Keith Robison

My quote of the day

The factory of the future will have only two employees, a man and a dog. The man will be there to feed the dog. The dog will be there to keep the man from touching the equipment.

Warren Bennis

ATP synthesis driven by atmospheric hydrogen concentrations | PNAS All cells require a continuous supply of the universal energy currency, adenosine triphosphate (ATP), to drive countless cellular reactions. The un...

Our article showing energy production from air alone is in PNAS today. This paper provides an ultimate biochemical proof that microbes can survive simply by 'making' energy from air (making two ATP per molecule atmospheric H2 consumed) and has biotech applications. www.pnas.org/doi/10.1073/...

After 15 years of controversy, Science retracts ‘arsenic life’ paper Science has retracted a 2010 paper describing a strain of bacteria that purportedly substituted arsenic for phosphorus, an element present in all known life. Science/AAAS Fifteen years after publis…

After 15 years of controversy, @science.org retracts ‘arsenic life’ paper

"Higher education policy in the United States is now being developed through ad hoc deals, a mode of regulation that is not only inimical to the ideal of the university as a site of critical thinking but also corrosive to the democratic order and to law itself."
#AcademicSky

For a top pharma partner, CIRQ doubled the duration of expression of one protein to 14 days and tripled another to 28 days (vs. 7 days with linear, modified mRNA).

Ginkgo RNA Solutions - CIRQ Platform R&D solutions for mRNA & circRNA.

rna.ginkgo.bio/blog/circula...

CIRQ has launched!

Customers can now order our circRNA to screen in own lab (10 designs, starts at $50,000), or 3 month long design and screening project at Ginkgo (50 designs, starts at $300k)

Amid Fear of Retaliation, N.S.F. Workers Sign Letter of Dissent

"In the letter, the signatories warned that National Science Foundation grants now underwent a 'covert and ideologically driven secondary review process'...”

www.nytimes.com/2025/07/22/s...

Well that's interesting.... here "pooling" refers to cofolding multiple proteins all at once and then assessing their pairwise ipTMs as shown in this figure from the preprint, never thought of doing that before and remarkable that it actually works *better* (I guess you'll need lots of VRAM though)

Cell Free Protein Synthesis (E. coli) Ginkgo’s cell free protein synthesis (CFPS) kit is an E. coli transcription/translation system optimized to produce proteins from a T7 RNA Polymerase promoter.  Reactions consist of a bacterial cell l...

Ginkgo has launched an E.coli-based Cell Free Protein Synthesis reagent!

reagents.ginkgo.bio/products/cel...

YouTube video by Science Communication Lab The Most Beautiful Experiment: Meselson and Stahl

NYT reported the passing of Franklin Stahl

Invest 20+ minutes of your time in this masterful documentary on “the most beautiful experiment in biology” as two friends joyfully relate how as young graduate students at they were entrusted with testing the Watson-Crick model

youtu.be/7-tnuAqEp9g?...

I Worked at U.S.A.I.D. for Over 8 Years. This Is Our Biggest Failure.

I worked for U.S.A.I.D. in East Africa over the past eight and a half years, selling the story of American foreign aid to people in Rwanda, Ethiopia and Kenya. Our inability to tell this same story to Americans is our great failure. It is what put the agency into the Department of Government Efficiency’s wood chipper first. It’s what allows Secretary of State Marco Rubio to get away with insisting that lifesaving humanitarian aid would continue while the administration drastically slashed its funding. And it’s what I fear will let this presidency cast the deaths from the next preventable catastrophe as unstoppable or inevitable.

You hear this a lot on the left but it isn't true. USAID did not "fail to tell its story to Americans," the right targeted the agency with lies and misinformation.

Ultimately this narrative turns conservative attacks into even more calls for the left to reform.
www.nytimes.com/2025/06/29/o...

Seriously. You know who has *great* messaging? Cancer researchers! Literally curing cancer! Sells itself!

Still got fed to the DOGE woodchipper.

FEMA and the National Weather Service got fed to the DOGE woodchipper, too. Nobody thought poorly of them until the right did the thing they always do.

Coukd It Have BEEN Found With Short Reads?

🧬🖥️

omicsomics.blogspot.com/2025/06/coul...

Food For Thought On ONT's Proteomics Push

🧬🖥️

omicsomics.blogspot.com/2025/06/food...

A process server delivered a letter regarding my "hostile" and "defamatory" attacks on #ColossalBio co-founder Ben Lamm, insinuating I'm a misogynist and a failed scientist. Nothing I've said is defamation, but you can read it a judge for yourself. I've redacted my home address 1/n

The Extinction of Truth Or, a Colossal Pile of Bullshit

Updated a broken link in my substack post about the
#ColossalBio #DeExtinction #DisInformation campaign – dire wolves are still extinct.

open.substack.com/pub/devoevom...

‘Magic Tree House’ Author, ‘Calvin and Hobbes’ among hundreds of Tennessee book bans - PEN America The removals in Tennessee are the result of a growing political movement to control information through book banning.

How profoundly sad. The kids deprived of reading Calvin and Hobbes are the kids who need them the most. My brother put it best: "We know we’re fucked when they come for your cartoon stuffed tigers."

Let's go sit in the grass and crack open "The Days are Just Packed."
pen.org/magic-tree-h...

Defining ultra-slow-growing extremophilic microorganisms as aeonophiles - Nature Microbiology In environments like the deep subsurface, microorganisms with long doubling times can remain metabolically active for millions of years — we propose referring to this class of extremophile as aeonophi...

Defining ultra-slow-growing extremophilic microorganisms as aeonophiles #USC_earth #USC_MEB #jcampubs www.nature.com/articles/s41...

Now published! Note that since Vikram's original post (quoted here), he's made it easy to dynamically update a set of multi-MUMs (e.g. when more genomes are added to a pangenome) and to find multi-MUMs for huge collections like HPRCv2 genomebiology.biomedcentral.com/articles/10....

EP 56 Open Conversation with Keith Robison Ketih's Blog, Omics Omics: https://omicsomics.blogspot.com/ Summary In this conversation, Keith Robison discusses the inception of his blog Omix, the evolution of social media in the scientific comm

Had a fun chat recently with Kevin Libuit on his The Bioinformatics Lab podcast

on.soundcloud.com/2hxiS7sDlK0x...

What a great loss. He was a giant, yet very humble and positive. I met Atul the first time at PSB, when he came to present in a session co-organized by his mentor Zack Kohane and myself in 2001. He will be greatly missed.

It is with great sadness that we mourn the loss of our friend and colleague Dr. Atul Butte. A hui hou Atul. We will miss you.

2024 Morris F. Collen Award Winner - Atul Butte, MD, PhD, FACMI This is "2024 Morris F. Collen Award Winner - Atul Butte, MD, PhD, FACMI" by AMIA on Vimeo, the home for high quality videos and the people who love them.

For those of you who may not have known him, Dr. Atul Butte, a pioneer in informatics, was the winner of the 2024 Morris F. Collen award, a pinnacle achievement in our field, as part of his storied career.

His passing is a major loss to us all.

RIP Dr. Butte

#MedSky

My favourite bit about the MAHA report is that every section with dot points comes back as ~100% AI generated and almost all of them contain hallucinations.

None of these references really supports the argument here, and the actual statements are also a bit contradictory.

vampirejuno Apr 2 Follow .. . Watching the mummy 1999 for shits and giggles, thought it'd be fun to bitch abt the inaccurate hieroglyphs now that I know smth abt all that. Disappointed and disgusted to find out that they hired an egyptologist consultant and the hieroglyphs are actually well done. Night ruined

See, I always love it when a film throws a bunch of money at a couple of academics like this. Fuck yeah Professor Adler, go hog wild in the set shop being uptight about the color of the stone walls

Roche Gives SBX Updates - and a Name!

🧬🖥️

omicsomics.blogspot.com/2025/06/roch...

Bacteria in Honeybee Crops Are Decoupled from Those in Floral Nectar and Bee Mouths - Microbial Ecology Bacteria in the honeybee gut are a well-recognized factor affecting bee health. However, the primary focus of this research has been the hindgut, while the crop, or honey stomach, is assumed to be dom...

New paper where we suggest bacteria in the honeybee stomach may be more interesting to study than generally thought.

doi.org/10.1007/s002...

The latent cis-regulatory potential of mobile DNA in Escherichia coli - Nature Communications The mechanism and extent to which transposons can alter the gene expression of their hosts is not well understood. This study finds that in the IS3 family of transposable elements in E.coli, de-novo p...

Happy to announce that our study on the latent cis-regulatory potential of mobile DNA is officially published!

TLDR: mobile DNA in bacteria (Insertion Sequences) have a proclivity for evolving new promoters. At least 25% of them probably already encode functional promoters as well.

Cartoon: a drawing of various whales. Caption: The pilot whale was so successful they went ahead and commissioned all the other whales

Pilot Whale

You know what time it is? That's right! It's time to plug my work again! Yay!

www.worldofmoose.com/products/pil...

Ira Deveson discusses how they are using Oxford Nanopore sequencing as a single technology to provide genome assemblies to detect complex genomic regions, providing insights into underrepresented populations, rare disease and more. #NanoporeConf