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Ed Cunningham-Oakes

@edcoakes.bsky.social
321 followers 220 following 47 posts

📍 Liverpool 👨🏾‍💻 Bioinformatics and EDI 💭 Microbiome and Genomic Diagnostics 🏋🏾‍♂️ Powerlifter Views and typos my own

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Reposted by Ed Cunningham-Oakes
Paul Bernal @paulbernal.bsky.social · 08/09/2026
No, you can’t. The line on immigration is exactly what fuels the fascists. The line is ‘immigrants are bad’. That’s a fascist line.
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Ed Cunningham-Oakes @edcoakes.bsky.social · 23/08/2026
This is absolutely critical context. I would urge those who are signing open letters to consider the official position on this. Moreover, I would consider all academics to consider the impact of rallying behind said views on your black colleagues.
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Jonathan W. Gray @elmcitytree.blacksky.app · 22/08/2026
There’s a petition signed by more than one hundred academics (& counting!) in support of Nathan Cofnas—the racist who instigated the pile on that led to J. Arday’s death—because he lost his postdoc. Apparently there’s nothing a white man can do that deserves consequences.
forbetterscience.com
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Emma Monk @monkemma.bsky.social · 22/08/2026
One of the first "outrageous" claims I saw as Jason Arday's media hounding unfolded was that he ran 30 marathons in 35 days! Wow! What a thing to claim! And the newspapers all suggested there was no evidence he actually did it. Well, they clearly didn't look very hard 🙄 🧵 1/26
Photo after Jason's final marathon taken from his archived blog showing Jason surrounded by supporters in orange charity t-shirts
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Chaminda Jayanetti @cjayanetti.bsky.social · 06/08/2026
fwiw I don't think "Cambridge University professor most people have never heard of committed professional malpractice" should actually be national headline news
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Ulrike Franke @rikefranke.eu · 21/07/2026
“While operating in our sandboxed testing environment, our models spent a substantial amount of inference compute finding a way to obtain open Internet access…” Yeah, that’s not reassuring at all openai.com/index/huggin...
openai.com
OpenAI and Hugging Face partner to address security incident during model evaluation
OpenAI and Hugging Face share early findings from a security incident during AI model evaluation, highlighting advanced cyber capabilities and lessons for defenders.
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Ed Cunningham-Oakes @edcoakes.bsky.social · 17/07/2026
We are advertising an exciting PhD opportunity based at Newcastle University. You’ll use epidemiological and genomic data to characterise Campylobacter burden… and work with me on some cool datasets! Deadline: 28th July 2026 - NB UK Students only due to funding restrictions. Don’t miss out!
findaphd.com
NIHR PhD Studentship: Modernising Campylobacter burden assessment using integrated genomics, symptoms and surveillance data at Newcastle University on FindAPhD.com
PhD Project - NIHR PhD Studentship: Modernising Campylobacter burden assessment using integrated genomics, symptoms and surveillance data at Newcastle University, listed on FindAPhD.com
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Ed Cunningham-Oakes @edcoakes.bsky.social · 11/06/2026
Our paper is now published in eBioMedicine and I'm genuinely thrilled it's out 🎉 🧵 www.thelancet.com/journals/EBI... Despite the fact that this is a 2026 paper (such is peer review!), I wanted to write something and take you back to 2023, where the story of this work began. (1/7)
thelancet.com
Implementing portable, real-time 16S rRNA sequencing in the healthcare sector enhances antimicrobial stewardship
The integration of ONT 16S sequencing into routine NHS diagnostics has enabled antimicrobial stewardship by offering a faster method with improved taxonomic resolution. Its earlier use in cases where ...
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Nick Loman @pathogenomenick.bsky.social · 16/05/2026
Rapid release of multiplex PCR amplicon scheme for Andes hantavirus whole genome sequencing validated on control material: www.biorxiv.org/content/10.6... @scalene.bsky.social @stevepullan.bsky.social @ukhsa.bsky.social output from HPRU in Public Health Genomics
biorxiv.org
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Craig Winstanley @cwinstan.bsky.social · 17/05/2026
Bit of advice to Labour members. I’d treat any Streeting pledges as equivalent to Starmer pledges…
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Daniel Padfield @padpadpadpad.bsky.social · 14/05/2026
BBSRC Early Independence Fellowships had an Outline stage this year to try help with amount of peer review. Turns out they received 586 applications, a 110% increase on 2025, and only typically fund 15 a year. They are cancelling this stage and going straight to full app with an institutional sift.
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Ed Cunningham-Oakes @edcoakes.bsky.social · 17/04/2026
Not long now until #ESCMIDGlobal2026. I will see you all there!
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Ed Cunningham-Oakes @edcoakes.bsky.social · 13/04/2026
Working on bringing #genomics into diagnostics? 🧬 I’m presenting a poster at #ESCMIDGlobal2026 on some exciting work with @livuni-livsrf.bsky.social and Liverpool Clinical Laboratories, using nanopore sequencing for rapid fungal pathogen ID 🧬 📅 18 April | ⏰ 12:00–13:00 CEST See you there!
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Ed Cunningham-Oakes @edcoakes.bsky.social · 13/04/2026
Working on bringing #genomics into diagnostics? 🧬 I’m presenting a poster at #ESCMIDGlobal2026 on some exciting work with @livuni-livsrf.bsky.social and Liverpool Clinical Laboratories, using nanopore sequencing for rapid fungal pathogen ID 🧬 📅 18 April | ⏰ 12:00–13:00 CEST See you there!
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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 08/03/2026
Big update for #gbdraw! - Multi-record circular plots: Genomes with multiple replicons can now be displayed in a single view! - Advanced linear plots: Focus on regions of interest with granular control over feature selection and color-coding! Try now: gbdraw.app #microbiology #bioinformatics
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Dr Emma Hodcroft @firefoxx66.bsky.social · 10/03/2026
1/5 Introducing SimPlot-CL! 🧬 Recombination plays an important role in viral evolution. Similarity plots are a great way to visualize recombination patterns, but generating them across many genomes can be cumbersome (Work with my student, Keno Strotjohann!) 📂 github.com/hodcroftlab/simplot-cl
A figure showing a 'Simplot' which plots the similarity of a genome to other genomes across a graph, with similarity on the Y-axis and the genome position on the x-axis. Many coloured lines show the sequences being compared - those closest to the top (similarity of 1) are the closest matches in different parts of the genome.
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Craig Winstanley @cwinstan.bsky.social · 17/02/2026
Over the years I’ve been willing to put up with quite a lot in order to go to football matches, but the possibility of being randomly scooped up & sent to a concentration camp for months is a bit too much of an inconvenience.
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Matthew Freeman @mjafreeman.bsky.social · 03/02/2026
I watched much of Ian Chapman's (Head of @ukri.org) appearance this morning at @ukparliament.parliament.uk Science, Innovation and Technology Committee.. A few points and new information that bioscientists may find interesting... A 🧵
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Ed Cunningham-Oakes @edcoakes.bsky.social · 02/02/2026
First day back @liverpooluni.bsky.social as Co-I on a Wellcome Discovery Award 🦠🏫 (in an exciting new office!) Grateful to have worked with @wvschaik.bsky.social @halllab.bsky.social & @pathogenomenick.bsky.social on public health genomics at @unibirmingham.bsky.social - papers to come! ✍️
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Lucy Evans 🧫🦠👩🏻‍🔬 @biolucy.bsky.social · 22/01/2026
Presenting my work in fabulous Newcastle for #VOMUK26! Come chat to me about my poster (or your opinions on The Traitors/Formula 1/crafting). #microsky #phagesky 🧪
My poster entitled ‘Elucidating phage resistance in Enterococcus’
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Ryan Wick @rrwick.bsky.social · 21/01/2026
New blog post with some thoughts on @nanoporetech.com and their recent announcement that the P2 Solo will be discontinued: rrwick.github.io/2026/01/21/p...
rrwick.github.io
P2 Solo announcement and the trade-offs of a more stable ONT
a blog for miscellaneous bioinformatics stuff
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Ed Cunningham-Oakes @edcoakes.bsky.social · 16/01/2026
Love microbes & omics? 🦠🧬 We’re hiring a Postdoc in Public Health Genomics at @unibirmingham.bsky.social Work on cutting-edge research with wonderful people! @wvschaik.bsky.social @halllab.bsky.social @pathogenomenick.bsky.social @scalene.bsky.social @alanmcn1.bsky.social 📅 Closes 4th Feb
edzz.fa.em3.oraclecloud.com
Research Fellow - Department of Microbes, Infection and Microbiomes - 105518 - Grade 7
The post holder will work within the newly established NIHR Health Protection Unit for Public Health Genomics, a partnership between the University of Birmingham and the UK Health Security Agency. You...
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Reposted by Ed Cunningham-Oakes
Zoe Gardner @zoejardiniere.bsky.social · 07/01/2026
Subtweet: You do not feel safer in London *despite* it being more diverse than other towns. You feel safer in London because it is generally safe, and there being a lot of brown people here has LITERALLY NOTHING to do with how safe you are.
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Dr Emma Yhnell 🧬🔬🧪🧠 🏴󠁧󠁢󠁷󠁬󠁳󠁿 @emmayhnell.bsky.social · 02/01/2026
A wonderful way to start the year, with a new publication. We examine ethnic representation across UK bioscience by exploring the structural factors shaping career progression, and proposing recommendations for meaningful change. Full article: pubmed.ncbi.nlm.nih.gov/41474708/
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Ed Cunningham-Oakes @edcoakes.bsky.social · 31/12/2025
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
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PacBio @pacbio.bsky.social · 26/12/2025
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
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Ed Cunningham-Oakes @edcoakes.bsky.social · 24/12/2025
‘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...
nature.com
Quantifying the bystander effect of antimicrobial use on the gut microbiome and resistome in Malawian adults - Nature Communications
Here, the authors analyze the microbiome composition and resistome pre-, during- and post-antibiotic exposure in Malawian adults, and find that commonly used antibiotics, such as ceftriaxone, exert st...
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Lisa Maier Lab | Tübingen @lisamaierlab.bsky.social · 22/12/2025
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...
lisamaierlab.com
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Torsten Seemann @torstenseemann.bsky.social · 22/12/2025
💾 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...
github.com
Releases · tseemann/mlst
:id: Scan contig files against PubMLST typing schemes - tseemann/mlst
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Stephen Turner @stephenturner.us · 21/12/2025
UnigeneFinder: An automated pipeline for gene calling from transcriptome assemblies without a reference genome
biorxiv.org
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…
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Reposted by Ed Cunningham-Oakes
Angie Rasmussen @angierasmussen.bsky.social · 19/12/2025
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...
notus.org
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.”
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Rob Moran @prob91.bsky.social · 18/12/2025
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...
microbiologyresearch.org
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...
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Alan McNally @alanmcn1.bsky.social · 16/12/2025
The first preprint from @izziepotterill.bsky.social PhD. A clone within ST131 clade C with a totally unique capsule region.
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Ed Cunningham-Oakes @edcoakes.bsky.social · 16/12/2025
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)
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Hall Lab @halllab.bsky.social · 15/12/2025
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...
doi.org
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 ...
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Ryan Marino, MD @ryanmarino.bsky.social · 14/12/2025
He really doesn’t understand any of the most basic biology concepts at all, huh
@Vision4theBlind

Elon Musk in an interview saying you can turn someone into a butterfly with mRNA.
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Willem van Schaik @wvschaik.bsky.social · 13/12/2025
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.
findaphd.com
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
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Hannah Trivett @hannahtriv.bsky.social · 10/12/2025
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...
biorxiv.org
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...
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Torsten Seemann @torstenseemann.bsky.social · 05/12/2025
💾 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...
github.com
Releases · tseemann/abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes - tseemann/abricate
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Sebastian Schmidt @tsbschm.bsky.social · 20/11/2025
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/...
academic.oup.com
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
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Ed Cunningham-Oakes @edcoakes.bsky.social · 21/11/2025
It is a disgrace that an alternative is even being entertained by the CDC
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Pathoplexus @pathoplexus.org · 18/11/2025
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.
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Bede Constantinides @bede.im · 17/11/2025
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.
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Kevin Fox @michigrim.bsky.social · 07/11/2025
What a banger
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Ian Dunt @iandunt.bsky.social · 29/10/2025
Your daily reminder that the government continues to commercially support an individual who wants to destroy it through fascist violence.
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Ed Cunningham-Oakes @edcoakes.bsky.social · 27/10/2025
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
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Rick Beeloo @rickbitloo.bsky.social · 23/10/2025
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...
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BWJones @bwjones.bsky.social · 24/09/2025
This remarkable therapy uses an approach the Trump administration just cancelled funding for.
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Ed Cunningham-Oakes @edcoakes.bsky.social · 07/09/2025
Has anyone given this a go? Tempted to let Reviewer 2 weigh in on my hobbies..
publishorperish.games
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....
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Ed Cunningham-Oakes @edcoakes.bsky.social · 29/07/2025
A great reminder of why it's important to consider the shape of your data before diving into microbiome analysis!
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