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Thom Booth

@thombooth.bsky.social
494 followers 187 following 111 posts

NNF Postdoctoral Fellow at DTU Biosustain. Interested in the discovery and evolution of biosynthetic pathways.

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Reposted by Thom Booth
Alex Crits-Christoph @acritschristoph.bsky.social · 16/08/2026
I think this 'LittleLearner' paper is SO interesting. They trained an LLM just on 5th grade material. It is not able to answer questions beyond a 5th grade level. Increasing the model size, post-training, and in-context learning don't help: littlelearner-ll.github.io#levers arxiv.org/abs/2608.13545
littlelearner-ll.github.io
LittleLearner: Language Models Under Pedagogically-Controlled Knowledge Exposure
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Reposted by Thom Booth
STCmicrobeblog @stcmicrobeblog.bsky.social · 16/08/2026
#MicroSky how to put GyrB into turbo mode...
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Thom Booth @thombooth.bsky.social · 11/05/2026
Our study into the incredible genome of Embleya australiensis has been published in Microbial Genomics. We've shown that Embleya carry gigantic secondary chromosomes around 4 - 6 Mb in size! Enjoy reading and don't hesitate to reach out! www.microbiologyresearch.org/content/jour... 🧪💻🦠 1/4
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Tom McAdam @tomm.org · 09/04/2026
Oh what, the singling out of British citizens abroad for caps on donations to political parties doesn’t work? Colour me surprised. Cap all donations, not just donations from citizens abroad.
independent.co.uk
Billionaire returning to UK from Hong Kong to donate millions to Reform UK
Ben Delo says he will return to so he can give millions more to fund the party’s ‘war chest’
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Lib Dems Abroad @libdemsabroad.org · 16/02/2026
The voices of thousands of overseas voters weren't heard due to postal delays at the last General Election. Yet the government has proposed a new law with no improvements for Brits abroad: ❌ No postal vote improvements ❌ No dedicated overseas representation ❌ No automatic voter registration
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Thom Booth @thombooth.bsky.social · 07/02/2026
A heads up to my dual citizenship friends. 🇬🇧 🇺🇳 They are updating the rules about which passports you can use to enter the UK - so don't get caught out! If you will be negatively impacted by this change, please reach out and make your voice heard!
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Reposted by Thom Booth
Marie-Eve VAL @val-meve.bsky.social · 09/01/2025
1/ 🔬 Our work, "Dynamic transitions of initiator binding coordinate the replication of the two chromosomes in Vibrio cholerae", is now published in Nature Communications. Here's a thread on how we think Chr1 and Chr2 replication is coordinated in Vibrio. 🧵 Link : www.nature.com/articles/s41...
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Reposted by Thom Booth
Tue Sparholt Jørgensen @tuesparholt.bsky.social · 15/10/2025
Then @thombooth.bsky.social used the presence/absence of known telomere proteins to identify a potentially new telomere protein which is linked to the Sg2247 class telomere, which previously did not have an identified maintenance system (notice the dot in the red circle)
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Thom Booth @thombooth.bsky.social · 24/10/2025
Did you know most 'complete' Streptomyces genomes are missing their telomeres? Thanks to David and Tues hard work, we now have a new tool to recover them! A pleasure to be part of a team. :) 🦠🧪💻 #microsky
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Reposted by Thom Booth
Christopher Whitford @chriiswh.bsky.social · 20/10/2025
Check out this new amazing preprint by David, @tuesparholt.bsky.social , @thombooth.bsky.social, and @tilmweber.bsky.social!
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Reposted by Thom Booth
PLOS Biology @plosbiology.org · 06/08/2025
More than a billion tons of #chitin are produced on Earth each year. This study shows that the soil #bacterium #Streptomyces venezuelae thrives on chitin from #insect #exoskeletons, using a potent mix of chitinases and a dedicated chitobiose importer @plosbiology.org 🧪 plos.io/45sg4S5
Images of Streptomyces venezuelae consuming the chitin-rich exoskeleton of a dead grasshopper (top), cricket (middle) and superworm (bottom).
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Thom Booth @thombooth.bsky.social · 27/07/2025
Very cool! More labs should do this! :)
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Reposted by Thom Booth
Nadine Ziemert @nadineziemert.bsky.social · 08/07/2025
Check out the Ziemert Lab’s new YouTube channel m.youtube.com/@ZiemertLab We’ve uploaded short tutorial videos on how to use our tools for genome mining and natural product discovery. Thanks Semih, @martinaadamek.bsky.social @turgutmesut.bsky.social ! #GenomeMining #SecMet #naturalproducts
m.youtube.com
ZiemertLab
The Ziemert lab is interested in the evolution and distribution of bacterial secondary metabolites. These bioactive compounds are especially important in human medicine as the chemical scaffolds are t...
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Reposted by Thom Booth
Team Thomma @teamthomma.bsky.social · 24/07/2025
📣 Happy to see the journal publication 📄 of our work on Starships 🚀 in Verticillium fungi: terrific work led by @yukiyosato.bsky.social rdcu.be/exBSp
rdcu.be
Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution
Nature Communications - Giant transposons, known as ‘Starships’, mediate horizontal gene transfer between fungal genomes. Here, Sato et al. show that Starships occupy genome regions...
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Science Magazine @science.org · 17/07/2025
The mantra “location, location, location” isn’t just about real estate. For life scientists, more than 50% of their productivity can be attributed to the institution where they work, according to a new study. scim.ag/4kKs1YO
scim.ag
Large study of scientists who move their labs reveals how location drives productivity
Concentrating funding at high-powered universities can maximize output, paper argues, but may sacrifice broader benefits
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Keith Trujillo @neurochicano.bsky.social · 17/07/2025
go.bsky.app/8zZNEGV Great resource to connect early career folks with more senior scientists looking to hire postdocs! 🧪
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Brodie Bulcock @brodiebulcock.bsky.social · 04/07/2025
Crystal clear? Not quite! Our new paper explores how atoms with similar atomic numbers can be misidentified with X-ray crystallography, and revises the chemical structures of a series of nucleoside natural products. pubs.acs.org/doi/10.1021/...
pubs.acs.org
Reconsidering the Structures of Tetillapyrone, Nortetillapyrone, Ochraceopyronide, and Rhizoaspergillin A
In this study, we revise the structures of the marine sponge-derived pyrone-deoxyribosides tetillapyrone and nortetillapyrone, as well as the semisynthetic derivative tetillapyrone diacetate, to the n...
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Reposted by Thom Booth
Barrie Wilkinson @barriewilks.bsky.social · 15/07/2025
A great story begun by Siobhan Dorai-Raj and taken over the line by @thombooth.bsky.social and Juan Pablo Gomez-Escribano. It's been tremendous fun and wonderful to watch old lab members become collaborators and leaders!
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Susan Schlimpert @s-lab.bsky.social · 10/07/2025
New Independent Fellowship position in Microbiology to launch your lab in our department @johninnescentre.bsky.social (UK). We are conducting a broad search in the area of plant-associated microbial interactions. Message me if you have any questions. Apply here: www.jic.ac.uk/vacancies/in...
jic.ac.uk
Independent Fellowship in Plant-Associated Microbial Interactions | John Innes Centre
An exciting opportunity for an Independent Fellowship in Plant-Associated Microbial Interactions has arisen at the John Innes Centre. To read the full job description for this role…
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Tung Le @tunglejic.bsky.social · 10/07/2025
Fantastic opportunity to start your independent career at the JIC here. Great startup package. Repost = nice. Thank you!!!
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Thom Booth @thombooth.bsky.social · 09/07/2025
Our new preprint is out! EEC1 is a massive 4.2 Mb secondary chromosome from Embleya australiensis. Conserved across Embleya, these are the first replicons of their kind in Actinobacteria and the largest secondary replicons in bacteria identified to-date! 1/6 🦠🧪🧬🔬 www.biorxiv.org/content/10.1...
biorxiv.org
Evidence supporting the first secondary chromosome in actinobacteria as a hallmark of the Embleya genus
Embleya is a genus within the family Streptomycetaceae, a group of actinobacteria with outstanding capacity for production of specialised metabolites and a strikingly complex life cycle. In this work, we sequenced the complete genome of the new species Embleya australiensis MST-11070 and validated the assembly using optical mapping. The genome of E. australiensis MST-11070 consists of a 7.1 Mb linear chromosome and three additional replicons, including a 4.2 Mb linear replicon, EEC1, significantly larger than all previously described secondary replicons from bacteria. EEC1 is typified by its similar composition to the chromosome in terms of GC-content, codon usage and gene functions. It also carries terminal inverted repeats identical to the chromosome. EEC1 is enriched in biosynthetic gene clusters (BGCs), including the only copy of the BGCs for the spore pigment and the surfactant peptide SapB, metabolites essential for the organism's lifecycle. EEC1 contains an origin of replication with at least some chromosomal properties, and its replication is likely to depend on functions provided by chromosomally located genes. Further comparison of Embleya spp. genomes suggests that EEC1-like replicons are conserved across the genus, in contrast to other known large linear extrachromosomal replicons (megaplasmids) in the order. EEC1 is thus a hallmark of the Embleya genus and is central to its evolution within the Streptomycetaceae family. We propose EEC1 as a secondary chromosome, distinct from previously described secondary chromosomes that utilise plasmid-like replication mechanisms (chromids) and the largest secondary replicon reported in bacteria, to date. ### Competing Interest Statement Ernest Lacey is a Founder, Board Member, and the Managing Director of Microbial Screening Technology Pty. Ltd. The authors declare no competing financial interests. Biotechnology and Biological Sciences Research Council, https://ror.org/00cwqg982, BB/P021506/1, BBS/E/J/000PR9790, BB/X01097X/1, BB/M011216/1 Novo Nordisk Foundation, https://ror.org/04txyc737, NNF22OC0078997
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José Cediel-Becerra @jcedielbecerra.bsky.social · 08/07/2025
GATOR-GC is out at @narjournal.bsky.social!! Check out our new targeted genome mining tool featuring a novel similarity metric to efficiently compare and deduplicate gene clusters. We uncover biosynthetic diversity missed by other genome mining tools academic.oup.com/nar/article/...
academic.oup.com
Targeted genome mining with GATOR-GC maps the evolutionary landscape of biosynthetic diversity
Abstract. Gene clusters, groups of physically adjacent genes that work collectively, are pivotal to bacterial fitness and valuable in biotechnology and med
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Nature Communications @natcomms.nature.com · 01/06/2025
Genetic compatibility and environmental co-occurrence drive the dissemination of #AntibioticResistance genes Co-occurrence of bacteria in the human #microbiome and #wastewater contributes to gene transfer
bit.ly
Genetic compatibility and ecological connectivity drive the dissemination of antibiotic resistance genes - Nature Communications
The dynamics of antimicrobial resistance gene transfer remain unclear. Here, by integrating bacterial genome and metagenome data with machine learning the authors show that genetic incompatibility is a main limiting factor, while co-occurrence of bacteria in the human microbiome and wastewater contributes to gene transfer.
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Natural Product Reports @natprodreports.rsc.org · 15/05/2025
🔥Be sure to read the latest Hot Off the Press article by Bob Hill & @andysuth14.bsky.social at @uofgchem.bsky.social on their selection of 32 recent papers covering the latest research in bioorganic chemistry & novel natural products #natprod Find it below🔽 pubs.rsc.org/en/content/a...
pubs.rsc.org
Hot off the Press
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as melichuniione A from Melicope chunii.
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Thom Booth @thombooth.bsky.social · 17/05/2025
Can we all agree to stop using the word 'bacterial' in the titles of studies that only investigate proteobacteria. Okay? Thanks! 🧪🦠
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Peter Andersen @germline.bsky.social · 16/05/2025
📣 🥳 🧑‍💻 Our department is hiring: Tenure-Track Assistant Professor / Associate Professor in Bioinformatics at Aarhus University, Denmark Deadline June 1st Thanks for sharing! mbg.au.dk/en/news-and-...
mbg.au.dk
Tenure-Track Assistant Professor / Associate Professor in Bioinformatics at Aarhus University, Denmark - Vacancy at Aarhus University
Vacancy at Department of Molecular Biology and Genetics - BiRC - Bioinformatics Research Center, Aarhus University
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Thom Booth @thombooth.bsky.social · 16/05/2025
🚨getphylo workshop announcement🚨 (Please share!) Are you interested in building genome-scale phylogenies - fast? Or want to explore the evolution of gene clusters? Then getphylo might be the tool for you! I will be running online workshops on the 26th and 27th May. 🧪💻 1/3
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Rafael Peña-Miller @penamiller.bsky.social · 15/05/2025
New preprint led by @brunoluviano.bsky.social & Fernando Santos. We show that filamentation enhances bacterial survival under toxic stress — not as collateral damage, but as a regulated morphological response. TL;DR: Filamentation isn’t a symptom, it’s a strategy! www.biorxiv.org/content/10.1...
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STCmicrobeblog @stcmicrobeblog.bsky.social · 15/05/2025
#MicroSky
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BacDive @bacdive.bsky.social · 13/05/2025
A new look for BacDive 🖥️🦠! We are excited to introduce the new BacDive design✨ and now invite all users to try it out. Tell us what you think, we look forward to your feedback! You can find it at 👉 beta.bacdive.dsmz.de or by clicking the red “New Design” button on every BacDive page.
Screenshot of the new BacDive front page.
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Reposted by Thom Booth
Chemical Science @chemicalscience.rsc.org · 11/05/2025
Weed control, essential for food security, normally relies on herbicides but these have limited modes of action. In this study, the authors explore COT-metsulfuron methyl as a herbistatic, offering an alternative route to weed control. Read for free: doi.org/10.1039/D4SC... #ChemSky
doi.org
In search of herbistasis: COT-metsulfuron methyl displays rare herbistatic properties
Weed management is an essential intervention for maintaining food security and protecting biodiversity but is heavily reliant on chemical control measures (i.e., herbicides). Concerningly, only one herbicide has been developed with a new mode of action (MOA) since the 1980s. Therefore, alternative strategies
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Kermit Murray @kkmurray.bsky.social · 11/05/2025
(BioRxiv All) Nova: A library for rapid development of mass spectrometry software applications: Nova is a software library for the reading, writing, and management of mass spectrometry data natively in the C# language. It complements similar software libraries ubiquitously… #BioRxiv #MassSpecRSS
dlvr.it
Nova: A library for rapid development of mass spectrometry software applications
Nova is a software library for the reading, writing, and management of mass spectrometry data natively in the C# language. It complements similar software libraries ubiquitously used in application development for C++, Python, and Java. Few software libraries and resources for mass spectrometry data analysis have been developed for C# relative to other languages. C#, however, remains the dominant language of choice for development of real time mass spectrometry (RTMS) analysis and instrument control applications, illustrating the need for native C# libraries when developing RTMS software. Nova provides fast, easy-to-use structures and classes built upon interfaces that support open community standards, and are easily extensible for current or future mass spectrometry software development needs.
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Tung Le @tunglejic.bsky.social · 09/05/2025
1/ Excited to share our latest work on gene transfer agents (GTAs) in Caulobacter crescentus, led by Emma Banks in collaboration with Pavol Bardy and Mai Nguyen from York!!! See a brief thread below. shorturl.at/o6S1w
shorturl.at
A bacterial CARD-NLR immune system controls the release of gene transfer agents
Bacteria have evolved a wide array of immune systems to detect and defend against external threats including mobile genetic elements (MGEs) such as bacteriophages, plasmids, and transposons. MGEs are ...
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Thomas Clavel @tclavel.bsky.social · 06/05/2025
Very happy that HiBC is out: rdcu.be/ekSCO 🔥 @natcomms.nature.com Excellent team spirit, and, as always, great driving factor by @tcahitch.bsky.social ⭐⭐⭐⭐ We hope that these bacterial isolates from the human gut will facilitate many studies by others... 😀
rdcu.be
HiBC: a publicly available collection of bacterial strains isolated from the human gut
Nature Communications - Here, the authors present and characterise a collection of human gut bacteria including novel taxa associated with health conditions and a large diversity of plasmids. All...
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Thom Booth @thombooth.bsky.social · 07/05/2025
I recently joined the Editorial Board of BMC Genomic Data. Alongside research and reviews, they also publish data notes. I often come across cool genomes with no publication associated with them and data notes can provide ever important context! 💻🦠🧪
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Alex Crits-Christoph @acritschristoph.bsky.social · 25/04/2025
Unique investigation of some errors in long read assemblers. In particular these remarkably chimeric contigs are 😱, if rare.... Improving long read assemblers is definitely the space to be in when it comes to the future of metagenomics, as short reads won't be part of it 😉
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Kai Blin @kblin.bsky.social · 10/04/2025
The Quadram Institute has a pretty cool setup over there. This sounds like a fun job.
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Michael Baym @baym.lol · 09/04/2025
Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social: rdcu.be/eg4OA 1/
rdcu.be
Efficient and robust search of microbial genomes via phylogenetic compression
Nature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks.
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Adam Rutherford @adamrutherford.bsky.social · 09/04/2025
The resurrection circus keeps clowning, but make no mistake, Dire wolves remain very extinct. An angry, sweary piece by a frustrated geneticist. arutherford.substack.com/p/dire-wolve...
arutherford.substack.com
Dire wolves remain very extinct
Despite what you are being fed, de-extinction is a con, full of gloss, bullshit and ghoulish greed.
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Thom Booth @thombooth.bsky.social · 09/04/2025
Scientific journalism needs to be more than just uncritically regurgitating press releases. time.com/7274542/colo... They have not ressurected the Dire Wolf and they never will. To quote Adam Rutherford: 'This is a House of Cards built on scientific illiteracy and actual lies.' 🧪
time.com
The Return of the Dire Wolf
Colossal Biosciences has genetically engineered the first dire wolf to live in over 10,000 years. Here's what that means for other extinct species.
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Tilmann Weber @tilmweber.bsky.social · 05/04/2025
Have a look at our latest tool: ActinoMation - a toolkit for automated E. coli – Streptomyces conjugation on Opentron laboratory automation systems: www.sciencedirect.com/science/arti...
sciencedirect.com
ActinoMation: A literate programming approach for medium-throughput robotic conjugation of Streptomyces spp
The genus Streptomyces are valuable producers of antibiotics and other pharmaceutically important bioactive compounds. Advances in molecular engineeri…
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Anna Svetlova @annasve.bsky.social · 30/03/2025
What do Actinomycetes and northern lights have in common? - The beautiful colours that they bring to life! 🍋‍🟩🍇🍊 Northern lights in Kiruna, 06.03.2025. #northernlights #auroraborealis #kiruna #sweden #actinomycetes #nightsky #microbiology #arcticcircle #aurora #biotech #phdlife #streptomyces
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 29/03/2025
Run BioEmu in Colab - just click "Runtime → Run all"! Our notebook uses ColabFold to generate MSAs, BioEmu to predict trajectories, and Foldseek to cluster conformations. Thanks @jjimenezluna.bsky.social for the help! 🌐 colab.research.google.com/github/sokry... 📄 www.biorxiv.org/content/10.1...
colab.research.google.com
Google Colab
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Tobias Engl @tcsengl.bsky.social · 27/03/2025
A long, long time ago, we started this review project during the first Coron lockdown, but if finally made it out into the world - Origin and function of beneficial bacterial symbioses in insects! @naturerevmicro.bsky.social
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Stephen Curry @scurry.bsky.social · 03/03/2025
Only very sparse details have emerged so far from the meeting of Royal Society Fellows tonight: www.theguardian.com/technology/2...
theguardian.com
Elon Musk survives as fellow of Royal Society despite anger among scientists
Questions remain over whether further action will be taken after resignations and calls for the Tesla CEO to be expelled
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Stephen Curry @scurry.bsky.social · 03/03/2025
My profound thanks to all 3494 members of the scientific community who signed my open letter calling on the Royal Society to stand up for its values in respect of concerns raised by the statements and actions of one of its fellows, Elon Musk. occamstypewriter.org/scurry/2025/... 1/2
occamstypewriter.org
An open letter to the President of the Royal Society – time to stand up for your values | Reciprocal Space
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Stephen Curry @scurry.bsky.social · 04/03/2025
Good piece by @kityates.bsky.social gets to the heart of why yesterday's statement from the Royal Society felt so empty. www.theguardian.com/commentisfre...
theguardian.com
Elon Musk is a proven danger to good science, but the Royal Society won’t say so. That’s why I resigned | Kit Yates
It is vital to act, and I urge colleagues to do so. How can we stand by and laud this man while he undermines scientific integrity? asks academic and author Kit Yates
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Marnix Medema @marnixmedema.bsky.social · 03/03/2025
Short perspective from @gillesvanwezel.bsky.social and yours truly on opportunities for antibiotic discovery from natural products. Was fun to write!
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Pieter Dorrestein @pieterdorrestein.bsky.social · 27/02/2025
It’s not every day one gets to publish an article with NASA astronauts. This journey started in 2019 and withe the goal to understand the microbial and chemical make-up of the space station. We had lots of experience with analysis from swabs on earth.
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Rauf Salamzade @raufs.bsky.social · 24/02/2025
Our minireview on BGC evolution being shaped by genomic & ecological context is now live on mSystems: journals.asm.org/doi/10.1128/... #secmet #MEvoSky
journals.asm.org
Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution | mSystems
Microbial secondary metabolites are compounds produced by bacteria and fungi that are not required for their replication and unconditional survival (1, 2). While they are thus not expected to be unive...
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