JS Gounot
@jsgounot.bsky.social
Microbiology x population genetic
Post-doctoral fellow in the Genome Institute of Singapore.
Post-doctoral fellow in the Genome Institute of Singapore.
Reposted by JS Gounot
How did @Nature become "prestigious" to scientists?
In our opening article of Issue 09, writer Robert Reason traces the journal's history.
By understanding how Nature’s prestige was constructed, we can also clarify which elements are deserved and which are entrenched.
In our opening article of Issue 09, writer Robert Reason traces the journal's history.
By understanding how Nature’s prestige was constructed, we can also clarify which elements are deserved and which are entrenched.
January 5, 2026 at 4:14 PM
How did @Nature become "prestigious" to scientists?
In our opening article of Issue 09, writer Robert Reason traces the journal's history.
By understanding how Nature’s prestige was constructed, we can also clarify which elements are deserved and which are entrenched.
In our opening article of Issue 09, writer Robert Reason traces the journal's history.
By understanding how Nature’s prestige was constructed, we can also clarify which elements are deserved and which are entrenched.
Reposted by JS Gounot
Troubleshooting common errors in assemblies of long-read metagenomes - @merenbey.bsky.social @banfieldlab.bsky.social go.nature.com/44P7nSm
Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology
Long-read sequence assemblies from metagenomes contain frequent errors.
go.nature.com
January 2, 2026 at 4:39 PM
Troubleshooting common errors in assemblies of long-read metagenomes - @merenbey.bsky.social @banfieldlab.bsky.social go.nature.com/44P7nSm
Our new paper on high-throughput isolation of Bifidobacterium just got published! A very nice adventure starting with the supervision of @lamhaiha.bsky.social, a talented intern, and a nice collab with our BSight expert @isaacyueyuan.bsky.social! Stay tuned for more isolation and Bifido work! :)
Thrilled to share our high-throughput Bifidobacterium isolation work in Microbiology Spectrum! journals.asm.org/doi/10.1128/...
By integrating a single-cell dispenser into a culturomics workflow, we accelerated the isolation of individual bacterial cells, allowing robust strain-level resolution.
By integrating a single-cell dispenser into a culturomics workflow, we accelerated the isolation of individual bacterial cells, allowing robust strain-level resolution.
High-throughput single-cell isolation of Bifidobacterium strains from the human gut microbiome | Microbiology Spectrum
The field of high-throughput microbial culturomics is still in its early stages. Enhancing
our ability to isolate and phenotypically test bacterial strains from complex communities
is crucial for adva...
journals.asm.org
January 1, 2026 at 9:20 AM
Our new paper on high-throughput isolation of Bifidobacterium just got published! A very nice adventure starting with the supervision of @lamhaiha.bsky.social, a talented intern, and a nice collab with our BSight expert @isaacyueyuan.bsky.social! Stay tuned for more isolation and Bifido work! :)
Reposted by JS Gounot
✨ Latest exciting story of the group in @nature.com. Here, we go beyond SNPs and built a species-wide atlas of genetic variants in yeast. With >1,000 near T2T genomes, we show how large genomic variations affect trait diversity.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes - Nature
A newly compiled atlas of species-wide structural variants and gene-based and graph pangenomes derived from highly complete assemblies of genomes from 1,086 natural isolates enable integrative genome-...
www.nature.com
October 16, 2025 at 7:49 AM
✨ Latest exciting story of the group in @nature.com. Here, we go beyond SNPs and built a species-wide atlas of genetic variants in yeast. With >1,000 near T2T genomes, we show how large genomic variations affect trait diversity.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by JS Gounot
New blog post – A quick look at Roche's SBX
lh3.github.io/2025/09/11/a...
lh3.github.io/2025/09/11/a...
September 12, 2025 at 3:26 AM
New blog post – A quick look at Roche's SBX
lh3.github.io/2025/09/11/a...
lh3.github.io/2025/09/11/a...
Reposted by JS Gounot
Reposted by JS Gounot
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
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
High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
September 7, 2025 at 11:35 PM
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
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
Reposted by JS Gounot
The latest story from the @haploteam highlights the phenotypic impact of acquired subgenomes in allopolyploids, through the lens of 1,060 Brettanomyces bruxellensis genomes. Nice collaboration with @univbordeaux.bsky.social
@unistra.fr @cnrsbiologie.bsky.social
www.nature.com/articles/s41...
@unistra.fr @cnrsbiologie.bsky.social
www.nature.com/articles/s41...
Whole-genome sequencing of 1,060 Brettanomyces bruxellensis isolates reveals significant phenotypic impact of acquired subgenomes in allopolyploids - Nature Communications
The authors sequence and phenotype over 1,000 isolates of the yeast Brettanomyces bruxellensis, and show how allopolyploidization reshapes genome evolution and enhances phenotypic diversity, highlight...
www.nature.com
July 3, 2025 at 7:08 PM
The latest story from the @haploteam highlights the phenotypic impact of acquired subgenomes in allopolyploids, through the lens of 1,060 Brettanomyces bruxellensis genomes. Nice collaboration with @univbordeaux.bsky.social
@unistra.fr @cnrsbiologie.bsky.social
www.nature.com/articles/s41...
@unistra.fr @cnrsbiologie.bsky.social
www.nature.com/articles/s41...
Reposted by JS Gounot
The most viruslike microbe to date was discovered by accident when researchers sequenced the DNA inside this tiny ocean critter. That story and more of the best from @science.org and science in this edition of #ScienceAdviser: www.science.org/content/arti... 🧪
June 16, 2025 at 8:08 PM
The most viruslike microbe to date was discovered by accident when researchers sequenced the DNA inside this tiny ocean critter. That story and more of the best from @science.org and science in this edition of #ScienceAdviser: www.science.org/content/arti... 🧪
Reposted by JS Gounot
Short-read metagenomic sequencing cannot recover genomes from many abundant marine prokaryotes due to high strain heterogeneity and platform-inherent GC bias (likely viruses, too), but Nanopore long reads can address this. A results thread on our recent preprint 🧵.
May 25, 2025 at 10:27 AM
Short-read metagenomic sequencing cannot recover genomes from many abundant marine prokaryotes due to high strain heterogeneity and platform-inherent GC bias (likely viruses, too), but Nanopore long reads can address this. A results thread on our recent preprint 🧵.
Reposted by JS Gounot
Super thrilled to share our labor of love from the Asian Skin Microbiome Program! We collected >3,500 skin samples, built metagenomic libraries w/ >70 billion reads and >10TB of data to study heterogeneity of the skin microbiome in the general population (200 adults, 18 sites) t.co/ZylbJMpvpw
Large-scale skin metagenomics reveals extensive prevalence, coordination, and functional adaptation of skin microbiome dermotypes across body sites
The human skin microbiome is increasingly recognized to influence skin health, immune function and disease susceptibility. However, large-scale, multi-site metagenomic studies in the general populatio...
www.biorxiv.org
April 28, 2025 at 4:52 AM
Super thrilled to share our labor of love from the Asian Skin Microbiome Program! We collected >3,500 skin samples, built metagenomic libraries w/ >70 billion reads and >10TB of data to study heterogeneity of the skin microbiome in the general population (200 adults, 18 sites) t.co/ZylbJMpvpw
Reposted by JS Gounot
I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers,
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
Assemblies of long-read metagenomes suffer from diverse errors
Genomes from metagenomes have revolutionised our understanding of microbial diversity, ecology, and evolution, propelling advances in basic science, biomedicine, and biotechnology. Assembly algorithms...
www.biorxiv.org
April 28, 2025 at 8:08 AM
I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers,
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
Reposted by JS Gounot
LLMs hallucinating nonexistent software packages with plausible names leads to a new malware vulnerability: "slopsquatting."
LLMs can't stop making up software dependencies and sabotaging everything
: Hallucinated package names fuel 'slopsquatting'
www.theregister.com
April 12, 2025 at 10:31 PM
LLMs hallucinating nonexistent software packages with plausible names leads to a new malware vulnerability: "slopsquatting."
Reposted by JS Gounot
Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:
rdcu.be/eg4OA
1/
rdcu.be/eg4OA
1/
Efficient and robust search of microbial genomes via phylogenetic compression
Nature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks.
rdcu.be
April 9, 2025 at 9:07 PM
Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:
rdcu.be/eg4OA
1/
rdcu.be/eg4OA
1/
Reposted by JS Gounot
In 1904, a physician took soil he had “impregnated with a living emulsion” of a virulent bacterium, Serratia marcescens, and sprinkled it in front of the UK House of Commons.
This was an early experiment to study how microbes spread through buildings and cause infections...
This was an early experiment to study how microbes spread through buildings and cause infections...
March 23, 2025 at 3:52 PM
In 1904, a physician took soil he had “impregnated with a living emulsion” of a virulent bacterium, Serratia marcescens, and sprinkled it in front of the UK House of Commons.
This was an early experiment to study how microbes spread through buildings and cause infections...
This was an early experiment to study how microbes spread through buildings and cause infections...
Reposted by JS Gounot
New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
Home
A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler
github.com
December 31, 2024 at 11:43 PM
New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
Interactive online show about the microbial world from the Museum of Natural history at Oxford Uni. Cool ideas. www.oum.ox.ac.uk/bacterialwor...
December 13, 2024 at 8:33 AM
Interactive online show about the microbial world from the Museum of Natural history at Oxford Uni. Cool ideas. www.oum.ox.ac.uk/bacterialwor...
Another great piece from Asimov press: www.asimov.press/p/mirror-life
The Dangers of Mirrored Life
Creating mirrored organisms using synthetic biology could seriously harm extant life, a 300-page report claims. While the risks from mirrored life are uncertain, it is best not to find out.
www.asimov.press
December 13, 2024 at 6:23 AM
Another great piece from Asimov press: www.asimov.press/p/mirror-life
Reposted by JS Gounot
A new view of #SpeciesConcepts by @jeannettewhitton.bsky.social and me, clarifying time frames while unifying interbreeding, genealogy, and traits. A general-purpose species should be a reproductive community (bound by cohesive processes) viewed retrospectively (RRCC). doi.org/10.18061/bss...
December 9, 2023 at 7:49 PM
A new view of #SpeciesConcepts by @jeannettewhitton.bsky.social and me, clarifying time frames while unifying interbreeding, genealogy, and traits. A general-purpose species should be a reproductive community (bound by cohesive processes) viewed retrospectively (RRCC). doi.org/10.18061/bss...
Another small and interesting historical story from Asimov press. This time about the Watson's central dogma.
Francis Crick Was Misunderstood
The Central Dogma is not a
doi.org
December 6, 2024 at 2:45 AM
Another small and interesting historical story from Asimov press. This time about the Watson's central dogma.
Reposted by JS Gounot
Excited to share our latest work, where we show how to achieve high-throughput sequencing of DNA containing non-canonical bases using Nanopore (@nanoporetech.com) and de novo basecalling enabled by spliced-based data-augmentation.
#nanopore #basecaller #syntheticbiology
#nanopore #basecaller #syntheticbiology
Direct high-throughput deconvolution of unnatural bases via nanopore sequencing and bootstrapped learning
The discovery of synthetic xeno-nucleic acids (XNAs) that can basepair as unnatural bases (UBs) to expand the genetic alphabet has spawned interest in many applications, from synthetic biology to DNA ...
biorxiv.org
December 5, 2024 at 9:52 AM
Excited to share our latest work, where we show how to achieve high-throughput sequencing of DNA containing non-canonical bases using Nanopore (@nanoporetech.com) and de novo basecalling enabled by spliced-based data-augmentation.
#nanopore #basecaller #syntheticbiology
#nanopore #basecaller #syntheticbiology
A fun idea, using Bacillus subtilis to sense the TNT explosive
An autonomous microbial sensor enables long-term detection of TNT explosive in natural soil - Nature Communications
Engineered microbes can detect harmful chemicals, but may not work well in complex environments. Here, the authors built microbial sensors for detection of TNT explosive and tested their response over...
www.nature.com
December 3, 2024 at 1:23 AM
A fun idea, using Bacillus subtilis to sense the TNT explosive
