Gerry Tonkin-Hill
@gerrythill.bsky.social
Group leader at Peter Mac & the Doherty Institute in Melbourne, Australia
microbial genomics, statistics, machine learning
microbial genomics, statistics, machine learning
Reposted by Gerry Tonkin-Hill
We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7
#microsky
#microsky
Metalog
Metalog is a repository of manually annotated metadata (or contextual data) for metagenomic sequencing data from across the globe.
metalog.embl.de
August 15, 2025 at 8:07 AM
We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7
#microsky
#microsky
Reposted by Gerry Tonkin-Hill
Reposted by Gerry Tonkin-Hill
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
September 25, 2025 at 9:29 PM
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
Reposted by Gerry Tonkin-Hill
Happy to see that Spacedust is now published on Nature Methods!
It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes.
1/6🧵
It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes.
1/6🧵
Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data.
@ruoshiz.bsky.social @milot.bsky.social
www.nature.com/articles/s41...
@ruoshiz.bsky.social @milot.bsky.social
www.nature.com/articles/s41...
De novo discovery of conserved gene clusters in microbial genomes with Spacedust - Nature Methods
This work presents Spacedust, a tool for de novo identification of conserved gene clusters from metagenomic data.
www.nature.com
September 16, 2025 at 8:26 PM
Happy to see that Spacedust is now published on Nature Methods!
It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes.
1/6🧵
It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes.
1/6🧵
Reposted by Gerry Tonkin-Hill
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 Gerry Tonkin-Hill
Large AI models are reported to achieve high accuracy (AUROC) predicting pathogenic variants across the genome.
A preprint reports that the predictions are based on splice variants. Using only this info (no sequences, no AI) achieves AUROC=0.944 across noncoding variants.
1/2
A preprint reports that the predictions are based on splice variants. Using only this info (no sequences, no AI) achieves AUROC=0.944 across noncoding variants.
1/2
September 9, 2025 at 11:01 PM
Large AI models are reported to achieve high accuracy (AUROC) predicting pathogenic variants across the genome.
A preprint reports that the predictions are based on splice variants. Using only this info (no sequences, no AI) achieves AUROC=0.944 across noncoding variants.
1/2
A preprint reports that the predictions are based on splice variants. Using only this info (no sequences, no AI) achieves AUROC=0.944 across noncoding variants.
1/2
Reposted by Gerry Tonkin-Hill
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
September 3, 2025 at 8:39 AM
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Reposted by Gerry Tonkin-Hill
What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years?
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics
Antibiotic resistance is frequently observed shortly after the clinical introduction of an antibiotic. Whether and how frequently that resistance occurred before the introduction is harder to determin...
www.microbiologyresearch.org
September 1, 2025 at 5:49 PM
What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years?
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
Reposted by Gerry Tonkin-Hill
The 10th anniversary #ABACBS conference will be held in Adelaide from Nov 24-28. If you're thinking of coming, get in quick, as it's going to be a big week: A fantastic #bioinformatics conference with outstanding national and international speakers, and we're wrapping up the ABACBS week an AC/DC gig
July 17, 2025 at 5:43 AM
The 10th anniversary #ABACBS conference will be held in Adelaide from Nov 24-28. If you're thinking of coming, get in quick, as it's going to be a big week: A fantastic #bioinformatics conference with outstanding national and international speakers, and we're wrapping up the ABACBS week an AC/DC gig
Reposted by Gerry Tonkin-Hill
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
July 16, 2025 at 9:59 PM
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
Reposted by Gerry Tonkin-Hill
The day is finally here! 🎉 We’re releasing the invited speaker line-up, key dates, and lots more info for ABACBS 2025.
Check it out and share widely: www.abacbs.org/abacbs2025
Registrations and abstract submissions open next week, with abstracts due in August!
Check it out and share widely: www.abacbs.org/abacbs2025
Registrations and abstract submissions open next week, with abstracts due in August!
ABACBS 2025 Conference
Adelaide, South Australia. Nov. 24-
www.abacbs.org
July 4, 2025 at 4:34 AM
The day is finally here! 🎉 We’re releasing the invited speaker line-up, key dates, and lots more info for ABACBS 2025.
Check it out and share widely: www.abacbs.org/abacbs2025
Registrations and abstract submissions open next week, with abstracts due in August!
Check it out and share widely: www.abacbs.org/abacbs2025
Registrations and abstract submissions open next week, with abstracts due in August!
Reposted by Gerry Tonkin-Hill
Are you a recent PhD (or soon to be PhD) from outside Canada looking to do a postdoc in Quebec?
Get in touch if you are excited about microbes, evolution, ecology, genomics (or all of the above!) and I'd be happy to help develop a project together!
www.mcgill.ca/gps/funding/...
Get in touch if you are excited about microbes, evolution, ecology, genomics (or all of the above!) and I'd be happy to help develop a project together!
www.mcgill.ca/gps/funding/...
PBEEE/Quebec Merit Scholarship for Foreign Postdocs and Visiting Research Student and Visiting Researchers
**Note that the FRQ is in the process of revamping their webpages. We will update links soon as we can with the current 2025 year's information. Be sure to check back to see if any eligibility or docu...
www.mcgill.ca
June 11, 2025 at 7:00 PM
Are you a recent PhD (or soon to be PhD) from outside Canada looking to do a postdoc in Quebec?
Get in touch if you are excited about microbes, evolution, ecology, genomics (or all of the above!) and I'd be happy to help develop a project together!
www.mcgill.ca/gps/funding/...
Get in touch if you are excited about microbes, evolution, ecology, genomics (or all of the above!) and I'd be happy to help develop a project together!
www.mcgill.ca/gps/funding/...
Reposted by Gerry Tonkin-Hill
www.bath.ac.uk/jobs/Vacancy...
Post doc available to work on Candida genomics with me at the Milner Centre for Evolution (U Bath, UK) as part of the JPIAMR funded project Fugaci www.jpiamr.eu/projects/fug...
For queries, email me!
Post doc available to work on Candida genomics with me at the Milner Centre for Evolution (U Bath, UK) as part of the JPIAMR funded project Fugaci www.jpiamr.eu/projects/fug...
For queries, email me!
FuGACI – JPIAMR
JPIAMR is a global collaborative organisation and platform, engaging 28 nations to curb antimicrobial resistance (AMR) with a One Health approach.
www.jpiamr.eu
May 20, 2025 at 12:39 PM
www.bath.ac.uk/jobs/Vacancy...
Post doc available to work on Candida genomics with me at the Milner Centre for Evolution (U Bath, UK) as part of the JPIAMR funded project Fugaci www.jpiamr.eu/projects/fug...
For queries, email me!
Post doc available to work on Candida genomics with me at the Milner Centre for Evolution (U Bath, UK) as part of the JPIAMR funded project Fugaci www.jpiamr.eu/projects/fug...
For queries, email me!
Reposted by Gerry Tonkin-Hill
Delighted our study (7+ years in the making) is out today in Nature. In a nutshell, 48 hours of antibiotics in week 1 led to impaired vaccine responses up to 15 months later in infants. We show (in-vivo) a probiotic can fix it #microbiome #science #immunology
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Bifidobacteria support optimal infant vaccine responses - Nature
Neonatal antibiotic use is shown to reduce immune response to infant vaccines, accompanied by reduced abundance of Bifidobacteria in the gut microbiota, with experiments in mice indicating that probio...
www.nature.com
April 2, 2025 at 11:33 PM
Delighted our study (7+ years in the making) is out today in Nature. In a nutshell, 48 hours of antibiotics in week 1 led to impaired vaccine responses up to 15 months later in infants. We show (in-vivo) a probiotic can fix it #microbiome #science #immunology
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Gerry Tonkin-Hill
Being able to data plasmid acquisition, and to see the diversity of plasmids being gained and lost from lineages, was really eye opening! It was a pleasure to contribute my tiny bit to this huge paper and the data has so much more to give! @arredondo.bsky.social @gerrythill.bsky.social et al.
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 11:34 AM
Being able to data plasmid acquisition, and to see the diversity of plasmids being gained and lost from lineages, was really eye opening! It was a pleasure to contribute my tiny bit to this huge paper and the data has so much more to give! @arredondo.bsky.social @gerrythill.bsky.social et al.
Reposted by Gerry Tonkin-Hill
We are recruiting a group leader in laboratory research at Peter Mac Cancer Centre in
Melbourne, Australia 🔬🦘💥
Work in a cutting edge research environment in a vibrant world city!
We value research excellence, creativity and diversity.
Join us!
careers.petermac.org/job/MELBOURN...
Melbourne, Australia 🔬🦘💥
Work in a cutting edge research environment in a vibrant world city!
We value research excellence, creativity and diversity.
Join us!
careers.petermac.org/job/MELBOURN...
Group Leader
Group Leader
careers.petermac.org
March 5, 2025 at 8:04 AM
We are recruiting a group leader in laboratory research at Peter Mac Cancer Centre in
Melbourne, Australia 🔬🦘💥
Work in a cutting edge research environment in a vibrant world city!
We value research excellence, creativity and diversity.
Join us!
careers.petermac.org/job/MELBOURN...
Melbourne, Australia 🔬🦘💥
Work in a cutting edge research environment in a vibrant world city!
We value research excellence, creativity and diversity.
Join us!
careers.petermac.org/job/MELBOURN...
Reposted by Gerry Tonkin-Hill
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 by Gerry Tonkin-Hill
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)
Reposted by Gerry Tonkin-Hill
I just made a first release of TNA - new tool to compare 2 bacterial genomes. Is shamelessly inspired by ACT, but should be simpler to use. Drag-n-drop two genomes: it runs BLAST for you and then you can visualize. For Mac, Windows 11, Linux tna.readthedocs.io
TNA documentation — TNA 0.0.1 documentation
tna.readthedocs.io
November 29, 2024 at 11:38 AM
I just made a first release of TNA - new tool to compare 2 bacterial genomes. Is shamelessly inspired by ACT, but should be simpler to use. Drag-n-drop two genomes: it runs BLAST for you and then you can visualize. For Mac, Windows 11, Linux tna.readthedocs.io
Reposted by Gerry Tonkin-Hill
Brisk: Exact resource-efficient dictionary for k-mers https://www.biorxiv.org/content/10.1101/2024.11.26.625346v1
Brisk: Exact resource-efficient dictionary for k-mers https://www.biorxiv.org/content/10.1101/2024.11.26.625346v1
The rapid advancements in DNA sequencing technology have led to an unprecedented increase in the gen
www.biorxiv.org
November 29, 2024 at 5:47 AM
Brisk: Exact resource-efficient dictionary for k-mers https://www.biorxiv.org/content/10.1101/2024.11.26.625346v1
Reposted by Gerry Tonkin-Hill
How invasive are different E .coli capsules and how many are there? Find out here and use the group 2 and 3 database to type your own!
medrxiv.org/cgi/content/...
medrxiv.org/cgi/content/...
Group 2 and 3 ABC-transporter dependant capsular K-loci contribute significantly to variation in the invasive potential of Escherichia coli
The major opportunistic pathogen Escherichia coli is the largest cause of antimicrobial resistance (AMR) associated infections and deaths globally. Considerable antigenic diversity has been documented...
medrxiv.org
November 27, 2024 at 2:44 AM
How invasive are different E .coli capsules and how many are there? Find out here and use the group 2 and 3 database to type your own!
medrxiv.org/cgi/content/...
medrxiv.org/cgi/content/...
Reposted by Gerry Tonkin-Hill
Super excited that our JPIAMR grant on Candida has been funded 🙌https://www.jpiamr.eu/projects/fugaci/
Keep your eyes peeled as there will be a lot of postdoc positions available on this grant, and a PhD position with me and Anita!
Keep your eyes peeled as there will be a lot of postdoc positions available on this grant, and a PhD position with me and Anita!
November 19, 2024 at 1:38 AM
Super excited that our JPIAMR grant on Candida has been funded 🙌https://www.jpiamr.eu/projects/fugaci/
Keep your eyes peeled as there will be a lot of postdoc positions available on this grant, and a PhD position with me and Anita!
Keep your eyes peeled as there will be a lot of postdoc positions available on this grant, and a PhD position with me and Anita!
Reposted by Gerry Tonkin-Hill
Always exciting to see journals publish negative results on the microbiome!
www.cell.com/med/fulltext...
www.cell.com/med/fulltext...
No association between the early-life gut microbiota and childhood body mass index and body composition
The gut microbiota has been implicated in the development of obesity, and especially
early life has been proposed to be important. Poulsen et al. followed 700 children
from birth and found no consiste...
www.cell.com
November 14, 2024 at 6:41 PM
Always exciting to see journals publish negative results on the microbiome!
www.cell.com/med/fulltext...
www.cell.com/med/fulltext...
Reposted by Gerry Tonkin-Hill
New preprint up! We sequenced hundreds of samples from across one of Earth's oldest living organisms - the Pando aspen clone - to understand how mutations accumulate and spread in long-lived clonal organisms. Our results were…surprising. 1/30
October 26, 2024 at 5:45 PM
New preprint up! We sequenced hundreds of samples from across one of Earth's oldest living organisms - the Pando aspen clone - to understand how mutations accumulate and spread in long-lived clonal organisms. Our results were…surprising. 1/30
Reposted by Gerry Tonkin-Hill
This is amazing and important work by Glen Carter and colleagues at the University of Melbourne
'Rifaximin prophylaxis causes resistance to the last-resort antibiotic daptomycin in Enterococcus'
www.nature.com/articles/s41...
'Rifaximin prophylaxis causes resistance to the last-resort antibiotic daptomycin in Enterococcus'
www.nature.com/articles/s41...
Rifaximin prophylaxis causes resistance to the last-resort antibiotic daptomycin - Nature
Rifaximin use, particularly in patients with liver cirrhosis, may be compromising the clinical use of daptomycin.
www.nature.com
October 24, 2024 at 7:09 AM
This is amazing and important work by Glen Carter and colleagues at the University of Melbourne
'Rifaximin prophylaxis causes resistance to the last-resort antibiotic daptomycin in Enterococcus'
www.nature.com/articles/s41...
'Rifaximin prophylaxis causes resistance to the last-resort antibiotic daptomycin in Enterococcus'
www.nature.com/articles/s41...