William Navarre
@drxenogene.bsky.social
Professor of microbiology at the University of Toronto Department of Molecular Genetics
Reposted by William Navarre
www.nature.com/articles/d41...
Coverage of our collaboration with the Liu group..
' “This is crazy directed evolution!” - Makoto Saito'
Coverage of our collaboration with the Liu group..
' “This is crazy directed evolution!” - Makoto Saito'
Powerful CRISPR system inserts whole gene into human DNA
‘Directed’ evolution in the laboratory creates an editing tool that outperforms classic CRISPR systems.
www.nature.com
May 16, 2025 at 5:54 PM
www.nature.com/articles/d41...
Coverage of our collaboration with the Liu group..
' “This is crazy directed evolution!” - Makoto Saito'
Coverage of our collaboration with the Liu group..
' “This is crazy directed evolution!” - Makoto Saito'
Reposted by William Navarre
Extracting @NCBI SRA files with fasterq-dump can require 17x the size of the accession while decompressing. Our new tool xsra extracts sequences at 5x throughput with significantly less disk usage, built-in compression, and optional BINSEQ outputs
github.com/arcInstitute...
github.com/arcInstitute...
GitHub - ArcInstitute/xsra: An efficient CLI to extract sequences from the SRA
An efficient CLI to extract sequences from the SRA - ArcInstitute/xsra
github.com
April 29, 2025 at 9:03 PM
Extracting @NCBI SRA files with fasterq-dump can require 17x the size of the accession while decompressing. Our new tool xsra extracts sequences at 5x throughput with significantly less disk usage, built-in compression, and optional BINSEQ outputs
github.com/arcInstitute...
github.com/arcInstitute...
Reposted by William Navarre
Wow.
Colon cancer is on the rise around the world. This new report concludes that early-life exposure to gut bacteria that produces colibactin, which is mutagenic, may be contributing
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Geographic and age variations in mutational processes in colorectal cancer - Nature
Nature - Geographic and age variations in mutational processes in colorectal cancer
www.nature.com
April 23, 2025 at 8:29 PM
Wow.
Reposted by William Navarre
Structure of the Pseudomonas aeruginosa PAO1 Type IV pilus
Finally out in PLOS Pathogens. Congrats Hannah Ochner and co-authors. @mrclmb.bsky.social
journals.plos.org/plospathogen...
Finally out in PLOS Pathogens. Congrats Hannah Ochner and co-authors. @mrclmb.bsky.social
journals.plos.org/plospathogen...
December 16, 2024 at 3:53 PM
Structure of the Pseudomonas aeruginosa PAO1 Type IV pilus
Finally out in PLOS Pathogens. Congrats Hannah Ochner and co-authors. @mrclmb.bsky.social
journals.plos.org/plospathogen...
Finally out in PLOS Pathogens. Congrats Hannah Ochner and co-authors. @mrclmb.bsky.social
journals.plos.org/plospathogen...
Reposted by William Navarre
The latest discovery from the lab and great colleagues at McMaster and U Illinois, Chicago. Lariocidin, a new lasso peptide antibiotic that inhibits the ribosome. rdcu.be/efdha
A broad-spectrum lasso peptide antibiotic targeting the bacterial ribosome
Nature - A new lasso peptide antibiotic exhibits broad-spectrum activity against Gram-negative and Gram-positive bacteria by interfering with bacterial protein synthesis, is unaffected by common...
rdcu.be
March 26, 2025 at 7:28 PM
The latest discovery from the lab and great colleagues at McMaster and U Illinois, Chicago. Lariocidin, a new lasso peptide antibiotic that inhibits the ribosome. rdcu.be/efdha
Reposted by William Navarre
Finally in peer-reviewed form: Mapping the ultrastructural topology of the corynebacterial cell surface. @bupbuse.bsky.social @vikramalva.bsky.social
Please also see concurrent beautiful work from @adriasogues.bsky.social and Han Remaut.
Please also see concurrent beautiful work from @adriasogues.bsky.social and Han Remaut.
The unique #CellEnvelope of #corynebacteria: @tbharat-lab.bsky.social &co map the C. glutamicum cell surface, revealing a patchy S-layer & specific assembly of the PS2 protein, thereby informing our understanding of cell envelopes that contain #MycolicAcids @plosbiology.org 🧪 plos.io/3Y6JNgw
April 23, 2025 at 2:07 PM
Finally in peer-reviewed form: Mapping the ultrastructural topology of the corynebacterial cell surface. @bupbuse.bsky.social @vikramalva.bsky.social
Please also see concurrent beautiful work from @adriasogues.bsky.social and Han Remaut.
Please also see concurrent beautiful work from @adriasogues.bsky.social and Han Remaut.
Reposted by William Navarre
People spend a lot of time wondering why the left is worse at using independent media to control the national narrative.
A useful exercise is to ask why the left is also worse at selling snake oil and pyramid schemes, because I think the reasons are basically exactly the same.
A useful exercise is to ask why the left is also worse at selling snake oil and pyramid schemes, because I think the reasons are basically exactly the same.
April 21, 2025 at 1:31 AM
People spend a lot of time wondering why the left is worse at using independent media to control the national narrative.
A useful exercise is to ask why the left is also worse at selling snake oil and pyramid schemes, because I think the reasons are basically exactly the same.
A useful exercise is to ask why the left is also worse at selling snake oil and pyramid schemes, because I think the reasons are basically exactly the same.
@nytimes.com - it’s not “deportation” if you aren’t returned to your home country and you’re put in a foreign prison without a trial or any legal representation. Call it what it is and quit obfuscating.
April 20, 2025 at 5:57 PM
@nytimes.com - it’s not “deportation” if you aren’t returned to your home country and you’re put in a foreign prison without a trial or any legal representation. Call it what it is and quit obfuscating.
Reposted by William Navarre
Excited to share a main project from my PhD, out now in
@naturecomms.bsky.social! 📝
We've designed and brought to life the “CORE cycle” – a new-to-nature pathway that provides a novel route for biological CO2 capture 🦠🌱
nature.com/articles/s41...
Take a look! Thread below... 🧵
@naturecomms.bsky.social! 📝
We've designed and brought to life the “CORE cycle” – a new-to-nature pathway that provides a novel route for biological CO2 capture 🦠🌱
nature.com/articles/s41...
Take a look! Thread below... 🧵
April 4, 2025 at 10:03 AM
Excited to share a main project from my PhD, out now in
@naturecomms.bsky.social! 📝
We've designed and brought to life the “CORE cycle” – a new-to-nature pathway that provides a novel route for biological CO2 capture 🦠🌱
nature.com/articles/s41...
Take a look! Thread below... 🧵
@naturecomms.bsky.social! 📝
We've designed and brought to life the “CORE cycle” – a new-to-nature pathway that provides a novel route for biological CO2 capture 🦠🌱
nature.com/articles/s41...
Take a look! Thread below... 🧵
Reposted by William Navarre
Read ‘Plasmid-driven strategies for clone success in Escherichia coli.’ From @sangerinstitute.bsky.social @uitnorgesarktiske.bsky.social, the University of Oslo, and others, in @naturecomms.bsky.social, here ⤵️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Plasmid-driven strategies for clone success in Escherichia coli - Nature Communications
Plasmids can encode multiple traits that contribute to the emergence and dissemination of their bacterial hosts. Here the authors use Nanopore long-read technology to sequence the complete genomes of ...
www.nature.com
April 3, 2025 at 10:33 AM
Read ‘Plasmid-driven strategies for clone success in Escherichia coli.’ From @sangerinstitute.bsky.social @uitnorgesarktiske.bsky.social, the University of Oslo, and others, in @naturecomms.bsky.social, here ⤵️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by William Navarre
Quick weekend read when you get the chance! I’m excited to announce that the preprint for a major chapter of my thesis work is out on BioRxiv! In this study, we highlight the essential role that pyrimidine metabolism plays in promoting activity of the SaeRS TCS in Staphylococcus aureus! 1/3
Pyrimidine sufficiency is required for Sae two-component system signaling in Staphylococcus aureus https://www.biorxiv.org/content/10.1101/2025.03.20.644390v1
March 22, 2025 at 3:09 AM
Quick weekend read when you get the chance! I’m excited to announce that the preprint for a major chapter of my thesis work is out on BioRxiv! In this study, we highlight the essential role that pyrimidine metabolism plays in promoting activity of the SaeRS TCS in Staphylococcus aureus! 1/3
Reposted by William Navarre
If you generate, or use MAGs, you should really read the work we have done benchmarking their limitations. Using complex mock communities (70 species), we assessed how deeply you need to sequence to accurately conduct common metaG analyses. Webwere shocked to see even HQ MAGs are often chimeric!
Benchmarking of shotgun sequencing depth highlights strain-level limitations of metagenomic analysis https://www.biorxiv.org/content/10.1101/2025.03.27.645659v1
March 28, 2025 at 9:17 AM
If you generate, or use MAGs, you should really read the work we have done benchmarking their limitations. Using complex mock communities (70 species), we assessed how deeply you need to sequence to accurately conduct common metaG analyses. Webwere shocked to see even HQ MAGs are often chimeric!
Reposted by William Navarre
March 21, 2025 at 7:29 PM
Reposted by William Navarre
we recently found some really neat RNA-guided DNA-cutting systems in phages. Despite remarkable similarities to CRISPR systems, including encoding guide RNAs in arrays, they appear entirely evolutionarily distinct (but definitely related to snoRNAs 🤓)
We decided to call them TIGR-Tas systems 🐯
We decided to call them TIGR-Tas systems 🐯
March 1, 2025 at 12:18 AM
we recently found some really neat RNA-guided DNA-cutting systems in phages. Despite remarkable similarities to CRISPR systems, including encoding guide RNAs in arrays, they appear entirely evolutionarily distinct (but definitely related to snoRNAs 🤓)
We decided to call them TIGR-Tas systems 🐯
We decided to call them TIGR-Tas systems 🐯
Reposted by William Navarre
THIS IS INCREDIBLE! Cohen Children’s Medical Center has confirmed that it has successfully ELIMINATED sickle cell disease from Sebastien Beauzile, using the groundbreaking genetic treatment Lyfgenia. He has made HISTORY by becoming the FIRST in New York to be CURED of sickle cell anemia! 🧪🧵⬇️
March 15, 2025 at 4:00 PM
THIS IS INCREDIBLE! Cohen Children’s Medical Center has confirmed that it has successfully ELIMINATED sickle cell disease from Sebastien Beauzile, using the groundbreaking genetic treatment Lyfgenia. He has made HISTORY by becoming the FIRST in New York to be CURED of sickle cell anemia! 🧪🧵⬇️
Reposted by William Navarre
1/ @nabroderick.bsky.social and @harmitmalik.bsky.social have posed questions asking how to US students may seek opportunities outside the US (EU and Canada). As a Department Chair in Canada in #immunosky, I offer my perspective in this "bluetorial".
March 4, 2025 at 3:29 PM
1/ @nabroderick.bsky.social and @harmitmalik.bsky.social have posed questions asking how to US students may seek opportunities outside the US (EU and Canada). As a Department Chair in Canada in #immunosky, I offer my perspective in this "bluetorial".
Reposted by William Navarre
Hate that it has come to this, but it's time to consider PubMed vulnerable to enshittification. My latest post @plos.org discusses the lines we need to fight to hold – and alternatives we can rely on internationally:
absolutelymaybe.plos.org/2025/02/14/w...
#medlibs
absolutelymaybe.plos.org/2025/02/14/w...
#medlibs
What if We Can't Rely on PubMed? - Absolutely Maybe
PubMed is incredibly reliable. And a lot depends on it. It’s an ecosystem built around MEDLINE, the steady feed of new publications…
absolutelymaybe.plos.org
February 14, 2025 at 6:06 AM
Hate that it has come to this, but it's time to consider PubMed vulnerable to enshittification. My latest post @plos.org discusses the lines we need to fight to hold – and alternatives we can rely on internationally:
absolutelymaybe.plos.org/2025/02/14/w...
#medlibs
absolutelymaybe.plos.org/2025/02/14/w...
#medlibs
Reposted by William Navarre
Reposted by William Navarre
Visibility matters. In fact, I am sure that many deserving colleagues are not even nominated because they do not have AAM fellows who can act a main nominator and co-nominator (you need two).
February 15, 2025 at 6:18 PM
Visibility matters. In fact, I am sure that many deserving colleagues are not even nominated because they do not have AAM fellows who can act a main nominator and co-nominator (you need two).
Reposted by William Navarre
The quickest way to a man’s heart is to insert a needle between the xiphoid process and left costal margin at a 15-to-30-degree angle, directed towards the left shoulder
February 14, 2025 at 12:26 PM
The quickest way to a man’s heart is to insert a needle between the xiphoid process and left costal margin at a 15-to-30-degree angle, directed towards the left shoulder
Reposted by William Navarre
A newly discovered microbial enzyme efficiently breaks down cellulose, leading to enhanced glucose release from biomass when expressed in engineered fungi #NBTHighlight nature.com/articles/s41...
A metagenomic ‘dark matter’ enzyme catalyses oxidative cellulose conversion - Nature
A metalloenzyme capable of oxidatively cleaving cellulose, found in a microbial community specialized in lignocellulose degradation, could enable sustainable biofuel production.
nature.com
February 13, 2025 at 6:22 PM
A newly discovered microbial enzyme efficiently breaks down cellulose, leading to enhanced glucose release from biomass when expressed in engineered fungi #NBTHighlight nature.com/articles/s41...
Reposted by William Navarre
Microbiome science needs more microbiologists- A new commentary authored by myself and @abaumler.bsky.social www.nature.com/articles/s41...
Microbiome science needs more microbiologists - Nature Microbiology
Microbiome science is a multi-disciplinary field, but classical microbiologists are needed to ensure advances are grounded in our understanding of basic microbiological concepts.
www.nature.com
January 23, 2025 at 5:14 PM
Microbiome science needs more microbiologists- A new commentary authored by myself and @abaumler.bsky.social www.nature.com/articles/s41...
Reposted by William Navarre
Read the full paper here: journals.asm.org/doi/full/10.... @zaminiqbal.bsky.social @uni-freiburg.de Many thanks go to the BMBF for funding my junior research group!
Tracking clonal and plasmid transmission in colistin- and carbapenem-resistant Klebsiella pneumoniae | mSystems
Antimicrobial resistance occupies a central stage in global public health emergencies. Recently, efforts to track the genetic elements that facilitate the spread of resistance genes in plasmids outbreaks, utilizing short-read sequencing technologies, have ...
journals.asm.org
January 14, 2025 at 2:20 PM
Read the full paper here: journals.asm.org/doi/full/10.... @zaminiqbal.bsky.social @uni-freiburg.de Many thanks go to the BMBF for funding my junior research group!
Reposted by William Navarre
💊🦠OUT NOW - comprehensive analysis of the propensity of ESKAPE pathogens to evolve resistance to new and in development antibiotics by Csaba Pal, Balint Kintses, Balazs Papp and colleagues. Dive in here...
www.nature.com/articles/s41...
www.nature.com/articles/s41...
ESKAPE pathogens rapidly develop resistance against antibiotics in development in vitro - Nature Microbiology
An extensive experimental analysis of resistance to antibiotics in development or introduced post-2017 in ESKAPE bacteria reveals the dynamics of resistance acquisition, mutational targets and the pre...
www.nature.com
January 13, 2025 at 1:57 PM
💊🦠OUT NOW - comprehensive analysis of the propensity of ESKAPE pathogens to evolve resistance to new and in development antibiotics by Csaba Pal, Balint Kintses, Balazs Papp and colleagues. Dive in here...
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by William Navarre
Valuable contribution to the issue of how we ight look at data that have evolved in a hierarchical manner: www.nature.com/articles/s41...
A phylogenetic approach to comparative genomics - Nature Reviews Genetics
Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests. The authors review the application ...
www.nature.com
January 12, 2025 at 10:17 PM
Valuable contribution to the issue of how we ight look at data that have evolved in a hierarchical manner: www.nature.com/articles/s41...