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Ian Holmes

@ianholmes.org

4.7K followers 3.1K following 1.4K posts

Berkeley professor (Bioeng, Compbio). Visiting Scientist at Calico. JBrowse genome browser / Apollo annotation editor, ML for gene regulation / molecular evolution / synbio. Occasional music, games, jokes

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Ian Holmes @ianholmes.org · Jan 25

I feel moved to write about one of my technological heroes, possibly the most influential on my youth as an 8-bit hacker: a trans woman named Sophie Wilson. en.m.wikipedia.org/wiki/Sophie_...

Sophie Wilson - Wikipedia

en.m.wikipedia.org

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Ian Holmes @ianholmes.org · 16h

Pompous lectures on pronunciation… could you sound any primmer?

Reposted by Ian Holmes

Richard Waite @waiterich.bsky.social · 3d

Brassica oleracea / Brassica oleracea / Brassica oleracea

Three dudes dressed three very different ways - first in a more conservative suit and tie, second in a short sleeve shirt and hat, third in a pink vest and tie

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Reposted by Ian Holmes

Federico Adolfi @fedeadolfi.bsky.social · 3d

**Me at a Halloween party**

Them, looking at my costume: what are you supposed to be?

Me: that’s a great question! Let’s think about it carefully step by step. You’re asking about my costu—

Them: no stop it

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Ian Holmes @ianholmes.org · 2d

This is like when Apple started running BSD. Nice work.

Reposted by Ian Holmes

gavin jones @ecologyofgavin.bsky.social · 3d

Gaussian, beta, Poisson

Anil Kalhan @akalhan.bsky.social · 3d

University general counsel, university trustee, university president

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Reposted by Ian Holmes

Edward T Eng @edwardteng.bsky.social · 6d

Muyuan Chen has turned structural biology into an immersive experience with his new video game Meowtabolism, now available on Steam.
Try the demo here: store.steampowered.com/app/4045010/...
Give Muyuan feedback: steamcommunity.com/app/4045010
#ScienceGaming #StructuralBiology #CryoEM #STEMOutreach

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Ian Holmes @ianholmes.org · 5d

SIMULATION - when a phone card is happy

Ian Holmes @ianholmes.org · 5d

Magic Alex would have made a better UI than this

Ian Holmes @ianholmes.org · 5d

I’d put it off as long as you can. The design changes are just really tacky and awful. It’s as if Harrods decided, all of a sudden, it was only going to sell track suits

Ian Holmes @ianholmes.org · 6d

Interesting! When carcinogenic mutations actually help…

Yale Cancer Center @yalecancer.bsky.social · 7d

Some #lungcancers with #KRAS G12C mutations respond to #immunotherapy bc of⬆️ mutation load from #tobacco exposure. Smoking history + overall mutation burden are better guides for treatment than KRAS status alone.
lungcancerjournal.info/article/S016...
@jeffreytownsend.bsky.social

KRAS G12C-associated immunotherapy benefit in NSCLC is substantially mediated by tobacco-induced tumor mutation burden, not allele-specific effects

KRAS G12C mutations in non-small cell lung cancer (NSCLC) have been associated with improved immune-checkpoint inhibition (ICI) outcomes. However, it remains unclear whether this benefit reflects alle...

lungcancerjournal.info

Ian Holmes @ianholmes.org · 7d

Any university that signs onto this is a finishing school for chumps

www.nytimes.com/2025/10/02/o...

Opinion | Trump’s ‘Compact’ With Universities Is Just Extortion

www.nytimes.com

Ian Holmes @ianholmes.org · 7d

New iOS is buggy as hell, juddery and slow due to pointless animations, previously convenient options now buried deep in menus, but at least it sends twice as many notifications thanks to “Apple Intelligence” great work guys

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Ian Holmes @ianholmes.org · 7d

Interesting. A competing school of thought says that the “Time Orange” refers to Scorsese’s use of oranges as a metaphor for death in the Godfather movies. A Half Time Orange is an orange that signifies a recoverable injury (Don Corleone getting shot early in the movie) as opposed to the final act

Ian Holmes @ianholmes.org · 7d

Popped into what was my local Berkeley coffee shop in 2020, I’m reminded of the right wing groups who traveled to Berkeley specifically to start fights that year, and how the coffee shop’s window - which had a big BLM sign - was cracked by a bullet that day. Left wing violence? My fat liberal ass.

Ian Holmes @ianholmes.org · 8d

Reposted by Ian Holmes

Alexandria Ocasio-Cortez @aoc.bsky.social · 9d

Most of the power authoritarians have is freely given. We should not comply with them in advance.

Trump is far weaker than he looks. So is the GOP. We should draw them out, drain them at every opportunity, and fight for people’s wellbeing at every turn.

We have been sent here to fight for people.

Acyn @acyn.bsky.social · 9d

AOC: I think there's two things that are happening at once: One, there absolutely is an unprecedented abuse of power, destruction of norms, erosion of our government and our democracy in order to prop up an authoritarian style of governance

However, they are weaker than they look…

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Reposted by Ian Holmes

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 9d

Systematic comparative benchmarking of computational methods for the detection of transposable elements in long-read sequencing data https://www.biorxiv.org/content/10.1101/2025.09.29.679192v1

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Ian Holmes @ianholmes.org · 9d

This is the best ad for a synthesizer ever made youtu.be/hbO1z13WP8o

"How to Orchid" by Telepathic Instruments

YouTube video by Telepathic Instruments

youtu.be

Reposted by Ian Holmes

Brandon Rohrer @brandonrohrer.com · 9d

Setting: Classic Tintin and Captain Haddock meme, modified

Wednesday Addams: What a week, huh Sergeant?

Captain: Wednesday, it's Captain

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Ian Holmes @ianholmes.org · 9d

I’m a vampire. Sewage systems are my road network.

Reposted by Ian Holmes

Jacqueline Antonovich @jackiantonovich.bsky.social · 9d

For those of you professors who are team “you erase the boards when you come in, not before you leave,” I would like to let you know that I lectured about the history of vaginal and rectal fistulas today and i am sure the prof coming in after me appreciates that i erased the board before i left.

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Ian Holmes @ianholmes.org · 9d

(Some bioinformatics file formats, eg PDB format for protein structures, still bear the traces of their punchcard roots.)

Ian Holmes @ianholmes.org · 9d

Oh man. I always tell my students that every OG punchcard operator has a story about a dropped deck. But have left it vague beyond that. This is some juicy detail, thank you

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Reposted by Ian Holmes

Jeremy Berg @jeremymberg.bsky.social · 10d

Compelling and quite disturbing...

LorennaCleary.bsky.social @lorennacleary.bsky.social · 10d

Land of the free. Home of the brave.

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Ian Holmes @ianholmes.org · 9d

It’s not Christianity as I see Christianity. It is however entirely consistent with certain historical movements that have gained sway in that religion, such as Muscular Christianity en.wikipedia.org/wiki/Muscula...

Muscular Christianity - Wikipedia

en.wikipedia.org