Thomas Haverkamp

So if you get sick in the next pandemic, it is because you did too little to be healthy ...
It just ignores what pathogens are /do... sigh...

A table with a stripped mug of black coffee. Next to it, a green pear and on top a with tray that is blurry. On the lower right a piece of my breakfast plate.

My morning coffee, today I used the french press again. #photography #square #coffee

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.

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-...

A blue box with books sorted by color, and surrounded by plants.

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

A lighthouse, surrounded by water, off the coast in Scotland.

Ah, okay well my interest is phages in poultry samples, so i was wondering if i could find this system in my metagenomes. Maybe i can, i will check out your preprint.

Okay, but that is interesting. Are those 300 related organisms, or are they found in very different phyla?

Hey Ilya, that is nice work.
Have you any idea how widespread this mentis system is in bacteria?

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...

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 Thanks Ilya for making it outdated already :).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!

A park landscape with a blue sky in the back, and a tree in yellow autumn colors.

The morning sun giving bright colors #berlin #gernany #yellow #photography

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

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/...

That is a scenario I had not thought of for an outbreak....

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

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

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 🧪

My daughter loves playing this especially when she can be the criminal.

Competitive metagenomic read recruitment explained A tutorial on the nuts and bolts of competitive read recruitment

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...

YouTube video by Global News Avian flu “real disaster” as over 1K cranes found dead at key German roosting spot: experts

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?...

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.

"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...

Cooooooooool

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...

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...

Stacked bargraph where the x-axis the year-month and the values are the number of bla*{NDM,OXA,VIM,GES,IMP,KPC}* genes identified in sequencing efforts that month. The legend is to the right in order for general matching of AMR gene to value.

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.

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?

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.

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...

Incredible new paper from @schacherer.bsky.social et al rdcu.be/eLcTH

Dank je wel Hilde.

A forrest path covered with leaves. The trees have autumn colors

Ww cycled today along the #Berlin wall. Some very straight paths in the autumn forrests #trees #autumn #square #photography

Okay, thanks.