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Stepan Denisov @stepadenisov.bsky.social · 6d

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

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Reposted by Stepan Denisov

Deepa Agashe @deepaagashe.bsky.social · 22d

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

Sofya Garushyants @garushyants.bsky.social · 23d

hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!

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Reposted by Stepan Denisov

Bryan Gitschlag @bryangitschlag.bsky.social · Sep 8

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!

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

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.

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Stepan Denisov @stepadenisov.bsky.social · Sep 4

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

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Kelly Turnbull @coelasquid.bsky.social · Aug 31

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. 🖊️🦑

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.

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Stepan Denisov @stepadenisov.bsky.social · Aug 14

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/...

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....

www.science.org

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Paula Ramiro-Martínez @paularamiro.bsky.social · Jul 22

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! 🧵👇

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...

www.biorxiv.org

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Stepan Denisov @stepadenisov.bsky.social · Jul 23

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

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Stepan Denisov @stepadenisov.bsky.social · Jul 22

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

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Selene FeRNAndez @selfdz.bsky.social · Jul 22

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

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Stepan Denisov @stepadenisov.bsky.social · Jul 22

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

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Stepan Denisov @stepadenisov.bsky.social · Jul 22

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

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Cameron Thrash @jcamthrash.bsky.social · Jul 21

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

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...

www.nature.com

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Stepan Denisov @stepadenisov.bsky.social · Jul 20

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

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Michael Baym @baym.lol · Jul 4

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

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”

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Reposted by Stepan Denisov

Timothy Fuqua 🏳‍🌈 @timothyfuqua.bsky.social · Jun 24

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

Home | Timothy Fuqua

timothyfuqua.com

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Reposted by Stepan Denisov

Paula Ramiro-Martínez @paularamiro.bsky.social · Jul 2

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 👇

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...

doi.org

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Stepan Denisov @stepadenisov.bsky.social · Jun 23

Glad to take part in #AIxBio25

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Science Magazine @science.org · Jun 9

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.

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

scim.ag

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Vladimir (Vova) Seplyarskiy @vseplyarskiy.bsky.social · Jun 4

🚨 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!

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Reposted by Stepan Denisov

SMBE Chile Adaptation & Evolution Meeting @smbe-chile2025.bsky.social · Jun 1

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

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Reposted by Stepan Denisov

Matt Hutchings @matthutchings.bsky.social · Jun 2

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

www.biorxiv.org

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Michael Brockhurst @brockhurstlab.bsky.social · May 28

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...

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’

www.theguardian.com

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Steve Rosenberg @bbcstever.bsky.social · May 29

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.

Stalin statue appears in the Moscow Metro

YouTube video by Steve Rosenberg

youtu.be

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Stepan Denisov @stepadenisov.bsky.social · May 24

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...

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...

petition.parliament.uk

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