Is SARS-cov-2 evolution inevitable?

On Friday I had a very interesting chat with Jesse Bloom about his work that showed the mutations the coronavirus can acquire to evade antibodies and, perhaps, ultimately the immune response. Jessie showed that the virus can escape individual antibodies, probably natural immunity and even vaccine-induced immunity (in the worst …

Setting a biological agenda for deep learning

I’ve always been fascinated with the concept of discovery in biology. Perhaps this is the reason why I work with microscopy images as my data of choice. The whole reason we have the word “cell” is because scientists placed corks and plants under microscopes in the 16th century and observed …

lab “pizza” lunch

Here’s most of us having our a “pizza” lunch. We are saying farewell to Amy (again) and celebrating Gang and Dina’s projects. Obviously, this semester has been different. Still, I hope we’ve learned. It helped me to put our semester in perspective: Cambridge sent home its students in the 1660s, …

BADR codes and data

We have recently been working on classifying disordered regions for different functions and phenotypes using evolutionary signatures (and signatures comprised of “bulk” feature calculations from disordered sequences). The code and data related to this project currently lives at: https://github.com/taraneh-z/BADR! Check it out and let us know what you think. Hopefully …

Journal club pre-print “Molecular evolution across developmental time reveals rapid divergence in early embryogenesis” by Cutter, A. D., et al

In this pre-print, the authors characterized the transcriptome of C. elegans at 30 timepoints during development. They used fPCA to cluster 14 co-expression modules from 19,711 genes and then fitted a cubic function to the expression profile of each module. The authors then conducted hierarchical clustering on the parameter values …