Reposted by Barış EkimNiema Moshiri @niema.net · 23/10/2025Again, 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 051
Reposted by Barış EkimRob Patro @robp.bsky.social · 10/10/2025Hi 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! 🖥️🧬 03137
Barış Ekim @ekimb.bsky.social · 16/09/2025Happy (a^2, b^2, c^2)! www.npr.org/2025/09/16/n...npr.orgOn 9/16/25, celebrate a date of mathematical beautyPythagorean Triple Square Day, as one man affectionately calls 9/16/25, is a day like no other this century. 092
Reposted by Barış EkimHuman Pangenome Reference Consortium @humanpangenome.bsky.social · 22/08/2025Accurate 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.orgHighly accurate assembly polishing with DeepPolisherAccurate 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... 021
Reposted by Barış EkimRan Blekhman @blekhman.bsky.social · 09/08/2025This 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. 419690
Barış Ekim @ekimb.bsky.social · 08/07/2025Actually 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 25After a quarter of a century, the website remains an essential tool for navigating the genome and understanding its structure, function and clinical impact. 021
Barış Ekim @ekimb.bsky.social · 06/06/2025Recently 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! 060
Barış Ekim @ekimb.bsky.social · 16/05/2025HHMI 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/ 175
Barış Ekim @ekimb.bsky.social · 09/05/2025I 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... 11537
Reposted by Barış EkimHeng Li @lh3lh3.bsky.social · 18/04/2025Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...biorxiv.orgEfficient near telomere-to-telomere assembly of Nanopore Simplex readsTelomere-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... 513977
Reposted by Barış EkimMichael Baym @baym.lol · 09/04/2025Our 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.beEfficient and robust search of microbial genomes via phylogenetic compressionNature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks. 11254104