Glad to see our review on polyploid phasing out today. Here, we also present the Phasing Toolkit, an open source project to simplify benchmarking and the use of phasing tools. Great work from @OmarAbouSaada1. sciencedirect.com/science/articl…

Nature research paper: Synonymous mutations in representative yeast genes are mostly strongly non-neutral go.nature.com/3Mx58Hd

The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments nature.com/articles/s4159…

CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning biorxiv.org/content/10.110…

Excited that our work on tracking Carbapenemase-producing Enterobacteriaceae in the gut microbiome is finally out open access! The result of great bench-to-bedside collaborations with Kalisvar Marimuthu Oon-Tek YunnHwen Gan Highlights thread: tinyurl.com/2p8tzrdv nature.com/articles/s4156…

A collaborative effort by GIS, TLL & NUS, comprehensively characterised 109 SGs’ gut microbiomes. Knowledge gained from the study will be key in developing future population-specific therapies to improve human health & potential. Niranjan Nagarajan Read more: bit.ly/3uoRlvH

Looking back, 2022 has been an incredible year for long-read #metagenomics! I have been busy creating a resource for all publicly available PacBio HiFi datasets (github.com/PacificBioscie…). Below is a visual snapshot of what these 35+ metagenomics datasets look like. 1/3

Me and Yun William Yu's new preprint on skani, a new tool for calculating ANI for metagenomic assembled genomes, is out. It's available on GitHub here: github.com/bluenote-1577/… 1/6

Presenting sylph (github.com/bluenote-1577/…), a fast, precise metagenomic profiler. Work done with Yun William Yu. sylph is highly accurate at the species level and takes ~1 minute and 16 GB RAM to profile against 85k prokaryotes and 2.9 million viral genomes. 1/10

The MetageNN paper is finally out on bioRxiv! MetageNN outperforms recent machine learning based approaches for taxonomic classification, and shows higher sensitivity than kmer based tools for novel taxa ... w/ Rafael Peres Chayaporn Nok Suphavilai biorxiv.org/content/10.110…

Check out our latest paper, just published in Nucleic Acids Res which focuses on translation variation across genetic backgrounds. Great work by Elie Teyssoniere. And great collaboration with Yuichi Shichino and Iwasaki_Lab_RIKEN. Schacherer Lab Institut universitaire de France (IUF) European Research Council (ERC) academic.oup.com/nar/advance-ar…

Our preprint is out! A new step toward strain-level resolved metagenomes. Very happy to have worked on this with Jim, we hope that Floria will be helpful for many of you to distinguish your favorite species' strain diversity and dynamics within metagenome.

Shotgun metagenomics data for >200 healthy Asian octogenerians helped us identify key gut microbial hallmarks of healthy aging, including some that are only consistently seen in Asian cohorts! 4 Major results in thread #aging #microbiome biorxiv.org/content/10.110…

📢Our publication on gut metagenomes of Asian octogenarians is now online in Nature Communications! 🎊 nature.com/articles/s4146… indrik wijaya Niranjan Nagarajan #HealthyAging #GutMicrobiome #AgingResearch #MicrobiomeScience Interesting results in thread 🧵