Research Interests

As a researcher at the National Cancer Institute, part of the National Institutes of Health, I work broadly in the areas of genomics and bioinformatics of high-throughtput data analysis. In addition to data analysis and biologically-driven projects, I have a strong interest in developing software and tools for analysing and interpreting genomic data and help to lead the Bioconductor project. Take a look at my publications page or my Google Scholar Profile for details.

Recent Blog Posts

  • Latex conversion notes
    Tuesday, February 28, 2012

    I have been avoiding latex lately because of a desire to publish documents in HTML as well as PDF and my sense was that converters from latex to other formats were lacking. After watching several beautiful presentations given based on the latex beamer class and being immersed in a Bioconductor course where vignettes are the coin of the realm, I decided to look a bit more fully.

  • Accessing mongodb from R
    Monday, January 23, 2012

    Mongodb is a scalable, high-performance, document-oriented NoSQL database. Since R is one of my main compute environments and languages, I have been playing with the rmongodb package to access mongodb from R.

  • After years of Apache, I have switched over to nginx for proxying and for serving as much content as possible. Recently, I had a need to have basic auth against ldap. On Apache, that meant adding mod_auth_ldap or another module. On nginx, that meant proxying through to a process to do the authentication and authorization and then to serve up an X-Accel-Redirect. This post is just a few notes on that process.

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