🚨 New postdoc opportunity in Aotearoa 🇳🇿 with @drhhnz.bsky.social RA / Postdoctoral Fellow in honeybee bacteriophages, microbial genetics & molecular evolution at the University of Canterbury (Christchurch). 3-year position, starts March 2026. 🔗 jobs.canterbury.ac.nz/jobdetails/a...

Fresh news on de novo genes! Happy to present our latest work published in Nature communications: www.nature.com/articles/s41... Keywords not in specific order: intergenic ORFs, de novo genes, GC content, foldability, genetic code, ancestral sequence reconstruction and more :)

We discovered a universal scaling law linking copy number and plasmid size, which can be used to predict the PCN of your favorite plasmid! 6/7

1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start? We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes! www.biorxiv.org/content/10.1...

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...

Recent paper from the lab studying predictors of phage cocktail efficacy against complex clinical Pseudomonas populations royalsocietypublishing.org/doi/epdf/10.... Led by Rosanna Wright with extraordinary MSc (PhD) student Maisie Czernuska

The Peters lab is looking for a new team member! The role transposons play in evolution, basic mechanisms regulating transposition, and applying transposons as tools for genome modification with a special focus on guide RNA-directed transposition. cornell.wd1.myworkdayjobs.com/CornellCaree...

EvANI benchmarking workflow for evolutionary distance estimation academic.oup.com/bib/article/... An great teamwork by @mohsenzakeri.bsky.social, @stephenhwang.bsky.social and me, with the excellent mentorship of @benlangmead.bsky.social

The LSRF post-doc fellowship is open (due Oct 31)! The LSRF is a supportive and kind community. We *always* celebrate each other. On a personal level, they've always greeted me with open arms and an abundance of kindness. If you are thinking of applying and have questions, feel free to reach out!

Bacteria–phage infection network structure and genomic defence system content predict efficacy of a phage therapy cocktail against Pseudomonas aeruginosa from chronic lung infections #phage #phagesky #microsky royalsocietypublishing.org/doi/10.1098/...

Gene co-occurrence and its association with phage infectivity in bacterial pangenomes #phage #phagesky #microsky royalsocietypublishing.org/doi/10.1098/...

Do you love phage? I have an opening for a postdoc in my lab at the University of South Florida College of Marine Science (@cmarinescience.bsky.social) looking at interactions between marine phage and iron, which is an important limiting trace metal in the oceans (1/5) 🧵#phagesky 🦠🌊

Excited to share new #program, STEPS, which can simulate #dynamics of the E. coli Long-Term Evolution Experiment (#LTEE) or other microbes in serial transfer regime. telliamedrevisited.wordpress.com/2025/08/12/s... STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.

Tn7 family transposons that include all of the guide RNA-directed transposons (CAST) are common in bacteria. We now find diverse representatives across archaea, with many in the Asgard group. Reviving an Asgard element confirmed the exciting behaviors of the family #MicroSky #TESky

We made structural predictions of representatives of each #PHROG from #phage genomes, and put the whole lot online. You can browse through montages or go to your favourite phrog directly and download its PDB. 💻🧬 #phagesky linsalrob.github.io/PHROG_struct...

Go work for @linsalrob.bsky.social ! I would if I could!!!

😳 microcins #microsky www.nature.com/articles/s41...

A @csisingapore.bsky.social team showed D-I-Tasser can outperform AlphaFold2/3, elevating high-accuracy protein structure & function predictions. We wonder if this moves us closer to resolving protein–protein complex structure prediction? @natbiotech.nature.com www.nature.com/articles/s41...

Scihub stopped uploading new articles. SciDB is a continuing effort which has the entire scihub collection AND new papers. annas-archive.org/scidb

Now published: Systematic comparison of protein language models for transfer learning. Key points: - You don't need gigantic models. The two smaller ESM C variants work great. - There is huge variability in performance across datasets. We have no idea why. www.nature.com/articles/s41...

Alignment-free Bacterial Taxonomy Classification with Genomic Language Models www.biorxiv.org/content/10.1... #jcampubs

An assessment of DNA language models concludes: ◼️ They do not offer compelling gains over baseline models Their performance is inconsistent and requires much more compute. arxiv.org/abs/2412.05430

New pre-print out \o/ All about CRISPR, metagenomes, and what you learn when you collect (a lot of) spacers from natural communities, with @apcamargo.bsky.social @urineri.bsky.social @lhug.bsky.social but also Uri Gophna, Nikhil George (not on Bsky I think) & others at JGI doi.org/10.1101/2025...

The Koonin Law of Computatoinal Biology: Whenever you think you have a great idea in computational or evolutionary biology, it will already have been published by Eugene Koonin in the mid 90ies.

Evolution of gene order in prokaryotes is driven primarily by gene gain and loss www.pnas.org/doi/abs/10.1... #jcampubs 🌊

Our work on the facial skin microbiome of non-human primates is out in mSystems! We show there is no close relative of Cutibacterium on the faces of gorillas and chimps at the Lincoln Park Zoo, furthering the mysterious origin of the dominant human skin colonizer. journals.asm.org/doi/10.1128/...

Looking for a postdoc on bacterial-insect symbiosis, combining evolution and molecular mechanisms? I'll have one open in my lab starting Sept 2025. If interested contact me (or find me at the GRC on Animal-microbe symbiosis if you'll be there). #SymbioSky

One of the coolest papers I've ever read: www.nature.com/articles/s41... Within-colony bacterial dynamics. And the figures are absolutely striking and clear.

Happy to share this resource of 568 closed Klebsiella pneumoniae species complex hybrid assemblies, including 1416 plasmids! ⭕️🦠 We hope this will be useful - short reads, long reads, hybrid assembly or all combined - for your own tools/validations 🥳 #Microsky journals.asm.org/doi/10.1128/...

With nearly all of Harvard Chan School’s direct federal grants terminated, we are relying on philanthropy to power our research and support our educational programs. Every gift, regardless of size, advances our vision of health, dignity, and justice for every human. Support our work: hsph.me/whygive

Interested in phages ? Want to work as team that will isolate, genome sequence and charachterise 1000s of phage to build a biobank . Come work with me and Martha Clokie at Leicester jobs.le.ac.uk/vacancies/va...

A new preprint from the lab in collaboration with Feng Jiang. www.biorxiv.org/content/10.1... This is a thread for you if you're interested in secretion systems, phages, and evolution. The extracellular contractile injection system (eCIS) is a mysterious microbial toxin delivery system.

Hidden in plain sight: Bacterial genomes reveal thousands of lytic phages with therapeutic potential https://www.biorxiv.org/content/10.1101/2025.05.06.652010v1

Cutting-edge tools for structural biology: bringing AlphaFold to the people @cp-trendsmicrobiol.bsky.social Forum by @c-elfmann.bsky.social and @joergstuelke.bsky.social www.cell.com/trends/micro...

For those with despair about today's extreme proposed funding cuts for NIH, NSF, NASA, NOAA, etc... remember: CONGRESS 👏 SETS 👏 BUDGET 👏 LEVELS Today's news is simply just the President's **request**. Tell your elected representatives to REJECT this assault on science and scientific training.

"That telomere phages are so prevalent means that they are a selective force, one that we know little about. We now want to understand how the telomere-toxin is secreted and also understand how this ‘telocin’ wheedles its way into unsuspecting bacterial neighbors” www.science.org/doi/10.1126/...

This was quite a beautiful paper--definitely a must-read for folks that want to do these kinds of comparisons

www.sciencedirect.com/science/arti... Nearly missed my bus stop reading this fascinating review :)

Come join us at @mcgill.ca as an assistant professor in virus-host interactions! Please share widely. mcgill.wd3.myworkdayjobs.com/en-US/McGill...

Federal research cuts impact local economies, and stall progress. Publish an opinion piece in your hometown paper on June 16th to SPREAD THE WORD about how scientific research contributes to the everyday health and wealth of the general public. #McClintockLetters blogs.cornell.edu/asap/events-...

Very excited to finally see this out! 🦠🧬 Huge thanks to all of my amazing co-authors! @lpachter.bsky.social @delaneyksull.bsky.social Original paper thread: x.com/neuroluebber... Free access link to the paper: rdcu.be/eiIWC

This looks like a very big deal. See thread below and consider commenting like your research program depends on it. (It just might.)

ACTION ITEM-----ACTION ITEM Implementation of Schedule F This is what a lot of us have been worried about. This allows for many civil service positions to replaced with political appointees. This could include NIH institute directors and even POs. BUT THERE IS A COMMENT PERIOD... 1/n

New paper @isme-microbes.bsky.social : Among a sample of 1044 vibrio phages, we found 17 new Schizotequatrovirus with large genomes (>250kb), a broad host range, and yet a low frequency in our samples (?!). #MicroSky #PhageSky

Exploring and expanding the natural chemical space of bacterial diterpenes www.nature.com/articles/s41... #jcampubs

Did you know that there is so much DNA packed inside a phage capsid that the pressure is 10X higher than in a bottle of champagne? In our latest preprint, we wondered how that is contained in a phage that lives at extremely high temperatures. /1 www.biorxiv.org/content/10.1...

If you have a lost NSF or NIH grant. Colleagues inside government agencies are tracking terminated grants in hopes of assisting organizing efforts and perhaps litigation. The link takes you to the NSF tracker; the NIH tracker is linked from there. Pass this on. 🧪🥼 airtable.com/appGKlSVeXni...

Know any soon to graduate or recently graduated postbac researchers interested in / with experience working with phages? We are hiring a junior specialist/research tech! Apply here: aprecruit.berkeley.edu/JPF04863 (start date more flexible than stated in ad!)