Sergey Kryazhimskiy

Magnesium depletion by Candida albicans unleashes two unusual modes of colistin resistance in Pseudomonas aeruginosa with different fitness costs Bacterial resistance to the vital last-resort antibiotic colistin is an increasing challenge. This study shows that magnesium sequestration by C. albicans enables P. aeruginosa to evolve much higher l...

Our story on the evolution of colistin resistance is just out on @plosbiology.org (journals.plos.org/plosbiology/... Evolution doesn’t happen in isolation. We show that competing fungi can rewire the evolutionary trajectory of colistin resistance in P. aeruginosa. Great teamwork with the Ernst lab

LAB of PIE We study the mechanisms of cross-kingdom microbial competition and how it influences microbial evolution and interaction with hosts

Curious about why polymicrobial interaction matters? Check out more future work from my lab (www.labofpie.org)

Researchers in the US might be having feelings about writing grants atm-I know I am!

We still need to write them. In this Evolution Exchange, I again chat with Sam Scheiner, who summarizes how to write a competitive proposal.

His advice is gold, and helpful regardless of funder. Pls RT!

a headshot of David Botstein

We are deeply saddened to share the news of the passing of David Botstein, a towering figure in modern #genetics and a foundational force behind SGD.
www.yeastgenome.org/blog/in-memo... #yeast #modelOrganism

Preposterous! Saying that Russell Vought is a leech would be an insult to leeches.

Very sad news. David Botstein made enormous contributions to molecular biology & genetics. I first met him in a grad school interview. I learned something from him each of the few times I saw him since. Indelible personality. Here he is giving a keynote at the 2015 UCSD Genetics Retreat.

I was sad to learn that my postdoctoral mentor, David Botstein, died yesterday. I started with David as a postdoc in 1998, and he had a profound effect on both my life and scientific career. He was a giant in the field of genetics, making seminal contributions in both yeast and human genetics. 1/

Would love to hear about recent AI experiences of other researchers? @wcratcliff.bsky.social, @baym.lol?

It often goes down rabbit holes and gets confused, but usually manages to pull itself out and eventually focuses on the most reasonable trains of thought. Overall, while it did not offer any new brilliant ideas, the conversation gave me at least one small lead that could be useful. Very cool!

I have to say, I am quite impressed with Claude-Opus-4.6. I had very interesting conversation with it trying to explain a puzzling phenomenon that we observed in our experiments. The internal monologue is fascinating and reveals solid reasoning characteristic of a very good 1st year PhD student.

Federal funding for US biomedical research is moribund.

Since October 1 2025, NIH is -80% in new grants and -70% in values (total dollars).

Labs are closing down and researchers are leaving science.

To what end?

Jeffrey Epstein’s tissue samples ignited a furor in the Harvard lab of George Church Exclusive: Harvard geneticist George Church knew more about Jeffrey Epstein's activities than he has previously said, before accepting new donations from the sex offender.

OK I don't have access to the whole article but the overall point / summary is very very troubling www.statnews.com/2026/02/24/e... #epstein

It's just something else that is getting educated 🥲

How to avoid getting an education while paying for one:

It is incredible how out of touch with reality these people are

#Genomics methodologies can often introduce bias, resulting in inaccurate predictions.

In #GENETICS, Michael Overton and @skryazhi.bsky.social present an improved genotyping pipeline for analyzing mutation accumulation in #yeast with a more reliable statistical estimations. buff.ly/1rcGasy

Country's budget is the clearest quantification of society's values.

Can we simulate realistic evolutionary trajectories and “replay the tape of life”? In this work, we propose a flexible, generalizable deep learning framework for modeling how the entire protein sequence evolves over time while capturing complex interactions across sites. 1/n
doi.org/10.64898/202...

Thanks! I'll reach out by email and we'll coordinate.

It actually looks like complex mutations that we detect carry *more* non-synonymous changes than simple mutations. Hmm...

We see no evidence of that (correlation btw allele frequencies does not decay with genomic distance).

I know! Would love to chat and get your input. We are still trying to find any technical explanations, but we already ruled out most of the things we could think of. The graph above is from Chlamy. Yeast in the same flasks evolves "normally" and dN/dS increases with multiplicity, as expected.

My current hypothesis is that there are more complex mutations among high multiplicity genes, meaning that complex mutations are drivers. But dN/dS estimates become essentially meaningless for such mutations.

Thanks! We are seeing such complex mutations occurring at very high rates in one of our evolution experiments. And they appear to drive down dN/dS. On the plot below, the x-axis show the multiplicity of a gene (how many times it was hit by mutations in independent lines).

1/5) Re-reading this excellent paper on using mutation-selection balance models to quantify positive selection. The discussed lack of congruence between MK approaches and classic dN/dS test is entirely unsurprising, see thread below.
www.pnas.org/doi/10.1073/...

Presumably, complex multi-nucleotide mutations/substitutions could also lead to false negatives. What's a good reference that discusses such substitutions?

Thanks!

For example, they asked to add a separate reference list to my supplementary data file. Anyone experienced this? I think it's would create unnecessary confusion.

(1) So far, I received 3 sequential requests to update the ms and the supp files. Why can't they just send one complete list? How many more rounds should I expect?

(2) And I have not encountered weirder and stricter requirements for formatting supp files in any other journal!

I have never had a more painful, awkward and inefficient post-acceptance/production experience than in PLoS Computational Biology. [Apparently not on Blue Sky, so tagging @plos.org and EiC @fmacg.bsky.social.]

Is it just me or do others have issues there too?