My PhD Thesis

03 September 2018

With the publication of the last major chapter of my thesis in Molecular Systems Biology, I’m happy to finally be able to put the full text of my thesis on this website.1

tl;dr: here’s the PDF.

My PhD thesis was called “Multiscale analysis of infectious diseases: integrating omics and clinical informatics data into patient care” and I wrote it under the dedicated guidance of Andrew Kasarskis, PhD, my thesis advisor. It was a dissertation comprising exclusively computational work. The motivating premise is that “big data” on infectious diseases are becoming more prevalent, and we should attempt new and ambitious methods to combine these data to solve urgent problems affecting our patients. Some examples of these new data sources are:

  • Next-generation sequencing of pathogen genomes
  • Electronic medical records
  • Mass cytometry of immune cell subpopulations during infection
  • RNA-seq of host gene expression changes during infection

Some of the problems that I tackled in this thesis were:

  • Using bacterial genome sequencing to explain the development of antibiotic resistance in patients undergoing treatment in the hospital
  • Tracking the patient-to-patient spread of hospital-acquired infections with nearly real-time analysis of genomic surveillance data
  • Estimating the cost of a hospital-acquired infection from electronic medical record data
  • Dissecting the human immune response to a recently emerging viral infection in the Americas (Chikungunya) in unprecedented depth

To read the thesis, you can:

I’ve also put the source code for typesetting the thesis on my GitHub.

  1. Although Molecular Systems Biology is an open access journal and is fairly liberal about accepting work already posted online, even encouraging posts to preprint servers and explicitly exempting theses as prior publication, many journals reserve the right to reject manuscripts that were disseminated in any way prior to submission. And until an article is published, you never know what other journals you might submit it to. Therefore, at least in the life sciences, I’d still recommend caution on putting thesis chapters online until they are accepted somewhere, or unless you’ve reviewed the editorial policies of every possible target journal.