Ton Ngoc Minh Quan
@tnmquann.bsky.social
@oucru - MolEpi. Currently working on human microbiome, using @nextflow.io to create scalable and reproducible pipelines
Reposted by Ton Ngoc Minh Quan
15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵
October 10, 2025 at 4:47 PM
15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵
Reposted by Ton Ngoc Minh Quan
Please, #microbiome and #sequencing data are NOT zero-inflated. Let's stop repeating this nonsense. Zero-inflated compared to what?? Those zeroes carry important information about abundance and sequencing depth, and are not "inflated" in any sense. 1/6
May 6, 2025 at 7:15 PM
Please, #microbiome and #sequencing data are NOT zero-inflated. Let's stop repeating this nonsense. Zero-inflated compared to what?? Those zeroes carry important information about abundance and sequencing depth, and are not "inflated" in any sense. 1/6
Reposted by Ton Ngoc Minh Quan
Excited to share that our paper on the relationship between viral load and metagenomic outputs in wildlife samples is now published in Microbial Genomics @microbiologysociety! 🎉 Fantastic collaboration with a brilliant team.
More info: 📖 tinyurl.com/ywb7tvjm
More info: 📖 tinyurl.com/ywb7tvjm
Quantifying viral load and characterizing virus diversity in wildlife samples with target enrichment sequencing
Metagenomics is a powerful tool for characterizing viruses, with broad applications across diverse disciplines, from understanding the ecology and evolutionary history of viruses to identifying causat...
tinyurl.com
September 29, 2025 at 11:23 AM
Excited to share that our paper on the relationship between viral load and metagenomic outputs in wildlife samples is now published in Microbial Genomics @microbiologysociety! 🎉 Fantastic collaboration with a brilliant team.
More info: 📖 tinyurl.com/ywb7tvjm
More info: 📖 tinyurl.com/ywb7tvjm
Reposted by Ton Ngoc Minh Quan
Pipeline release! nf-core/mag v5.0.0 - mag 5.0.0 - Green Squirrel!
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.0.0
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.0.0
Release mag 5.0.0 - Green Squirrel · nf-core/mag
Added
#718 - Add support for independent long-read metagenomic assembly (requested by @ljmesi and many others, added by @muabnezor)
#718 - Added metaMDBG and (meta)Flye as long read assemblers (ad...
github.com
September 30, 2025 at 7:37 AM
Pipeline release! nf-core/mag v5.0.0 - mag 5.0.0 - Green Squirrel!
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.0.0
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.0.0
Reposted by Ton Ngoc Minh Quan
Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/o.... Work with Alvin Qin
September 30, 2025 at 2:19 AM
Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/o.... Work with Alvin Qin
Reposted by Ton Ngoc Minh Quan
Working memory expands shared task representations in cortex https://www.biorxiv.org/content/10.1101/2025.09.29.679345v1
September 30, 2025 at 7:15 AM
Working memory expands shared task representations in cortex https://www.biorxiv.org/content/10.1101/2025.09.29.679345v1
Reposted by Ton Ngoc Minh Quan
Why early birds sing early: rebound singing from nighttime suppression can explain dawn chorus https://www.biorxiv.org/content/10.1101/2025.09.29.679172v1
September 30, 2025 at 7:45 AM
Why early birds sing early: rebound singing from nighttime suppression can explain dawn chorus https://www.biorxiv.org/content/10.1101/2025.09.29.679172v1
Reposted by Ton Ngoc Minh Quan
Out now in National Science Review! Our recent perspective on horizontal gene transfer in metagenomics analysis. Congrats @hpeng.bsky.social! academic.oup.com/nsr/article/...
Unveiling horizontal gene transfer in the gut microbiome: bioinformatic strategies and challenges in metagenomics analysis
Microorganisms can inhabit diverse environments, including the human gut [1]. Gut bacteria can continuously evolve in response to changes in the intestinal
academic.oup.com
July 3, 2025 at 1:36 PM
Out now in National Science Review! Our recent perspective on horizontal gene transfer in metagenomics analysis. Congrats @hpeng.bsky.social! academic.oup.com/nsr/article/...
Reposted by Ton Ngoc Minh Quan
Manually curated and harmonized metadata for over 110k metagenomic samples! (58k samples from the human gut alone!)🦠
Proud to have contributed to Metalog, the latest @borklab.bsky.social resource:
www.biorxiv.org/content/10.1...
#microsky #microbiome
Proud to have contributed to Metalog, the latest @borklab.bsky.social resource:
www.biorxiv.org/content/10.1...
#microsky #microbiome
August 15, 2025 at 1:54 PM
Manually curated and harmonized metadata for over 110k metagenomic samples! (58k samples from the human gut alone!)🦠
Proud to have contributed to Metalog, the latest @borklab.bsky.social resource:
www.biorxiv.org/content/10.1...
#microsky #microbiome
Proud to have contributed to Metalog, the latest @borklab.bsky.social resource:
www.biorxiv.org/content/10.1...
#microsky #microbiome
Reposted by Ton Ngoc Minh Quan
Thrilled to share our recent review on multidimensional metagenomics analysis, in which we highlight cutting edge technologies and AI applications at 1D to 4D levels. Congrats @hpeng.bsky.social and Angel Ruiz-Moreno.
www.nature.com/articles/s44...
www.nature.com/articles/s44...
Multi-dimensional metagenomics - Nature Reviews Bioengineering
High-throughput sequencing and artificial intelligence-driven structural biology have vastly expanded our understanding of the human metagenome, yet microbial functions remain largely elusive. In this...
www.nature.com
August 26, 2025 at 11:44 AM
Thrilled to share our recent review on multidimensional metagenomics analysis, in which we highlight cutting edge technologies and AI applications at 1D to 4D levels. Congrats @hpeng.bsky.social and Angel Ruiz-Moreno.
www.nature.com/articles/s44...
www.nature.com/articles/s44...
Reposted by Ton Ngoc Minh Quan
How do you long-read sequence metagenomes? I would argue it starts with the right sample storage & DNA extraction, to enable efficient @nanoporetech.com /@pacbio.bsky.social sequencing, which we investigated in our new paper: www.biorxiv.org/content/10.1...
Massive thanks to Klara for driving this
Massive thanks to Klara for driving this
September 9, 2025 at 3:35 PM
How do you long-read sequence metagenomes? I would argue it starts with the right sample storage & DNA extraction, to enable efficient @nanoporetech.com /@pacbio.bsky.social sequencing, which we investigated in our new paper: www.biorxiv.org/content/10.1...
Massive thanks to Klara for driving this
Massive thanks to Klara for driving this
Reposted by Ton Ngoc Minh Quan
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology
LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.
www.nature.com
September 10, 2025 at 9:12 AM
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Reposted by Ton Ngoc Minh Quan
Our new tool "X-Mapper: fast and accurate sequence alignment via gapped x-mers" now published on Genome Biology! Please try it if you work on DNA sequences :) github.com/mathjeff/Map...
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
X-Mapper: fast and accurate sequence alignment via gapped x-mers - Genome Biology
Sequence alignment is foundational to many bioinformatic analyses. Many aligners start by splitting sequences into contiguous, fixed-length seeds, called k-mers. Alignment is faster with longer, uniqu...
genomebiology.biomedcentral.com
August 30, 2025 at 1:45 AM
Our new tool "X-Mapper: fast and accurate sequence alignment via gapped x-mers" now published on Genome Biology! Please try it if you work on DNA sequences :) github.com/mathjeff/Map...
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
Reposted by Ton Ngoc Minh Quan
agtools: a software framework to manipulate assembly graphs https://www.biorxiv.org/content/10.1101/2025.09.14.676178v1
September 16, 2025 at 8:48 PM
agtools: a software framework to manipulate assembly graphs https://www.biorxiv.org/content/10.1101/2025.09.14.676178v1
Reposted by Ton Ngoc Minh Quan
Surprising discoveries about the species responsible for 90 per cent of mushroom-related deaths is revealing the fungi kingdom to be even stranger than we had thought.
The deadliest mushroom, the death cap, is still concocting new poisons
Surprising discoveries about the species responsible for 90 per cent of mushroom-related deaths is revealing the fungi kingdom to be even stranger than we had thought
www.newscientist.com
September 13, 2025 at 9:20 AM
Surprising discoveries about the species responsible for 90 per cent of mushroom-related deaths is revealing the fungi kingdom to be even stranger than we had thought.
Reposted by Ton Ngoc Minh Quan
Integrated metabolomics data analysis to generate mechanistic hypotheses with MetaProViz https://www.biorxiv.org/content/10.1101/2025.08.18.670781v1
August 22, 2025 at 2:04 PM
Integrated metabolomics data analysis to generate mechanistic hypotheses with MetaProViz https://www.biorxiv.org/content/10.1101/2025.08.18.670781v1
Reposted by Ton Ngoc Minh Quan
Beloved #bioinformatics tool users, we are redoing our database download pages for #sourmash with automated templates; see sourmash--3754.org.readthedocs.build/en/3754/data... for an example. What extra/advanced info would be helpful??
Collection: GTDB RS226 — sourmash 4.9.4.dev0 documentation
sourmash--3754.org.readthedocs.build
August 4, 2025 at 1:51 PM
Beloved #bioinformatics tool users, we are redoing our database download pages for #sourmash with automated templates; see sourmash--3754.org.readthedocs.build/en/3754/data... for an example. What extra/advanced info would be helpful??
Reposted by Ton Ngoc Minh Quan
The beginning of the end of mitochondrial disease? We only make progress, if we invest in research... 🧪 #MedSky #PoliSky #EconSky #AcademicSky
www.nejm.org
July 23, 2025 at 10:17 PM
The beginning of the end of mitochondrial disease? We only make progress, if we invest in research... 🧪 #MedSky #PoliSky #EconSky #AcademicSky
Reposted by Ton Ngoc Minh Quan
Inkscape plugin to rescale figures without distorting the text, and other useful features!
github.com/burghoff/Sci...
github.com/burghoff/Sci...
June 2, 2025 at 12:15 PM
Inkscape plugin to rescale figures without distorting the text, and other useful features!
github.com/burghoff/Sci...
github.com/burghoff/Sci...
Reposted by Ton Ngoc Minh Quan
A short preprint describing the GlobDB is now on arXiv: arxiv.org/abs/2506.11896
If you find the resource useful, please also check globdb.org for info on how to cite the underlying resources and tools.
If you find the resource useful, please also check globdb.org for info on how to cite the underlying resources and tools.
I'm happy to announce the latest release of the GlobDB, available at globdb.org.
The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
home | GlobDB
globdb.org
June 16, 2025 at 8:44 PM
A short preprint describing the GlobDB is now on arXiv: arxiv.org/abs/2506.11896
If you find the resource useful, please also check globdb.org for info on how to cite the underlying resources and tools.
If you find the resource useful, please also check globdb.org for info on how to cite the underlying resources and tools.
Reposted by Ton Ngoc Minh Quan
Interesting paper on precisely detecting species of interest in metagenomes. I thought this was a thoughtful investigation for a problem that most folks don't discuss much, but implicitly think about often.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Comparative performance of reference-based metagenomic tools to identify species-level taxa among families of bacteria: benchmarking Mycobacteriaceae and Neisseriaceae
Hypotheses concerning the ecology and evolution of bacteria commonly relate to the presence and abundance of species in various settings and conditions. Shotgun metagenomics may address these hypothes...
www.biorxiv.org
July 3, 2025 at 9:09 PM
Interesting paper on precisely detecting species of interest in metagenomes. I thought this was a thoughtful investigation for a problem that most folks don't discuss much, but implicitly think about often.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Ton Ngoc Minh Quan
Leviathan: A fast, memory-efficient, and scalable taxonomic and pathway profiler for next generation sequencing (pan)genome-resolved metagenomics and metatranscriptomics https://www.biorxiv.org/content/10.1101/2025.07.14.664802v1
July 18, 2025 at 10:47 PM
Leviathan: A fast, memory-efficient, and scalable taxonomic and pathway profiler for next generation sequencing (pan)genome-resolved metagenomics and metatranscriptomics https://www.biorxiv.org/content/10.1101/2025.07.14.664802v1
Reposted by Ton Ngoc Minh Quan
We prepared an additional sylph database for the GlobDB with subsampling rate 1000 (-c 1000) requiring lower RAM than the default 200.
Both databases and taxonomy are available at globdb.org
Both databases and taxonomy are available at globdb.org
July 23, 2025 at 4:36 PM
We prepared an additional sylph database for the GlobDB with subsampling rate 1000 (-c 1000) requiring lower RAM than the default 200.
Both databases and taxonomy are available at globdb.org
Both databases and taxonomy are available at globdb.org
Reposted by Ton Ngoc Minh Quan
Reposted by Ton Ngoc Minh Quan
#NatMicroPicks
Tracking the gut microbiome evolution 🦠
A big data analysis of gut microbiome of kids from infancy to 8 years of age.
#MicroSky #MicrobiomeSky
www.nature.com/articles/s41...
Tracking the gut microbiome evolution 🦠
A big data analysis of gut microbiome of kids from infancy to 8 years of age.
#MicroSky #MicrobiomeSky
www.nature.com/articles/s41...
Gut microbiome evolution from infancy to 8 years of age - Nature Medicine
In a unique cohort of twins followed from birth to 8 years of age, shotgun sequencing of stool samples reveals that the transmission, persistence and evolutionary adaptation of bacterial strains are s...
www.nature.com
June 26, 2025 at 3:32 PM
#NatMicroPicks
Tracking the gut microbiome evolution 🦠
A big data analysis of gut microbiome of kids from infancy to 8 years of age.
#MicroSky #MicrobiomeSky
www.nature.com/articles/s41...
Tracking the gut microbiome evolution 🦠
A big data analysis of gut microbiome of kids from infancy to 8 years of age.
#MicroSky #MicrobiomeSky
www.nature.com/articles/s41...