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Stepan Denisov

@stepadenisov.bsky.social
81 followers 92 following 24 posts

Bioinformatics, molecular biology & evolution The University of Manchester, UK

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Stepan Denisov @stepadenisov.bsky.social · 14/10/2026
www.findaphd.com/phds/program... Deadlines: 23 November (Manchester) and 1 December (Oxford)
findaphd.com
FindAPhD : MRC CoRE in Exposome Immunology at The University of Manchester
Apply for a PhD: MRC CoRE in Exposome Immunology at The University of Manchester
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Stepan Denisov @stepadenisov.bsky.social · 22/04/2026
www.nature.com/articles/d41...
nature.com
Dozens of AI disease-prediction models were trained on dubious data
The models are designed to predict someone’s risk of diabetes or stroke. A few might already have been used on patients.
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Qiyun Zhu @zhuqiyun.bsky.social · 11/12/2025
The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource
nature.com
Scikit-bio: a fundamental Python library for biological omic data analysis - Nature Methods
Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis
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Vladimir (Vova) Seplyarskiy @vseplyarskiy.bsky.social · 08/12/2025
Job AD. Research Directions: 1. Selection in early development; Pop gen methods applied to new technologies, i.e. scDNA-seq with D. Shao 2. Study of hypermutability and selection using population cohorts with E. Koch 3. Evolution of Mutagenesis with M. Penenell & @jgschraiber.bsky.social
jobs.utsouthwestern.edu
POSTDOCTORAL RESEARCHER - McDermott Center HG&D - Seplyarskiy Lab
Discover POSTDOCTORAL RESEARCHER - McDermott Center HG&D - Seplyarskiy Lab and other PostDoc jobs in Dallas, TX and apply online today!
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Oded Rechavi @odedrechavi.bsky.social · 15/12/2025
When your PI presents your work
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Michael Baym @baym.lol · 20/11/2025
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/...
science.org
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...
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Axel Visel @axelvisel.bsky.social · 18/11/2025
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...
A stylized infographic showing the workflow for building a global soil plasmidome resource on the left and a textured world map on the right. The workflow depicts three input data streams from metagenomic datasets and isolate plasmids, which pass through steps like quality control, clustering, functional annotation, CRISPR analysis, host assignment, and detection of gene categories such as biosynthetic clusters, antimicrobial resistance, antimicrobial peptides, and CAZymes. All outputs feed into a central SQL database. The world map shows sample locations across the globe as teal circles of varying size, highlighting regions from many plasmids were recovered. Adapted from Fig 1A and 1B in Fiamenghi et al., doi:10.1038/s41467-025-65102-6
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Louis-Marie Bobay @lbobay.bsky.social · 18/11/2025
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
rdcu.be
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...
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Genetics Society UK @gensocuk.bsky.social · 14/11/2025
Congratulations to Joe Felsenstein on being awarded the 2026 Mendel Medal!
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Roland Hatzenpichler @environmicrobio.bsky.social · 14/11/2025
“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.”
science.org
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
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Stepan Denisov @stepadenisov.bsky.social · 13/11/2025
My talk 🤗
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Georgii "Yegor" Bazykin @gbazykin.bsky.social · 18/09/2025
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/...
faculty-emory.icims.com
Careers | Emory University | Atlanta GA
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Martin Taylor @mstaylor.bsky.social · 04/11/2025
The exciting next instalment of Mutations in Time and Space... Open for registration now
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Jean-Michel Ané @jeanmichelane.bsky.social · 04/11/2025
Please, my friends, vote for this brilliant idea from Lego! beta.ideas.lego.com/product-idea...
beta.ideas.lego.com
Biomedicine Institute | LEGO® Ideas
It all started by building a small microscope with my 8-years old daughter following her visit at my work place, a biomedical research center. She loved it and …
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Fiona J Whelan @whelanfj.bsky.social · 27/10/2025
📣 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...
findaphd.com
(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
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Stepan Denisov @stepadenisov.bsky.social · 27/10/2025
I mean it’s all the bacteria from your paper, it doesn’t include all the other bacteria to which this method can be applied.
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Stepan Denisov @stepadenisov.bsky.social · 27/10/2025
Yes. But not all the bacteria
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Stepan Denisov @stepadenisov.bsky.social · 27/10/2025
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The University of Manchester @manchester.ac.uk · 21/10/2025
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...
Discover our Bicentenary PhD Studentships and Fellowships
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Stepan Denisov @stepadenisov.bsky.social · 21/10/2025
Glad to take part!
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Stepan Denisov @stepadenisov.bsky.social · 15/10/2025
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!
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Stepan Denisov @stepadenisov.bsky.social · 02/10/2025
As a first sanity check we tested the bacteria from your paper. Results looks quite similar but not identical.
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Deepa Agashe @deepaagashe.bsky.social · 16/09/2025
Sofya is a fantastic scientist and a super nice person. Definitely recommend finding a way to work with her!
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Bryan Gitschlag @bryangitschlag.bsky.social · 08/09/2025
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...
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 · 04/09/2025
Quite similar idea to what’s done in our group in 2022: elifesciences.org/articles/64543
elifesciences.org
Predicting bacterial promoter function and evolution from random sequences
An inferred mechanistic model that connects sequence (genotype) to function (constitutive gene expression phenotype) for any random sequence in Escherichia coli reveals the structure of constitutive p...
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Kelly Turnbull @coelasquid.bsky.social · 31/08/2025
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 · 14/08/2025
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/...
science.org
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....
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Paula Ramiro-Martínez @paularamiro.bsky.social · 22/07/2025
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! 🧵👇
biorxiv.org
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...
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Stepan Denisov @stepadenisov.bsky.social · 23/07/2025
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 · 23/07/2025
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 · 22/07/2025
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 · 22/07/2025
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 · 22/07/2025
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 · 21/07/2025
Experimental evolution in an era of molecular manipulation www.nature.com/articles/s41... #jcampubs
nature.com
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...
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Stepan Denisov @stepadenisov.bsky.social · 20/07/2025
It’s great to be at #SMBE2025 in Beijing and meet good friends!
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Michael Baym @baym.lol · 04/07/2025
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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Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 24/06/2025
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
timothyfuqua.com
Home | Timothy Fuqua
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Paula Ramiro-Martínez @paularamiro.bsky.social · 02/07/2025
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 👇
doi.org
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...
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Stepan Denisov @stepadenisov.bsky.social · 23/06/2025
Glad to take part in #AIxBio25
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Science Magazine @science.org · 09/06/2025
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.
scim.ag
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
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Vladimir (Vova) Seplyarskiy @vseplyarskiy.bsky.social · 04/06/2025
🚨 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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SMBE Chile Adaptation & Evolution Meeting @smbe-chile2025.bsky.social · 01/06/2025
📣 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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Matt Hutchings @matthutchings.bsky.social · 02/06/2025
A genomic catalog of Earth's bacterial and archaeal symbionts (bioRxiv pdf): www.biorxiv.org/content/10.1...
biorxiv.org
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Michael Brockhurst @brockhurstlab.bsky.social · 28/05/2025
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...
theguardian.com
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’
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Steve Rosenberg @bbcstever.bsky.social · 29/05/2025
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.
youtu.be
Stalin statue appears in the Moscow Metro
YouTube video by Steve Rosenberg
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Stepan Denisov @stepadenisov.bsky.social · 24/05/2025
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.parliament.uk
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...
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Christian Odendahl @codendahl.bsky.social · 22/05/2025
America is in danger of experiencing an academic brain drain  economist.com/science-and-...
website views of PhD programmes up in Netherlands. canada, sweden etc website views from outside the US down massively in the US, up elsewhere
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Conor (Conchúr) Meehan @conmeehan.bsky.social · 22/05/2025
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...
futurelearn.com
Antimicrobial Databases and Genotype Prediction - Online Course - FutureLearn
Transform your understanding of antimicrobial resistance (AMR) and elevate your research or clinical practice with Wellcome Connecting Science.
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Scott Delaney @scott-delaney.bsky.social · 14/05/2025
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.
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Brian D. Wade @astrobrian.bsky.social · 22/04/2025
The evolution of robustness and fragility during long-term bacterial adaptation #mevoSky #evoSky #evolSky #evolution #ExperimentalEvolution #LTEE www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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