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Charlie Vaske

@seavaske.com
577 followers 811 following 404 posts

Genomics, bioinformatics, diagnostics, cancer, housing, and transit. Слава Україні orcid.org/0000-0001-8151-6612

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Reposted by Charlie Vaske
Jenna Norton @jenna-m-norton.bsky.social · 29/09/2026
A great overview of how the Trump admin cultivated fear inside NIH to force compliance, even with harmful, unethical & unlawful orders. Also covers origins of the Bethesda Declaration community. From my friend & co-organizer Dr. Wen-Ying Sylvia Chou. www.psychologicalscience.org/publications...
psychologicalscience.org
NIH Employees Lived in A Culture of Fear, So They Started Keeping Receipts
Sylvia Chou, former NIH program director, says “nobody’s OK” after massive disruptions to funding policies and infrastructure.
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Charlie Vaske @seavaske.com · 29/09/2026
This is the YIMBYest politician ever elected.
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Reposted by Charlie Vaske
Science Magazine @science.org · 24/09/2026
Thomas Jefferson’s genome has been sequenced to substantiate the idea that the president fathered children with Sally Hemings, a Black woman he enslaved. But one of Hemings’s descendants has criticized the work and withdrawn her participation in the study. Learn more: scim.ag/4iKdSxA
DNA analysis strengthens evidence that Thomas Jefferson fathered children with Sally Hemings
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Charlie Vaske @seavaske.com · 21/09/2026
I love this representation of scRNA data, showing yet again that compression leads to some of the best insights on data.
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Californians for Electric Rail @calelectricrail.org · 18/09/2026
In 2024 the US Department of Energy proposed these routes for electrification. No time like the present to get to work making it a reality.
Map of High-potential routes for catenary feasibility studies. Includes line-haul freight, intercity passenger, commuter, and other. Major freight routes include LA-Chicago, WA-Chicago, SLC-Chicago via both Wyoming and Colorado, LA-Houston, Houstin-Chicago via Oklahoma, Chicag-NYC via PA. Commuter routes include Metra, Metrolink, Frontrunner, and NY-area diesel routes
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Scott McGrath @smcgrath.phd · 11/09/2026
Fewer than 20% of EHR data sits in coded fields; the rest stays trapped in clinician notes. A new framework extracts atomic facts into an 88M-node knowledge graph across 1M visits, matching physician review with a 99.4% F1 score to reconstruct longitudinal patient journeys. #MedSky
nature.com
Computable longitudinal patient journeys from structured and unstructured EHR data - Nature Medicine
A suite of large pre-trained language models accurately extracts computable clinical data from unstructured electronic health records and integrates the findings into knowledge graphs that can…
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Dr Grace S Peng @gspeng.bsky.social · 09/09/2026
I am an actual scientist and I did the math badmomgoodmom.blogspot.com/2022/12/urba...
badmomgoodmom.blogspot.com
Urban trees and the zombie carbon sequestration myth
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Charlie Vaske @seavaske.com · 05/09/2026
This is a fascinating and beautiful new visualization for single-cell RNA datasets as an alternative to UMAP. I will definitely be trying it out soon...
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Charlie Vaske @seavaske.com · 04/09/2026
We need a vacancy tax on all that wasted space.
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Reposted by Charlie Vaske
Richard Lenski @relenski.bsky.social · 19/08/2026
If Zachary Blount had one dollar for every cell he plated in his dissertation looking for new Cit+ mutations, he could single handedly pay off the US debt of $40,000,000,000,000. www.npr.org/2026/08/19/n...
Zachary Blount with giant stacks of petri dishes used in his research on historical contingency and the evolution of citrate use in the LTEE.
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Reposted by Charlie Vaske
Stan Oklobdzija @stano.bsky.social · 19/08/2026
Bigger picture: LLMs are perfectly fine tools to use to automate drudgery and to augment skills you already have. The problem is that they present a gigantic marshmallow test for those with no impulse control to never learn how to do anything and to remove all friction from their lives.
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Charlie Vaske @seavaske.com · 17/08/2026
After weeks of brow-beating Claude about "load-bearing," I finally got it to self censor: "already load-bear– already central..."
Screenshot of Claude conversation: "Option 2 is the low-friction one if Forgejo is already load-bear— already central to your workflow. Caveat: issues/PRs opened on Tangled live in atproto records and won't sync back to Forgejo."
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Reposted by Charlie Vaske
Nature Portfolio @natureportfolio.nature.com · 12/08/2026
Ticklish areas of the body appear to be shared across cultures, according to a study of individuals with Chinese, Dutch, and Greek backgrounds published in Nature Human Behaviour. 🧪
go.nature.com
Human ticklishness is a widespread, culturally shared and bodily organized sensory experience - Nature Human Behaviour
Ticklishness is a familiar but poorly understood experience. Xiong and Kilteni show that ticklishness is culturally shared and follows a distinct bodily topography. They evaluate different theories on why some body regions are more ticklish than others.
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Reposted by Charlie Vaske
Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 09/08/2026
Our paper on the active form of human protein kinases is out in Biochemical Journal from @biochemsoc.bsky.social . Great experience with the journal, unlike another journal that begins with "Nat" and ends with "omms." doi.org/10.1042/BCJ2... Made the cover in August (paper came out in July)...
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Charlie Vaske @seavaske.com · 04/08/2026
For the dozen people out there into urban planning and cloud computing arcana: Inclusionary availability zoning will finally solve our affordability problems.
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Jeffrey Tumlin 🏳️‍🌈 🌁 @jeffreytumlin.bsky.social · 02/08/2026
Your periodic reminder that my 1991 SF Mission apt was $980/mo in today's dollars - an unaffordable sum for me then. This is what decades of NIMBY SF politics stole from you and our beloved city's creative spark
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Gregg Gonsalves @gregggonsalves.bsky.social · 07/07/2026
Yale President McInnis and the trustees are out of step with their faculty, including the current and present deans of the law school, in seeking a settlement from the Trump administration. Students and alumni also oppose. Who does Yale leadership actually represent? www.nytimes.com/2026/07/07/u...
nytimes.com
Yale Law School Fights to Stop Trump Deal
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Reposted by Charlie Vaske
Joshua Shapiro @josh.shapiro.foo · 30/06/2026
Hey look, our paper about the Single-cell Pediatric Cancer Atlas that we at @cancerdatalab.bsky.social have been working on for a while is out! www.cell.com/cell-genomic... It's a pretty good resource, if I do say so myself, and we are expanding: if you have data you want to share, get in touch!
cell.com
The Single-Cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors
Hawkins et al. introduce the Single-Cell Pediatric Cancer Atlas: a uniformly processed collection of sc/snRNA-seq data from pediatric cancer samples and models. 700 samples from 55 pediatric cancer ty...
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Reposted by Charlie Vaske
Dr PattiJones @drpattijones.bsky.social · 29/06/2026
very cool paper. Also contains an author that has the best name for a scientific consultancy that I have seen yet: “Middle Author Bioinformatics, LLC, Phoenix, AZ, USA Arkadiy Garber“
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Charlie Vaske @seavaske.com · 24/06/2026
Fans of #RNA should check out the RNA Futures Meeting at UCSC in the fall, looks to be a great lineup of speakers, including Mark Akeson, Laurence Ettwiller, and Miten Jain: rnacenter.ucsc.edu/rna-futures-...
rnacenter.ucsc.edu
RNA Futures Meeting – UCSC RNA Center
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Manny Ares 👀 @mannyares.bsky.social · 20/06/2026
Thanks to @jmcoller.bsky.social for writing this important piece. Describes exactly what we stand to lose from the Lysenkoization of US science. 💪🏼
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Zamin Iqbal @zaminiqbal.bsky.social · 19/06/2026
One for the bioinformaticians
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Ben Vezina @bananabenana.bsky.social · 20/06/2026
Spoke at The Australian Society for Microbiology 2026 Annual Meeting earlier this week. I covered our work on >100k carbapenemase-encoding genomes. Also here's a gimmick slide I spent way too much time on: "The Microbe's Digest". It's carba-pandemonium out there folks 🙏 @aussocmic.bsky.social
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CAHSR's Strongest Soldier @emoscientist.bsky.social · 18/06/2026
The end of Roe coincided with the near-complete destruction of feminist organizing or women's issues as a salient issue. Nobody in politics talks about abortion or gender equality, and the discourse is all about how "the Left is failing men". Hard to succinctly explain why but it's not salient.
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Charlie Vaske @seavaske.com · 11/06/2026
Just how bad is housing affordability in Santa Cruz? Median house prices are currently 9.3x the median wage here, and though housing prices fluctuate, the average increase is 1.2% per year. Can any social scientists comment on my use of FHFA house price data and SAIPE household income?
Plot of price-to-income ratio of housing in Santa Cruz County, from 1990 to 2024. Housing prices come from FHFA (ATNHPIUS42100Q), income from SAIPE (MHICA06087A052NCEN). There are wide fluctuations due to housing boom and bust, but the trend is from a ratio of 6.3x in 1990 to 9.3x in 2024.
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Charlie Vaske @seavaske.com · 05/06/2026
Santa Cruz County is so NIMBY that it even $117k/year for a single person is considered "low-income." SC wages are far lower than SF or Silicon Valley, but HUD has to apply a special correction for exceptional housing-cost-to-income ratio. Even a median incomes qualifies for subsidized housing!
Table of 2026 HCD income bands for affordable and subsidized housing in Santa Cruz county. The "low income" cutoffs are all significantly higher than the "median income" line.
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Maureen Barr @barrlab.bsky.social · 16/05/2026
“Most Chinese scientists came to the U.S. with the hope of staying for their careers,” Innes says. “But now they are getting the clear message that the government doesn’t want them to be here.” 1/2 @policyhound.bsky.social 👏👏👏 www.science.org/content/arti...
science.org
Chinese postdocs in U.S. hit with a wave of prosecutions and deportations
The U.S. government has recently convicted multiple postdocs for improper shipments of biological materials. Some see a replay of the 2018 China Initiative
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David Roberts @volts.wtf · 15/05/2026
If you follow energy at all, you're probably familiar with the fact that the IEA and other energy analysts have a long record of underestimating the growth of solar and batteries. But did you know that they also have a long record of *overestimating* the growth of nuclear?
sciencedirect.com
The “Nuclear Energy Paradox”- Investigating nuclear imaginaries in energy projections
Current energy projections often envision an expansion of nuclear capacities to decarbonize future energy systems. However, this contrasts with the hi…
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Sam (ABeardedPanda) @abeardedpanda.bsky.social · 15/05/2026
"we're willing to trade kidnapped children for POWs" is a completely insane admission of guilt
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工an Monroe 🚰 @eean.dev · 06/05/2026
Spiderman: How does $54/Mhw sound?

Dinosaur, labeled new data centers: I don't want $54/Mhw. I want diesel jet turbines.
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Charlie Vaske @seavaske.com · 27/04/2026
This newly-discovered DNA recognition system is a perfect fit for matching gene sequences that produce the same protein, by skipping over the wobble base in the protein code. Very cool system...
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Reposted by Charlie Vaske
Clay Kosonocky @kosonocky.bsky.social · 21/04/2026
Have you wondered what the wet lab success rates are for current AI-driven protein design models? Look no further! In our new review, @kevinkaichuang.bsky.social @avapamini.bsky.social, @sarahalamdari.bsky.social, and I report wet lab success rates for *over 200* different protein design tasks 🧬💻
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Charlie Vaske @seavaske.com · 20/04/2026
There was a time when the dictatorial and punitive power of Steve Jobs ensured that Apple would never let this sort of "I have two Outlooks" problem persist:
macOS Finder listing of two different Numbers.app programs right next to each other.
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Charlie Vaske @seavaske.com · 13/04/2026
Currently trying to translate dinner discussion about Orban's defeat to our 7yo, and landed on the metaphor of JD Vance as Bowser Jr. This feels very right.
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Charlie Vaske @seavaske.com · 12/04/2026
Ben Patton: "They [the Ukrainians] need us a lot less than we [the US] need them right now." US support to Ukraine has been cut off for more than a year, and in that year Ukraine has shifted the tide of the war. The US is blockading the Strait of Hormuz while Ukraine fights for freedom.
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Reposted by Charlie Vaske
Dmitry Grozoubinski @explaintrade.com · 12/04/2026
Very Ukrainian accent: "Oh Mr Vance, is it hard to negotiate peace? Is it difficult to come to a deal when both sides have fundamentally irreconcilable positions on key issues? Does not being able to trust your counterparty make things tricky? Why do you hate peace, Mr Vance?"
media.tenor.com
a man with a beard is sitting in a chair .
ALT: a man with a beard is sitting in a chair .
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Richard Sever @richardsever.bsky.social · 11/04/2026
Nobel Laureate Jack Szostak “This country has given me endless opportunities…: The America we inhabit today bears almost no resemblance to the country I chose all those years ago” newsletter.ofthebrave.org/p/im-a-nobel...
newsletter.ofthebrave.org
I’m a Nobel Prize-winning immigrant. I can no longer recognize this country.
Attacks on science and immigrants are destroying America.
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Alex Rubinsteyn @alexr.bsky.social · 10/04/2026
The neoantigen vaccine selection logic at the end of the OpenVax pipeline (code behind Mount Sinai PGV trials) is called Vaxrank inputs: HLA + VCF + RNA BAM outputs: vaccine design output Hadn't changed much since 2010s Just shipped 2.0 (new predictors, per-trial configs, &c)
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Ashwin Varma @ashwinvarma97.bsky.social · 05/04/2026
Oh my god, this is my job!!! I can finally add something back to all the people who’ve given me knowledge
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Iva Tolić @ivatolic.bsky.social · 28/03/2026
Chromosomes stuck behind the spindle are ticking time bombs for aneuploidy. We uncovered a mechanical rescue mechanism where microtubule pivoting repositions these high-risk chromosomes! Out last week in @natcomms.nature.com, here's a thread 🧵 shorturl.at/OD89x
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Sloposition 13 Iconoclast🚰🔰 @josh.hawn.xyz · 27/03/2026
I'm Josh Hawn, and I support this message.
screenshot from the end of the video where Mayor Mamdani says "Because to deliver public goods, you have to first deliver public excellence."
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Glonzo In Exile 🇨🇦🇬🇱🇨🇦🇬🇱 @glonzo-in-exile.bsky.social · 22/03/2026
Everyone I know with practically any knowledge of global supply chains be like:
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Needhi Bhalla 💅🏽 @needhibhalla.bsky.social · 15/03/2026
“No for-profit company could possibly withstand all the false leads required by that process,” he recalled telling them, “all the weird, random science that never panned out.” Super grateful for this piece highlighting the threats to this country’s biomedical research infrastructure
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Charlie Vaske @seavaske.com · 05/03/2026
Most cloud infrastructure engineering amounts to this, but is a bit less fun
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Sundance @sundance.bikesky.social · 05/03/2026
Zone 2 cardio. Mobility maxxing. There will be no further discussion.
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Jason Moore @moorejh.bsky.social · 03/03/2026
Epistasis and co-adaptation in bacterial genome evolution www.nature.com/articles/s41... #epistasis #microbiology #evolution #genomics
nature.com
Epistasis and co-adaptation in bacterial genome evolution - Nature Reviews Genetics
Bacterial genome evolution is shaped by epistasis, which can constrain or promote specific evolutionary paths. The authors review how integrating the effects of epistatic interactions into population-...
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Charlie Vaske @seavaske.com · 26/02/2026
You can always tell when Russia is scared about the status of their genocidal invasion, because they activate ludicrously false propaganda pushes in US media. Russian lines are breaking for the first time in a long while, so Foreign Affairs is publishing Michael Desch carrying water for Putin.
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Theo Sanderson @theo.io · 25/02/2026
Realised I can display live posts on the map bluesky-map.theo.io?live=1 (there's also an option under the settings cog to display post text, in case you really want to be overstimulated)
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Alfred Twu @alfredtwu.com · 23/02/2026
Several hundred turned out for today's Bay Area rally for continued support of Ukraine's fight for freedom and survival! Berkeley councilmember @igortregub.bsky.social led the march, councilmember @markhumbert.bsky.social was also at the rally. ✊💙💛🇺🇦
Alfred, Igor, and Mark on a stage at a rally for Ukraine in San Francisco. Igor is at the mic. There are US and Ukrainian flags in the backgroundA large crowd marches down a wide sidewalk in San Francisco, holding Ukrainian flags and signs
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Isabel @isabelott.bsky.social · 15/02/2026
“Asked how the cuts have affected science, one [researcher] said, ‘This is like asking, how do you think dropping an atomic bomb on New York City will affect the future of Broadway musicals? This is a generational loss of innovation, technology, and economic power.’” 🔗 archive.ph/2026.02.12-1...
archive.ph
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