Wei Shen 沈 伟
@shenwei356
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Associate professor of Bioinformatics at Chongqing Medical University, China. Lab: https://t.co/67yy7iIrgx Personal: https://t.co/E5GOnSMIRW https://t.co/mXnnqslpi1
Chongqing, China
Joined November 2013
Excited to share this collaborative work with @ZaminIqbal ! We're thrilled about the potential impact LexicMap could have on advancing microbial genomics research! . Imagine how cool it is to search for a gene (with >30k hits) against 2 million bacterial genomes within 1 minute!.
Great pleasure to work with @shenwei356 on a new indexing and alignment scheme, called LexicMap:.We have been working on uniformly reassembling, QC-ing and annotating all bacterial (+ now archaeal) data, & wanted to be able to do full alignment to it. .
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RT @jim_elevator: skani v0.3.0 is released. * 30-40% potential reduction in memory .* Breaking changes to indexing….
github.com
Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs. - bluenote-1577/skani
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Yes, I just recommended it to my students.
is shaping up to becoming one of the absolute top resources for learning hands on #bioinformatics and #genomics today!.
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RT @RayanChikhi: Slides from my talk (with Kamil Jaron) on an history of k-mers in bioinformatics:
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RT @nomad421: This seems like an awesome course! If there were more hours in the day, I'd want to put something l….
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Also updated .- taxid-changelog to May, 2025 - gtdb-taxdump to GTDB r226 - ictv-taxdump to VMR_MSL40
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TaxonKit v0.20.0 is adapted to recent rank changes in NCBI Taxonomy.
github.com
Changes TaxonKit v0.20.0 This version is mainly for maintaining compatibility with NCBI's recent changes(1, 2). Please remove the ranks.txt file in ~/.taxonkit/ or other directories containi...
Updates coming to #NCBITaxonomy! We are introducing two new ranks, domain and realm, and discontinuing the rank superkingdom. Learn more:
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⚡️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
v0.7.0 - 2025-04-11 Please rebuild the index, as some seeds in the genome end regions were missed during computation. lexicmap index: Fix a little bug in seed desert filling -- forgot to fill the...
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RT @KarelBrinda: A decade ago, we had thousands of bacterial genomes. Now, we have millions. How to scale computational methods?. Our paper….
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RT @baym: Thrilled that our work on this problem with @KarelBrinda, @ZaminIqbal, and others is out in @naturemethods today! . We used phylo….
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RT @krsahlin: As for my project (Project 1 in the list), please help spread the word to students interested in doing a PhD in Computational….
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🚀 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:
github.com
v0.6.0 - 2025-03-25 This version is compatible with indexes created by previous versions (requires a one-time, automatic preprocessing), but rebuilding the index is recommended for more accurate re...
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Thrilled to finally debut my lab site 🎉: — which stands for Microbial Bioinformatics, a domain I purchased 9 years ago and has been waiting for this moment ever since!"
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Bacteriophage protein Dap2 inhibits bacterial type III secretion system and synergizes with Dap1 to evade anti-phage immunity
biorxiv.org
The evolutionary arms race between bacterial immunity and phages has driven the emergence of sophisticated anti-defense systems (ADSs). However, certain ADSs exhibit incomplete suppression of their...
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Just updated seqkit, csvtk, taxonkit, and rush. Click to see changes:.- - - -
github.com
rush v0.6.1 Fix issue with stopping orphan children. #69 by @bburgin When the field index is larger than the number of fields, do not replace it with the last field as before. #68
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RT @IgorMartayan: I'm glad to announce that the simd-minimizers library is out!.@curious_coding and I have been optimizing the computation….
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RT @curious_coding: I did a project on making an optimized implementation of the S+ tree. The result is 40x speedup over plain binary searc….
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