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Life update: just started a postdoc with Heng Li at Dana-Farber Data Science/Harvard DBMI. Let me know if you wanna talk bioinformatics around Boston the next year :)

Published in 2009, bwa-aln is one of the oldest short-read aligners. It remains a popular choice for aligning ancient DNA reads. The following blog post explains the algorithmic reasons. lh3.github.io/2024/09/28/why…

A new paper from our amazing Ondřej Sladký (jointly supervised with Pavel Veselý) on super space-efficient indexing of arbitrary k-mer sets, introducing the Masked Burrows-Wheeler Transform (MBWT).

I gave a talk recently at Ben Langmead's group on my post on fast computation of random minimizers. Was super fun! Blogpost: curiouscoding.nl/posts/fast-min… Recording: curiouscoding.nl/talks/minimize…

Just tried Sylph github.com/bluenote-1577/… by Jim Shaw. Processed >2000 samples in a few hours on google cloud powered by Terra. Roughly 15min per sample. Briefly checked the abundances and they match pretty well with what we got using an independent workflow.

Happy to see our method for T2T genome assembly published! It addresses an important limitation of string graph, that is, the contained reads. Led by Sudhanva Kamath "Telomere-to-telomere assembly by preserving contained reads" doi.org/10.1101/gr.279…

Hifiasm 0.21.0 has been released. It now has a beta module for direct assembly of ONT R10 simplex reads. Initial tests with regular simplex reads show very promising results! github.com/chhylp123/hifi…

Tech Alert! 🚀🧬 We can now determine the sequence of DNA with non-canonical bases in a direct and high-throughput manner with Nanopore sequencing. Check out our preprint for details: biorxiv.org/content/10.110…

GASTON, our method to learn “topographic maps” of gene expression, is out now Nature Methods! IMO the coolest part is a new model of *spatial gradients in sparse data*. As is typical for bio papers, it’s buried in Methods, but see below for a quick outline on the math 👇

NENG HUANG developed longcallR for joint SNP calling and phasing from long RNA-seq reads, AND for identifying allele-specific splicing/junctions (ASJ). Although ASJs of statistical significance are rare, a large fraction involve unannotated junctions. In Rust!

New life update! 🎆 🎓 This Fall, I will be joining the Department of Computer Science at Johns Hopkins University (JHU Computer Science) as an Assistant Professor, with an affiliation at the new Data Science and AI Institute (Johns Hopkins Data Science and AI Institute).

Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment. arxiv.org/abs/2506.12986

I'm excited to share that I will soon join UCLA's Bioengineering department as an Assistant Professor. I am incredibly fortunate to have landed my dream job in this current atmosphere, and I would like to thank my mentors, colleagues, and friends for their support.