Thomas Haverkamp
@thomieh73.bsky.social
Microbiology / bioinformatics / photography and running around
November 15, 2025 at 8:12 AM
Reposted by Thomas Haverkamp
I've done a lot of work in Python this fall, and it hasn't endeared me to the language at all. Why does stuff have to be so complicated when you're doing it in Python?
blog.genesmindsmachines.com/p/python-is-...
blog.genesmindsmachines.com/p/python-is-...
Python is not a great language for data science. Part 1: The experience
It may be a good language for data science, but it’s not a great one.
blog.genesmindsmachines.com
November 13, 2025 at 4:16 PM
I've done a lot of work in Python this fall, and it hasn't endeared me to the language at all. Why does stuff have to be so complicated when you're doing it in Python?
blog.genesmindsmachines.com/p/python-is-...
blog.genesmindsmachines.com/p/python-is-...
We decided to sort the #books by color in this box in a kleingarten here in #Berlin. We found a almost complete dutch encyclopedia of 20 books inside. Why do some people think one can dump such things in a book sharing box.... #photography
November 9, 2025 at 7:41 PM
We decided to sort the #books by color in this box in a kleingarten here in #Berlin. We found a almost complete dutch encyclopedia of 20 books inside. Why do some people think one can dump such things in a book sharing box.... #photography
Reposted by Thomas Haverkamp
A lighthouse, surrounded by water, off the coast in Scotland.
November 9, 2025 at 8:09 AM
A lighthouse, surrounded by water, off the coast in Scotland.
Reposted by Thomas Haverkamp
Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides.
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:00 AM
Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides.
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Reposted by Thomas Haverkamp
Such an elegant mechanism. Perfect to make November more fun.
Also, we wrote a review about NAD+ and bacterial immunity, that came out last month. Thanks Ilya for making it outdated already :).
Congrats to everyone for a beautiful discovery!
Also, we wrote a review about NAD+ and bacterial immunity, that came out last month. Thanks Ilya for making it outdated already :).
Congrats to everyone for a beautiful discovery!
Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides.
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
November 6, 2025 at 8:50 AM
Such an elegant mechanism. Perfect to make November more fun.
Also, we wrote a review about NAD+ and bacterial immunity, that came out last month. Thanks Ilya for making it outdated already :).
Congrats to everyone for a beautiful discovery!
Also, we wrote a review about NAD+ and bacterial immunity, that came out last month. Thanks Ilya for making it outdated already :).
Congrats to everyone for a beautiful discovery!
November 6, 2025 at 8:20 AM
I am working for years with microbiome data, and one of the things I find tough is the differential abundance analysis. Currently reading a paper that promotes non-parametric testing, and I wonder about the results I produced in the past:
academic.oup.com/bib/article/...
academic.oup.com/bib/article/...
Elementary methods provide more replicable results in microbial differential abundance analysis
Abstract. Differential abundance analysis (DAA) is a key component of microbiome studies. Although dozens of methods exist, there is currently no consensus
academic.oup.com
November 5, 2025 at 10:31 AM
I am working for years with microbiome data, and one of the things I find tough is the differential abundance analysis. Currently reading a paper that promotes non-parametric testing, and I wonder about the results I produced in the past:
academic.oup.com/bib/article/...
academic.oup.com/bib/article/...
That is a scenario I had not thought of for an outbreak....
October 29, 2025 at 4:24 PM
That is a scenario I had not thought of for an outbreak....
Reposted by Thomas Haverkamp
From a crewmember on yesterday's Teal 74 mission into now-Category 5 Hurricane #Melissa. As clear of an eye as you will see in the Atlantic basin.
October 27, 2025 at 4:11 PM
From a crewmember on yesterday's Teal 74 mission into now-Category 5 Hurricane #Melissa. As clear of an eye as you will see in the Atlantic basin.
My sunday morning coffee #photography
October 26, 2025 at 8:45 AM
My sunday morning coffee #photography
Reposted by Thomas Haverkamp
Researchers harvested the coffee bean–containing scat of wild Asian palm civets, which is used to make kopi luwak, to do a chemical analysis of the beans. cen.acs.org/food/ferment... #chemsky 🧪
This coffee comes from civet poop. What makes it chemically distinct?
Kopi luwak is a specialty coffee that’s fermented in the gut of a civet. It’s also rich in fatty acids
cen.acs.org
October 25, 2025 at 6:11 PM
Researchers harvested the coffee bean–containing scat of wild Asian palm civets, which is used to make kopi luwak, to do a chemical analysis of the beans. cen.acs.org/food/ferment... #chemsky 🧪
Reposted by Thomas Haverkamp
I wrote a new tutorial on competitive metagenomic read recruitment (and profiling of the results with #anvio), for those of us nerds who would like to get their hands dirty with data:
anvio.org/tutorials/co...
anvio.org/tutorials/co...
Competitive metagenomic read recruitment explained
A tutorial on the nuts and bolts of competitive read recruitment
anvio.org
October 25, 2025 at 10:50 AM
I wrote a new tutorial on competitive metagenomic read recruitment (and profiling of the results with #anvio), for those of us nerds who would like to get their hands dirty with data:
anvio.org/tutorials/co...
anvio.org/tutorials/co...
Reposted by Thomas Haverkamp
It’s everywhere except Australia. I don’t know if H5N1 will make the jump to human adaptation and pandemic potential, but it’s never had more opportunities.
youtu.be/sRJeCLgzcKY?...
youtu.be/sRJeCLgzcKY?...
Avian flu “real disaster” as over 1K cranes found dead at key German roosting spot: experts
YouTube video by Global News
youtu.be
October 24, 2025 at 8:03 AM
It’s everywhere except Australia. I don’t know if H5N1 will make the jump to human adaptation and pandemic potential, but it’s never had more opportunities.
youtu.be/sRJeCLgzcKY?...
youtu.be/sRJeCLgzcKY?...
Reposted by Thomas Haverkamp
Really exciting that the preprint on Barbell, a new demultiplexer, is finally out!
It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.
It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.
Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it:
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
October 23, 2025 at 9:28 PM
Really exciting that the preprint on Barbell, a new demultiplexer, is finally out!
It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.
It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.
Reposted by Thomas Haverkamp
"The Kasai outbreak emphasises the case that genomic stasis might be a recurring feature of Ebola virus ecology. A lineage that is virtually unchanged since 1976 challenges assumptions about Ebola's evolution and exposes the blind spots of surveillance."
www.thelancet.com/journals/lan...
www.thelancet.com/journals/lan...
October 21, 2025 at 3:03 PM
"The Kasai outbreak emphasises the case that genomic stasis might be a recurring feature of Ebola virus ecology. A lineage that is virtually unchanged since 1976 challenges assumptions about Ebola's evolution and exposes the blind spots of surveillance."
www.thelancet.com/journals/lan...
www.thelancet.com/journals/lan...
Reposted by Thomas Haverkamp
Cooooooooool
Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?
Today, we report the discovery of telomerase homologs in a family of antiviral reverse transcriptases, revealing an unexpected evolutionary origin in bacteria.
doi.org/10.1101/2025...
Today, we report the discovery of telomerase homologs in a family of antiviral reverse transcriptases, revealing an unexpected evolutionary origin in bacteria.
doi.org/10.1101/2025...
October 18, 2025 at 4:09 AM
Cooooooooool
Reposted by Thomas Haverkamp
Ik ontdekte een blinde vlek in het stikstofbeleid 👇🏼
Maatregelen die de uitstoot moeten drukken zijn én nauwelijks effectief, maar pakken óók nog eens slecht uit voor de gezondheid en het welzijn van dieren. 🐄 🐖
Morgen in de papieren krant, nu al online:
www.volkskrant.nl/wetenschap/k...
Maatregelen die de uitstoot moeten drukken zijn én nauwelijks effectief, maar pakken óók nog eens slecht uit voor de gezondheid en het welzijn van dieren. 🐄 🐖
Morgen in de papieren krant, nu al online:
www.volkskrant.nl/wetenschap/k...
Koeien, varkens en kippen gaan gebukt onder stikstofbeleid: ‘Diergezondheid staat bijna altijd achteraan’
In de strijd tegen stikstof zijn miljarden gestoken in emissiearme stallen, luchtwassers en aangepast veevoer. Niet alleen halen die maatregelen weinig uit: ze brengen ook de gezondheid van koeien, va...
www.volkskrant.nl
October 17, 2025 at 10:36 AM
Ik ontdekte een blinde vlek in het stikstofbeleid 👇🏼
Maatregelen die de uitstoot moeten drukken zijn én nauwelijks effectief, maar pakken óók nog eens slecht uit voor de gezondheid en het welzijn van dieren. 🐄 🐖
Morgen in de papieren krant, nu al online:
www.volkskrant.nl/wetenschap/k...
Maatregelen die de uitstoot moeten drukken zijn én nauwelijks effectief, maar pakken óók nog eens slecht uit voor de gezondheid en het welzijn van dieren. 🐄 🐖
Morgen in de papieren krant, nu al online:
www.volkskrant.nl/wetenschap/k...
Reposted by Thomas Haverkamp
I probably need some different colors, but I've made a graph detailing the number of AMR genes we've seen in organisms that we've sequenced for the last few months.
October 16, 2025 at 6:10 PM
I probably need some different colors, but I've made a graph detailing the number of AMR genes we've seen in organisms that we've sequenced for the last few months.
Reposted by Thomas Haverkamp
The Long Quest to Uncover a Sea Star Killing Bacteria daily.jstor.org/the-long-que...
The Long Quest to Uncover a Sea Star Killing Bacteria - JSTOR Daily
Scientists say they’ve found the cause of a marine epidemic more than ten years after it started. What took so long?
daily.jstor.org
October 16, 2025 at 12:26 PM
The Long Quest to Uncover a Sea Star Killing Bacteria daily.jstor.org/the-long-que...
Please people, don't publish your work in a MDPI journal, just so you can get it accepted quickly. For me it is a sign you are cutting corners to do science so you ignore the fact MDPI has troublesome standards when it comes to peer-review.
I won't read your paper because it is in MDPI. It is sad.
I won't read your paper because it is in MDPI. It is sad.
October 16, 2025 at 8:22 AM
Please people, don't publish your work in a MDPI journal, just so you can get it accepted quickly. For me it is a sign you are cutting corners to do science so you ignore the fact MDPI has troublesome standards when it comes to peer-review.
I won't read your paper because it is in MDPI. It is sad.
I won't read your paper because it is in MDPI. It is sad.
Reposted by Thomas Haverkamp
Incredible new paper from @schacherer.bsky.social et al rdcu.be/eLcTH
From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes
Nature - A newly compiled atlas of species-wide structural variants and gene-based and graph pangenomes derived from highly complete assemblies of genomes from 1,086 natural isolates enable...
rdcu.be
October 15, 2025 at 9:06 PM
Incredible new paper from @schacherer.bsky.social et al rdcu.be/eLcTH
Ww cycled today along the #Berlin wall. Some very straight paths in the autumn forrests #trees #autumn #square #photography
October 12, 2025 at 2:38 PM
Ww cycled today along the #Berlin wall. Some very straight paths in the autumn forrests #trees #autumn #square #photography
This is nicely explained why it is important to have more whale poo in the oceans.
The global whaling industry experienced a boom c. 1840-1950 as technology allowed whalers to hunt the Southern Ocean around Antarctica.
Under standard models, we would have expected krill populations to have *exploded*.
Instead, they DROPPED exponentially.
Let's talk about the KRILL PARADOX.
Under standard models, we would have expected krill populations to have *exploded*.
Instead, they DROPPED exponentially.
Let's talk about the KRILL PARADOX.
October 9, 2025 at 3:08 PM
This is nicely explained why it is important to have more whale poo in the oceans.
Good morning from a sunny balcony
October 9, 2025 at 6:28 AM
Good morning from a sunny balcony