Ed Cunningham-Oakes
@edcoakes.bsky.social
📍 Birmingham
👨🏾💻 Bioinformatics and EDI
💭 Microbiome and Genomic Diagnostics
🦠 HPRU in Public Health Genomics
🏋🏾♂️ Powerlifter
Views and typos my own
👨🏾💻 Bioinformatics and EDI
💭 Microbiome and Genomic Diagnostics
🦠 HPRU in Public Health Genomics
🏋🏾♂️ Powerlifter
Views and typos my own
New year, new PhD? 🧑🎓
If you’re fed up of leftovers, and out of ideas for festive fun, here’s a quick reminder to apply to these posts! 🧫 🧬
#PhD #Microbiology #Genomics
If you’re fed up of leftovers, and out of ideas for festive fun, here’s a quick reminder to apply to these posts! 🧫 🧬
#PhD #Microbiology #Genomics
We are recruiting for a number of PhDs in the HPRU in Public Health Genomics, based at @unibirmingham.bsky.social, in collaboration with UKHSA. 🦠🧬
Apply below to work on cutting-edge science and public health priorities! (NB deadline of 9th January / UK only due to funding restrictions)
(1/7)
Apply below to work on cutting-edge science and public health priorities! (NB deadline of 9th January / UK only due to funding restrictions)
(1/7)
December 31, 2025 at 10:17 AM
New year, new PhD? 🧑🎓
If you’re fed up of leftovers, and out of ideas for festive fun, here’s a quick reminder to apply to these posts! 🧫 🧬
#PhD #Microbiology #Genomics
If you’re fed up of leftovers, and out of ideas for festive fun, here’s a quick reminder to apply to these posts! 🧫 🧬
#PhD #Microbiology #Genomics
Reposted by Ed Cunningham-Oakes
Happy holidays! 🦌🎄
A new chromosome-level genome assembly of Norwegian wild alpine reindeer was generated using #PacBio HiFi long reads, delivering accurate, haplotype-resolved results.
See more HiFi-powered science at #PAG33 and visit us at booth 219!
Read the paper: bit.ly/3Y0tEZu
A new chromosome-level genome assembly of Norwegian wild alpine reindeer was generated using #PacBio HiFi long reads, delivering accurate, haplotype-resolved results.
See more HiFi-powered science at #PAG33 and visit us at booth 219!
Read the paper: bit.ly/3Y0tEZu
December 26, 2025 at 4:55 PM
Happy holidays! 🦌🎄
A new chromosome-level genome assembly of Norwegian wild alpine reindeer was generated using #PacBio HiFi long reads, delivering accurate, haplotype-resolved results.
See more HiFi-powered science at #PAG33 and visit us at booth 219!
Read the paper: bit.ly/3Y0tEZu
A new chromosome-level genome assembly of Norwegian wild alpine reindeer was generated using #PacBio HiFi long reads, delivering accurate, haplotype-resolved results.
See more HiFi-powered science at #PAG33 and visit us at booth 219!
Read the paper: bit.ly/3Y0tEZu
‘Twas the night before Christmas,
and all through the house,
Not a creature was stirring…
apart from journal editorial teams who have made this my final paper of the year!
Happy to announce that this work has been published in Nature Comms.
www.nature.com/articles/s41...
and all through the house,
Not a creature was stirring…
apart from journal editorial teams who have made this my final paper of the year!
Happy to announce that this work has been published in Nature Comms.
www.nature.com/articles/s41...
December 24, 2025 at 3:59 PM
‘Twas the night before Christmas,
and all through the house,
Not a creature was stirring…
apart from journal editorial teams who have made this my final paper of the year!
Happy to announce that this work has been published in Nature Comms.
www.nature.com/articles/s41...
and all through the house,
Not a creature was stirring…
apart from journal editorial teams who have made this my final paper of the year!
Happy to announce that this work has been published in Nature Comms.
www.nature.com/articles/s41...
Reposted by Ed Cunningham-Oakes
We’re hiring 2 Postdocs (f/m/d) in Drug–Microbiome–Host Interactions 🦠💊
Focus: how non-antibiotic drugs shape the gut microbiome, drug efficacy & side effects.
#PostdocJobs #Microbiome #AcademicJobs
Full job ad:
lisamaierlab.com/wp-content/u...
Focus: how non-antibiotic drugs shape the gut microbiome, drug efficacy & side effects.
#PostdocJobs #Microbiome #AcademicJobs
Full job ad:
lisamaierlab.com/wp-content/u...
lisamaierlab.com
December 22, 2025 at 2:08 PM
We’re hiring 2 Postdocs (f/m/d) in Drug–Microbiome–Host Interactions 🦠💊
Focus: how non-antibiotic drugs shape the gut microbiome, drug efficacy & side effects.
#PostdocJobs #Microbiome #AcademicJobs
Full job ad:
lisamaierlab.com/wp-content/u...
Focus: how non-antibiotic drugs shape the gut microbiome, drug efficacy & side effects.
#PostdocJobs #Microbiome #AcademicJobs
Full job ad:
lisamaierlab.com/wp-content/u...
Reposted by Ed Cunningham-Oakes
💾 mlst 2.25.0 has been released!
Fixed a bug that missed alleles in increasingly larger schemes like senterica (thanks @microbiologikat.bsky.social) and updated the databases.
#bioinformatiocs #microbiology #genomics
github.com/tseemann/mls...
Fixed a bug that missed alleles in increasingly larger schemes like senterica (thanks @microbiologikat.bsky.social) and updated the databases.
#bioinformatiocs #microbiology #genomics
github.com/tseemann/mls...
Releases · tseemann/mlst
:id: Scan contig files against PubMLST typing schemes - tseemann/mlst
github.com
December 22, 2025 at 9:15 PM
💾 mlst 2.25.0 has been released!
Fixed a bug that missed alleles in increasingly larger schemes like senterica (thanks @microbiologikat.bsky.social) and updated the databases.
#bioinformatiocs #microbiology #genomics
github.com/tseemann/mls...
Fixed a bug that missed alleles in increasingly larger schemes like senterica (thanks @microbiologikat.bsky.social) and updated the databases.
#bioinformatiocs #microbiology #genomics
github.com/tseemann/mls...
Reposted by Ed Cunningham-Oakes
UnigeneFinder: An automated pipeline for gene calling from transcriptome assemblies without a reference genome
UnigeneFinder: An automated pipeline for gene calling from transcriptome assemblies without a reference genome
For most species in nature, transcriptome data is much more readily available than genome data. Without a reference genome, however, gene calling is cumbersome and inaccurate due to the high degree…
www.biorxiv.org
December 21, 2025 at 10:42 AM
UnigeneFinder: An automated pipeline for gene calling from transcriptome assemblies without a reference genome
Reposted by Ed Cunningham-Oakes
This is not the first time RFK Jr or his fellow anti-vax travelers conducted a study they knew would harm or kill children in low-income countries. It is a dehumanizing, colonialist model of manufacturing evidence: sacrificing foreign kids for political pseudoscience.
www.notus.org/health-scien...
www.notus.org/health-scien...
CDC to Fund Controversial Study in West Africa on Infant Hepatitis B Vaccines
The study prompted swift outcry from scientists in the U.S. who say it’s “unethical.”
www.notus.org
December 19, 2025 at 5:46 PM
This is not the first time RFK Jr or his fellow anti-vax travelers conducted a study they knew would harm or kill children in low-income countries. It is a dehumanizing, colonialist model of manufacturing evidence: sacrificing foreign kids for political pseudoscience.
www.notus.org/health-scien...
www.notus.org/health-scien...
Reposted by Ed Cunningham-Oakes
Our new paper in MGen traces the evolution of a plasmid lineage associated with MDR in Enterococcus faecium, primarily driven by IS1216
For anyone interested in plasmid structures and the smaller MGEs that shape them 🧵👇 [1/14]
@microbiologysociety.org
www.microbiologyresearch.org/content/jour...
For anyone interested in plasmid structures and the smaller MGEs that shape them 🧵👇 [1/14]
@microbiologysociety.org
www.microbiologyresearch.org/content/jour...
IS1216 drives the evolution of pRUM-like multidrug resistance plasmids in Enterococcus faecium
pRUM-like plasmids are commonly found in multidrug-resistant Enterococcus faecium, but the evolution of these plasmids has not been characterised in detail. When we analysed the genome sequences of tw...
www.microbiologyresearch.org
December 18, 2025 at 7:46 AM
Our new paper in MGen traces the evolution of a plasmid lineage associated with MDR in Enterococcus faecium, primarily driven by IS1216
For anyone interested in plasmid structures and the smaller MGEs that shape them 🧵👇 [1/14]
@microbiologysociety.org
www.microbiologyresearch.org/content/jour...
For anyone interested in plasmid structures and the smaller MGEs that shape them 🧵👇 [1/14]
@microbiologysociety.org
www.microbiologyresearch.org/content/jour...
Reposted by Ed Cunningham-Oakes
The first preprint from @izziepotterill.bsky.social PhD. A clone within ST131 clade C with a totally unique capsule region.
Genomic rearrangement of the capsule operon in a phylogenetically distinct cluster of the multi-drug resistant Escherichia coli lineage ST131 https://www.biorxiv.org/content/10.64898/2025.12.15.689991v1
December 16, 2025 at 7:52 PM
The first preprint from @izziepotterill.bsky.social PhD. A clone within ST131 clade C with a totally unique capsule region.
We are recruiting for a number of PhDs in the HPRU in Public Health Genomics, based at @unibirmingham.bsky.social, in collaboration with UKHSA. 🦠🧬
Apply below to work on cutting-edge science and public health priorities! (NB deadline of 9th January / UK only due to funding restrictions)
(1/7)
Apply below to work on cutting-edge science and public health priorities! (NB deadline of 9th January / UK only due to funding restrictions)
(1/7)
December 16, 2025 at 6:50 PM
We are recruiting for a number of PhDs in the HPRU in Public Health Genomics, based at @unibirmingham.bsky.social, in collaboration with UKHSA. 🦠🧬
Apply below to work on cutting-edge science and public health priorities! (NB deadline of 9th January / UK only due to funding restrictions)
(1/7)
Apply below to work on cutting-edge science and public health priorities! (NB deadline of 9th January / UK only due to funding restrictions)
(1/7)
Reposted by Ed Cunningham-Oakes
Delighted to share Magda's new review in Annual Review of Food Science and Technology 🎉
We explore how microbe-diet interactions shape health across the life course and the promise (and challenges!) of microbiome-informed precision nutrition 👇
doi.org/10.1146/annu...
We explore how microbe-diet interactions shape health across the life course and the promise (and challenges!) of microbiome-informed precision nutrition 👇
doi.org/10.1146/annu...
Microbe–Diet Interactions and Personalized Nutrition
Nutrition plays a fundamental role in shaping human health across the life course, influencing both host physiology and the composition and function of the gut microbiota. In turn, the gut microbiota ...
doi.org
December 15, 2025 at 8:57 AM
Delighted to share Magda's new review in Annual Review of Food Science and Technology 🎉
We explore how microbe-diet interactions shape health across the life course and the promise (and challenges!) of microbiome-informed precision nutrition 👇
doi.org/10.1146/annu...
We explore how microbe-diet interactions shape health across the life course and the promise (and challenges!) of microbiome-informed precision nutrition 👇
doi.org/10.1146/annu...
Reposted by Ed Cunningham-Oakes
He really doesn’t understand any of the most basic biology concepts at all, huh
December 14, 2025 at 8:50 PM
He really doesn’t understand any of the most basic biology concepts at all, huh
Reposted by Ed Cunningham-Oakes
New PhD project, supervision by @alanmcn1.bsky.social and me.
'Nationwide Clostridioides difficile population dynamics'
www.findaphd.com/phds/project...
Deadline for applications 9 Jan 2026, UK students only.
'Nationwide Clostridioides difficile population dynamics'
www.findaphd.com/phds/project...
Deadline for applications 9 Jan 2026, UK students only.
Nationwide Clostridioides difficile population dynamics. at University of Birmingham on FindAPhD.com
PhD Project - Nationwide Clostridioides difficile population dynamics. at University of Birmingham, listed on FindAPhD.com
www.findaphd.com
December 13, 2025 at 4:59 PM
New PhD project, supervision by @alanmcn1.bsky.social and me.
'Nationwide Clostridioides difficile population dynamics'
www.findaphd.com/phds/project...
Deadline for applications 9 Jan 2026, UK students only.
'Nationwide Clostridioides difficile population dynamics'
www.findaphd.com/phds/project...
Deadline for applications 9 Jan 2026, UK students only.
Reposted by Ed Cunningham-Oakes
I am pleased to share that my first postdoc paper from the @halllab.bsky.social is now on bioRxiv! 🎉
We used long-read #metagenomics to explore how the gut microbiome and #antimicrobialresistance landscape shift across advanced chronic #liverdisease (ACLD)
www.biorxiv.org/content/10.6...
We used long-read #metagenomics to explore how the gut microbiome and #antimicrobialresistance landscape shift across advanced chronic #liverdisease (ACLD)
www.biorxiv.org/content/10.6...
Decoding the microbiome and resistome of advanced chronic liver disease through long-read metagenomics
Introduction - Patients with advanced chronic liver disease (ACLD) and underlying cirrhosis frequently require repeated courses of antimicrobial therapy, with both the frequency and spectrum of antimi...
www.biorxiv.org
December 10, 2025 at 12:09 PM
I am pleased to share that my first postdoc paper from the @halllab.bsky.social is now on bioRxiv! 🎉
We used long-read #metagenomics to explore how the gut microbiome and #antimicrobialresistance landscape shift across advanced chronic #liverdisease (ACLD)
www.biorxiv.org/content/10.6...
We used long-read #metagenomics to explore how the gut microbiome and #antimicrobialresistance landscape shift across advanced chronic #liverdisease (ACLD)
www.biorxiv.org/content/10.6...
Reposted by Ed Cunningham-Oakes
💾 ABRicate 1.2.0 has been released!
This 'oversight' lasted 6 years, but with help from @finlaym.bsky.social we got CI working and updated all the databases. #bioconda #conda #bioinformatics #microbiology #genomics
github.com/tseemann/abr...
This 'oversight' lasted 6 years, but with help from @finlaym.bsky.social we got CI working and updated all the databases. #bioconda #conda #bioinformatics #microbiology #genomics
github.com/tseemann/abr...
Releases · tseemann/abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes - tseemann/abricate
github.com
December 5, 2025 at 11:27 PM
💾 ABRicate 1.2.0 has been released!
This 'oversight' lasted 6 years, but with help from @finlaym.bsky.social we got CI working and updated all the databases. #bioconda #conda #bioinformatics #microbiology #genomics
github.com/tseemann/abr...
This 'oversight' lasted 6 years, but with help from @finlaym.bsky.social we got CI working and updated all the databases. #bioconda #conda #bioinformatics #microbiology #genomics
github.com/tseemann/abr...
Reposted by Ed Cunningham-Oakes
Congrats @fullam.bsky.social @pangenomics.bsky.social @borklab.bsky.social & team(s). Great to see this published!
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes: academic.oup.com/nar/article/...
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes: academic.oup.com/nar/article/...
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes
Abstract. The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands rob
academic.oup.com
November 20, 2025 at 8:50 AM
Congrats @fullam.bsky.social @pangenomics.bsky.social @borklab.bsky.social & team(s). Great to see this published!
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes: academic.oup.com/nar/article/...
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes: academic.oup.com/nar/article/...
It is a disgrace that an alternative is even being entertained by the CDC
Should you find yourself - for whatever reason - looking for a new set of authoritative, accessible summaries of the risks and benefits of vaccines to share with people, the NHS website is still doing a good job at this www.nhs.uk/vaccinations...
November 21, 2025 at 7:59 AM
It is a disgrace that an alternative is even being entertained by the CDC
Reposted by Ed Cunningham-Oakes
1/ 🚀 Big thanks to our community - since August we’ve added thousands of new sequences, rolled out major new features, and welcomed fresh faces into the #Pathoplexus world. Let’s dive into what’s new.👇🏻
Read the full update: pathoplexus.org/news/2025-11...
Read the full update: pathoplexus.org/news/2025-11...
November 18, 2025 at 7:01 PM
1/ 🚀 Big thanks to our community - since August we’ve added thousands of new sequences, rolled out major new features, and welcomed fresh faces into the #Pathoplexus world. Let’s dive into what’s new.👇🏻
Read the full update: pathoplexus.org/news/2025-11...
Read the full update: pathoplexus.org/news/2025-11...
Reposted by Ed Cunningham-Oakes
My account's upload and bulk download access were terminated permanently in 2021 without explanation after I published *checksums* of GISAID genomes. GISAID and its SAB have since ignored a dozen emails seeking explanation.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
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 17, 2025 at 1:32 PM
My account's upload and bulk download access were terminated permanently in 2021 without explanation after I published *checksums* of GISAID genomes. GISAID and its SAB have since ignored a dozen emails seeking explanation.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
Reposted by Ed Cunningham-Oakes
Reposted by Ed Cunningham-Oakes
Your daily reminder that the government continues to commercially support an individual who wants to destroy it through fascist violence.
Elon musk: ‘Civil war in Britain is inevitable. Just a question of when.’
October 29, 2025 at 8:10 AM
Your daily reminder that the government continues to commercially support an individual who wants to destroy it through fascist violence.
I am delighted to be a co-investigator on this newly funded Wellcome Discovery Award. Excited to begin work with the team (including those not on Bluesky!)
@jayhinton.bsky.social @roygoodacre.bsky.social @lisamaierlab.bsky.social @blancaps.bsky.social
@jayhinton.bsky.social @roygoodacre.bsky.social @lisamaierlab.bsky.social @blancaps.bsky.social
NEWS | Professor @jayhinton.bsky.social and an international team have been awarded £4.56M Wellcome Discovery Award to investigate natural human resistance to Salmonella
🔗 bit.ly/4hujsRG
@livuninews.bsky.social | #TeamLivUni
🔗 bit.ly/4hujsRG
@livuninews.bsky.social | #TeamLivUni
October 27, 2025 at 3:30 PM
I am delighted to be a co-investigator on this newly funded Wellcome Discovery Award. Excited to begin work with the team (including those not on Bluesky!)
@jayhinton.bsky.social @roygoodacre.bsky.social @lisamaierlab.bsky.social @blancaps.bsky.social
@jayhinton.bsky.social @roygoodacre.bsky.social @lisamaierlab.bsky.social @blancaps.bsky.social
Reposted by Ed Cunningham-Oakes
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 Ed Cunningham-Oakes
This remarkable therapy uses an approach the Trump administration just cancelled funding for.
September 24, 2025 at 12:29 PM
This remarkable therapy uses an approach the Trump administration just cancelled funding for.
Has anyone given this a go? Tempted to let Reviewer 2 weigh in on my hobbies..
Publish or Perish: A Humorous Party Game about Academic Publish
Welcome to the chaotic life of academic publishing. In this game, you are a clueless researcher trying to do the one and only thing that matters in your academic life: churning out publications, fast....
publishorperish.games
September 7, 2025 at 5:19 PM
Has anyone given this a go? Tempted to let Reviewer 2 weigh in on my hobbies..