A. Murat Eren (Meren)
@merenbey.bsky.social
Professor of Ecosystem Data Science at @hifmb.bsky.social studying the ecology and evolution of microbes through high-resolution 'omics and #anvio
.. and we were lucky to receive a generally positive feedback from the attendees (read more of the survey results here: anvio.org/blog/oldenbu...).
We strive to do better, come and be the judge of it yourself!
We strive to do better, come and be the judge of it yourself!
November 20, 2025 at 6:42 PM
.. and we were lucky to receive a generally positive feedback from the attendees (read more of the survey results here: anvio.org/blog/oldenbu...).
We strive to do better, come and be the judge of it yourself!
We strive to do better, come and be the judge of it yourself!
Just so you know, the previous iteration of the workshop went quite well (see more photos here: anvio.org/blog/oldenbu...)
November 20, 2025 at 6:42 PM
Just so you know, the previous iteration of the workshop went quite well (see more photos here: anvio.org/blog/oldenbu...)
We have a date for the free-to-attend #anvio workshop and ECR Symposium for 2026, and we look forward to meeting you at the @hifmb.de in Oldenburg, Germany!
Please find more information on the venue, program, and the application form here, and spread the word 😇
anvio.org/workshops/20...
Please find more information on the venue, program, and the application form here, and spread the word 😇
anvio.org/workshops/20...
November 20, 2025 at 6:42 PM
We have a date for the free-to-attend #anvio workshop and ECR Symposium for 2026, and we look forward to meeting you at the @hifmb.de in Oldenburg, Germany!
Please find more information on the venue, program, and the application form here, and spread the word 😇
anvio.org/workshops/20...
Please find more information on the venue, program, and the application form here, and spread the word 😇
anvio.org/workshops/20...
My first thought was that this probably some AI flop. The authors asked an LLM for help, and this is what they got, and didn't have the resources to triple-check it.
So I asked ChatGPT to see if that's how they messed up this bad .. and now I wish the authors had done the same.
So I asked ChatGPT to see if that's how they messed up this bad .. and now I wish the authors had done the same.
October 10, 2025 at 8:03 AM
My first thought was that this probably some AI flop. The authors asked an LLM for help, and this is what they got, and didn't have the resources to triple-check it.
So I asked ChatGPT to see if that's how they messed up this bad .. and now I wish the authors had done the same.
So I asked ChatGPT to see if that's how they messed up this bad .. and now I wish the authors had done the same.
One of the things I find hardest to get used to in science is seeing how scientists can completely mischaracterize approaches developed by others just to justify their own. Here is a fresh example in which the highlighted statements are 100% objectively wrong about what PlasX or MobMess does
October 10, 2025 at 8:03 AM
One of the things I find hardest to get used to in science is seeing how scientists can completely mischaracterize approaches developed by others just to justify their own. Here is a fresh example in which the highlighted statements are 100% objectively wrong about what PlasX or MobMess does
Have you ever looked at some differentially occurring gene clusters in a microbial #pangenome and thought to yourself "I wonder if they contribute to any metabolic modules"?
With the most recent changes, the answer is a few clicks away in #anvio 😇
With the most recent changes, the answer is a few clicks away in #anvio 😇
September 18, 2025 at 10:05 AM
Have you ever looked at some differentially occurring gene clusters in a microbial #pangenome and thought to yourself "I wonder if they contribute to any metabolic modules"?
With the most recent changes, the answer is a few clicks away in #anvio 😇
With the most recent changes, the answer is a few clicks away in #anvio 😇
PSA: This is what the real male loneliness syndrome looks like.
July 31, 2025 at 1:24 PM
PSA: This is what the real male loneliness syndrome looks like.
POV: When you're a middle author of a study, and everything is a matter of life and death 💀
I AM BECOME REVIEWER #2, DESTROYER OF RELATIONSHIPS BEFORE THE STUDY WENT OUT TO REVIEW.
I AM BECOME REVIEWER #2, DESTROYER OF RELATIONSHIPS BEFORE THE STUDY WENT OUT TO REVIEW.
July 16, 2025 at 3:53 PM
POV: When you're a middle author of a study, and everything is a matter of life and death 💀
I AM BECOME REVIEWER #2, DESTROYER OF RELATIONSHIPS BEFORE THE STUDY WENT OUT TO REVIEW.
I AM BECOME REVIEWER #2, DESTROYER OF RELATIONSHIPS BEFORE THE STUDY WENT OUT TO REVIEW.
Not that you care, but I still wanted to let you know that if I see a paper full of bogus citations with your name on it, I'm not talking to you anymore.
I was so triggered by a paper I was reading this morning, I am drinking my second coffee.
I was so triggered by a paper I was reading this morning, I am drinking my second coffee.
May 30, 2025 at 9:03 AM
Not that you care, but I still wanted to let you know that if I see a paper full of bogus citations with your name on it, I'm not talking to you anymore.
I was so triggered by a paper I was reading this morning, I am drinking my second coffee.
I was so triggered by a paper I was reading this morning, I am drinking my second coffee.
An excellent letter by Dennis Hazelett:
www.nature.com/articles/s41...
And below is my attempt to motivate people in my group and others elsewhere to read it. Putting it here as well in case it may work on you, too :p
www.nature.com/articles/s41...
And below is my attempt to motivate people in my group and others elsewhere to read it. Putting it here as well in case it may work on you, too :p
March 19, 2025 at 8:07 AM
An excellent letter by Dennis Hazelett:
www.nature.com/articles/s41...
And below is my attempt to motivate people in my group and others elsewhere to read it. Putting it here as well in case it may work on you, too :p
www.nature.com/articles/s41...
And below is my attempt to motivate people in my group and others elsewhere to read it. Putting it here as well in case it may work on you, too :p
The best opening slide doesn't exi...
March 11, 2025 at 8:15 AM
The best opening slide doesn't exi...
The first #anvio workshop at our brand new @hifmb.de building in Oldenburg has just started with around 50 individuals who represent a wide range of locations, scientific interests and career levels :')
Very excited for this week and thankful for Iva Veseli and Florian Trigodet!
Very excited for this week and thankful for Iva Veseli and Florian Trigodet!
March 3, 2025 at 11:00 AM
If you have been using #anvio to analyze your microbial pangenomes, we have a new program for you to calculate rarefaction curves or Heaps' Law fit for your gene clusters:
anvio.org/help/main/pr...
Sorry it took this long :/ But at least t will run on any existing anvi'o pangenome :)
anvio.org/help/main/pr...
Sorry it took this long :/ But at least t will run on any existing anvi'o pangenome :)
March 2, 2025 at 3:13 PM
If you have been using #anvio to analyze your microbial pangenomes, we have a new program for you to calculate rarefaction curves or Heaps' Law fit for your gene clusters:
anvio.org/help/main/pr...
Sorry it took this long :/ But at least t will run on any existing anvi'o pangenome :)
anvio.org/help/main/pr...
Sorry it took this long :/ But at least t will run on any existing anvi'o pangenome :)
I'm very happy to report that Matt Schechter's PhD work is now online as a pre-print:
"Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities", www.biorxiv.org/content/10.1...
Here's a little 🧵 about it.
"Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities", www.biorxiv.org/content/10.1...
Here's a little 🧵 about it.
January 17, 2025 at 3:31 PM
I'm very happy to report that Matt Schechter's PhD work is now online as a pre-print:
"Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities", www.biorxiv.org/content/10.1...
Here's a little 🧵 about it.
"Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities", www.biorxiv.org/content/10.1...
Here's a little 🧵 about it.
Very proud that these just appeared in bioRxiv:
www.biorxiv.org/content/10.1... (reports 71 new SAR11 isolates, proposes names for 24 SAR11 genera).
www.biorxiv.org/content/10.1... (investigates the pangenome and metabolic determinants of habitat specificity in SAR11).
Wishing you a great 2025!
www.biorxiv.org/content/10.1... (reports 71 new SAR11 isolates, proposes names for 24 SAR11 genera).
www.biorxiv.org/content/10.1... (investigates the pangenome and metabolic determinants of habitat specificity in SAR11).
Wishing you a great 2025!
December 25, 2024 at 9:57 AM
Very proud that these just appeared in bioRxiv:
www.biorxiv.org/content/10.1... (reports 71 new SAR11 isolates, proposes names for 24 SAR11 genera).
www.biorxiv.org/content/10.1... (investigates the pangenome and metabolic determinants of habitat specificity in SAR11).
Wishing you a great 2025!
www.biorxiv.org/content/10.1... (reports 71 new SAR11 isolates, proposes names for 24 SAR11 genera).
www.biorxiv.org/content/10.1... (investigates the pangenome and metabolic determinants of habitat specificity in SAR11).
Wishing you a great 2025!
I just wanted to send a quick update and thank the 70+ people who applied for the upcoming #anvio workshop and ECR symposium in Oldenburg so far.
We are very encouraged with the geographical diversity, which has been one of our main concerns. The applications are open until January 10.
We are very encouraged with the geographical diversity, which has been one of our main concerns. The applications are open until January 10.
December 19, 2024 at 11:02 AM
I just wanted to send a quick update and thank the 70+ people who applied for the upcoming #anvio workshop and ECR symposium in Oldenburg so far.
We are very encouraged with the geographical diversity, which has been one of our main concerns. The applications are open until January 10.
We are very encouraged with the geographical diversity, which has been one of our main concerns. The applications are open until January 10.
We are very happy to announce a free-to-attend #anvio workshop and ECR symposium in Oldenburg to discuss integrated microbial 'omics and learn applications of anvi'o.
More information and application link (application deadline is Jan 10): anvio.org/workshops/20...
Please apply and/or circulate 😇
More information and application link (application deadline is Jan 10): anvio.org/workshops/20...
Please apply and/or circulate 😇
December 16, 2024 at 10:38 AM
We are very happy to announce a free-to-attend #anvio workshop and ECR symposium in Oldenburg to discuss integrated microbial 'omics and learn applications of anvi'o.
More information and application link (application deadline is Jan 10): anvio.org/workshops/20...
Please apply and/or circulate 😇
More information and application link (application deadline is Jan 10): anvio.org/workshops/20...
Please apply and/or circulate 😇
The code is open, developers are around and responsive, and the distance metric and clustering algorithm are literally shown in the interface and can be changed to anything available in scipy.
Of course most people use most methods blindly, but I hope it is not everyone as you suspect :)
Of course most people use most methods blindly, but I hope it is not everyone as you suspect :)
December 11, 2024 at 8:46 AM
The code is open, developers are around and responsive, and the distance metric and clustering algorithm are literally shown in the interface and can be changed to anything available in scipy.
Of course most people use most methods blindly, but I hope it is not everyone as you suspect :)
Of course most people use most methods blindly, but I hope it is not everyone as you suspect :)
Please take a look at the reviews a colleague of mine received for a paper they submitted to a respectable journal.
The first review is for the first submission, the second one is for the revisions, and both of them will leave you wondering what the editor thinks about their role in this process 🤦♂️
The first review is for the first submission, the second one is for the revisions, and both of them will leave you wondering what the editor thinks about their role in this process 🤦♂️
November 15, 2024 at 1:56 PM
Please take a look at the reviews a colleague of mine received for a paper they submitted to a respectable journal.
The first review is for the first submission, the second one is for the revisions, and both of them will leave you wondering what the editor thinks about their role in this process 🤦♂️
The first review is for the first submission, the second one is for the revisions, and both of them will leave you wondering what the editor thinks about their role in this process 🤦♂️
It is a different kind of magic to be at the Cold Spring Harbor Laboratory during one of the best times of the year to visit this part of the world.
October 30, 2024 at 10:56 AM
It is a different kind of magic to be at the Cold Spring Harbor Laboratory during one of the best times of the year to visit this part of the world.
Today I gave a talk at the Karolinska Institute for the Swedish Bioinformatics Workshop.
My title was "Writing code for those who are looking for a kitchen in a world of restaurants", and there is a lot to talk unpack there.
BUT I JUST WANTED TO SHOW YOU THIS ABSOLUTE UNIT OF A SEMINAR ROOM,:
My title was "Writing code for those who are looking for a kitchen in a world of restaurants", and there is a lot to talk unpack there.
BUT I JUST WANTED TO SHOW YOU THIS ABSOLUTE UNIT OF A SEMINAR ROOM,:
November 7, 2023 at 6:54 PM
Today I gave a talk at the Karolinska Institute for the Swedish Bioinformatics Workshop.
My title was "Writing code for those who are looking for a kitchen in a world of restaurants", and there is a lot to talk unpack there.
BUT I JUST WANTED TO SHOW YOU THIS ABSOLUTE UNIT OF A SEMINAR ROOM,:
My title was "Writing code for those who are looking for a kitchen in a world of restaurants", and there is a lot to talk unpack there.
BUT I JUST WANTED TO SHOW YOU THIS ABSOLUTE UNIT OF A SEMINAR ROOM,: