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Barış Ekim @ekimb.bsky.social · 24d

Not aware of anything other than docs.rs/debruijn/lat..., which is what I ended up using. Seems like a bespoke HashMap impl is the best way to go, although I hate rewriting the simplification and compaction routines that must (and does, just not in Rust) exist somewhere…

debruijn - Rust

debruijn: a De Bruijn graph library for DNA seqeunces in Rust.

docs.rs

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Barış Ekim @ekimb.bsky.social · 24d

Happy (a^2, b^2, c^2)!

www.npr.org/2025/09/16/n...

On 9/16/25, celebrate a date of mathematical beauty

Pythagorean Triple Square Day, as one man affectionately calls 9/16/25, is a day like no other this century.

www.npr.org

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Barış Ekim @ekimb.bsky.social · Aug 22

Skeet of the week award!

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Reposted by Barış Ekim

Human Pangenome Reference Consortium @humanpangenome.bsky.social · Aug 22

Accurate genome assemblies just got better. DeepPolisher improves base-level accuracy, cutting errors by 50%+ and indels by >70%, applied to 180 HPRC assemblies.

Uncover the science behind it:
www.biorxiv.org/content/10.1...

Highly accurate assembly polishing with DeepPolisher

Accurate genome assemblies are essential for biological research, but even the highest quality assemblies retain errors caused by the technologies used to construct them. Base-level errors are typical...

www.biorxiv.org

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Reposted by Barış Ekim

Ran Blekhman @blekhman.bsky.social · Aug 9

This is not just HHMI. All Chan Zuckerberg Initiative funding calls are CLOSED. The Gates Foundation has no Grand Challenges funding opportunities. I've never seen anything like this. Private foundations have just decided to stop supporting biomedical research.

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Barış Ekim @ekimb.bsky.social · Jul 8

Actually wild how it’s been free and accessible for over two decades... 🎉🎉

’We couldn’t live without it’: the UCSC Genome Browser turns 25

After a quarter of a century, the website remains an essential tool for navigating the genome and understanding its structure, function and clinical impact.

www.nature.com

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Barış Ekim @ekimb.bsky.social · Jun 6

Recently said goodbye to a home away from home after almost a decade (in exchange for a title only in writing). Now moving onto greener pastures!

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Barış Ekim @ekimb.bsky.social · Jun 6

To be honest I expected a minimum number of edit operations instead of retyping… Congrats Giulio!

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Barış Ekim @ekimb.bsky.social · May 16

Sadly, academia is already perceived as a rat race and a cutthroat battle arena. By taking away the one chance to sustain themselves in this environment, you’re not doing international scholars, who actively chose to survive in a place that consistently attempts to get rid of them, any favors. 5/5

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Barış Ekim @ekimb.bsky.social · May 16

I might come across as quasi-entitled here — since it only makes sense that a country would support solely its citizens (which I, incidentally, oppose as an ideology); however, when fellowships are often what makes or breaks a faculty/job application, why would a non-citizen choose to work here? 4/

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Barış Ekim @ekimb.bsky.social · May 16

I understand that perhaps this is the best strategy for protecting HHMI as a supportive institution long-term; however, it’s a sad predicament that taking this stance, paradoxically, alienates international scientists who’re already doubting if US is a welcoming enough country to be in right now. 3/

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Barış Ekim @ekimb.bsky.social · May 16

The Hanna Gray Fellowship was one of the few (frankly, currently maybe the only) fellowships I could apply for this year. It focuses on diversity and representation in medicine, but this was not a factor for me; on the contrary, I felt obliged to apply because there was, simply, no other option. 2/

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Barış Ekim @ekimb.bsky.social · May 16

HHMI made the decision to discontinue the Hanna Gray Fellows program (indefinitely, presumably).

There is, of course, something to be said about the volatile nature of academia (re: funding) in the US, but the flipside is that this is actively pushing away international scholars. 1/

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Barış Ekim @ekimb.bsky.social · May 10

Thank you, Igor! We should chat re: more min-space stuff :)

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Barış Ekim @ekimb.bsky.social · May 10

Thanks Shuvom! Probably will be back for more later :)