PhD student @pharmabiotic @ucc | Microbes, Biofilms and Antimicrobial Resistance | All views my own | @aforestsomewher[email protected]
Cork, Ireland
Joined March 2013
- Tweets1.6K
- Following1.4K
- Followers533
- Likes11.1K
Katie O'Mahony retweeted
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/
Katie O'Mahony retweeted
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: asm.social/2Fk
ALT Average microbiome composition for each method employed by the participants (n = 5), aligned to the ground truth (Actual) of each DNA RR. (A) Relative species level composition (%) of the DNA-Gut-HiLo and DNA-Gut-Mix RRs resulting from shotgun sequencing data analysis. (B) Relative genus level composition (%) of the DNA-Gut-HiLo and DNA-Gut-Mix RRs resulting from 16S rRNA gene amplicon sequencing data analysis.
Katie O'Mahony retweeted
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.
biorxiv.org/content/10.1101/…
Katie O'Mahony retweeted
Unassigning bacterial species for microbiome studies journals.asm.org/doi/full/10…
Katie O'Mahony retweeted
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
Some weekend reading…great to see GROND, our new database for long-read amplicon sequencing of the ribosomal operon, is out. Congrats @calumari_walsh @meghana_srini @VanSinderenLab @pauldcotter @tstinear microbiologyresearch.org/con…
Katie O'Mahony retweeted
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
doi.org/10.1099/mgen.0.00125…
@rrwick, myself and the team (@JuddLmj @tstinear @linsalrob & Sarah) have recently looked at the effect of depth on short-read polishing almost-perfect Nanopore bacterial genomes
biorxiv.org/content/10.1101/…
(1/7)
Katie O'Mahony retweeted
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)
biorxiv.org/content/10.1101/…
Katie O'Mahony retweeted
MicrobeMod: A computational toolkit for identifying prokaryotic methylation and restriction-modification with nanopore sequencing biorxiv.org/cgi/content/shor… #biorxiv_micrbio
Katie O'Mahony retweeted
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!
journals.plos.org/plosbiolog…
This work was led by @marion_bichet and out on World Phage Week! #WorldPhageWeek
Katie O'Mahony retweeted
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 – at Cork, Ireland
Katie O'Mahony retweeted
@N_RoseEdwin knocking it out of the park (digging in the weeds?) of soil microbiomes @MicrobioSoc Irish meeting
Katie O'Mahony retweeted
Our third speaker is @EmmanuelKuffo15, talking about Streptococcus suis as a model for phage based biocontrol agents #MicrobioIrish23 @MicrobioSoc @UccMicrobiology @SEFSUCC @UCC @JenniferMahony7
Katie O'Mahony retweeted
And now @meghana_srini speaking about her work to apply long read sequencing to metagenomics #MicrobioIrish23
Katie O'Mahony retweeted
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.
Katie O'Mahony retweeted
ggCaller paper now out in its final form
genome.cshlp.org/content/33/…
Call your genes, get your pangenome
(and a great cover thanks to laurenbellcreative.com/)
Katie O'Mahony retweeted
#Microbiome twitter, we are looking for negative control samples from as many sources and kits as possible. If you've included blanks in your 16S or ITS amplicon seq project and the data is publicly available, drop a link in the thread!
RTs appreciated!
Katie O'Mahony retweeted
🏠Seeking Rental Help in South Dublin.
Due to a house fire, we're urgently searching for a rental from Sep to Dec/Jan. No injuries, but handling this #shitshow from Germany.
If you know of any options within budget for two #academics, DM me😢 #HousingEmergency
Please retweet 🩷
Katie O'Mahony retweeted
If anyone wants to help spread the word about @SkypeScientist, it's one of two things we need the most.
You can send people to: skypeascientist.com/sign-up.…
And feel free to share this flyer with anyone who you think could benefit from our program!
ALT An explainer for skype a scientist that says "Skype a Scientist chat with scientists FOR FREE" followed by "Skype a Scientist matches classrooms, scout troops, libraries and other groups with scientists for Q&As about science! " and then "How it works: Step 1: Sign up on SkypeAScientist.com Step 2: Pick a category of science your group would like to talk about (e.g. marine biology, chemistry, astronomy) Step 3: Get a match via email Step 4: Connect with your scientist, discuss your class's needs, and pick a time to chat Step 5: Talk to your scientist!"
Katie O'Mahony retweeted
Great to see this out with @MicrobioSoc Many congrats @BMC2203 and @meghana_srini Isolation and identification of chlorate-reducing Hafnia sp. from milk microbiologyresearch.org/con…