iiinova — where your digital self keeps evolving

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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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 · 21/05/2026

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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Chris Miller @chrismiller.science · 17/03/2026

An argument from @nilshomer.com that in the long run, your tool's intermediate data may be just as important as the end results. blog.fulcrumgenomics.com/p/your-bioin...

I want to make a simple argument: every new bioinformatics tool and method you write should be AI-ready. AI assistants need to work with your code, your outputs, and your analysis logic. Machine learning needs to train on the rich data your tools produce. If you’re not gathering this data as you go, you’re leaving value on the table.

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Chris Miller @chrismiller.science · 06/10/2025

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)

Plot showing how many records need to be returned to ensure that each completely typed gene will be in the list.

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Chris Miller @chrismiller.science · 06/10/2025

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)

199 AR
120 PC
100 KL
78 ZNF7
67 ZNF2
67 CS
58 CP
58 ADA
57 SI
55 ZNF3
52 TH
51 C2
43 MAG
42 ZNF8
42 TNF
41 GPR1
37 DEFB1
36 USP1
36 GAL
34 PLEK
31 MET

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Chris Miller @chrismiller.science · 21/04/2025

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...

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Chris Miller @chrismiller.science · 14/04/2025

There's the traditional solution:

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Chris Miller @chrismiller.science · 15/01/2025

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?"

Newsweek - On target - Genetic Sequencing is creating bespoke cancer cures.

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Chris Miller @chrismiller.science · 12/12/2024

JFC. "Mirror bacteria" (with entirely opposite chirality) was not on my list of existential threats until today.

$Our analysis suggests that mirror bacteria would likely evade many immune mechanisms mediated by chiral molecules, potentially causing lethal infection in humans, animals, and plants. They are likely to evade predation from natural-chirality phage and many other predators, facilitating spread in the environment. We cannot rule out a scenario in which a mirror bacterium acts as an invasive species across many ecosystems, causing pervasive lethal infections in a substantial fraction of plant and animal species, including humans. Even a mirror bacterium with a narrower host range and the ability to invade only a limited set of ecosystems could still cause unprecedented and irreversible harm.$

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Chris Miller @chrismiller.science · 25/11/2024

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-...

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Chris Miller @chrismiller.science · 20/11/2024

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!

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Chris Miller @chrismiller.science · 19/11/2024

But, since we put lots of candidates into each patient, 14 of the 18 patients had a response to at least one of them.

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Chris Miller @chrismiller.science · 19/11/2024

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)

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Chris Miller @chrismiller.science · 19/11/2024

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!

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Chris Miller @chrismiller.science · 16/11/2024

If you see this, please repost with a favourite photo of the sky you’ve taken recently

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Chris Miller @chrismiller.science · 15/11/2024

Indeed! I still show this in the bioinformatics class I teach

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Chris Miller @chrismiller.science · 11/11/2024

Woah. All ~50Pb of SRA in one kmer index 🖥️🧬 logan-search.org Paper on @biorxiv-bioinfo.bsky.social: www.biorxiv.org/content/10.1...

There are 50 petabases of freely-available DNA sequencing data. We introduce "Logan Search" which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips.

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Chris Miller @chrismiller.science · 18/09/2024

Trying out a new motto this week

Do you want to be good at science, or do you want to be good at emails?

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Chris Miller @chrismiller.science · 12/09/2024

The record for most people in orbit at once has been tied, with 19 people hanging out there right now whoisinspace.com

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Chris Miller @chrismiller.science · 15/07/2024

Questions to ask of your data before giving that seminar:

Is it hot? does it look good? Are you proud to serve it?

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Chris Miller @chrismiller.science · 13/06/2024

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/

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Chris Miller @chrismiller.science · 15/05/2024

Solid statistics joke from @mikebenchcapon.bsky.social that isn't getting nearly the love it deserves on twitter

The weird thing about The Simpsons is that while the average quality of the jokes has decreased over time, the average quality of each individual character's jokes has actually increased over time

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Chris Miller @chrismiller.science · 11/05/2024

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?

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Chris Miller @chrismiller.science · 08/05/2024

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...

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Chris Miller @chrismiller.science · 01/03/2024

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

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Chris Miller @chrismiller.science · 26/02/2024

"Sorry for the slow response" --Every academic, every day

the secret to multi-tasking is apologizing constantly to everyone you know forever

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Chris Miller @chrismiller.science · 23/02/2024

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.

Shipping Household Goods Inside an Ocean Container

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Chris Miller @chrismiller.science · 23/11/2023

It's STAR under the hood, and the attached applies, AFAIK. The bam header contains the actual STAR command used, but the older bams I have handy (cellranger 3.0) have `--outSAMmultNmax -1` set, but no other options relevant to multimapping that I see.

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Chris Miller @chrismiller.science · 25/10/2023

I believe the field has landed on "Computeral Bioinfologist" @mikelove.bsky.social @robp.bsky.social

Chris Miller
I get that I'm not the arbiter of terminology but it all seems like meaningless distinctions to me. If you're using computers to study biological information, then use any combination of those words as a title, Then more importantly, tell me what you *actually do*

Michael Love
so you're cool with me saying I study Computeral Bioinfology

Rob Patro
As long as you sound drunk whenever you say it, I’d be fine with this.

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Chris Miller @chrismiller.science · 11/10/2023

I quite like this word cloud of my publications. via @morinryan.bsky.social 's tool: shiny.rcg.sfu.ca/u/rdmorin/se... (The semantic scholar tool worked much better than google scholar or pubmed for me!)

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Chris Miller @chrismiller.science · 06/10/2023

Sycamores don't have the most vibrant colors in the fall, but I'm a sucker for those white branches and mottled bark

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Chris Miller @chrismiller.science · 02/10/2023

Since the official Nobel prize isn't on bsky yet, here's today's announcement.

Nobel prize awarded to Katalin Kariko and Drew Weissman for their discoveries concerning nucleoside base modifications that enabled the development of effective mRNA vaccines against COVID-19

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Chris Miller @chrismiller.science · 24/09/2023

Fun way to visualize your scholarly works in a word cloud. Here's mine

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Chris Miller @chrismiller.science · 14/09/2023

Me: This time is different. This is going to be the bioinformatics tool that is well designed and easy to run! 🖥️ 🧬

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Chris Miller @chrismiller.science · 11/09/2023

Using an image, show a movie you are sure you have watched more than 10 times. VHS-taped off of a TV airing, including 5-second fragments of commercials from the breaks. I always fast-forwarded past all the icky love scenes.

Top Gun: I feel the need, the need for speed!

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