This plots Rt as a function of intrinsic transmissibility and immune escape. With high levels of population immunity, a hypothetical Omicron virus with modest R0 but partial immune escape will spread faster than a Delta-like virus with high R0 but little immune escape. 9/15

Following up here with speculative estimates of the rate of spread of Omicron and a stab at how to apportion this rapid rate of spread between intrinsic transmissibility and immune escape. 1/18

I wrote a short and, uh, slightly provocative piece on a stumbling block of my PhD:

prize for the first person who figures out what this is

Major release: Infomap 2.0 with regularized map equation – reveal flow-based communities in weighted, directed networks with incomplete data without overfitting. pip install infomap or git clone [email protected]:mapequation/infomap.git cd infomap make -j

7. Stochastic and non-linear dynamics: these fields have often developed independently from each other. But most interesting problems on biology (and beyond) are probably subject to both non-linearity and stochasticity 8/9

These epidemics have proceeded in a similar fashion across states with initial rapid exponential growth that slowed as epidemics grew in size. It appears that states are largely on the same curve, just some are farther ahead on this curve compared to others. 4/9

Assuming between a 1 in 4 and 1 in 5 case reporting rate suggests that between 18% and 23% of the country was infected by Omicron by Jan 17, with the large majority infected in a span of just ~4 weeks. 6/9 x.com/trvrb/status/1…

Having ~40% of the population infected by a single pathogen in the span of 8 weeks is remarkable and I can't think of an obvious modern precedent. Flu seasons generally have perhaps 10% infected in the span of 16 weeks. 8/9

The cost of information acquisition by natural selection biorxiv.org/content/10.110… From Ryan Seamus McGee, Olivia Kosterlitz, @kaznatcheev, Benjamin Kerr, and Carl T. Bergstrom See 🧵👇

Let's say you had a species of blue beetles. They do quite well in a certain environment, but then birds start noticing them and they become a major food source. A mutant green form happens to arise and it is not noticed by the birds and does much better than the blue form. 🧵

Announcing a new tool for exploring federal grant data: GrantExplorer.org. With support from @Moorefound, Cole Chamberlin, Jason P & I built a tool for answering questions like, how much U.S. National Science Foundation funding has supported “data science”? Feedback welcome. grantexplorer.org

Someone on here (I forget who I'm sorry) linked to this paper and it derives this statistical identity that is completely mind blowing and I want to tweet about it. bias = data quality × data quantity × problem difficulty statistics.fas.harvard.edu/files/statisti…

someone said that trees aren't a thing phylogenetically and i was like "oh sure palm trees etc must be unrelated" BUT NO your standard OAK is more closely related to a DANDELION than to a GIANT REDEOOD trees are a CONVERGENT GROWTH HABIT, they're the crab of the plant world

How does exposure to different hosts affect evolution of bacterial genes on mobile elements? In Molecular Biology and Evolution, Olivia Kosterlitz et al use barcode methods to compare adaptive landscapes across species & show alignment enables a form of adaptive “crowdsourcing”🧵academic.oup.com/mbe/article/40…

Now out in MBE! Fitness assays often involve barcoding, but barcode-dependent amplification bias can cause fitness misestimates. We present a method to detect/remove such bias with no changes to the exp. protocol. doi.org/10.1093/molbev… Ryan Seamus McGee Grant Kinsler Dmitri Petrov 1/2