Erik Garrison
@thinks.lol
computational biologist: genomes, evolution, DNA
Reposted by Erik Garrison
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
September 3, 2025 at 5:41 PM
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!
July 17, 2025 at 7:53 AM
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!
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
February 25, 2025 at 7:35 AM
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...
January 22, 2025 at 3:17 PM
Memory makes computation universal, remember? thinks.lol/2025/01/what...
Reposted by Erik Garrison
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!
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!
October 25, 2024 at 1:34 PM
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!
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.
November 8, 2024 at 3:24 PM
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
"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...
September 27, 2024 at 2:15 PM
"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
September 15, 2023 at 3:48 PM
@timtriche.bsky.social so this really is a public forum. No DMs. Fun
Reposted by Erik Garrison
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
September 13, 2023 at 2:32 PM
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...
September 12, 2023 at 7:48 PM
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
Reposted by Erik Garrison
"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...
September 12, 2023 at 7:43 PM
"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...