October 2025

Papers:

Accelerated design of Escherichia coli reduced genomes using a whole-cell model and machine learning

Gherman I.M., et al. 2025. Cell Syst 16: 101392.

With the current climate, it's interesting to read about how people are using ML in research. This is an interesting use! But I'm always interested in ML research in where the model fails. What is it about the single deletions that the model gets wrong?

Individual-based modeling unravels spatial and social interactions in bacterial communities

Wang J., et al. 2025. ISME J. 19:

Been reading up on agent-based modeling of bacterial communities and enjoyed this recent review.

Books:

"Yellowface" By: R.F. Kuang

"BoyMom" By: Ruth Whippman

Sorry, faculty applications are cutting into my reading time and I'm still working in these two ...

TV/Movies:

Deep Cover - really enjoyed watching this the other day while I was getting over a cold!

September 2025

Papers:

Biophysics and systems biology

Noble D. 2010. Phil. Trans. R. Soc. A 368: 1125-1139.

Some interesting viewpoints on the high's and low's of molecular biology. I think we've come a long way since the 2010's in understanding how biology uses noise, but maybe that's because I have embraced a systems biology mindset.

Stochastic Pulse Regulation in Bacterial Stress Response.

Locke JCW, et al. 2011. Sci. 334: 366-369.

An older paper, but a great one! I really enjoyed revisiting one of the early stochastic/noisy gene circuit papers from the Elowitz lab.

Elementary 3D organization of active and silenced E. coli genome.

Gavrilov AA, et al. 2025. Nature. 645: 1060-1070.

An in-depth look at how the 3D structure regulates the bacterial genome. It's cool to compare and contrast this with eukaryotic genome structure.

Books:

"Yellowface" By: R.F. Kuang

"BoyMom" By: Ruth Whippman

TV:

Taskmaster