Lightnews — Scholar-powered news

Reposted by John Lees

Josie Bryant @josiebryant.bsky.social · 7d

Proud to see my lab's work on M. tuberculosis and P. aeruginosa highlighted in this blog post

Mat Beale @typemat12.bsky.social · 7d

sangerinstitute.blog/2025/10/01/t... @sangerinstitute.bsky.social #microsky

Ten ways the Sanger Institute is tackling the global fight against AMR - Wellcome Sanger Institute Blog

Our scientists and collaborators are working together to tackle one of the biggest public health threats: antimicrobial resistance. We are using cutting-edge genomics to hunt down drug-resistant micro...

sangerinstitute.blog

1 5

John Lees @bacpop.org · 9d

Now published, our tool to run (almost) all biological models interactively in your web browser

Paper: academic.oup.com/bioinformati...
Website: biomodels.bacpop.org
Code: github.com/bacpop/SBMLt...

1 9 15

Reposted by John Lees

Sam Horsfield @samuelhorsfield.bsky.social · 14d

A new ggCaller version is out! v1.4 includes tweaks to improve efficiency, outputs Panaroo-friendly GFFs, and enables iterative gene calling; if you have already called a gene set, you can now add more genomes either one by one or in batches github.com/bacpop/ggCal...

GitHub - bacpop/ggCaller: Bifrost graph gene caller.

Bifrost graph gene caller. Contribute to bacpop/ggCaller development by creating an account on GitHub.

github.com

1 7 11

Reposted by John Lees

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

40 19

John Lees @bacpop.org · 16d

Thanks for all the trainers and attendees on this course, which was a lot of fun to run, and hopefully filled a gap in genomics/modelling training

And especially co-organisers @leonielorenz.bsky.social @sonjalehtinen.bsky.social Joel Hellewell

EMBL-EBI Training @training.ebi.embl.org · 19d

Thank you to everyone who joined us this week for the @embo.org Practical Course 'Methods for infectious disease modelling using genomics'.

Join us for 2026's EMBO Practical Course. Sign up for 'Causality in biomedicine' alerts and hear as this new course develops: www.ebi.ac.uk/training/eve...
🧬🧫

1 4 12

Reposted by John Lees

EMBL-EBI Training @training.ebi.embl.org · 19d

Thank you to everyone who joined us this week for the @embo.org Practical Course 'Methods for infectious disease modelling using genomics'.

Join us for 2026's EMBO Practical Course. Sign up for 'Causality in biomedicine' alerts and hear as this new course develops: www.ebi.ac.uk/training/eve...
🧬🧫

5 5

John Lees @bacpop.org · 16d

Oops sorry yes!! But should be the same yep

1

John Lees @bacpop.org · 16d

Yes I think so: www.johnlees.me/index.xml

www.johnlees.me

1

Reposted by John Lees

David Hodgson @dchodge.bsky.social · 19d

Just launched an interactive Bayesian epidemic modelling platform that runs entirely in your browser!

No downloads, no installations, no expensive software licenses. Just open the link and start modelling disease dynamics with real-time parameter estimation.

>> widget-bayesian-sir.davidhodgson.me

Interactive Bayesian Epidemic Modelling

widget-bayesian-sir.davidhodgson.me

2 6 22

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

40 19

John Lees @bacpop.org · 27d

alignmentalignment.ai

Center for the Alignment of AI Alignment Centers

We align the aligners

alignmentalignment.ai

2 4

Reposted by John Lees

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

5 98 190

John Lees @bacpop.org · 28d

Not massively convinced by the Covid bit after a quick read through, I think it’s probably quite overfitted (but not totally confident, I only had a quick look at the code)

1 2

Reposted by John Lees

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
🧬💻

2 10 42

Reposted by John Lees

Giulio Ermanno Pibiri @jermp.bsky.social · Aug 28

Wow, more than 2.4M of assembled bacteria in the new release of ABT! We plan to index these using our efficient colored De Bruijn graph index, Fulgor. We recently conducted experiments with nearly 1M genomes…getting there :)
www.biorxiv.org/content/10.1...

AllTheBacteria - all bacterial genomes assembled, available and searchable

The bacterial sequence data publicly available via the global DNA archives is a vast potential source of information on the evolution of bacteria. However, most of this sequence data is unassembled, o...

www.biorxiv.org

30 67

Reposted by John Lees

Ben Langmead @benlangmead.bsky.social · Aug 26

📢🚨📢🚨 Genome Informatics deadline extended to September 8! meetings.cshl.edu/meetings.asp....
Please spread the word. If you are like me and had at least one abstract that wasn't quite ready by last week's deadline, you get another swing. See you there!

Genome Informatics

Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.

meetings.cshl.edu

1 19 29

Reposted by John Lees

Josie Bryant @josiebryant.bsky.social · Aug 20

Closing soon. Great opportunity to do spatial transcriptomics on pre-antibiotic TB

Josie Bryant @josiebryant.bsky.social · Jul 16

⭐ Excellence fellowships accepting applications ⭐ for Black ECRs who have a degree from the UK. sanger.wd103.myworkdayjobs.com/en-US/Wellco...
I have an amazing spatial transcriptomics project available on the world's most important pathogen, TB: www.sanger.ac.uk/wp-content/u...
Please reach out!

www.sanger.ac.uk

5

Reposted by John Lees

🎃nisillos @onisillos.bsky.social · Aug 18

It's interesting to draw these parallels.

(We definitely need to move beyond purely technological solutions to how we deal with infections in a future where antimicrobials are more scarce.)

www.theguardian.com/books/2025/a...

Why antibiotics are like fossil fuels

They helped create the modern world but are dangerously overused. How can we harness them sustainably?

www.theguardian.com

1 5 17

Reposted by John Lees

Bede Constantinides @bedec.bsky.social · Aug 15

Deacon 0.9.0 can filter FASTA at well over 2Gbp/s on an AMD CPU from 2021. Compression is very limiting, but I suspect ~1Gbp/s is possible for fastq.gz with a modern CPU. Thanks @curiouscoding.nl for a monumental perf PR!

Release 0.9.0
github.com/bede/deacon/...
www.biorxiv.org/content/10.1...

Thread scaling performance for compressed and uncompressed sequence input

1 4 9

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

7 56 110

Reposted by John Lees

EMBL-EBI @ebi.embl.org · Aug 13

Recruitment is now open for the EMBL-EBI–Sanger Postdoctoral Programme.

ESPOD builds on the collaborative relationship between EMBL-EBI and the @sangerinstitute.bsky.social, offering projects that combine experimental and computational approaches.

www.ebi.ac.uk/research/pos...

🧬🖥️🔬#postdocjob

ESPOD, the EMBL-EBI/Sanger postdoctoral fellowship. Applications deadline 30 September. Image credit: Karen Arnott / EMBL-EBI

1 31 31

Reposted by John Lees

Bede Constantinides @bedec.bsky.social · Aug 11

📣 Deacon 0.8.0 available on Bioconda
- Much faster search and depletion through improved work distribution on multicore systems. My fastq.gz benchmark now runs at 400Mbp/s on Apple M1.
- Dual default match thresholds for greater accuracy

Details: github.com/bede/deacon/...

1k downloads! 🐥

Release 0.8.0 · bede/deacon

Faster filtering on multicore systems through improved work allocation using the Paraseq library (@noamteyssier). Filtering at >1Gbp/s is possible with uncompressed long sequences, and >500Mbp/s is...

github.com

2 6 15

John Lees @bacpop.org · Aug 5

Two take-aways from a nice talk by John Jumper last week
www.johnlees.me/posts/alphaf...

Lessons from a Nobel Laureate (on deep learning and academia/industry)

Last week I saw John Jumper give a presentation on his team’s development of AlphaFold 1/2/3. He started explaining how AlphaFold1 worked, essentially a convolutional neural network. He spent most of ...

www.johnlees.me

1 7

John Lees @bacpop.org · Aug 5

I'll put you in touch with Victor who did our analysis!

1

John Lees @bacpop.org · Aug 4

Yes, two splits before, and always above 63. Also didn't try k>1023. We also thought it was weird and don't really understand!!

1 1