Lightnews — Scholar-powered news

Marco Galardini @mgalactus.bsky.social · 14h

New AI term just dropped

Simon Willison @simonwillison.net · 1d

Vibe coding is irresponsibly building software through dice rolls, not caring what code is produced

What about when engineers at the top of their game use AI tools responsibly to accelerate their work?

I propose "vibe engineering"!

simonwillison.net/2025/Oct/7/v...

Vibe engineering

I feel like vibe coding is pretty well established now as covering the fast, loose and irresponsible way of building software with AI—entirely prompt-driven, and with no attention paid to …

simonwillison.net

Reposted by Marco Galardini

Pedro Beltrao @pedrobeltrao.bsky.social · 1d

Our group has a PhD position open in this Doctoral network. Our topic is around combining proteomics AI and protein structures. Look through the website below to look at all of the projects/groups and apply.

protaiomics.bsky.social @protaiomics.bsky.social · 1d

🌟Ready to apply?
16 fully funded PhD positions are open in ProtAIomics Doctoral Network!
Join 16 labs across Europe to advance AI-powered proteomics and drive discoveries in health & biotechnology.
👉 Apply here: www.protaiomics.eu
#Proteomics #ArtificialIntelligence #MSCA #PhDOpportunities

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Reposted by Marco Galardini

Claus Wilke @clauswilke.com · 1d

Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...

We still can’t predict much of anything in biology

Biology is hard. Yes, even for AI.

blog.genesmindsmachines.com

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Marco Galardini @mgalactus.bsky.social · 1d

Nor can it automatically fetch any page from their docs

Marco Galardini @mgalactus.bsky.social · 3d

So, Claude Code won't implement almost anything using openAI's API, stopping with a generic error 💯

Reposted by Marco Galardini

Alan McNally @alanmcn1.bsky.social · 2d

After being with the journal since its very inception, the time has come for me to step back from Microbial Genomics. This is a wonderful opportunity to have a leadership role in one of the leading journals for microbial genomics research

microbiologysociety.org/news/society...

<i>Microbial Genomics </i> Deputy Editor-in-Chief: Call for Expressions of interest

microbiologysociety.org

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Marco Galardini @mgalactus.bsky.social · 1d

Chatbots in a nutshell

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Marco Galardini @mgalactus.bsky.social · 2d

vibe coding in a nutshell

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Marco Galardini @mgalactus.bsky.social · 3d

So, Claude Code won't implement almost anything using openAI's API, stopping with a generic error 💯

Reposted by Marco Galardini

Judit Burgaya @jburgaya.bsky.social · 6d

On Wednesday I started my postdoc at the Institut für Infektionskrankheiten (IFIK) @unibe.ch 🧬💻 Excited to get started on my project exploring Streptococcus pneumoniae virulence and all the science ahead!

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Marco Galardini @mgalactus.bsky.social · 7d

I see so much "static" AI slop for advertising already that I'm pretty sure it will move onto video as soon as cost comes down (hopefully energy use as well)

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Reposted by Marco Galardini

Tami Lieberman @contaminatedsci.bsky.social · 9d

Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise.

Until now, using AccuSNV.

Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV

Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission events, and identifying antimicrobial resistance mutati...

www.biorxiv.org

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Reposted by Marco Galardini

Craig MacLean @craigmaclean.bsky.social · 13d

New ERC funded computational postdoc position in my lab! We are looking for someone who will study the genomics of bacterial evolution using samples from experimental evolution and clinical trials. Lots of opportunities for interesting and fun collaboration!
my.corehr.com/pls/uoxrecru...

Job Details

my.corehr.com

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Reposted by Marco Galardini

James McInerney @jomcinerney.bsky.social · 14d

OK, here it is. Come work with me at the University of Liverpool making ALL THE AI models from ALL THE prokaryote pangenome data. Heck, we will make models from ALL the pangenomes, even eukaryotes!!! (link below👇) 1/4

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Reposted by Marco Galardini

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

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Reposted by Marco Galardini

Anna Cusco @annacusco.bsky.social · 15d

If you made it this far, thanks for reading. I hope you enjoyed the thread.

I am currently looking for my next research adventure. If you have insights on the microbiome/microbial genomics🧬🦠 job market in Europe (academia and industry), or want to chat about this work, please reach out!

At Handan Campus, Fudan University, Shanghai.

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Reposted by Marco Galardini

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 18d

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com

GPU-accelerated homology search with MMseqs2 - Nature Methods

Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

www.nature.com

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Marco Galardini @mgalactus.bsky.social · 20d

We are looking to integrate a fluorescent marker in an E. coli BW strain we built; what's your favorite integration site (and why)?

(asking here seemed to have worked quite well for @wvschaik.bsky.social and so I figured why not trying?)

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Reposted by Marco Galardini

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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Marco Galardini @mgalactus.bsky.social · 21d

Yes!

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Reposted by Marco Galardini

Anshul Kundaje @anshulkundaje.bsky.social · 23d

I'm curious if other mid career PIs have considered completely abandoning the trad publication model. We've been making gradual moves towards that end goal. But it's been difficult to completely jump ship for one main reason for me at least. 1/

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Marco Galardini @mgalactus.bsky.social · 23d

This comment tho: "Took me a while to realize that Grace Blackwell refers to a person and not an Nvidia chip :)"

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Marco Galardini @mgalactus.bsky.social · 24d

just leaving this gem here :)

A tweet from Tom Ellis about the lack of rules in biology:

"As I tell my undergrads, there are only 2 rules in biology:

Rule 1: If people think there is a rule, then somewhere out there an organism or virus will be breaking it.

Rule 2: The person who finds that gets a paper in Cell"

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Marco Galardini @mgalactus.bsky.social · 24d

My German might still be rusty, but I'm locked in culturally

A photo of a cucumber/lime Popsicle, bright green

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Reposted by Marco Galardini

Max Planck Institute for Infection Biology @mpiib-berlin.mpg.de · 26d

#Job opportunity
The Key Lab @keyfm.bsky.social is looking for a #postdoc in evolutionary genetics - join a young team in the heart of #Berlin to investigate the evolution of ancient microbial pathogens.

⏰ Deadline: October 17
📌 More info and how to apply: www.mpiib-berlin.mpg.de/2193291/job_...

Max Planck Institute for Infection Biology

Postdoc in Evolutionary Genetics

Job Offer

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Reposted by Marco Galardini

Tami Lieberman @contaminatedsci.bsky.social · 26d

We are looking for a postdoc to study single-cell transcriptional heterogeneity in the human skin microbiome.

We have a new protocol mostly developed, but need someone to see it through. Experience with protocol dev or RNAseq appreciated.

Funded by a new grant from MIT-HEALS.

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