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Zhiyuan Hu

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Single-Cell Analysis, Ovarian Cancer, Genomics

I am an Oxford CSC-NDM Prize student with Chris Holmes, Christopher Yau and Ahmed Ahmed at the Wellcome Trust Centre for Human Genetics and at the MRC Weatherall Institute of Molecular Medicine at the University of Oxford.

I am working on single cell methods for understanding ovarian cancer. I also work on computational methods for understanding the role of nonsense mediated decay in cancer.

Publications

2020

• Z. Hu , R. J. Evans , Faster algorithms for Markov equivalence, in Proceedings of the 36th Conference on Uncertainty in Artificial Intelligence (UAI-20), 2020, vol. 2020.
  

  @inproceedings{hu20,
    author = {Hu, Z. and Evans, R. J.},
    title = {Faster algorithms for {M}arkov equivalence},
    booktitle = {Proceedings of the 36th Conference on Uncertainty in Artificial Intelligence (UAI-20)},
    volume = {2020},
    year = {2020}
  }
  

2017

• Z. Hu , C. Yau , A. A. Ahmed , A pan-cancer genome-wide analysis reveals tumour dependencies by induction of nonsense-mediated decay, Nature communications, vol. 8, 15943, Jun. 2017.
  
  Nonsense-mediated decay (NMD) eliminates transcripts with premature termination codons. Although NMD-induced loss-of-function has been shown to contribute to the genesis of particular cancers, its global functional consequence in tumours has not been characterized. Here we develop an algorithm to predict NMD and apply it on somatic mutations reported in The Cancer Genome Atlas. We identify more than 73 K mutations that are predicted to elicit NMD (NMD-elicit). NMD-elicit mutations in tumour suppressor genes (TSGs) are associated with significant reduction in gene expression. We discover cancer-specific NMD-elicit signatures in TSGs and cancer-associated genes. Our analysis reveals a previously unrecognized dependence of hypermutated tumours on hypofunction of genes that are involved in chromatin remodelling and translation. Half of hypermutated stomach adenocarcinomas are associated with NMD-elicit mutations of the translation initiators LARP4B and EIF5B. Our results unravel strong therapeutic opportunities by targeting tumour dependencies on NMD-elicit mutations.

  @article{Hu:2017bra,
    author = {Hu, Zhiyuan and Yau, Christopher and Ahmed, Ahmed Ashour},
    title = {{A pan-cancer genome-wide analysis reveals tumour dependencies by induction of nonsense-mediated decay}},
    journal = {Nature communications},
    year = {2017},
    volume = {8},
    pages = {15943},
    month = jun
  }