Ed Cunningham-Oakes
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edcoakes.bsky.social
Ed Cunningham-Oakes
@edcoakes.bsky.social
280 followers 210 following 25 posts
📍 Birmingham
👨🏾‍💻 Bioinformatics and EDI
💭 Microbiome and Genomic Diagnostics
🦠 HPRU in Public Health Genomics
🏋🏾‍♂️ Powerlifter
Views and typos my own
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Reposted by Ed Cunningham-Oakes
tsbschm.bsky.social
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
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
edcoakes.bsky.social
It is a disgrace that an alternative is even being entertained by the CDC
socialinfluenza.bsky.social Ed Hutchinson @socialinfluenza.bsky.social · 4d
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...
Text box reading: Vaccines do not... do not overload or weaken the immune system – it's safe to give children and adults several vaccines at a time and this reduces the amount of injections needed do not contain mercury (thiomersal) do not contain any ingredients that cause harm – only ingredients essential to making them safer and more effective and only in very small amounts do not cause autism – studies have found no evidence of a link between the MMR vaccine and autism
November 21, 2025 at 7:59 AM
Reposted by Ed Cunningham-Oakes
pathoplexus.org
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...
Graph showing the change in number of directly submitted sequences to Pathoplexus since August 2024. 0 in Aug 2024 to almost 9000 today.
November 18, 2025 at 7:01 PM
Reposted by Ed Cunningham-Oakes
bedec.bsky.social
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.
nextstrain.org Nextstrain @nextstrain.org · 17d
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
Reposted by Ed Cunningham-Oakes
michigrim.bsky.social
What a banger
November 7, 2025 at 4:51 PM
Reposted by Ed Cunningham-Oakes
iandunt.bsky.social
Your daily reminder that the government continues to commercially support an individual who wants to destroy it through fascist violence.
fintwitter.bsky.social FinTwitter @fintwitter.bsky.social · 26d
Elon musk: ‘Civil war in Britain is inevitable. Just a question of when.’
October 29, 2025 at 8:10 AM
edcoakes.bsky.social
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
livuni-ives.bsky.social Institute of Infection, Veterinary and Ecological Sciences @livuni-ives.bsky.social · 27d
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
A news title card with a transparent image of salmonella bacteria against a navy blue background. The text reads '£4.56M Wellcome Discovery Award to investigate natural human resistance to Salmonella' in white.
October 27, 2025 at 3:30 PM
Reposted by Ed Cunningham-Oakes
rickbitloo.bsky.social
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...
October 23, 2025 at 8:16 PM
Reposted by Ed Cunningham-Oakes
bwjones.bsky.social
This remarkable therapy uses an approach the Trump administration just cancelled funding for.
September 24, 2025 at 12:29 PM
edcoakes.bsky.social
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
edcoakes.bsky.social
A great reminder of why it's important to consider the shape of your data before diving into microbiome analysis!
July 29, 2025 at 4:31 PM
Reposted by Ed Cunningham-Oakes
axelvisel.bsky.social
🧬Viromics🧬 = using (meta-)genomics to study uncultivated viruses has yielded unprecedented insights into the diversity and global distribution of viruses

@jgi.doe.gov's @simrouxvirus.bsky.social and Clement Coclet review the state of the field, available tools, and remaining challenges
July 22, 2025 at 1:49 PM
Reposted by Ed Cunningham-Oakes
widdowquinn.bsky.social
Thank you to everyone who has used pyani over the years (I know it's thousands of people!) but we have now archived the repository.

But we have replaced it with a completely rewritten and extended implementation: pyani-plus!

github.com/pyani-plus/p...

1/
han solo from star wars is pointing at the camera in a room .
ALT: han solo from star wars is pointing at the camera in a room .
media.tenor.com
July 1, 2025 at 2:04 PM
edcoakes.bsky.social
Yesterday was my last day after an exciting four years in @acdarby.bsky.social's lab at Liverpool.

The lab photo below was taken in Birmingham, where I’ll soon be working!

Excited to join @wvschaik.bsky.social, @pathogenomenick.bsky.social, @halllab.bsky.social to work on Public Health Genomics.
July 1, 2025 at 12:52 PM
Reposted by Ed Cunningham-Oakes
trishgreenhalgh.bsky.social
Plenty studies showing that your postcode is a better predictor of your health outcomes than your genome.
carolinejmolloy.bsky.social CarolineJMolloy @carolinejmolloy.bsky.social · Jun 21
The BBC & Telegraph are trailing Wes Streeting’s technophile health plans, including genomic mapping at birth.
Is this really gonna transform the NHS into a prevention service within 10 yrs, as Wes claims? For v rare genetic conditions, praps. But for the real burden of disease?

Thoughts, #medsky?
June 22, 2025 at 6:43 AM
Reposted by Ed Cunningham-Oakes
albertvilella.bsky.social
@andywatson on the NGS Sequencing market and the prisoner's dilemma
June 21, 2025 at 10:59 AM
Reposted by Ed Cunningham-Oakes
fascinatorfun.bsky.social
Keir Starmer, Yvette Cooper, David Lammy, and McSweeney @teamlabouruk.bsky.social should take note if what they really want is growth.
maartenpvink.bsky.social Maarten Vink @maartenpvink.bsky.social · May 31
Academic studies consistently show that access to citizenship has positive effects. Immigrants who become citizens experience lower unemployment, earn higher income, less likely to be overqualified for jobs & experience stronger sense of belonging

eg @gathmannch.bsky.social

doi.org/10.1016/j.la...
June 1, 2025 at 9:10 AM
Reposted by Ed Cunningham-Oakes
jimshaw.bsky.social
Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).

myloasm-docs.github.io
myloasm - metagenomic assembly with (noisy) long reads
myloasm-docs.github.io
May 28, 2025 at 5:54 PM
Reposted by Ed Cunningham-Oakes
tommytang.bsky.social
🧵 You’re not behind in bioinformatics. The field just evolves faster than anyone can follow.
1/ It’s not you.
Bioinformatics evolves too fast.
And not just from new algorithms—
But from how fast technology itself changes.
May 22, 2025 at 1:15 PM
edcoakes.bsky.social
1/12 🎉 We're excited to announce our Genome Medicine paper benchmarking 1000+ metagenomes (DNA) and metatranscriptomes (RNA) from infectious intestinal disease patients against pathogen diagnostics. The full dataset is public to accelerate pathogen discovery & surveillance: doi.org/10.1186/s130...
May 20, 2025 at 9:20 AM
Reposted by Ed Cunningham-Oakes
microbiologysociety.org
It’s Black Inclusion Week this week. If you are a Black microbiologist we would recommend connecting with the Black Microbiologists Association. They are working hard to increase visibility and facilitate connections: blackinmicrobiology.org #BlackInMicro #BIW2025
Black Microbiologists Association
Moving Microbiology Forward
blackinmicrobiology.org
May 12, 2025 at 9:02 AM
Reposted by Ed Cunningham-Oakes
tanjabueltmann.net
My letter to the Prime Minister. #immigration
Slightly amended so I can fit this here: I am writing to you as an immigrant who chose to make the UK my home. As someone who is now also a British citizen. And as a German-born historian who understands where the complete normalisation of the far right can end. I write to say: For shame! I first came to the UK in the 1990s for a visit with my grandmother. Objectively, much was backwards here. No mixer taps in the bathroom; awful ‘bread’; and strings had to be pulled to switch on lights. But however I felt about this, my own string had been pulled: I loved this Cool Britannia. It was quite possibly then that I decided that the UK was to be my home. When I arrived to settle here permanently, I made a choice: to contribute my skills, my knowledge—all I have to offer—to this country rather than another one. I am deeply disgusted by your comment today that immigration has done ‘incalculable damage’ to the country. This is the language of the far right. It is insulting, hateful & will fuel xenophobia. And it is just wrong. Migration is a normal part of the human existence. None of us would be where we are without it. Open your fridge and you will see migration. Immigrants help make the UK tick every single day, whether we clean toilets in our hospitals or provide care for the elderly; whether we empty our bins or carry out cancer research. We are mothers, sons-in-law, aunts and uncles, friends, neighbours and colleagues. I ask you not tell me that you do not mean me. I know that you do not—at least not primarily—mean a white woman from Europe who has a PhD. But who do you mean? And, much more importantly, who do you think those racists who were engaged in riots on our streets last summer think you mean? Anti-immigration narratives have defined UK policymaking for the best part of two decades. And fundamentally so. They were the key driver in delivering Brexit, for example, and, as such, have directly limited the rights and opportunities of British citizens. This obsessive focus on immigration as the ‘problem’—that is the real problem. And it is consistently delivering poor outcomes for the UK. Instead of tackling this, you are choosing to consolidate it, sowing divisions along the way. You may point me to polling and tell me that this is what voters want. Do they? I am not surprised at all that over 50% of voters might say they want to see immigration reduced if that is the question they are being asked. What we need to know is what they would answer to the question: “Would you like to see immigration reduced? What this would mean for you and your local community is XYZ.” That is not how surveys can ask questions, but governments absolutely can choose to make policy using such a more informed position. Prime Minister, you continue to talk a lot about making the tough choices. But let’s be clear: setting immigrants up as the ‘other’, as a scapegoat—describing us as a threat ‘pulling the country apart’, a ‘squalid chapter’, a risk that might make the UK an ‘island of strangers’—these are not tough choices at all. These are the easy choices. They are the choices that populists make who have no solutions to the real problems a country faces. What I would like to know, Prime Minister, is what you will do when your policies lead to the implosion of the UK’s Higher Education sector. What you will tell communities when they can no longer provide any care for the elderly. The policies you announced today will not solve anything at all. They will have exclusively negative impacts. For those immediately affected; for our communities; and for our economy. Being pro-immigration—it is progressive, yes, but the much more crucial point is that it is also the most pro-UK policy approach that any politician in the country can pursue. And you are choosing to do the opposite. This, Prime Minister, is the real damage—and it will be very calculable indeed. Tanja Bueltmann
May 12, 2025 at 2:46 PM
edcoakes.bsky.social
Delighted to share this preprint on the mosquito #virome with some excellent collaborators 🦠🦟
biorxiv-genomic.bsky.social bioRxiv Genomics @biorxiv-genomic.bsky.social · May 7
Emergence Risks from Within? Metagenomic Analysis of Mosquito Viromes from Two Zoos Reveals Mosquito-associated Orthobunyaviruses in the UK https://www.biorxiv.org/content/10.1101/2025.05.01.651672v1
May 9, 2025 at 3:54 PM
edcoakes.bsky.social
Great to see the Pseudomonas sp. PP3 genome published in @asm.org journals, and to be included based on sequencing I did during my PhD @cardiffuni.bsky.social!

journals.asm.org/doi/full/10....

PP3’s genome reveals how microbes adapt to (and help clean up) halo-organic pollutants. 🌱🧬
Complete genome sequence of Pseudomonas sp. PP3, a dehalogenase-producing bacterium, confirms the unusual mobile genetic element DEH | Microbiology Resource Announcements
Halo-organic compounds are used as herbicides, pesticides, preservatives, solvents, and other applications. The persistence and toxicity of many of these compounds raise serious environmental concerns regarding their use (1). Biodegradation of such compounds, including haloalkanoic acids, by Pseudomonas species is well known (2).
journals.asm.org
April 22, 2025 at 12:26 PM
Reposted by Ed Cunningham-Oakes
jessicamablair.bsky.social
Really delighted to see this out in npj antimicrobials and resistance! @emmabeansworth.bsky.social @blancaps.bsky.social & @edcoakes.bsky.social have done a fantastic job with this 🤩
April 15, 2025 at 8:06 AM