Amy H Fitzpatrick

Don't know who to follow for the best in microbial bioinformatics?

This is the Starter Pack you need!

bsky.app/starter-pack...

It could possibly have only been written by a teenage boy but we are lucky to have it. Check it out here - celt.ucc.ie/published/T5...

Big Irish Head - BT Young Scientist Awards

The world is not ready for gen z. They are shitposters in real life.

I made a quick Starter Pack for scientists working on virus discovery - please reply if you’d like me to add you to the pack (or remove you) or to recommend anyone! #scisky go.bsky.app/HK1wxRb

🚨Postdoc position(s) alert🚨 If you like to develop new bioinformatic tools for *human* microbiome analysis, are interested by virus/phages, we (JGI Viral Genomics and Microbiome Data groups) may have a great position for you ! No official job posting yet, but email or DM if you are interested !

We are already planning the next @rdrpsummit.bsky.social for 2025. If you enjoy the consensus statement or you want to tear it apart, then you should get involved!

Consensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communities Improved RNA virus understanding is critical to studying animal and plant health, and environmental processes. However, the continuous and rapid RNA virus evolution makes their identification and char...

You can read this article in detail here: t.ly/Uwqge
And follow us to be updated on the upcoming #RdRpSummit

Unfortunately, a lack of standards in data collection, storage, and analysis methodologies serves as the biggest obstacle in standardizing RNA virus discovery.

The field of RNA virus discovery is booming! We observed an exponential rise in studies published exploiting RNA-dependent RNA polymerase (#RdRp) sequences to explore diversity, uncovering novel RNA viruses. Over 80 quadrillion bases have been deposited in the NCBI SRA database!

Consensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communities Improved RNA virus understanding is critical to studying animal and plant health, and environmental processes. However, the continuous and rapid RNA virus evolution makes their identification and char...

We just published a consensus statement (with 47 institutes) on advancing #RdRp-based RNA virus discovery! We sum up the challenges identified at the 1st #RdRpSummit and propose solutions to ensure greater interoperability. Here’s a summary-
t.ly/Uwqge

Peeking out from the great firewall:

I wrote a little commentary about the significance of @jomcinerney.bsky.social et al paper about predictable evolution in microbial genomes, enjoy!

🧪 #evosky

authors.elsevier.com/a/1it5ycZ3X0...

Application deadline: 9 April

Check out our new paper in collaboration with Travis Wheeler's group out today in NAR Genomics & Bioinformatics! Editors choice!

VIBES: a workflow for annotating and visualizing viral sequences integrated into bacterial genomes

#microsky
#phagesky
🧫🧪🔬

doi.org/10.1093/narg...

Microbial hitchhikers on microplastics: The exchange of aquatic microbes across distinct aquatic habitats

#envmicro by Máté Vass from Agneta Andersson

enviromicro-journals.onlinelibrary.wiley.com/doi/full/10....

Using Narrative CVs: Identifying shared objectives and monitoring effectiveness | DORA In February 2022, DORA organized the online workshop series “Using Narrative CVs: Identifying shared objectives and monitoring effectiveness” in partnership with FORGEN CoP, Science Foundation Ireland...

Setting clear objectives 🎯 for the use of narrative CVs in grant applications can support optimization. Common objectives are:
• More recognition of a wider range of research contributions
• More flexibility for researchers to demonstrate contributions
sfdora.org/resource/usi...

Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters - Microbiome Background Aerobic anoxygenic phototrophic (AAP) bacteria are heterotrophic bacteria that supply their metabolism with light energy harvested by bacteriochlorophyll-a-containing reaction centers. Desp...

Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters microbiomejournal.biomedcentral.com/articles/10.... #jcampubs

Follow @roseedwin.bsky.social for more updates on shotgun metagenomics applied to the soil microbiome! There is lots more to come from her PhD

From there, Rose's study blossomed (and ballooned). There were so many challenges, computationally; as well as varying taxonomic systems ⚠️ and my dislike of capital letters in bash scripts ☮️. It was great to work with Rose on this study and wonderful to see her grow as a scientist 🥲

I had applied simulation approaches to evaluate bioinformatic pipelines for norovirus but could we apply the same process to the soil microbiome? 🤪
Thanks to her supervisors' soil expertise, the generosity of other researchers and lots of grunt work; Rose had a soil database!

An in-depth evaluation of metagenomic classifiers for soil microbiomes - Environmental Microbiome Background Recent endeavours in metagenomics, exemplified by projects such as the human microbiome project and TARA Oceans, have illuminated the complexities of microbial biomes. A robust bioinformati...

Congratulations to #Vision1 PhD student Rose on the publication of her first PhD paper! The study stemmed from numerous lab meetings where Rose shared her 🙃 shotgun metagenomic analysis of soil samples......

Job claxon!

Uni of Birmingham biosciences is looking to appoint two Assistant Professors in the broad field of microbiology.

edzz.fa.em3.oraclecloud.com/hcmUI/Candid...

and

edzz.fa.em3.oraclecloud.com/hcmUI/Candid...

Come and join us at the IMI!

If you can do it, individual animals are the way to go for virus metagenomics: www.nature.com/articles/s41...

Replication efficiencies of human cytomegalovirus-infected epithelial cells are dependent on source of virus production https://www.biorxiv.org/content/10.1101/2024.03.19.585739v1 Human cytomegalovirus (HCMV) is a prevalent betaherpesvirus, and infection can lead to a range of sy

Replication efficiencies of human cytomegalovirus-infected epithelial cells are dependent on source of virus production https://www.biorxiv.org/content/10.1101/2024.03.19.585739v1

Antarctica wildlife at risk as bird flu surges around globe Since H5N1 arrived in Antarctica, there have been deaths of elephant seals, ifur seals, kelp gulls, penguins, according to SCAR.

Avian influenza is a serious threat to biodiversity, it’s honestly so scary

🧪🦑🌎🦉

cosmosmagazine.com/my-cosmos/an...

Males Aren’t Larger Than Females in Most Mammalian Species A new study corrects a biased assumption promoted by Charles Darwin 150 years ago and repeated ever since

Do all mammals have boy bois? Darwin thought it was the way of the world.

Darwin was incorrect (no one is perfect). 🧪

Turns out only 45% of mammals have bigger males, 39% have the same size in both sexes, and 16%? Bigger females. www.scientificamerican.com/article/male...

A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics journals.asm.org/doi/full/10.... #jcampubs

Interested in Influenza? Check out the Options XII meeting in Brisbane, Australia! Abstracts due April 5th, Meeting Dates Sept 29- Oct 2, 2024. www.optionsxii2024.org.uk

"Tradwives" offer an alluring vision of-right wing Christianity — meet the people fighting back The #FundieSnark movement battles to "deconstruct" those picture-perfect images of Christian social media

It's here! I've been working on this since January: "Tradwives" have been rightly getting a lot of criticism from feminists.

Less discussed: They're largely Christian propaganda.

Meet the people exposing the truth behind the pretty pictures.

www.salon.com/2024/03/08/t...

Many of us in Ireland feel the proposed rewording falls short in addressing the issue and abandons the state's responsibility to support carers. It is a conundrum: damned if you vote yes, damned if you vote no. The current government are wasting our time and money with this half-arsed attempt.

Exciting chance to join our Wellcome Trust collaborative project understanding AMR evolution in human infections! Genomics, experimental evolution, Pseudomonas. Research Assistant 4-days per week for 2-years, deadline 18.03. www.jobs.manchester.ac.uk/Job/JobDetai... #microsky