When even your own publication list makes no sense

A few years ago, the head of my research group asked if I’d like to help write a chapter for a book. I weighed up the pros: it was an updated version of a previous book (so not too much work), it was invited (so not too many battles with reviewers) and it’s another item to go on the CV. The cons: typically, this kind of article appears in an obscure, closed publication that no-one ever reads or cites. So I said sure, why not and we wrote it.

It’s listed on my publications page at this blog as:

Saunders, N.F.W., Brinkworth, R.I., Kemp, B.E. and Kobe, B. (2010). Substrates of Cyclic Nucleotide-Dependent Protein Kinases. In: Handbook of Cell Signalling (Bradshaw, R.A., Dennis, E., eds.). Academic Press San Diego, 182:1489-1495. [DOI]

and sure enough, if you visit that DOI (and have a Science Direct subscription), you’ll find chapter 182 in the Handbook of Cell Signalling.

I thought no more about it, until I updated my Google Scholar citations page, where I found this:

Substrates of Cyclic Nucleotide-Dependent Protein Kinases
Neil FW Saunders, Ross I Brinkworth, Bruce E Kemp, Bostjan Kobe
2011/4/12
Transduction Mechanisms in Cellular Signaling: Cell Signaling Collection 399
Academic Press

And here’s the link at Google Books. Same article, same editors – but in chapter 41 of a different book: Transduction Mechanisms in Cellular Signaling: Cell Signaling Collection, on pages 399-405.

So apparently, my chapter has been “repurposed” for a completely different publication. Perhaps this transpired in consultation with the research group after I left. Perhaps there’s a long-forgotten email trail in which I agreed to this. Or perhaps we have so little control over our own work that strange things like this can just happen.

PhosphoGRID

I no longer work on protein kinases but when I did, PhosphoGRID is the kind of database that I would have wanted to see. It features:

• A nice clean interface, with good use of Javascript
• Useful information returned from a simple search form
• Data for download in plain text format with no restrictions or requirements for registration

All it lacks is a RESTful API, but nothing is perfect :-)

Published in the little-known but often-useful journal Database:

PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae.
doi:10.1093/database/bap026.

Prokaryotes: not so “simple” after all

One of my research challenges for 2008 is to marry my previous work (and my “true interest”), microbial genomics, with my current project which focuses on protein kinase substrate prediction. It should prove to be fascinating and fun, provided that publications such as this one keep appearing:

Schneiker, S. et al. (2007)
Complete genome sequence of the myxobacterium Sorangium cellulosum.
Nature Biotech. 25: 1281-1289
doi:10.1038/nbt1354 | Abstract | Full Text (subscription) | PubMed

It’s years since I read a textbook but I imagine that many of them will tell you that cell signalling via serine/threonine/tyrosine phosphorylation is “eukaryotic”, whereas Bacteria and Archaea use two-component sensor/histidine kinase systems. Some far-sighted individuals have been educating us otherwise for years, but only with the advent of microbial genomics has it become apparent that eukaryotic-like protein kinases (ELKs) are widespread in prokaryotes.

Back to Sorangium. This bacterium has the largest-known bacterial genome to date (~ 13 Mbp), encodes ~ 50% more proteins than the eukaryote S. cerevisiae and – get this – has 317 putative ELKs. That’s a greater length of DNA encoding for ELKs than some entire bacterial genomes and the highest percentage of the genome devoted to ELKs of any organism (bear in mind that the human/rat/mouse kinome comprises ~ 600 kinases). On top of that Sorangium synthesises a heap of interesting secondary metabolites, including an anti-cancer compound.

Let’s hear it for those prokaryotes.