Hello, world! Richard Neher, Adrian Egli and I just finished a project quantifying the importance of HGT in the spread+evolution of carbapenem resistance. Using ONT and Illumina tech, we assembled 115 complete genomes and found huge structural diversity. doi.org/10.1101/456897

Finishing a project with Sebastian Streichan and Boris Shraiman! We found a connection between epithelial geometry and delaunay triangulations that encode mechanics. Used to accurately infer global myosin distributions in Drosophila. Would love feedback! arxiv.org/abs/1812.04678

Just finished our first ONT sequencing run with 24 barcodes. Got 1x coverage on all 24 within a few minutes! All credit goes to Eric Ulrich. Oxford Nanopore we still need more barcodes!

Marginally amplifying the tweet. I hope it helps inform decisions! Let me know if you have questions or find bugs.

Takeaways agree with intuition obtained from our simulations at scratch.neherlab.org. Early action now has an exponential benefit in later outcomes.

We updated our #COVID19 scenarios app (Ivan Aksamentov Nicholas Noll Jan Albert ). It now contains historical case counts for many countries (by Our World in Data). We also revised our presets: the outbreak is/was growing faster than our initial assumptions. neherlab.org/covid19/

The folks at Neher Lab have produced a startling model of COVID-19 proliferation: neherlab.org/covid19/ The code is on GitHub: github.com/neherlab/covid… Developers who want to help in this unprecedented time should check out the `help wanted` issues on the repo.

Comparing confirmed #COVID19 case counts & deaths with models (neherlab.org/covid19) reveals striking patterns. In many countries (example France), confirmed deaths and case counts are much closer to each other than the model predictions, suggesting many missed cases.

Tonight #DeborahBirx stated that models anticipating large-scale transmission of COVID-19 do not match reality on the ground. Our modeling (done by Stephen Kissler based on work with Christine Tedijanto Wen and @yhgrad and me) is one of the models she is talking about.

This is tragic

We have just released a new version of covid19-scenarios.org (prev neherlab.org/covid19), our tool to explore #COVID19 outbreaks! We now have: * allow for custom age distributions * discrete infection control measures * scenarios fit to case counts * PDF export

It's been a unique, awesome experience having this project morph from scientific research into open source development to provide a useful tool. Thanks to everyone involved!

I am sorry to confirm the passing of my colleague John Conway. An incomparable mathematician, a pleasant neighbor, and an excellent coffee acquaintance. His passing was sudden (fever started only Wednesday morning). Part of coronavirus's hard toll in New Jersey.

All models are wrong, some models are useful bloomberg.com/opinion/articl…

Glad to see the covid19-scenarios,org site get some traction, especially after watching Nicholas Noll grind away at improvements 16 hours/day since early March. bloomberg.com/opinion/articl…