Please use this identifier to cite or link to this item: https://ah.lib.nccu.edu.tw/handle/140.119/136968
題名: 以資料分析和機器學習用於HiChIP解析T細胞衰竭機制
Using HiChIP investigate T Cell exhaustion by data analysis and machine learning
作者: 楊明翰
Yang, Ming-Han
貢獻者: 張家銘
Chang, Jia-Ming
楊明翰
Yang, Ming-Han
關鍵詞: 染色體構象捕獲
T細胞衰竭
T cell exhaustion
Hi-C
HiChIP
T cell exhaustion
Hi-C
HiChIP
日期: 2021
上傳時間: 2-Sep-2021
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Pan-Cancer Analysis Reveals Disrupted Circadian Clock Associates With T Cell Exhaustion. Frontiers In Immunology, 10. doi: 10.3389/fimmu.2019.02451\n\nKim, Y., Marhon, S., Zhang, Y., Steger, D., Won, K., & Lazar, M. (2018). Rev-erbα dynamically modulates chromatin looping to control circadian gene transcription. Science, 359(6381), 1274-1277. doi: 10.1126/science.aao6891\n\nLiang, C., Huang, S., Zhao, Y., Chen, S., & Li, Y. (2021). TOX as a potential target for immunotherapy in lymphocytic malignancies. Biomarker Research, 9(1). doi: 10.1186/s40364-021-00275-y\n\nLieberman-Aiden, E., van Berkum, N., Williams, L., Imakaev, M., Ragoczy, T., & Telling, A. et al. (2009). Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science, 326(5950), 289-293. doi: 10.1126/science.1181369\n\nRobertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., & Zeng, T. et al. (2007). 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Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Nature, 511(7510), 428-434. doi: 10.1038/nature13379\n\nZimmerman, M., Liu, Y., He, S., Durbin, A., Abraham, B., & Easton, J. et al. (2017). MYC Drives a Subset of High-Risk Pediatric Neuroblastomas and Is Activated through Mechanisms Including Enhancer Hijacking and Focal Enhancer Amplification. Cancer Discovery, 8(3), 320-335. doi: 10.1158/2159-8290.cd-17-0993\n\nBhattacharyya, S., Chandra, V., Vijayanand, P., & Ay, F. (2019). Identification of significant chromatin contacts from HiChIP data by FitHiChIP. Nature Communications, 10(1). doi: 10.1038/s41467-019-11950-y\n\nLareau, C., & Aryee, M. (2017). hichipper: A preprocessing pipeline for assessing library quality and DNA loops from HiChIP data. doi: 10.1101/192302\n\nAnders, S., & Huber, W. (2010). Differential expression analysis for sequence count data. Genome Biology, 11(10). doi: 10.1186/gb-2010-11-10-r106\n\nZhi, D. (2019). Gene2vec: distributed representation of genes based on co-expression. BMC Genomics, 20(S1). doi: 10.1186/s12864-018-5370-x\n\n\nZufferey, M., Tavernari, D., Oricchio, E., & Ciriello, G. (2018). Comparison of computational methods for the identification of topologically associating domains. Genome Biology, 19(1). doi: 10.1186/s13059-018-1596-9\n\nLazaris, C., Kelly, S., Ntziachristos, P., Aifantis, I., & Tsirigos, A. (2017). HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking. BMC Genomics, 18(1). doi: 10.1186/s12864-016-3387-6\n\nSanders, J., Freeman, T., Xu, Y., Golloshi, R., Stallard, M., & Hill, A. et al. (2020). Radiation-induced DNA damage and repair effects on 3D genome organization. Nature Communications, 11(1). doi: 10.1038/s41467-020-20047-w\n\nDylan Skola (2018).python-genome-browser. Github,from https://github.com/phageghost/python-genome-browser\n\nKnight, P., & Ruiz, D. (2012). A fast algorithm for matrix balancing. IMA Journal Of Numerical Analysis, 33(3), 1029-1047. doi: 10.1093/imanum/drs019\n\nMumbach, M., Satpathy, A., Boyle, E., Dai, C., Gowen, B., & Cho, S. et al. (2017). Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements. Nature Genetics, 49(11), 1602-1612. doi: 10.1038/ng.3963\n\nQuinlan, A., & Hall, I. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26(6), 841-842. doi: 10.1093/bioinformatics/btq033\n\nChen, Z., Ji, Z., Ngiow, S., Manne, S., Cai, Z., & Huang, A. et al. (2019). TCF-1-Centered Transcriptional Network Drives an Effector versus Exhausted CD8 T Cell-Fate Decision.\nImmunity, 51(5), 840-855.e5. doi: 10.1016/j.immuni.2019.09.013\n\nIm, S., Hashimoto, M., Gerner, M., Lee, J., Kissick, H., & Burger, M. et al. (2016). Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy. Nature, 537(7620), 417-421. doi: 10.1038/nature19330\n\nSanders, J., Freeman, T., Xu, Y., Golloshi, R., Stallard, M., & Hill, A. et al. (2020). Radiation-induced DNA damage and repair effects on 3D genome organization. Nature Communications, 11(1). doi: 10.1038/s41467-020-20047-w\n\nBlank, C., Haining, W., Held, W., Hogan, P., Kallies, A., & Lugli, E. et al. (2019). Defining ‘T cell exhaustion’. Nature Reviews Immunology, 19(11), 665-674. doi: 10.1038/s41577-019-0221-9
描述: 碩士
國立政治大學
資訊科學系
108753203
資料來源: http://thesis.lib.nccu.edu.tw/record/#G0108753203
資料類型: thesis
Appears in Collections:學位論文

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