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Erik Garrison

@thinks.lol

2.3K followers 61 following 21 posts

computational biologist: genomes, evolution, DNA

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Reposted by Erik Garrison

The Matrix.org Foundation @matrix.org · Sep 3

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.

Matrix, the open protocol for secure decentralised communications

Erik Garrison @thinks.lol · Jul 17

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

Erik Garrison @thinks.lol · Feb 25

Memphis

Erik Garrison @thinks.lol · Feb 25

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

Andrea Guarracino @andreaguarracino.bsky.social · Feb 24

Want to level up in #pangenomics? Join our workshop, conference & biohackathon in #Memphis, May 11-15, 2025. Connect with leading scientists, embrace genomic diversity, and contribute to cutting-edge software. Register now! pangenome.github.io/MemPanG25/ #Bioinformatics #MemPanG25

Erik Garrison @thinks.lol · Jan 22

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

Reposted by Erik Garrison

Fritz Sedlazeck @sedlazeck.bsky.social · Oct 25

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!

Erik Garrison @thinks.lol · Nov 8

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.

Erik Garrison @thinks.lol · Nov 8

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.

Erik Garrison @thinks.lol · Nov 8

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.

Erik Garrison @thinks.lol · Nov 8

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.

Erik Garrison @thinks.lol · Nov 8

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.

Erik Garrison @thinks.lol · Nov 8

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

Erik Garrison @thinks.lol · Nov 8

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.

Erik Garrison @thinks.lol · Nov 8

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.

Erik Garrison @thinks.lol · Nov 8

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.

Reposted by Erik Garrison

Adam Phillippy @aphillippy.bsky.social · Sep 27

"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...

Schematic of Robertsonian chromosome formation

FISH image and schematic of a complete Robertsonian chromosome

Erik Garrison @thinks.lol · Oct 23

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?

Erik Garrison @thinks.lol · Oct 23

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.

Erik Garrison @thinks.lol · Oct 23

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.

Erik Garrison @thinks.lol · Oct 23

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.

Erik Garrison @thinks.lol · Oct 23

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.

Erik Garrison @thinks.lol · Sep 15

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

Reposted by Erik Garrison

Adam Phillippy @aphillippy.bsky.social · Sep 13

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...

Unraveling the Mysteries Of The Y Chromosome

Assembling the complete sequence of the Y chromosome is an important step toward understanding the human genome.

www.sciencefriday.com

Erik Garrison @thinks.lol · Sep 12

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

Adam Phillippy @aphillippy.bsky.social · Sep 12

"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...

Reposted by Erik Garrison

Adam Phillippy @aphillippy.bsky.social · Sep 12

"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...