Jane Hawkey
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yekwah.bsky.social
Jane Hawkey
@yekwah.bsky.social
320 followers 160 following 21 posts
Microbial genomics - bacterial evolution, AMR, mobile elements, phylogenetics. Located at Monash University/Alfred Hospital
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Reposted by Jane Hawkey
mattbevan.bsky.social
I can’t explain why but reading the news feels like this at the moment
November 13, 2025 at 7:02 AM
yekwah.bsky.social
Very interesting to see what amendments were pushed by different parties for this bit of legislation. The One Nation amendment to remove a focus on public health issues caused by climate change (thankfully voted down) was typically 🙄
November 6, 2025 at 4:50 AM
Reposted by Jane Hawkey
natrevgenet.nature.com
New online! Microbial genomics for antimicrobial resistance ecology and action
Microbial genomics for antimicrobial resistance ecology and action
Nature Reviews Genetics, Published online: 03 November 2025; doi:10.1038/s41576-025-00909-zMicrobial genomics can improve our understanding of antimicrobial resistance dynamics across ecosystems. In this Comment, Kathryn Holt emphasizes the interconnectedness of human, animal and environmental health and calls for greater integration of microbial genomic data through robust analytical frameworks to unravel the complexity of antimicrobial resistance dynamics.
www.nature.com
November 3, 2025 at 1:07 PM
Reposted by Jane Hawkey
ksbakes.bsky.social
Are you hungry for some Shigella news? Why not come to the 1st International Shigella meeting www.shigella2026.conferences-pasteur.org/home 20-24 April 2026 Paris
October 29, 2025 at 6:29 PM
Reposted by Jane Hawkey
ebi.embl.org
There are millions of openly available microbial genomes, but searching them can be slow.

Until now 🥁

Introducing LexicMap, a new alignment tool that lets scientists search these data in minutes, helping track antibiotic resistance, trace outbreaks, and more.

www.ebi.ac.uk/about/news/r...
🦠
How to rapidly search the world’s microbial DNA
By making the world’s microbial DNA easier to explore, LexicMap helps researchers track outbreaks, study antibiotic resistance, and understand microbial diversity.
www.ebi.ac.uk
September 30, 2025 at 9:47 AM
Reposted by Jane Hawkey
rrwick.bsky.social
Happy to share that the paper describing Autocycler is now 100% up:
doi.org/10.1093/bioi...
(1/3)
Autocycler: long-read consensus assembly for bacterial genomes
AbstractMotivation. Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-l
doi.org
September 29, 2025 at 4:11 AM
Reposted by Jane Hawkey
dotnagy.bsky.social
To summarise our recent pre-print: Autocycler, the automated consensus assembler, when used with Nanopore long-read only Enterobacterales assemblies, produces more complete chromosomes and plasmids, with an accuracy comparable to hybrid assemblies.
Figure 2 from my recently pre-printed manuscript on the completeness and accuracy of Nanopore long-read only bacterial genome assembly for Enterobacterales. a) tile plot of chromosome circularisation, with assembler on the x-axis and sample on the y-axis, shows that the consensus long-read only assembler, Autocycler, circularised more chromosomes at 95% (87/92) than any other long-read or hybrid assembler. b) complex upset plot of plasmid reconstruction, showing that the best plasmid reconstruction was achieved by long-read assemblers incorporating the separate plasmid assembly tool, Plassembler, namely Autocycler and Hybracter, reconstructing >96% of plasmids.
September 29, 2025 at 6:57 AM
Reposted by Jane Hawkey
christinafaher1.bsky.social
A great opportunity to attend the #Shigella meeting April 20-24, 2026! Abstract submissions are open! @shigellameeting.bsky.social #Microsky
microbiologysociety.org Microbiology Society @microbiologysociety.org · Sep 26
External Event Grant awards of up to £750 are available for eligible members as a contribution towards the costs of registration, travel, and accommodation to attend an event beginning 01 Jan – 30 April 2026. Apply now before the deadline 01 Nov at 23:59: microb.io/ExternalEven...
External Event Grant
Login to apply
microb.io
September 27, 2025 at 12:03 PM
Reposted by Jane Hawkey
ksbakes.bsky.social
Come and join us at @shigellameeting.bsky.social in Paris 2026. Registrations are now open! www.shigella2026.conferences-pasteur.org/home and follow the Shigella starter pack go.bsky.app/6Vbwhjc (message to be added)! 215 days to go!
September 17, 2025 at 11:58 AM
Reposted by Jane Hawkey
thomasp85.com
I am beyond excited to announce that ggplot2 4.0.0 has just landed on CRAN.

It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package.

Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats
ggplot2 4.0.0
A new major version of ggplot2 has been released on CRAN. Find out what is new here.
www.tidyverse.org
September 11, 2025 at 11:20 AM
Reposted by Jane Hawkey
aluckmann.bsky.social
Academia may not give you job security, flexibility, or wealth, but it will let you unexpectedly connect to eduroam in foreign cities
August 20, 2025 at 4:58 PM
yekwah.bsky.social
Really liked the explanation about human understanding, and what we miss when we use black box models. This has always been my gripe with prediction models for eg AMR - I want to know why that feature is associated with resistance!
schwessinger.bsky.social The Tattooed Professor @schwessinger.bsky.social · Aug 11
This is an excellent long-read on AI and science with lots of useful further reading www.aisnakeoil.com/p/could-ai-s.... Well worth your time to actually read it.
Could AI slow science?
Confronting the production-progress paradox
www.aisnakeoil.com
August 12, 2025 at 4:56 AM
Reposted by Jane Hawkey
escmid.bsky.social
Register today for the 14th International Meeting on Microbial Epidemiological Markers (IMMEM XIV)! Topics range from how genomics inform resistance profiling to pathogen surveillance in a #OneHealth framework. 🧬

✍️ Register: ow.ly/gjOZ50WpOXX
👀 Programme: ow.ly/Whj850WpOXY

#IDSky
August 7, 2025 at 8:14 AM
Reposted by Jane Hawkey
nature.com
This surprisingly relaxing footage is from SIX MILES under the ocean – and it’s the deepest ecosystem yet discovered
July 31, 2025 at 3:38 PM
yekwah.bsky.social
Huge amount of work in this paper, very proud of Hugh getting through all these benchmarking tests. We’re much more confident now using ONT-only data for our clinical questions
hughcottingham.bsky.social Hugh Cottingham @hughcottingham.bsky.social · Jul 30
Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1
www.medrxiv.org/content/10.1...
July 30, 2025 at 8:34 AM
Reposted by Jane Hawkey
bananabenana.bsky.social
New preprint where we analysed IS loads in 🦠 #Klebsiella pneumoniae lineages and found they're inversely associated with nutrient usage. We propose an insertional tolerance model, whereby IS can only insert into metabolically-tolerable sites.

#IDSky #MicroSky 🧪

www.biorxiv.org/content/10.1...
Graph showing IS loads by Klebsiella sub-lineage
July 29, 2025 at 2:29 AM
Reposted by Jane Hawkey
linsalrob.bsky.social
Fold first, ask later: structure-informed function annotation of Pseudomonas phage proteins

Structural predictions to improve #phage genome annotation!

@hannelorelongin.bsky.social @gbouras13.bsky.social y.social @susiegriggo.bsky.social @veravannoort.bsky.social

www.biorxiv.org/content/10.1...
Fold first, ask later: structure-informed function annotation of Pseudomonas phage proteins
Phages, the viruses of bacteria, harbor an incredibly diverse repertoire of proteins capable of manipulating their bacterial hosts, inspiring many medical and biotechnological applications. However, t...
www.biorxiv.org
July 22, 2025 at 12:27 AM
Reposted by Jane Hawkey
microseqasm.bsky.social
🚨Abstract submission & registration for #MicroSeq2025 is OPEN! 🚨Get in quick! The first 50 registrations are FREE for PhD students and ECRs who are current ASM members, thanks to @aussocmic.bsky.social.

Head to our website to register now 👇
www.microseqconference.com/registration...
Registration and abstract submission for MicroSeq2025 is open. Abstract submission closes August 8, 2025. Participants can register at microseqconference.com. MicroSeq2025 is an online meeting being held on September 3rd and 4th, focused on research being conducted on sequencing data generated from microbiological samples (bacteria, fungi, and viruses). MicroSeq2025 is supported by The Australian Society for Microbiology, the Australasian Virology Society, and Microbial Genomics.
July 21, 2025 at 2:16 AM
Reposted by Jane Hawkey
biorxiv-bioinfo.bsky.social
A periodic table of bacteria?: Mapping bacterial diversity in trait space https://www.biorxiv.org/content/10.1101/2025.07.11.664459v1
July 17, 2025 at 4:47 PM
Reposted by Jane Hawkey
linsalrob.bsky.social
The 10th anniversary #ABACBS conference will be held in Adelaide from Nov 24-28. If you're thinking of coming, get in quick, as it's going to be a big week: A fantastic #bioinformatics conference with outstanding national and international speakers, and we're wrapping up the ABACBS week an AC/DC gig
The view of the Adelaide Oval, site of the 2025 Australian Biology and Computational Biology Society (ABACBS) conference, from across the River Torrens. The conference will be held in Adelaide from 24 to 28 November and celebrates 10 years of ABACBS.
July 17, 2025 at 5:43 AM
yekwah.bsky.social
Doesn’t destroy the planet if you use solar energy to power it - in summer our house regularly produces way more solar than we can use, our AC runs entirely off solar during the day with energy to spare
July 14, 2025 at 12:36 AM
Reposted by Jane Hawkey
microseqasm.bsky.social
🦋Hello BlueSky!🦋 Let's get right into it. MicroSeq is back September 3-4, 2025! Stay tuned for more details on registration and abstract submission coming soon here and at www.microseqconference.com. 🌟Save the date!🌟
#MicroSeq2025
A call to save the date for MicroSeq2025, returning September 3-4. MicroSeq is an online meeting where microbiology meets sequencing, including bacteria, viruses, and fungi.
July 3, 2025 at 5:47 AM
Reposted by Jane Hawkey
esgmap.bsky.social
🚨Plasmid ALERT – new @eurosurveillance.org rapid comms!

@ecdc.europa.eu-led study finds mosaic IncHI1B(pNDM-MAR) plasmid with blaOXA-48 + aerobactin in 492 K. pneumoniae isolates across 8 EU countries (2019–2024).

First ESGMAP-backed paper: tinyurl.com/4acezh92
#AMR #plasmids #OneHealth #ESGMAP
Cross-border spread of a mosaic resistance (OXA-48) and virulence (aerobactin) plasmid in Klebsiella pneumoniae: a European Antimicrobial Resistance Genes Surveillance Network investigation, Europe, F...
An investigation of the European Antimicrobial Resistance Genes Surveillance Network (EURGen-Net) detected the same mosaic IncHI1B(pNDM-MAR) resistance (OXA-48) and virulence (aerobactin) plasmid in 4...
tinyurl.com
July 11, 2025 at 8:57 AM
Reposted by Jane Hawkey
mackayim.bsky.social
Israel: silencing dissent everywhere theshot.net.au/uncategorize...
Israel: silencing dissent everywhere - The Shot
The pro-Israel lobby isn’t designed to balance debate nor to enrich it – it is designed to silence it.
theshot.net.au
July 10, 2025 at 11:33 PM
Reposted by Jane Hawkey
jerorb.bsky.social
🚨🚨New paper out in @natcomms.nature.com!!

Come for the first large-scale analysis of plasmid copy number across species,
stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬

👉 www.nature.com/articles/s41...
Universal rules govern plasmid copy number - Nature Communications
Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...
www.nature.com
July 2, 2025 at 11:08 AM