Barış Ekim
@ekimb.bsky.social
🇹🇷. Postdoc @Yale, formerly @MIT @Broad. Skeets(?) in TR/EN, views my own.
Reposted by 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
October 23, 2025 at 3:26 PM
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
Reposted by Barış Ekim
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! 🖥️🧬
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!
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
October 10, 2025 at 1:02 PM
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! 🖥️🧬
Reposted by Barış Ekim
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...
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
August 22, 2025 at 5:47 PM
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...
Uncover the science behind it:
www.biorxiv.org/content/10.1...
Reposted by Barış Ekim
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.
August 9, 2025 at 4:50 PM
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.
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
July 8, 2025 at 3:03 PM
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!
June 6, 2025 at 1:42 PM
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!
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/
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/
May 16, 2025 at 3:22 PM
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/
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/
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...
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...
May 9, 2025 at 5:28 PM
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...
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...
Reposted by Barış Ekim
Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
April 18, 2025 at 9:54 PM
Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...
Reposted by Barış Ekim
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/eg4OA
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.
rdcu.be
April 9, 2025 at 9:07 PM
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/eg4OA
1/