Here is a small collection of explainers, articles and discussions I have written on some topics. Most of these relate to microbiology because it’s always on my mind 🦠 💚.
Articles
What were Prototaxites? - A wee article on the mysterious organism Prototaxites, a possible hero of all life as we know it.
Help, I’m a Frog! - A one pager on endangered froggies and who is hanging around to rescue them (spoiler alert: it’s bacteria).
Explainers & Research articles
News & Views article: Yeast-based synthetic genomics brewing up a storm against COVID-19
Nature publishes articles called “News and Views” where researchers summarise recently published papers to a more general science crowd. I wrote my own about a microbial genetics paper published by Thi Nhu Thao et al. (2020) in which they developed a method to reconstruct a viruses (like COVID-19) in yeast to enable research on pathogens without having to risk catching the virus themselves. Here is a link to the draft.
Primer: A brief overview of how to set up evolutionary experiments
A Primer is a short explanation of sparkly new techniques within a field to give other researchers the opportunity to use these in their own research. Inspired by Richard Lenski’s research, the worlds’ longest-running evolution experiment (since 1988!), my primer describes different techniques to set up an evolutionary experiment. Have a read here , and if you liked it maybe you’d like to follow the references in the sources and read up some more.
TLDR: Assembling a genome with the help of de Bruijn graphs
In this article I explain how the computer assembles genomes after we sequence them in the lab. This article assumes general knowledge of genetic lab techniques.
Into the woodwork - An investigation into the composition and structure of the termite gut microbiome
As part of an assignment I received some datasets of genomes from termite gut microbiome samples of two different locations. This technical research article digs deep into the composition and structure of these microbiomes and compares the microbial life of the termite guts to each other. Even for someone not familiar with genomics the graphs in the article should make it easy to spot differences between then two locations.
Paper Reviews
Phylogeography/Phylogenetics of SARS-CoV-2 - Right on topic in 2021, I wrote a small review of a paper that conducted a quantitative analysis on mutations in SARS-CoV-2 genomes. The original paper was the first of its kind and published very shortly after the WHO declared the COVID outbreak a pandemic so it received quite a bit of attention in the science community.
Natural Selection in SARS-CoV-2 - Another small review of a paper that came from sequencing genomes of SARS-CoV-2 but this one is on the topic of natural selection. I decided to review this paper because (in my opinion) it had some analytical flaws that I wanted to briefly address.
Yet to come!!!! <3
shipwreck paper discussion
broad bean paper review
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