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Erik Garrison

@thinks.lol
2.4K followers 73 following 30 posts

computational biologist: genomes, evolution, DNA

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Reposted by Erik Garrison
Alex Crits-Christoph @acritschristoph.bsky.social · 06/08/2026
see also this work, which helps provide some helpful framing of how novel these phages are: www.biorxiv.org/content/10.6... tl;dr: I believe this work generates only marginally novel phages, which have only a moderate likelihood of working, that decreases the more novel they get.
biorxiv.org
Quantifying evolutionary novelty and design efficiency in generative genome design
Generative genome design models can now produce previously unobserved genome-length sequences, but assessing their capabilities is complicated by limitations in functional prediction. The ability to e...
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Rob Edwards @linsalrob.bsky.social · 06/08/2026
This is a much more impressive reimagination of phiX174, which, alas, didn't get an NYTimes article about it because of, well, the other used AI. www.biorxiv.org/content/10.6...
biorxiv.org
Complete Mutagenesis of the Genome and Proteome of ΦX174
The bacteriophage ΦX174 was the first genome to be sequenced and the first to be chemically synthesised. Here we present a complete map of the consequences of changing every nucleotide in the ΦX174 ge...
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Erik Garrison @thinks.lol · 17/06/2026
seqwish is now implemented in rust! github.com/pangenome/se... github.com/pangenome/se...
github.com
GitHub - pangenome/seqwish: alignment to variation graph inducer
alignment to variation graph inducer. Contribute to pangenome/seqwish development by creating an account on GitHub.
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Erik Garrison @thinks.lol · 11/06/2026
@edzitron.com next level safety
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Erik Garrison @thinks.lol · 11/06/2026
biology = bad. thanks for saving me from myself @anthropic.com !
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Erik Garrison @thinks.lol · 15/05/2026
new jam: don't just test, but prove algorithms by writing them in lean4, then porting to rust. example: overlap graph bluntifier for dbg/syncmer graphs to variation graphs github.com/pangenome/bl...
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Reposted by Erik Garrison
Society for Molecular Biology and Evolution @official-smbe.bsky.social · 16/12/2025
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
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)
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The Matrix.org Foundation @matrix.org · 03/09/2025
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.org
Matrix.org
Matrix, the open protocol for secure decentralised communications
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Erik Garrison @thinks.lol · 17/07/2025
Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!
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Erik Garrison @thinks.lol · 25/02/2025
We've had a wonderful series of pangenome meetings in Memphis. Join us for the next edition in May!
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Erik Garrison @thinks.lol · 22/01/2025
Memory makes computation universal, remember? thinks.lol/2025/01/what...
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Fritz Sedlazeck @sedlazeck.bsky.social · 25/10/2024
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!
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Erik Garrison @thinks.lol · 08/11/2024
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.
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Reposted by Erik Garrison
Adam Phillippy @aphillippy.bsky.social · 27/09/2024
"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 formationFISH image and schematic of a complete Robertsonian chromosome
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Erik Garrison @thinks.lol · 15/09/2023
@timtriche.bsky.social so this really is a public forum. No DMs. Fun
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Adam Phillippy @aphillippy.bsky.social · 13/09/2023
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...
sciencefriday.com
Unraveling the Mysteries Of The Y Chromosome
Assembling the complete sequence of the Y chromosome is an important step toward understanding the human genome.
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Erik Garrison @thinks.lol · 12/09/2023
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
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Reposted by Erik Garrison
Adam Phillippy @aphillippy.bsky.social · 12/09/2023
"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...
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