Ellis Torrance

🚨 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

Technician III - Department of Microbiology Position Summary This position will be in the lab of Dr. Joseph E. Peters in the Department of Microbiology. Research in the Peters’ lab broadly involves deciphering mechanisms in genome stability and...

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 Abstract. Advances in long-read sequencing technology have led to a rapid increase in high-quality genome assemblies. These make it possible to compare gen

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/...

Electron micrograph of two phage infecting a host cell side-by-side, with hearts between them

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 🦠🌊

STEPS To It Announcing a new program, called STEPS, to simulate the dynamics of evolving microbial populations.

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!!!

Antibacterial microcins are ubiquitous and functionally diverse across bacterial communities - Nature Communications Bacteria produce antibacterials to aid competition in complex communities. Here, the authors show that class II microcins, an understudied group of secreted antibacterials, are abundant, with diverse ...

😳 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

Fig. 3 from the paper, showing that model performance levels off around 300M parameters and ESM C variants tend to outperform the other available protein language models.

Figure 5 from the paper, showing a wide range of model performance across datasets, with R^2 values ranging from 0.1 to 0.8. Only a small fraction of this variation is explained by either dataset size or protein length.

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

Congrats @simrouxvirus.bsky.social ! Well deserved! 👏👏👏

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 | PNAS Evolution of bacterial and archaeal genomes is highly dynamic, including extensive gene gain via horizontal gene transfer (HGT) and gene loss as we...

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

The microbiome of the human facial skin is unique compared to that of other hominids | mSystems Understanding how and why human skin bacteria differ from our closest animal relatives provides crucial insights into human evolution and health. While we have known that human facial skin hosts disti...

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

Spatiotemporal development of expanding bacterial colonies driven by emergent mechanical constraints and nutrient gradients - Nature Communications Bacterial colonies growing on solid surfaces can exhibit robust expansion kinetics, with constant radial growth and saturating vertical expansion. Here, the authors use modeling and experiments to sho...

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.

Complete genomes of 568 diverse Klebsiella pneumoniae species complex isolates from humans, animals, and marine sources in Norway from 2001 to 2020 | Microbiology Resource Announcements Klebsiella pneumoniae species complex are opportunistic pathogens that can transmit between humans, animals, and the environment (1). Here, we report hybrid genome assemblies of 578 (568 complete) gen...

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/...