Chris Miller

I have a joke about cram files, but it's no good if you don't get the reference

@tycheleturner Cool. Always glad to see new experiments, and very intrigued. Please report back on whether you think it was successful!

Hi @chrisamiller! Yes, in regards to your question. But also, I am mainly looking to reach researchers and/or teams who already have research participant genomic data and are exploring how or what they can do with it. The goal is to showcase what OUR new genomic tools make possible, so someone can quickly see a capability, and think, “We could apply that to our dataset,” and then either bring it to their bioinformatics team to evaluate and implement or contact us directly to discuss a potential collaboration. I am aiming this at a broader research audience across the human genetics/genomics and medical research community. Linking and collaborating across specialities. Just thought I would try this white paper strategy out! Thanks for your question.

Outreach note from @TNTurnerLab. One part of our research work since joining the faculty at @WashUGenetics has been building new and original genomics software out of necessity. Over ~7 years, driven by our interests in my research area of neurodevelopmental disorders, we have developed a steady stream of state of the art new original tools, and some now also apply to other phenotypes. Encouraged by other research scientists and to make this work more accessible for the community, I am releasing our first white paper: CNPI (zenodo.org/records/188421…) #GenomicsWhitePapers #genomics #computation #bioinformatics

I study measles. I’ve seen the devastating toll it takes on children’s immune systems It drives immunological amnesia and erases parts of protective immune memory and sets kids up for secondary infections months and years later Its not benign nytimes.com/2025/04/02/opi…

@iskander No, but neither did clinical WGS. Far too many places are still using panels, even in cancer cases where WGS would provide clinical benefit in a decent fraction of cases.

Did consumer WGS ever take off?

@sinabooeshaghi @i000 @ensembl I thought this was common knowledge? It's the main reason to work in ENSG/ENST space until you come up to the surface for interpretation and context.

@i000 @ensembl The issue is the "Gene Synonym" which maps to another gene name with a conflicting Ensembl ID. I've found 2,122 cases of this happening.

What's your one-sentence bioinformatics horror-story? I'll start: Today I found two completely different genes with the same @ensembl ID.

cancer research saves lives - including mine Trump wants to cut National Cancer Institute's 2026 funding by $2.7B his proposed tax cut would give 18 times that much - $48.9B - to the top one-tenth-of-one-percent income bracket my @zeteo_news column zeteo.com/p/trump-cut-ca…

We have two identical groups of 8 gauges with anomalous gauge at position (3,1). The degree of anomaly is identical in both groups ~ 8 deg. Humans have extreme hyperacuity with respect to detecting angular orientation of line segments—needle gauge is so much faster to read. The arc gauges all look the same even though the amount of deviation is the same, about 8 degrees. Even if you concentrate, it's hard to tell which one is off.

I have a thread on bsky about our new paper, describing a phase I clinical trial where we designed neoantigen vaccines against people's tumors (triple-negative breast cancer). Check it out there! bsky.app/profile/did:pl… genomemedicine.biomedcentral.com/articles/10.11… @obigriffith @malachigriffith

@vsbuffalo My take is that Twitter was never going to be the end-all platform. Like everything else on the internet, it got enshittified, and people moved on. The same thing will happen to Bsky eventually, once they need to, y'know, actually make money. And then we'll move on again.

x.com/AmericanGwyn/s… For better or worse, I think this tweet captures the vibe there. But, there is a lot more science happening there now — by at least 5-10x. Both places have become echo chambers due to selection effects of who leaves and who stays.

The exodus of scientists to "the other site" (apparently we have to speak in code due to algorithmic filtering) is now quite perceptible. I've been bearish on X dying as a platform for a while because of network effects. Not so anymore. X has a human capital shortage problem.

Activity on ⁦@bluesky⁩ is extraordinary since last week’s election. Scientific Twitter seems to be migrating en masse, my followers have tripled in a week. bsky.app/profile/greall…

Amazing stuff. Talking about this over on bsky: bsky.app/profile/chrism…

New paper 📣 - "A comprehensive survey of RNA modifications in a human transcriptome" by @logan_mulroney, Lucia Coscujuela Tarrero and colleagues from an excellent collaboration between Francesco Nicassio's lab at @IITalk and my group @emblebi biorxiv.org/content/10.110…

Lots of activity happening on bluesky in the bioinformatics /genomics space. Get started with these folks: bsky.app/starter-pack/d… Would love to see more cancer over there - come join us, it's nice!

No, this isn't great, but look at that reduction! 25% down from our peak and dropping. There's cause for concern and also cause for optimism here.

Big shout out to those researchers who made their data available in PDB over the years The Chemistry Nobel Prize winners today relied on that open academic data to train their models We wouldn't have these advances if researchers hadn't made 200,000 protein structures available

@vsbuffalo There's a lot of shit out there, but the best sports journalism isn't about sports, it's about the human condition, and it can be sublime

I rarely read sports journalism, is it always like this? This article on the record number of White Sox losses is probably the single best NYT piece I’ve read all year. nytimes.com/2024/09/24/mag…

This is a beautifully done tribute to the Oakland A’s. The first baseball game I ever saw was the A’s at the coliseum 🥲 nytimes.com/2024/09/26/sty…

@aaronquinlan This is the stat that blew my mind: reddit.com/r/baseball/com…

I have no tattoos. "Ohtani" might be my first. What an absolute legend. mlb.com/dodgers/video/…

This is a great essay on the “Duplication Crisis”: academic science incentivizes the creation of new methods and software, not the refinement (or even maintenance) of existing tools. This is a serious problem that’s well-known among software folks in science.

Exciting opportunity! I am hiring a postdoc to join the group and to develop computational methods for the analysis of biomedical data including imaging and genomics data at a single-cell or spatial resolution 🧬 stephaniehicks.com/join

Just a reminder that Bluesky is a nice replacement and gathering more and more of the science community. I check Twitter less and less these days