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Reposted by Gerry Tonkin-Hill

Ryan Wick @rrwick.bsky.social · 10d

Happy to share that the paper describing Autocycler is now 100% up:
doi.org/10.1093/bioi...
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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

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Zamin Iqbal @zaminiqbal.bsky.social · 13d

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
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Ruoshi @ruoshiz.bsky.social · 22d

Happy to see that Spacedust is now published on Nature Methods!
It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes.
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Nature Methods @natmethods.nature.com · 22d

Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data.
@ruoshiz.bsky.social @milot.bsky.social

www.nature.com/articles/s41...

De novo discovery of conserved gene clusters in microbial genomes with Spacedust - Nature Methods

This work presents Spacedust, a tool for de novo identification of conserved gene clusters from metagenomic data.

www.nature.com

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Zamin Iqbal @zaminiqbal.bsky.social · 29d

Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology

LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

www.nature.com

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Nikolai Slavov @slavov-n.bsky.social · 29d

Large AI models are reported to achieve high accuracy (AUROC) predicting pathogenic variants across the genome.

A preprint reports that the predictions are based on splice variants. Using only this info (no sequences, no AI) achieves AUROC=0.944 across noncoding variants.

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Rayan Chikhi @rayanchikhi.bsky.social · Sep 3

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024...

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Michael Baym @baym.lol · Sep 1

What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years?

Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...

Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics

Antibiotic resistance is frequently observed shortly after the clinical introduction of an antibiotic. Whether and how frequently that resistance occurred before the introduction is harder to determin...

www.microbiologyresearch.org

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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.

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Reposted by Gerry Tonkin-Hill

Ben J Woodcroft @benjwoodcroft.bsky.social · Jul 16

Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵

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abacbs.bsky.social @abacbs.bsky.social · Jul 4

The day is finally here! 🎉 We’re releasing the invited speaker line-up, key dates, and lots more info for ABACBS 2025.
Check it out and share widely: www.abacbs.org/abacbs2025

Registrations and abstract submissions open next week, with abstracts due in August!

ABACBS 2025 Conference

Adelaide, South Australia. Nov. 24-

www.abacbs.org

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Jesse Shapiro @bjesseshapiro.bsky.social · Jun 11

Are you a recent PhD (or soon to be PhD) from outside Canada looking to do a postdoc in Quebec?

Get in touch if you are excited about microbes, evolution, ecology, genomics (or all of the above!) and I'd be happy to help develop a project together!

www.mcgill.ca/gps/funding/...

PBEEE/Quebec Merit Scholarship for Foreign Postdocs and Visiting Research Student and Visiting Researchers

**Note that the FRQ is in the process of revamping their webpages. We will update links soon as we can with the current 2025 year's information. Be sure to check back to see if any eligibility or docu...

www.mcgill.ca

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Ed Feil @edfeil.bsky.social · May 20

www.bath.ac.uk/jobs/Vacancy...
Post doc available to work on Candida genomics with me at the Milner Centre for Evolution (U Bath, UK) as part of the JPIAMR funded project Fugaci www.jpiamr.eu/projects/fug...
For queries, email me!

FuGACI – JPIAMR

JPIAMR is a global collaborative organisation and platform, engaging 28 nations to curb antimicrobial resistance (AMR) with a One Health approach.

www.jpiamr.eu

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Feargal Ryan @feargalr.bsky.social · Apr 2

Delighted our study (7+ years in the making) is out today in Nature. In a nutshell, 48 hours of antibiotics in week 1 led to impaired vaccine responses up to 15 months later in infants. We show (in-vivo) a probiotic can fix it #microbiome #science #immunology
www.nature.com/articles/s41...

Bifidobacteria support optimal infant vaccine responses - Nature

Neonatal antibiotic use is shown to reduce immune response to infant vaccines, accompanied by reduced abundance of Bifidobacteria in the gut microbiota, with experiments in mice indicating that probio...

www.nature.com

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Reposted by Gerry Tonkin-Hill

Rebecca Gladstone @becctococcus.bsky.social · Apr 3

Being able to data plasmid acquisition, and to see the diversity of plasmids being gained and lost from lineages, was really eye opening! It was a pleasure to contribute my tiny bit to this huge paper and the data has so much more to give! @arredondo.bsky.social @gerrythill.bsky.social et al.

Wellcome Sanger Institute @sangerinstitute.bsky.social · Apr 3

Read ‘Plasmid-driven strategies for clone success in Escherichia coli.’ From @sangerinstitute.bsky.social @uitnorgesarktiske.bsky.social, the University of Oslo, and others, in @naturecomms.bsky.social, here ⤵️

www.nature.com/articles/s41...

Plasmid-driven strategies for clone success in Escherichia coli - Nature Communications

Plasmids can encode multiple traits that contribute to the emergence and dissemination of their bacterial hosts. Here the authors use Nanopore long-read technology to sequence the complete genomes of ...

www.nature.com

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Ben Hogan @benjhogan.bsky.social · Mar 5

We are recruiting a group leader in laboratory research at Peter Mac Cancer Centre in
Melbourne, Australia 🔬🦘💥

Work in a cutting edge research environment in a vibrant world city!

We value research excellence, creativity and diversity.

Join us!

careers.petermac.org/job/MELBOURN...

Group Leader

careers.petermac.org

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Lars Barquist @lbarquist.bsky.social · Jan 17

Interested in predicting AMR in bacteria? We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. With @nwheeler443.bsky.social and former PhD student Yanying Yu. 🦠🧫🧬🖥️🧪

www.biorxiv.org/content/10.1...

Biased sampling confounds machine learning prediction of antimicrobial resistance

Antimicrobial resistance (AMR) poses a growing threat to human health. Increasingly, genome sequencing is being applied for the surveillance of bacterial pathogens, producing a wealth of data to train...

www.biorxiv.org

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Reposted by Gerry Tonkin-Hill

Ryan Wick @rrwick.bsky.social · Dec 31

New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
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Home

A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler

github.com

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Martin Hunt @martibartfast.bsky.social · Nov 29

I just made a first release of TNA - new tool to compare 2 bacterial genomes. Is shamelessly inspired by ACT, but should be simpler to use. Drag-n-drop two genomes: it runs BLAST for you and then you can visualize. For Mac, Windows 11, Linux tna.readthedocs.io

TNA documentation — TNA 0.0.1 documentation

tna.readthedocs.io

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Nov 29

Brisk: Exact resource-efficient dictionary for k-mers https://www.biorxiv.org/content/10.1101/2024.11.26.625346v1

The rapid advancements in DNA sequencing technology have led to an unprecedented increase in the gen

www.biorxiv.org

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Rebecca Gladstone @becctococcus.bsky.social · Nov 27

How invasive are different E .coli capsules and how many are there? Find out here and use the group 2 and 3 database to type your own!
medrxiv.org/cgi/content/...

Group 2 and 3 ABC-transporter dependant capsular K-loci contribute significantly to variation in the invasive potential of Escherichia coli

The major opportunistic pathogen Escherichia coli is the largest cause of antimicrobial resistance (AMR) associated infections and deaths globally. Considerable antigenic diversity has been documented...

medrxiv.org

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Reposted by Gerry Tonkin-Hill

Jo Rhodes @drjorhodes.com · Nov 19

Super excited that our JPIAMR grant on Candida has been funded 🙌https://www.jpiamr.eu/projects/fugaci/

Keep your eyes peeled as there will be a lot of postdoc positions available on this grant, and a PhD position with me and Anita!

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Duncan Ng @duncan-ng.bsky.social · Nov 14

Always exciting to see journals publish negative results on the microbiome!

www.cell.com/med/fulltext...

No association between the early-life gut microbiota and childhood body mass index and body composition

The gut microbiota has been implicated in the development of obesity, and especially early life has been proposed to be important. Poulsen et al. followed 700 children from birth and found no consiste...

www.cell.com

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Will Ratcliff @wcratcliff.bsky.social · Oct 26

New preprint up! We sequenced hundreds of samples from across one of Earth's oldest living organisms - the Pando aspen clone - to understand how mutations accumulate and spread in long-lived clonal organisms. Our results were…surprising. 1/30

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Willem van Schaik @wvschaik.bsky.social · Oct 24

This is amazing and important work by Glen Carter and colleagues at the University of Melbourne

'Rifaximin prophylaxis causes resistance to the last-resort antibiotic daptomycin in Enterococcus'

www.nature.com/articles/s41...

Rifaximin prophylaxis causes resistance to the last-resort antibiotic daptomycin - Nature

Rifaximin use, particularly in patients with liver cirrhosis, may be compromising the clinical use of daptomycin.

www.nature.com

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Eduardo Rocha @epcrocha.bsky.social · Oct 15

Our study on the (huge) variations in transformation rates is now out in OA! Key question: why are so many strains non-transformable if the many recent transitions to non-transformability seem deleterious? doi.org/10.1371/jour...

Intragenomic conflicts with plasmids and chromosomal mobile genetic elements drive the evolution of natural transformation within species

Bacterial species exhibit large variations in their transformation rates. This study of Legionella pneumophila and Acinetobacter baumannii shows that their transformation rates evolve by sudden quick ...

doi.org

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