Johan Nystrom-Persson
@jtnystrom.bsky.social
Metagenomics, algorithmic bioinformatics, programming languages. Performance engineering, esp w. Scala and Spark. Swedish, living in Japan. Consulting: https://jnpsolutions.io/
Reposted by Johan Nystrom-Persson
Every reputable expert I know considers mRNA vaccine technology to be one of the most revolutionary advances in medicine in our lifetimes. Its inventors won the Nobel Prize in 2023. Shutting it down now is pointless self-harm to humanity.
Release from HHS: HHS will wind down its development of the mRNA vaccine development activities under the Biomedical Advanced Research and Development Authority (BARDA).
August 5, 2025 at 10:54 PM
Every reputable expert I know considers mRNA vaccine technology to be one of the most revolutionary advances in medicine in our lifetimes. Its inventors won the Nobel Prize in 2023. Shutting it down now is pointless self-harm to humanity.
Explaining in simple terms the two main results achieved by our #metagenomic classifier #Slacken - scaling independently of RAM, and sample-tailored libraries. jnpsolutions.io/2025/07/03/s...
Slacken paper published in NAR Genomics and Bioinformatics
Our paper on Slacken, a metagenomic classifier based on the Kraken 2 method, was recently published in NAR Genomics and Bioinformatics. In this post I (Johan) would like to break down the main results...
jnpsolutions.io
July 3, 2025 at 4:55 AM
Explaining in simple terms the two main results achieved by our #metagenomic classifier #Slacken - scaling independently of RAM, and sample-tailored libraries. jnpsolutions.io/2025/07/03/s...
Excited to announce our paper "Precise and scalable metagenomic profiling with sample-tailored minimizer libraries". academic.oup.com/nargab/artic...
#metagenomics #kraken2 #slacken
#metagenomics #kraken2 #slacken
Precise and scalable metagenomic profiling with sample-tailored minimizer libraries
Abstract. Reference-based metagenomic profiling requires large genome libraries to maximize detection and minimize false positives. However, as libraries g
academic.oup.com
June 18, 2025 at 2:37 AM
Excited to announce our paper "Precise and scalable metagenomic profiling with sample-tailored minimizer libraries". academic.oup.com/nargab/artic...
#metagenomics #kraken2 #slacken
#metagenomics #kraken2 #slacken
Reposted by Johan Nystrom-Persson
“Why I stopped using AI code editors”
The article is spot on. I've gained my intuition & expertise, aka good taste in software engineering, by suffering through learning and taking care of the nitty-gritty while thinking of abstraction and reuse.
lucianonooijen.com/blog/why-i-s...
The article is spot on. I've gained my intuition & expertise, aka good taste in software engineering, by suffering through learning and taking care of the nitty-gritty while thinking of abstraction and reuse.
lucianonooijen.com/blog/why-i-s...
Why I stopped using AI code editors ·
Luciano Nooijen
In the past I used AI code editors for all of my programming, but I stopped using it and recommend others to consider this as well
lucianonooijen.com
April 4, 2025 at 6:11 AM
“Why I stopped using AI code editors”
The article is spot on. I've gained my intuition & expertise, aka good taste in software engineering, by suffering through learning and taking care of the nitty-gritty while thinking of abstraction and reuse.
lucianonooijen.com/blog/why-i-s...
The article is spot on. I've gained my intuition & expertise, aka good taste in software engineering, by suffering through learning and taking care of the nitty-gritty while thinking of abstraction and reuse.
lucianonooijen.com/blog/why-i-s...
Reposted by Johan Nystrom-Persson
CDC datasets have been saved. But you can still help by seeding.
CDC datasets uploaded before January 28th, 2025 : Centers for Disease Control and Prevention : Free Download, Borrow, and Streaming : Internet Archive
An archive of all CDC datasets uploaded to https://data.cdc.gov/browse before January 28th, 2025. Excludes corrupt datasets and data not publicly accessible.
archive.org
February 2, 2025 at 4:38 AM
CDC datasets have been saved. But you can still help by seeding.
Reposted by Johan Nystrom-Persson
Number theorists: please get in touch. xenaproject.wordpress.com/2025/01/20/t...
Think of a number.
My feed was recently clogged up with news articles reporting that Sam Altman thinks that AGI is here, or will be here next year, or whatever. I will refrain from giving even more air to this nonsen…
xenaproject.wordpress.com
January 20, 2025 at 2:21 PM
Number theorists: please get in touch. xenaproject.wordpress.com/2025/01/20/t...
Our new #metagenomics paper. What if the Kraken 2 library was specifically built for the samples being classified, every time? We show that this improves precision significantly while also being surprisingly cheap, using a new clone of Kraken 2 based on Apache Spark. www.biorxiv.org/content/10.1...
Precise and scalable metagenomic profiling with sample-tailored minimizer libraries
Reference-based metagenomic profiling requires large genome libraries to maximize detection and minimize false positives. However, as libraries grow, classification accuracy suffers, particularly in k...
www.biorxiv.org
January 21, 2025 at 2:17 AM
Our new #metagenomics paper. What if the Kraken 2 library was specifically built for the samples being classified, every time? We show that this improves precision significantly while also being surprisingly cheap, using a new clone of Kraken 2 based on Apache Spark. www.biorxiv.org/content/10.1...
Reposted by Johan Nystrom-Persson
Precise and scalable metagenomic profiling with sample-tailored minimizer libraries https://www.biorxiv.org/content/10.1101/2024.12.22.629657v1
December 25, 2024 at 4:34 PM
Precise and scalable metagenomic profiling with sample-tailored minimizer libraries https://www.biorxiv.org/content/10.1101/2024.12.22.629657v1