Alison Mather
@alisonmather.bsky.social
Epidemiology, microbial (meta)genomics, antimicrobial resistance, One Health, Professor of Microbial Genomic Epidemiology at Quadram Institute Bioscience & University of East Anglia.
Reposted by Alison Mather
Happy New Year – new role! 🎉
We’re looking for a PostDoc to join us in @halllab.bsky.social @unibirmingham.bsky.social.
Full-time, fixed-term to March 2028. Note tight closing date: 11 Jan 2026. CV + cover letter (submit via portal).
Further details 👇
edzz.fa.em3.oraclecloud.com/hcmUI/Candid...
We’re looking for a PostDoc to join us in @halllab.bsky.social @unibirmingham.bsky.social.
Full-time, fixed-term to March 2028. Note tight closing date: 11 Jan 2026. CV + cover letter (submit via portal).
Further details 👇
edzz.fa.em3.oraclecloud.com/hcmUI/Candid...
Research Fellow - Department of Microbes, Infection and Microbiomes - 106849 - Grade 7
To create and contribute to the creation of knowledge by undertaking a specified range of activities as part of an Investigator project funded by Wellcome, focusing on understanding microbial and diet...
edzz.fa.em3.oraclecloud.com
January 7, 2026 at 5:06 PM
Happy New Year – new role! 🎉
We’re looking for a PostDoc to join us in @halllab.bsky.social @unibirmingham.bsky.social.
Full-time, fixed-term to March 2028. Note tight closing date: 11 Jan 2026. CV + cover letter (submit via portal).
Further details 👇
edzz.fa.em3.oraclecloud.com/hcmUI/Candid...
We’re looking for a PostDoc to join us in @halllab.bsky.social @unibirmingham.bsky.social.
Full-time, fixed-term to March 2028. Note tight closing date: 11 Jan 2026. CV + cover letter (submit via portal).
Further details 👇
edzz.fa.em3.oraclecloud.com/hcmUI/Candid...
Reposted by Alison Mather
8/
Authored by Aldert Zomer, Sam Nooij, Cailean Carter, and Alison Mather (@alisonmather.bsky.social).
Supported by the JPIAMR MEGAISurv project: jpiamr.eu/projects/meg...
Thanks to all contributing to strengthening mutation-focused AMR surveillance in metagenomic data.
Authored by Aldert Zomer, Sam Nooij, Cailean Carter, and Alison Mather (@alisonmather.bsky.social).
Supported by the JPIAMR MEGAISurv project: jpiamr.eu/projects/meg...
Thanks to all contributing to strengthening mutation-focused AMR surveillance in metagenomic data.
MEGAISurv – JPIAMR
JPIAMR is a global collaborative organisation and platform, engaging 28 nations to curb antimicrobial resistance (AMR) with a One Health approach.
jpiamr.eu
December 8, 2025 at 10:00 AM
8/
Authored by Aldert Zomer, Sam Nooij, Cailean Carter, and Alison Mather (@alisonmather.bsky.social).
Supported by the JPIAMR MEGAISurv project: jpiamr.eu/projects/meg...
Thanks to all contributing to strengthening mutation-focused AMR surveillance in metagenomic data.
Authored by Aldert Zomer, Sam Nooij, Cailean Carter, and Alison Mather (@alisonmather.bsky.social).
Supported by the JPIAMR MEGAISurv project: jpiamr.eu/projects/meg...
Thanks to all contributing to strengthening mutation-focused AMR surveillance in metagenomic data.
Reposted by Alison Mather
7/
The code is open-source, with both a web-based interface and the full repository available:
Web tool: klif.uu.nl/metapointfin...
GitHub: github.com/aldertzomer/...
Feedback on extending reference sets and integrating the approach into surveillance pipelines is welcome.
The code is open-source, with both a web-based interface and the full repository available:
Web tool: klif.uu.nl/metapointfin...
GitHub: github.com/aldertzomer/...
Feedback on extending reference sets and integrating the approach into surveillance pipelines is welcome.
December 8, 2025 at 10:00 AM
7/
The code is open-source, with both a web-based interface and the full repository available:
Web tool: klif.uu.nl/metapointfin...
GitHub: github.com/aldertzomer/...
Feedback on extending reference sets and integrating the approach into surveillance pipelines is welcome.
The code is open-source, with both a web-based interface and the full repository available:
Web tool: klif.uu.nl/metapointfin...
GitHub: github.com/aldertzomer/...
Feedback on extending reference sets and integrating the approach into surveillance pipelines is welcome.
Reposted by Alison Mather
6/
We applied the tool to public datasets on fluoroquinolone, β-lactam, and rifamycin resistance, showing how mutation-level profiling resolves discrepancies between phenotypes and gene-only predictions.
We applied the tool to public datasets on fluoroquinolone, β-lactam, and rifamycin resistance, showing how mutation-level profiling resolves discrepancies between phenotypes and gene-only predictions.
December 8, 2025 at 10:00 AM
6/
We applied the tool to public datasets on fluoroquinolone, β-lactam, and rifamycin resistance, showing how mutation-level profiling resolves discrepancies between phenotypes and gene-only predictions.
We applied the tool to public datasets on fluoroquinolone, β-lactam, and rifamycin resistance, showing how mutation-level profiling resolves discrepancies between phenotypes and gene-only predictions.
Reposted by Alison Mather
5/
In benchmarks using simulated reads (100–5000 bp), MetaPointFinder outperformed existing mutation mappers and showed strong recovery of mutation-positive reads, particularly from long-read metagenomes.
In benchmarks using simulated reads (100–5000 bp), MetaPointFinder outperformed existing mutation mappers and showed strong recovery of mutation-positive reads, particularly from long-read metagenomes.
December 8, 2025 at 10:00 AM
5/
In benchmarks using simulated reads (100–5000 bp), MetaPointFinder outperformed existing mutation mappers and showed strong recovery of mutation-positive reads, particularly from long-read metagenomes.
In benchmarks using simulated reads (100–5000 bp), MetaPointFinder outperformed existing mutation mappers and showed strong recovery of mutation-positive reads, particularly from long-read metagenomes.
Reposted by Alison Mather
4/
The outputs enable calculation of both relative abundance of mutation-driven AMR and the proportion of resistant reads among all reads mapping to a locus (WT + R). Metrics can be summarised at read, gene, or antibiotic-class level, extending metagenomic resistome profiling beyond gene presence.
The outputs enable calculation of both relative abundance of mutation-driven AMR and the proportion of resistant reads among all reads mapping to a locus (WT + R). Metrics can be summarised at read, gene, or antibiotic-class level, extending metagenomic resistome profiling beyond gene presence.
December 8, 2025 at 10:00 AM
4/
The outputs enable calculation of both relative abundance of mutation-driven AMR and the proportion of resistant reads among all reads mapping to a locus (WT + R). Metrics can be summarised at read, gene, or antibiotic-class level, extending metagenomic resistome profiling beyond gene presence.
The outputs enable calculation of both relative abundance of mutation-driven AMR and the proportion of resistant reads among all reads mapping to a locus (WT + R). Metrics can be summarised at read, gene, or antibiotic-class level, extending metagenomic resistome profiling beyond gene presence.
Reposted by Alison Mather
3/
MetaPointFinder performs read-level protein and DNA alignment (DIAMOND + KMA) against curated AMRFinder mutation references. A custom scoring engine evaluates each substitution, enabling accurate detection across both long- and short-read datasets.
MetaPointFinder performs read-level protein and DNA alignment (DIAMOND + KMA) against curated AMRFinder mutation references. A custom scoring engine evaluates each substitution, enabling accurate detection across both long- and short-read datasets.
December 8, 2025 at 10:00 AM
3/
MetaPointFinder performs read-level protein and DNA alignment (DIAMOND + KMA) against curated AMRFinder mutation references. A custom scoring engine evaluates each substitution, enabling accurate detection across both long- and short-read datasets.
MetaPointFinder performs read-level protein and DNA alignment (DIAMOND + KMA) against curated AMRFinder mutation references. A custom scoring engine evaluates each substitution, enabling accurate detection across both long- and short-read datasets.
Reposted by Alison Mather
2/
In metagenomic data, most AMR tools detect only acquired genes, while point mutations in gyrA, parC, folA, rpoB, 23S rRNA and others are major drivers of resistance. These variants are rarely quantified because they require precise alignment and position-specific evaluation.
In metagenomic data, most AMR tools detect only acquired genes, while point mutations in gyrA, parC, folA, rpoB, 23S rRNA and others are major drivers of resistance. These variants are rarely quantified because they require precise alignment and position-specific evaluation.
December 8, 2025 at 10:00 AM
2/
In metagenomic data, most AMR tools detect only acquired genes, while point mutations in gyrA, parC, folA, rpoB, 23S rRNA and others are major drivers of resistance. These variants are rarely quantified because they require precise alignment and position-specific evaluation.
In metagenomic data, most AMR tools detect only acquired genes, while point mutations in gyrA, parC, folA, rpoB, 23S rRNA and others are major drivers of resistance. These variants are rarely quantified because they require precise alignment and position-specific evaluation.
Reposted by Alison Mather
1/
Our preprint on MetaPointFinder is online:
www.biorxiv.org/content/10.6...
Current resistome profiling has a major gap: it misses mutation-driven AMR, even though chromosomal mutations underpin resistance to key antimicrobials. MetaPointFinder addresses this at the read level in metagenomes.
Our preprint on MetaPointFinder is online:
www.biorxiv.org/content/10.6...
Current resistome profiling has a major gap: it misses mutation-driven AMR, even though chromosomal mutations underpin resistance to key antimicrobials. MetaPointFinder addresses this at the read level in metagenomes.
December 8, 2025 at 10:00 AM
1/
Our preprint on MetaPointFinder is online:
www.biorxiv.org/content/10.6...
Current resistome profiling has a major gap: it misses mutation-driven AMR, even though chromosomal mutations underpin resistance to key antimicrobials. MetaPointFinder addresses this at the read level in metagenomes.
Our preprint on MetaPointFinder is online:
www.biorxiv.org/content/10.6...
Current resistome profiling has a major gap: it misses mutation-driven AMR, even though chromosomal mutations underpin resistance to key antimicrobials. MetaPointFinder addresses this at the read level in metagenomes.
A new tool we’ve developed to identify AMR-associated SNPs in short- and long-read metagenome data….allows a greater understanding of the total resistome of a sample
MetaPointFinder:
A new approach for detecting mutation-driven antimicrobial resistance directly from metagenomic reads.
Fills a major gap in current resistome profiling by capturing chromosomal AMR mutations that metagenome tools miss.
github.com/aldertzomer/...
A new approach for detecting mutation-driven antimicrobial resistance directly from metagenomic reads.
Fills a major gap in current resistome profiling by capturing chromosomal AMR mutations that metagenome tools miss.
github.com/aldertzomer/...
December 8, 2025 at 10:51 AM
A new tool we’ve developed to identify AMR-associated SNPs in short- and long-read metagenome data….allows a greater understanding of the total resistome of a sample
Reposted by Alison Mather
🆕 We’re looking for a motivated candidate to investigate whether differences in E. coli types increase risk of UTIs in pregnancy. This will help inform better patient care 🧪
🗓️ Apply by 6 January 2025
➡️https://buff.ly/sFpuQWo
@alisonmather.bsky.social
🗓️ Apply by 6 January 2025
➡️https://buff.ly/sFpuQWo
@alisonmather.bsky.social
October 27, 2025 at 2:30 PM
🆕 We’re looking for a motivated candidate to investigate whether differences in E. coli types increase risk of UTIs in pregnancy. This will help inform better patient care 🧪
🗓️ Apply by 6 January 2025
➡️https://buff.ly/sFpuQWo
@alisonmather.bsky.social
🗓️ Apply by 6 January 2025
➡️https://buff.ly/sFpuQWo
@alisonmather.bsky.social
Reposted by Alison Mather
🆕We’re looking for a motivated candidate to examine drivers and evolutionary factors influencing antimicrobial resistance in pigs from Brazil🐖
🗓️ Apply by 6 January 2025
➡️https://buff.ly/sFpuQWo
@alisonmather.bsky.social
🗓️ Apply by 6 January 2025
➡️https://buff.ly/sFpuQWo
@alisonmather.bsky.social
October 27, 2025 at 2:30 PM
🆕We’re looking for a motivated candidate to examine drivers and evolutionary factors influencing antimicrobial resistance in pigs from Brazil🐖
🗓️ Apply by 6 January 2025
➡️https://buff.ly/sFpuQWo
@alisonmather.bsky.social
🗓️ Apply by 6 January 2025
➡️https://buff.ly/sFpuQWo
@alisonmather.bsky.social
Reposted by Alison Mather
📣Call for abstracts — WBF 2026, Session NEX5: “Microbial communities as One Health drivers.”
Davos, 14–19 Jun 2026. Community-level mechanisms, AMR & practical interventions (experimental/computational/interventional).
Deadline: 18 Nov 2025 → tinyurl.com/4un5a8a4
#OneHealth #Microbiome #AMR
Davos, 14–19 Jun 2026. Community-level mechanisms, AMR & practical interventions (experimental/computational/interventional).
Deadline: 18 Nov 2025 → tinyurl.com/4un5a8a4
#OneHealth #Microbiome #AMR
October 13, 2025 at 6:09 AM
📣Call for abstracts — WBF 2026, Session NEX5: “Microbial communities as One Health drivers.”
Davos, 14–19 Jun 2026. Community-level mechanisms, AMR & practical interventions (experimental/computational/interventional).
Deadline: 18 Nov 2025 → tinyurl.com/4un5a8a4
#OneHealth #Microbiome #AMR
Davos, 14–19 Jun 2026. Community-level mechanisms, AMR & practical interventions (experimental/computational/interventional).
Deadline: 18 Nov 2025 → tinyurl.com/4un5a8a4
#OneHealth #Microbiome #AMR
Reposted by Alison Mather
Was great to put the dream team back together for a commentary on this with @alisonmather.bsky.social very cool study on AMR flow through food production chains in Europe www.nature.com/articles/s41...
July 31, 2025 at 10:26 AM
Was great to put the dream team back together for a commentary on this with @alisonmather.bsky.social very cool study on AMR flow through food production chains in Europe www.nature.com/articles/s41...
Reposted by Alison Mather
🎓 #PhDPosition !
🤰 Understanding the relationship between the maternal microbiome and fetal growth restriction with Professor Mark Webber @webberma.bsky.social and Professor Alison Mather @alisonmather.bsky.social
📅Apply by Monday 14 April
➡️ buff.ly/QL3JFtg
🤰 Understanding the relationship between the maternal microbiome and fetal growth restriction with Professor Mark Webber @webberma.bsky.social and Professor Alison Mather @alisonmather.bsky.social
📅Apply by Monday 14 April
➡️ buff.ly/QL3JFtg
March 18, 2025 at 3:00 PM
🎓 #PhDPosition !
🤰 Understanding the relationship between the maternal microbiome and fetal growth restriction with Professor Mark Webber @webberma.bsky.social and Professor Alison Mather @alisonmather.bsky.social
📅Apply by Monday 14 April
➡️ buff.ly/QL3JFtg
🤰 Understanding the relationship between the maternal microbiome and fetal growth restriction with Professor Mark Webber @webberma.bsky.social and Professor Alison Mather @alisonmather.bsky.social
📅Apply by Monday 14 April
➡️ buff.ly/QL3JFtg
Reposted by Alison Mather
Starting the new year with a new pre-print from the Hall Lab @halllab.bsky.social looking at the impact of empirical antibiotics on gut microbiome and resistome of both probiotic and non-probiotic supplemented VLBW preterm infants: www.biorxiv.org/content/10.1...
#resistome #amr #microbiome #preterm
#resistome #amr #microbiome #preterm
Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants
Preterm infants (<37 weeks’ gestation) are often administered broad-spectrum antibiotics in hospitals due to their vulnerability to severe morbidity, including necrotising enterocolitis and sepsis. Ho...
www.biorxiv.org
January 3, 2025 at 5:03 PM
Starting the new year with a new pre-print from the Hall Lab @halllab.bsky.social looking at the impact of empirical antibiotics on gut microbiome and resistome of both probiotic and non-probiotic supplemented VLBW preterm infants: www.biorxiv.org/content/10.1...
#resistome #amr #microbiome #preterm
#resistome #amr #microbiome #preterm
Reposted by Alison Mather
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 Alison Mather
🚨#PhD opportunity!🚨Do plasmids help soil microbiomes adapt to climate change? Join me and Raj Whitlock to investigate, using the world's longest-running climate experiment 🌾🥵🦠 Please share, and get in touch if you are interested! www.findaphd.com/phds/project...
November 7, 2023 at 4:15 PM
🚨#PhD opportunity!🚨Do plasmids help soil microbiomes adapt to climate change? Join me and Raj Whitlock to investigate, using the world's longest-running climate experiment 🌾🥵🦠 Please share, and get in touch if you are interested! www.findaphd.com/phds/project...
Reposted by Alison Mather
The HZI will hire up to twenty (20!) tenure-track research groups under the broad topic of "Microbial Stargazing" (🦠🌌). The first round of 4 positions is now open; the call closes on the 10th of December. Please share! www.helmholtz-hzi.de/en/career/jo...
November 6, 2023 at 12:52 PM
The HZI will hire up to twenty (20!) tenure-track research groups under the broad topic of "Microbial Stargazing" (🦠🌌). The first round of 4 positions is now open; the call closes on the 10th of December. Please share! www.helmholtz-hzi.de/en/career/jo...
Reposted by Alison Mather
Come work with us! The Quadram is in search of a Head of Bioinformatics to lead and cultivate a specialised bioinformatics core support team. Applications Close 04 December 2023
quadram.ac.uk/vacancies/he...
quadram.ac.uk/vacancies/he...
October 21, 2023 at 3:52 PM
Come work with us! The Quadram is in search of a Head of Bioinformatics to lead and cultivate a specialised bioinformatics core support team. Applications Close 04 December 2023
quadram.ac.uk/vacancies/he...
quadram.ac.uk/vacancies/he...
Reposted by Alison Mather
PhD studentship with myself and Ed Feil at the University of Bath looking at the evolution and epidemiology of plasmids - in particular looking at plasmid fusions/hybrids/recombinants. Lots of fun bioinformatics! Open to UK or international students.
#microsky
www.findaphd.com/phds/project...
#microsky
www.findaphd.com/phds/project...
October 18, 2023 at 4:17 PM
PhD studentship with myself and Ed Feil at the University of Bath looking at the evolution and epidemiology of plasmids - in particular looking at plasmid fusions/hybrids/recombinants. Lots of fun bioinformatics! Open to UK or international students.
#microsky
www.findaphd.com/phds/project...
#microsky
www.findaphd.com/phds/project...
Reposted by Alison Mather
PhD studentship (co-sup with Ed Feil, collaborators incl. Edze Westra): using GWAS to find bacterial susceptibility loci to phage infection, and machine learning for prediction. Amazing dataset, great application for machine learning
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
October 19, 2023 at 8:54 AM
PhD studentship (co-sup with Ed Feil, collaborators incl. Edze Westra): using GWAS to find bacterial susceptibility loci to phage infection, and machine learning for prediction. Amazing dataset, great application for machine learning
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
Reposted by Alison Mather
PhD available with me at NTU. Metabolomics and cell-line work (... maybe some microbiota ...). Open to UK and international students.
Host–microbiota interactions in pancreatic cancer: determining whether they exist, and their influence on disease
Please RT. #MicrobiomeSky
Host–microbiota interactions in pancreatic cancer: determining whether they exist, and their influence on disease
Please RT. #MicrobiomeSky
Host–microbiota interactions in pancreatic cancer: determining whether they exist, and their influ...
Discover our PhD Studentship opportunities in the School of Science and Technology
www.ntu.ac.uk
October 19, 2023 at 10:58 AM
PhD available with me at NTU. Metabolomics and cell-line work (... maybe some microbiota ...). Open to UK and international students.
Host–microbiota interactions in pancreatic cancer: determining whether they exist, and their influence on disease
Please RT. #MicrobiomeSky
Host–microbiota interactions in pancreatic cancer: determining whether they exist, and their influence on disease
Please RT. #MicrobiomeSky
PhD opportunity with me and Mark Webber! Some microbial genomics, some molecular biology, all fun. Apply here: buff.ly/3FjzrzS
October 19, 2023 at 7:55 AM
PhD opportunity with me and Mark Webber! Some microbial genomics, some molecular biology, all fun. Apply here: buff.ly/3FjzrzS