Lightnews — Scholar-powered news

Reposted by Jane Hawkey

EMBL-EBI @ebi.embl.org · 9d

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

1 16 41

Reposted by Jane Hawkey

Ryan Wick @rrwick.bsky.social · 10d

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

1 35 62

Reposted by Jane Hawkey

Dorottya Nagy @dotnagy.bsky.social · 10d

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.

1 16 25

Reposted by Jane Hawkey

Christina Faherty @christinafaher1.bsky.social · 11d

A great opportunity to attend the #Shigella meeting April 20-24, 2026! Abstract submissions are open! @shigellameeting.bsky.social #Microsky

Microbiology Society @microbiologysociety.org · 13d

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

5 7

Reposted by Jane Hawkey

Kate Baker @ksbakes.bsky.social · 21d

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!

2 9 18

Reposted by Jane Hawkey

Thomas Lin Pedersen @thomasp85.com · 27d

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

9 280 850

Reposted by Jane Hawkey

Alexander Luckmann @aluckmann.bsky.social · Aug 20

Academia may not give you job security, flexibility, or wealth, but it will let you unexpectedly connect to eduroam in foreign cities

29 160 1K

Jane Hawkey @yekwah.bsky.social · Aug 12

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!

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

2 9

Reposted by Jane Hawkey

ESCMID @escmid.bsky.social · Aug 7

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

6 5

Reposted by Jane Hawkey

Nature @nature.com · Jul 31

This surprisingly relaxing footage is from SIX MILES under the ocean – and it’s the deepest ecosystem yet discovered

440 3.5K 14K

Jane Hawkey @yekwah.bsky.social · Jul 30

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

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...

1 6

Reposted by Jane Hawkey

Ben Vezina @bananabenana.bsky.social · Jul 29

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

1 8 18

Reposted by Jane Hawkey

Rob Edwards @linsalrob.bsky.social · Jul 22

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

25 46

Reposted by Jane Hawkey

MicroSeq2025 @microseqasm.bsky.social · Jul 21

🚨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.

1 13 8

Reposted by Jane Hawkey

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jul 17

A periodic table of bacteria?: Mapping bacterial diversity in trait space https://www.biorxiv.org/content/10.1101/2025.07.11.664459v1

3 2

Reposted by Jane Hawkey

Rob Edwards @linsalrob.bsky.social · Jul 17

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.

5 9

Jane Hawkey @yekwah.bsky.social · Jul 14

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

The Guardian @theguardian.com · Jul 13

How do I feel about air conditioning? I’m very hot – but it’s destroying the planet | Emma Beddington

Yes, temperatures are rising. But more and more AC means more and more CO2 – and then more and more global heating. Let’s have some long-term thinking instead, writes Guardian columnist Emma Beddington

www.theguardian.com

1 5

Reposted by Jane Hawkey

MicroSeq2025 @microseqasm.bsky.social · Jul 3

🦋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.

11 20

Reposted by Jane Hawkey

esgmap.bsky.social @esgmap.bsky.social · Jul 11

🚨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

8 6

Reposted by Jane Hawkey

Ian M. Mackay, PhD (he/him) 🦠🤧🧬📑🦟🧀 @mackayim.bsky.social · Jul 10

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

4 7

Reposted by Jane Hawkey

Jerónimo Rodríguez-Beltrán @jerorb.bsky.social · Jul 2

🚨🚨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

4 84 180

Reposted by Jane Hawkey

Kelly Wyres @kelwyres.bsky.social · Jul 2

So excited that this is now online. It's been a huge collaborative effort to estimate the prevalence of capsule and O antigens associated with #klebsiella neonatal sepsis in Africa and South Asia. The first step to prioritising antigens for a vaccine to protect 1000s of newborns. #MicroSky #AMR

Kat Holt @katholt.bsky.social · Jul 1

I'm super happy to share this preprint on ‘Distribution of capsule and O types in #Klebsiella pneumoniae causing neonatal sepsis in Africa and South Asia: meta-analysis of genome-predicted serotype prevalence and potential vaccine coverage’
doi.org/10.1101/2025...

Distribution of capsule and O types in Klebsiella pneumoniae causing neonatal sepsis in Africa and South Asia: meta-analysis of genome-predicted serotype prevalence and potential vaccine coverage

Background: Klebsiella pneumoniae causes ~20% of sepsis in neonates, with ~40% crude mortality. A vaccine administered to pregnant women, protecting against 70% of K. pneumoniae infections, could aver...

doi.org

4 12

Reposted by Jane Hawkey

Wellcome Connecting Science Learning and Training @eventswcs.bsky.social · Jun 20

Explore the important role of #genomics and data-driven technologies for accelerating advances in #AMRresearch, at our Antimicrobial Resistance meeting! #AMR2026

Discover the latest developments informing a dynamic global response to controlling this crisis.

🗓️ 23–25 March 2026

📎 bit.ly/3SWzJUm

Wellcome Connecting Science hybrid conference
Antimicrobial Resistance – Genomes, Big Data and Emerging Technologies
Conference dates: 23–25 March 2026
Location: Hinxton Hall Conference Centre, Wellcome Genome Campus, UK and online

Bursary deadline: 01 December 2025
Abstract deadline: 15 December 2025
Registration deadlines: In person: 24 February 2026 | Virtual: 17 March 2026

8 11

Reposted by Jane Hawkey

Jose F. Delgado-Blas @josefdelgadoblas.bsky.social · Jun 23

Excited to share this preprint focused on the genomic taxonomy of C. diphtheriae #diphtheria
➡️ www.biorxiv.org/content/10.1...
Hope it helps advance research and surveillance of this relevant bacterial pathogen. Thanks to @sylvainbrisse.bsky.social and BEBP and BIGSdb teams for making it possible!

4 11