iiinova — where your digital self keeps evolving

Chris Miller @chrismiller.science · 04/10/2026

The first two dozen of these are pretty darn good as a set of guiding principles for an academic scientist (whether tenure-track or not)

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Jeremy Berg @jeremymberg.bsky.social · 01/10/2026

From a discussion of updating a department website...

A photo with baby Yoda and adult Yoda with the caption "Could it be time for a new photo?"

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Chris Miller @chrismiller.science · 25/09/2026

I don't know CIHR details, but with NIH grants, you get a page to address the concerns of the original reviewers for a revision/resubmission. It makes sense that if it goes back to those three reviewers, that their most pressing concerns are addressed, but new reviewers may bring in new criticisms.

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Bart⚓️ @bartgonnissen.bsky.social · 23/09/2026

The Facial Expressions of Tethys by artist Julius von Bismarck. A suspended high-sea buoy that moves in real time. Sensors on a twin buoy out in the Atlantic Ocean send live satellite data to motors inside the museum. This makes the indoor buoy copy the exact, real-time movements of the ocean waves.

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Chris Miller @chrismiller.science · 22/09/2026

Thanks. Sadly, the data is human, and needs dbGaP-like protections for human subjects. I suspect that the repo doesn't exist, at least partially because the data is huge (~1TB per sample)

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Chris Miller @chrismiller.science · 21/09/2026

Is there a sequence data repository that will accept ONT POD5 files? We've shared the bams from our study in dbGaP, and would like to do the same for raw data. It's easy for me to imagine that folks working on things like base modifications might want to dig into that data in the future.

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Chris Miller @chrismiller.science · 17/09/2026

Here's hoping! We've put too much effort into creating rich supplementary files for them to sit hidden forever. (There's a whole other conversation about what 100+ page supplements mean, in terms of the sky-high benchmark for a publishable unit, but we'll save that for another thread!)

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Chris Miller @chrismiller.science · 07/09/2026

Thanks for all the suggestions. I ended up using a heavily modified version of github.com/sbryngelson/... Still a work in progress (always!), but I'm happy with the outcome so far: chrismiller.science

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Alex Rubinsteyn @alexr.bsky.social · 03/09/2026

Curious if there's a nimble manufacturing partner who could make personalized mRNA for 20-50 patients in a ph1 oncology trial, ideally for <$100k/pt & in <=2 months each. If you can encapsulate in LNPs, even better (otherwise we'll do it) (seems good to check more before building everything at UNC)

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Chris Miller @chrismiller.science · 31/08/2026

Still, it's cool to see an idea that we dreamed up over a decade ago moving into the clinic. This is how the fight against cancer plays out: better outcomes for a few % of patients, or extending lifespans by a little, year after year, eventually adds up to better lives for a lot of people! (7/n)

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Chris Miller @chrismiller.science · 31/08/2026

This is definitely just the first step - there are still lots of questions: What's the right threshold for detection (especially now that ultra-deep barcode sequencing is available)? Is 30 days post-chemo the best timepoint? Why did some of the "clear" patients relapse anyway? (6/n)

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Chris Miller @chrismiller.science · 31/08/2026

After multiple grants failed, a team here at WashU eventually secured funding and set out to see if this idea had legs. There are lots of subtleties in the results, but at it's core, the idea worked: Using genomics to split patients into more or less aggressive therapy improved outcomes. (5/n)

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Chris Miller @chrismiller.science · 31/08/2026

We figured that we could sequence patients, identify those who didn't effectively clear their AML, and treat them more aggressively, often with a bone-marrow transplant. Turning an idea into standard of care takes a clinical trial, though, and those are expensive, and take a long time (4/n)

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Chris Miller @chrismiller.science · 31/08/2026

Back in 2015, we took a deeper look at these patients who were in "remission", and found that if you sequenced them, we could often find the residual AML cells hanging around, sometimes at quite high levels. Unsurprisingly, these patients do really poorly (3/n) pmc.ncbi.nlm.nih.gov/articles/PMC...

KM plot - AML survival is worse when mutations persist

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Chris Miller @chrismiller.science · 31/08/2026

When someone gets chemotherapy for AML, pathologists look at samples from the patient's bone marrow. If there are few or no tumor cells hanging around, they say the patient is in remission, and has cleared their cancer. For a good number of patients, this turns out to be dead wrong. (2/n)

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Kristian G. Andersen @kgandersen.bsky.social · 31/08/2026

"What really bothers me about these stories about how AI will design killer viruses is that they are pure fear mongering, and more importantly they divert attention from the things that matter". Indeed 🎯.

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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 28/08/2026

I am delighted to announce that The Department of Human Genetics at the University of Utah is continuing a multi-year recruiting initiative for multiple tenure-track faculty positions at the rank of Assistant Professor. Please share and consider applying! utah.peopleadmin.com/postings/208...

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Chris Miller @chrismiller.science · 29/08/2026

I really need to get one of the sandbox wrappers set up. I've noticed an uptick in Claude reaching outside the working directory too, and it makes me increasingly uncomfortable. Would love suggestions from anyone who's happy with their sandboxing strategy.

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Chris Miller @chrismiller.science · 28/08/2026

a) How'd that turn out for the Luddites? b) I understand the impulse, but I don't think there are many people who actually like pipetting tiny amounts of colorless liquid over and over. If we can reduce grunt work (and human errors), that's more time to like, actually think about science, right?

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Stephen Turner @stephenturner.us · 27/08/2026

Extremely cool. Some Scientists Have ‘Magic Hands’ in the Lab. This A.I. Is Learning Why: www.nytimes.com/2026/08/27/s...

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Chris Miller @chrismiller.science · 27/08/2026

What are the best personal/CV websites you've seen from academic researchers? My site is dated (hand-coded HTML from ~2012!), and I'm looking for inspiration. I know about the great lab templates from @casey.greenelab.com, but I'm looking for a single-person site - CV, publications, research, etc

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Chris Miller @chrismiller.science · 26/08/2026

While backpacking in Colorado, a buckle broke on my nearly 30 year-old Kelty pack. Contacted them to ask about buying a replacement, and they're shipping out a part for free. That's pretty great customer service! Here's hoping I get another 30 years out of this pack!

A red Kelty external frame backpack covered in patches from places I've hiked

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Chris Miller @chrismiller.science · 21/08/2026

We've been banging this drum for 20 years. Will the need to feed the gaping maw of AI change funding priorities?

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Tychele Turner @tycheleturner.bsky.social · 06/08/2026

The Turner Lab at WashU is looking for a postdoc to work on chromosome 9p deletion and duplication syndromes. Feel free to share with anyone who might be interested: wustl.wd1.myworkdayjobs.com/en-US/Extern... #9p #genetics

wustl.wd1.myworkdayjobs.com

Postdoctoral Research Associate - Genetics

Location ST. LOUIS, MO 63110 Position Summary The Postdoctoral Researcher will support a multidisciplinary research program focused on understanding the genomic and molecular mechanisms underlying 9p-...

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Derek Lowe @dereklowe.bsky.social · 23/07/2026

Thoughts on the various Trump administration proposals to revamp US science funding - and what they all have in common:

science.org

The Assault On Science Funding Continues

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Mike Schatz @mikeschatz.bsky.social · 22/07/2026

Application portal is open for travel and registration scholarships from the @jxtxfoundation.bsky.social to the CSHL Biological Data Science conference. Applications are due by Aug 5 #cshldata26 #methodsmatter Apply here: jxtxfoundation.org/news/2026-06... Learn more: bit.ly/cshl-biodata26

jxtxfoundation.org

JXTX + CSHL 2026 Biological Data Science Scholarship

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Tuomas Mattila @tuomasjmattila.eurosky.social · 22/07/2026

I've noticed that without the very basics, higher level R becomes sorcery: yelling incantations to the machine and trying to get it right.

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Chris Miller @chrismiller.science · 22/07/2026

I pushed a package to bioconda 2 weeks ago and it's still waiting for review. Anyone here a maintainer that could help get it unstuck? github.com/bioconda/bio... (We have a paper in review that mentions an option for bioconda install - would like to make that aspirational sentence reality!)

github.com

Add vatools by chrisamiller · Pull Request #67110 · bioconda/bioconda-recipes

Adds a new recipe for vatools (https://github.com/griffithlab/vatools), a package designed to ease manipulation of genomic data stored in VCF format

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Adam Rogers @jetjocko.bsky.social · 22/07/2026

Like I said in Scientific American last month, this is the military-industrial, for-profit approach to research funding. It presupposes an ability to guess at (and fund) successful research, and most scholarship on it says it generates neither new knowledge *nor* higher productivity.

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Danny Miller, MD, PhD @danrdanny.bsky.social · 06/07/2026

Hi everyone! I'm excited to announce that our lab at UW will soon be recruiting a postdoc to work on DNA methylation signatures in rare disease. This will be a mostly computational position. Please share and reach out if interested! millerlaboratory.com

millerlaboratory.com

Miller Lab | University of Washington

Led by Danny E. Miller, MD, PhD, the Miller Lab uses long-read Nanopore sequencing to investigate the significance of structural genomic variation, methylation, and RNA in human disease, and to impro...

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Chris Miller @chrismiller.science · 02/07/2026

This is also often true of faculty on the research track. Promotions to Assoc or Full don't necessarily come with tenure.

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Julian Sanchez @normative.bsky.social · 01/07/2026

It‘s just insane to me that a sitting president has made MORE THAN A BILLION DOLLARS peddling fucking fairy dust with no intrinsic value beyond his stature and power AS president, and it’s not treated as the biggest corruption scandal in American history.

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Jon Bois @jonbois.bsky.social · 21/06/2026

tired of the "#1 dad" nonsense. if you're a dad, stop treating it like a joke and post your actual national dad ranking. i'm # 492,018, which is actually really high up there, but more importantly it lets me enter ranked dad lobbies where i can get matched up for fistfights with dads of my caliber

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Jenna Norton @jenna-m-norton.bsky.social · 21/06/2026

“A single Tomahawk cruise missile runs about $3.6 million, roughly what it takes to fund one scientist’s multiyear grant. The entire National Science Foundation budget is less than what we spent in the first week of the war with Iran.” www.nytimes.com/2026/06/20/o...

nytimes.com

Opinion | The Science That Turned Lizard Venom Into GLP-1s Is Under Attack

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Chris Miller @chrismiller.science · 18/06/2026

I like the biscuit toolchain - pileup and vcf2bed huishenlab.github.io/biscuit/docs... I have not looked to see if it's compatible with minibwa, but from a first pass, I'd imagine so

huishenlab.github.io

Read Pileup

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Heng Li @lh3lh3.bsky.social · 16/06/2026

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

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Liam McHugh-Russell @xntl.info · 06/06/2026

Someone help me with time management please my family is starving * 40 hours working * 20 hours cooking and cleaning * 10 hours childcare * 30 hours email * 50 hours 2-factor authentication

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Derek Lowe @dereklowe.bsky.social · 28/05/2026

An unapologetically angry post about what’s being done to US science:

science.org

The Current Crisis: What's Happening to Science in America

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Kelly Sovacool @kelly.sova.cool · 21/05/2026

Deeply worried about deskilling in bioinformatics and software development. In parallel, also worried about low quality code being churned out rapidly by folks using these tools without doing proper quality control on the outputs 😬

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Chris Miller @chrismiller.science · 21/05/2026

+1. If it is "fits in 100Mb of memory, but takes three weeks to align a 30x genome", then it's not necessarily useful for human applications (though I can think of targeted or microbial applications, for sure)

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Chris Miller @chrismiller.science · 21/05/2026

Pleased to see our preprint on expanding the transcriptome of AML go live. Includes splicing factor-mutants, healthy BM populations, and 170k+ new transcripts Explore the long-read data here: leylab.org/isoforms Look up your favorite gene, and see which transcripts are actually being expressed!

Screenshot of a long read transcriptome explorer, showing YBX1 alternative splicing in SRSF2 mutant samples

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Jesse Eisinger @jeisinger.bsky.social · 13/05/2026

This would constitute one of the most brazen, most appalling acts of corruption in U.S. history. I know we’re numb to all of this but this is a seven-alarm fire. www.nytimes.com/2026/05/12/b...

nytimes.com

Justice Dept. Officials Consider Settling Trump Suit Against I.R.S.

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Chris Miller @chrismiller.science · 07/05/2026

(And if there's one thing humans have proven adept at, it's dealing with slow-moving crises...) The techno-optimist take is that robotics/AI may help an awful lot, both by taking on some unglamorous work of caring for the elderly, and by increasing productivity so that we can afford the elderly

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