Stepan Denisov
@stepadenisov.bsky.social
Bioinformatics, molecular biology & evolution The University of Manchester, UK
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
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
nature.com
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
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!
jobs.utsouthwestern.edu
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/...
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...
science.org
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...
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
Congratulations to Joe Felsenstein on being awarded the 2026 Mendel Medal!
“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
science.org
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/...
Careers | Emory University | Atlanta GA
faculty-emory.icims.com
The exciting next instalment of Mutations in Time and Space... Open for registration now
Wellcome Connecting Science Learning and Training@eventswcs.bsky.social · 11mo agoExplore 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
Please, my friends, vote for this brilliant idea from Lego! beta.ideas.lego.com/product-idea...
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 …
beta.ideas.lego.com
📣 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...
(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
findaphd.com
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...
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!
Sofya is a fantastic scientist and a super nice person. Definitely recommend finding a way to work with her!
Sofya Garushyants@garushyants.bsky.social · last yr.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!
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
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...
elifesciences.org
Alejandro Montenegro@aemonten.bsky.social · last yr."We propose a model in which TF binding is not determined by individual binding sites, but rather by the sum of multiple, overlapping binding sites." www.nature.com/articles/s41...
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....
science.org
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...
biorxiv.org
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 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...
nature.com
It’s great to be at #SMBE2025 in Beijing and meet good friends!
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
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