News

  • publication
    Sunday, January 1, 2017
    In a very reproducible fashion, we assess a wide variety of computational techniques in metagenomics, including assembly (putting together pieces of genomes, called contigs, from short reads), binning (figuring out where the contigs came from), and taxonomic profiling (determining which organisms are present in a sample and at what relative amount).
  • publication
    Sunday, January 1, 2017
    Rapidly answers “why are these data sets different” by leveraging hierarchical/relatedness information. In short, we develop an algorithm to quickly compute the Unifrac distance by leveraging the earth mover's distance, prove its correctness, and derive time and space complexity characterizations.
  • publication
    Tuesday, November 1, 2016
    After introducing the notion of a random substitution Markov chain, we relate it to other notions of a "random substitution" and give a complete description of the Martin boundary for a few interesting examples.
  • publication
    Saturday, October 1, 2016
    In a network of interacting quantities (such as a food web), we examine how qualitative and quantitative predictions change when a quantity (such as the abundance of an organism or a set of organisms) is increased. This is quantified in terms of which model parameters cause the largest change in predictions.
  • publication
    Tuesday, May 24, 2016
    We present the idea of using the "earth mover's distance" (aka the first Wasserstein metric) to measure the distance between samples of DNA. This reduces to finding the most efficient way to transform one kind of graph (known as de Bruijn graphs) into another.