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My PhD thesis.
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README.md

My PhD thesis

This is the complete source, including figures, for my PhD thesis, deposited at the Icahn School of Medicine at Mount Sinai on July 5, 2017. The title of the thesis is:

"Multiscale analysis of infectious diseases: integrating omics and clinical informatics data into patient care."

My thesis advisor was Andrew Kasarskis, PhD.

The LaTeX code for typesetting was forked from @scientiffic's tufte-latex-mit template, which is itself an amalgamation of components of the MIT's LaTeX thesis template and the Tufte-LaTeX template.

Reading

You can view and download the complete PDF.

I also wrote a short blog post about my thesis.

The typeset PDF is also included in the repository as main.pdf.

Publications

Four chapters of this thesis were published, after reformatting and revisions, as individual peer-reviewed articles. Citations for those publications are as follows:

Chapter 1: Pak TR, Kasarskis A. "How next-generation sequencing and multiscale data analysis will transform infectious disease management." Clin Infect Dis. 2015 Aug 6. pii: civ670. doi:10.1093/cid/civ670.

Chapter 2: Pak TR, Altman DR, Attie O, Sebra R, Hamula CL, Lewis M, Deikus G, Newman LC, Fang G, Hand J, Patel G, Wallach F, Schadt EE, Huprikar S, van Bakel H, Kasarskis A, Bashir A. "Whole-genome sequencing identifies emergence of a quinolone resistance mutation in a case of Stenotrophomonas maltophilia bacteremia." Antimicrob Agents Chemother. 2015 Aug 31. pii: AAC.01723-15. doi:10.1128/AAC.01723-15.

Chapter 5: Pak TR, Chacko KI, O’Donnell T, Huprikar S, van Bakel H, Kasarskis A, Scott ER. "Estimating local costs associated with Clostridium difficile infection using machine learning and electronic medical records." Infect Control Hosp Epidemiol. 2017 Dec;38(12):1478-1486. doi:10.1017/ice.2017.214.

Chapter 6: Michlmayr D,* Pak TR,* Rahman A, Amir ED, Kim E-Y, Kim-Schulze S, Suprun M, Stewart MG, Thomas G, Balmaseda A, Wang L, Zhu J, Suarez-Farinas M, Wolinsky SM, Kasarskis A, Harris E. "Comprehensive innate immune profiling of chikungunya virus infection in pediatric cases." Mol Syst Biol. 2018 Aug; 14(8): e7862. doi:10.15252/msb.20177862.

* denotes equal authorship.

Compiling

I compiled this with MacTeX 2014 using the wrappers for latexmk in the LaTeX bundle for TextMate 2.0. The main (and only) file that you should compile is main.tex, and to support all features used, you need to use XeTeX, not pdflatex.

In theory, it should also be compilable with TeX Live 2014 on any UNIX, but I haven't tested that. There are breaking updates in certain packages, particularly biblatex, that seem to prevent this from being compiled as-is with newer distributions like 2015 or 2016. With TeX debugging being the pile of worms that it is, I haven't had time to figure out why that is. Fortunately, TUG maintains an archive of all old MacTeX and TeX Live distributions, and it is fairly simple (at least with MacTeX) to have multiple distributions installed and switch between them as needed. So for now, MacTeX 2014 it shall be.

Besides MacTex or Tex Live 2014, you'll also need the Minion Pro, Bitstream Vera Sans Mono, Palatino, and Cochin fonts, which XeTeX should be able to find if they are installed for your operating system.

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