Welcome to emmahodcroft.com
I am currently a PhD student at the University of Edinburgh, Scotland, studying under Andrew Leigh Brown. My research is concentrated on investigating the use of quantitative genetic methods to estimate the heritability (viral genetic effect) of virulence in HIV.
The sections below will let you find out a little about me, my current and past research, and some of the programs I've written. Please look around!
The most exciting phrase to hear in science, the one that heralds
the most discoveries, is not "Eureka!" but "That's funny..."
About Emma Hodcroft
"Scientists don't have dreams unless they are within 2 standard deviations from reality."
Academic
Recent
In the autumn of 2009, I moved from Texas to Edinburgh, Scotland, and began my master's degree at the University of Edinburgh on the Quantitative Genetics and Genome Analysis course. Though a challenging year, the course gave me an excellent introduction to the world of population and quantitative genetics. During the course, I prepared reports and did research projects on the evolution of SIV & HIV, the co-evolution of hantavirus and its hosts, genes involved in vitamin D production and colon cancer, and, for my final dissertation, the evidence of adaptive selection in coding and non-coding DNA in Drosophila.
After receiving my MSc degree with distinction in the autumn of 2010, I took a year-long research assistant position with Prof. Andrew Leigh Brown investigating virulence in HIV. Having been thoroughly won-over by the wonderful world of viruses, I began my PhD with Prof. Leigh Brown in September 2011 to continue my work on HIV. (More information in the 'Research' section.)
Distant
My education through high school (secondary school) was mostly in Texas, though I did attend some school in Scotland during the summer holidays until I was 16. During high school was when I was first introduced to genetics, evolution, and programming - three things still at the heart of my life many years on!
I originally planned to become a medical doctor, and spent my first two years of university at Southwestern University in Texas. Though an excellent university and a good experience, the tiny campus and small student population weren't right for me, and I transferred to Texas Christian University (TCU) at the beginning of my junior (third) year.
At TCU, I helped to set up and run the Purple Bike Program, a green initiative that rented free bikes to students to help reduce pollution and carbon emissions on campus. I also worked as a Java programming tutor, a job I really enjoyed.
Though unsure about my post-university plans for a while, an evolution class with Dr. John Horner during my senior (final) year left me decided in my interests and determined to pursue a life in academia and research.
After graduating in December of 2008, I took a research assistant position with Dr. Horner investigating how carnivorous Sarracenia alata pitcher plants attract their prey, as well as the genetic diversity of Sarracenia populations in the Southern US. (Obligatory research-in-action photo above-left.)
Personal
Born in Norway, and raised spending half the year in Scotland with my father and half the year in Texas with my mother, I'm a strange mix of two countries more similar than one might expect!
My half-and-half upbringing has given me an interesting perspective on life, as well as an interesting vocabulary and an amusing accent. A fan of both kilts and cowboy boots, I feel equally at home in both places.
I'm lucky enough to have had the opportunity to travel around North and South America, Europe, and even venture a little into Asia. My bi-annual migrations between Texas and Scotland all my life mean I'm quite at home in airports and on planes, and am no stranger to travel at all.
As well as my love of biology and evolution, I'm an armchair sociologist and feminist, and very much enjoy a good debate on any controversial topic. I love reading a wide variety of books, from popular fiction and 'pop-sci' to non-fiction and classics. Being a third-generation computer geek, I enjoy all things tech-y and have had a deep love of programming since 15.
I played violin regularly in various orchestras from age 10 to 21 and still enjoy it, though I don't play as much as I'd like to at the moment. Like everyone else on the planet, I enjoy photography. Finally, I have a fondness for the colour purple, cephalopods, potatoes, and cats.
Current
I am currently investigating the heritability of virulence in HIV. It is well-known that host
genetics and environmental factors play a large part in determining disease progression in people with HIV, but
despite long-standing speculation on whether the HIV virus could be evolving, the effect that the viral
genome may have on determining disease progression has only been investigated by a few studies.
The highly variable estimates obtained in these studies, which usually rely on transmission partners,
may be limited by small sample size, the confounding effects of studying sexual partners, and overly-strict
inclusion criteria. In my research, I'm using population genetic techniques to develop a more rigorous way of determining an
accurate measure of the influence of the HIV viral genome on virulence and disease progression.
I presented a poster on this work at the 2012 CROI Conference in Seattle, Washington, USA.
Post-Graduate
- During my MSc, I wrote minor assignment papers on the evolution of SIV and HIV and the co-evolution of hantavirus to its hosts.
- For my minor research project, I investigated the link between vitamin D level and colo-rectal cancer stage and conducted a genome-wide analysis study (GWAS) to look for an association between vitamin D level and SNPs on chromosome 16. No significant associations were found.
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For my major research project, I looked for evidence of adaptive selection in coding and
non-coding genes in Drosophila. Adaptive substitution rates in coding regions and
5' and 3' UTRs (untranslated regions) were analysed by tissue-specific, time-specific,
and immune-related gene function.
Coding regions of immune-related genes were found to have significantly higher adaptive rates than non-immune-related genes, but no difference was found in UTRs. All three regions were shown to have similar rates of adaptive evolution in most tissue-specific and time-specific genes, though UTRs had significantly higher adaptive rates than coding regions in some cases. The study provided evidence that UTRs have a faster overall adaptive rate but also more non-adaptive substitutions, and that the adaptive rate of UTRs and coding regions varies by gene function.
Graduate/Under-Graduate
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After graduating from TCU, I worked with Dr. John Horner on the carnivorous pitcher plant
Sarracenia alata. I aided in preliminary studies on the aromatic compounds that
Sarracenia may use to attract prey, and also investigated the genetic variation
in four geographically separate populations of Sarracenia. Using AFLP analysis,
our study concluded that though long suspected to be primarily clonally reproducing,
only 14% of the genetic variation in Sarracenia alata occurred among populations,
while 86% occurred within populations, indicating that clonal spread is actually quite low
in these populations.
I presented a poster on this work at the Evolution 2010 Conference in Portland, Oregon. - During my time at TCU, I conducted a three-week long guided research project on the effects of thyroxine on the development of Xenopus tadpoles. I independently examined the resulting data to write a report tying the results to potential real-world parallels caused by excreted synthetic thyroid hormones.
"Research is what I'm doing when I don't know what I'm doing."
My love of programming means I'm always trying to find an excuse to code something. During my
MSc programme and in the course of my current research, I've written a few simple programs to aid
me in my tasks. Most are probably not too useful, but a few may be. In particular, TreeCollapserCL,
which I've developed to use in my current research, is the most meticulously written and potentially
the most useful to others.
All of these programs are Java, but I very much like R, and have dabbled in Perl.
Useful
*New!*PareTree 1.0
A basic, command-line Java program that allows users to 'pare' down their tree by either
removing unwanted sequences/leaf-nodes or removing bootstrap information - or both - quickly
and efficiently.
TreeCollapserCL 3.1.1 (Most Popular)
A new, improved version of TreeCollapseCL that can root trees and find lengths of branches
and average bootstraps of nodes before as well as collapsing nodes with bootstraps
below a user-specified threshold.
Updated with bugs for file type and bootstraps fixed.
TreeCollapserCL 1.0
A command-line Java program that takes in a NEXUS-style phylogenetic tree file (two formats accepted) with bootstraps and returns NEXUS-style code for the same tree, but with all nodes with bootstraps falling below a user-specified threshold collapsed into polytomies. This program is outdated, it is recommended that you use TreeCollapser3 (above) instead.
SeqMatcher
A program written to match sequences across HIV database downloads. Because sequence and
patient names are re-anonymised before each download release, it has so far been impossible
to track the differences in how the sequences cluster from download-to-download. This program
attempts to identify matching sequences between downloads. Because sequences are thousands of
characters long, and each download contains tens of thousands of sequences, running efficiency
and memory allocation are important in this program. Because of the amount of information and
data returned, finding a way to present this in an intuitive and useful way to the user was a
major challenge for this program.
Unfortuantely, because this program is written specifically for the HIV database, it would not
be useful for me to provide it here for public use.
Less Useful
TreeCoder
Allows the user to copy a visual phylogenetic tree (say out of a paper) into phyloXML or Nexus-type code easily so they can mess with it. Might be potentially useful, though only in limited circumstances, since I doubt many people do this regularly. It was really useful (and originally written) for a paper I wrote on coevolution of hantavirus during my MSc. (I used it to point out that a published tanglegram had been left partially tangled to support the paper's premise, but could actually be resolved much better than the author seemed to be implying.)
Word Counter
Does what it says, but doesn't count references in quotes!
Data Finder
A program that combines files on common ID (something you could probably do better in R).
I am rarely happier than when spending an entire day programming my computer to perform automatically a task that would otherwise take me a good ten seconds to do by hand.
I can be contacted at the address and phone number below:
Phone: 0131 650 8683 (International: +44 131 650 8683)
The prevalence of spam-bots keeps me from posting my email address, but you can contact me via the feedback form.
“Science may never come up with a better office communication system than the coffee break.”
