POSTDOC POSITION --- Bernd Blasius has just opened a PostDoc position to model viral evolution. The project is a collaboration with me Dirk Brockmann and famous virologist Christian Drosten, among others. uol.de/en/job/postd...
Β» A new simplification in modeling enables us to predict system failures before they begin. Β« (@mhab.bsky.social)
How? β‘οΈ Read in our latest newsletter: 241806.seu2.cleverreach.com/m/16915050
Also news about Red Sea coral reef protection, BBNJ, a new working group and... a special cemetery π±
ππ‘ππ π©π«π¨πππ¬π¬ππ¬ π π¨π―ππ«π§ π©π‘π¨ππ¨π¬π²π¦ππ’π¨π¬π’π¬ ππ¬ππππ₯π’π¬π‘π¦ππ§π ππ§π ππ«πππ€ππ¨π°π§? πͺΈ
Join us for a 3-year #Postdoc and help us find out! Our ERC-funded project at @hifmb.de offers excellent facilities and an international collaborative work environment.
Apply by April 1st: jobs.awi.de/Vacancies/21...
#ScienceJobs
Rossella Alba, our new colleague at @hifmb.de leading the Marine Policy and Management working group, offers two fully funded PhD positions here: jobs.awi.de/Vacancies/21... apply until March 18, and feel free to make potential applicants aware. π§ͺ @icbm-uol.bsky.social
Our new paper, out today! We resurrected ancient nitrogenases first used by life on Earth 3 billion years ago. We combined synthetic biology and geology & validated their chemical #biosignature in rocks that helps reveal ancient life on Earth!(and beyond!)
Link: www.nature.com/articles/s41...
With the release of anvi'o v9, the 300k+ contigs databases available for download on the GlobDB website are now compatible with both the development version and the latest stable release (v9) of anvi'o.
More info:
globdb.org/news
Thanks #anvio team!
π₯οΈπ§¬π¦
Yes, many plans :) We are still working on it, and we wish that branch to reach a level of maturity before we merge it for anvio-dev. But it is accessible to those who don't mind switching branches in their anvio-dev setup, and any help would be most welcome. We would love to collaborate.
Some more:
anvi-script-find-misassemblies: anvio.org/m/anvi-scrip...
anvi-display-codon-frequencies: anvio.org/m/anvi-displ...
anvi-reorient-genomes: anvio.org/m/anvi-reori...
Some of the new programs in this release:
anvi-compute-rarefaction-curves: anvio.org/m/anvi-compu...
anvi-draw-kegg-pathways: anvio.org/m/anvi-draw-...
anvi-predict-metabolic-exchanges: anvio.org/m/anvi-predi...
We just released #anvio v9, "eunice" π
This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.
Read the release notes:
github.com/merenlab/anv...
Visit our up-to-date web page:
anvio.org
Now published in Nature Biotechnology:
go.nature.com/44P7nSm
If you missed it, the TL;DR is in my April thread below
Troubleshooting common errors in assemblies of long-read metagenomes - @merenbey.bsky.social @banfieldlab.bsky.social go.nature.com/44P7nSm
In my opinion, in theory nothing can be more reliable than the assembly graph. So if the graph says something is circular, I'd take that more seriously than the other way around :)
With ONT and PacBio you do get many many genuinely circular elements. Some of which are excellent, some others are quite questionable, but luckily finding the poop ones and being more careful with them is not that difficult:
anvio.org/help/main/pr...
Here is the boring fact: it depends on the environment, lib prep, & depth of sequencing. Quite a large number of plasmids and viruses will circularize with Illumina.
One can curate Bacterial genomes manually to circularity, but I'd say it would be unlikely to get them assembled circular :/
If a tandem repeat collapses to a single copy of itself during the assembly, it certainly would become indistinguishable from a circular element through RF evidence. Probably that is a very big problem for eukaryotic genomics, but we don't assemble many euks from metagenomes.
Of course tandem repeats can also produce end-localized RF pairs, but I'd say it will be a rare event compared to circular elements in a metagenome. Probably that's why almost all circular elements we capture in metagenomes resolve to plasmids or viruses (at least in human gut metagenomes).
Proper pairs will unlikely map exclusively to contig ends when they originate from tandem repeats. That's why in addition to measuring distance between RF pairs, one needs to track precisely where those proper pairs map on a given contig, their coverage, and the insert size dist in the dataset.
But if you mean one needs to be 'lucky' because most people prepare libraries without proper size selection (which leads to garbage insert size distribution that ruin robust RF statistics), and most assemblies break at low-complexity / repeat regions, then yes, you need to be lucky there :)
A circle does not have an end, but a linear contig that represents a circular molecule after assembly does, in which case the paired-end reads that span the artificial breakpoint will have RF orientation. It works pretty well actually (and I'm not a very lucky person in general .. so, IDK).
What does luck have anything to do with it?
It is pretty simple for all domains of life. You need proper RF reads exclusively at contig ends :)
HIFMB newsletter out now! π¦
In our top story, Bettina Meyer outlines the Krill Stock Hypothesis, a scientific framework for setting krill catch quotas to protect the ecological balance in the Southern Ocean.
That and more here: 241806.seu2.cleverreach.com/m/16677411
New blog post for my microbiologist colleagues:
merenlab.org/2025/12/15/r...
In which Meren talks about a paper by Valentina Marcheselli on how microbiologists navigate the tension between reductionism and complexity in their everyday practices.
More than a year ago researchers from @hifmb.de and @icbm-uol.bsky.social started to write about different perspectives on marine biodiversity change from natural and social science perspectives. This morphed into a review paper that was published online today link.springer.com/article/10.1... π§ͺ
π We need YOUR input!
We're writing a perspective piece to share a vision for a future global observatory for marine microbial 'omics. One aspect of the perspective piece is to synthesize ongoing marine microbiome time-series.
Please review our list and add any we've missed: tinyurl.com/4bmeenp9
What would a marine microbiome observing system meant to last decades look like? ππ¦
We explored this at the recent MMOFF Workshop, which brought together diverse partners to envision the future of marine microbiome observations.
merenlab.org/workshops/MM...
I am happy to share that our data descriptor on the HawaiΚ»i Diel Sampling is now published! ππ¦ https://www.nature.com/articles/s41597-025-06166-3
Every 1.5 hours for 48 hours, we collected ocean microbes from within and adjacent to KΔneΚ»ohe Bay, OΚ»ahu, HawaiΚ»i and produced a multi-omics dataset.
This was possible primarily thanks to Sarah, Jessika FΓΌssel, Kelle Freel, and others, and Mike RappΓ©'s leadership that enabled a high-resolution sampling effort that covered two full days, which I had described in greater detail here:
merenlab.org/data/hads/
