Ed Cunningham-Oakes

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.

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 🧵

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! ✍️

My poster entitled ‘Elucidating phage resistance in Enterococcus’

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 🧪

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...

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...

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

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.

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/

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

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

‘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...

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...

Releases · tseemann/mlst :id: Scan contig files against PubMLST typing schemes - tseemann/mlst

💾 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...

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…

UnigeneFinder: An automated pipeline for gene calling from transcriptome assemblies without a reference genome

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.”

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...

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...

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...

The first preprint from @izziepotterill.bsky.social PhD. A clone within ST131 clade C with a totally unique capsule region.

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

- Nationwide Clostridioides difficile population dynamics

Supervisors: Willem van Schaik, David Williams, Alan McNally

www.findaphd.com/phds/project...

(7/7)

Rational analysis of metagenomic diagnostic data at University of Birmingham on FindAPhD.com PhD Project - Rational analysis of metagenomic diagnostic data at University of Birmingham, listed on FindAPhD.com

- Rational analysis of metagenomic diagnostic data

Supervisors: Mike Cox, Meera Chand, David Cleary, Dhruv Parekh, Miruna David

www.findaphd.com/phds/project...

(6/7)

Multi-omic surveillance of microbial dynamics in river and flood-impacted environments: implications for public health in a changing climate at University of Birmingham on FindAPhD.com PhD Project - Multi-omic surveillance of microbial dynamics in river and flood-impacted environments: implications for public health in a changing climate at University of Birmingham, listed on FindAP...

- Multi-omic surveillance of microbial dynamics in river and flood-impacted environments: implications for public health in a changing climate

Supervisors: Johanna Rhodes, Willem van Schaik, Marie Anne Chattaway, Claire Jenkins

www.findaphd.com/phds/project...

(5/7)

Using novel genomic tools to understand the evolution of Acinetobacter baumannii pathogenicity in clinical environments at University of Birmingham on FindAPhD.com PhD Project - Using novel genomic tools to understand the evolution of Acinetobacter baumannii pathogenicity in clinical environments at University of Birmingham, listed on FindAPhD.com

- Using novel genomic tools to understand the evolution of Acinetobacter baumannii pathogenicity in clinical environments

Supervisors: David Grainger, Katie Hopkins, Jessica Blair, Willem van Schaik

www.findaphd.com/phds/project...

(4/7)

Leveraging genomics for improved metagenomic surveillance of Streptococcus pneumoniae at University of Birmingham on FindAPhD.com PhD Project - Leveraging genomics for improved metagenomic surveillance of Streptococcus pneumoniae at University of Birmingham, listed on FindAPhD.com

- Leveraging genomics for improved metagenomic surveillance of Streptococcus pneumoniae

Supervisors: David Cleary, Alan McNally, Meera Chand

www.findaphd.com/phds/project...

(3/7)

Utilising large scale metagenomic surveillance data sets to identify and track pathogen population dynamics at University of Birmingham on FindAPhD.com PhD Project - Utilising large scale metagenomic surveillance data sets to identify and track pathogen population dynamics at University of Birmingham, listed on FindAPhD.com

- Utilising large scale metagenomic surveillance data sets to identify and track pathogen population dynamics

Supervisors: Alan McNally, Meera Chand, Nick Loman

www.findaphd.com/phds/project...

(2/7)

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)

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 ...

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...

@Vision4theBlind Elon Musk in an interview saying you can turn someone into a butterfly with mRNA.

He really doesn’t understand any of the most basic biology concepts at all, huh

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

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.

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...

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...

Releases · tseemann/abricate :mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes - tseemann/abricate

💾 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...

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

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/...