@article{coons_sullivant_2021, title={Quasi-independence models with rational maximum likelihood estimator}, volume={104}, ISSN={["1095-855X"]}, DOI={10.1016/j.jsc.2020.10.006}, abstractNote={We classify the two-way quasi-independence models (independence models with structural zeros) that have rational maximum likelihood estimators, or MLEs. We give a necessary and sufficient condition on the bipartite graph associated to the model for the MLE to be rational. In this case, we give an explicit formula for the MLE in terms of combinatorial features of this graph. We also use the Horn uniformization to show that for general log-linear models M with rational MLE, any model obtained by restricting to a face of the cone of sufficient statistics of M also has rational MLE.}, journal={JOURNAL OF SYMBOLIC COMPUTATION}, author={Coons, Jane Ivy and Sullivant, Seth}, year={2021}, pages={917–941} }
 @article{coons_rusinko_2016, title={A note on the path interval distance}, volume={398}, ISSN={["1095-8541"]}, DOI={10.1016/j.jtbi.2016.03.027}, abstractNote={The path interval distance accounts for global congruence between locally incongruent trees. We show that the path interval distance provides a lower bound for the nearest neighbor interchange distance. In contrast to the Robinson-Foulds distance, random pairs of trees are unlikely to be maximally distant from one another under the path interval distance. These features indicate that the path interval distance should play a role in phylogenomics where the comparison of trees on a fixed set of taxa is becoming increasingly important.}, journal={JOURNAL OF THEORETICAL BIOLOGY}, author={Coons, Jane Ivy and Rusinko, Joseph}, year={2016}, month={Jun}, pages={145–149} }