Every year, I need my annual hit of this www.tiktok.com/@fashiongirl...

If you tell people a simplified story that conforms to their biases and preferences, and ignores important facts and critical complexities, and they'll believe and parrot it regardless of its accuracy. This seems true across so many areas; a true failure mode of human cognition.

Meet the keynote speakers for the 2025 scverse conference! Elham Azizi, Associate Professor of Cancer Data Research and Biomedical Engineering at Columbia University 🧵 @elhamazizi.bsky.social @columbiauniversity.bsky.social #scverse #scverse2025 #machinelearning #genomics #cancerimmunology

Fantastic talk by @vikramshivakumar.bsky.social Mumemto—Scalable multi-MUM finding for pangenomes Papers biorxiv.org/content/10.1101/2025.05.20.654611 & doi.org/10.1186/s13059-025-03644-0 Code: github.com/vikshiv/mume... Very efficient pangenome visualization tool, revealing synteny and variations!

Man; @typst.app is so good! That's all; that's the skeet.

#GI2025 is about to start. I hope you'll enjoy this edition!

I don't find it surprising at all. Historically, this is perfectly in line with what you'd expect. Political takeover, followed by erasure of legal protections and civil liberties and capture of the media. This is how hostile ends to civil governments play out, again and again.

They're laying it on thick, huh?

Let's go Bills!

Also @robp.bsky.social 's work spotted in a museum already :o things deprecate so fast

Our soon-to-be Surgeon General has some unscientific views. I have some thoughts about that... open.substack.com/pub/stevensa...

Funders have decided to execute US science (and even much of tech) development. I don't think it's reasonable to argue the knowledge gap here. The destruction is intentional.

My algorithmic friends (@camillemrcht.bsky.social) doing LLM stuff : www.biorxiv.org/content/10.1...! And also, screaming last names in the author list ;P. Given my level of trust in Camille, though, perhaps it's time for me to engage more seriously with these models in research...

This framing is a bit problematic I think, b/c the main thesis is incomplete. Parsing touches on both linguistics & math (& a particularly mathematical part of linguistics). But, what you use programming FOR (i.e. algorithms) is absolutely math, as is the theory of computation & a lot of compilers.

Following ish's `filter` and bqtools' `grep`, Sassy now also has initial support for grep and filter! Grep mode shows all matches, grouped per record, and is meant for human consumption. Filter mode prints full matching (or non-matching) records to stdout or output files.

Huge congratulations to Steven Tan, a superb undergraduate junior at JHU CS whose first-author paper "Movi Color: fast and accurate taxonomic classification with the move structure" won best paper at ACM-BCB. Please check it out: www.biorxiv.org/content/10.1.... Congrats, Steven!!

Many people do not know that Dante's inferno originally had 10 circles of hell. The 10th level was reserved for people writing "clever" but error prone code. In the 10th circle, you have to programm C++ against a changing standard that a hostile committee updates every 3 hours!

Our department (Comp Sci) at UMD is hiring this cycle. We have an open-rank search (umd.wd1.myworkdayjobs.com/en-US/UMCP/j...). Consider applying to join our department; we’re a pretty cool group if I say so myself ☺️!

Yes, but pay attention to what, exactly? Nothing here is being done in secret. What is being done since January is the illegal, unapologetic, un-American, wanton destruction of the American republic. Not just its social contract, but even its strategic advantages. It's national seppuku.

Damn; it is so fun to watch the Ravens when they are doing well and firing on all cylinders. Will this be a Jackson 5 evening?

IMO, the biggest implication here should be for legal challenges to AI companies. This demonstrates that they should *not* fall under fair use exemptions to copyright. They are not akin to a human reading the content, they are akin to copying the content! www.arxiv.org/abs/2510.15511

IMO, the biggest implication here should be for legal challenges to AI companies. This demonstrates that they should *not* fall under fair use exemptions to copyright. They are not akin to a human reading the content, they are akin to copying the content.

I mean, to be clear, hunger and poverty are also not "existential threats" to humanity as a species, just the root of immeasurable suffering for a huge number of people (as climate change will be). futurism.com/science-ener...

So Netflix is considering a Crash Bandicoot series?! Honestly, if there is another videogame to series conversion, I'd want to see the Ghost series (Tsushima & Yoeti). I think they would make a great series. collider.com/last-of-us-c...

End qualified immunity.

Do I have any @typst.app folks in my bsky sphere? If so, I'm trying to figure out how to generate an outline for a document where only headings having a specific label are included. For example, imagine I have a label <in-outline>; how can I just collect only these for inclusion in the ToC?

This is some very neat foundational work on suffix array limits and the relationship to prefix range queries! arxiv.org/pdf/2510.19815

As a Ravens fan, I am looking forward to our crushing and embarrassing loss to the Bears this afternoon as we continue to fail to score points in the absence of a single player from the team...

I've been around long enough & seen enough attempts to form the opinion that all metrics that attempt to summarize scientific productivity as a number are bad. Not just in practice, but conceptually fawed. They incentivize faculty to take shortcuts where they shouldn't, in peer evaluation.

Hilariously bad idea. In my subfield author lists are almost always alphabetical!

Ok, clarification. UCLA has not agreed to these terms. Rather, this is ongoing "negotiations" that they are "considering". They should not enter into any negation with an administraton where these are the demands. The demands are absurd. UCLA should walk away and face the administration in court.

This is *shocking*. The fact that UCLA agreed to this raises many questions and concerns. Apart from the obvious ones (why would you agree to this?!), it also makes one wonder why!? Fighting this seems like it would be cheaper unless they were engaging in *actually illegal* discrimination practices.

The description of pthash as "academic" but not practical is outrageous! news.ycombinator.com/item?id=4569.... It demonstrates, on the part of the poster, a complete ignorance of the idea and purpose of MPHFs as well as an immense ignorance of the actual implementation they are mentioning.

Because Ghost of Yoeti is a phenomenal game! Phenomenal. Period. End of sentence. search.app/ThkTL

Really exciting that the preprint on Barbell, a new demultiplexer, is finally out! It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.

Barbell Resolves Demultiplexing and Trimming Issues in Nanopore Data doi.org/10.1101/2025...

Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it: www.biorxiv.org/content/10.1... Want to get started? github.com/rickbeeloo/b...

Barbell Resolves Demultiplexing and Trimming Issues in Nanopore Data https://www.biorxiv.org/content/10.1101/2025.10.22.683865v1

1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...

San Diego is pretty nice 🙂!

Movi 2: Fast and Space-Efficient Queries on Pangenomes. #Pangenomes #SequenceQueries #Genomics #Bioinformatics @biorxiv-genomic.bsky.social 🧬 🖥️ www.biorxiv.org/content/10.1...

I'm low-key excited for the term "DNS resolution" to enter the broader public vernacular. I just wish it had a more positive association...

I find this conference where both the submissions and reviews are AI generated at least a bit distressing. Also, it would seem state of the art generative models still can’t solve the LaTeX formatting problem 😜 agents4science.stanford.edu

"That they see as authoritarian"? No, his actions are unequivocally authoritarian...

Ohh no; will they have to stop making constitutionally braindead decisions that defy logic and precedent? search.app/jGRD3

If you were a foreign adversary nation directing the coordinated downfall of the US, this is basically exactly what it would look like.

UVA rejects the compact. www.vpm.org/news/2025-10...

F*ing SalesForce. They call it SalesForce because you are *forced* to use their software. We use this software for PhD admissions at UMD and it sucks! Waaay worse than the software cooked up by one of our own faculty (alone) like a dozen years ago (which the Uni forced us to drop).