Viewing profile — chrisamiller

I don't mean this to sound snarky, but if a blog doesn't have a good ratio of signal to noise, you just unsubscribe from the feed. The solution is to be okay with missing some thin…

Our middle school has banned phones during school hours, and it's been great. Even though most kids own phones and have them in their backpacks, they aren't seen. There are less pr…

At any given time, I'm working on like 10 different projects. tmux lets me set up sessions for each of these projects, so that when I leave one and come back in a week, all the con…

Are you claiming that declining fertility is due to plastic, rather than to increasing wealth, education of women, and access to contraception? If so, then I'm going to have to ask…

Absolutely. We're not there yet, but it's not inconceivable.

The short answer is, we sequence their genomes, identify mutations that change a protein sequence and are highly expressed, then run those all through suites of algorithms that pre…

Look, I get the impulse, and might have agreed with you 10 years ago. At the end of the day, though, we have to work with non-computationally savvy people who (reasonably) want to …

It's too late, the genetics community already caved :-( [Scientists rename human genes to stop Microsoft Excel from misreading them as dates]( https://www.theverge.com/2020/8/6/213…

These are ballpark numbers to be sure, and yeah, my off the cuff comment didn't get that exactly right. I also simplified things quite a bit to try to get the broader point across …

This is a great example of where cancer treatment is headed and why it's so hard - namely that cancer isn't one disease, it's many thousands of diseases. This is a drug that target…

I do cancer research, including using mouse models, so believe me, I know the difficulty :-) Getting promising drugs into humans is -hard-, and this research is interesting, but th…

I hate to be that guy, because it seems like there is some interesting science behind this press release hype. There are, however, many many miles between "effects in a mouse model…

You're going to want to start with the PCAWG consortium, who looked very closely at viral involvement across a host of cancers. Their numbers: Cohort: 2,658 cancers across 38 tumor…

It's true that the whole problem of cancer therapy is "how do I target these cells over here, while avoiding the rest of your healthy cells, when they look mostly the same" And you…

There is a lot of great work going on thinking about this very problem. One common theory goes like this: There are lots of tumor "driver mutations" that are causative and occur in…

I'm as critical of pharma pricing as the next guy, but this really is a case where you're getting a custom vaccine design just for you, and the profit margins probably aren't very …

This isn't a preventative vaccine like that. It's something that has to be developed after you have cancer to target your tumor's specific mutational profile. So mass production (j…

That's not far off from the rates for producing custom order medical-grade peptides and/or mRNA vaccines, coupled with the expertise needed to design, administer, and monitor them.…

There are lots of folks working on problems surrounding automation and reproducibility to enable science in this space. One such effort that I contribute to is [pVACtools]( https:/…

You're right that there are a variety of folks working on these things, both in academia and industry, but it's more complicated than "PhDs do this, others do that". It comes down …

Part of my research involves designing these cancer vaccines. There are different delivery mechanisms, but the need to synthesize medical-grade peptides or mRNA vaccines is one of …

The amount of energy needed to get out of earth's gravity well is incredibly high. It would be silly to try to boost a massive object like the ISS out.

That's a pretty expansive statement. Are you doing error-corrected sequencing to look for rare mosaic variants? Do you care about transcripts expressed at very low levels? Are you …

In most cases* the raw data can be recreated from the aligned BAM/CRAM file, so it's often sensible to toss the raw FASTQs after alignment. But yeah, I go back to 10+ year old geno…