chrisamiller

9 ms·

31.
by chrisamiller 5y ago
People are living longer and age is a dominant risk factor for cancer. In a world where cancer care wasn't improving, we'd expect to see massive increases in deaths due to cancer. What's also not captured by that number are
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by chrisamiller 5y ago
Maybe your car hasn't changed, but your cancer care sure as hell has. The medical and biological sciences are where a lot of innovation has taken place, and the pace of technological advancement in things like DNA sequencing (as one ex
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by chrisamiller 5y ago
I firmly agree that we've crossed several tipping points and that adaptation is a large and necessary part of our response. You seem to ignore that there are degrees of badness here, though! Limiting warming to 2 or 3 degrees C is goi
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by chrisamiller 6y ago
LastPass costs $36 per year. Operating on the principle of being the customer and not the product, that seems very reasonable for a secure way to store and share the keys to my digital life. That said, it does make it a little bit harder fo
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by chrisamiller 6y ago
That all depends what you want to do with the data. For assembling new genomes, they produce very long reads that are essential for "scaffolding". They're also great for structural variant detection (large rearrangements of
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by chrisamiller 6y ago
The economy cares very much about this virus. The stock market does not. The disconnect between the two is yet another sign of how vast the inequality gap is at the moment.
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by chrisamiller 6y ago
I'm sure this is abnormal for the Bay Area, but insane seems kind of overblown - this doesn't sound out of the ordinary for the midwest at all. Thunderstorms, hail, and occasional tornados are routine in the summer. Just last wee
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by chrisamiller 6y ago
Preprint servers have been an amazing boost to the speed at which science is able to progress. The benefits unambiguously outweigh the small number of cons, in nearly everyone's opinion. The fact that the press can't help sensatio
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by chrisamiller 6y ago
This thread from another virologist casts some doubt about the claims of selective advantage proposed in this preprint: https://twitter.com/trvrb/status/1257825352660877313?s=19 Science in action, folks. It's
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by chrisamiller 7y ago
FWIW, I have this same BoA issue and have been trying for months to escalate it to someone who can actually do something about it. It's frustrating, to say the least.
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by chrisamiller 7y ago
Unfortunately, there still is no such thing as "basic" analysis of DNA. :)Ewan Birney has a great quote about this: Sequencing, analysing and interpreting genomes is ‘routine’ in the same way the US Navy ‘routinely’ lands planes o
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by chrisamiller 7y ago
> How would such a mutation help her lineage? But that same question, more broadly, how do mutations that benefit people past their child bearing age factor into human evolution? To oversimplify a bit, you can think of most mutations as
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by chrisamiller 7y ago
All the time! People propose hypotheses, supported by some preliminary data, and then they need to be tested. Some problems are easy, some take years or decades to be overturned. It's messy sometimes, but that's how science is
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by chrisamiller 7y ago
I often recommend Aaron Quinlan's excellent course if people want to learn a more hands-on and practical set of skills related to computational genomics and bioinformatics. https://github.com/quinlan-lab/applied-co
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by chrisamiller 8y ago
Very few places, but there's no reason that it couldn't be. Such a plan would have to come with some substantial changes/restrictions on colleges to help rein in the ballooning costs (e.g. lazy rivers, gourmet cuisine) that a
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by chrisamiller 8y ago
So you get an education for free, then pay back into the system after you're in the workforce? Congratulations, silicon valley, you've just re-invented public education! Imagine what our public universities could look like with s
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by chrisamiller 8y ago
The biggest difference between academic tools and those in industry is that they're sinking major funds into producing (expensive, hard to produce at scale) training data. That, in theory, should allow them to develop better algorithms
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by chrisamiller 8y ago
Not sure why this is grey - many animals adapt to their environments very quickly. If all the drones are doing is buzzing the birds, they may very well learn to ignore them.
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by chrisamiller 8y ago
Those of us in academia are (mostly) pushing hard for open access policies. We want our work to be disseminated as widely as possible! What makes it difficult is that publications and journal reputation are still used as a measure of succes
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by chrisamiller 8y ago
Yeah the desktop web version is a massively better experience (though not stellar either, tbh). It says something that it's still a good tool despite those shortcomings
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by chrisamiller 9y ago
It's a SNP chip and only covers a few common mutations. To anyone who wants to know for sure whether you're at increased risk of breast cancer, you'll want to get a test that sequences all the known mutations, along with an
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by chrisamiller 9y ago
I'd urge you to be cautious when interpreting those data. The effect size of most of these SNPs is tiny, often explaining (at most) only very small amounts of the variability observed between groups. This is especially true for things
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by chrisamiller 9y ago
It might be marginally more feasible to build an enormous space tether ( https://www-istp.gsfc.nasa.gov/Education/wtether.html ). By dragging it through Earth's magnetic field (which extends out past the moon on the
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by chrisamiller 9y ago
It's really comparing apples and oranges. If you want a 30x whole genome for genotyping, you'll use short read technologies and it'll be way less expensive. The enormous reads offer a different window into genomes, by spannin
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by chrisamiller 9y ago
Culturing is the problem, though, right? Many types of bacteria (including some pathogens) really do not like to grow on most media. There's no doubt that sequencing is the future of infection diagnosis. It's just a matter of how
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by chrisamiller 9y ago
It far outstrips Moore's law :) https://www.researchgate.net/profile/Orit_Shaer/publication/...
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by chrisamiller 9y ago
Niche uses where long-read sequencing is required (denovo assembly, reference improvement, bacterial genomes, whole-isoform transcriptomes. Nanopore is starting to eat into that market, though.
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by chrisamiller 9y ago
Be careful about defining "high coverage" as 30x. Many applications (especially cancer) really require 100x or more to overcome purity and ploidy, or to identify subclonal populations.
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by chrisamiller 9y ago
It's definitely a good starting place for people from a CS background, but if you really want to learn biology, don't get too attached! As you get deeper, you'll quickly discover the limitations of that analogy.
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by chrisamiller 9y ago
And the public reference genome is about 2/3 from a single African American individual from Buffalo, New York!

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