Protein words

Posted on December 7, 2016 by spencer

In my post about creating a DNA font, I mentioned the idea of doing a similar thing for proteins. There are 20 standard amino acids, each with a single character abbreviation. When combined with symbo... Read More

CE-CP

Posted on April 13, 2015 by spencer

Our latest paper on the CE-CP method for finding protein circular permutations is in this month’s issue of Bioinformatics. Spencer E. Bliven, Philip E. Bourne, and Andreas Prlić. (2015) Detecti... Read More

Using BioJava from R

Posted on April 10, 2015 by spencer

I’m a fan of literate programming. When I’m writing a paper, I typically use LaTeX to draft the paper, Java to generate the data, and R to create figures and do basic analysis. With Sweave (or the... Read More

A PDB-wide, evolution-based assessment of protein–protein interfaces

Posted on October 21, 2014 by spencer

My first paper in collaboration with the Capitani team has been published online: Kumaran Baskaran, Jose M Duarte, Nikhil Biyani, Spencer Bliven and Guido Capitani. (2014) A PDB-wide, evolution-based ... Read More

Regiomeeting at Mont Sainte-Odile

Posted on October 1, 2014 by spencer

Last week I attended the Rhine-Knee Regional Meeting on Biocrystallography at the Hohenburg Abbey on Mont Sainte-Odile, France. It’s a smaller conference, with a focus on short PhD and Postdoc p... Read More

ISMB 2014

Posted on July 24, 2014 by spencer

I had a great time at the ISMB conference & related events in Boston last week. As always, it is an exciting event scientifically and socially. First there was the Open Bio Foundation’s Cod... Read More

Babies

Posted on July 23, 2014December 7, 2016 by spencer

I learned some interesting facts about fetal development recently. So interesting, they can only be properly delivered by Doctor McNinja (using the awesome Dinosaur Comic mashup template)... Read More

New publication on CE-Symm

Posted on April 25, 2014 by spencer

My latest paper with Douglas, Peter, Zaid, Andreas, Philippe, and Phil is out! Douglas Myers-Turnbull, Spencer E. Bliven, Peter W. Rose, Zaid K. Aziz, Philippe Youkharibache, Philip E. Bourne, Andreas... Read More

How do insertions affect the structure of the Rossmann fold?

Posted on September 10, 2013 by spencer

I presented journal club today on the paper: Pandya, C., Brown, S., Pieper, U., Šali, A., Dunaway-Mariano, D., Babbitt, P. C., et al. (2013). Consequences of domain insertion on sequence-structure di... Read More

Castle Panic pieces

Posted on August 28, 2013 by spencer

I’m quite proud of my recently-released Castle Panic game pieces. Castle Panic is a great game, and it is fun to have some sturdy walls and towers to replace the flimsy cardboard ones it comes w... Read More