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Got an email to say your manuscript had failed manuscripts checks as the corresponding author email was missing and is required ... I am the corresponding author 🤔..

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-…

Submitted my first set of annual review stuff for my PhD (yes I started end of September but the annual review is due 1st June) and looking back on the past 8 months... Wow I have grown into even more of a badass girlie 😎🧪 #phd #microsky

New preprint up on the changes in the bovine virome though different life stages led by @milja001.bsky.social @ryancook94.bsky.social www.biorxiv.org/content/10.1...

This is probably my last piece of work from my @medresfdn.bsky.social funded PhD at @uniofnottingham.bsky.social (thanks for all the support over the years!). Contributions from @milja001.bsky.social @evelienadri.bsky.social (and many others not yet on Bluesky) 13/13

The dairy cow gut virome is a dynamic ecosystem that could be an under-studied player in sustainable agriculture 🔑 Preprint: www.biorxiv.org/content/10.1... #Microbiome #Virome #ClimateScience #Agriculture #Dairy #Cows #Methanogens 12/13

1,338 vOTUs were predicted complete. @milja001.bsky.social and I agreed to manually inspect the annotations of every single one. I started at the top, he started at the bottom (I think he only did 50 though despite agreeing to do half 💁‍♂️). All of them looked viral in origin, and most were novel 4/13

We profiled the faecal virome of dairy cows across key life stages with ultra-deep Nanopore and Illumina sequencing 🐮 We recovered over 30,000 vOTUs (approximate to species), and included shallow bulk metagenomes for each sample to place the viruses within the context of their microbial hosts 3/13

Why does this matter? Dairy cows = 265 million worldwide, huge importance in food production and greenhouse gas emissions. Yet we know very little about their gut viral communities across key life stages 🐄 2/13

🧬🐄 NEW PREPRINT: Really happy to finally share the last big piece of work from my PhD! Spoiler: Cows are great and so are their viromes 🧵1/13 www.biorxiv.org/content/10.1...

Interested in phages ? Want to work as team that will isolate, genome sequence and charachterise 1000s of phage to build a biobank . Come work with me and Martha Clokie at Leicester jobs.le.ac.uk/vacancies/va...

Take away coffees are served differently in Vietnam..bit fancier than standard Costa slop ,😁

www.biorxiv.org/content/10.1... Searching for lytic phages in bacterial genome assemblies ..!

We @ryancook94.bsky.social , updated number of phage genomes we can find in NCBI .... Took longer than it should to do this months ... millardlab.org/home/bacteriop…

Many congratulations to Mickey @mickey-tad.bsky.social for successfully defending his viva today!! My warmest thanks to Andy @milja001.bsky.social and Lona Alkhalaf for being his examiners and to @nezislab.bsky.social for serving as Exam Advisor! @warwicklifesci.bsky.social @albertilab.bsky.social

Job claxon! Senior postdoc research associate position at the Becky Mayer Centre for Phage Research at the University of Leicester, working with @milja001.bsky.social and Martha Clokie. Brilliant opportunity! jobs.le.ac.uk/vacancies/11...

taxMyPhage made Jans pick...in this month's Capsid and tail .. phage.directory ptax.ku.dk github.com/amillard/tax_m…

we ( @ryancook94.bsky.social ) updated genomes in INPHARED millardlab.org/phage-genomes-… There are more genomes than last month! Shocker. Haven't had a chance to analyse yet

Great to have you involved @remidenise.bsky.social .might even meet in person at some point :-)

Phage taxonomy doesn’t have to be taxing, my latest cartoon for the Phage journal. To illustrate 𝘁𝗮𝘅𝗠𝘆𝗣𝗵𝗮𝗴𝗲 lnkd.in/dAXK4sSt @milja001.bsky.social

Found a lot of use through phage genomics workshop hosted by @milja001.bsky.social and it was great learning so much from his genomic pipelines. Lots to learn for me in this field, and very complimentary to my work done in the labs (and scraping alpaca poop for phage isolations!)

And I finally got round to updating the GitHub links... github.com/RyanCook94/i...

First update of the Bluesky era! #PhageSky

New year ... new lot of genomes. With @ryancook94.bsky.social updated what we can find in Genbank millardlab.org/phage-genome-j… With entire set annotated with PHROGs millardlab-inphared.s3.climb.ac.uk/GenomesDB_Jan2…

New year, new assemblies! I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes! It's the successor to Trycycler, designed to be faster and less reliant on user intervention. Check it out: github.com/rrwick/Autoc... (1/5)

Published just in time for the holidays! I learned so much while writing about the past, present, and future of E. faecalis research with Gary. Check it out! 🦠🧫🧪🔬 journals.asm.org/doi/10.1128/...

Isolation, characterization, and genomic analysis of BUCT627: a lytic bacteriophage targeting Stenotrophomonas maltophilia. DOI: 10.1093/femsle/fnae076 https://pubmed.ncbi.nlm.nih.gov/39349986/

We are getting a new name and a £4 Million donation . Thanks to Jimmy Mayer, we will become the " Becky Mayer Centre for Phage Research " le.ac.uk/news/2024/de...

We ( @ryancook94.bsky.social ) updated number complete phage genomes we can find in Genbank. downloads and links on millardlab.org/phage-genomes-…

We updated complete genomes we can find in Genbank . Big increase this month with lots of new Microviridae from what looks like a single study . All links on millardlab.org/phages-genomes… and github.com/RyanCook94/inp  to download latest data

Two Post-Doc positions in my group in collaboration with Claudio Avignone-Rossa & GSK using #engineeringbiology to improve #sustainability of industrial #Streptomyces fermentations strathvacancies.engageats.co.uk/Vacancies/W/... pls RT-happy to chat MicrobioSoc conference next wk,reach out by email

Hostile 1.0.0 released and live on Bioconda - Adds human genomes masked against bacteria, viruses and phage (thanks for phage genomes @milja001.bsky.social!) - Improved automatic index download - Improved genome masking - Bug fixes

Christina Hazard gave us a great talk on this work a few weeks ago. Really nice study.

New PhD position in the MRC Doctoral Training Programme for an Oct 2024 start with @milja001.bsky.social and myself as supervisors. The gut phageome as a driver for microbiome dynamics in critically ill patients Scroll down on more.bham.ac.uk/mrc-aim/phd-... for details