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Nicolas Tromas

@cyanophage.bsky.social
1.3K followers 753 following 47 posts

Cyano lover, working on Cyanobacteria-cyanophages dynamic, bloom toxicity prediction, cyano microbiome. Evolutionary ecologist, fake-bioinformatician & author of children book.

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Reposted by Nicolas Tromas
Craig MacLean @craigmaclean.bsky.social · 30/09/2026
Postdoc position available in my group to work on ERC funded project on evolutionary biology of antibiotic resistance. Looking for someone with expertise in bacterial genetics, AMR, and evolutionary biology. www.jobs.ac.uk/job/DSZ416/p...
jobs.ac.uk
Postdoctoral Research Associate at University of Oxford
Explore an exciting academic career as a Postdoctoral Research Associate. Don't miss out on other academic jobs. Click to apply and explore more opportunities.
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
Our latest, spearheaded by the truly indefatigable @emderrick.bsky.social in which we search for selective sweeps in nature and genetic targets of selection within a species in the context of a diverse background community @isme-microbes.bsky.social doi.org/10.1093/isme... 🧵 1/n
doi.org
Validate User
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Didier Mazel @amazeld.bsky.social · 18/09/2026
Dear all, I have the pleasure to inform you that the online course "Resistance to Antibacterial Agents", produced by the Institut Pasteur, will start on November 3, 2026. How does ABR emerge and spread? ... 🔗 www.fun-mooc.fr/en/courses/r...
fun-mooc.fr
Resistance to antibacterial agents
The origin, risks, diagnosis, epidemiology of resistance to antibacterial agents in man and livestock worldwide, as well as preventive and countermeasures, in a « one health » perspective.
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Will Ratcliff @wcratcliff.bsky.social · 15/09/2026
1/17 Submissions are now open for the 2027 Microbial Population Biology GRC! We expect this meeting to be extraordinarily oversubscribed. If you want to come, time is of the essence--apply ASAP! June 27–July 2 • Andover, NH www.grc.org/microbial-po...
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Asher Leeks @asherleeks.bsky.social · 16/09/2026
Come work with @viromehunter.bsky.social and myself at UBC! We have a postdoctoral position available for someone with an interest in bioinformatics and genomics, using sociovirology to understand disease dynamics in plant viruses. Advert: ppvlab.sites.olt.ubc.ca/files/2026/0...
ppvlab.sites.olt.ubc.ca
Browser Verification | UBC Cybersecurity
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Nicolas Tromas @cyanophage.bsky.social · 13/09/2026
ici.radio-canada.ca/info/videos/...
ici.radio-canada.ca
IA : pourquoi certains chercheurs craignent-ils de perdre le contrôle?
Dans la dernière année, les intelligences artificielles ont menti, dissimulé, fait du chantage. De plus en plus d’experts du domaine ont peur que ces intelligences gagnent en pouvoir et échappent à no...
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Meaghan Castledine @mcastd.bsky.social · 10/09/2026
🦠Fully funded PhD project with myself, Angus Buckling, Jo Lello and Phil Mitchelmore🦠 How should we design phage therapeutics for bacterial co-infections? How do interactions between pathogens affect treatment efficacy? Please get in touch if you have any Qs 💃 shorturl.at/39Xea
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David Sünderhauf @davvi36.bsky.social · 10/09/2026
Please share! We are looking for a PhD student excited about gene transfer, and tackling Antimicrobial Resistance in Klebsiella pneumoniae. 🧬 More details & applications on funder website by 21st Oct 👇🏻 gw4biomed.ac.uk/developing-c...
gw4biomed.ac.uk
Developing CRISPR-Cas antimicrobials to tackle antibiotic resistance spread in Klebsiella pneumoniae - GW4 BioMed MRC DTP
Project Code IIAR27Ex van Houte Project Type Wet lab Research Theme Infection, Immunity, and Antimicrobial Resistance Project Summary Download Summary Antimicrobial resistance (AMR) poses a major thre...
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Ché Pillay @chepillay.bsky.social · 08/09/2026
The cited Microbiology Spectrum paper is here: journals.asm.org/doi/10.1128/... Interesting reading - the way I was taught aseptic technique may have just been a waste of time.
journals.asm.org
As a component of aseptic technique, Bunsen burners do not universally decrease deposition of microbe-containing particles | Microbiology Spectrum
The ability to manipulate and control microbial presence in built environments is imperative to research and medicine. The lack of documented evidence relating Bunsen burner use and airborne contamina...
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John Lees @johnlees.bacpop.org · 03/09/2026
I am hiring in this round – please do apply if you are interested in: machine learning (protein/genome/gene language models), methods for pathogen data analysis, pangenomes (or share with any students who might want to work with us)
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Nicolas Tromas @cyanophage.bsky.social · 11/08/2026
@tf1info.bsky.social Pas sûr que promouvoir des solutions miracles contre les cyanobactéries ne soit une bonne idée. Avant d'indiquer que ces solutions court-terme fonctionnent, essayer de faire un peu de recherche svp :)
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Nicolas Tromas @cyanophage.bsky.social · 19/07/2026
With such FIFA leaders, football is dead. Probably one of the worst World Cups ever.
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Libération @liberation.fr · 19/07/2026
Le texte, lancé par la coalition «Désarmer Bolloré», reproche à la SNCF le contrat qui la lie aux enseignes Relay, devenues «les vitrines de l’extrême droite et du climato-négationnisme». ➡️ l.liberation.fr/yr6
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Florian Altermatt @florianaltermatt.bsky.social · 17/07/2026
I am #hiring! In my group 📍Universität Zürich | University of Zurich & Eawag I have #two open #Postdoc #Positions, with application deadlines in early August 2026. 🧬 🦐 🐠🌐🌍 Here a quick reminder & 🧵with all details, thanks for 🔄 redistributing to interested candidates.
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Rosalie Bruel @rosaliebruel.bsky.social · 08/07/2026
📢 postdoc offer @umrcarrtel.bsky.social, France National-scale modelling of lake warming and water-level dynamics under climate change More: ℹ️ jobs INRAE : jobs.inrae.fr/en/ot-29378 👨‍💻 lab website, includes a pdf containing all the information: carrtel.lyon-grenoble.hub.inrae.fr/news/postdoc...
A poster presenting the project. The poster reads:

Postdoc offer 2026 - National-scale modelling of lake warming and water-level dynamics under climate change

The project will combine in situ data (A), remote sensing (B), and modelling (C) to model the 1D lake thermal structure of at least 210 reservoirs (D), i.e., sites for which a proof of concept is available. The model outputs will then be analysed to assess reservoir responses to climate change and water level management practices at the national scale.Your future lunch view? 
Picture taken from the lab’s private access to Lake Geneva. The lake is clear, the sky is blue.Picture taken from the main building: a large daphnia made a drift wood is seen in the park, Lake Geneva is visible in the back.
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Deborah Bourc’his @deborahbourchis.bsky.social · 27/06/2026
Coupes drastiques du budget de la recherche + durcissement des règles d’attribution des financements ANR «Allez à l’ERC!» qu’ils disent, mais l’ERC saturée prend des mesures pour limiter les candidatures #deadend#recherchefrançaise Une petition semble vaine mais il faut commencer quelque part 👉
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Abbey @abbeyarletto.bsky.social · 23/06/2026
When reality surpasses fiction! Top: fictional forecast for August 2050, broadcast by French TV in 2014 to warn about the consequences of global warming. Bottom: Real French forecast for yesterday, June 22, 2026.
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Tim Dickinson @timdickinson.bsky.social · 14/06/2026
The world's first trillionaire did this
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Margot Foley @mfoley25.bsky.social · 14/06/2026
#ObamaDay #ObamaAppreciationDay #BarackObama
A photograph of Barack Obama receiving the Nobel Peace Prize. The man standing with Barack Obama in the photo is Thorbjørn Jagland, who was the chairman of the Norwegian Nobel Committee at the time. Below the photo, large white text on a black background reads: "IT'D BE A REAL SHAME IF THIS PHOTO OF PRESIDENT OBAMA RECEIVING HIS NOBEL PEACE PRIZE WENT VIRAL TODAY, FOR  CB NO PARTICULAR REASON." A laughing emoji is centered at the bottom, and a circular logo with a silhouette of the Statue of Liberty and the words "THE RESISTANCE" is in the top right corner.
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Yoshua Bengio @yoshuabengio.bsky.social · 03/06/2026
J'ai beaucoup apprécié mon récent passage à C dans lair pour discuter des risques de l'IA pour nos sociétés, nos économies, et nos démocraties. Merci Caroline Roux pour l'invitation! www.youtube.com/watch?v=TNCu...
youtube.com
Le cri d'alarme d'un des pères fondateurs de l'IA - Rencontre avec Yoshua Bengio
YouTube video by C dans l'air - France Télévisions
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Teppo Hiltunen @teppo-h.bsky.social · 28/05/2026
Evolution induced state shifts in a long-term microbial community experiment (now out, but previously posted here as a preprint) with Ville Mustonen, Lutz Becks @jcairns.bsky.social & others. Experiment continues @utu.fi and now 5+ years www.pnas.org/doi/10.1073/...
pnas.org
Evolution induced state shifts in a long-term microbial community experiment | PNAS
Biological communities are complex, dynamic systems that underpin ecosystem functionality, yet their long-term dynamics and predictability remain p...
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Elisabeth (Lilli) Janssen @elisabethjanssen.bsky.social · 04/05/2026
This advanced education course on #toxic #cyanobacteria ranges from understanding #morphology, #genetics and chemical toxin #analysis with examples of Swiss case studies! 29. June @eawag.bsky.social
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Asher Leeks @asherleeks.bsky.social · 28/04/2026
We're recruiting! We're looking for two graduate students to join us at UBC in Vancouver. Fully funded and open to global applicants, with flexible start-date. Topics include theory, bioinformatics, and microbiology. More details: asherleeks.com/apply #socialviruses #evosky #virosky 🧪
Leeks Lab is recruiting. We study social evolution in viruses. We're recruiting for two fully funded PhD or MSc positions, starting from September 2026. Evolutionary theory / experimental microbiology / viral bioinformatics. Experience optional / enthusiasm essential. asherleeks.com/apply
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Michael Brockhurst @brockhurstlab.bsky.social · 01/05/2026
Why does antibiotic resistance evolution vary between patients? Come to @officialuom.bsky.social @mermanchester.bsky.social to help us find out! 2.5 year @wellcometrust.bsky.social postdoc position in experimental evolution Closing 15 May. Apply here: www.jobs.manchester.ac.uk/Job/JobDetai...
jobs.manchester.ac.uk
Research Associate in Microbial Evolution:Oxford Road
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Yoshua Bengio @yoshuabengio.bsky.social · 24/04/2026
AI is advancing faster than our ability to manage it. We still have the opportunity to build the societal & technical guardrails needed to keep people, institutions and democracies safe—we shouldn't let it pass us by. Interview with @elconfidencial.bsky.social www.elconfidencial.com/tecnologia/2...
elconfidencial.com
Yoshua Bengio ayudó a crear la IA. Ahora lanza su aviso más serio: "No estamos preparados"
Considerado uno de los pioneros de la IA moderna, Yoshua Bengio lleva años alertando de los riesgos "catastróficos" si esta tecnología no se controla y regula. Su preocupación, igual que el poder de la IA, no ha hecho más que aumentar
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Fiona J Whelan @whelanfj.bsky.social · 13/03/2026
📣 The Whelan lab is hiring a bioinformatics postdoc 📣 Together with @fabricejpierre.bsky.social, we are offering a 1-year bioinformatic PDRA position in comparative genomics of Pseudomonas aeruginosa. To find out more please visit whelanlab.co.uk/contact/. Applications close 3 April 2026!
jobs.manchester.ac.uk
Research Associate in Microbial Genomics:Manchester
This postdoctoral research position is part of a Cystic Fibrosis Canada Early Career Investigator Award funded for 3-years led by Dr. Fabrice Jean-Pierre and Dr. Fiona Whelan. The aim of this project is to identify the genetic changes that arise in the Pseudomonas aeruginosa genome following perturbations – such as antibiotic treatment – in an in vitro system. The PDRA will use a large dataset of P. aeruginosa genomes and experimental metadata to predict key mutationsto the organism.
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Times Higher Education (THE) @timeshighered.bsky.social · 30/01/2026
Scientists are concerned that curiosity-driven research is set to be further cut back after three research councils confirmed they have paused funding opportunities. @jgro-the.bsky.social reports #academicsky #researchfunding ow.ly/lpvO50Y67ku
ow.ly
Three UK research councils suspend funding opportunities
Temporary block on grant applications by MRC, BBSRC and EPSRC heightens concerns over funding cuts
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Steven Robbins @stevenjrobbins.bsky.social · 28/01/2026
Curious, what's the best-practice tool at this point for taxonomically classifying long reads from metagenomes from less well-characterised environments? My impression is that Kraken will give lots of false positives and mis-classify taxa not in its database. Please share around for visibility.
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Prof Gavin Yamey MD MPH @gavinyamey.bsky.social · 24/01/2026
The most important public health story in America right now is that the Trump administration is kidnapping 2-year olds
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Rachel M. Wheatley @rachelmwheatley.bsky.social · 15/01/2026
🚨4-year fully funded PhD in the lab of @magicmicrobe.bsky.social (& collaborating with me!): How does iron availability shape the ability of pathogens to invade the gut microbiome? Apply by Jan 26th Advert: research.reading.ac.uk/foodbiosyste... How to apply: research.reading.ac.uk/foodbiosyste...
research.reading.ac.uk
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StrictlyChristo 🇺🇦🌻 @strictlychristo.bsky.social · 09/01/2026
Stephen Colbert on the ICE murder of Renee Nicole Good: “The message from this administration is clear. Only they determine the truth. And when their forces come to your city: obey or die. And if you die, you clearly didn’t obey. This should be an alarm bell for the entire country.”
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Nandita Garud @nanditagarud.bsky.social · 17/12/2025
Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible. www.nature.com/articles/s41...
nature.com
Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature
Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...
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Simon Roux @simrouxvirus.bsky.social · 08/12/2025
100%, both ONT and PacBio (although most of what we do is not marine / streamlined genome). We just published a specific study of soil metag short- vs long-read, and we see that, among other things, long-reads assemble regions too complex for short reads academic.oup.com/nargab/artic...
academic.oup.com
Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations
Abstract. Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but stru
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Torsten Seemann @torstenseemann.bsky.social · 05/12/2025
💾 ABRicate 1.2.0 has been released! This 'oversight' lasted 6 years, but with help from @finlaym.bsky.social we got CI working and updated all the databases. #bioconda #conda #bioinformatics #microbiology #genomics github.com/tseemann/abr...
github.com
Releases · tseemann/abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes - tseemann/abricate
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Nicolas Tromas @cyanophage.bsky.social · 05/12/2025
For metagenomics folks: what would be alternative approach to recover MAGs from highly diverse taxa where "classical" approaches have failed (megahit + mulitple binners like metabat2,vamb,...). I am trying metaSpades now...
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Nicolas Tromas @cyanophage.bsky.social · 04/12/2025
Some days are tougher than others... 2 rejected grants in the same day
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Thomas Gerbet @thomasgerbet.bsky.social · 03/12/2025
Une importante étude concluant à la sûreté du glyphosate vient d'être désavouée par la revue scientifique qui l'a publiée, il y a 25 ans. Cette étude avait été utilisée par Santé Canada pour sa réévaluation de l'herbicide. Les réels auteurs de l'étude ne seraient pas les chercheurs, mais Monsanto.
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PLOS Biology @plosbiology.org · 28/11/2025
Capsule diversity limits #phage host range by affecting receptor-binding protein (RBP) interactions in capsulated #bacteria. @pilardomingoc.bsky.social &co show that generalist phages evolve host range via RBP mutation & recombination, but specialists remain stable @plosbiology.org 🧪 plos.io/48nvOqY
Graphic representation of the recombination events in the Sugarlandvirus I and J variants. Top left: Representation of the variants isolates in the different strains in the three lines. Genome fragments of each parent are represented in a different color. Regions with the most abundant recombination events are marked and associated with a schematic representation of the functional annotation and intergenomic similarity between the two parental phages. Bottom left: 3D folding of the RBPγ. The consensus recombinant region, which is associated with the infection of the K-type 47, is represented in light orange. Variable positions detected in the protein sequence alignment of the variants are represented as hot pink spheres. The table indicates the percentage of identity of the parental protein sequences in three protein regions limited by the amino acids indicated. Right: Transmission electron microscopy (TEM) image of Klebsiella myoviruses artificially coloured, showing their characteristic contractile tails and icosahedral capsids. Image acquired by the Environmental and Biomedical Virology group (Institute for Integrative Systems Biology, Universitat de València-CSIC).
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Jean-Guillard.bsky.social @jean-guillard.bsky.social · 28/11/2025
Le parcours (singulier) de mon (dernier) thésard mis en avant dans une revue internationale : www.science.org/content/arti...
science.org
I dropped out of high school. Now, I’m living my dream as a fish scientist
This Ph.D. student from a working class background writes that no one should be made to feel inferior because of their roots
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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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Kathrin Rousk @kathrinrousk.bsky.social · 17/11/2025
Still time to apply to work on #symbioses #mosses #cyanobacteria! Join us in #Copenhagen! @voltcenter.bsky.social
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Anne Chevallereau @annechevallereau.bsky.social · 22/10/2025
JOB OFFER #PhageSky We have a postdoc position opening in my group to investigate phage-MGE interactions ! We're based in the very nice city of Lyon, France @mmsb-lyon.bsky.social Contact me for more info ! >> Apply on the CNRS webpage emploi.cnrs.fr/Offres/CDD/U...
emploi.cnrs.fr
Portail Emploi CNRS - Offre d'emploi - Postdoctoral researcher Microbiology (M/F)
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Teppo Hiltunen @teppo-h.bsky.social · 11/10/2025
Evolution induced state shifts in a long-term microbial community experiment www.biorxiv.org/content/10.1...
biorxiv.org
Evolution induced state shifts in a long-term microbial community experiment
Biological communities are complex, dynamic systems that underpin ecosystem functionality, yet their long-term dynamics and predictability remain poorly understood. Understanding how Darwinian evoluti...
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KOJAMF🤘🖤🤘 @kojamf.bsky.social · 05/10/2025
Dr. Jane Goodall filmed an interview with Netflix in March 2025 that she understood would only be released after her death.
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Mya Breitbart @viromegirl.bsky.social · 02/10/2025
We're hiring for several positions (a post-bac researcher in #transcriptomics, a #phage #postdoc, a senior researcher (broad topics) and a graduate student to work on #ciliates) - find info here: www.marine.usf.edu/genomics/app...
marine.usf.edu
Apply - Genomics
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Nicolas Tromas @cyanophage.bsky.social · 01/10/2025
www.lemonde.fr/disparitions... Elle était de celles dont on ne peut que s'inspirer. Son travail est juste énorme et j'espère que ses paroles et ses conseils continueront d'être partagés.
lemonde.fr
Jane Goodall, la primatologue qui a révolutionné le regard porté sur les chimpanzés, est morte
Pionnière de l’éthologie moderne, devenue ambassadrice de la protection de la faune sauvage, la chercheuse britannique est morte à 91 ans.
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Willem van Schaik @wvschaik.bsky.social · 23/09/2025
Come on @theguardian.com! Wrong, incorrect, irresponsible. Not contentious.
Headline in the Guardian.

Trump warns pregnant women not to take paracetamol making contentious autism claim.
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Lukas VF Novak @animalculum.bsky.social · 13/09/2025
#Arctic #algae aren't immobile or entombed. They're not just surviving either—they're gliding into record books phys.org/news/2025-09... Ice gliding #diatoms establish record-low temperature limits for motility in a eukaryotic cell www.pnas.org/doi/10.1073/... #protists #microbes #extremophiles
schematic pictures and microscopic photos showing various aspects of movement in single-celled algae
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Heike Zimmermann @heikezimm.bsky.social · 05/09/2025
📣We seek a talented and enthusiastic postdoc - 3 yrs Join our team at #GEUS, and use environmental genomics applied to marine sediment cores from the #Arctic to decipher past dynamics of toxic #phytoplankton species. 🌊❄️🧬 #protistsonsky #ancientDNA #PHATE candidate.hr-manager.net/ApplicationI...
candidate.hr-manager.net
Postdoc in marine environmental DNA/sedimentary ancient DNA
The Department of Glaciology and Climate at the Geological Survey of Denmark and Greenland (GEUS) is looking for a talented and enthusiastic postdoctoral resear
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Anna-Liisa Laine @annaliisalaine.bsky.social · 10/09/2025
A few more days to apply!!!
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