Translational human genetics, computational genomics, 🏳️🌈, @UVA, @Columbia_Bio, @MIT_CSAIL. Views expressed are my own and not of my employer (@Alnylam)
Cambridge, MA
Joined March 2009
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Published today in @NatureComms! In this study from @Alnylam Human Genetics we describe a rare missense variant in manganese transporter SLC30A10 associating with biomarkers of hypermanganesemia and diagnosis of cholangiocarcinoma. nature.com/articles/s41467-0…
Happy to share this new preprint from our group at @Alnylam, with @hochoutu @iammegparker @AimeeDeaton @PNioi. (1/14)
teapawt.net/biorxivpreprint/status…
Luke Ward retweeted
I'm sorry, but all you have to do is Google something you have real expertise in to know "AI Overview" is total horseshit
Luke Ward retweeted
AI for bio teams in academia & industry have been playing "offense" pumping out billion parameter models every other week that are worth less than a paper weight. How can anyone claim that the field needs "more offense" & less "rigor", when it requires literally the opposite?!?
This applies to academic labs too — maybe more than anywhere.
Defense in academia looks like rigor: protect your niche, optimize your pipeline, wait for the field to settle. It isn't rigor. It's just slower irrelevance.
The labs that matter in five years aren't asking "how do we use AI to do our old experiments faster." They're asking "what questions are now askable that weren't before?"
That's the offensive posture. And academics have something founders don't — the freedom to chase questions with no obvious payoff. That's an enormous edge, if you use it.
Luke Ward retweeted
Regeneron's 23andMe buyout is the best possible outcome. A Big Pharma would just bobble it, then watch it die. REGN is far more purposeful and directed. They get it cheap, keep their eyes on the ball and manage things. I like it.
endpts.com/why-regeneron-is-…
Luke Ward retweeted
Every so often I relive the unsettling realization that ~8% of my genome is basically ancient viruses. Like you have less DNA coding for your own proteins (1-2% of the genome) than you have DNA of some virus from forever ago. You are basically mostly a virus.
Luke Ward retweeted
Nope! These are all Chinese participants of the Kadoorie biobank, color-coded by the cities they were recruited from. Ancestry inference can be extremely sensitive with enough data.
(pubmed.ncbi.nlm.nih.gov/3760…)
Luke Ward retweeted
everyone needs to read this from @jsomers
jsomers.net/i-should-have-lo…
Luke Ward retweeted
OH MY FUCKING GOD. YOUR ENTIRE BUSINESS RUNS ON MASSIVE AMOUNTS OF UNPAID LABOUR YOU HYPOCRITICAL SHITGIBBONS.
It can be hard to say no to service requests in academia.
We sought advice on how to ensure researchers don’t get stuck doing unpaid labour
go.nature.com/4bUX6WN
Luke Ward retweeted
TIL when you sort the codon wheel by the second base the quadrants align with the properties of the amino acids being coded for and also it looks like the mystic sigil of the coven of the four bases
journals.asm.org/doi/pdf/10.…
Luke Ward retweeted
In dramatic overhaul, Cambridge becomes one of the first cities in Mass. to eliminate single-family zoning trib.al/n2sS3Up
Luke Ward retweeted
just one more striped hyena block bro, I promise. DNA is all you need dog, trust me. the only thing we're missing is ring attention, I swear. once we have the context length to capture long-range interactions we'll solve mammalian genome modeling. yeah yeah I know the human genome is 45% retrotransposons and there were those recent genome scrambling results but I think if we just scale up compute a bit more and finally train the model chinchilla optimal—what? you want to curate pretraining data using gnomad conservation z-scores? are you not scaling-pilled bro?! incoherent mumbling... just need... one more... mammalian clade... I promise the marsupial reference genomes will unlock everything...
Luke Ward retweeted
Agreed! That's why I wrote ggpubfigs, a ggplot2 extension that *only colorblind-friendly color palettes.
Easily make your figures colorblind-friendly with ggpubfigs! teapawt.net/NKWhiteman/status/1852…
Luke Ward retweeted
Statistics is hard enough for most people as it is; please stop using the phrases "type I" and "type II" errors.
Unless, of course, your goal is to confuse people - in which case, congrats - you've succeeded!
Just say "false positive" and "false negative" instead.
If you are at #ASHG2024, head to Room 104 for lunch today (Friday) to hear Alnylam's @AimeeDeaton and others discuss the @ukfuturehealth study, which has currently recruited 1M participants and plans to recruit 5M!
Luke Ward retweeted
My quest to find the most boring WikiCrow page is off to a good start. Meet uncharacterized protein C17orf50. Terrible AlphaFold 2 structure. Not much is known about it, so not much material for PaperQA2 to work with. wikicrow.ai/C17orf50
ALT WikiCrow C17orf50
Luke Ward retweeted
For all its flaws, I would argue the biotech industry is still *the* single best place to work today with a tech background
1- Intellectually, you get to work on some of the hardest problems of our time and they won’t be solved anytime soon.
2- The field is undergoing a fundamental shift from qualitative to quantitative. Today, you get to pioneer a direction that will be the future of biomedicine.
3- It is immensely fulfilling to know that your work contributes to addressing the many still grave unmet health needs. You literally get to work on ensuring your friends and family live longer and healthier.
4- There is almost infinite potential for learning and growth - and every slice of the drug discovery pipeline has incredible depth of existing knowledge. If you are keen to learn, there is always another area you haven’t learnt about yet.
Sure, the business side of it can be unpredictable and its likely you would be compensated more working on ad optimization or image generation apps - but I don’t know anyone that is excited about the above that would even consider that an alternative.
Luke Ward retweeted
I wrote about the paucity of genetic evidence for very recent selective sweeps and the generally odd and sporadic nature of the ones we do see. A 🧵:
Luke Ward retweeted
New manuscript "Addressing the credibility crisis in Mendelian randomization" is out at @BMCMedicine: bmcmedicine.biomedcentral.co…. We discuss the explosion in MR studies, and what can be done by authors and editors/reviewers to improve the quality of published MR research. Thread:
Luke Ward retweeted
The Li + Durbin 2011 paper showing that you can infer an entire population history from just a single genome is still one of the most mind-blowing results in genetics I have ever seen.
nature.com/articles/nature10…
