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Ryan Cook

@ryancook94.bsky.social

300 followers 190 following 39 posts

Viral ecologist with Evelien Adriaenssens at The Quadram | All things phage (but mostly viromes) | Formerly at Uni of Nottingham with Andy Millard | All opinions my own.

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Ryan Cook @ryancook94.bsky.social · Jun 17

New pre-print alert! 🚨🫁

COPD affects millions worldwide. While we know bacterial dysbiosis drives disease, the role of bacteriophages remains unexplored. We re-analysed 135 COPD metagenomes to characterise the lung virome for the first time 🫁 1/9

www.biorxiv.org/content/10.1...

www.biorxiv.org

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Reposted by Ryan Cook

Tung Le @tunglejic.bsky.social · 5d

Independent research fellowships leading to tenured positions at the John Innes Centre.

Repost = nice. Thank you very much!!!

John Innes Centre @johninnescentre.bsky.social · 5d

Shortlisted candidates will be invited to give a seminar at the Fellows Conference, which will be held on 10 March 2026.

Candidates who win Fellowships will be offered a Tenure Track Group Leader position from the outset, initially for 5 years.

Find out more: www.jic.ac.uk/training-car...

Independent Research Fellowships Leading to Tenured Faculty Positions | John Innes Centre

The John Innes Centre (JIC), is a world leading centre of excellence in plant and microbial sciences based on the Norwich Research Park, UK. We are inviting applications from outstanding researchers…

www.jic.ac.uk

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Mya Breitbart @viromegirl.bsky.social · 6d

We're hiring for several positions (a post-bac researcher in #transcriptomics, a #phage #postdoc, a senior researcher (broad topics) and a graduate student to work on #ciliates) - find info here: www.marine.usf.edu/genomics/app...

Apply - Genomics

www.marine.usf.edu

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Reposted by Ryan Cook

A. Murat Eren (Meren) @merenbey.bsky.social · 20d

Have you ever looked at some differentially occurring gene clusters in a microbial #pangenome and thought to yourself "I wonder if they contribute to any metabolic modules"?

With the most recent changes, the answer is a few clicks away in #anvio 😇

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Reposted by Ryan Cook

Vijini Mallawaarachchi @vijinim.bsky.social · 21d

Excited to share our latest preprint on agtools, an open-source Python framework for analysing and manipulating assembly graphs. (1/n)

www.biorxiv.org/content/10.1...

#Bioinformatics #genomics #assembly #assemblygraphs #software

agtools: a software framework to manipulate assembly graphs

Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap information, facilitating the assembler to construct longer genomic f...

www.biorxiv.org

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Reposted by Ryan Cook

Franklin Nobrega @fnobrega.bsky.social · 22d

Three new kids on the block. ARMADA, BRIGADE, and TALON. Impressive how multiple labs all come together to contribute to discovery. Great collaboration with Simon, Chase, and Eugene. From the very talented Ryan Bell, together with Thomas Gaudin and our own Yi Wu.

www.biorxiv.org/content/10.1...

YprA family helicases provide the missing link between diverse prokaryotic immune systems

Bacteria and archaea possess an enormous variety of antivirus immune systems that often share homologous proteins and domains, some of which contribute to diverse defense strategies. YprA family helic...

www.biorxiv.org

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Reposted by Ryan Cook

Daniel Figeys @dfigeys.bsky.social · 22d

Interested in healthy aging and the microbiome? Join my lab to explore how ex vivo microbiome assays can guide personalized interventions that modulate specific microbiome-derived metabolites critical for health.

Quadram Institute @quadraminstitute.bsky.social · 22d

🆕 Vacancy! We're looking for a Research Scientist (Clinical Microbiome) to advance precision prebiotic microbiome intervention trials aimed at promoting healthy ageing.

💷 £37,500 to £45,350
🗓️ Apply by 2 October 2025
➡️ buff.ly/KGl7eiG

A photo of someone pipetting in the lab and the text "Research Scientist (Clinical Microbiome) to advance precision prebiotic microbiome intervention trials aimed at promoting trials aimed at promoting healthy ageing, Salary: £37,500 to £43,350, Contract length: 2.5 years, Apply by 2 October"

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Reposted by Ryan Cook

Daniel Figeys @dfigeys.bsky.social · 22d

Interested in compound- microbiome interactions, and how they affect health? Join my lab at the Quadram Institute.

Quadram Institute @quadraminstitute.bsky.social · 23d

🆕 Vacancy! We're looking for a Research Scientist (Xenobiotics) to investigate xenobiotic–microbiome interactions and understand the variation in responses across different individual microbiomes.

💷 £37,500 to £45,350
🗓️ Apply by 2 October 2025
➡️ buff.ly/8abEye5

A social card with an illustration of a molecules like forms, forming a person in part of the image, plus the text "Research Scientist (Xenobiotics) to investigate xenobiotic-microbiome interactions and understand variation across different individual microbiomes. Salary: £37,500 to £43,350, Contract length: 2.5 Years, Apply by 2 October 2025

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Ann Gregory, PhD @gregoryannc.bsky.social · 22d

🚨 We’re hiring! 🚨

The Integrative Viromics Lab @UCalgary 🇨🇦 is looking for a Lab Technician!

🔬 Phage isolation & culture
🧫 Anaerobic chamber work
📦 Lab management & student mentoring

Apply now & help us explore the virosphere!

You must have work authorization to work in Canada already.

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Ryan Cook @ryancook94.bsky.social · 22d

Dangers of no confirmation screen + me being an idiot. I'm gonna make some coffee ☕️

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Quadram Institute @quadraminstitute.bsky.social · 26d

🆕 Vacancy! We’re looking for a Chief Scientific Officer to support the development of the institute’s scientific strategy and scientific leadership of the institute.

💷 Competitive
🗓️ Apply by 12 October 2025
➡️ buff.ly/mKUhD3K

A social card with an image of the Quadram Institute labs and the sentence "To support the development of the institute's scientific strategy and scientific leadership of the institute. Salary: Competitive, Contract length: indefinite, apply by 12 October 2025

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Falk Hildebrand @bioinf.bsky.social · 26d

Only 5 days left to apply for our Soil metagenomics position: estimating the impact microbiomes in restored agricultural sites can have on climate change (closing 19th Sep):
jobs.earlham.ac.uk/Details.asp?...

Earlham Institute

jobs.earlham.ac.uk

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Reposted by Ryan Cook

Quadram Institute @quadraminstitute.bsky.social · 26d

🆕 Blog! Our Research Scientist Dr Revathy Krishnamurthi reflects on her recent visit to the village where she grew up in India to inspire the next generation to discover the world of science 🔍

@norwichmicro.bsky.social

Inspiring the next generation: exploring the invisible microbial world with students in Koothanoor, India - Quadram Institute

Research Scientist Dr Revathy Krishnamurthy reflects on her visit to the village where she grew up in India and inspiring the next generation to discover the world of science.

buff.ly

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Reposted by Ryan Cook

Willem van Schaik @wvschaik.bsky.social · 27d

I thought I'd try this technical molecular microbiology question here. #MicroSky

Does anyone have experience with cloning 7-10 kbp fragments into a vector for Gram-positives?

We are trying, but the vectors we generally use become quite unstable when we try to clone in a fragment of that size.

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Reposted by Ryan Cook

Anita Tarasenko @anitatarasenko.bsky.social · Sep 9

🚨New Review Out🚨
We explore how phage-antibiotic synergy can dismantle efflux-driven resistance in multidrug-resistant ESKAPEE pathogens. By reprogramming bacterial defences, phages offer a precision strategy to restore antibiotic efficacy.

journals.asm.org/doi/10.1128/...

Reprogramming resistance: phage-antibiotic synergy targets efflux systems in ESKAPEE pathogens | mBio

Antimicrobial resistance (AMR) is one of the greatest threats to global health. If unaddressed, it is projected to cause over 39 million cumulative deaths globally by 2050 (1). While resistance is a b...

journals.asm.org

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Reposted by Ryan Cook

Quadram Institute @quadraminstitute.bsky.social · Sep 3

🆕 Vacancy! We’re looking for a #Metagenomics Research Scientist to join the Laboratory of Dr Falk Hildebrand @bioinf.bsky.social to study diet impact on the gastrointestinal microbiome.

💷 £37,500 - £42,000
🗓️ Apply by 30 September 2025
➡️ buff.ly/uwqGQQm

An illustration of a network with the text "Metagenomics Research Scientist, to join Falk Hildebrand's group to study the diet impact on the gastrointestinal microbiome. Salary: £37,500 to £42,000, Contract length: 2.5 years, Apply by 30 September 2025"

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Evelien Adriaenssens @evelienadri.bsky.social · Sep 3

Today, I'm excited to announce the publication of the Duplodnaviria realm Profile and Chapter.
The realm includes viruses of archaea, bacteria and eukaryotes and is best known for its inclusion of herpesviruses and tailed phages.

www.microbiologyresearch.org/content/jour...

ICTV Virus Taxonomy Profile: Duplodnaviria 2025

The realm Duplodnaviria includes viruses of archaea, bacteria and eukaryotes, with linear dsDNA genomes. Duplodnavirians share a distinct morphogenetic module of four hallmark genes encoding the HK97-...

www.microbiologyresearch.org

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Evelien Adriaenssens @evelienadri.bsky.social · Sep 3

The ICTV Report chapters, which are linked to the profiles and get updated when the taxonomy changes, can be found on the ICTV website:
ictv.global/report

ICTV Report Chapters | ICTV

ictv.global

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Evelien Adriaenssens @evelienadri.bsky.social · Sep 3

We have expanded our ICTV Virus Taxonomy profiles and chapters to include higher ranks, which have been recently introduced and may not be familiar to all virologists.

You can find our 2-page Profiles (citable record) in JGV @microbiologysociety.org
www.microbiologyresearch.org/content/ictv...

ICTV Virus Taxonomy Profiles | Microbiology Society

Journal of General Virology ICTV Virus Taxonomy Profiles are a freely available series of concise, review-type articles that provide overviews of the classification, structure and properties of indivi...

www.microbiologyresearch.org

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Karthik Anantharaman @karthik-a.bsky.social · Aug 27

New paper alert! We suggest caution in the analyses of viral auxiliary metabolic genes and propose a new overarching term - 'auxiliary viral genes' (AVGs) to describe different types of such genes. @simrouxvirus.bsky.social #phagesky #Microsky www.nature.com/articles/s41...

A call for caution in the biological interpretation of viral auxiliary metabolic genes - Nature Microbiology

This Perspective discusses virus-encoded auxiliary metabolic genes and provides a framework for the biological interpretation of these genes.

www.nature.com

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Reposted by Ryan Cook

Rob Edwards @linsalrob.bsky.social · Aug 22

New in @asm.org #MMBR Computational function prediction of bacteria and phage proteins. How to annotate your #phage and #bacteria genomes

by @susiegriggo.bsky.social @bedutilh.bsky.social @gbouras13.bsky.social and Bob

#phagesky #microsky

journals.asm.org/doi/epub/10....

Examples of protein annotations across functional classification schemes. Yellow: hierarchical classification schemes, red: orthologous/homologous groups, and blue: methods using protein domain information. Protein structures were generated using the ColabFold Alphafold MMseqs2 interactive notebook (version 1.5.2) (57) and visualized using ChimeraX (58). (A) Functional labels associated with the glycogen synthase protein in Escherichia coli (UniprotKB P0A6U8). (B) Functional labels associated with Kehishuvirus sp. tikala major capsid protein (NCBI WEU69752.1).

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Britt Koskella @bkoskella.bsky.social · Aug 20

Have to take a deep breath and remember that I am a grown-up and not an angry toddler. But still, reviewing a paper in your field that directly ignores (aka doesn’t cite) all of your papers despite them being pretty much the only other papers like it can hit hard sometimes : /

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Andrew Millard @milja001.bsky.social · Aug 11

After a busy period , @ryancook94.bsky.social and I have have updated links to latest INPHARED dataset. With 37.5K genomes now. If some "iffy" genomes have got thought the automated and then out manual filters. Let us know the accession numbers so we can exclude

millardlab.org/bacteriophage-…

https://millardlab.org/bacteriophage-…

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Aug 7

Protein Structure Informed Bacteriophage Genome Annotation with Phold https://www.biorxiv.org/content/10.1101/2025.08.05.668817v1

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