We built the first complete genome for the common marmoset, fully resolving regions that were previously missing: centromeres, acrocentric short arms, and more. A new reference genome for anyone working with marmosets. This was an awesome collaborative effort & I’m grateful to all my co-authors! 🧬
I wrote this song on Saturday, recorded it yesterday and released it to you today in response to the state terror being visited on the city of Minneapolis. It’s dedicated to the people of Minneapolis, our innocent immigrant neighbors and in memory of Alex Pretti and Renee Good.
Stay free
Today, The New York Times published a guest essay by former federal judges Shira A. Scheindlin and John E. Jones III, introducing a new Keep Our Republic initiative: The Principles on Preserving the Independence of the Legal Profession.
Read more here:
www.nytimes.com/2026/01/19/o...
I've joined @keepourrepublic.bsky.social
to work on defending the independence of the Legal Profession. The NYT published our guest essay today: nyti.ms/4bMkVC2
For attorneys: endorse and help here: keepourrepublic.org/what-we-do/i...
I've added 7 videos to my Burrows-Wheeler indexing playlist (www.youtube.com/playlist?lis...), rounding out the r-index series and adding a 5-part series on the move structure. Now 27 videos in that playlist. I aim to add videos on prefix-free parsing, PBWT, Wheeler languages/automata in the future.
@acarroll.bsky.social @kishwar.bsky.social Pi-Chuan Chang, Faith Okamoto, @humanpangenome.bsky.social
Big thanks to everyone involved in the paper! @benedictpaten.bsky.social @adamnovak.graphs.vg Jordan Eizenga @jltsiren.bsky.social @jmonlong.bsky.social @shlokanegi.bsky.social Francesco
Andreace @sagorika03.bsky.social @kokyriakidis.bsky.social Glenn Hickey, Stephen Hwang, Emmanuele Delot
A cartoon of a variation graph and a sequencing read with seed alignments between the read and graph. The snarl tree corresponding to the variation graph is shown to the right. Below is the zip code tree representing the seeds, snarl and chain boundaries, and the distances among them.
My favorite part: co-linear chaining in cyclic graphs using zip code trees, a new data structure for quickly finding distances in the graph that best match corresponding distances in the read
Also featuring a cool demo of pangenome-guided regional assembly of complex loci from @shlokanegi.bsky.social Francesco Andreace @sagorika03.bsky.social @kokyriakidis.bsky.social
🦒Long read giraffe is out!🦒
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Republicans are shutting down the government to stop you from having healthcare—there’s the message!!!!
Last talk of the day (before posters) "Lossless Pangenome Indexing Using Tag Arrays" presented by Parsa Eskandar! #WABI25
Thanks so much!
Huge thank you to my incredible advisor @benedictpaten.bsky.social at @ucscgenomics.bsky.social for all his support and guidance, and to my committee David Haussler, @russcd.bsky.social, and @jianma.bsky.social
I'm very excited to share that I defended my thesis this week! I helped develop algorithms to combat reference #bias and make genomics more #equitable and #representative by incorporating genetic #diversity into genomics pipelines
We use personalized references with our Giraffe aligner. Each chromosome is partitioned into a sequence of blocks. We sample the most relevant haplotypes in each block using kmer counts. Mapping to this personalized reference improves variant calling accuracy. www.nature.com/articles/s41...
Welcome to the Bluesky account for Stand Up for Science 2025!
Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide!
#scienceforall #sciencenotsilence
Variation graph representing the names of long read pangenome mappers: MiniGraph, GraphChainer, GraphAligner, PanAligner, and Giraffe
New figure for my thesis showing why Giraffe is the best long read pangenome mapper. No further evidence will be provided.
Quote: Long read sequencing is likely the next best test for unsolved cases... It can serve as a single diagnostic test, reducing the need for multiple clinical visits and transforming a years-long diagnostic journey into a matter of hours. Shloka Negi, UC Santa Cruz
Researchers at @ucsantacruz.bsky.social have demonstrated how long-read sequencing could improve detection of diseases that have eluded diagnosis, at a fraction of the cost. New clinical tests could be on the way.
🗞 news.ucsc.edu/2025/01/pate...
👏🏼👏🏿👏🏾 @khmiga.bsky.social @benedictpaten.bsky.social