After many years of beautiful experiments, breakthroughs and graphic designs (e.g., here, here and here), Taraneh is leaving us. We commemorated with a lunch in December and we were lucky to have a special guest on hand. It was hard to say good bye, but we at least we got …
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 …
Given all the changes and excitement around our lab in the last few months, Bob’s choice of theme for this year’s retreat seems more appropriate than ever! Our plans to go hiking were dashed by rainy weather, and we still had no trouble filling up the two days with challenging …
If anyone is interested in the raw z-scores underlying Figure 3 from our latest pre-print, you can find them here. You can open the .cdt file as you would any spreadsheet, or import it into TreeView to explore the clusters. UPDATE: The paper is now accepted for publication at eLife, …
I recently had the opportunity to present some of the super-exciting research progress we are making on image analysis and intrinsically disordered regions. I am making slides available here in case anyone wants to have a closer look.
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 …
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.
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 …
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 …
