Reposted by Amy H FitzpatrickTorsten Seemann @torstenseemann.bsky.social · 13/01/2025Don't know who to follow for the best in microbial bioinformatics? This is the Starter Pack you need! bsky.app/starter-pack... 02713
Reposted by Amy H FitzpatrickDr Gillian Kenny @medievalgill.bsky.social · 12/01/2025It 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.ieArchduke Ferdinand's visit to Kinsale in Ireland, an extract from Le Premier Voyage de Charles-Quint en Espagne, de 1517 à 1518 2624
Reposted by Amy H FitzpatrickMiriam IRL @miriam.blacksky.app · 10/01/2025Big Irish Head - BT Young Scientist Awards The world is not ready for gen z. They are shitposters in real life. 1830992
Reposted by Amy H FitzpatrickKaty Brown @thekatybrown.bsky.social · 16/11/2024I 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 278137
Reposted by Amy H FitzpatrickSimon 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 ! 07476
Amy H Fitzpatrick @amyhfitzpatrick.bsky.social · 01/05/2024We 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! 062
Reposted by Amy H FitzpatrickRdRp Summit @rdrpsummit.bsky.social · 30/04/2024You can read this article in detail here: t.ly/Uwqge And follow us to be updated on the upcoming #RdRpSummitt.lyConsensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communitiesImproved 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... 021
Reposted by Amy H FitzpatrickRdRp Summit @rdrpsummit.bsky.social · 30/04/2024Unfortunately, a lack of standards in data collection, storage, and analysis methodologies serves as the biggest obstacle in standardizing RNA virus discovery. 101
Reposted by Amy H FitzpatrickRdRp Summit @rdrpsummit.bsky.social · 30/04/2024The 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! 121
Reposted by Amy H FitzpatrickRdRp Summit @rdrpsummit.bsky.social · 30/04/2024We 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/Uwqget.lyConsensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communitiesImproved 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... 2139
Reposted by Amy H FitzpatrickJo Wolfe, PhD @jopabinia.bsky.social · 04/04/2024Peeking 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... 0115
Reposted by Amy H FitzpatrickWillem van Schaik @wvschaik.bsky.social · 04/04/2024Application deadline: 9 April 0714
Reposted by Amy H FitzpatrickPatrick R. Secor @prsecor.bsky.social · 04/04/2024Check 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... 0178
Reposted by Amy H FitzpatrickÁkos T Kovács @evolvedbiofilm.bsky.social · 03/04/2024Microbial 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.... 044
Reposted by Amy H FitzpatrickDORA @dorassessment.bsky.social · 29/03/2024Setting 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.orgUsing Narrative CVs: Identifying shared objectives and monitoring effectiveness | DORAIn 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... 031
Reposted by Amy H FitzpatrickCameron Thrash @jcamthrash.bsky.social · 29/03/2024Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters microbiomejournal.biomedcentral.com/articles/10.... #jcampubsmicrobiomejournal.biomedcentral.comPhenology and ecological role of aerobic anoxygenic phototrophs in freshwaters - MicrobiomeBackground Aerobic anoxygenic phototrophic (AAP) bacteria are heterotrophic bacteria that supply their metabolism with light energy harvested by bacteriochlorophyll-a-containing reaction centers. Desp... 011
Amy H Fitzpatrick @amyhfitzpatrick.bsky.social · 29/03/2024Congratulations 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.comAn in-depth evaluation of metagenomic classifiers for soil microbiomes - Environmental MicrobiomeBackground 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... 162
Reposted by Amy H FitzpatrickJessica Blair @jessicamablair.bsky.social · 25/03/2024Job 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! 11024
Reposted by Amy H FitzpatrickEddie Holmes @eddieholmes.bsky.social · 22/03/2024If you can do it, individual animals are the way to go for virus metagenomics: www.nature.com/articles/s41... 32114
Reposted by Amy H FitzpatrickbioRxiv Microbiology @biorxiv-microbiol.bsky.social · 19/03/2024Replication efficiencies of human cytomegalovirus-infected epithelial cells are dependent on source of virus production www.biorxiv.org/content/10.1101/202… biorxiv.orgReplication 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 012
Reposted by Amy H FitzpatrickDr Michelle LaRue @drmichellelarue.bsky.social · 19/03/2024Avian influenza is a serious threat to biodiversity, it’s honestly so scary 🧪🦑🌎🦉 cosmosmagazine.com/my-cosmos/an...cosmosmagazine.comAntarctica wildlife at risk as bird flu surges around globeSince H5N1 arrived in Antarctica, there have been deaths of elephant seals, ifur seals, kelp gulls, penguins, according to SCAR. 26631
Reposted by Amy H FitzpatrickBethany Brookshire @beebrookshire.bsky.social · 13/03/2024Do 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.comMales Aren’t Larger Than Females in Most Mammalian SpeciesA new study corrects a biased assumption promoted by Charles Darwin 150 years ago and repeated ever since 0287
Reposted by Amy H FitzpatrickCameron Thrash @jcamthrash.bsky.social · 08/03/2024A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics journals.asm.org/doi/full/10.... #jcampubs 021
Reposted by Amy H FitzpatrickAmerican Society for Virology @amersocvirology.bsky.social · 08/03/2024Interested 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 011
Reposted by Amy H FitzpatrickAmanda Marcotte @amandamarcotte.bsky.social · 08/03/2024It'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 backThe #FundieSnark movement battles to "deconstruct" those picture-perfect images of Christian social media 17518218
Amy H Fitzpatrick @amyhfitzpatrick.bsky.social · 07/03/2024Many 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. 112
Reposted by Amy H FitzpatrickMichael Brockhurst @brockhurstlab.bsky.social · 05/03/2024Exciting 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 01637
Reposted by Amy H FitzpatrickbioRxivpreprint @biorxivpreprint.bsky.social · 06/03/2024Microbe 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.orgMicrobe 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 011
Reposted by Amy H FitzpatrickKatharine Hayhoe @katharinehayhoe.com · 06/03/2024Still laughing hours after I read this. So true so true 4458371196
Reposted by Amy H FitzpatrickKobe Desender @kobedesender.bsky.social · 08/02/2024PhD 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/ 11519
Reposted by Amy H FitzpatrickPaul Hoskisson 🧫 🦠🐸 @paulhoskisson.bsky.social · 03/03/2024Adaptive Evolution of Pseudomonas aeruginosa in Human Airways Shows Phenotypic Convergence Despite Diverse Patterns of Genomic Changes academic.oup.com/mbe/article/... #MicroSkyacademic.oup.comAdaptive Evolution of Pseudomonas aeruginosa in Human Airways Shows Phenotypic Convergence Despite Diverse Patterns of Genomic ChangesAbstract. Selective forces in the environment drive bacterial adaptation to novel niches, choosing the fitter variants in the population. However, in dynamic an 0138
Reposted by Amy H FitzpatrickKat Holt @katholt.bsky.social · 28/02/2024JOB 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... 11228
Reposted by Amy H FitzpatrickJavier Brumós @jbrumos.bsky.social · 28/02/2024Arabidopsis 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 🧪 #PlantScienceacademic.oup.comArabidopsis as a model for translational researchThis review discusses the benefits and challenges of translating Arabidopsis-generated knowledge to crop plants and beyond. 11210
Amy H Fitzpatrick @amyhfitzpatrick.bsky.social · 22/02/2024We 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 042
Reposted by Amy H FitzpatrickSiobhán O'Brien @siderophile.bsky.social · 22/02/2024This 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.orgEcological dependencies and the illusion of cooperation in microbial communitiesEcological 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... 34225
Reposted by Amy H FitzpatrickLachlan Fetterplace @fiskeforbrains.bsky.social · 22/02/2024Postdoc: 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... 🧪🌏🦑 0178
Reposted by Amy H FitzpatrickGregor Kalinkat @gkalinkat.bsky.social · 22/02/2024New 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.comSpecies sensitivities to artificial light at night: A phylogenetically controlled multilevel meta‐analysis on melatonin suppressionEcology Letters is a broad-scope ecology journal considering all taxa, in any biome and geographic area, and spanning community, microbial & evolutionary ecology. 074
Reposted by Amy H FitzpatrickÁkos T Kovács @evolvedbiofilm.bsky.social · 22/02/2024Active 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/... 021
Reposted by Amy H FitzpatrickDaniel S. Goldberg @profgoldberg.bsky.social · 20/02/2024Oh 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.” 48558
Reposted by Amy H FitzpatrickAlan McNally @alanmcn1.bsky.social · 20/02/2024Our 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.orgMultidrug resistance plasmids commonly reprogram the expression of metabolic genes in Escherichia coli | mSystemsThe 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... 03917
Reposted by Amy H FitzpatrickCaroline Hu @hudrewthis.bsky.social · 20/02/2024Scientist 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!! 2235
Reposted by Amy H FitzpatrickMichelle Wille @duckswabber.bsky.social · 19/02/2024New 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/ 0129
Reposted by Amy H FitzpatrickArthur Gessler @arthurobuntspecht.bsky.social · 18/02/2024A trait‐based framework linking the soil metabolome to plant–soil feedbacks nph.onlinelibrary.wiley.com/doi/10.… 051
Reposted by Amy H FitzpatrickCosta Samaras @costasamaras.com · 18/02/2024Every 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 1015056
Reposted by Amy H FitzpatrickBen Neely @benneely.com · 14/02/2024ATCC 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.orgBehind the Biology, Episode 1Learn 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... 2113
Reposted by Amy H FitzpatrickAlex Crits-Christoph @acritschristoph.bsky.social · 15/02/2024Remarkable 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. 23521
Reposted by Amy H FitzpatrickZhiru Liu @zzzhiru.bsky.social · 14/02/2024Excited (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.coDynamics of bacterial recombination in the human gut microbiomeRecombination 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... 37631
Reposted by Amy H FitzpatrickRhys White @rhystwhite.bsky.social · 14/02/2024It’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.orgGenomic epidemiology reveals geographical clustering of multidrug-resistant Escherichia coli ST131 associated with bacteraemia in Wales - Nature CommunicationsEscherichia 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... 063
Reposted by Amy H FitzpatrickÁkos T Kovács @evolvedbiofilm.bsky.social · 14/02/2024How does evolution work in superabundant microbes? -in #TrendsMicrobiol by Dmitry A. Filatov and Mark Kirkpatrick www.sciencedirect.com/science/arti... 034