Stepan Denisov @stepadenisov.bsky.social · 22/04/2026www.nature.com/articles/d41...nature.comDozens of AI disease-prediction models were trained on dubious dataThe models are designed to predict someone’s risk of diabetes or stroke. A few might already have been used on patients. 000
Reposted by Stepan DenisovQiyun Zhu @zhuqiyun.bsky.social · 11/12/2025The 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 #OpenSourcenature.comScikit-bio: a fundamental Python library for biological omic data analysis - Nature MethodsNature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis 39852
Reposted by Stepan DenisovVladimir (Vova) Seplyarskiy @vseplyarskiy.bsky.social · 08/12/2025Job 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.socialjobs.utsouthwestern.eduPOSTDOCTORAL RESEARCHER - McDermott Center HG&D - Seplyarskiy LabDiscover POSTDOCTORAL RESEARCHER - McDermott Center HG&D - Seplyarskiy Lab and other PostDoc jobs in Dallas, TX and apply online today! 198
Reposted by Stepan DenisovOded Rechavi @odedrechavi.bsky.social · 15/12/2025When your PI presents your work 621729
Reposted by Stepan DenisovMichael Baym @baym.lol · 20/11/2025Hot 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.orgIntracellular competition shapes plasmid population dynamicsFrom populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g... 11437199
Reposted by Stepan DenisovAxel Visel @axelvisel.bsky.social · 18/11/2025Soils 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... 0127
Reposted by Stepan DenisovLouis-Marie Bobay @lbobay.bsky.social · 18/11/2025Our 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/eQAMfrdcu.beIntrogression impacts the evolution of bacteria, but species borders are rarely fuzzyNature 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... 16043
Reposted by Stepan DenisovGenetics Society UK @gensocuk.bsky.social · 14/11/2025Congratulations to Joe Felsenstein on being awarded the 2026 Mendel Medal! 010131
Reposted by Stepan DenisovRoland 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.orgU.S. Congress considers sweeping ban on Chinese collaborationsResearchers speak out against proposal that would bar funding for U.S. scientists working with Chinese partners or training Chinese students 56583299
Reposted by Stepan DenisovGeorgii "Yegor" Bazykin @gbazykin.bsky.social · 18/09/2025Now 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.comCareers | Emory University | Atlanta GA 01528
Reposted by Stepan DenisovMartin Taylor @mstaylor.bsky.social · 04/11/2025The exciting next instalment of Mutations in Time and Space... Open for registration now 077
Reposted by Stepan DenisovJean-Michel Ané @jeanmichelane.bsky.social · 04/11/2025Please, my friends, vote for this brilliant idea from Lego! beta.ideas.lego.com/product-idea...beta.ideas.lego.comBiomedicine Institute | LEGO® IdeasIt 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 … 2298
Reposted by Stepan DenisovFiona 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.comPhD 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 068
Reposted by Stepan DenisovThe University of Manchester @manchester.ac.uk · 21/10/2025Applications 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... 025
Stepan Denisov @stepadenisov.bsky.social · 15/10/2025Hey 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! 020
Reposted by Stepan DenisovDeepa Agashe @deepaagashe.bsky.social · 16/09/2025Sofya is a fantastic scientist and a super nice person. Definitely recommend finding a way to work with her! 031
Reposted by Stepan DenisovBryan Gitschlag @bryangitschlag.bsky.social · 08/09/2025NEW 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... 23013
Stepan Denisov @stepadenisov.bsky.social · 04/09/2025Quite similar idea to what’s done in our group in 2022: elifesciences.org/articles/64543elifesciences.orgPredicting bacterial promoter function and evolution from random sequencesAn 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... 010
Reposted by Stepan DenisovKelly Turnbull @coelasquid.bsky.social · 31/08/2025Sometimes 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. 🖊️🦑 153258748947
Stepan Denisov @stepadenisov.bsky.social · 14/08/2025Dierks 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.orgAn orthogonal T7 replisome for continuous hypermutation and accelerated evolution in E. coliSystems 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.... 021
Reposted by Stepan DenisovPaula Ramiro-Martínez @paularamiro.bsky.social · 22/07/2025New 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.orgPlasmids promote bacterial evolution through a copy number-driven increase in mutation ratePlasmids 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... 27336
Reposted by Stepan DenisovSelene FeRNAndez @selfdz.bsky.social · 22/07/2025Super 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 283
Stepan Denisov @stepadenisov.bsky.social · 22/07/2025Aerobic 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 2276
Stepan Denisov @stepadenisov.bsky.social · 22/07/2025Really impressing and perfectly conceptualised work of how Genotype-Phenotype map structure influence DNA-protein specificity evolution by @joethorntonlab.bsky.social. #SMBE2025 0112
Reposted by Stepan DenisovCameron Thrash @jcamthrash.bsky.social · 21/07/2025Experimental evolution in an era of molecular manipulation www.nature.com/articles/s41... #jcampubsnature.comExperimental evolution in an era of molecular manipulation - Nature Reviews GeneticsIn 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... 02319
Stepan Denisov @stepadenisov.bsky.social · 20/07/2025It’s great to be at #SMBE2025 in Beijing and meet good friends! 052
Reposted by Stepan DenisovMichael Baym @baym.lol · 04/07/2025GRC insisting on the vote for the next location being in person in the name of democracy 1409
Reposted by Stepan DenisovTimothy Fuqua @timothyfuqua.bsky.social · 24/06/2025Hey 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.comtimothyfuqua.comHome | Timothy Fuqua 149
Reposted by Stepan DenisovPaula Ramiro-Martínez @paularamiro.bsky.social · 02/07/2025Curious 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.orgUniversal rules govern plasmid copy number - Nature CommunicationsPlasmids 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... 411754
Reposted by Stepan DenisovScience Magazine @science.org · 09/06/2025Breaking 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.agNIH staff and biomedical community sound alarm about agency politicization, funding slowdownIn test of NIH director’s support of dissent, NIH staff sign Bethesda Declaration urging reversal of grant cuts and freezes 9403159
Reposted by Stepan DenisovVladimir (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! 064
Reposted by Stepan DenisovSMBE 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 036
Reposted by Stepan DenisovMatt Hutchings @handle.invalid · 02/06/2025A genomic catalog of Earth's bacterial and archaeal symbionts (bioRxiv pdf): www.biorxiv.org/content/10.1...biorxiv.org 01810
Reposted by Stepan DenisovMichael Brockhurst @brockhurstlab.bsky.social · 28/05/2025It’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.comManchester 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’ 083
Reposted by Stepan DenisovSteve Rosenberg @bbcstever.bsky.social · 29/05/2025First, 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.beStalin statue appears in the Moscow MetroYouTube video by Steve Rosenberg 45445147
Stepan Denisov @stepadenisov.bsky.social · 24/05/2025Many 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.ukPetition: Keep the 5-Year ILR pathway for existing Skilled Worker visa holdersDo 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... 010
Reposted by Stepan DenisovChristian Odendahl @codendahl.bsky.social · 22/05/2025America is in danger of experiencing an academic brain drain economist.com/science-and-... 571118421
Reposted by Stepan DenisovConor (Conchúr) Meehan @conmeehan.bsky.social · 22/05/2025Myself 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.comAntimicrobial Databases and Genotype Prediction - Online Course - FutureLearnTransform your understanding of antimicrobial resistance (AMR) and elevate your research or clinical practice with Wellcome Connecting Science. 11719
Reposted by Stepan DenisovScott Delaney @scott-delaney.bsky.social · 14/05/2025My 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. 15437396
Reposted by Stepan DenisovBrian D. Wade @astrobrian.bsky.social · 22/04/2025The evolution of robustness and fragility during long-term bacterial adaptation #mevoSky #evoSky #evolSky #evolution #ExperimentalEvolution #LTEE www.pnas.org/doi/10.1073/...pnas.orgPNASProceedings 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... 0225
Reposted by Stepan DenisovRoli Roberts @roliroberts.bsky.social · 08/05/2025Q: 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/...journals.plos.orgExplosion of formulaic research articles, including inappropriate study designs and false discoveries, based on the NHANES US national health databaseThe 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... 0148
Reposted by Stepan Denisovlauren-stadler.bsky.social @lauren-stadler.bsky.social · 18/03/2025Fresh in @NatureBiotech! We developed a synthetic biology tool for tracking gene transfer in microbial communities and applied it to study plasmid hosts in a wastewater microbiome. Awesome collab with James Chappell & @joffsilberg.bsky.social and incredible students. www.nature.com/articles/s41...nature.comInformation storage across a microbial community using universal RNA barcoding - Nature BiotechnologyBarcoding microbial ribosomal RNA creates a recording of gene transfer events without requiring translation. 37532
Reposted by Stepan DenisovInternational Society of Antimicrobial Chemotherapy @isacworld.bsky.social · 22/04/2025📢ISAC webinar announcement Darwin meets the antibiotic crisis: how to use evolutionary principles to optimise #antibiotic therapy Organised by the Early Career Working Group 📆2 May 🕰 12.00 Register⬇️ tinyurl.com/yc6df5w7 @jinxin-zhao.bsky.social @souhakanj.bsky.social @heiman-wertheim.bsky.social 122
Reposted by Stepan DenisovMaxim Greenberg @maxvcg.bsky.social · 11/04/2025The Americans are doing to Kseniia what the Russians did to Brittney Griner for having 0.7 grams of cannabis oil. Except no one is coming to negotiate her freedom and Harvard is sitting on their hands. I am so ashamed. Please share this story. www.nytimes.com/2025/04/11/s...nytimes.comShe Worked in a Harvard Lab to Reverse Aging, Until ICE Jailed Her (Gift Article)President Trump’s immigration crackdown ensnared Kseniia Petrova, a scientist who fled Russia after protesting its invasion of Ukraine. She fears arrest if she is deported there. 07664
Reposted by Stepan DenisovOlivier Borkowski @oborkowski.bsky.social · 05/04/2025Sustainable regeneration of 20 aminoacyl-tRNA synthetases in a reconstituted system toward self-synthesizing artificial systems www.science.org/doi/10.1126/...science.orgSustainable regeneration of 20 aminoacyl-tRNA synthetases in a reconstituted system toward self-synthesizing artificial systemsAn in vitro system is capable of sustainably regenerating 20 aminoacyl-tRNA synthetases toward artificial cells. 0249
Reposted by Stepan DenisovShaily Patel @vox-magica.bsky.social · 28/03/2025Although the legal penalty for improperly importing… is simply a fine of up to $500, immigration officers decided to deny Petrova re-entry to the US. When she informed [them] of her very real fear of being jailed for protesting Putin’s war on Ukraine…, “she was transferred to ICE, into detention.theguardian.comRussian scientist working at Harvard detained by Ice at Boston airportKseniia Petrova was returning to the US from a trip to France when officials revoked her visa and detained her 1137
Reposted by Stepan DenisovFiona J Whelan @whelanfj.bsky.social · 28/03/2025Come join us! Next week marks my 1 year anniversary at @uniofmanchester.bsky.social and I've never looked back! 01213
