Katie O'Mahony

PhD student @pharmabiotic @ucc | Microbes, Biofilms and Antimicrobial Resistance | All views my own | @[email protected]

[Thomas G. Dietterich @tdietterich]

Attention @arxiv authors: Our Code of Conduct states that by signing your name as an author of a paper, each author takes full responsibility for all its contents, irrespective of how the contents were generated. 1/

[ASM @ASMicrobiology]

In a study involving 23 labs, researchers tested various sequencing/bioinformatic approaches for taxonomic profiling of DNA reference reagents consisting of 20 common gut bacteria, revealing the reality of technical bias in the microbiome field. #mSystems: https://t.co/W6zFtW9b3S

[Katie O'Mahony @forestsomewhere]

@BissonGiulia @pauldcotter @teagasc Bravissima!!!! Congratulatioms Giulia

[Peter Dougherty @PeterEDougherty]

Are there virulent phages hiding in your bacterial culture? Here we find hundreds of virulent phage genomes in bacterial genome assemblies. Bioinformatic and experimental evidence indicate these are not contaminations, but represent persistent infections.
https://t.co/fPDQ10bThT

[Rainer Melzer @UCDflowerpower]

GWAS for Nobel prize laureates.

[Cameron Thrash @jcamthrash]

Unassigning bacterial species for microbiome studies https://t.co/fa8N9YAESZ

[Paul Cotter @pauldcotter]

Great to see this finally published! GROND is a new 16S-ITS-23S rRNA database that will allow the full potential of long read sequencing be applied to amplicon-based metataxonomics

[George Bouras @GB13Faithless]

The final version of our short-read polishing manuscript (headed by @rrwick of course) is out in @MicrobioSoc MGen!

Tldr: with R10.4.1+Dorado ONT assemblies, few errors remain, so short-read polishing can make assemblies worse at low depth; target >=25x

https://t.co/qrsiXFuuFN

[Katie O'Mahony @forestsomewhere]

@OrlaOS @TeagascFood @pauldcotter @jgskenny @Ant__Lourenco You know when you're in a scientific meeting about fermented foods when a massive vat of fermented veg has pride of place during each lunch buffet! Thanks to Rain Kuldjärv and all at TFTAK for hosting and to new colleagues for a friendly introduction to #DOMINOEU

[Ryan Cook @RyanCookAMR]

Happy to share my first pre-print with @EvelienAdri in my new role at @TheQuadram. We sequenced three human faecal viromes with Illumina and Nanopore, and tested a number of long, short and hybrid assembly approaches (1/10)

https://t.co/iRyrIhvHP6

[bioRxiv Microbiology @biorxiv_micrbio]

MicrobeMod: A computational toolkit for identifying prokaryotic methylation and restriction-modification with nanopore sequencing https://t.co/Yhfz9ConOh #biorxiv_micrbio

[Jeremy J Barr @JeremyJBarr]

Our latest work, out today in @PLOSBiology suggests that not only do mammalian cells absorb bacteriophages, but they appear to use them as a resource to enhance growth!

https://t.co/6oGAXcD4Jp

This work was led by @marion_bichet and out on World Phage Week! #WorldPhageWeek

[J.O.K.Emmanuel🏳️‍🌈🏳️‍⚧️ @EmmanuelKuffo15]

What are fermented foods and why should we care? @RamyaBalasubr13 presents her work on understanding the role of fermented foods in modulating the microbioata-gut-brain axis… #APCSymposium2023

[John Kenny @jgskenny]

⁦@N_RoseEdwin⁩ knocking it out of the park (digging in the weeds?) of soil microbiomes ⁦@MicrobioSoc⁩ Irish meeting

[microSCRUM @micro_SCRUM]

Our third speaker is @EmmanuelKuffo15, talking about Streptococcus suis as a model for phage based biocontrol agents #MicrobioIrish23 @MicrobioSoc @UccMicrobiology @SEFSUCC @UCC @JenniferMahony7

[John Kenny @jgskenny]

And now @meghana_srini speaking about her work to apply long read sequencing to metagenomics #MicrobioIrish23

[Mike Tisza @MikeTisza]

PSA to folks who have bioinformatics tools with required databases hosted on Zenodo: all the URLs for Zenodo data files have changed slightly. It may affect your DB set up scripts.

[John Lees @johnlees6]

ggCaller paper now out in its final form

https://t.co/200jrT68xK

Call your genes, get your pangenome

(and a great cover thanks to https://t.co/ZrzZx9ZcQF)

[Katie O'Mahony @forestsomewhere]

@EmmanuelKuffo15 @haleybiont @RamyaBalasubr13

[Katie O'Mahony @forestsomewhere]

@EmmanuelKuffo15 @PWO_Ireland 👏 well said, especially when universities and postgrad students are essentially fighting on the same team against chronic and ongoing undervalorisation and underfunding of tertiary education... And it is of such direct and concrete relevance to #EDI