Previously, I took advantage of a dataset that linked preprints to their published counterparts to look at the fraction of papers in a journal that are preprinted. This linkage can be used to answer other interesting questions. Such as: when do authors preprint their papers relative to submission? And does this differ by journal? There’s a bit of preamble. If you just want to know the answer, click here.
A new paper means a new paper explainer. This post is all about our new paper on clathrin assembly. Some background info Endocytosis is the way that cells take up material from the outside world. The cell can make tiny vesicles that bud inwards from the cell surface and pinch off to travel inside the cell. This process is important for lots of things that cells do, so there is a lot of interest in how endocytosis works.
The aim of this post is to look at revisions of bioRxiv preprints. I’m interested how long preprint versions exist on bioRxiv. In other words: how long do revisions to preprints take? The data from bioRxiv is a complex dataset with many caveats as I’ll explain further down, but some interesting details do emerge. Consider this a sketch of the dataset rather than an in-depth analysis. I’ll walk you through the code.
As the COVID-19 pandemic continues, different countries are experiencing various restrictions including lockdowns. Some of these restrictions alter our ability to do science: by hindering lab access or taking time away from researchers for homeschooling. So, what impact has the pandemic had on scientific output? One way to look at this – for biology – is to look at newly deposited papers on bioRxiv.
We have a new paper out! I am a bit late with this post, since the accepted version went online in December 2020, and the final version appeared a few weeks ago. It will shortly appear in a finished issue of the journal so I can tell myself that I am not too late yet. What’s it about? A complex of TACC3-chTOG-clathrin-GTSE1 is important for stabilising the mitotic spindle during cell division.
We have a new preprint out. This is a short post to describe our findings and highlight some of the software I developed for analysing cell migration and cell shape data.
When a preprint is uploaded to bioRxiv, it undergoes screening before it appears online. How long does it take for Affiliates to screen preprints at bioRxiv? tl;dr I used R to look at bioRxiv screening times. Even though bioRxiv has expanded massively, screening happens quickly (in about 24 h). I am a bioRxiv Affiliate – one of the people who does the screening. Preprints wait in a queue to be screened.
I’m posting this the morning after generating a graph, and it’s already out-of-date. During the worldwide COVID-19 outbreak, preprint servers such as bioRxiv and medRxiv have again shown that they are the most effective way of communicating science rapidly. A collection of all papers on COVID-19 deposited on these two servers is available here, and it is growing daily.
I run a Masters module called MD997. Over six weeks, students have to write a grant proposal and then assess their peers’ proposals at a mock grant panel. Each student bases their proposal on a paper. They present that paper to the class and then they write their proposal using the paper as a springboard. I refreshed my paper list this year to consist of solely papers published (or posted on bioRxiv) in 2019. The previous list is here.
We have a new preprint out – it is a cautionary tale about using GFP nanobodies in cells. This short post gives a bit of background to the work. Please read the paper if you are interested in using GFP nanobodies in cells, you can find it here. Paper in a nutshell: Caution is needed when using GFP nanobodies because they can inhibit their target protein in cells.
