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Now out in @AnnualReviews of Genetics!!

We review the use of functional assays for the study of human coding and noncoding SNVs, exploring current applications and outlining key methods and principles of experimental design.

An enormous thank you to Victoria Parikh, Prashant Mali, Fritz Roth (@fritzroth), and Melina Claussnitzer who I count myself very lucky to have worked with!!

And a thank you to the AVE ETS working group and of course, to @AnnualReviews!

annualreviews.org/eprint/TK7RF

function box() { t="$1xxxx";c=${2:-=}; echo ${t//?/$c}; echo "$c $1 $c"; echo ${t//?/$c}; } # Make box around text. By bartonski
I made an explanation of how this works a while ago here: youtube.com/watch?v=9bZ85aMuf6

Question: If you have a little R package floating around on github with a few useful functions that other people are using, where would you publish it to be "citeable"?

(I don't have the strength or patience to send it to CRAN.)

Updated benchmarking of variant effect predictors using deep mutational scanning biorxiv.org/content/10.1101/20

Updated benchmarking of variant effect predictors using deep mutational scanning

Variant effect predictors (VEPs) provide a potential solution to the influx of variants of uncertain clinical significance produced by genome sequencing studies. However, the assessment of VEP performance is fraught with biases introduced by benchmarking against clinical observations. In this study, building on our previous work, we use independently generated measurements of protein function from deep mutational scanning (DMS) experiments for 26 human proteins to benchmark 55 different VEPs, while introducing minimum data circularity. The top VEPs are dominated by unsupervised methods including EVE, DeepSequence and ESM-1v, a new protein language model that ranked first overall. However, the strong performance of recent supervised VEPs, in particular VARITY, shows that developers are taking data circularity and bias issues seriously. We also assess the performance of DMS and unsupervised VEPs for discriminating between known pathogenic and putatively benign missense variants. Our findings are mixed, demonstrating that some DMS datasets perform exceptionally at variant classification, while others are poor. Notably, we observe a striking correlation between VEP agreement with DMS data and performance in identifying clinically relevant variants, with EVE, DeepSequence and ESM-1v performing best, further supporting the utility of DMS as an independent benchmark. ### Competing Interest Statement The authors have declared no competing interest.

www.biorxiv.org

🚨 BIG EXOPLANET NEWS! 🚨

Our team has released FIVE papers today on the most COMPREHENSIVE study of an #exoplanet atmosphere to date!

Using #JWST we obtained four transit observations of #WASP-39b early in the telescope's operations to study both the planet itself, and the telescope's capabilities to observe exoplanet atmospheres.

We detected numerous molecules in the planet's atmosphere, including CO2, CO, H2O, and SO2 🧵

The future is here! ⭐ 🪐 🔭 #Astrodon #Science

webbtelescope.org/contents/new

@monotrox99 Agreed. I suspect qoto is running a modded fork of mastodon v3.2.1. So our hashtag subscription feature may have been implemented independently from the one that was introduced in v4 on other instances.

Maybe "following hashtags from search results" would be worth a feature request with our admin @freemo ? :)

@monotrox99 In the browser (not on mobile), go to "Settings" -> "Follows and Subscriptions" -> "Following Hashtags" -> "Add new Hashtag follow".

Hope this helps :)

The duf is a better 'df' command. It gives you a single tool for checking disk usage and free space on Linux, macOS, *BSD, Windows, Android and Unix. Try duf today
cyberciti.biz/open-source/comm

My abstract got accepted to '23 today! 🎉
Anyone else planning to go?

@freemo

That's great to hear! I did try to make a latex test toot earlier and noticed that bug.
Thanks for putting so much work into this!

@arinbasu @SteveZissou

@arinbasu @SteveZissou @freemo I was also pleasantly surprised by QOTO's LaTeX support! Altogether a really cool set of features!

A reminder for anyone new to mastodon who might not be happy with some of the racist and bad actors out there on other servers... Just import the fediblock list to your personal blocks and you will be safe from the vast majority of bad actors.

𝑺𝑻𝑶𝑹𝑴⛈️  
I took all the domains from https://fediblock.neocities.org/ block list and put it in a csv file that can be imported so you can block all hateful ...

Real long aggregation of Mastodon etiquette for birdsite expats 

Some Mastodon thoughts, for bird-site expats (which include myself). I'm aggregating these from posts I've boosted before, so little of this is my own brain.

- There's no algorithm here. That means favoriting/liking doesn't do anything except communicate approval to the OP and others (which is still nice!).

- No algorithm means boosting ("retweeting") is the true method to increase a post's visibility. Do that more than you did on birdsite.

- There's no post-quoting here, and that's by design. Look at quote-tweets on the birdsite; it's a feature primarily used for toxicity.

- There's no direct word-search here either; that means you want to use hashtags to make posts more searchable. This is also intended, since word-searching posts was often used to harass/stalk on the birdsite and elsewhere, so that was left by the wayside here. This also means hashtags are much more a thing here than any of the algorithm-powered sites.

- It's encouraged to put in text descriptions when you post images; a lot of Mastodon users use screen-readers due to various disabilities, and getting an image description read out loud helps them immensely.

- Speaking of screen-readers: using capitalization in your hashtags allows the screen-readers to read them more easily, especially if you're smashing multiple words together. #rockmusic = unreadable. #RockMusic = readable.

- The best way to make threads is to make set your first post as public, but "unlist" all of your replies. This prevents your whole thread from clogging up feeds.

- Content Warnings should be used more liberally here. If you haven't gotten the impression yet, much of Mastodon was built and populated by marginalized groups who were harassed/bullied off of other platforms. This is the culture they built, to respect each other's mental health. It's not a rule, but it's well-appreciated.

- Consider chipping a few bucks towards whomever runs the server you're on; the strain is real, and most server admins were likely paying out of pocket before so don't have an existing donation base. The growth here has been extremely fast, and that means money's needed.

- DMs are just posts with privacy settings. So if you @ someone in a DM, you pull them into the thread. That could be embarrassing.

- Also, no, DMs aren't end-to-end encrypted, but they aren't on Twitter either. Don't use either if you want true privacy.

- Including your Mastodon handle in your birdsite profile will help people find you here; there's a tool (pruvisto.org/debirdify/ is one of them that's used) people can use to pull Mastodon handles from Twitter profile.

- Use the blocking and reporting features liberally, if needed. This should go without saying, but they work, and work well!

- If there's an entire Mastodon server you don't want to hear from, you can block the whole thing too.

- Preferences -> Appearance -> "Slow Mode": this can make larger "Local" feeds and any "Federated" feed much more readable.

I'll reply with some more as I see them, or reply here too. I've only been here 4 days but I'm loving it so far.

Early adopter?

The Donnelly Centre @ University of Toronto is hiring 3 (❗) tenure-track positions in computational biology & functional #genomics.

Learn more about the positions & how to apply here: bit.ly/DonnellyRecruitment2022

Applications close January 16, 2023.
#bioinformatics #job

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