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

2015: growing almonds consumes too much energy and water 2026: growing kids consumes too much energy and eater bsky.app/profile/x2y....

In pretty sure I’m thoroughly radiated after this

Spotify wrap up is so last year

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

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

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

Happy Q4 for those who celebrate

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

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 🙏🙏🙏

Perfect marketing doesn’t exi…

It is by the juice of coffee that thoughts acquire speed …

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...

I misread that as “message” which would have been more impressive 🚩

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.

In Iceland spring is not something you define as season based on weather but more from the arrival of migratory birds

My favorite brainrot is an account on TikTok that solves complicated integrals on a blackboard with colored chalk.

There is something refreshingly honest about moving the goalpost this blatantly. Adjusting for multiple testing? Not in my house ☝️

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

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

I might need to replicate this paper www.nature.com/articles/s44...

Somehow I would be more confident that the Tesla could drive autonomously if the auto mode on the windshield wipers worked.

Ironically this is the best content on that other place

Beautiful polar stratospheric clouds today

Productivity tip: set your phone to do not disturb, close all messaging software and email apps on your laptop, put on your headphones and Koyaanisqatsi on repeat. Don’t forget coffee.

Let’s see if this bsky thing works. I have a 4K monitor at home and I want to connect a Mac mini and a Mac laptop to the monitor and external keyboard/mouse. Any recommendations on a KVM setup or favorite keyboard & mouse?

Heading out to #genomeinformatics2024 remember to bring your adapters

Today I almost obsessed over a piece of code that turns out took 7.6 seconds to run. Writing the code to measure the time took half a second, I just wrote a comment and cursor filled in the rest and I hit tab. Prior to AI I would have spent half an hour reading docs or stack overflow

Reposting! This faculty search is open through December

Adam Rutherford delivered a great overview of how the past of eugenics is still with us in today’s education of genetics and how it shapes the public view #ashg23 Fascinating to see the origin and paths of these ideas and phenotypes, accepted as truths (eye and hair color) even if they are false

Robert Handsaker just delivered a mind blowing talk at #ashg23 Beautiful application of single cell omics to disentangle the expansion of CAG repeats to specific cell types in patients of Huntington’s disease

I fought the linker and the linker won

2017 vs 2023