@xinehc.bsky.social
Reposted
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 10, 2025 at 11:20 AM
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.
Reposted
Unique investigation of some errors in long read assemblers.
In particular these remarkably chimeric contigs are 😱, if rare....
Improving long read assemblers is definitely the space to be in when it comes to the future of metagenomics, as short reads won't be part of it 😉
In particular these remarkably chimeric contigs are 😱, if rare....
Improving long read assemblers is definitely the space to be in when it comes to the future of metagenomics, as short reads won't be part of it 😉
April 25, 2025 at 2:46 PM
Unique investigation of some errors in long read assemblers.
In particular these remarkably chimeric contigs are 😱, if rare....
Improving long read assemblers is definitely the space to be in when it comes to the future of metagenomics, as short reads won't be part of it 😉
In particular these remarkably chimeric contigs are 😱, if rare....
Improving long read assemblers is definitely the space to be in when it comes to the future of metagenomics, as short reads won't be part of it 😉
Reposted
GTDB release 10 based on RefSeq 226 (R10-RS226) is live at gtdb.ecogenomic.org. This release covers 732,475 genomes (22% increase) and has 143,6141 species clusters (37% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r226.
GTDB - Genome Taxonomy Database
The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.
gtdb.ecogenomic.org
April 18, 2025 at 7:13 PM
GTDB release 10 based on RefSeq 226 (R10-RS226) is live at gtdb.ecogenomic.org. This release covers 732,475 genomes (22% increase) and has 143,6141 species clusters (37% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r226.
Reposted
I was waiting two years to see this out!! The genomic location of bacterial genes is not random!!! Congratulation on the authors (Martin Lercher and Team!). www.science.org/doi/10.1126/...
Most bacterial gene families are biased toward specific chromosomal positions
The arrangement of genes along bacterial chromosomes influences their expression through growth rate–dependent gene copy number changes during DNA replication. Although translation- and transcription-...
www.science.org
April 10, 2025 at 7:43 PM
I was waiting two years to see this out!! The genomic location of bacterial genes is not random!!! Congratulation on the authors (Martin Lercher and Team!). www.science.org/doi/10.1126/...
Reposted
In 2016, the Kishony Lab at Harvard Medical School put together this demonstration of acquired antibiotic resistance in E. coli bacteria, creating a mega-Petri dish (2' x 4') with a stepped gradient of antibiotic.
Seeing the mutants emerge & spread is an elegant demo of evolutionary change.
Seeing the mutants emerge & spread is an elegant demo of evolutionary change.
The Evolution of Bacteria on a “Mega-Plate” Petri Dish (Kishony Lab)
YouTube video by Harvard Medical School
youtu.be
April 13, 2025 at 2:01 PM
In 2016, the Kishony Lab at Harvard Medical School put together this demonstration of acquired antibiotic resistance in E. coli bacteria, creating a mega-Petri dish (2' x 4') with a stepped gradient of antibiotic.
Seeing the mutants emerge & spread is an elegant demo of evolutionary change.
Seeing the mutants emerge & spread is an elegant demo of evolutionary change.
Reposted
In a new Science study, researchers present ESM3, a protein language model that enables the programmed generation of protein structure and sequence in response to user prompts.
Learn more: scim.ag/40l2z3J
Learn more: scim.ag/40l2z3J
Simulating 500 million years of evolution with a language model
More than 3 billion years of evolution have produced an image of biology encoded into the space of natural proteins. Here, we show that language models trained at scale on evolutionary data can genera...
scim.ag
February 26, 2025 at 8:08 PM
In a new Science study, researchers present ESM3, a protein language model that enables the programmed generation of protein structure and sequence in response to user prompts.
Learn more: scim.ag/40l2z3J
Learn more: scim.ag/40l2z3J
Reposted
🚨 Our latest research in @naturecomms.bsky.social shows a promising strategy for less resistance-prone #antibiotics. For details, see the thread below and read the paper “Exploring the principles behind antibiotics with limited resistance” here: #MEvoSky www.nature.com/articles/s41...
Exploring the principles behind antibiotics with limited resistance - Nature Communications
This study shows that only those dual-targeting antibiotics limit resistance in Gram-negative pathogens that also target the membrane of the bacteria. This mechanism provides a basis for designing fut...
www.nature.com
February 24, 2025 at 11:09 AM
🚨 Our latest research in @naturecomms.bsky.social shows a promising strategy for less resistance-prone #antibiotics. For details, see the thread below and read the paper “Exploring the principles behind antibiotics with limited resistance” here: #MEvoSky www.nature.com/articles/s41...
Reposted
7️⃣ New drugs are getting rare:
90% of the major classes of antibiotics have been discovered before 1980, only 3 out of 29 after 1980.
Pharma companies have little financial incitation to invest, as new compounds often have to be kept as “last resource” drugs.
Still, new approaches exist.
/end
90% of the major classes of antibiotics have been discovered before 1980, only 3 out of 29 after 1980.
Pharma companies have little financial incitation to invest, as new compounds often have to be kept as “last resource” drugs.
Still, new approaches exist.
/end
November 22, 2024 at 9:01 AM
7️⃣ New drugs are getting rare:
90% of the major classes of antibiotics have been discovered before 1980, only 3 out of 29 after 1980.
Pharma companies have little financial incitation to invest, as new compounds often have to be kept as “last resource” drugs.
Still, new approaches exist.
/end
90% of the major classes of antibiotics have been discovered before 1980, only 3 out of 29 after 1980.
Pharma companies have little financial incitation to invest, as new compounds often have to be kept as “last resource” drugs.
Still, new approaches exist.
/end
Reposted
Many people talk about the "Golden Age of Antibiotics", but I hadn't seen it visualized properly.
Just how many types of antibiotics were discovered during that time?
So, I visualized it myself!
Just how many types of antibiotics were discovered during that time?
So, I visualized it myself!
December 23, 2024 at 10:09 AM
Many people talk about the "Golden Age of Antibiotics", but I hadn't seen it visualized properly.
Just how many types of antibiotics were discovered during that time?
So, I visualized it myself!
Just how many types of antibiotics were discovered during that time?
So, I visualized it myself!
Reposted
Interested in predicting AMR in bacteria? We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. With @nwheeler443.bsky.social and former PhD student Yanying Yu. 🦠🧫🧬🖥️🧪
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Biased sampling confounds machine learning prediction of antimicrobial resistance
Antimicrobial resistance (AMR) poses a growing threat to human health. Increasingly, genome sequencing is being applied for the surveillance of bacterial pathogens, producing a wealth of data to train...
www.biorxiv.org
January 17, 2025 at 10:08 PM
Interested in predicting AMR in bacteria? We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. With @nwheeler443.bsky.social and former PhD student Yanying Yu. 🦠🧫🧬🖥️🧪
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted
This paper has been a long time coming: We looked at the genomes of historical bacterial samples over a century to look for trends of antibiotic resistance genes, finding multiple instances of them in infections before the age of antibiotics, but an increase in both frequency and mobility after
Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics https://www.biorxiv.org/content/10.1101/2025.01.16.633422v1
January 17, 2025 at 8:53 PM
This paper has been a long time coming: We looked at the genomes of historical bacterial samples over a century to look for trends of antibiotic resistance genes, finding multiple instances of them in infections before the age of antibiotics, but an increase in both frequency and mobility after
Reposted
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)