jsgounot

[jsgounot @jsgounot]

Our new paper on high-throughput isolation of Bifidobacterium just got published! A very nice adventure starting with the supervision of Hai, a talented intern, and a nice collab with our BSight expert @isaacyueyuan ! Stay tuned for more isolation and Bifido work! :)

[Yue Yuan On (Isaac) @isaacyueyuan]

Thrilled to share our high-throughput Bifidobacterium isolation work!
Now out in https://t.co/JVN00fXHND

By integrating a single-cell dispenser into a culturomics workflow, we accelerated the isolation of individual bacterial cells, allowing robust strain-level resolution.

[Cherry Chengchen Li 李成辰 @ChengchenliC]

Thrilled to share our work offering a fresh lens into the skin microbiome across body sites! Incredible support from @NiranjanTW @john_common @atViduall @aarthiravikrish @indrikwijaya @jsgounot @minghao_chia+Asian Skin Microbiome Program & the HELIOS study team! Check it out 👇

[Mauricio Lisboa Perez @mlisboaperez]

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: https://t.co/VuYZ5wEO5l
@nanopore

[Niranjan Nagarajan @NiranjanTW]

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: https://t.co/mSOSzubouc

[jsgounot @jsgounot]

@MishaKolmogorov Congratulation! Were you able to compare Strainy to (disclaimer, I'm one author) Floria? I'm curious. https://t.co/UflrDkW29A

[Aarthi Ravikrishnan @aarthiravikrish]

📢Our publication on gut metagenomes of Asian octogenarians is now online in Nature Communications! 🎊
https://t.co/SdjMbaznGP
@indrikwijaya @NiranjanTW
#HealthyAging #GutMicrobiome #AgingResearch #MicrobiomeScience
Interesting results in thread 🧵

[Karrie Ko @karriekkko]

Check out our paper now on @LancetMicrobe ! We @nokcs @NiranjanTW @JacquesMeis @km_tsui 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!
https://t.co/TVZ3Bmwd2A #candidia #candidaauris #Genomics

[Niranjan Nagarajan @NiranjanTW]

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
https://t.co/Qxl37PRBJQ

[jsgounot @jsgounot]

@ace_gtdb @jim_elevator they used skani for the new release ;)

[jsgounot @jsgounot]

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.

[Jim Shaw @jim_elevator]

Our method for recovering strains in long-read (e.g. nanopore) or short-read metagenomes is out!

Work with Jean-Sebastien Gounot (*Co-lead*, @jsgounot), Hanrong Chen and supervised by Niranjan Nagarajan (@NiranjanTW), and Yun William Yu (@YunWilliamYu) 1/8

[Joseph Schacherer @jo_schacherer]

Check out our latest paper, just published in @NAR_Open which focuses on translation variation across genetic backgrounds. Great work by Elie Teyssoniere. And great collaboration with @u1_7no and @IwasakiLabRIKEN.
@haploteam @InstUnivFr @ERC_Research
https://t.co/EwKjrJh5d0

[Niranjan Nagarajan @NiranjanTW]

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/ @rafaelperes @nokcs

https://t.co/stONibv4kF

[Jim Shaw @jim_elevator]

Presenting sylph (https://t.co/WGX3W1yOjT), a fast, precise metagenomic profiler. Work done with @YunWilliamYu.

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

[jsgounot @jsgounot]

@jim_elevator Looks good mate, congrat!

[jsgounot @jsgounot]

@DPortik I'm working on building a nice and updated human gut metagenome database. I remember you refined the MAGs obtained with HiFi reads. Are there publicly available? Thanks!

[Jim Shaw @jim_elevator]

Me and @YunWilliamYu's new preprint on skani, a new tool for calculating ANI for metagenomic assembled genomes, is out. It's available on GitHub here: https://t.co/dEkIzxHDNT 1/6

[Daniel Portik @DPortik]

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 (https://t.co/KPWyzBwHE4). Below is a visual snapshot of what these 35+ metagenomics datasets look like. 1/3

[A*STAR Genome Institute of Singapore (A*STAR GIS) @astar_gis]

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. @NiranjanTW
Read more: https://t.co/Eq1UaSdtu8

[jsgounot @jsgounot]

It would be our great pleasure if you find other ways to use this dataset. Let us know if you need more specific information to leverage the data for your analysis! You can already find all the MAGs and reads both on ENA and on Figshare (https://t.co/jP2mt8p0VY)

[jsgounot @jsgounot]

Very excited that our Singaporean Platinum Metagenome Project study is finally out open access! https://t.co/QltkPVJUy3

[jsgounot @jsgounot]

with 2) 10% of our MAGs defined as novel, suggesting a untouched diversity within South Asia. Finally, 3) high-quality genomes help to identify meaningful genetic features, allowing @minghao_chia to find a very cool BGC with a potential impact on community structure.