@santiagomarco.bsky.social you def need to guide agents to do your bidding. "in rust" too lol

SMBE2026 Symposium 21 | From genomic graphs to evolutionary insights: standardising pangenomes for population inference Organisers - Robert Waterhouse — SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland (Male) - Chiara Bortoluzzi - SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland (Female) - Tristan Cumer — Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland (Male) - Landen Gozashti — Department of Integrative Biology, University of California Berkeley, Berkeley, USA (Male) Invited Speaker - Erik Garrison — University of Tennessee Health Science Center, United States of America (Male)

Organisers
- @rmwaterhouse.bsky.social | @sib.swiss
- Chiara Bortoluzzi | @sib.swiss
- Tristan Cumer | University of Lausanne
- Landen Gozashti | UC Berkeley

Invited Speaker
- @thinks.lol | University of Tennessee Health Science Center

great analysis! the increase in run length is more than I expected but it makes perfect sense! fwiw HPRCv2 is recently released. not sure that citing Liao 2023 is correct, it might cause confusion

who is presenting?

Matrix.org Matrix, the open protocol for secure decentralised communications

Right, matrix.org is back online as of 17:00 UTC. The server is struggling a bit as it catches up. Huge apologies again for the outage; postmortem + ways to avoid a repeat will be forthcoming. See also www.theregister.com/2025/09/03/m... & www.heise.de/en/news/Matr.... Thanks all for your patience.

Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!

Memphis

We've had a wonderful series of pangenome meetings in Memphis. Join us for the next edition in May!

Memory makes computation universal, remember? thinks.lol/2025/01/what...

Excited to get DRAGEN from Illumina out in Nature Biotechnology: www.nature.com/articles/s41...

Graph genome based detection of SNV, STR, SV, CNV all in 30 min! Improvements in all variants classes. Plus we worked on how to merge and combine variant classes making it easier to study them!

This is an invitation. If you think that this is a way to operate, let me know. Let's start a group chat and see what happens.

I'm willing to bet that that kind of environment doesn't look a whole lot like Blue Sky or Twitter, where you have only 300 characters to say what you mean to say. What you realize when you start speaking to type is that that can be filled in seconds.

But where are people practicing together, not just alone talking with machines or using this as a faster way to type, but really in a group setting where people are encouraged to speak their mind without adulteration and to directly flow their thoughts into a collective consciousness.

We can put our thoughts into words in a dynamic flow, and it's also something you can learn to do better. It's not something we're practicing as much now because we sub-vocalize ideas into text using our fingers, and then we go back and edit them.

It's not just the raw words per minute of the typing versus speaking that matters. It's that we're dramatically better at speaking. It is what we've evolved to do for millions of years.

The biggest problem in my experience is that actually the recipients have trouble parsing what's been said because so much can be said so quickly like dramatically faster than you can write

You could set this up a few ways. You could have a group chat where, by convention, people are behaving this way. Or you could have a kind of application that makes it seamless for the user to do this.

I'm really fascinated by the dynamics that might arise in a group chat or asynchronous messaging system where everyone is encouraged to use speech-to-text and to do minimal correction of what they write.

Speech to text is the most efficient way to communicate, but you have to learn how to do it, just like you learn how to touch type or tap on your phone. And it's not just writing, but reading that we have to learn how to do, because we're not used to reading speech-to-text transcriptions.

Schematic of Robertsonian chromosome formation

FISH image and schematic of a complete Robertsonian chromosome

"The formation and propagation of human Robertsonian chromosomes" ROBs are the most common translocation in humans, approx. ~1 per 800 people. Last year we proposed a simple mechanism for ROB formation; This year we prove it by finishing some T2T! New preprint: www.biorxiv.org/content/10.1...

There's a lot of talk about not having enough resources for science. The journals are eating them. What are they giving back to the scientific community? Is it enough to justify the cost?

The journals' propositions are becoming inappropriate. They say, "For only four months of PhD stipend, you can publish a paper that everyone can read for free online." That's something that we can do without them---If we can agree to break with their brand signaling.

It's a very hard social problem. The political and brand power of major scientific journals is overwhelming. But maybe a solid majority of us are fed up.

It will take collective action by scientists. It is possible if enough of us agree that publishers' margins indicate something very wrong and parasitic is going on.

We can end all of this. It's time for a completely open publication system. Like a preprint server, but with reviews. A system supporting these two things at once is a journal. At least, it replaces a journal with something better.

@timtriche.bsky.social so this really is a public forum. No DMs. Fun

Unraveling the Mysteries Of The Y Chromosome Assembling the complete sequence of the Y chromosome is an important step toward understanding the human genome.

Kateryna Makova and I were excited to be guests on Science Friday to discuss the Y chromosome. Congrats to the amazing @arhie.bsky.social, Sergey Nurk, and others on completing this last unfinished chromosome! Tune in here if you’re curious about ChrY: www.sciencefriday.com/segments/y-c...

We are already using this at scale to build an all-to-all homology map for the vegetate genomes project 290 genome set! It let us find similarities at down to 70% ANI in "only" ~200k CPU hours. Was totally impossible with minimizer mashmap

"Minmers are a generalization of minimizers that enable unbiased local jaccard estimation" aka MashMap3 with Bryce Kille, @erikg.bsky.social, and @treangen.bsky.social is now accepted in Bioinformatics! Many thanks to the reviewers for their very careful reviews doi.org/10.1093/bioi...

Hello! Happy to join