Calum Walsh 🇮🇪🇦🇺
@calumwalsh.bsky.social
Microbiome Bioinformatician
Centre for Pathogen Genomics
Doherty Institute
University of Melbourne
https://scholar.google.com.au/citations?user=CV66a6sAAAAJ&hl=en
Psyduck is my spirit animal.
Centre for Pathogen Genomics
Doherty Institute
University of Melbourne
https://scholar.google.com.au/citations?user=CV66a6sAAAAJ&hl=en
Psyduck is my spirit animal.
@secondcaptains.bsky.social Declan Rice halfway through a game of SOCOM
October 2, 2025 at 4:03 AM
@secondcaptains.bsky.social Declan Rice halfway through a game of SOCOM
Delighted to be able to contribute (barely) to the Data Reuse Consortium. A great idea - looking forward to the DRI tag becoming standard in microbiome research
New article on equitable reuse of public sequencing data, published in @natmicrobiol.nature.com!
Led by the Data reuse core team @lhug.bsky.social @environmicrobio.bsky.social Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and with Anke Heyer and The Data Reuse Consotrium!
Led by the Data reuse core team @lhug.bsky.social @environmicrobio.bsky.social Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and with Anke Heyer and The Data Reuse Consotrium!
September 30, 2025 at 4:35 AM
Delighted to be able to contribute (barely) to the Data Reuse Consortium. A great idea - looking forward to the DRI tag becoming standard in microbiome research
Timely reminder to add some art to the wall of my home office
Final presentation by Calum J. Walsh @calumwalsh.bsky.social
Rational Engineering of Live Bacterial Therapeutics from a Human Microbiome Biobank
Rational Engineering of Live Bacterial Therapeutics from a Human Microbiome Biobank
September 11, 2025 at 4:17 AM
Timely reminder to add some art to the wall of my home office
First output of our collaboration with Australian Red Cross Lifeblood - using genomics and culturing to look at the impact of processing on microbial composition and viability in FMT products
Stability and Processing Impacts on Faecal Microbiota Transplant Products: An Integrated Metagenomic-Culturomic Analysis https://www.biorxiv.org/content/10.1101/2025.09.02.673862v1
September 4, 2025 at 11:29 PM
First output of our collaboration with Australian Red Cross Lifeblood - using genomics and culturing to look at the impact of processing on microbial composition and viability in FMT products
Congrats Sai!
📣Publication alert!
Another great output from @metagymomics.bsky.social for his PhD. Looking at strain level genetic variation within members of the vaginal microbiome. #microsky @pauldcotter.bsky.social @calumwalsh.bsky.social
www.nature.com/articles/s41...
Another great output from @metagymomics.bsky.social for his PhD. Looking at strain level genetic variation within members of the vaginal microbiome. #microsky @pauldcotter.bsky.social @calumwalsh.bsky.social
www.nature.com/articles/s41...
Strain-level variation among vaginal Lactobacillus crispatus and Lactobacillus iners as identified by comparative metagenomics - npj Biofilms and Microbiomes
npj Biofilms and Microbiomes - Strain-level variation among vaginal Lactobacillus crispatus and Lactobacillus iners as identified by comparative metagenomics
www.nature.com
March 24, 2025 at 10:10 AM
Congrats Sai!
Reposted by Calum Walsh 🇮🇪🇦🇺
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
Great job all! Really interesting project to be a part of.
📣 New high-throughput method for determining genes involved in #AMR, Quantitative Mutational Scan Sequencing (QMS-Seq)
Special congratulations to MERMAN PhD student Matt @mattjago.bsky.social for his 1st first author paper & supervisor Mato Lagator!
#MicroSky 🦠🧫
www.nature.com/articles/s41...
Special congratulations to MERMAN PhD student Matt @mattjago.bsky.social for his 1st first author paper & supervisor Mato Lagator!
#MicroSky 🦠🧫
www.nature.com/articles/s41...
High-throughput method characterizes hundreds of previously unknown antibiotic resistance mutations - Nature Communications
Resistance mutations are challenging to characterize because their effects are highly context dependent. Here, authors present a quantitative mutant screening technique that deconstructs how factors l...
www.nature.com
January 17, 2025 at 10:56 PM
Great job all! Really interesting project to be a part of.
Reposted by Calum Walsh 🇮🇪🇦🇺
Big news from Finnish publication forum. Almost all MDPI and Frontiers journals will be downgraded to level 0 and thus are not considered as properly peer reviewed trustworthy scientific journals.
julkaisufoorumi.fi/en/news/chan...
julkaisufoorumi.fi/en/news/chan...
Changes to the classification
julkaisufoorumi.fi
December 16, 2024 at 10:12 AM
Big news from Finnish publication forum. Almost all MDPI and Frontiers journals will be downgraded to level 0 and thus are not considered as properly peer reviewed trustworthy scientific journals.
julkaisufoorumi.fi/en/news/chan...
julkaisufoorumi.fi/en/news/chan...
New Genus who dis?
The complete genome sequence of the crayfish pathogen Candidatus Paracoxiella cheracis n.g. n.sp. provides insight into pathogenesis and the phylogeny of the Coxiellaceae family https://www.biorxiv.org/content/10.1101/2024.12.02.626477v1
The complete genome sequence of the crayfish pathogen Candidatus Paracoxiella cheracis n.g. n.sp. provides insight into pathogenesis and the phylogeny of the Coxiellaceae family https://www.biorxiv.org/content/10.1101/2024.12.02.626477v1
The Coxiellaceae bacterial family, within the order Legionellales, is defined by a collection of poo
www.biorxiv.org
December 4, 2024 at 7:50 AM
New Genus who dis?
Reposted by Calum Walsh 🇮🇪🇦🇺
Security pro tip: if you find a USB key on the ground somewhere, DO NOT plug it in to your home computer.
Take it to the office and plug it in there. They have way better software that will mitigate any threats.
Take it to the office and plug it in there. They have way better software that will mitigate any threats.
November 27, 2024 at 6:09 PM
Security pro tip: if you find a USB key on the ground somewhere, DO NOT plug it in to your home computer.
Take it to the office and plug it in there. They have way better software that will mitigate any threats.
Take it to the office and plug it in there. They have way better software that will mitigate any threats.
Reposted by Calum Walsh 🇮🇪🇦🇺
I’m looking to recruit PhD candidates to work with me at Flinders University in #Bioinformatics. Details at the link below 👇 Please share to your networks!
www.flinders.edu.au/scholarships...
www.flinders.edu.au/scholarships...
PhD scholarship in bioinformatics - Flinders University
www.flinders.edu.au
November 13, 2024 at 2:25 AM
I’m looking to recruit PhD candidates to work with me at Flinders University in #Bioinformatics. Details at the link below 👇 Please share to your networks!
www.flinders.edu.au/scholarships...
www.flinders.edu.au/scholarships...
Reposted by Calum Walsh 🇮🇪🇦🇺
Our latest paper is out now. The brilliant Chris Connor’s entire PhD in one paper. And I hope a new avenue of research opened in MDR E. coli
journals.plos.org/plosbiology/...
1/n
journals.plos.org/plosbiology/...
1/n
October 18, 2023 at 6:49 AM
Our latest paper is out now. The brilliant Chris Connor’s entire PhD in one paper. And I hope a new avenue of research opened in MDR E. coli
journals.plos.org/plosbiology/...
1/n
journals.plos.org/plosbiology/...
1/n
Reposted by Calum Walsh 🇮🇪🇦🇺
Did a big thread on Twitter, but will keep it short here.
We have a new paper out! If you're into signal transduction, staph aureus, and/or nifty molecular biology then check it out.
journals.asm.org/doi/10.1128/...
We have a new paper out! If you're into signal transduction, staph aureus, and/or nifty molecular biology then check it out.
journals.asm.org/doi/10.1128/...
The two-component system WalKR provides an essential link between cell wall homeostasis and DNA repl...
The opportunistic human pathogen Staphylococcus aureus uses an array of protein sensing systems called two-component systems (TCS) to sense
environmental signals and adapt its physiology in response b...
journals.asm.org
October 17, 2023 at 7:02 AM
Did a big thread on Twitter, but will keep it short here.
We have a new paper out! If you're into signal transduction, staph aureus, and/or nifty molecular biology then check it out.
journals.asm.org/doi/10.1128/...
We have a new paper out! If you're into signal transduction, staph aureus, and/or nifty molecular biology then check it out.
journals.asm.org/doi/10.1128/...