Author Archives : sasha

GSPE: Genomics of Social Parasite Evolution Workshop

We were happy to host our excellent US and European-based collaborators to jointly work on the evolution of social parasite genomes. In the few days of the workshop we made major progress, finally bringing the project over the hill and hopefully en route to eventual publication. Participants (as ordered in photo): Ti Eriksson (Arizona State [...]


“Degenerate adaptor sequences for detecting PCR duplicates in reduced representation sequencing data improve genotype-calling accuracy” paper published!

Together with our collaborators from the National University of Singapore we just published a paper describing an improved method for making double-digest RAD-tag libraries. By adding a small run of degenerate nucleotides to the end of one of the Illumina indexes, you can barcode each individual ligation reaction and determine how many molecules participate in [...]

2014-08-28 07-52-07 Degenerate adaptor sequences for detecting PCR duplicates in reduced representation sequencing data imp

It belongs in a museum!

Over lunch during one of his visits to OIST, my former boss Sydney Brenner suggested that I try a ribo-tailing technique for attaching adaptors to short DNA molecules. The idea is that the action of terminal transferase on riboguanidines creates a 3′ tail of controlled length, which can be used for attaching adaptors and synthesizing [...]

Extracted carpenter ant

NTU Group Visit

OIST-NTU Invasive Ant Symposium

We were the proud hosts of Dr. Scotty Yang’s research group and his colleagues from Taiwan National University. His research group specializes in studying the patterns of ¬†dispersal in a variety of invasive ant species. We were treated to a wide range of topics, including a few fascinating finding about Wolbachia distributions in invasive ants. [...]

home-made rack

Goodbye Invitrogen ripoff product

With the help of Ken Meacham of the Bandi Unit, we have successfully used some magnets to inexpensively 3D print our own magnetic stands based on this design and some inexpensive magnets. They look like cheap imitations, but just as well, if not better, and cost orders of magnitude less (last I checked the commercial stand [...]

Host-associated genomic differentiation paper recommended by F1000

It was a long, hard road, but our paper is getting some recognition! F1000′s Dr. Ian Wang writes that “this finding highlights the importance of considering multiple factors, including dispersal, population sizes, spatial variation in ecologically-important traits, and population histories, for understanding how ecological adaptation contributes to patterns of differentiation throughout the genome.” I hope [...]