Our most recent manuscript was almost ready for submission. We were planning to send it to an open access journal. It was then that I had the thought: how many papers in the reference list are freely available? It somehow didn’t make much sense to point readers towards papers that they might not be able to access. So, I wondered if there was a quick way to determine how papers in my reference list were open access.

Following on from the last post about publication lag times at cell biology journals, I went ahead and crunched the numbers for all journals in PubMed for one year (2013). Before we dive into the numbers, a couple of points about this kind of information. Some journals “reset the clock” on the received date with manuscripts that are resubmitted. This makes comparisons difficult.

My interest in publication lag times continues. Previous posts have looked at how long it takes my lab to publish our work, how often trainees publish and I also looked at very long lag times at Oncogene. I recently read a blog post on automated calculation of publication lag times for Bioinformatics journals. I thought it would be great to do this for Cell Biology journals too.

I thought I’d share this piece of analysis looking at productivity of people in the lab. Here, productivity means publishing papers. This is unfortunate since some people in my lab have made some great contributions to other peoples’ projects or have generally got something going, but these haven’t necessarily transferred into print. Also, the projects people have been involved in have varied in toughness.

I thought I’d compile a list of songs related to biomedical science. These were all found in my iTunes library. I’ve missed off multiple entries for the same kind of thing, as indicated.

In this post I’ll describe a computational method for splitting two sides of a cell biological structure. It’s a simple method that relies on principal component analysis , otherwise known as PCA.

We have a new paper out! You can access it here. The work was mainly done by Cristina Gutiérrez Caballero, a post-doc in the lab. We had some help from Selena Burgess and Richard Bayliss at the University of Leicester, with whom we have an ongoing collaboration. The paper in a nutshell We found that TACC3 binds the plus-ends of microtubules via an interaction with ch-TOG. So TACC3 is a +TIP.

Having recently got my head around violin plots, I thought I would explain what they are and why you might want to use them. There are several options when it comes to plotting summary data. I list them here in order of granularity, before describing violin plots and how to plot them in some detail.

When I started this blog, my plan was to write about interesting papers or at least blog about the ones from my lab. This post is a bit of both. I was recently asked to write a “Journal Club” piece for Nature Reviews Molecular Cell Biology, which is now available online. It’s paywalled unfortunately. It’s also very short, due to the format. For these reasons, I thought I’d expand a bit on the papers I highlighted.

I have been doing paper of the day (#potd) again in 2014. See my previous post about this. My “rules” for paper of the day are: Read one paper each working day. If I am away, or reviewing a paper for a journal or colleague, then I get a pass. Read it sufficiently to be able to explain it to somebody else, i.e. don’t just scan the abstract and look at the figures.

Back of the envelope calculations for this post. An old press release for a paper on endocytosis by Tom Kirchhausen contained this fascinating factoid: If this is true it is absolutely staggering. Let’s check it out. A synaptic vesicle is ~40 nm in diameter.