Poppy Hesketh Best
@pjhesbes.bsky.social
Infectious Disease Genomics, Environmental Microbiology, all things bugs and viruses.
IGTP, Catalonia, Spain.
IGTP, Catalonia, Spain.
Reposted by Poppy Hesketh Best
Amazing novel mpox recombination between epidemic clade 1 and 2 in returning traveller detected in UK: virological.org/t/inter-clad...
Inter-Clade Recombinant Mpox Virus Detected in England in a Traveller Recently Returned from Asia
Inter-Clade Recombinant Mpox Virus Detected in England in a Traveller Recently Returned from Asia Authors: Steven T. Pullan1, Isobel Everall1, Rebecca Doherty1, Lucy Crossman1, Emma Wise1, Hassan Ha...
virological.org
December 8, 2025 at 6:17 PM
Amazing novel mpox recombination between epidemic clade 1 and 2 in returning traveller detected in UK: virological.org/t/inter-clad...
Reposted by Poppy Hesketh Best
It was great to write a brief commentary with @sociovirology.bsky.social on @nanamikubota.bsky.social and @vscooper.micropopbio.org's recent discovery of cheat-driven cycles in Pseudomonas (www.cell.com/current-biol... - amazing example of the tragedy of the commons!
🧪 #socialviruses #evosky
🧪 #socialviruses #evosky
Phage–bacteria dynamics: The tragedy of the commons at hyperspeed
A recent study found that apparently stable coexistence between a clinically important
pathogen, Pseudomonas aeruginosa, and its integrated prophages can break down, setting
off an evolutionary cycle ...
www.cell.com
December 4, 2025 at 8:56 PM
It was great to write a brief commentary with @sociovirology.bsky.social on @nanamikubota.bsky.social and @vscooper.micropopbio.org's recent discovery of cheat-driven cycles in Pseudomonas (www.cell.com/current-biol... - amazing example of the tragedy of the commons!
🧪 #socialviruses #evosky
🧪 #socialviruses #evosky
Reposted by Poppy Hesketh Best
Feeling festive?
Why not deck the halls with @cvrinfo.bsky.social's papercraft #VirusSnowflakes and celebrate the science of viruses and the fight against viral diseases.
Download for free: cvr-engagement.co.uk/virus-snowfl...
#scicomm #sciart #decorations
Why not deck the halls with @cvrinfo.bsky.social's papercraft #VirusSnowflakes and celebrate the science of viruses and the fight against viral diseases.
Download for free: cvr-engagement.co.uk/virus-snowfl...
#scicomm #sciart #decorations
December 1, 2025 at 9:51 AM
Feeling festive?
Why not deck the halls with @cvrinfo.bsky.social's papercraft #VirusSnowflakes and celebrate the science of viruses and the fight against viral diseases.
Download for free: cvr-engagement.co.uk/virus-snowfl...
#scicomm #sciart #decorations
Why not deck the halls with @cvrinfo.bsky.social's papercraft #VirusSnowflakes and celebrate the science of viruses and the fight against viral diseases.
Download for free: cvr-engagement.co.uk/virus-snowfl...
#scicomm #sciart #decorations
Reposted by Poppy Hesketh Best
Out now in Nature Communications: Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses
www.nature.com/articles/s41...
@luisvalentin.bsky.social @lingdong-shi.bsky.social @martianmicrobe.bsky.social @mschoelmerich.bsky.social
www.nature.com/articles/s41...
@luisvalentin.bsky.social @lingdong-shi.bsky.social @martianmicrobe.bsky.social @mschoelmerich.bsky.social
Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses - Nature Communications
Borgs are large extrachromosomal elements of anaerobic methane-oxidizing archaea. Here, via in silico protein structure prediction of ~10,000 Borg proteins, the authors reveal that Borgs share numerou...
www.nature.com
November 28, 2025 at 9:01 PM
Out now in Nature Communications: Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses
www.nature.com/articles/s41...
@luisvalentin.bsky.social @lingdong-shi.bsky.social @martianmicrobe.bsky.social @mschoelmerich.bsky.social
www.nature.com/articles/s41...
@luisvalentin.bsky.social @lingdong-shi.bsky.social @martianmicrobe.bsky.social @mschoelmerich.bsky.social
Reposted by Poppy Hesketh Best
New version of macrel released (v1.6.0)
The biggest change is internal, using a much better approach to saving and loading models (thus removing the dependency on particular versions of scikit-learn)
A few other bugfixes were included
github.com/BigDataBiolo...
The biggest change is internal, using a much better approach to saving and loading models (thus removing the dependency on particular versions of scikit-learn)
A few other bugfixes were included
github.com/BigDataBiolo...
GitHub - BigDataBiology/macrel: Predict AMPs in (meta)genomes and peptides
Predict AMPs in (meta)genomes and peptides. Contribute to BigDataBiology/macrel development by creating an account on GitHub.
github.com
November 25, 2025 at 5:05 AM
New version of macrel released (v1.6.0)
The biggest change is internal, using a much better approach to saving and loading models (thus removing the dependency on particular versions of scikit-learn)
A few other bugfixes were included
github.com/BigDataBiolo...
The biggest change is internal, using a much better approach to saving and loading models (thus removing the dependency on particular versions of scikit-learn)
A few other bugfixes were included
github.com/BigDataBiolo...
Reposted by Poppy Hesketh Best
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Poppy Hesketh Best
ICYMI: catch up with our pangenomics webinar series. The recordings are now available on-demand: www.ebi.ac.uk/training/eve...
Webinars were given by: Raymond Cheng, Leanne Haggerty, @samuelhorsfield.bsky.social, Alexander Leonard, Neil MacAlasdair, and @camillemrcht.bsky.social.
🧬🖥️📊🦠
Webinars were given by: Raymond Cheng, Leanne Haggerty, @samuelhorsfield.bsky.social, Alexander Leonard, Neil MacAlasdair, and @camillemrcht.bsky.social.
🧬🖥️📊🦠
November 20, 2025 at 10:28 AM
ICYMI: catch up with our pangenomics webinar series. The recordings are now available on-demand: www.ebi.ac.uk/training/eve...
Webinars were given by: Raymond Cheng, Leanne Haggerty, @samuelhorsfield.bsky.social, Alexander Leonard, Neil MacAlasdair, and @camillemrcht.bsky.social.
🧬🖥️📊🦠
Webinars were given by: Raymond Cheng, Leanne Haggerty, @samuelhorsfield.bsky.social, Alexander Leonard, Neil MacAlasdair, and @camillemrcht.bsky.social.
🧬🖥️📊🦠
Reposted by Poppy Hesketh Best
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 11, 2025 at 5:15 PM
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Poppy Hesketh Best
What is the most profitable industry in the world, this side of the law? Not oil, not IT, not pharma.
It's *scientific publishing*.
We call this the Drain of Scientific Publishing.
Paper: arxiv.org/abs/2511.04820
Background: doi.org/10.1162/qss_...
Thread @markhanson.fediscience.org.ap.brid.gy 👇
It's *scientific publishing*.
We call this the Drain of Scientific Publishing.
Paper: arxiv.org/abs/2511.04820
Background: doi.org/10.1162/qss_...
Thread @markhanson.fediscience.org.ap.brid.gy 👇
November 12, 2025 at 10:31 AM
What is the most profitable industry in the world, this side of the law? Not oil, not IT, not pharma.
It's *scientific publishing*.
We call this the Drain of Scientific Publishing.
Paper: arxiv.org/abs/2511.04820
Background: doi.org/10.1162/qss_...
Thread @markhanson.fediscience.org.ap.brid.gy 👇
It's *scientific publishing*.
We call this the Drain of Scientific Publishing.
Paper: arxiv.org/abs/2511.04820
Background: doi.org/10.1162/qss_...
Thread @markhanson.fediscience.org.ap.brid.gy 👇
Reposted by Poppy Hesketh Best
Know metagenomics and could spare 2 mins? I'm applying for funding to build a visual repository for metagenomic classification data (not sequence data). To support the application, I have a short 2 minute survey and it would be a big help if you could fill it in: docs.google.com/forms/d/e/1F...
November 12, 2025 at 12:01 PM
Know metagenomics and could spare 2 mins? I'm applying for funding to build a visual repository for metagenomic classification data (not sequence data). To support the application, I have a short 2 minute survey and it would be a big help if you could fill it in: docs.google.com/forms/d/e/1F...
Reposted by Poppy Hesketh Best
📢 Just released 0.5.0 of SciCommander, a tool to automatically track provenance information about shell commands, into HTML reports with the full provenance graph for every output. This version brings much improved usability and better looks.
github.com/samuell/scic...
#provenance #bioinformatics
github.com/samuell/scic...
#provenance #bioinformatics
November 6, 2025 at 8:27 PM
📢 Just released 0.5.0 of SciCommander, a tool to automatically track provenance information about shell commands, into HTML reports with the full provenance graph for every output. This version brings much improved usability and better looks.
github.com/samuell/scic...
#provenance #bioinformatics
github.com/samuell/scic...
#provenance #bioinformatics
Reposted by Poppy Hesketh Best
Know metagenomics and could spare 2 mins? I'm applying for funding to build a visual repository for metagenomic classification data (not sequence data). To support the application, I have a short 2 minute survey and it would be a big help if you could fill it in: docs.google.com/forms/d/e/1F...
Metagenomic classification survey
Background: We're seeking the views of researchers on the possibility of a repository for metagenomic classification data, which we're hoping to build. The rationale is that people are familiar with t...
docs.google.com
November 10, 2025 at 6:24 PM
Know metagenomics and could spare 2 mins? I'm applying for funding to build a visual repository for metagenomic classification data (not sequence data). To support the application, I have a short 2 minute survey and it would be a big help if you could fill it in: docs.google.com/forms/d/e/1F...
Reposted by Poppy Hesketh Best
The hitchhiker’s guide to cross-species DNA delivery
@cp-trendsmicrobiol.bsky.social Spotlight by Kotaro Kiga and Rodrigo Ibarra-Chávez
www.cell.com/trends/micro...
@cp-trendsmicrobiol.bsky.social Spotlight by Kotaro Kiga and Rodrigo Ibarra-Chávez
www.cell.com/trends/micro...
The hitchhiker’s guide to cross-species DNA delivery
Microbial hitchhikers are rewriting the rules of horizontal gene transfer. He, Patkowski,
et al. reveal how phage satellites assemble chimeric infective particles that deliver
DNA across species bound...
www.cell.com
November 9, 2025 at 9:39 AM
The hitchhiker’s guide to cross-species DNA delivery
@cp-trendsmicrobiol.bsky.social Spotlight by Kotaro Kiga and Rodrigo Ibarra-Chávez
www.cell.com/trends/micro...
@cp-trendsmicrobiol.bsky.social Spotlight by Kotaro Kiga and Rodrigo Ibarra-Chávez
www.cell.com/trends/micro...
Reposted by Poppy Hesketh Best
1. Postdoc in plant-fungal interactions: jobsite.sheffield.ac.uk/job/Research...
2. Postdoc in molecular plant-microbe interactions: jobsite.sheffield.ac.uk/job/Research...
3. Research technician: jobsite.sheffield.ac.uk/job/Technici...
(Pls share!)
2. Postdoc in molecular plant-microbe interactions: jobsite.sheffield.ac.uk/job/Research...
3. Research technician: jobsite.sheffield.ac.uk/job/Technici...
(Pls share!)
Research Associate: Plant-fungal interactions
Research Associate: Plant-fungal interactions
jobsite.sheffield.ac.uk
November 8, 2025 at 1:00 PM
1. Postdoc in plant-fungal interactions: jobsite.sheffield.ac.uk/job/Research...
2. Postdoc in molecular plant-microbe interactions: jobsite.sheffield.ac.uk/job/Research...
3. Research technician: jobsite.sheffield.ac.uk/job/Technici...
(Pls share!)
2. Postdoc in molecular plant-microbe interactions: jobsite.sheffield.ac.uk/job/Research...
3. Research technician: jobsite.sheffield.ac.uk/job/Technici...
(Pls share!)
Reposted by Poppy Hesketh Best
Worried about identification of human samples from microbial sequencing? We were too- this is what we've done about it! www.sciencedirect.com/science/arti...
Benchmarking of human read removal strategies for viral and microbial metagenomics
Human reads are a key contaminant in microbial metagenomics and enrichment-based studies, requiring removal for computational efficiency, biological a…
www.sciencedirect.com
November 6, 2025 at 4:19 PM
Worried about identification of human samples from microbial sequencing? We were too- this is what we've done about it! www.sciencedirect.com/science/arti...
Reposted by Poppy Hesketh Best
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....
genzplyr is dplyr, but bussin fr fr no cap.
genzplyr is dplyr, but bussin fr fr no cap.
GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap
dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.
github.com
November 6, 2025 at 11:25 PM
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....
genzplyr is dplyr, but bussin fr fr no cap.
genzplyr is dplyr, but bussin fr fr no cap.
Reposted by Poppy Hesketh Best
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 6, 2025 at 9:46 PM
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
Reposted by Poppy Hesketh Best
Our method for genome size estimation from long-read overlaps is now published 🥳
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Genome size estimation from long read overlaps
AbstractMotivation. Accurate genome size estimation is an important component of genomic analyses such as assembly and coverage calculation, though existin
academic.oup.com
November 7, 2025 at 3:19 AM
Our method for genome size estimation from long-read overlaps is now published 🥳
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Reposted by Poppy Hesketh Best
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:26 PM
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
Reposted by Poppy Hesketh Best
Want to make some new conceptual graphics.
Tried to give Powerpoint's AI 'copilot' a spin. Asked it to make me a slide with 100 circle shape objects randomly distributed. Was excited when it made me a pptx to download...
except this is what it came up with.
Why can't we have nice things?
Tried to give Powerpoint's AI 'copilot' a spin. Asked it to make me a slide with 100 circle shape objects randomly distributed. Was excited when it made me a pptx to download...
except this is what it came up with.
Why can't we have nice things?
November 4, 2025 at 9:01 PM
Want to make some new conceptual graphics.
Tried to give Powerpoint's AI 'copilot' a spin. Asked it to make me a slide with 100 circle shape objects randomly distributed. Was excited when it made me a pptx to download...
except this is what it came up with.
Why can't we have nice things?
Tried to give Powerpoint's AI 'copilot' a spin. Asked it to make me a slide with 100 circle shape objects randomly distributed. Was excited when it made me a pptx to download...
except this is what it came up with.
Why can't we have nice things?
Reposted by Poppy Hesketh Best
🐝🦠 New paper: rdcu.be/eOf7A
Phages may drive microbial diversity, yet we often don’t even know how phages & bacteria correlate in nature. Our new study tackles this in the honeybee gut, thanks to the great work of PhD student @malickndiaye.bsky.social at @dmf-unil.bsky.social @fbm-unil.bsky.social
Phages may drive microbial diversity, yet we often don’t even know how phages & bacteria correlate in nature. Our new study tackles this in the honeybee gut, thanks to the great work of PhD student @malickndiaye.bsky.social at @dmf-unil.bsky.social @fbm-unil.bsky.social
Phage diversity mirrors bacterial strain diversity in the honey bee gut microbiota - Nature Communications
Authors analyse paired viral and bacterial shotgun metagenomics data from individual honeybee guts, revealing modular, nested phage–bacteria networks, with viral diversity mirroring bacterial strain c...
www.nature.com
November 4, 2025 at 8:36 PM
🐝🦠 New paper: rdcu.be/eOf7A
Phages may drive microbial diversity, yet we often don’t even know how phages & bacteria correlate in nature. Our new study tackles this in the honeybee gut, thanks to the great work of PhD student @malickndiaye.bsky.social at @dmf-unil.bsky.social @fbm-unil.bsky.social
Phages may drive microbial diversity, yet we often don’t even know how phages & bacteria correlate in nature. Our new study tackles this in the honeybee gut, thanks to the great work of PhD student @malickndiaye.bsky.social at @dmf-unil.bsky.social @fbm-unil.bsky.social
Reposted by Poppy Hesketh Best
Relying on the beneficence of private actors leaves the world vulnerable to the shifting opinions (or, conversely, the intransigence) of a handful of people
gh.bmj.com/content/10/1...
gh.bmj.com/content/10/1...
Who’s leading WHO? A quantitative analysis of the Bill and Melinda Gates Foundation’s grants to WHO, 2000-2024
Introduction The Bill and Melinda Gates Foundation (BMGF) has been the World Health Organization’s (WHO) second biggest source of funding in recent years, contributing 9.5% of WHO’s revenues between 2...
gh.bmj.com
October 31, 2025 at 9:18 AM
Relying on the beneficence of private actors leaves the world vulnerable to the shifting opinions (or, conversely, the intransigence) of a handful of people
gh.bmj.com/content/10/1...
gh.bmj.com/content/10/1...
Reposted by Poppy Hesketh Best
"Since 1850, human & domesticated mammal populations have grown rapidly. During the same period, the total biomass of wild mammals decreased by more than 2-fold." www.nature.com/articles/s41...
October 29, 2025 at 2:56 PM
"Since 1850, human & domesticated mammal populations have grown rapidly. During the same period, the total biomass of wild mammals decreased by more than 2-fold." www.nature.com/articles/s41...
Reposted by Poppy Hesketh Best
Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it:
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
October 23, 2025 at 8:16 PM
Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it:
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
Reposted by Poppy Hesketh Best
Are you interested in studying RNA phages? We are looking for a PhD student and a postdoc to join the lab!
For more information and how to apply, see below 👇
Please RT!
For more information and how to apply, see below 👇
Please RT!
📢 The #HIRI is looking for a #postdoc & a #PhD student to join the research group of @jenshoer.bsky.social. His lab focuses on understanding the molecular mechanisms of #phages with #RNA genomes during infection, host takeover & anti-phage defense. 🧫🦠 More info: www.helmholtz-hiri.de/en/jobs-tale...
Working at HIRI
At the HIRI, we do not just value excellent research. Short distances, an open door policy, and a good working atmosphere—this is what distinguishes us from others. Have a look at our current job…
www.helmholtz-hiri.de
October 17, 2025 at 12:52 PM
Are you interested in studying RNA phages? We are looking for a PhD student and a postdoc to join the lab!
For more information and how to apply, see below 👇
Please RT!
For more information and how to apply, see below 👇
Please RT!