Karen Cranston PhD

Postdoctoral Research Associate

Karen is a computational phylogeneticist. Her research focuses on developing methods for inferring evolutionary trees, especially using large, complex data sets. She doesn't have a formal connection to any particular group of organisms, although she has been seen associating with plant biologists. One of her goals at BioSynC is to incorporate evolutionary information surrounding the Tree of Life into the Encyclopedia of Life.

Education

2007 PhD, Department of Medical Genetics, University of Alberta, Edmonton, AB. Thesis title: “Inferring, testing and summarizing a posterior distribution of phylogenies”. Supervisor: Dr. Bruce Rannala.

1996 B.Sc. (Honours, First Class) in Genetics. University of Manitoba, Winnipeg, MB

Research

PhyLoTA browser: PhyLoTA is a web-accessible database of homologous sequence clusters, alignments and phylogenies constructed using a bioinformatics pipeline and GenBank nucleotide sequences as input.

Gene trees and species trees: Phylogenies built from different genes can show different topologies, and we can use the differences in phylogenetic signal to construct species trees and make inferences about evolutionary processes. I am currently working on methods for summarizing incongruence across gene trees.

Bayesian phylogenetic inference: My doctoral work focused on improving the computational algorithms used in Bayesian phylogenetic inference and summarizing the sample of trees that is the output from such methods.

Biodiversity informatics: Online resources for biological data necessitate the development of standards to facilitate storage, sharing and re-use of online biological data. Phylogenies can serve as a central organizing structure for a wide variety of biodiversity data. I am a member of the EvoIO data standards community that is building file formats, web services and ontologies for evolutionary data.

Tree Visualization: As phylogenies get larger and we assemble metadata that links to phylogenies, we need tools to visualize trees and associated metadata. I am the team lead of the iPlant Tree of Life working group on TreeViz. I believe this challenge is largely aesthetic - how do we explore the tree of life within an intuitive, visually pleasing interface?