Publications, Software & Data

Publications, open-source software, and datasets.

Publications

  1. Ping, Z., Chen, S., Zhou, G., Huang, X., Zhu, S. J., Zhang, H., Lee, H. H., Lan, Z., Cui, J., Chen, T., Zhang, W., Yang, H., Xu, X., Church, G. M., & Shen, Y. (2022). Towards practical and robust DNA-based data archiving using the yin–yang codec system. Nature Computational Science, 2(4), 234–242. https://doi.org/10.1038/s43588-022-00231-2
  2. Baumdicker, F., Bisschop, G., Goldstein, D., Gower, G., Ragsdale, A. P., Tsambos, G., Zhu, S. J., Eldon, B., Ellerman, C. E., Galloway, J. G., Gladstein, A. L., Gorjanc, G., Guo, B., Jeffery, B., Kretzschmar, W. W., Lohse, K., Matschiner, M., Nelson, D., Pope, N. S., Quinto-Cortés, C. D., Rodrigues, M. F., Saunack, K., Sellinger, T., Thornton, K., van Kemenade, H., Wohns, A. W., Wong, H. Y., Gravel, S., Kern, A. D., Koskela, J., Ralph, P. L., & Kelleher, J. (2022). Efficient ancestry and mutation simulation with msprime 1.0. Genetics, 220(3). https://doi.org/10.1093/genetics/iyab229
  3. Cole, C. B., Zhu, S. J., Mathieson, I., Prufer, K., & Lunter, G. (2020). Ancient admixture into Africa from the ancestors of non-Africans. bioRxiv. https://doi.org/10.1101/2020.06.01.127555
  4. Baumdicker, F., Bisschop, G., Goldstein, D., Gower, G., Ragsdale, A. P., Tsambos, G., Zhu, S. J., … Kelleher, J. (2021). Efficient ancestry and mutation simulation with msprime 1.0. bioRxiv. https://doi.org/10.1101/2021.08.31.457499
  5. Henderson, D., Zhu, S. J., Cole, C. B., & Lunter, G. (2021). Demographic inference from multiple whole genomes using a particle filter for continuous Markov jump processes. PLOS ONE, 16(3), 1–24. https://doi.org/10.1371/journal.pone.0247647
  6. 平质, 张颢龄, 陈世宏, 倪鸣, 徐讯, 朱砂, & 沈玥. (2021). Chamaeleo：DNA存储碱基编解码算法的可拓展集成与系统评估平台. 合成生物学, 2(3), 412. https://doi.org/10.12211/2096-8280.2020-083
  7. Ping, Z., Ma, D., Huang, X., Chen, S., Liu, L., Guo, F., Zhu, S. J., & Shen, Y. (2019). Carbon-based archiving: current progress and future prospects of DNA-based data storage. GigaScience, 8(6). https://doi.org/10.1093/gigascience/giz075
  8. Zhu, S. J., Hendry, J. A., Almagro-Garcia, J., Pearson, R. D., Amato, R., Miles, A., Weiss, D. J., Lucas, T. C. D., Nguyen, M., Gething, P. W., Kwiatkowski, D., & McVean, G. (2019). The origins and relatedness structure of mixed infections vary with local prevalence of P. falciparum malaria. eLife, 8, e40845. https://doi.org/10.7554/eLife.40845
  9. Zhu, S. J., Almagro-Garcia, J., & McVean, G. (2018). Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data. Bioinformatics, 34(1), 9–15. https://doi.org/10.1093/bioinformatics/btx530
  10. Staab, P. R., Zhu, S. J., Metzler, D., & Lunter, G. (2015). scrm: efficiently simulating long sequences using the approximated coalescent with recombination. Bioinformatics, 31(10), 1680–1682. https://doi.org/10.1093/bioinformatics/btu861
  11. Zhu, S. J., Degnan, J. H., & Steel, M. (2011). Clades, clans, and reciprocal monophyly under neutral evolutionary models. Theoretical Population Biology, 79(4), 220–227. https://doi.org/10.1016/j.tpb.2011.03.002
  12. Zhu, S. J., Degnan, J. H., Goldstien, S. J., & Eldon, B. (2015). Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. BMC Bioinformatics, 16(1), 292. https://doi.org/10.1186/s12859-015-0721-y
  13. Zhu, S. J., & Steel, M. (2013). Does random tree puzzle produce Yule–Harding trees in the many-taxon limit? Mathematical Biosciences, 243(1), 109–116. https://doi.org/10.1016/j.mbs.2013.02.003
  14. Zhu, S. J., & Degnan, J. H. (2017). Displayed trees do not determine distinguishability under the network multispecies coalescent. Systematic Biology, 66(2), 283–298. https://doi.org/10.1093/sysbio/syw097
  15. Zhu, S. J., Than, C., & Wu, T. (2015). Clades and clans: a comparison study of two evolutionary models. Journal of Mathematical Biology, 71(1), 99–124. https://doi.org/10.1007/s00285-014-0817-4
  16. Yu, G. Z., Reilly, S., Lewandowski, A. J., Aye, C. Y. L., Simpson, L. J., Newton, L. D., Davis, E. F., Zhu, S. J., Fox, W. R., Goel, A., Watkins, H., Channon, K. M., Watt, S. M., Kyriakou, T., & Leeson, P. (2018). Neonatal MicroRNA profile determines endothelial function in offspring of hypertensive pregnancies. Hypertension, 72(4), 937–945.

Software

Tools that I have built and contributed to that you may also find useful.

autoslider. [R] The normal process of creating clinical study slides is that a statistician manually types in the numbers from outputs and a separate statistician double-checks them. This is time-consuming, resource-intensive, and error-prone. Automatic slide generation reduces the work and time required, and the risk of errors from manually copying numbers to slides.

formatters. [R] A framework for rendering complex tables to ASCII, and a set of formatters for transforming values or sets of values into ASCII-ready display strings.

rtables. [R] Reporting tables often have structure beyond simple rectangular data. rtables provides a framework for declaring complex multi-level tabulations and applying them to data, modelling both tabulation and the resulting tables as hierarchical, tree-like objects.

rtables.officer. [R] Supports export of rtables objects to Microsoft Office formats, including Word (docx) and PowerPoint (pptx).

rlistings. [R] A framework for the specific formatting features often used when displaying large datasets in clinical-trial submission listings.

tern. [R] Table, Listings, and Graphs (TLG) library for common outputs used in clinical trials.

teal.modules.clinical. [R] A set of standard teal modules to be used with CDISC data to generate many of the standard outputs used in clinical trials.

DEploid. [C++, R] Deconvolves mixed Plasmodium falciparum sequence data and reports the mixture proportions. An R version is available on CRAN.

Hybrid-Lambda. [C++] A simulation tool for the lambda coalescent of a given species network; the population structure (species tree/network) is expressed as a Newick string.

Hybrid-Coal. [C++] Computes gene tree probabilities given a species network under the coalescent process using dynamic programming.

smcsmc. [C++] Infers demographic events and rates from multiple-sample whole-genome sequence data.

scrm. [C++] A Kingman coalescent simulator suitable for large-scale whole-genome sequence simulations.

Chamaeleo. [Python] A collection focused on different codec methods for DNA storage, developed and operated by BGI-Research (Shenzhen).

I have also contributed to the code base of the following programs:

GA4GH-server. [Python] Reference implementation of the APIs defined in ga4gh-schemas.

msprime. [C, Python] A reimplementation of Hudson’s classical ms simulator for modern data sets.

TreeWAS. [R] Uses tree-structured healthcare data to perform genetic association studies using UK Biobank data.

Data

Pf3k. Deconvoluted Plasmodium falciparum haplotypes.