. 2636-2647. PubMed Web Address
    • Rao, S., Chiu, T. P., Kribelbauer, J. F., Mann, R. S., Bussemaker, H. J., Rohs, R. (2018). Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein-DNA binding. Epigenetics & chromatin. Vol. 11 (1), pp. 6. PubMed Web Address
    • Li, J., Sagendorf, J. M., Chiu, T. P., Pasi, M., Perez, A., Rohs, R. (2017). Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding. Nucleic acids research. Vol. 45 (22), pp. 12877-12887. PubMed Web Address
    • Chiu, T. P., Rao, S., Mann, R. S., Honig, B., Rohs, R. (2017). Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding. Nucleic acids research. Vol. 45 (21), pp. 12565-12576. PubMed Web Address
    • Mathelier, A., Xin, B., Chiu, T. P., Yang, L., Rohs, R., Wasserman, W. W. (2016). DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo. Cell systems. Vol. 3 (3), pp. 278-286.e4. PubMed Web Address
    • Chiu, T. P., Comoglio, F., Zhou, T., Yang, L., Paro, R., Rohs, R. (2016). DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding. Bioinformatics (Oxford, England). Vol. 32 (8), pp. 1211-3. PubMed Web Address
    • Deng, Z., Wang, Q., Liu, Z., Zhang, M., Machado, A. C., Chiu, T. P., Feng, C., Zhang, Q., Yu, L., Qi, L., Zheng, J., Wang, X., Huo, X., Qi, X., Li, X., Wu, W., Rohs, R., Li, Y., Chen, Z. (2015). Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator. Nature communications. Vol. 6, pp. 7642. PubMed Web Address
    • Chiu, T. P., Yang, L., Zhou, T., Main, B. J., Parker, S. C., Nuzhdin, S. V., Tullius, T. D., Rohs, R. (2015). GBshape: a genome browser database for DNA shape annotations. Nucleic acids research. Vol. 43 (Database issue), pp. D103-9. PubMed Web Address
    • Fang, H. Y., Wang, H. M., Chang, K. F., Hu, H. T., Hwang, L. J., Fu, T. F., Lin, Y. C., Chang, W. C., Chiu, T. P., Wen, Z. H., Fong, Y., Chiu, C. C., Chen, B. H. (2013). Feruloyl-L-arabinose attenuates migration, invasion and production of reactive oxygen species in H1299 lung cancer cells. Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association. Vol. 58, pp. 459-66. PubMed Web Address
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