Jul 31, 2015

Coffee Berry Borer genome published

Our paper on the de novo genome sequence and annotation of the Coffee Berry Borer (a beetle) is published today in Nature Scientific Reports. This was a really fun project, where I was pushed to do a lot more in-depth study of insect biology (such as antimicrobial and cytochrome P450 proteins). We also discovered that this beetle has captured a bunch of bacterial proteins into its genome (horizontal gene transfer) - which seems odd, but was actually previously reported for this insect and many others. Interestingly, most of these captured bacterial proteins provide starch digesting enzymes, which support the beetle's lifestyle of living entirely inside of the coffee bean and eating nothing but coffee! We are of course hoping that these genes can be used as some sort of target for control of the pest, which causes something like a billion $$ of annual damage worldwide to our beloved coffee. 

Jul 29, 2015

I am writing new lectures and organizing a lot of teaching material to teach 4 (!) classes this fall at two different universities (NYU and Fordham). I would like to keep the teaching materials in a nice easily accessible online location, and easily share with my students without a lot of hassle to sign them all up or whatever. I had a fairly good experience with Google Drive for a short course this Spring, so I'm trying it out now. Here is the master link to all of my 2015 teaching material:


Stuff will appear, change, possibly disappear from this location as I keep sorting and rewriting, up to and during the classes. Most of the material is my own, some journal articles that I provide as readings to my students, and some shameless theft of good lectures, exercises, and tutorials from other folks smarter or better at explaining stuff than I am.

We are also planning to make Screencast type videos of most of the lectures, which get dumped on YouTube. I will try to find some sensible way of organizing them and sharing via this NGS blog.

Jul 16, 2015

CSHL Press has made the RNA-seq chapter of my Next-Gen Seq book available free from their website: RNA Sequencing with Next-Generation Sequencing.


Cold Spring Harbor Laboratory Press banner image
Next-Generation DNA Sequencing Informatics, Second Edition banner image