Hayley Thompson
@hayleyt77.bsky.social
Lecturer in Food Science @ The Natural Resources Institute
Foodborne Pathogens /Microbiomes / AMR / Metagenomics
Foodborne Pathogens /Microbiomes / AMR / Metagenomics
Amazing!
🚨Our paper is out! 🥳
Hijacking a bacterial ABC transporter for efficient genetic code expansion.
Many congrats to everyone involved - a multi-year effort led by @taruniype.bsky.social @maxfottner.bsky.social
www.nature.com/articles/s41...
it all started years ago with a failed experiment
🧵👇 1/9
Hijacking a bacterial ABC transporter for efficient genetic code expansion.
Many congrats to everyone involved - a multi-year effort led by @taruniype.bsky.social @maxfottner.bsky.social
www.nature.com/articles/s41...
it all started years ago with a failed experiment
🧵👇 1/9
Hijacking a bacterial ABC transporter for genetic code expansion - Nature
Bacterial ATP-binding cassette (ABC) transporters can be utilized and engineered to transport non-canonical amino acids into Escherichia coli for highly efficient synthesis of proteins with novel func...
www.nature.com
October 17, 2025 at 7:07 PM
Amazing!
Do you have an interest in AMR and OneHealth?
Then apply for our PhD, exploring the prevalence of resistance of Enterobacterales across poultry farms, fresh produce systems, and wastewater treatment plants.
www.gre.ac.uk/docs/rep/com...
#AMR #OneHealth #PhD #Microbiology #Genomics #FoodSafety
Then apply for our PhD, exploring the prevalence of resistance of Enterobacterales across poultry farms, fresh produce systems, and wastewater treatment plants.
www.gre.ac.uk/docs/rep/com...
#AMR #OneHealth #PhD #Microbiology #Genomics #FoodSafety
Cultural Surveillance of Antibiotic Resistant Enterobacterales: A One Health Approach to Tracking Antimicrobial Resistance from Farm to Community | Documents | University of Greenwich
Closing Date: 15th October 2025
www.gre.ac.uk
October 4, 2025 at 8:55 PM
Do you have an interest in AMR and OneHealth?
Then apply for our PhD, exploring the prevalence of resistance of Enterobacterales across poultry farms, fresh produce systems, and wastewater treatment plants.
www.gre.ac.uk/docs/rep/com...
#AMR #OneHealth #PhD #Microbiology #Genomics #FoodSafety
Then apply for our PhD, exploring the prevalence of resistance of Enterobacterales across poultry farms, fresh produce systems, and wastewater treatment plants.
www.gre.ac.uk/docs/rep/com...
#AMR #OneHealth #PhD #Microbiology #Genomics #FoodSafety
Reposted by Hayley Thompson
My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology:
www.ebi.ac.uk/training/onl...
Including both molecular and epidemiological examples
www.ebi.ac.uk/training/onl...
Including both molecular and epidemiological examples
Mathematical modelling for biologists - Modelling concepts in biological research
Mathematical modelling for biologists - Modelling concepts in biological research
www.ebi.ac.uk
August 15, 2025 at 10:39 AM
My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology:
www.ebi.ac.uk/training/onl...
Including both molecular and epidemiological examples
www.ebi.ac.uk/training/onl...
Including both molecular and epidemiological examples
Reposted by Hayley Thompson
Our high-precision metagenomic strain caller, PHLAME, is now published in Cell Reports!! www.cell.com/cell-reports...
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
August 15, 2025 at 4:33 PM
Our high-precision metagenomic strain caller, PHLAME, is now published in Cell Reports!! www.cell.com/cell-reports...
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
Reposted by Hayley Thompson
The new version of MetaPhlAn v4.2.2 released!
📌taxonomic profiling of long-read metagenomes for the first time
📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs
Try it out & @hutlab.bsky.social and we are looking forward to your feedback!
forum.biobakery.org/t/metaphlan-...
📌taxonomic profiling of long-read metagenomes for the first time
📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs
Try it out & @hutlab.bsky.social and we are looking forward to your feedback!
forum.biobakery.org/t/metaphlan-...
MetaPhlAn 4.2.2 release (initial long-read sequencing support and database update)
Announcement We are pleased to share that MetaPhlAn 4.2.2 is now available, which incorporates taxonomic profiling of long-read metagenomes for the first time and includes a new version of the MetaPhl...
forum.biobakery.org
June 11, 2025 at 6:15 AM
The new version of MetaPhlAn v4.2.2 released!
📌taxonomic profiling of long-read metagenomes for the first time
📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs
Try it out & @hutlab.bsky.social and we are looking forward to your feedback!
forum.biobakery.org/t/metaphlan-...
📌taxonomic profiling of long-read metagenomes for the first time
📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs
Try it out & @hutlab.bsky.social and we are looking forward to your feedback!
forum.biobakery.org/t/metaphlan-...
Reposted by Hayley Thompson
The 👏 point 👏 of 👏 vaccination 👏 is 👏 that 👏 we 👏 don’t 👏 have 👏 to 👏 urgently 👏 treat 👏 severely 👏 ill 👏 children
RFK Jr on measles: "We need to do better at treating kids who have this disease, and not just saying the only answer is vaccination."
April 10, 2025 at 8:35 PM
The 👏 point 👏 of 👏 vaccination 👏 is 👏 that 👏 we 👏 don’t 👏 have 👏 to 👏 urgently 👏 treat 👏 severely 👏 ill 👏 children
Reposted by Hayley Thompson
I'm delighted to share a useful FREE web-based app portal of powerful bioinformatics tools for microbial genomes and shotgun microbiome sequences!
It's called Micromics and is built by Middle Author Bioinformatics, led by co-founder @ironark.bsky.social
omix.midauthorbio.com
It's called Micromics and is built by Middle Author Bioinformatics, led by co-founder @ironark.bsky.social
omix.midauthorbio.com
Microbial Omics
A suite of bioinformatics tools for microbial genome and metagenome analysis.
omix.midauthorbio.com
April 8, 2025 at 12:11 PM
I'm delighted to share a useful FREE web-based app portal of powerful bioinformatics tools for microbial genomes and shotgun microbiome sequences!
It's called Micromics and is built by Middle Author Bioinformatics, led by co-founder @ironark.bsky.social
omix.midauthorbio.com
It's called Micromics and is built by Middle Author Bioinformatics, led by co-founder @ironark.bsky.social
omix.midauthorbio.com
Reposted by Hayley Thompson
Do you (like me) create a bunch of conda environments, then later forget what they're for, when they were last updated, or which tools are in them?
If so, you might this little project: github.com/rrwick/conda...
If so, you might this little project: github.com/rrwick/conda...
GitHub - rrwick/condaenvlist: a simple tool for listing conda environments with descriptions
a simple tool for listing conda environments with descriptions - rrwick/condaenvlist
github.com
March 27, 2025 at 4:34 AM
Do you (like me) create a bunch of conda environments, then later forget what they're for, when they were last updated, or which tools are in them?
If so, you might this little project: github.com/rrwick/conda...
If so, you might this little project: github.com/rrwick/conda...
Reposted by Hayley Thompson
Master the art of food safety and quality management! #StudyatNRI
Our MSc in Applied Food Safety and Quality Management offers a comprehensive approach, ensuring safe and high-quality food for consumers.
#FoodSafety
www.nri.org/study/postgr...
Our MSc in Applied Food Safety and Quality Management offers a comprehensive approach, ensuring safe and high-quality food for consumers.
#FoodSafety
www.nri.org/study/postgr...
March 20, 2025 at 9:57 AM
Master the art of food safety and quality management! #StudyatNRI
Our MSc in Applied Food Safety and Quality Management offers a comprehensive approach, ensuring safe and high-quality food for consumers.
#FoodSafety
www.nri.org/study/postgr...
Our MSc in Applied Food Safety and Quality Management offers a comprehensive approach, ensuring safe and high-quality food for consumers.
#FoodSafety
www.nri.org/study/postgr...
Reposted by Hayley Thompson
I am beyond excited to share that you can now apply to observe a @wellcometrust.bsky.social #DiscoveryResearch shortlisting Committee! If you plan to apply to us in the next 2 years, apply to be an Observer now to better understand what happens once you click submit! wellcome.org/grant-fundin...
Apply to observe a Wellcome funding advisory committee | Prepare to Apply | Wellcome
Find out how to observe a Wellcome funding advisory committee. Researchers who are considering applying for Wellcome funding in the next two years can apply to observe a shortlisting committee.
wellcome.org
February 21, 2025 at 12:00 PM
I am beyond excited to share that you can now apply to observe a @wellcometrust.bsky.social #DiscoveryResearch shortlisting Committee! If you plan to apply to us in the next 2 years, apply to be an Observer now to better understand what happens once you click submit! wellcome.org/grant-fundin...
Reposted by Hayley Thompson
Incredible graphic - the myriad of ways that bacteria defend themselves against antibiotics.
14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell
www.sciencedirect.com/science/arti...
14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell
www.sciencedirect.com/science/arti...
November 13, 2024 at 12:46 PM
Incredible graphic - the myriad of ways that bacteria defend themselves against antibiotics.
14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell
www.sciencedirect.com/science/arti...
14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell
www.sciencedirect.com/science/arti...
Reposted by Hayley Thompson
Would it be great to have a tool that harmonises all the different AMR prediction tool outputs? We agree and outline it in this paper!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
hAMRonization: Enhancing antimicrobial resistance prediction using the PHA4GE AMR detection specification and tooling
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
March 11, 2024 at 4:54 PM
Would it be great to have a tool that harmonises all the different AMR prediction tool outputs? We agree and outline it in this paper!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Hayley Thompson
GSR-DB: a manually curated and optimized taxonomical database for 16S rRNA amplicon analysis journals.asm.org/doi/full/10.... #jcampubs
January 9, 2024 at 2:30 PM
GSR-DB: a manually curated and optimized taxonomical database for 16S rRNA amplicon analysis journals.asm.org/doi/full/10.... #jcampubs
Reposted by Hayley Thompson
Reposting our work on sylph, a new fast and precise metagenomic profiler.
Check it out here github.com/bluenote-157...
Tldr: profile against 85k prokaryotes and 2.9 million viruses in a minute and 16 gb of ram. Seems to be accurate at the species level, ANI output too!
Check it out here github.com/bluenote-157...
Tldr: profile against 85k prokaryotes and 2.9 million viruses in a minute and 16 gb of ram. Seems to be accurate at the species level, ANI output too!
Tweet by @jim_elevator
twitter.com
November 21, 2023 at 4:52 AM
Reposting our work on sylph, a new fast and precise metagenomic profiler.
Check it out here github.com/bluenote-157...
Tldr: profile against 85k prokaryotes and 2.9 million viruses in a minute and 16 gb of ram. Seems to be accurate at the species level, ANI output too!
Check it out here github.com/bluenote-157...
Tldr: profile against 85k prokaryotes and 2.9 million viruses in a minute and 16 gb of ram. Seems to be accurate at the species level, ANI output too!
Reposted by Hayley Thompson
Blueskiers! I am starting a Practical bioinformatics for biologist course from scratch this spring semester focused on microbes 🦠 🧫. I am putting the finishing touches on it but want to make sure it’s well rounded. It’ll be heavily hands on. But anyone have lectures they’re willing to share?
December 29, 2023 at 12:48 AM
Blueskiers! I am starting a Practical bioinformatics for biologist course from scratch this spring semester focused on microbes 🦠 🧫. I am putting the finishing touches on it but want to make sure it’s well rounded. It’ll be heavily hands on. But anyone have lectures they’re willing to share?
Reposted by Hayley Thompson
New paper by Pat Schloss about rarefaction is definitely worth a read for microbiome aficionados
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
Waste not, want not: revisiting the analysis that called into question the practice of rarefaction |...
Over the past 10 years, the best method for normalizing the sequencing depth of samples
characterized by 16S rRNA gene sequencing has been contentious. An often cited article
by McMurdie and Holmes fo...
journals.asm.org
December 7, 2023 at 1:51 PM
New paper by Pat Schloss about rarefaction is definitely worth a read for microbiome aficionados
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
Reposted by Hayley Thompson
AMR folks! Come join a great conference: Antimicrobial Resistance – Genomes, Big Data and Emerging Technologies (13-15 March 2024).
Awesome line-up of speakers.
Bursary deadline 19 December.
Abstract deadline 16 January.
coursesandconferences.wellcomeconnectingscience.org/event/antimi...
Awesome line-up of speakers.
Bursary deadline 19 December.
Abstract deadline 16 January.
coursesandconferences.wellcomeconnectingscience.org/event/antimi...
Antimicrobial Resistance – Genomes, Big Data and Emerging Technologies — 20240313
Highlighting the importance of genomic data in the fight against AMR
coursesandconferences.wellcomeconnectingscience.org
November 30, 2023 at 10:42 AM
AMR folks! Come join a great conference: Antimicrobial Resistance – Genomes, Big Data and Emerging Technologies (13-15 March 2024).
Awesome line-up of speakers.
Bursary deadline 19 December.
Abstract deadline 16 January.
coursesandconferences.wellcomeconnectingscience.org/event/antimi...
Awesome line-up of speakers.
Bursary deadline 19 December.
Abstract deadline 16 January.
coursesandconferences.wellcomeconnectingscience.org/event/antimi...
Reposted by Hayley Thompson
Workshop‼️ One Health and antimicrobial resistance: role of antibiotics, antimicrobial peptides and biocides
29 & 30 January 2024 in Berlin, Germany and online
29 & 30 January 2024 in Berlin, Germany and online
November 23, 2023 at 7:30 PM
Workshop‼️ One Health and antimicrobial resistance: role of antibiotics, antimicrobial peptides and biocides
29 & 30 January 2024 in Berlin, Germany and online
29 & 30 January 2024 in Berlin, Germany and online
Reposted by Hayley Thompson
📢MicrobesNG POPUP Conference is coming to Oxford!
This is a FREE Microbial Genomics conference 7th Mar🦠🧬
We're accepting abstracts for talks now! Focus on ECRs. Please repost!
Submit abstract by 6th Dec 👉 www.surveymonkey.co.uk/r/Oxford_Abs...
Organised by @rwheatley8.bsky.social
#MNGPopUp #ECR
This is a FREE Microbial Genomics conference 7th Mar🦠🧬
We're accepting abstracts for talks now! Focus on ECRs. Please repost!
Submit abstract by 6th Dec 👉 www.surveymonkey.co.uk/r/Oxford_Abs...
Organised by @rwheatley8.bsky.social
#MNGPopUp #ECR
October 24, 2023 at 3:50 PM
📢MicrobesNG POPUP Conference is coming to Oxford!
This is a FREE Microbial Genomics conference 7th Mar🦠🧬
We're accepting abstracts for talks now! Focus on ECRs. Please repost!
Submit abstract by 6th Dec 👉 www.surveymonkey.co.uk/r/Oxford_Abs...
Organised by @rwheatley8.bsky.social
#MNGPopUp #ECR
This is a FREE Microbial Genomics conference 7th Mar🦠🧬
We're accepting abstracts for talks now! Focus on ECRs. Please repost!
Submit abstract by 6th Dec 👉 www.surveymonkey.co.uk/r/Oxford_Abs...
Organised by @rwheatley8.bsky.social
#MNGPopUp #ECR
Reposted by Hayley Thompson
Interesting preprint by Edwin et al. of possible interest:
An In-depth Evaluation of Metagenomic Classifiers for Soil Microbiomes
www.researchsquare.com/article/rs-3...
An In-depth Evaluation of Metagenomic Classifiers for Soil Microbiomes
www.researchsquare.com/article/rs-3...
An In-depth Evaluation of Metagenomic Classifiers for Soil Microbiomes
Background: Recent endeavours in metagenomics, exemplified by projects such as the human microbiome project and TARA Oceans, have illuminated the complexities of microbial biomes. A robust bioinformat...
www.researchsquare.com
October 21, 2023 at 7:50 PM
Interesting preprint by Edwin et al. of possible interest:
An In-depth Evaluation of Metagenomic Classifiers for Soil Microbiomes
www.researchsquare.com/article/rs-3...
An In-depth Evaluation of Metagenomic Classifiers for Soil Microbiomes
www.researchsquare.com/article/rs-3...
Reposted by Hayley Thompson
The hacked the @nanopore sequencer to read amino acids and PTMs along protein strands. This opens up the possibility for barcode sequencing at the protein level for highly multiplexed assays, PTM monitoring, and protein identification 🧬🧪🤯
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Multi-pass, single-molecule nanopore reading of long protein strands with single-amino acid sensitiv...
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
October 21, 2023 at 9:37 PM
The hacked the @nanopore sequencer to read amino acids and PTMs along protein strands. This opens up the possibility for barcode sequencing at the protein level for highly multiplexed assays, PTM monitoring, and protein identification 🧬🧪🤯
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Hayley Thompson
🚨 #DataVisualization in R for Scientists! 🔥
#DataViz protocols: An introduction to data visualization protocols for wet lab scientists#
A fantastic resource from @joachimgoedhart.bsky.social 🙏👏👍
joachimgoedhart.github.io/DataViz-prot...
#DataViz protocols: An introduction to data visualization protocols for wet lab scientists#
A fantastic resource from @joachimgoedhart.bsky.social 🙏👏👍
joachimgoedhart.github.io/DataViz-prot...
DataViz protocols
This is an introduction to data visualization protocols for wet lab scientists
joachimgoedhart.github.io
October 22, 2023 at 6:42 AM
🚨 #DataVisualization in R for Scientists! 🔥
#DataViz protocols: An introduction to data visualization protocols for wet lab scientists#
A fantastic resource from @joachimgoedhart.bsky.social 🙏👏👍
joachimgoedhart.github.io/DataViz-prot...
#DataViz protocols: An introduction to data visualization protocols for wet lab scientists#
A fantastic resource from @joachimgoedhart.bsky.social 🙏👏👍
joachimgoedhart.github.io/DataViz-prot...
Today has been a good day in the lab 😀 My first Nanopore sequencing run is on!
October 12, 2023 at 4:34 PM
Today has been a good day in the lab 😀 My first Nanopore sequencing run is on!
Reposted by Hayley Thompson
Scientist?
New to BlueSky?
Here's a list of over 80 science-related feeds you might want to follow and contribute to!
#AcademicSky #WomenInSTEM 🧪
New to BlueSky?
Here's a list of over 80 science-related feeds you might want to follow and contribute to!
#AcademicSky #WomenInSTEM 🧪
BlueSky Science-Related Feeds
Sheet1
Likes,Name (Click to visit feed),Tags,Contact to ask to be added to contributor list
2,<a href="https://bsky.app/profile/did:plc:ftnzzw4cnon2pzpw7i5m2xu7/feed/aaaiqnkwsgsz6">#AI&HCI</a>,#HCI, ...
docs.google.com
September 19, 2023 at 8:10 AM
Scientist?
New to BlueSky?
Here's a list of over 80 science-related feeds you might want to follow and contribute to!
#AcademicSky #WomenInSTEM 🧪
New to BlueSky?
Here's a list of over 80 science-related feeds you might want to follow and contribute to!
#AcademicSky #WomenInSTEM 🧪
Only been here 5 minutes and I’m already liking what I see! 😊
September 21, 2023 at 9:19 PM
Only been here 5 minutes and I’m already liking what I see! 😊