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.

Check out our paper now on The Lancet Microbe ! We Chayaporn Nok Suphavilai Niranjan Nagarajan Jacquomo Clement Tsui 徐健銘 made the discovery in June 2023 and made the data available for the community as a preprint in August 2023. Now it is finally here! thelancet.com/journals/lanmi… #candidia #candidaauris #Genomics

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 🧵

Tech Alert! 🚀🧬 We can now determine the sequence of DNA with non-canonical bases in a direct and high-throughput manner with Nanopore sequencing. Check out our preprint for details: biorxiv.org/content/10.110…

Excited to share our latest work, where we show how to achieve high-throughput sequencing of DNA containing non-canonical bases using Nanopore and de novo basecalling enabled by spliced-based data-augmentation. Check out our preprint: biorxiv.org/cgi/content/sh… Oxford Nanopore

Thrilled to share our work offering a fresh lens into the skin microbiome across body sites! Incredible support from Niranjan Nagarajan John Common @atViduall Aarthi Ravikrishnan indrik wijaya jsgounot Minghao Chia+Asian Skin Microbiome Program & the HELIOS study team! Check it out 👇