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Barış Ekim

@ekimb.bsky.social
723 followers 122 following 29 posts

🇹🇷. Postdoc @Yale, formerly @MIT @Broad. Skeets(?) in TR/EN, views my own.

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Reposted by Barış Ekim
Niema Moshiri @niema.net · 23/10/2025
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
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Reposted by Barış Ekim
Rob Patro @robp.bsky.social · 10/10/2025
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! 🖥️🧬
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Barış Ekim @ekimb.bsky.social · 16/09/2025
Happy (a^2, b^2, c^2)! www.npr.org/2025/09/16/n...
npr.org
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.
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Reposted by Barış Ekim
Human Pangenome Reference Consortium @humanpangenome.bsky.social · 22/08/2025
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...
biorxiv.org
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...
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Reposted by Barış Ekim
Ran Blekhman @blekhman.bsky.social · 09/08/2025
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 · 08/07/2025
Actually wild how it’s been free and accessible for over two decades... 🎉🎉
nature.com
’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.
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Barış Ekim @ekimb.bsky.social · 06/06/2025
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 · 16/05/2025
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 · 09/05/2025
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...
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Reposted by Barış Ekim
Heng Li @lh3lh3.bsky.social · 18/04/2025
Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...
biorxiv.org
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...
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Reposted by Barış Ekim
Michael Baym @baym.lol · 09/04/2025
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 1/
rdcu.be
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.
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