Xian Chang

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...

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

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...

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