Personal

I'm a PhD student in the Computational Biology Lab at the University of Toronto, working under the auspices of Mike Brudno. I moved from Seattle, where I studied at the University of Washington and researched in Bill Noble's lab in the Department of Genome Sciences. I am the current organizer of weekly CSGSBS cookiebreaks.

Recent side projects I've been involved with include:
  • EasyType French Accents, software that lets you type French accents, hassle-free,
    [Facebook, Twitter]
  • Map What's Up (now inactive), a twitter/foursquare/etc map that was significantly better than Bing's, and
  • Books For U, a textbook price engine to help subvert the University of Washington Bookstore's monopoly.

Research

In addition to the projects listed below, I've also been working on several projects in collaboration with the Hospital for Sick Children (SickKids) in Toronto. In one, we are sequencing a small portion of the genome (the exome) of 1,000 individuals with autism, in the hopes of finding variants associated with the disorder which can then be used for developing tests and treatments. In another, we have sequenced the exome of a number of individuals with congenital heart disease and are, similarly, looking for associated genetic variants in the hopes of shedding light on this disease.

  • SilVA: Silent variant analysis using random forests. 2011-2012

    SilVA (Latin for "forest") is a tool for the automated harmfulness prediction of synonymous (silent) mutations within the human genome. SilVA predicts the harmfulness of mutations using features that include CpG, codon usage, splice sites, splicing enhancers and suppressors, and mRNA folding free energy. Given variants in a VCF file, SilVA will rank the rare synonymous variants according to their predicted harmfulness.

  • Segtools 2009-2010

    The ENCODE Project Consortium has been using a variety of machine learning techniques to identify genomic "states". Unfortunately, these states are often hard to interpret and characterize. Toward this end, we developed a general software package to explore how classes of annotations relate to other known genomic features. Applications range from analyzing machine learned genomic states to exploring the pattern of transcription factor binding around transcription start sites.

  • Genomedata 2009-2010

    Next-generation sequencing has resulted in an explosion in the amount of data available to the researcher. Unfortunately, processesing this data is a large bottleneck in current research. To address this challenge, we developed the Genomedata format. Genomedata allows fast random access to hundreds of gigabytes of data while retaining a small disk footprint.

  • AutoOrthoGen 2009

    Gene orthology prediction is useful for characterizing the evolution of related organisms as well as identifying genes that are unique to a particular organism. We developed a tool to identify unique and orthologous genes between closely related strains of prokaryotes using a combination of sequence similarity and syntenic support. This work was done with Yogesh Saletore and Kris Weber, under the guidance of Martin Tompa.

    [writeup] [presentation]
  • HeartBeat 2009

    Heart rate monitors can be useful tools for general exercise, athletic training, and rehabilitation. For situations where electrocardiogram (ECG) monitors are not safe or convenient, we developed a prototype headphone-mounted infrared heart rate monitor. This device was at least as motion-resistant as medical infrared heart rate monitors and could be improved to provide voice feedback, music selection based upon heart rate, and measure other biological signals. This work was done under the supervision of Chris Neils and Michael Regnier.

    [ugrad thesis] [poster] [presentation]

Teaching

I love teaching, especially introductory material. It's wonderful to introduce students to a new field and present it in an exciting and accessible way. More than this, though, I value dedication to the students, something that the University of Washington fostered in me and Software Carpentry reinforced. This was my desktop for a while: [png] (from Mark Goetz).

Education

I have had one foot in biology and one in computing since high school, and I hope to use skills from both to research and teach until I'm old. Tenure would be lovely, at some point. Also, a couple successful entrepreneurial ventures, and perhaps a visit to the moon to sample the cheese, as long as we're fantasizing.

  • University of Toronto, Toronto, ON
    • PhD in Computer Science circa 2015
    • MSc in Computer Science 2012
  • University of Washington, Seattle, WA 2009
    • BSc in Bioengineering with Distinction, magna cum laude
    • BSc in Computer Engineering, magna cum laude
    • Minor in Music

Awesomeness

Some inspiring friends: Some fabulous entertainment: Some useful links: Etc.