Research on the population genetics of microbial organisms requires the use of specialized analyses designed for clonal organisms to avoid violating the assumptions of traditional population genetic models. The tools necessary for performing these analyses existed as a set of unrelated software with non-overlapping capabilities and did not cover all...
Sudden oak death caused by the oomycete Phytophthora ramorum was first discovered in California toward the end of the 20th century and subsequently emerged on tanoak forests in Oregon before its first detection in 2001 by aerial surveys. The Oregon Department of Forestry has since monitored the epidemic and sampled...
Initially reported in California as the causal agent of sudden oak death (SOD), efforts to limit spread of Phytophthora ramorum in Oregon natural forests have concentrated on quarantine regulations and eradication of the pathogen from infested areas. P. ramorum has four clonal lineages: NA1; NA2; EU1; and EU2 (Grünwald et...
For a certain class of Z²-actions, we provide a proof of a conjecture that the ratio of the Perron eigenvalues of the transfer matrices of the free boundary restrictions converge to the entropy of that action. Also, a novel method for computing the entropy of Z²-actions is conjectured.
Bacterial canker, caused by Pseudomonas syringae pv. syringae is
recognized as one of the greatest limiting factors in cherry production
in Oregon. Disease incidence may be decreased when susceptible
cultivars are high-grafted onto tolerant/resistant rootstocks. This
research was begun to develop a rapid screening method which could be
used to...
Many microbial, fungal, or oomcyete populations violate assumptions for population
genetic analysis because these populations are clonal, admixed, partially
clonal, and/or sexual. Furthermore, few tools exist that are specifically designed for
analyzing data from clonal populations, making analysis difficult and haphazard.
We developed the R package poppr providing unique tools...
The asymmetric nature of bit errors in several practical applications provides grounds for efficient error control techniques. The Z-channel model and special classes of codes like asymmetric error detection codes and t-asymmetric error correcting/d-asymmetric error detecting codes can be successfully used in ARQ protocols for feedback error control enhancement. This...
A common issue with extracorporeal medical devices is blood clotting due to bio-incompatibility. Systemic anticoagulants are often prescribed to mitigate the coagulation issues. However, such drugs can lead to further complications, for example hemorrhaging. One solution to improve the hemocompatibility of blood-contacting medical devices are biomaterials, such as slippery liquid...
Semi-supervised clustering aims to improve clustering performance by considering user supervision in the form of pairwise constraints. In this paper, we study the active learning problem of selecting pairwise must-link and cannot-link constraints for semisupervised clustering. We consider active learning in an iterative manner where in each iteration queries are...