Chris Miller
@chrismiller.science
I study cancer at Washington University in St Louis. Cancer Genomics, Bioinformatics, Data Viz, Tumor Evolution, AML, Immunotherapy, Irreverent humor 🧬 🖥️ mostly @chrisamiller on other platforms
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!)
(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!)
Bear in mind I have been joking of supplementary data for years that it is "Unreviewed, unindexed and unread". AI may mean it's time has finally come...
September 17, 2026 at 4:14 PM
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!)
(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!)
Reposted by Chris Miller
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)
(seems good to check more before building everything at UNC)
September 3, 2026 at 8:10 PM
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)
(seems good to check more before building everything at UNC)
This is the story of how a 2015 genomics paper turned into a clinical trial, then into a new manuscript showing how we can use sequencing data to better treat patients with Leukemia:
evidence.nejm.org/doi/10.1056/... (1/n)
evidence.nejm.org/doi/10.1056/... (1/n)
Consolidation Therapy Based on Mutation Clearance in Acute Myeloid Leukemia
Optimal consolidation therapy for patients with intermediate-risk acute myeloid leukemia
(AML) in first complete remission (CR1) is controversial. Retrospective studies have
suggested that the clea...
evidence.nejm.org
August 31, 2026 at 8:57 PM
This is the story of how a 2015 genomics paper turned into a clinical trial, then into a new manuscript showing how we can use sequencing data to better treat patients with Leukemia:
evidence.nejm.org/doi/10.1056/... (1/n)
evidence.nejm.org/doi/10.1056/... (1/n)
Reposted by Chris Miller
"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 🎯.
Indeed 🎯.
I'm really frustrated by the constant fear-mongering about AI-designed superviruses. Can we focus on the things that should actually worry us, such as measles?
blog.genesmindsmachines.com/p/im-sorry-y...
blog.genesmindsmachines.com/p/im-sorry-y...
I'm sorry, you're not going to die from an AI-engineered supervirus
God save us from economists who think they can competently talk about biology
blog.genesmindsmachines.com
August 31, 2026 at 7:26 AM
"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 🎯.
Indeed 🎯.
Reposted by Chris Miller
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...
utah.peopleadmin.com/postings/208...
August 28, 2026 at 6:47 PM
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...
utah.peopleadmin.com/postings/208...
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.
Maybe this is common knowledge, but it wasn't to me. I was using Claude Code in ~/scripts (a little collection of convenience utils of mine) to create a python script to manipulate a pptx file. CC reached outside the project dir to find other files it could use for testing. Confirmed when asked. 1/
August 29, 2026 at 1:39 PM
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.
Reposted by Chris Miller
Extremely cool. Some Scientists Have ‘Magic Hands’ in the Lab. This A.I. Is Learning Why: www.nytimes.com/2026/08/27/s...
August 27, 2026 at 1:16 PM
Extremely cool. Some Scientists Have ‘Magic Hands’ in the Lab. This A.I. Is Learning Why: www.nytimes.com/2026/08/27/s...
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
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
August 27, 2026 at 3:09 AM
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
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
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!
Here's hoping I get another 30 years out of this pack!
August 26, 2026 at 1:28 PM
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!
Here's hoping I get another 30 years out of this pack!
We've been banging this drum for 20 years. Will the need to feed the gaping maw of AI change funding priorities?
Treat biological databases as infrastructure, not projects www.nature.com/articles/d41...
Treat biological databases as infrastructure, not projects
Letter to the Editor
www.nature.com
August 21, 2026 at 5:26 PM
We've been banging this drum for 20 years. Will the need to feed the gaping maw of AI change funding priorities?
Reposted by Chris Miller
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
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-...
wustl.wd1.myworkdayjobs.com
August 6, 2026 at 12:25 PM
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
Reposted by Chris Miller
Thoughts on the various Trump administration proposals to revamp US science funding - and what they all have in common:
The Assault On Science Funding Continues
www.science.org
July 23, 2026 at 7:04 PM
Thoughts on the various Trump administration proposals to revamp US science funding - and what they all have in common:
Reposted by Chris Miller
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
Apply here: jxtxfoundation.org/news/2026-06...
Learn more: bit.ly/cshl-biodata26
JXTX + CSHL 2026 Biological Data Science Scholarship
JXTX + CSHL 2026 Biological Data Science Scholarship
jxtxfoundation.org
July 22, 2026 at 12:58 PM
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
Apply here: jxtxfoundation.org/news/2026-06...
Learn more: bit.ly/cshl-biodata26
Reposted by Chris Miller
I've noticed that without the very basics, higher level R becomes sorcery: yelling incantations to the machine and trying to get it right.
July 22, 2026 at 5:33 AM
I've noticed that without the very basics, higher level R becomes sorcery: yelling incantations to the machine and trying to get it right.
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/bioconda/bio...
(We have a paper in review that mentions an option for bioconda install - would like to make that aspirational sentence reality!)
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
github.com
July 22, 2026 at 5:25 PM
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/bioconda/bio...
(We have a paper in review that mentions an option for bioconda install - would like to make that aspirational sentence reality!)
Reposted by Chris Miller
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.
Ahead of a hearing before the House Science, Space and Technology Committee tomorrow, the White House Office of Science and Technology Policy has released a 120-pg report, "Science: A New Golden Age" www.whitehouse.gov/wp-content/u...
Here's the summary from the press release:
Here's the summary from the press release:
July 22, 2026 at 12:44 AM
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.
Reposted by Chris Miller
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
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...
millerlaboratory.com
July 6, 2026 at 8:39 PM
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
Reposted by Chris Miller
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.
“.. He also reported earning $636 million in royalties from Celebration Coins.”
@bloomberg.com
www.bloomberg.com/news/article...
@bloomberg.com
www.bloomberg.com/news/article...
July 1, 2026 at 12:58 AM
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.
Reposted by Chris Miller
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
June 21, 2026 at 6:42 PM
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
Reposted by Chris Miller
“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...
www.nytimes.com/2026/06/20/o...
Opinion | The Science That Turned Lizard Venom Into GLP-1s Is Under Attack
www.nytimes.com
June 21, 2026 at 7:05 PM
“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...
www.nytimes.com/2026/06/20/o...
Reposted by Chris Miller
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
June 16, 2026 at 4:13 PM
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
Reposted by Chris Miller
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
* 40 hours working
* 20 hours cooking and cleaning
* 10 hours childcare
* 30 hours email
* 50 hours 2-factor authentication
June 6, 2026 at 2:25 PM
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
* 40 hours working
* 20 hours cooking and cleaning
* 10 hours childcare
* 30 hours email
* 50 hours 2-factor authentication
Reposted by Chris Miller
An unapologetically angry post about what’s being done to US science:
The Current Crisis: What's Happening to Science in America
www.science.org
May 28, 2026 at 6:38 PM
An unapologetically angry post about what’s being done to US science:
Reposted by Chris Miller
Reposted by Chris Miller
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 😬
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 😬
The more I use AI for development, the more concerned I am about the fact that knowing what makes an effective prompt and the appropriate, opiniated, guardrails necessary to consistently get high quality output is much harder if you don't have quite a bit of experience doing things by hand first.
May 21, 2026 at 3:31 AM
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 😬
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 😬