@shenwei356
Joined November 2013
  • Tweets1.5K
  • Following1.1K
  • Followers1.6K
72Media
Wei Shen retweeted
Ben WoOdcroft@wwoodMay 27
Sandpiper 2 is up. 913,000 metagenomic community profiles w GTDB R232 via SingleM, 200k more than 1.0. sandpiper.qut.edu.au GlobDB coming. Thanks to @aroney_samuel @IAmTotesBrett Josh Mitchell and especially the new kid @StefanHerh
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I prefer rewritting some interesting packages by hands, which helps understanding the algorithm.
Heng Li@lh3lh3Apr 17
Blog post on "The AI Rewrite Dilemma": lh3.github.io/2026/04/17/the…
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10 years after the first FAMSA paper, its successor is now published in Nat Biotech! We believe that FAMSA2 can enable analyses of large protein collections that were previously unattainable. Thank you, @a_zielezinski and @cnotred, for great collaboration nature.com/articles/s41587-0…

Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2

Nature Biotechnology - FAMSA2 accurately aligns millions of protein sequences at high speed.

nature.com
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High-resolution metagenome assembly for modern long reads with myloasm - @lh3lh3 go.nature.com/3PBEwvR
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Clustering proteins using DIAMOND is out now @naturemethods nature.com/articles/s41592-0…

Clustering the protein universe of life using DIAMOND DeepClust

Nature Methods - DIAMOND DeepClust provides an ultra-fast clustering method for organizing the protein universe of life at low sequence identity, enabling large-scale dimensionality reduction and...

nature.com
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Wei Shen retweeted
Stephen Turner@strnrMar 15
Sassy2: Batch Searching of Short DNA Patterns biorxiv.org/content/10.64898… 🧬💻🧪 github.com/RagnarGrootKoerka…
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LexicMap v0.9.0 has been released with - a few bug fixes: CIGAR, bitscore and evalue calculation. - new features: better support for big genomes like human. - a new command to convert output to SAM format github.com/shenwei356/LexicM…

Release LexicMap v0.9.0 · shenwei356/LexicMap

v0.9.0 - 2026-03-13 New commands: lexicmap utils 2sam: Convert the default search output to SAM format (#26). Attention: This command requires search results generated by the current LexicMap ver...

github.com
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I was pleased to give an interview to @RadioPrague about my academic journey across Czechia, France, and the United States, and about my research. english.radio.cz/karel-brind…

Karel Břinda on research at Harvard and working with bacteria as if

Karel Břinda sheds light on how curiosity, mobility, and interdisciplinarity can shape a modern researcher’s path in a world where science increasingly transcends borders.

english.radio.cz
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1/ Our paper on Multi-Context Seeds is now out. We introduce a new seeding concept that improves read alignment accuracy while maintaining speed. link.springer.com/article/10…

Multi-context seeds enable fast and high-accuracy read mapping

Genome Biology - A key step in sequence similarity search is to identify shared seeds between a query and a reference sequence. A well-known tradeoff is that longer seeds offer fast searches but...

link.springer.com
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Wei Shen retweeted
Lior Pachter@lpachterMar 6
kallisto sped up RNA-seq quantification by 50x. Now another 50x speedup... quantify hundreds of millions of reads in a few seconds. This seems too good to be true. But it's true! Incredible accomplishment by @pmelsted.
Pall Melsted@pmelstedMar 6
Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv biorxiv.org/content/10.64898… Figure 1 shows they key result
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Can't wait to release a 10-year-old birthday version for SeqKit! - 10 years - 2 papers, 3500 citations - 20 contributors - 40 subcommands - 880 commits - 500 issues - 685.5K Bioconda total downloads Thank you all, dear contributors and users! github.com/shenwei356/seqkit…

Release SeqKit v2.13.0 (10-year-old birthday version) · shenwei356/seqkit

Changelog SeqKit is 10 years old! SeqKit v2.13.0 - 2026-02-28 seqkit: add support for reading and writing LZ4 compression format. new command: seqkit sample2: improved seqkit sample by @stahiga....

github.com
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🎇Very excited to share our perspective piece calling for higher standards for reports on microbial detection in cancers! It was great to put this together with some of the leaders in the field including @StevenSalzberg1 @barjammar @rafalab @minghao_chia: rdcu.be/e4IaU
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Wei Shen retweeted
Ya (Allen) Cui@YaCui7Feb 10
Haha, it's time to show my faculty page at UCI. My new lab website: wlcb.oit.uci.edu/allen
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Replying to @oxfordnanopore
@oxfordnanopore Help! I can't start my first run! "Unexpected error in RPC handling!" - Ubuntu 24.04 6.14.0-37-generic #37~24.04.1-Ubuntu - Latest MinKow 25.09.16 - Lenovo legion 2025, 64G ram, Nvidia 5080 - Hardware check is OK - a fresh R10.4 flowcell with 1400+ pores.
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Forgot to say the device is Minion Mk1D. In the end, we used a Windows PC to run it successfully.
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Tried my methods, still can't start it 💀
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A dream position! I wish I could go.
Heng Li@lh3lh3Jan 14
I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!
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Phage therapy of perinephric abscess in kidney transplantation recipients caused by drug‐resistant Pseudomonas aeruginosa - Liu - 2025 - mLife - Wiley Online Library onlinelibrary.wiley.com/doi/…

Phage therapy of perinephric abscess in kidney transplantation recipients caused by drug‐resistant...

Click on the article title to read more.

onlinelibrary.wiley.com
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The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. nature.com/articles/s41592-0… #Bioinformatics #OpenSource

Scikit-bio: a fundamental Python library for biological omic data analysis

Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis

nature.com
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It's Monday! ...and a new #MVIF program is out! 🤩 Free registration: cassyni.com/s/mvif-44 Highlights: 🇺🇸 Vanessa Hale 🇰🇷 Jun Hyung Cha Keynote: 🇺🇸 Katherine Lemon Talks: 🇺🇸 Meenakshi Chakraborty 🇨🇳 Wei Shen @shenwei356 🇺🇸 Johanna Gutleben @jo_goodlife
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Wei Shen retweeted
𝕐@nomad42111 Nov 2025
This paper highlights some recent security vulnerabilities in sequencers & directly related software (here, with a focus on ONT devices). The intersection of sequencing tech & security seems under-developed! nature.com/articles/s41467-0… ONT’s CVE guidelines: nanoporetech.com/es/products…

Toward security-aware portable sequencing

Nature Communications - Portable genome sequencers are revolutionizing genomic research. However, their reliance on external systems introduces new vulnerabilities that threaten the security of...

nature.com
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