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Rob Patro @robp.bsky.social · 9h

Yup!

Reposted by Rob Patro

Andre Kahles @akkah21.bsky.social · 1d

After years of research and continuous refinement, we’re thrilled to share that our paper on the MetaGraph framework — enabling Petabase-scale search across sequencing data — has been published today in Nature (www.nature.com/articles/s41...)

Efficient and accurate search in petabase-scale sequence repositories - Nature

MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

www.nature.com

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Rob Patro @robp.bsky.social · 12h

I did say coding (my bad), but I was considering the case of software engineering, which involves certain problem solving and invention that I have seen AI fall completely flat on, even when gently guided toward a good solution in multiple different ways / through different prompts. 2/2

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Rob Patro @robp.bsky.social · 12h

Yea, I reject that characterization. The process of coding involves applying specific practices, often in subtly different ways, in different contexts. I have seen several different AIs mess that up horribly in different domains on multiple occasions. Also 1/2

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Reposted by Rob Patro

Robert Aboukhalil @robert.bio · 18h

Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt

It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.

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Rob Patro @robp.bsky.social · 19h

Agreed; 100%

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Rob Patro @robp.bsky.social · 19h

This endorsement means a lot to me! This is because Mohsen (a) was my student, and so knows not just about the work we do in the lab but also about what it's like to work with me as an advisor/mentor and (b) has long since graduated and so is under no duress to provide such an endorsement 🤣!

Mohsen Zakeri @mohsenzakeri.bsky.social · 20h

An awesome opportunity, strongly recommended to anyone looking for a postdoc in algorithms and genomics!

Rob Patro @robp.bsky.social · 1d

And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....

If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!

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Reposted by Rob Patro

Mohsen Zakeri @mohsenzakeri.bsky.social · 20h

An awesome opportunity, strongly recommended to anyone looking for a postdoc in algorithms and genomics!

Rob Patro @robp.bsky.social · 1d

And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....

If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!

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Rob Patro @robp.bsky.social · 21h

Oh man; long-form interview with @jonhoo.eu about Rust and other things! I can't wait to watch this: youtu.be/nOSxuaDgl3s?...

Rust 2025: 400K Salaries, AI, Defence & Borrow Checker — Jon Gjengset on Rust & the Future of Coding

YouTube video by JetBrains

youtu.be

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Rob Patro @robp.bsky.social · 21h

The Metagraph paper is out in Nature; it showed up in my feeds today! Congratulations to Mikhail Karasikov, @gxxxr.bsky.social, @akkah21.bsky.social and all of the other authors (whom I'd love to follow on Bluesky if I can find you ;P) www.nature.com/articles/s41...

Efficient and accurate search in petabase-scale sequence repositories - Nature

MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

www.nature.com

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Reposted by Rob Patro

Jon Gjengset @jonhoo.eu · 21h

In August, I was interviewed by JetBrains about programming and Rust, ranging from the borrow checker, to agentic coding, to hiring. And it's now on YouTube! It's also general enough that it should be interesting even to those not already knee deep in Rust 😅
www.youtube.com/watch?v=nOSx...

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Rob Patro @robp.bsky.social · 23h

Even if not, you'll Google it again in 6 years or so when you've forgotten about this episode ;P.

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Rob Patro @robp.bsky.social · 1d

I agree interviews are hard, but disagree that AI covers the whole field (by discrete areas, not size ... by size, much software is already trivial copypasta that AI can handle just fine). But 80% of the hard stuff is in a small number of places.

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Rob Patro @robp.bsky.social · 1d

And as my second post pointed out. If you don't need those skills, why hire a person?

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Rob Patro @robp.bsky.social · 1d

Because for certain important skill sets, that is manifestly not true.

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Rob Patro @robp.bsky.social · 1d

Don't forget to turnoff the AI!

www.google.com/search?q=how...

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Reposted by Rob Patro

David Buchanan @retr0.id · 3d

how to deactivate torment nexus

torment nexus deactivation tutorial

torment nexus deactivation tutorial working 2025

deactivate torment nexus no survey

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Reposted by Rob Patro

Travis Wheeler @wheelerlab.org · 1d

Dream postdoc - Rob's science is excellent (and he's pretty great, too)

Rob Patro @robp.bsky.social · 1d

And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....

If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!

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Reposted by Rob Patro

Joshua Weitz @joshuasweitz.bsky.social · 1d

Best consideration deadline, Friday Oct 10:

#SCIMaP (scienceimacts.org) seeks to hire a Research Communications and Media Outreach Specialist at U-Maryland to facilitate public engagement related to federal investment in science and health research.

umd.wd1.myworkdayjobs.com/en-US/UMCP/j...

SCIMaP job opportunity - https://umd.wd1.myworkdayjobs.com/en-US/UMCP/job/Research-Communications-and-Media-Outreach-Specialist_JR102577

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Rob Patro @robp.bsky.social · 1d

Another amazing opportunity at UMD in Mihai Pop's lab! Mihai is looking for a bioinformatics software engineer. Consider applying here if you're interested: umd.wd1.myworkdayjobs.com/en-US/UMCP/j...

Bioinformatics engineer

Job Description Summary Organization's Summary Statement: We are seeking to hire a bioinformatics engineer in the Pop lab within the University of Maryland Institute for Advanced Computer Studies (UMI...

umd.wd1.myworkdayjobs.com

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Rob Patro @robp.bsky.social · 1d

🙏Thank you, Travis!

Rob Patro @robp.bsky.social · 1d

And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....

If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!

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Rob Patro @robp.bsky.social · 1d

Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...

Postdoc Description.docx

Title: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...

docs.google.com

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Rob Patro @robp.bsky.social · 1d

If what you need can be generated by mediocre AI code agents, you don't need a quality software engineer. If what you need is someone to write good, efficient, and clear code, their answers to this question will be enlightening. 2/2

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Rob Patro @robp.bsky.social · 1d

Idea for a coding interview question. Give the applicant the code generated by ChatGPT or Claude for a marginally esoteric problem, and ask them to fix or improve the code. 1/2

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