Hey Greg, thank you for looking into this, and I will be curious to hear about the outcome.

We didn't follow up with their questions because there is no study objective or preliminary data apart from wanting to test published claims as we wrote in our request.

That sounds such a great idea (and one that would give Iva and I much honor and pleasure). Thank you!

Oh, yes, absolutely! I owe my career to those good datasets out there and cooperative authors :) They are the best.

As far as my experience goes with data availability issues, I don't see any progress myself. Which makes me believe that without a fundamental, systemic change to publishing, we should expect things to get better. But I so hope that I am wrong, and you are correct and things are getting better.

This is from 7 years ago (merenlab.org/2019/02/24/f...). We are talking about the same things today. We will be talking about the same things 7 years from now. There is no one to blame for this apart from ourselves. I find it very depressing.

Reviewers must uphold these values much more rigorously. This is from 7 years ago (merenlab.org/2019/02/24/f...). We are still talking about the same things, and it is very depressing.

Hey Jesse! We are sorry for this one. But we are also working on other things that hopefully those who think a lot about comparative genomics will enjoy reading :)

Thank you very much for reading the blog post and for your comment, Willem.

I have now read this piece and it is very good.

Massive respect for @merenbey.bsky.social and Iva for their persistence and documenting this torturous process.

Highly recommended reading for anyone who cares about reproducibility in science.

Thank you, Kevin! And thank you for this great perspective -- I updated the blog post to make sure the readers are aware of it.

In return, you may find the Conclusions of these two studies interesting/relevant:

link.springer.com/article/10.1...

elifesciences.org/articles/89862

Unfalsifiable by Design: A Year of Trying and Failing to Reproduce a Human Microbiome and Autism Study The myth of open data, reproducibility, responsibility, and accountability in science, and your role in it

How every layer of science's "self-correcting machinery" failed when Iva Veseli and I simply wanted to reproduce the findings of a high-profile study on gut microbiome and autism:

merenlab.org/2026/04/15/u...

"A data-conscious checklist for the reviewers of 'omics studies who champion open science", a Comment Iva Veseli and I wrote is now online at metaRxiv:

doi.org/10.31222/osf...

Please read it and consider sharing it with your friends, colleagues, trainees, or editors of your favorite journals.

Have you listened to the #MVIFconversations podcast?

There is a new episode where @cpavloud.bsky.social and I talked to @merenbey.bsky.social about open source, mentoring, and believe me it's a GREAAAT one!!

Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social

Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback.

rdcu.be/famFj

Our new paper on the presence of xenobiotics in marine dissolved organic matter just come out. Thanks to Jarmo Kalinski and our awesome collaborators, we were able to reanalyze more than 20 public LC-MS/MS datasets from seawater and ask how many anthropogenic compounds we can detect. rdcu.be/e8q6C

OMFG. Reading this piece immediately convinced me that you are on the right track.

I wish you strength and patience against these charlatans.

Global Observations Reveal Rapid Reorganization of Ocean Nutrients - Eos Data reveal that changes in nutrient levels vary depending on depth and distance from shore—and that these changes are happening more quickly than scientists realized.

New research in @aguadvances.bsky.social examined more than 14 million nitrate and phosphate measurements captured around the world between 1925 and 2025.

eos.org/research-spo...

Water mass specific genes dominate the Southern Ocean microbiome Nature Communications - Southern Ocean microbial communities are less well studied. Here, the authors generate a circumpolar-scale gene catalog from 218 metagenomics samples revealing broadscale...

Very happy to share the latest paper of our group (et al.)! rdcu.be/e7zyX . This one has a special place… 1/n

Did I nail it? :p

As of this week, I have begun a new part-time role as a Professor at Aalborg University in Denmark. I’m very excited to join AAU’s Center for Microbial Communities’ ambitious team while continuing my research programs and serving as SCGC director at Bigelow Laboratory for Ocean Sciences in the US.

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...

» A new simplification in modeling enables us to predict system failures before they begin. « (@mhab.bsky.social)
How? ➡️ 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 😱

𝐖𝐡𝐚𝐭 𝐩𝐫𝐨𝐜𝐞𝐬𝐬𝐞𝐬 𝐠𝐨𝐯𝐞𝐫𝐧 𝐩𝐡𝐨𝐭𝐨𝐬𝐲𝐦𝐛𝐢𝐨𝐬𝐢𝐬 𝐞𝐬𝐭𝐚𝐛𝐥𝐢𝐬𝐡𝐦𝐞𝐧𝐭 𝐚𝐧𝐝 𝐛𝐫𝐞𝐚𝐤𝐝𝐨𝐰𝐧? 🪸

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. 🧪 @icbm-uol.bsky.social

Resurrected nitrogenases recapitulate canonical N-isotope biosignatures over two billion years - Nature Communications The study shows that nitrogenase enzymes have maintained stable isotope signatures over billions of years, revealing how ancient microbes shaped Earth’s nitrogen cycle and offering a new experimental ...

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!
🖥️🧬🦠

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" 🎉

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