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 …

Pi day

Shadi brought us a pie. I proposed to draw a circle with a diameter of 2R and have uniformly random knife cuts on the pie to estimate π with Monte Carlo method. My proposal was rejected.

Journal Club Review: “Mitigating Data Scarcity in Protein Binding Prediction using Meta-Learning”

In our recent journal club, we discussed the pre-print, “Mitigating Data Scarcity in Protein Binding Prediction using Meta-Learning”. Here, Luo et al. apply the recent trend of meta-learning to predicting phosphorylation sites for a poorly characterized kinase family. Meta-learning algorithms aim to discover models that generalize to new predictions with …

ISMB at Chicago

I recently attended the ISMB (Intelligent Systems for Molecular Biology) conference in Chicago.  This conference is one of the biggest bioinformatics conferences, with scientists from different corners of the world studying a whole range of organisms, systems, models…In fact, the ISMB conference seems to be typically split up into different …

Thoughts after SMBE

(Sunrise on top of Mt. Fuji) This is the first time I attended a conference of this size, and I expected myself to explore the various topics currently studied in the molecular biology of evolution. One variation among different symposia is the definition of evolution at which the researchers are …

Lab retreat 2018

As we have done for the last few years, the lab decided to organize a retreat this year to take some time to think about the big picture: where we are and where we are going. However, this year being the 10th anniversary of the lab, we decided to follow …