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Reposted by Andries van Tonder

Josie Bryant @josiebryant.bsky.social · 3h

New respiratory 🫁 infection and microbiomes conference in Hinxton with stellar line up of speakers.

🚨 Submit your abstracts now! 🚨

Please RT

coursesandconferences.wellcomeconnectingscience.org/event/air-20...

AIR 2026: Genomic and Systems Approaches to Respiratory Infection, Microbiomes and Immunity — 20260211

Course exploring how genomics, microbiome profiling, and systems biology reshape our understanding of respiratory infections and immune dynamics.

coursesandconferences.wellcomeconnectingscience.org

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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 6d

Phylodynamics and genome-wide association studies reveal the expansion of modern Streptococcus canis in Germany https://www.biorxiv.org/content/10.1101/2025.09.29.679251v1

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Zamin Iqbal @zaminiqbal.bsky.social · 12d

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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John Lees @bacpop.org · 21d

The EMBL PhD programme is open until 13th October (entry ~Sep 2026):
www.embl.org/about/info/e...

We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them

EMBL International PhD Programme – Unique in the world and waiting for you!

www.embl.org

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Iain Johnston @mitomaths.bsky.social · 16d

Great to see this out there! We infer the evolutionary pathways behind patterns of AMR in Klebsiella across 102 states, finding globally consistent principles, state-specific deviations (and covariates), and validating evol predictions with new genomes. biorxiv.org/content/10.1... 1/

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Phil Ewels @ewels.bsky.social · 21d

Really excited to announce the v1.9 release of the `rich-click` library 🎉 It's a Python library that uses builds on top of command-line help output from click, giving you beautiful output with only a couple of lines of code 🪄 ✨ 🌈

v1.9 TLDR: We have themes!

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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!

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Lucy Weinert @lucyweinert.bsky.social · 21d

Introducing AMR cartography - work by Andrew Balmer

bioRxiv Genomics @biorxiv-genomic.bsky.social · 21d

Antimicrobial Resistance Cartography: A Generalisable Framework for Studying Multivariate Drug Resistance https://www.biorxiv.org/content/10.1101/2025.09.12.675231v1

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Hall Lab @halllab.bsky.social · 21d

🚨 An excellent opportunity for scientists in Africa, at all career stages, working on maternal & child microbiome research 🚨

📚 Blended learning (3 months) incl. prep modules, hands-on training (12-17 Apr 2026) & mentoring.

coursesandconferences.wellcomeconnectingscience.org/event/human-...

Human Gut Microbiome Metagenomics – Africa — 20260412

Build skills in microbiome metagenomics, bioinformatics, and data interpretation to advance maternal and child health research

coursesandconferences.wellcomeconnectingscience.org

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 23d

X-Mapper 🦠🧬🧪 - a sequence aligner developed for microbes, now on Bioconda! 🚀
• 11–24× fewer suboptimal alignments (same for human genome)
• 3–579× lower inconsistency
• improves on ~30% of reads aligned to non-target species
github.com/mathjeff/map...
bioconda.github.io/recipes/x-ma...
#microsky

Alignment algorithms represent a balance between speed and accuracy. We evaluated this balance across aligners, with accuracy measured by suboptimal alignments. We found that the relationship between alignment time (with 30 threads) and suboptimal alignment rates exhibits diminishing returns, where X-Mapper stands out as an outlier, offering the highest accuracy with competitive speed.

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Zamin Iqbal @zaminiqbal.bsky.social · 28d

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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Andries van Tonder @andriesvt.bsky.social · Sep 8

The next online version of our "Working with Bacterial Genomes" course is now open for registration. We aim to provide you with comprehensive training in analysing bacterial genomes covering everything from QC to clustering plasmids. Sign up here: www.training.cam.ac.uk/bioinformati...

Research Informatics - Working with Bacterial Genomes (ONLINE LIVE TRAINING) - Mon 27 Oct 2025

www.training.cam.ac.uk

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EMBL-EBI @ebi.embl.org · Sep 8

Mathematical models in biology are powerful, but often hard to run, visualise, or reuse without specialist skills.

Menelmacar is a new platform that makes biological models interactive and easy to explore directly in the browser: biomodels.bacpop.org
🧬💻

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Nature @nature.com · Sep 5

This study describes the oldest microbial DNA ever sequenced

go.nature.com/4nfIzcU

A mammoth toothache: bacterial community discovered in mouth of ancient mammal

Genetic-sequencing techniques have uncovered the oldest host-associated microbial DNA ever recorded — inside samples of teeth and bones from woolly and steppe mammoths.

go.nature.com

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James McInerney @jomcinerney.bsky.social · Aug 29

New preprint reveals bacteria can't just collect all resistance genes like Pokemon cards.
We found mutually exclusive evolutionary pathways to multidrug resistance in E. coli & P. aeruginosa - some resistance mechanisms actively prevent others from coexisting www.biorxiv.org/content/10.1...

Genomic constraints shape the evolution of alternative routes to drug resistance in prokaryotes

Background Variation within the prokaryotic pangenome is not random, and natural selection that favours particular combinations of genes appears to dominate over random drift. What is less clear is wh...

www.biorxiv.org

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Stephen Turner @stephenturner.us · Aug 28

New blog post: Using OpenAI Codex in @posit.co Positron with a demo on developing an #Rstats package using the OpenAI Codex agent doi.org/10.59350/ste...

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Nature @nature.com · Aug 15

A coffee variety called liberica, which is gaining popularity for the distinctive flavour of its beans, is actually three species

go.nature.com/4fFfx3F

Mysterious coffee species turns out to be a blend

A coffee variety called liberica, which is gaining popularity for the distinctive flavour of its beans, is actually three species.

go.nature.com

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John Lees @bacpop.org · Aug 15

My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology:
www.ebi.ac.uk/training/onl...

Including both molecular and epidemiological examples

Mathematical modelling for biologists - Modelling concepts in biological research

www.ebi.ac.uk

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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Aug 5

A cross-environment comparison of nontuberculous mycobacterial diversity https://www.biorxiv.org/content/10.1101/2025.08.04.668438v1

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Alan McNally @alanmcn1.bsky.social · Aug 5

If ever a species needed a large scale long-read genomics project it is Y. pestis. Great paper!

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

Insights into Yersinia pestis evolution through rearrangement analysis of 242 complete genomes - Nature Genetics

Analysis of synteny blocks and genomic rearrangement patterns of 178 newly sequenced and 64 publicly available complete genomes of Yersinia pestis highlights the impact of key variations on genes invo...

www.nature.com

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Segata Lab @cibiocm.bsky.social · Jun 11

The new version of MetaPhlAn v4.2.2 released!

📌taxonomic profiling of long-read metagenomes for the first time
📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs

Try it out & @hutlab.bsky.social and we are looking forward to your feedback!
forum.biobakery.org/t/metaphlan-...

MetaPhlAn 4.2.2 release (initial long-read sequencing support and database update)

Announcement We are pleased to share that MetaPhlAn 4.2.2 is now available, which incorporates taxonomic profiling of long-read metagenomes for the first time and includes a new version of the MetaPhl...

forum.biobakery.org

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Mark A. Hanson @hansonmark.bsky.social · Jun 10

New from The Strain Team:
🎊 Springer Nature Discovers MDPI 🎊

Springer Nature has spawned a copycat journal series called "Discover" mimicking #MDPI journal titles and citation behaviours. We even made a browser game to prove it (see 🔗).

Gross! 😀 1/n

#ResearchIntegrity #SciPub #AcademicSky

Spinger Nature Discovers MDPI – The Strain on Scientific Publishing

Home page for the paper ‘The Strain on Scientific Publishing’ by Mark A Hanson, Dan Brockington, Paolo Crosetto and Pablo Gomez Barreiro

the-strain-on-scientific-publishing.github.io

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Jim Shaw @jimshaw.bsky.social · May 28

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).

myloasm-docs.github.io

myloasm - metagenomic assembly with (noisy) long reads

myloasm-docs.github.io

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Conor (Conchúr) Meehan @conmeehan.bsky.social · May 22

Myself and @yekwah.bsky.social are running our bacterial AMR databases and genotype prediction course again with @eventswcs.bsky.social. Completely free and study at your own pace.
Check out the course objectives below and sign up before June 9th to join us!
www.futurelearn.com/courses/anti...

Antimicrobial Databases and Genotype Prediction - Online Course - FutureLearn

Transform your understanding of antimicrobial resistance (AMR) and elevate your research or clinical practice with Wellcome Connecting Science.

www.futurelearn.com

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Ryan Wick @rrwick.bsky.social · May 27

New blog post!
In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup.
Check it out for the full results:
rrwick.github.io/2025/05/27/d...

Dorado v1.0.0 and the v5.2.0 basecalling models

a blog for miscellaneous bioinformatics stuff

rrwick.github.io

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