Barış Ekim

Again, everyone who looks like me, everyone who looks like Mamdani, etc. has been experiencing this type of casual racism for decades now. I won't hold my breath waiting for any politicians to condemn this blatant racism given how normalized it is 🤷 Representation matters

Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬

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…

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.

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

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

Skeet of the week award!

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...

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...

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.

’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.

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

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!

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

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

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/

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/

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/

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/

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

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

Tack, Kris!

Thank you!

Thank you!

Teşekkür ederim! :)

Thanks, Sam!

There was another meeting in G575 right after, had to get Facilities for cleanup, became this whole thing… :)

Congrats to yourself! We made it to the other side…

Thanks, Sumaiya!

Thanks for your support, Rob - really means a lot! There are lots of interesting things to explore (we should chat re: tx-ome once things settle down here)… :)

IYKYK (I need to frame this reply or something)… Thanks for being there, Rob!

I survived my defense (the snake was of substantial size)!

Huge thanks to my advisor Bonnie (@bergerlab.bsky.social), committee members Rayan (@rayanchikhi.bsky.social) at Pasteur and Srini and Ronitt from MIT, and friends and colleagues who attended.

www.mcsweeneys.net/articles/faq...

Efficient near telomere-to-telomere assembly of Nanopore Simplex reads Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads w...

Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...

Efficient and robust search of microbial genomes via phylogenetic compression Nature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks.

Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:

rdcu.be/eg4OA

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Many such cases… I always seqtk seq -AU all inputs because of this.