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Reposted by Ed Cunningham-Oakes

BWJones @bwjones.bsky.social · 14d

This remarkable therapy uses an approach the Trump administration just cancelled funding for.

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Ed Cunningham-Oakes @edcoakes.bsky.social · Sep 7

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

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Ed Cunningham-Oakes @edcoakes.bsky.social · Jul 29

A great reminder of why it's important to consider the shape of your data before diving into microbiome analysis!

Ákos T Kovács @evolvedbiofilm.bsky.social · Jul 29

Microbiome data: tell me which metrics and I will tell you which communities

in #ISMEComms

academic.oup.com/ismecommun/a...

Microbiome data: tell me which metrics and I will tell you which communities

Abstract. In microbial community studies, analyzing diversity is crucial for uncovering ecological complexity. However, the intrinsic characteristics of Ne

academic.oup.com

Reposted by Ed Cunningham-Oakes

Axel Visel @axelvisel.bsky.social · Jul 22

🧬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

Nature Reviews Genetics @natrevgenet.nature.com · Jul 21

New online! Viromics approaches for the study of viral diversity and ecology in microbiomes

Viromics approaches for the study of viral diversity and ecology in microbiomes

Nature Reviews Genetics, Published online: 21 July 2025; doi:10.1038/s41576-025-00871-wIn this Review, Roux and Coclet outline current viromics approaches and discuss how they have contributed to our growing understanding of viral genomic diversity, focusing on uncultivated viruses of microorganisms.

www.nature.com

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Reposted by Ed Cunningham-Oakes

Leighton Pritchard @widdowquinn.bsky.social · Jul 1

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...

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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

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Ed Cunningham-Oakes @edcoakes.bsky.social · Jul 1

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.

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Reposted by Ed Cunningham-Oakes

Trish Greenhalgh @trishgreenhalgh.bsky.social · Jun 22

Plenty studies showing that your postcode is a better predictor of your health outcomes than your genome.

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?

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Reposted by Ed Cunningham-Oakes

Albert Vilella, PhD. @albertvilella.bsky.social · Jun 21

@andywatson on the NGS Sequencing market and the prisoner's dilemma

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Reposted by Ed Cunningham-Oakes

Fionna O’Leary @fascinatorfun.bsky.social · Jun 1

Keir Starmer, Yvette Cooper, David Lammy, and McSweeney @teamlabouruk.bsky.social should take note if what they really want is growth.

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...

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Reposted by Ed Cunningham-Oakes

Jim Shaw @jimshaw.bsky.social · May 28

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

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Ed Cunningham-Oakes @edcoakes.bsky.social · May 24

EID?: wwwnc.cdc.gov/eid

Emerging Infectious Diseases - CDCCenters for Disease Control and Prevention. CDC twenty four seven. Saving Lives, Protecting Peoplehome4expandexpandexpandexpandexpandexpandedit_01 fil...

Emerging Infectious Diseases is a peer-reviewed, monthly journal published by the Centers for Disease Control and Prevention (CDC). It offers global health professionals the latest scientific informat...

wwwnc.cdc.gov

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Reposted by Ed Cunningham-Oakes

Ming Tommy Tang @tommytang.bsky.social · May 22

🧵 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.

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Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

12/12 📰 For more background and wider context, check out the @liverpooluni.bsky.social press release covering this study’s impact on understanding and diagnosing infectious intestinal diseases: news.liverpool.ac.uk/2025/05/20/a...

Advanced genomics study improves detection of hard-to-find diarrhoeal infections - University of Liverpool News

Advanced genomics study improves detection of hard-to-find diarrhoeal infections

news.liverpool.ac.uk

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Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

11/12 🙏 A big thank you to all my amazing collaborators who made this work possible @blancaps.bsky.social @jayhinton.bsky.social @acdarby.bsky.social (PI) and many of the INTEGRATE consortium not on BlueSky.
Thank you to @nihr.bsky.social for funding via the second HPRU-GI @livuni-ives.bsky.social.

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Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

10/12 🔍 This dual-omics approach captures both what pathogens are present and what they're doing, offering unmatched resolution for understanding infectious intestinal disease biology.

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Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

9/12 📊 RNA/DNA ratios differed significantly between positive and negative cases, helping distinguish true infection from bystander carriage and providing a molecular readout of microbial activity.

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Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

8/12 📦 Critically, RNA in stool remained stable enough for pathogen detection without preservatives (and after self-sample and surviving the mail service!), providing evidence for the routine potential of metatranscriptomics in clinical settings (with some work!)

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Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

7/12 🧫 For the first time, we captured a comprehensive snapshot of Salmonella gene expression from a human stool sample. These data reveal how bacteria survive and adapt after leaving the gut. Explore via Hinton Lab’s interactive browser: jb.hintonlab.com/index.html?d...

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Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

6/12 🦠➡️🧬 Metatranscriptomics also detected Cryptosporidium via its RNA virus, CSpV1, previously reported in diarrhoeic animals (doi.org/10.1186/s135...). Cryptosporidium was undetectable in metagenomic data, suggesting RNA sequencing can sensitively detect it when DNA methods fall short.

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Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

5/12 🦠 Metatranscriptomics captured active Adenovirus F infections via broad transcriptome coverage (in a couple of samples, near complete!), despite it being a DNA virus, highlighting its use in profiling ongoing viral activity during diarrhoeal illness.

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Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

4/12
🧪 Metatranscriptomics showed superior sensitivity, with strong correlation to conventional diagnostics for 6/15 pathogens and to Luminex for 8/14.
🧬 Metagenomics performed well for some targets but showed lower overall concordance.

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Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

🔬 3/12 As a part of the INTEGRATE study, we sequenced stool from 1,067 patients using both metagenomics and metatranscriptomics. We identified pathogens in these data and benchmarked against routine diagnostics and Luminex xTAG GPP, a multiplex test for key bacterial, viral, and parasitic pathogens.

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Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

2/12 💩 Diarrhoea affects ~18 million annually in the UK, yet traditional diagnostics often miss causes, especially hard-to-culture or emerging pathogens. Our work shows how next-generation sequencing can transform the detection and understanding of GI infections.

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Ed Cunningham-Oakes @edcoakes.bsky.social · May 20

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...

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Reposted by Ed Cunningham-Oakes

Microbiology Society @microbiologysociety.org · May 12

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

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