Stepan Denisov
@stepadenisov.bsky.social
Bioinformatics, molecular biology & evolution
The University of Manchester, UK
The University of Manchester, UK
Reposted by Stepan Denisov
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Stepan Denisov
Soils contain an amazing diversity of functions encoded in plasmids.
The Global Soil Plasmidome Resource: 98,728 soil plasmids from 6,860 samples.
Led by @mattlabguy.bsky.social and @apcamargo.bsky.social at @jgi.doe.gov @biosci.lbl.gov @berkeleylab.lbl.gov
www.nature.com/articles/s41...
The Global Soil Plasmidome Resource: 98,728 soil plasmids from 6,860 samples.
Led by @mattlabguy.bsky.social and @apcamargo.bsky.social at @jgi.doe.gov @biosci.lbl.gov @berkeleylab.lbl.gov
www.nature.com/articles/s41...
November 18, 2025 at 7:18 PM
Soils contain an amazing diversity of functions encoded in plasmids.
The Global Soil Plasmidome Resource: 98,728 soil plasmids from 6,860 samples.
Led by @mattlabguy.bsky.social and @apcamargo.bsky.social at @jgi.doe.gov @biosci.lbl.gov @berkeleylab.lbl.gov
www.nature.com/articles/s41...
The Global Soil Plasmidome Resource: 98,728 soil plasmids from 6,860 samples.
Led by @mattlabguy.bsky.social and @apcamargo.bsky.social at @jgi.doe.gov @biosci.lbl.gov @berkeleylab.lbl.gov
www.nature.com/articles/s41...
Reposted by Stepan Denisov
Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf
Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy
Nature Communications - It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core...
rdcu.be
November 18, 2025 at 9:01 PM
Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf
Reposted by Stepan Denisov
Congratulations to Joe Felsenstein on being awarded the 2026 Mendel Medal!
November 14, 2025 at 12:41 PM
Congratulations to Joe Felsenstein on being awarded the 2026 Mendel Medal!
Reposted by Stepan Denisov
“The prohibited activities would include joint research, co-authorship on papers, and advising a foreign graduate student or postdoctoral fellow. The language is retroactive, meaning any interactions during the previous 5 years could make a scientist ineligible for future federal funding.”
U.S. Congress considers sweeping ban on Chinese collaborations
Researchers speak out against proposal that would bar funding for U.S. scientists working with Chinese partners or training Chinese students
www.science.org
November 14, 2025 at 1:03 AM
“The prohibited activities would include joint research, co-authorship on papers, and advising a foreign graduate student or postdoctoral fellow. The language is retroactive, meaning any interactions during the previous 5 years could make a scientist ineligible for future federal funding.”
My talk 🤗
In this week’s seminar we learned about the evolution of intrinsic terminators from @stepadenisov.bsky.social 🧬
Made even more fun by snacks kindly sponsored by @microbesng.bsky.social 🍪
Made even more fun by snacks kindly sponsored by @microbesng.bsky.social 🍪
November 13, 2025 at 5:43 PM
My talk 🤗
Reposted by Stepan Denisov
Now hiring a computational postdoc (evolutionary genomics, molecular evolution) in my lab at Emory University.
If you’re interested in population genetics, fitness landscapes, and viral evolution — get in touch.
faculty-emory.icims.com/jobs/151181/...
If you’re interested in population genetics, fitness landscapes, and viral evolution — get in touch.
faculty-emory.icims.com/jobs/151181/...
Careers | Emory University | Atlanta GA
faculty-emory.icims.com
September 18, 2025 at 3:38 PM
Now hiring a computational postdoc (evolutionary genomics, molecular evolution) in my lab at Emory University.
If you’re interested in population genetics, fitness landscapes, and viral evolution — get in touch.
faculty-emory.icims.com/jobs/151181/...
If you’re interested in population genetics, fitness landscapes, and viral evolution — get in touch.
faculty-emory.icims.com/jobs/151181/...
Reposted by Stepan Denisov
The exciting next instalment of Mutations in Time and Space... Open for registration now
Explore the origins, patterns and consequences of mutations across biological systems! #MITS26
🗓️ Conference dates: 13-15 April 2026
Participate in expert-led knowledge exchange on how genome evolution shapes human health and ageing 🧬
Check out our exciting speakers ➡️ bit.ly/4hmbnyr
#Genomics
🗓️ Conference dates: 13-15 April 2026
Participate in expert-led knowledge exchange on how genome evolution shapes human health and ageing 🧬
Check out our exciting speakers ➡️ bit.ly/4hmbnyr
#Genomics
November 4, 2025 at 10:28 AM
The exciting next instalment of Mutations in Time and Space... Open for registration now
Reposted by Stepan Denisov
Reposted by Stepan Denisov
📣 PhD opportunity led by @madhvimenon.bsky.social with @kathelse.bsky.social , @tracyh9494.bsky.social , and me open now:
"Sex Differences in Immune Responses to Infection: The Role of the Microbiota in Shaping Lymphocyte Dynamics"
apps due 15 November 2025 📣
www.findaphd.com/phds/project...
"Sex Differences in Immune Responses to Infection: The Role of the Microbiota in Shaping Lymphocyte Dynamics"
apps due 15 November 2025 📣
www.findaphd.com/phds/project...
(Bicentenary) Sex Differences in Immune Responses to Infection: The Role of the Microbiota in Shaping Lymphocyte Dynamics at The University of Manchester on FindAPhD.com
PhD Project - (Bicentenary) Sex Differences in Immune Responses to Infection: The Role of the Microbiota in Shaping Lymphocyte Dynamics at The University of Manchester, listed on FindAPhD.com
www.findaphd.com
October 27, 2025 at 3:24 PM
📣 PhD opportunity led by @madhvimenon.bsky.social with @kathelse.bsky.social , @tracyh9494.bsky.social , and me open now:
"Sex Differences in Immune Responses to Infection: The Role of the Microbiota in Shaping Lymphocyte Dynamics"
apps due 15 November 2025 📣
www.findaphd.com/phds/project...
"Sex Differences in Immune Responses to Infection: The Role of the Microbiota in Shaping Lymphocyte Dynamics"
apps due 15 November 2025 📣
www.findaphd.com/phds/project...
Reposted by Stepan Denisov
Applications are now open for 200 new PhD Studentships and Fellowships.
We're investing in early career researchers, in partnership with philanthropic support - to develop the next generation of research leaders.
Share with someone you know!
www.manchester.ac.uk/research/bic...
We're investing in early career researchers, in partnership with philanthropic support - to develop the next generation of research leaders.
Share with someone you know!
www.manchester.ac.uk/research/bic...
October 21, 2025 at 8:19 AM
Applications are now open for 200 new PhD Studentships and Fellowships.
We're investing in early career researchers, in partnership with philanthropic support - to develop the next generation of research leaders.
Share with someone you know!
www.manchester.ac.uk/research/bic...
We're investing in early career researchers, in partnership with philanthropic support - to develop the next generation of research leaders.
Share with someone you know!
www.manchester.ac.uk/research/bic...
Glad to take part!
A fun little side project I've been working on with @stepadenisov.bsky.social , Mato Lagator, and Andreas Wagner: "Strong promoters are mutationally robust". Briefly...
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Strong promoters are mutationally robust
Mutational robustness is the persistence of a phenotype upon mutation. It facilitates molecular evolution and has been characterized in a variety of biological systems, but studies of prokaryotic prom...
www.biorxiv.org
October 21, 2025 at 9:13 AM
Glad to take part!
Hey Bluesky! 👋 I’m a bioinformatician (PostDoc, University of Manchester 🇬🇧) fascinated by eukaryotic & prokaryotic #genomics, #transcriptomics, and molecular #evolution.
I’m exploring new opportunities in the UK — let’s connect!
I’m exploring new opportunities in the UK — let’s connect!
October 15, 2025 at 8:01 AM
Hey Bluesky! 👋 I’m a bioinformatician (PostDoc, University of Manchester 🇬🇧) fascinated by eukaryotic & prokaryotic #genomics, #transcriptomics, and molecular #evolution.
I’m exploring new opportunities in the UK — let’s connect!
I’m exploring new opportunities in the UK — let’s connect!
Reposted by Stepan Denisov
Sofya is a fantastic scientist and a super nice person. Definitely recommend finding a way to work with her!
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!
September 16, 2025 at 10:57 AM
Sofya is a fantastic scientist and a super nice person. Definitely recommend finding a way to work with her!
Reposted by Stepan Denisov
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...
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...
September 8, 2025 at 7:38 PM
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...
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
September 4, 2025 at 12:03 PM
Quite similar idea to what’s done in our group in 2022: elifesciences.org/articles/64543
Reposted by Stepan Denisov
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. 🖊️🦑
August 31, 2025 at 9:04 AM
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. 🖊️🦑
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
August 14, 2025 at 1:17 PM
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/...
Reposted by Stepan Denisov
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.
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
July 22, 2025 at 9:38 AM
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.
We combine theory, simulations, experimental evolution, and bioinformatics to demonstrate that mutation rates scale with plasmid copy number.
Let's dive in! 🧵👇
Reposted by Stepan Denisov
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
#SMBE2025
July 22, 2025 at 9:34 AM
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
#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
July 22, 2025 at 1:13 PM
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
July 22, 2025 at 3:04 AM
Really impressing and perfectly conceptualised work of how Genotype-Phenotype map structure influence DNA-protein specificity evolution by @joethorntonlab.bsky.social. #SMBE2025
Reposted by Stepan Denisov
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
July 21, 2025 at 4:25 PM
Experimental evolution in an era of molecular manipulation www.nature.com/articles/s41... #jcampubs
Reposted by Stepan Denisov
GRC insisting on the vote for the next location being in person in the name of democracy
July 4, 2025 at 10:03 AM
GRC insisting on the vote for the next location being in person in the name of democracy