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This is how mass hysteria spreads. A media outlet betraying the trust of their viewers by sharing an out of focus light in the sky and presenting it as a UAP, which then gets amplified by people who trust them. This is exactly what Venus looks like when it’s not quite in focus.

The story behind Sylph, from Jim Shaw . It's quite inspiring to read. jim-shaw-bluenote.github.io/blog/2024/deve…

I did a project on making an optimized implementation of the S+ tree. The result is 40x speedup over plain binary search! It builds on Algorithmica's post on S-trees and the famous paper "Array layouts for comparison based searching" by Paul Khuong ([email protected]). 🧵 curiouscoding.nl/posts/static-s…

I'm glad to announce that the simd-minimizers library is out! Ragnar {Groot Koerkamp} 🦋 and I have been optimizing the computation of minimizers down to the smallest detail. The result is an order of magnitude faster than existing methods ; processing an entire human genome takes only 4s!

x.com/i/article/1898…

Just updated seqkit, csvtk, taxonkit, and rush. Click to see changes: - github.com/shenwei356/seq… - github.com/shenwei356/tax… - github.com/shenwei356/csv… - github.com/shenwei356/rus…

Bacteriophage protein Dap2 inhibits bacterial type III secretion system and synergizes with Dap1 to evade anti-phage immunity biorxiv.org/content/10.110…

🚀 ​LexicMap v0.6.0 is released! ✅ ​More accurate alignments! 🎯 ​Higher sensitivity for short queries (>100bp)! 💡 ​Denser seeds, same index size! 🔬 Function: Efficient seq alignment in millions of prokaryotic genomes! 📖 Docs: bioinf.shenwei.me/LexicMap github.com/shenwei356/Lex…

As for my project (Project 1 in the list), please help spread the word to students interested in doing a PhD in Computational Biology/Bioinformatics. Note that PhD students here are employed with a salary, that the position comes with benefits, and that there are no tuition fees

Thrilled that our work on this problem with Karel Břinda, Zamin Iqbal, and others is out in Nature Methods today! We used phylogenetic compression (described in the thread) to compress every microbe ever sequenced onto a flash drive so that it can be searched with a laptop!

A decade ago, we had thousands of bacterial genomes. Now, we have millions. How to scale computational methods? Our paper in Nature Methods answers this: use evolutionary history to guide compression and search. …From terabytes to tens of GBs… w/@Baym Zamin Iqbal et al. 🧵1/

⚡️LexicMap v0.7.0 fixed a minor bug in index building and improved the alignment accuracy! Please rebuild the existing index. Sorry for the inconvenience. 🥹 github.com/shenwei356/Lex…