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Amy H Fitzpatrick

@amyhfitzpatrick.bsky.social
1.1K followers 588 following 39 posts

RNA virus discovery 🦠🔎 Irish Research Council postdoc 👩🏼‍🔬 at University College Dublin (UCD) 🍀 Ballet and book lover 🩰 | Eurovision fanatic 🇮🇪 🇮🇹 🇩🇰 🇩🇪

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Reposted by Amy H Fitzpatrick
Torsten Seemann @torstenseemann.bsky.social · 13/01/2025
Don't know who to follow for the best in microbial bioinformatics? This is the Starter Pack you need! bsky.app/starter-pack...
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Dr Gillian Kenny @medievalgill.bsky.social · 12/01/2025
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...
celt.ucc.ie
Archduke Ferdinand's visit to Kinsale in Ireland, an extract from Le Premier Voyage de Charles-Quint en Espagne, de 1517 à 1518
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Miriam IRL @miriam.blacksky.app · 10/01/2025
Big Irish Head - BT Young Scientist Awards The world is not ready for gen z. They are shitposters in real life.
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Katy Brown @thekatybrown.bsky.social · 16/11/2024
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
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Simon Roux @simrouxvirus.bsky.social · 07/01/2025
🚨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 !
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Amy H Fitzpatrick @amyhfitzpatrick.bsky.social · 01/05/2024
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!
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RdRp Summit @rdrpsummit.bsky.social · 30/04/2024
You can read this article in detail here: t.ly/Uwqge And follow us to be updated on the upcoming #RdRpSummit
t.ly
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...
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Reposted by Amy H Fitzpatrick
RdRp Summit @rdrpsummit.bsky.social · 30/04/2024
Unfortunately, a lack of standards in data collection, storage, and analysis methodologies serves as the biggest obstacle in standardizing RNA virus discovery.
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RdRp Summit @rdrpsummit.bsky.social · 30/04/2024
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!
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RdRp Summit @rdrpsummit.bsky.social · 30/04/2024
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
t.ly
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...
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Reposted by Amy H Fitzpatrick
Jo Wolfe, PhD @jopabinia.bsky.social · 04/04/2024
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...
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Willem van Schaik @wvschaik.bsky.social · 04/04/2024
Application deadline: 9 April
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Patrick R. Secor @prsecor.bsky.social · 04/04/2024
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...
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Ákos T Kovács @evolvedbiofilm.bsky.social · 03/04/2024
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....
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Reposted by Amy H Fitzpatrick
DORA @dorassessment.bsky.social · 29/03/2024
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...
sfdora.org
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...
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Reposted by Amy H Fitzpatrick
Cameron Thrash @jcamthrash.bsky.social · 29/03/2024
Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters microbiomejournal.biomedcentral.com/articles/10.... #jcampubs
microbiomejournal.biomedcentral.com
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...
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Amy H Fitzpatrick @amyhfitzpatrick.bsky.social · 29/03/2024
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......
link.springer.com
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...
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Jessica Blair @jessicamablair.bsky.social · 25/03/2024
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!
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Eddie Holmes @eddieholmes.bsky.social · 22/03/2024
If you can do it, individual animals are the way to go for virus metagenomics: www.nature.com/articles/s41...
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 19/03/2024
Replication efficiencies of human cytomegalovirus-infected epithelial cells are dependent on source of virus production www.biorxiv.org/content/10.1101/202…
biorxiv.org
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
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Dr Michelle LaRue @drmichellelarue.bsky.social · 19/03/2024
Avian influenza is a serious threat to biodiversity, it’s honestly so scary 🧪🦑🌎🦉 cosmosmagazine.com/my-cosmos/an...
cosmosmagazine.com
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.
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Bethany Brookshire @beebrookshire.bsky.social · 13/03/2024
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...
scientificamerican.com
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
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Cameron Thrash @jcamthrash.bsky.social · 08/03/2024
A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics journals.asm.org/doi/full/10.... #jcampubs
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American Society for Virology @amersocvirology.bsky.social · 08/03/2024
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
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Amanda Marcotte @amandamarcotte.bsky.social · 08/03/2024
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...
salon.com
"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
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Amy H Fitzpatrick @amyhfitzpatrick.bsky.social · 07/03/2024
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.
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Michael Brockhurst @brockhurstlab.bsky.social · 05/03/2024
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
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bioRxivpreprint @biorxivpreprint.bsky.social · 06/03/2024
Microbe tree metabolite interactions in the soil - phyllosphere continuum of poplar tree: when microbes rewire poplar root exudate and metabolome www.biorxiv.org/content/10.1101/202…
biorxiv.org
Microbe tree metabolite interactions in the soil - phyllosphere continuum of poplar tree: when microbes rewire poplar root exudate and metabolome https://www.biorxiv.org/content/10.1101/2024.03.04.583280v1
Trees are associated with a broad range of microorganisms colonising the diverse tissues of their ho
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Katharine Hayhoe @katharinehayhoe.com · 06/03/2024
Still laughing hours after I read this. So true so true
Image of a tweet reading “I have been at conferences with many tools who will offer real time feedback”
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Kobe Desender @kobedesender.bsky.social · 08/02/2024
PhD and Post-Doc positions in my Lab! We are currently recruiting (i) a Marie-Curie "CODE" PhD student to work on confidence and reinforcement learning, (ii) a Post-Doc to work on metacognitive insight into latent cognitive parameters. Deadline 31 March, pls RT! Apply: desenderlab.com/job-openings/
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Paul Hoskisson 🧫 🦠🐸 @paulhoskisson.bsky.social · 03/03/2024
Adaptive Evolution of Pseudomonas aeruginosa in Human Airways Shows Phenotypic Convergence Despite Diverse Patterns of Genomic Changes academic.oup.com/mbe/article/... #MicroSky
academic.oup.com
Adaptive Evolution of Pseudomonas aeruginosa in Human Airways Shows Phenotypic Convergence Despite Diverse Patterns of Genomic Changes
Abstract. Selective forces in the environment drive bacterial adaptation to novel niches, choosing the fitter variants in the population. However, in dynamic an
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Reposted by Amy H Fitzpatrick
Kat Holt @katholt.bsky.social · 28/02/2024
JOB ALERT! Come work with me at LSHTM to investigate transmission of Klebsiella pneumoniae in neonatal units in Africa using bioinformatics and genomic epi. Great team, Gates funded, £44-50k/yr, 1-year postdoc to start with possibilities to extend. Closing March 26. jobs.lshtm.ac.uk/vacancy.aspx...
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Javier Brumós @jbrumos.bsky.social · 28/02/2024
Arabidopsis as a model for translational research We should capitalize on the use of Arabidopsis as a robust & convenient experimental system, its vast datasets, annotations, germplasm, constructs, methods, molecular & computational tools to address fundamental & applied questions 🧪 #PlantScience
academic.oup.com
Arabidopsis as a model for translational research
This review discusses the benefits and challenges of translating Arabidopsis-generated knowledge to crop plants and beyond.
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Amy H Fitzpatrick @amyhfitzpatrick.bsky.social · 22/02/2024
We covered this preprint in journal club today 🧐 👉This really is a mind boggling amount of work 👀 👉Lots of questions about coronaviruses and their narrow tropism 👉Would love to see prediction models using this metadata Definitely worth a read
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Siobhán O'Brien @siderophile.bsky.social · 22/02/2024
This paper was really fun to write! Unpicking the subtle differences between dependencies, facilitation and cooperation in microbial communities, and why it matters. With Elze Hesse (not here yet!)
microbiologyresearch.org
Ecological dependencies and the illusion of cooperation in microbial communities
Ecological dependencies – where organisms rely on other organisms for survival – are a ubiquitous feature of life on earth. Multicellular hosts rely on symbionts to provide essential vitamins and amin...
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Lachlan Fetterplace @fiskeforbrains.bsky.social · 22/02/2024
Postdoc: Spatial Ecology of Marine Megafauna Closes 28 Feb. Arendal, Norway. Focus - Movements, connectivity, and ecosystem impact of marine top predators (harbour seals and cod) in Skagerrak www.jobbnorge.no/en/available... 🧪🌏🦑
A small harbour on an inlet with small islands in the distance. a small research sits on the harbour and a research vessel is docked.
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Gregor Kalinkat @gkalinkat.bsky.social · 22/02/2024
New and important #lightpollution meta-study out in Ecology Letters Yang et al (2024) Species sensitivities to artificial light at night: A phylogenetically controlled multilevel meta-analysis on melatonin suppression 🧪 onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
Species sensitivities to artificial light at night: A phylogenetically controlled multilevel meta‐analysis on melatonin suppression
Ecology Letters is a broad-scope ecology journal considering all taxa, in any biome and geographic area, and spanning community, microbial & evolutionary ecology.
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Ákos T Kovács @evolvedbiofilm.bsky.social · 22/02/2024
Active microbial population dynamics and life strategies drive the enhanced carbon use efficiency in high-organic matter soils -in mBio journal journals.asm.org/doi/10.1128/...
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Daniel S. Goldberg @profgoldberg.bsky.social · 20/02/2024
Oh my god “Indeed, we show that tenants who were threatened with eviction experienced excess mortality that was ten times higher than that of the general population.”
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Alan McNally @alanmcn1.bsky.social · 20/02/2024
Our latest paper is out. The brainchild of @drrebeccajhall.bsky.social We had shown how different E. coli strains respond to the same MDR plasmid. Here we show how one strain responds to different MDR plasmids journals.asm.org/doi/10.1128/...
journals.asm.org
Multidrug resistance plasmids commonly reprogram the expression of metabolic genes in Escherichia coli | mSystems
The increase in infections that are resistant to multiple classes of antibiotics, including those isolates that carry carbapenamases, beta-lactamases, and colistin resistance genes, is of global conce...
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Caroline Hu @hudrewthis.bsky.social · 20/02/2024
Scientist collaborators have been selected for this spring semester's comics collabs! Thanks all who applied. The volume of apps made it loud & clear--scientists want to visually communicate their research!!
Marker drawings of symbiotic pairs of organisms. "Scientist collaborators have been selected!" "Thanks all who applied!" "More comics collabs in the fall"
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Michelle Wille @duckswabber.bsky.social · 19/02/2024
New update from BAS. Sadly HPAI now detected in wandering albatross on South Georgia Island. These are the largest albatross species in the world. 👉https://www.bas.ac.uk/media-post/avian-flu-now-detected-in-albatrosses-on-south-georgia/
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Arthur Gessler @arthurobuntspecht.bsky.social · 18/02/2024
A trait‐based framework linking the soil metabolome to plant–soil feedbacks nph.onlinelibrary.wiley.com/doi/10.…
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Costa Samaras @costasamaras.com · 18/02/2024
Every academic department in the humanities and social sciences should have multiple faculty working on climate change & the implications of the energy transition— it’s the landscape on which the future unfolds. Without social science scholars, there is zero chance we get to zero emissions. Let’s go
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Ben Neely @benneely.com · 14/02/2024
ATCC has a podcast "Behind the Biology", and it actually seems pretty cool. They open the series up with a banger from Jonathan Jacobs (over on twitter, not here) on the difficulties of BIG data in the biological sciences. You should listen to these when you're done with The Proteomics Show. 🧪
atcc.org
Behind the Biology, Episode 1
Learn about such as reproducibility in research, the pros and cons of crowd sourcing data, and a solution in ATCC’s approach to whole-genome sequencing, assembly, and annotation for producing high-qua...
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Alex Crits-Christoph @acritschristoph.bsky.social · 15/02/2024
Remarkable analysis that finds at least 17, up to an estimated 60 mink to human spillovers in Denmark occurred before the mink farms were culled in 2020.
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Zhiru Liu @zzzhiru.bsky.social · 14/02/2024
Excited (and relieved!) to share that my 1st paper in grad school finally came out in PLOS Biology! We were motivated by a very basic question: how fast, really, do bacteria exchange DNA in the human gut? (1/n)
t.co
Dynamics of bacterial recombination in the human gut microbiome
Recombination is a ubiquitous force in bacterial evolution, but its dynamics are poorly characterized in many natural populations. This study presents a metagenomic approach for quantifying the landsc...
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Rhys White @rhystwhite.bsky.social · 14/02/2024
It’s out! (despite surgeries, pandemic, floods, finishing the #PhD & relocating) 📌Genomic epidemiology reveals geographical clustering of multidrug- resistant Escherichia coli ST131 associated with bacteraemia in Wales | @NatureComms doi.org/10.1038/s414... 🖥️🧬💻 #AcademicSky #Microsky 🧪🧫🦠
doi.org
Genomic epidemiology reveals geographical clustering of multidrug-resistant Escherichia coli ST131 associated with bacteraemia in Wales - Nature Communications
Escherichia coli ST131 is a globally dominant multidrug resistant clone associated with high rates of recurring urinary tract infections. In this genomic epidemiology study, the authors describe the e...
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Ákos T Kovács @evolvedbiofilm.bsky.social · 14/02/2024
How does evolution work in superabundant microbes? -in #TrendsMicrobiol by Dmitry A. Filatov and Mark Kirkpatrick www.sciencedirect.com/science/arti...
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