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
For those who are interested, the plot showing cumulative percentage of human HUGO gene names (from ensembl protein-coding genes) covered by a set number of records looks like this. So 8 results covers 99% of genes, 34 results covers 99.9% of genes, and it takes 199 to cover everything. (7/n)
October 6, 2025 at 6:54 PM
For those who are interested, the plot showing cumulative percentage of human HUGO gene names (from ensembl protein-coding genes) covered by a set number of records looks like this. So 8 results covers 99% of genes, 34 results covers 99.9% of genes, and it takes 199 to cover everything. (7/n)
It introduces a new question, though - this failed on TP53 with 10 results, so how many results need to be returned to handle all genes correctly? A few seconds of bash/grep later, I get the following list of 21 genes that will still fail. (5/n)
October 6, 2025 at 6:54 PM
It introduces a new question, though - this failed on TP53 with 10 results, so how many results need to be returned to handle all genes correctly? A few seconds of bash/grep later, I get the following list of 21 genes that will still fail. (5/n)
It may not just be Lone Star ticks that cause Alpha-Gal syndrome (in which you become allergic to red meat).
If you hike in hotspot areas, like I do, don't forget the bug spray - it can be remarkably effective!
www.sciencenews.org/article/tick...
If you hike in hotspot areas, like I do, don't forget the bug spray - it can be remarkably effective!
www.sciencenews.org/article/tick...
April 21, 2025 at 7:40 PM
It may not just be Lone Star ticks that cause Alpha-Gal syndrome (in which you become allergic to red meat).
If you hike in hotspot areas, like I do, don't forget the bug spray - it can be remarkably effective!
www.sciencenews.org/article/tick...
If you hike in hotspot areas, like I do, don't forget the bug spray - it can be remarkably effective!
www.sciencenews.org/article/tick...
There's the traditional solution:
April 14, 2025 at 12:59 PM
There's the traditional solution:
Nice article on how using whole-genome sequencing to diagnose cancer is entering the mainstream (finally!). Great to see lots of familiar folks interviewed.
www.newsweek.com/2025/01/24/c...
This is one of those articles that I send to my family to help answer "What is it that you do, exactly?"
www.newsweek.com/2025/01/24/c...
This is one of those articles that I send to my family to help answer "What is it that you do, exactly?"
January 15, 2025 at 4:55 PM
Nice article on how using whole-genome sequencing to diagnose cancer is entering the mainstream (finally!). Great to see lots of familiar folks interviewed.
www.newsweek.com/2025/01/24/c...
This is one of those articles that I send to my family to help answer "What is it that you do, exactly?"
www.newsweek.com/2025/01/24/c...
This is one of those articles that I send to my family to help answer "What is it that you do, exactly?"
JFC. "Mirror bacteria" (with entirely opposite chirality) was not on my list of existential threats until today.
December 12, 2024 at 7:53 PM
JFC. "Mirror bacteria" (with entirely opposite chirality) was not on my list of existential threats until today.
The key lesson I try to impart over and over is "Don't trust your data". Programs aren't magic, p-values != validity. Assume your data is faulty/biased/wrong and then try to convince yourself otherwise.
The datasaurus dozen is a nice demonstration:
blog.revolutionanalytics.com/2017/05/the-...
The datasaurus dozen is a nice demonstration:
blog.revolutionanalytics.com/2017/05/the-...
November 25, 2024 at 8:40 PM
The key lesson I try to impart over and over is "Don't trust your data". Programs aren't magic, p-values != validity. Assume your data is faulty/biased/wrong and then try to convince yourself otherwise.
The datasaurus dozen is a nice demonstration:
blog.revolutionanalytics.com/2017/05/the-...
The datasaurus dozen is a nice demonstration:
blog.revolutionanalytics.com/2017/05/the-...
Wrapping up another year of teaching in the Advanced SeqTech and Bioinformatics course at @cshlaboratory.bsky.social
We had a really top-notch group of students, working on a wide range of really interesting projects. I can't wait to see the awesome science they produce with their new skills!
We had a really top-notch group of students, working on a wide range of really interesting projects. I can't wait to see the awesome science they produce with their new skills!
November 20, 2024 at 7:11 PM
Wrapping up another year of teaching in the Advanced SeqTech and Bioinformatics course at @cshlaboratory.bsky.social
We had a really top-notch group of students, working on a wide range of really interesting projects. I can't wait to see the awesome science they produce with their new skills!
We had a really top-notch group of students, working on a wide range of really interesting projects. I can't wait to see the awesome science they produce with their new skills!
But, since we put lots of candidates into each patient, 14 of the 18 patients had a response to at least one of them.
November 19, 2024 at 4:48 AM
But, since we put lots of candidates into each patient, 14 of the 18 patients had a response to at least one of them.
The hard part is finding neoantigens that are specific to the tumor and then well presented-to and recognized-by the immune system. The field as a whole is not great at this yet (it's complicated!). Only some of the neoantigens we tried hit the target and stimulated a response (3/n)
November 19, 2024 at 4:48 AM
The hard part is finding neoantigens that are specific to the tumor and then well presented-to and recognized-by the immune system. The field as a whole is not great at this yet (it's complicated!). Only some of the neoantigens we tried hit the target and stimulated a response (3/n)
Just out - our paper on a successful phase I trial of DNA vaccines against triple-negative breast cancer!
genomemedicine.biomedcentral.com/articles/10....
Key points:
- Neoantigen specific T cell responses were induced in 14/18 patients
- 87.5% recurrence-free survival at 36 months
Thread below!
genomemedicine.biomedcentral.com/articles/10....
Key points:
- Neoantigen specific T cell responses were induced in 14/18 patients
- 87.5% recurrence-free survival at 36 months
Thread below!
November 19, 2024 at 4:48 AM
Just out - our paper on a successful phase I trial of DNA vaccines against triple-negative breast cancer!
genomemedicine.biomedcentral.com/articles/10....
Key points:
- Neoantigen specific T cell responses were induced in 14/18 patients
- 87.5% recurrence-free survival at 36 months
Thread below!
genomemedicine.biomedcentral.com/articles/10....
Key points:
- Neoantigen specific T cell responses were induced in 14/18 patients
- 87.5% recurrence-free survival at 36 months
Thread below!
If you see this, please repost with a favourite photo of the sky you’ve taken recently
November 16, 2024 at 1:40 PM
If you see this, please repost with a favourite photo of the sky you’ve taken recently
Indeed!
I still show this in the bioinformatics class I teach
I still show this in the bioinformatics class I teach
November 15, 2024 at 5:24 AM
Indeed!
I still show this in the bioinformatics class I teach
I still show this in the bioinformatics class I teach
Woah. All ~50Pb of SRA in one kmer index 🖥️🧬
logan-search.org
Paper on @biorxiv-bioinfo.bsky.social:
www.biorxiv.org/content/10.1...
logan-search.org
Paper on @biorxiv-bioinfo.bsky.social:
www.biorxiv.org/content/10.1...
November 11, 2024 at 6:46 PM
Woah. All ~50Pb of SRA in one kmer index 🖥️🧬
logan-search.org
Paper on @biorxiv-bioinfo.bsky.social:
www.biorxiv.org/content/10.1...
logan-search.org
Paper on @biorxiv-bioinfo.bsky.social:
www.biorxiv.org/content/10.1...
Trying out a new motto this week
September 18, 2024 at 1:35 AM
Trying out a new motto this week
The record for most people in orbit at once has been tied, with 19 people hanging out there right now
whoisinspace.com
whoisinspace.com
September 12, 2024 at 2:30 AM
The record for most people in orbit at once has been tied, with 19 people hanging out there right now
whoisinspace.com
whoisinspace.com
Questions to ask of your data before giving that seminar:
July 15, 2024 at 4:23 AM
Questions to ask of your data before giving that seminar:
My first-pass attempt:
June 13, 2024 at 3:14 PM
My first-pass attempt:
Today's challenge:
Summarize your research using the UpGoer5 text editor, which only allows the 10,000 most common words in the English language.
splasho.com/upgoer5/
Summarize your research using the UpGoer5 text editor, which only allows the 10,000 most common words in the English language.
splasho.com/upgoer5/
June 13, 2024 at 3:13 PM
Today's challenge:
Summarize your research using the UpGoer5 text editor, which only allows the 10,000 most common words in the English language.
splasho.com/upgoer5/
Summarize your research using the UpGoer5 text editor, which only allows the 10,000 most common words in the English language.
splasho.com/upgoer5/
Solid statistics joke from @mikebenchcapon.bsky.social that isn't getting nearly the love it deserves on twitter
May 15, 2024 at 4:27 PM
Solid statistics joke from @mikebenchcapon.bsky.social that isn't getting nearly the love it deserves on twitter
Aurora borealis from a campground outside of St Louis (my first time ever seeing them!). My 9-year-old definitely does not realize how lucky she is to have seen a total solar eclipse and the Northern lights within about a month. What else should be on my astronomy bucket list?
May 11, 2024 at 10:46 AM
Aurora borealis from a campground outside of St Louis (my first time ever seeing them!). My 9-year-old definitely does not realize how lucky she is to have seen a total solar eclipse and the Northern lights within about a month. What else should be on my astronomy bucket list?
I've been studying biology for 25 years and until now, hadn't really thought about the fact that mRNA is much larger than the protein it codes for
book.bionumbers.org/which-is-big...
book.bionumbers.org/which-is-big...
May 8, 2024 at 5:04 PM
I've been studying biology for 25 years and until now, hadn't really thought about the fact that mRNA is much larger than the protein it codes for
book.bionumbers.org/which-is-big...
book.bionumbers.org/which-is-big...
This is great, and one of the only times I've ever been bummed that my tumors have purity that is too high!
github.com/jts/smrest
github.com/jts/smrest
March 1, 2024 at 2:55 AM
This is great, and one of the only times I've ever been bummed that my tumors have purity that is too high!
github.com/jts/smrest
github.com/jts/smrest
"Sorry for the slow response"
--Every academic, every day
--Every academic, every day
February 26, 2024 at 3:48 PM
"Sorry for the slow response"
--Every academic, every day
--Every academic, every day
Being in medical research, I'm used to a lot of weird spam for antibodies, instruments, and shady conferences. This one, was new though, and honestly, kind of a refreshing change of pace.
February 23, 2024 at 7:35 PM
Being in medical research, I'm used to a lot of weird spam for antibodies, instruments, and shady conferences. This one, was new though, and honestly, kind of a refreshing change of pace.