See Google Scholar for the full list.

2018

1. Deconvolution of multiple infections in \it Plasmodium falciparum from high throughput sequencing data Zhu, Sha Joe, Almagro-Garcia, Jacob, and McVean, Gil Bioinformatics 2018
2. Neonatal MicroRNA Profile Determines Endothelial Function in Offspring of Hypertensive Pregnancies Yu, Grace Z., Reilly, Svetlana, Lewandowski, Adam J., Aye, Christina Y.L., Simpson, Lisa J., Newton, Laura D., Davis, Esther F., Zhu, Sha J., Fox, Willow R., Goel, Anuj, Watkins, Hugh, Channon, Keith M., Watt, Suzanne M., Kyriakou, Theodosios, and Leeson, Paul Hypertension 2018

2017

1. Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent Zhu, Sha, and Degnan, James H. Systematic Biology 2017

2015

1. scrm: efficiently simulating long sequences using the approximated coalescent with recombination Staab, Paul R., Zhu, Sha, Metzler, Dirk, and Lunter, Gerton Bioinformatics 2015
2. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees Zhu, Sha, Degnan, James H., Goldstien, Sharyn J., and Eldon, Bjarki BMC Bioinformatics 2015 [Abs]

   There has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously.

3. Clades and clans: a comparison study of two evolutionary models Zhu, Sha, Than, Cuong, and Wu, Taoyang Journal of Mathematical Biology 2015 [Abs]

   The Yule–Harding–Kingman (YHK) model and the proportional to distinguishable arrangements (PDA) model are two binary tree generating models that are widely used in evolutionary biology. Understanding the distributions of clade sizes under these two models provides valuable insights into macro-evolutionary processes, and is important in hypothesis testing and Bayesian analyses in phylogenetics. Here we show that these distributions are log-convex, which implies that very large clades or very small clades are more likely to occur under these two models. Moreover, we prove that there exists a critical value }}\backslashkappa (n)}}κ(n)for each }}n\backslashgeqslant 4}}n⩾4such that for a given clade with size }}k}}k, the probability that this clade is contained in a random tree with }}n}}nleaves generated under the YHK model is higher than that under the PDA model if }}1<k<\backslashkappa (n)}}1<k<κ(n), and lower if }}\backslashkappa (n)<k<n}}κ(n)<k<n. Finally, we extend our results to binary unrooted trees, and obtain similar results for the distributions of clan sizes.

2013

1. Does random tree puzzle produce Yule–Harding trees in the many-taxon limit? Zhu, Sha, and Steel, Mike Mathematical Biosciences 2013 [Abs]

   It has been suggested that a random tree puzzle (RTP) process leads to a Yule–Harding (YH) distribution, when the number of taxa becomes large. In this study, we formalize this conjecture, and we prove that the two tree distributions converge for two particular properties, which suggests that the conjecture may be true. However, we present statistical evidence that, while the two distributions are close, the RTP appears to converge on a different distribution than does the YH. By way of contrast, in the concluding section we show that the maximum parsimony method applied to random two-state data leads a very different (PDA, or uniform) distribution on trees.

2011

1. Clades, clans, and reciprocal monophyly under neutral evolutionary models Zhu, Sha, Degnan, James H., and Steel, Mike Theoretical Population Biology 2011 [Abs]

   The Yule model and the coalescent model are two neutral stochastic models for generating trees in phylogenetics and population genetics, respectively. Although these models are quite different, they lead to identical distributions concerning the probability that pre-specified groups of taxa form monophyletic groups (clades) in the tree. We extend earlier work to derive exact formulae for the probability of finding one or more groups of taxa as clades in a rooted tree, or as ‘clans’ in an unrooted tree. Our findings are relevant for calculating the statistical significance of observed monophyly and reciprocal monophyly in phylogenetics.