Stepan Denisov

As a first sanity check we tested the bacteria from your paper. Results looks quite similar but not identical.

Sofya is a fantastic scientist and a super nice person. Definitely recommend finding a way to work with her!

Graph showing a positive correlation between "bias in adaptive outcome" on the vertical axis and "mutation bias" on the horizontal axis, with 14 data points representing 14 respective species, with a line of best fit equal to a slope of 0.82 on the log-scale axes. Each data point contains horizontal and vertical error bars to illustrate the uncertainty in both the mutational and adaptive data. The 95% confidence interval of the slope is shown in parentheses (0.44 to 1.24), based on 10,000 simulated data sets, where the simulated data sets are based on statistical resampling of the empirical data (i.e. "bootstrap" data sets). Regression lines based on these bootstrap data sets are shown as light gray lines. The type of bias reported here refers to the ratio of transitions versus transversions, where transitions are a DNA mutation that preserves the basic structure of the DNA base (i.e. a purine-to-purine or pyrimidine-to-pyrimidine mutation), and transversions are mutations that alter the structure of the DNA base at a particular site (i.e. replacing a purine with a pyrimidine or vice versa). In other words, this graph shows that transitions contribute more toward adaptive evolution in species where transitions arise at a higher rate.

NEW PAPER! Some kinds of genetic mutations are more likely to arise than others. Such "biases" in mutation vary between species.

Analyzing data from 14 species, we show that this variation explains species differences in the genetics of adaptation!

(1/3)

www.biorxiv.org/content/10.1...

Quite similar idea to what’s done in our group in 2022: elifesciences.org/articles/64543

Frustrated little dude gripping a pencil saying “how do I pack this down into something I can actually share?” While swirling rainbows labeled “INFINITE POTENTIAL” float around them. Little dude frowns at a tiny grey box, exclaiming “all that work for THIS?!” Little dude shoves the grey box into another little guy’s hands; Frowning, stomping off, and saying “Here you go, I made this, it sucks.” Second little dude cracks open the box, swirling rainbows project out onto their face. Second little dude stares in awe at all the swirling rainbows now floating around them.

Sometimes we’re unsatisfied with a thing we made because when it only existed in our head, we saw all the things it could have been and when it’s done we know all the things that it isn’t, but we can’t see the way it expands into a million new things when someone else unpacks it in their head. 🖊️🦑

An orthogonal T7 replisome for continuous hypermutation and accelerated evolution in E. coli Systems that perform continuous hypermutation of designated genes without compromising the integrity of the host genome can substantially accelerate the evolution of new or enhanced protein functions....

Dierks et al. engineered an replisome that replicates only target plasmids at mutation rates 100,000 times higher than normal but leaving the rest of the genome unchanged. They evolved TEM-1 β-lactamase to gain strong resistance to several antibiotics in under a week. www.science.org/doi/10.1126/...

Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate Plasmids are autonomously replicating DNA molecules that stably coexist with chromosomes in bacterial cells. These genetic elements drive horizontal gene transfer and play a fundamental role in bacter...

New paper alert! 🚨

Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate.

We combine theory, simulations, experimental evolution, and bioinformatics to demonstrate that mutation rates scale with plasmid copy number.

Let's dive in! 🧵👇

Depends on the specific species. I’ll check out the species from your paper and let you know!

They have higher GC-content (if I got you right): bmcecolevol.biomedcentral.com/articles/10.... Aerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have | BMC Ecology and Evolution

Super cool talk by Parker Crossland showing that DNA in single fixed cells can be amplified & sequenced (B. subtilis, E. coli & yeast). Only 14 cells needed to cover the full yeast genome 🤯 Adding barcodes captures rare genotypes missed by colony picking 🦠 Preprint 👇🏽

#SMBE2025

Aerobic bacteria show higher A>G (and lower G>A) mutation rate than anaerobes. First results in bioinformatic project to estimate mutation spectra across bacterial tree under my supervision. Qs and ideas are wellcome. #SMBE2025

Really impressing and perfectly conceptualised work of how Genotype-Phenotype map structure influence DNA-protein specificity evolution by @joethorntonlab.bsky.social. #SMBE2025

Experimental evolution in an era of molecular manipulation - Nature Reviews Genetics In this Review, Ascensao and Desai discuss how methodological advances in genotype and phenotype manipulation are transforming experimental evolution approaches and providing new insights into the und...

Experimental evolution in an era of molecular manipulation www.nature.com/articles/s41... #jcampubs

It’s great to be at #SMBE2025 in Beijing and meet good friends!

A cartoon titled “sampling bias” showing a slide with 99.8 of survey respondents saying they love responding to surveys, and only 0.2% saying “no, I toss them in the bin”

GRC insisting on the vote for the next location being in person in the name of democracy

Hey y'all, grant-pending, I may be unemployed starting from October. If you have any leads on biotech / postdoc positions in the German-speaking part of Switzerland, I'd greatly appreciate a message. I'm great with Data Analysis, Molecular Biology, and Teaching. (Plz RT!)

More at timothyfuqua.com

Universal rules govern plasmid copy number - Nature Communications Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...

Curious about plasmid biology? Our latest paper is out now in Nature Communications! 🚨

doi.org/10.1038/s414...

We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇

Glad to take part in #AIxBio25

NIH staff and biomedical community sound alarm about agency politicization, funding slowdown In test of NIH director’s support of dissent, NIH staff sign Bethesda Declaration urging reversal of grant cuts and freezes

Breaking news: Staff at the National Institutes of Health have issued a declaration calling on their director to depoliticize the agency and reverse spending cuts.

🚨 Looking for postdocs!
I'm starting my lab at UT Southwestern this September.

If you're interested in:
🧬 Somatic & germline mutagenesis
🐭 Evolution of mutation processes
🧠 Adjacent areas like Mendelian genomics & population genetics—please consider joining.

Formal ad coming soon. DM me!

📣 Attention!🚨🚨🚨🚨🚨🚨
We’ve extended the scholarship application deadline to June 27th.
Don’t miss your chance, submit your application and abstract

A genomic catalog of Earth's bacterial and archaeal
symbionts (bioRxiv pdf): www.biorxiv.org/content/10.1...

Manchester Museum named European museum of the year ‘Gobsmacked’ director says 138-year-old museum aims to ‘build empathy for other people and the natural world’

It’s a beautiful university museum with an aim to “build empathy for other people and the natural world”. Much needed. www.theguardian.com/uk-news/2025...

YouTube video by Steve Rosenberg Stalin statue appears in the Moscow Metro

First, a statue of Soviet dictator Joseph Stalin appears in the Moscow Metro. Then a Kremlin adviser says that “from a legal standpoint the USSR still exists.” In Russia the past hangs over the present. My report from Moscow.

Petition: Keep the 5-Year ILR pathway for existing Skilled Worker visa holders Do not apply the proposed 10-year ILR rule to existing Skilled Worker visa holders. Keep the 5-year ILR route for those already in the UK on this visa. Apply any changes only to new applicants from th...

Many skilled visa holders moved to the UK for better opportunities and in return have contributed to the UK economy, paid taxes, and supported critical sectors. We think that changing ILR rules mid-journey is unfair and causes stress for families.

petition.parliament.uk/petitions/72...

website views of PhD programmes up in Netherlands. canada, sweden etc

website views from outside the US down massively in the US, up elsewhere

America is in danger of experiencing an academic brain drain 
economist.com/science-and-...

Myself and @yekwah.bsky.social are running our bacterial AMR databases and genotype prediction course again with @eventswcs.bsky.social. Completely free and study at your own pace.
Check out the course objectives below and sign up before June 9th to join us!
www.futurelearn.com/courses/anti...

My ongoing request:

If your NSF or NIH grant was terminated--whether at Harvard or elsewhere--please report it here.

NSF: grant-watch.us/submit-nsf.h...

NIH: grant-watch.us/submit-nih.h...

Our trackers are actively used in lawsuits and are often the only record that terminations ever occurred.

The evolution of robustness and fragility during long-term bacterial adaptation
#mevoSky #evoSky #evolSky #evolution #ExperimentalEvolution #LTEE

www.pnas.org/doi/10.1073/...

Explosion of formulaic research articles, including inappropriate study designs and false discoveries, based on the NHANES US national health database The combination of AI and national health databases offers opportunities, but may also be exploited by unethical agents. This study shows that there has been an explosion of formulaic research article...

Q: What happens when a #PublishOrPerish" research culture meets #AI readable biomedical databases? A: "An explosion of formulaic research articles, including inappropriate study designs and false discoveries." New in @plosbiology.org... journals.plos.org/plosbiology/...