News

  • publication
    Thursday, June 20, 2013

    We introduce an extremely fast, light-weight, "big data" algorithm to quickly answer the question of "which bacteria are present?" in a given sample of DNA. The method is based on the theory of compressed sensing and aims to find the simplest explanation for the data in terms of known information.

  • publication
    Wednesday, January 22, 2014

    We demonstrate that a concept of "weighted information content" (known as topological pressure, from the ergodic theory literature) can be used to facilitate the analysis of genomic data (in particular, find areas of a genome that have many genes in them). This is a conceptual extension to topological entropy approach presented earlier.

  • publication
    Wednesday, May 7, 2014

    In this paper, we improve both the accuracy and speed of the Quikr approach to classifying a given set of metagenomic DNA sequences (16S rRNA). This is accomplished by increasing the number of "feature vectors" we use for each training genome, and by modifying the Lawson-Hanson algorithm for non-negative least squares.

  • Article

    This is a course that I created back in 2014 (that continues to run, typically in the Fall and Spring) to introduce students to Mathematica, Matlab, and LaTeX. In the future, I will be incorporating modules on Python and/or Julia.

  • 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.

Improving Min Hash for Metagenomic Classification

A presentation about work with Hooman Zabeti that used probabilistic data analysis to analyze metagenomic communities.

MTH 321: Introductory applications of mathematical software

This is a course that I created back in 2014 (that continues to run, typically in the Fall and Spring) to introduce students to Mathematica, Matlab, and LaTeX. In the future, I will be incorporating modules on Python and/or Julia. This hands-on course has been attended by over 80 undergradutes, as well as a handfull of graduate students and faculty as well!

I wrote a (~200 page) textbook to accompany this course which can be found here.

MetaPalette Summary video

Very brief explanation of how MetaPalette works.

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