PostDoc at Bhatt lab in the Stanford University.
https://yuyanoah.github.io/Homepage/index.html
Yuya Kiguchi
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Excited to share our review relating to the giant extrachromosomal elements (ECEs)
We cover: why long-read metagenomics enables their discovery, genomic comparisons across recently characterized examples, and limitations of current classification tools.
www.cell.com/trends/genet...
Prokaryotes harbor a diverse spectrum of extrachromosomal elements (ECEs), which are
intracellular replicons maintained independently of the primary chromosome. Historically,
the ECE research field ha...
Nature research paper: Long-read metagenomics reveals phage dynamics in the human gut microbiome
go.nature.com/44zgo1o
Happy to announce VIRE, a planetary-scale database of >1.7M viral genomes reconstructed from 100k+ metagenomes across diverse environments! In collaboration with @fullam.bsky.social, @tsbschm.bsky.social, and @borklab.bsky.social.
academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1225/8356007
Our review on the Japanese gut microbiome is now published!
By analyzing >30,000 gut metagenomes from 37 countries🧬, we re-evaluated the unique feature of the Japanese gut microbiome🦠 in a global context🌏.
doi.org/10.2183/pjab...
Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–bacterial interactions in the human gut microbiome.
go.nature.com
Mushuvirus is the most widespread phage genus in the human gut. 🌍
Together with other family members, these viruses occur in 89% of humans worldwide, including the Iceman Ötzi!
How is it possible that they were hidden in previous metagenomic analyses?
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Read: doi.org/10.64898/202...
Nature
Our method, savont, for generating amplicon sequence variants (ASVs) for long-read amplicons is now on bioRxiv.
Work with @lh3lh3.bsky.social and help from @mkddueholm.bsky.social and team (Marie Riisgaard-Jensen, @kirk3gaard.bsky.social, Kasper Skytte Andersen)
github.com/bluenote-157...
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Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social
Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback.
rdcu.be/famFj
Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
Abstract. Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a compr
Announcing a new tool for "denoising" long-read amplicon sequences: savont.
Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.
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github.com/bluenote-157...
Metagenomics has become a powerful approach for deciphering the structure and function of the human gut microbiome, a complex microbial ecosystem in t …
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
