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Páll Melsted

@pmelsted.bsky.social
1.6K followers 93 following 57 posts

Professor @hi.is in CS, head of rna seq data analysis at decode genetics (views are mine). Bioinformatician, epistemic trespasser, &c. ps. I hate GTF files

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Reposted by Páll Melsted
Nick Loman @pathogenomenick.bsky.social · 22/09/2026
Folks - if you're interested in how machine learning/AI can be used for microbial genomics, microbiome and metagenomics studies - please join us for a workshop in Birmingham on Thursday 8th October organised with CLIMB & NVIDIA. www.climb.ac.uk/blog/2026/09...
climb.ac.uk
Call for Applications: GPU-Accelerated Computing for Microbiome and Metagenomic Research · CLIMB
CLIMB is a cloud computing infrastructure for microbial bioinformatics — notebook servers, shared storage and reproducible workflows for genomics, metagenomics and pathogen surveillance researchers ac...
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Guillaume Holley @guillaumeolesan.bsky.social · 20/08/2026
I am delighted to present with @hannespetur.bsky.social our new study on the Icelandic pangenome reference HPRC-ICE. This work goes all the way from pangenome construction to disease association! (1/7) www.nature.com/articles/s41...
nature.com
An Icelandic pangenome reference - Nature
Newly developed methods enable construction of Icelandic haplotypes and mapping of population-scale short reads to a pangenome by reducing reference bias and improving discovery in low-mappability reg...
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Páll Melsted @pmelsted.bsky.social · 20/08/2026
Pantone or it didn’t happen
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Páll Melsted @pmelsted.bsky.social · 13/08/2026
It's hard to capture just how surreal the total eclipse was, even though it was cloudy. Darkness came instantly
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Páll Melsted @pmelsted.bsky.social · 05/05/2026
Is the link broken?
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Páll Melsted @pmelsted.bsky.social · 30/04/2026
Try the unsubscribe link, it’s leaking some email address information
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Reposted by Páll Melsted
Kristoffer Sahlin @ksahlin.bsky.social · 16/03/2026
𝗣𝗼𝘀𝘁𝗱𝗼𝗰 𝗮𝗻𝗱 𝗣𝗵𝗗 𝗽𝗼𝘀𝗶𝘁𝗶𝗼𝗻𝘀 𝗶𝗻 𝗖𝗼𝗺𝗽𝘂𝘁𝗮𝘁𝗶𝗼𝗻𝗮𝗹 𝗚𝗲𝗻𝗼𝗺𝗶𝗰𝘀 / 𝗔𝗹𝗴𝗼𝗿𝗶𝘁𝗵𝗺𝗶𝗰 𝗕𝗶𝗼𝗶𝗻𝗳𝗼𝗿𝗺𝗮𝘁𝗶𝗰𝘀 I am currently recruiting for both: 🔹 Postdoc position su.varbi.com/what:job/job... 🔹 PhD position su.varbi.com/en/what:job/... Please share with anyone who might be interested!
su.varbi.com
Postdoktor i Beräkningsbiologi
Matematiska institutionen består av cirka 120 forskare, lärare och administrativ personal och är organiserad i tre huvudsakliga avdelningar: Matematik, Matematisk statistik och Beräkningsmatematik
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Páll Melsted @pmelsted.bsky.social · 07/03/2026
media.tenor.com
a man stands in front of a sign that says microsoft web developers
ALT: a man stands in front of a sign that says microsoft web developers
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Páll Melsted @pmelsted.bsky.social · 06/03/2026
Cuda. I tried a long time ago to build something with opencl and found out that there is no support. AMD has had plenty of time to work with developers since then but nothing has happened. I guess NVIDIA figured out that Ballmer was right, it’s all about the developers
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Páll Melsted @pmelsted.bsky.social · 06/03/2026
Coming next week
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Páll Melsted @pmelsted.bsky.social · 06/03/2026
ok, that figure looked fine in the preview but was transparent, here's a better version
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Páll Melsted @pmelsted.bsky.social · 06/03/2026
The only downside to this work is that now I feel frustrated having to wait minutes for classical kallisto to finish
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Páll Melsted @pmelsted.bsky.social · 06/03/2026
like dealing with sparse arrays, variable sized lists and things we would solve with dynamic memory allocation on the CPU.
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Páll Melsted @pmelsted.bsky.social · 06/03/2026
and over again. Prefix scan. If you are interested in learning more about this then read this paper www.cs.cmu.edu/~guyb/papers... by Guy Blelloch from 1990. It is one of the most clearly written papers I've read and it gives you the algorithmic building blocks to solve problems on GPUs
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Páll Melsted @pmelsted.bsky.social · 06/03/2026
Contrary to regular scientific programming, where the state consist of a high dimensional vector and most operations are matrix multiplication, string processing does not have obvious programming paradigms that port easily to GPUs. And yet in this work we always wind up using the same tool over ...
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Páll Melsted @pmelsted.bsky.social · 06/03/2026
The key insight (aside from the speed) is that we need to reconsider all of the algorithmic framework if we want to use GPUs for large scale processing of sequencing datasets. It's nontrivial but I hope this paper gives some insight into how it's possible.
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Páll Melsted @pmelsted.bsky.social · 06/03/2026
For a large dataset (295M reads) the GPU version took 50 seconds. Just running zcat on the files takes 10 minutes! Decompression and parsing FASTQ is a major bottleneck . Instead of using kseq we moved this work parsing to the GPU which delivers amazing throughput.
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Páll Melsted @pmelsted.bsky.social · 06/03/2026
Figure 1 shows the main results, we can run 30M paired end reads in under 10 seconds using a RTX 5090 NVIDIA GPU. The average speedup is 30x for smaller reads and that includes startup time, on average we can process about 3.6M paired end reads per second.
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Páll Melsted @pmelsted.bsky.social · 06/03/2026
Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k... Figure 1 shows they key result
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Páll Melsted @pmelsted.bsky.social · 22/02/2026
2015: growing almonds consumes too much energy and water 2026: growing kids consumes too much energy and eater bsky.app/profile/x2y....
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Páll Melsted @pmelsted.bsky.social · 18/02/2026
Jafngóð og bókin?
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Páll Melsted @pmelsted.bsky.social · 10/01/2026
In pretty sure I’m thoroughly radiated after this
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Páll Melsted @pmelsted.bsky.social · 28/12/2025
I’ve been exploring different models in cursor and opus 4.5 is amazing. I often ask it to sketch out code with the prompt “do not make any modifications to the code” and ask about my assumptions and poke holes, only when I agree can it proceed
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Páll Melsted @pmelsted.bsky.social · 23/12/2025
Spotify wrap up is so last year
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Páll Melsted @pmelsted.bsky.social · 08/12/2025
I also learned today that Nirvana is not “niche”. But then again this is the generation that invented 6-7
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Páll Melsted @pmelsted.bsky.social · 08/12/2025
14yo: I need a niche music recommendation Me: how about Godspeed You! Black Emperor, let’s find it *not found on Spotify* Me: That’s how nice they are
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Páll Melsted @pmelsted.bsky.social · 31/10/2025
Today I found out that the Pacbio tools for working with barcodes and adapters in Kinnex are called lima and skera. To whomever came up with that joke, I salute you, you’ve reached 50% of the audience
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Páll Melsted @pmelsted.bsky.social · 21/10/2025
Retracting a paper is going to hurt
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Páll Melsted @pmelsted.bsky.social · 07/10/2025
All right, I posed this question to my PhD student this morning and he looked at me funny and asked if it was a trick question What is the running time of this code a, b = 0, 1 for _ in range(2, n+1): a, b = b, a + b return b
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Páll Melsted @pmelsted.bsky.social · 01/10/2025
Happy Q4 for those who celebrate
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Páll Melsted @pmelsted.bsky.social · 28/09/2025
Today I fixed a humming converter and an intercom receiver set from the 70’s. I’m surprised at how good ChatGPT is at diagnosing problems and coming up with fixes for hardware that is older than me. Since I didn’t have to replace the units I can justify the cost and environmental impact of AI
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Reposted by Páll Melsted
Ben Langmead @benlangmead.bsky.social · 22/08/2025
The Genome Informatics conference (@ Cold Spring Harbor Lab, Nov 5 - 8) abstract deadline is **today**. We welcome your submissions! Topics include: - PanGenomes - Genome Assembly & Seq. Algos. - Algorithmic Evo. Bio - Single Cell & Spatial Omics - Microbial Genomics - AI/ML & Integrative Omics 🙏🙏🙏
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Páll Melsted @pmelsted.bsky.social · 15/08/2025
media.tenor.com
a group of men in suits are dancing around a coffin .
ALT: a group of men in suits are dancing around a coffin .
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Páll Melsted @pmelsted.bsky.social · 05/07/2025
Perfect marketing doesn’t exi…
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Páll Melsted @pmelsted.bsky.social · 05/07/2025
Glengarry Glen Ross
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Páll Melsted @pmelsted.bsky.social · 27/06/2025
It is by the juice of coffee that thoughts acquire speed …
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Reposted by Páll Melsted
Oliver Stegle @oliverstegle.bsky.social · 26/06/2025
Job alert: Join us for a postdoc in AI in genetics at @EMBL Heidelberg! Great collaboration with @Adrian Cortes @GSK, aiming to develop new tools to elucidate genetic effects using population-scale cohorts and single-cell readouts. Please share! embl.wd103.myworkdayjobs.com/de-DE/EMBL/d...
embl.wd103.myworkdayjobs.com
Postdoctoral Researcher in Computational Genetics
The research group of Oliver Stegle looks for a postdoctoral researcher to join a collaborative project with GSK with the goal to apply computational methods to investigate the effects of rare variant...
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Páll Melsted @pmelsted.bsky.social · 24/06/2025
I misread that as “message” which would have been more impressive 🚩
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Reposted by Páll Melsted
Lior Pachter @lpachter.bsky.social · 03/06/2025
liorpachter.wordpress.com/2025/06/03/e...
liorpachter.wordpress.com
Epistemic failure of epistemic failure
Earlier this year I came across this interesting post by mathematician Daniel Litt, where he pondered how many intrinsically true results in mathematics have been published with erroneous proofs: D…
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Reposted by Páll Melsted
Jonathan Pritchard @jkpritch.bsky.social · 01/06/2025
I have an opportunity to hire a staff scientist for my lab. Looking for someone with outstanding skillset in ML/statistics, genomics applications; interest in mentoring, strong publication record, PD experience required. Email CV to me+cc my assistant (see 'contact' on my website). Ad to follow.
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Páll Melsted @pmelsted.bsky.social · 20/05/2025
I had Ágætis byrjun on repeat for a long time. Just happened upon this on Spotify the other day and I’d forgotten how good it was
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Páll Melsted @pmelsted.bsky.social · 09/05/2025
In Iceland spring is not something you define as season based on weather but more from the arrival of migratory birds
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Páll Melsted @pmelsted.bsky.social · 05/05/2025
For me it’s kind of in the same category as woodworking videos that create beautiful custom tables from slabs of oak. Looks great and maybe someday I can use this.
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Páll Melsted @pmelsted.bsky.social · 05/05/2025
vm.tiktok.com/ZNd6ebsjN/ I actually learned something new here
vm.tiktok.com
TikTok - Make Your Day
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Páll Melsted @pmelsted.bsky.social · 05/05/2025
My favorite brainrot is an account on TikTok that solves complicated integrals on a blackboard with colored chalk.
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Páll Melsted @pmelsted.bsky.social · 02/05/2025
When you refresh to see new posts you lose where you were. This is the only thing I miss about twitter
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Páll Melsted @pmelsted.bsky.social · 30/04/2025
There is something refreshingly honest about moving the goalpost this blatantly. Adjusting for multiple testing? Not in my house ☝️
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Reposted by Páll Melsted
Erna Magnúsdóttir @e-rna.bsky.social · 22/04/2025
Join our lab to study transcriptional regulation in mouse germ cells and embryonic stem cells at @haskoliislands.bsky.social in beautiful Reykjavík! Apply here: tinyurl.com/34y6jcrd #epigenetics #TranscriptionFactors #transcriptomics #stemCells #pluripotency
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Páll Melsted @pmelsted.bsky.social · 07/04/2025
Hold my mead. 1200 from Iceland handrit.is/manuscript/v...
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Páll Melsted @pmelsted.bsky.social · 04/03/2025
Today I gave a lecture in a brand new lecture hall where the projector was acting weird. Turned out that the control panel showed green for when the projector was off, you had to press the button wait 10 seconds and then it turned red. I think this should be a case study in UI design
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