Erik Garrison
@thinks.lol
computational biologist: genomes, evolution, DNA
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...
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
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, the open protocol for secure decentralised communications
matrix.org
Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!
We've had a wonderful series of pangenome meetings in Memphis. Join us for the next edition in May!
Andrea Guarracino@andreaguarracino.bsky.social · last yr.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
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!
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.
"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...
@timtriche.bsky.social so this really is a public forum. No DMs. Fun
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.
sciencefriday.com
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 · 3y ago"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...
"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...