iiinova — where your digital self keeps evolving

Human Pangenome Reference Consortium @humanpangenome.bsky.social · 22/08/2025

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...

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...

021

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.

419690

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!

060

Barış Ekim @ekimb.bsky.social · 06/06/2025

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

250

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

040

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/

Barış Ekim @ekimb.bsky.social · 10/05/2025

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/

175

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

Barış Ekim @ekimb.bsky.social · 10/05/2025

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

000

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

010

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

110

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)… :)

110

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

Barış Ekim @ekimb.bsky.social · 25/03/2025

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...

11537

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

I snorted… “This guy’s hard drive is full of files that are just large integers — divide all of them by 101 just to make sure he’s not carrying government secrets”.

Five years later and I still carry my passport with me everywhere I go…

140

First thing that came to mind when I read CNRS was you guys… It’s despicable.

130

For nucleotide-level alignment (in between seed matches)? Yeah, I think it’s affine gap semiglobal. This is to compute the highest scoring chain before that, no?

100