Remember the current NIH director going on about protecting researchers from government censorship? Today his people called the police in to forcibly remove my colleagues from their own society meeting for sharing an editorial published in their flagship journal that was critical of him. Gift link

Police Remove Diabetes Experts From Conference for Distributing Critique of Trump Administration

nytimes.com

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! 🧬

bioRxiv Genomics@biorxiv-genomic.bsky.social · 7mo ago

A Complete Genome for the Common Marmoset https://www.biorxiv.org/content/10.64898/2026.03.25.713844v1

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

Bruce Springsteen - Streets Of Minneapolis (Official Audio)

YouTube video by Bruce Springsteen

youtu.be

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...

Opinion | How the American Legal Profession Can Regain Its Dignity

nytimes.com

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.

Burrows-Wheeler Indexing - YouTube

Videos on : (a) the Burrows-Wheeler Transform (BWT), (b) the FM Index, which uses the BWT to construct a full-text index, (c) Wheeler graphs, (d) r-index, an...

youtube.com

🦒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

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · last yr.

Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe https://www.biorxiv.org/content/10.1101/2025.09.29.678807v1

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

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...

Personalized pangenome references - Nature Methods

This work introduces a k-mer-based approach to customizing a pangenome reference, making it more relevant to a new sample of interest. This method enhances the accuracy of genotyping small variants an...

nature.com

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

New figure for my thesis showing why Giraffe is the best long read pangenome mapper. No further evidence will be provided.

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