Lightnews — Scholar-powered news

Ewan Birney @ewanbirney.bsky.social · 2h

Some thoughts on the blossoming of genomic medicine stimulated by the excellent @ga4gh.org meeting in lovely Uppsala Sweden. www.linkedin.com/pulse/though...

Thoughts from Uppsala - Genomic Medicine blossoming

I have had a wonderful three days in Uppsala Sweden, at the Global Alliance for Genomics and Health plenary hosted locally by the generous SciLifeLab . It was a meeting of course focused on the standa...

www.linkedin.com

2 5

Ewan Birney @ewanbirney.bsky.social · 12h

The working language is English; you will have a short and productive course at the start and then work with your supervisor in one of the sites, always in a community of PhD students (predocs in EMBL speak) and postdocs, with support around you over the 4 years of a PhD.

1

Ewan Birney @ewanbirney.bsky.social · 12h

You get to work in Europe's flagship molecular biology laboratory in one of our 6 sites, getting a degree from our local partner universities (Sapienza, U. Heidelberg, U. Cambridge, U. Hamburg, U. Grenoble+UPF, Barcelona), be part of a vibrant scientific community and diverse future career options

1 2

Ewan Birney @ewanbirney.bsky.social · 12h

A reminder that the PhD program for EMBL is open for winter recruitment round. If you want to understand life at a molecular level and have a quantitative science (you don't have to have done biology - we love our mathematicians/physcists/chemists!) apply www.embl.org/about/info/e...

Application – EMBL International PhD Programme

www.embl.org

1 42 31

Reposted by Ewan Birney

Pragati Kore @pragskore.bsky.social · 2d

📃 We’re excited to share our latest work, now published in Nature Communications — a major update to the Genome Aggregation Database (gnomAD) that improves allele frequency resolution for two gnomAD-defined genetic ancestry groups using local ancestry inference (LAI).

Improved allele frequencies in gnomAD through local ancestry inference - Nature Communications

This study incorporates local ancestry into the Genome Aggregation Database (gnomAD) to improve allele frequency estimates for admixed populations, enhancing variant interpretation and enabling more accurate and equitable genomic research and clinical care.

www.nature.com

1 7 26

Reposted by Ewan Birney

Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 2d

📣Important update for #AlphaFold API users! New API fields launched on October 7th, 2025. We’ll maintain BOTH fields until June 25, 2026! Check the docs! 🔗
For more information, read the news item: www.ebi.ac.uk/pdbe/news/br...

2 7

Ewan Birney @ewanbirney.bsky.social · 2d

So sorry to hear this. He was a great - and generous - scientist

1

Reposted by Ewan Birney

The Guardian @theguardian.com · 2d

Sunder Katwala on race, patriotism and flag-waving: ‘The far right is vocal and angry because it is shrinking’

The director of British Future has spent his career trying to find common ground when it comes to race and immigration. He describes his own experience of racism – and why he’s still hopeful for the UK

www.theguardian.com

5 17 94

Reposted by Ewan Birney

Joannes Laveyne @jolaveyne.bsky.social · 2d

It may have escaped your attention, but the Belgian energy system has quietly passed an important test. During the weekend of 4-5 October 2025, our consumption was almost entirely covered by renewable energy. And yet the system ticked like a Swiss watch. /

3 57 190

Ewan Birney @ewanbirney.bsky.social · 2d

I’d love to know what happens next but presumably no one knows (or just Macron knows ??)

2 1

Ewan Birney @ewanbirney.bsky.social · 2d

So my French colleagues - am I right that France has had a prime minister with a shorter tenure than Liz Truss - 50 days. Or could he patch it all up this week? French parliamentary politics is murky enough from the outside but … this is pretty impressive

2 2

Ewan Birney @ewanbirney.bsky.social · 2d

10,000 foot take home message is ... biology is very complex. Gob-smakingly complex!

Bart Deplancke @bartdeplancke.bsky.social · 3d

🧵1/ Excited to share our new paper introducing a new #singlecell assay: scTF-seq, a high-throughput single-cell approach to explore how transcription factor (TF) dose shapes cell identity and reprogramming outcomes. 🔗 www.nature.com/articles/s41... Big congrats to the entire team @EPFL & @SIAT_China

Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq - Nature Genetics

This study introduces single-cell transcription factor (TF) sequencing, a single-cell barcoded and doxycycline-inducible TF overexpression approach that reveals dose-sensitive functional classes of TFs and cellular heterogeneity by mapping TF dose-dependent transcriptomic changes during the reprogramming of mouse embryonic multipotent stromal cells.

www.nature.com

2 13

Reposted by Ewan Birney

Randall Munroe @xkcd.com · 2d

Ping

xkcd.com/3150/

4-panel comic. (1) [person finds bottle on shore] (2) [person reads message from inside bottle: ICMP ECHO REQUEST...] (3) [person writes on message ICMP ECHO REPLY...] (4) [person puts bottle back in water and leaves]

29 240 2.3K

Reposted by Ewan Birney

Jonathan Pritchard @jkpritch.bsky.social · 2d

I want to try something again at #ASHG25 this year: I'll block some time on Thursday and Friday afternoons to meet with trainees who would be interested to chat on any topic.

I did this last year and it was great to meet a whole bunch of new people, at all career stages!

1 16 57

Ewan Birney @ewanbirney.bsky.social · 3d

Well - this is why I want to go air to water via the radiators - like for like.

1

Ewan Birney @ewanbirney.bsky.social · 3d

Why is it so high at 0? (Solar?)

2 2

Ewan Birney @ewanbirney.bsky.social · 4d

Ugh. Where is the dislike button !!

1 7

Reposted by Ewan Birney

Carmelo Ferrai @carmeloferrai.bsky.social · 4d

2- I feel that people shouldn’t be annoyed talking about “epigenetics” and a refresh every now an then probably is not bad 🤣 I don’t see any concern to the study of @jamiehackett.bsky.social that indeed is very nice… mainly the fight should point other fronts where epigenetic goes very South!!!👇🏽

2 1 7

Reposted by Ewan Birney

John Greally @greally.bsky.social · 4d

Using the word in the title to lull people into a false sense of security. It's very devious, I'll admit.

1 6

Ewan Birney @ewanbirney.bsky.social · 4d

That said, it is a word with a lot of history people have... or even are... writing books with it in the title right? and the word has it uses in particular in contexts where the definition being used is clear by context.

2 2

Ewan Birney @ewanbirney.bsky.social · 4d

We're in danger of the classic issue between academics - agreeing on many things but arguing passionately about the few things - often semantics and language - where we disagree. I am not a big fan of the word epigenetics, and it's multiple meanings absolutely confuse comms

1 4

Ewan Birney @ewanbirney.bsky.social · 4d

The tech for heat pumps is now fine and personally people have over empaised aspects like efficiency (requiring lower central heating temperatures at higher flow / more insulated houses) vs like-for-like swaps. This where we need tech, policy and social change /comfort (literally) to come together

3 2

Ewan Birney @ewanbirney.bsky.social · 4d

However the uk is in a blind spot on home heating; most is via gas via a near ubiquitous gas network , uk has a lot of old housing stock and it’s a culturally important thing to fix up, restore etc (compare to - say - Japan)

1

Ewan Birney @ewanbirney.bsky.social · 4d

As important as low carbon grid is moving consumption to electricity. Transport now is largely market barriers aspect (though the oversupply in batteries from China is a conundrum of exploiting this vs protecting longer view on technology)

1

Ewan Birney @ewanbirney.bsky.social · 4d

Both future modelling and practical considerations say that one can achieve a 90-95% low carbon grid relatively easily and cheaply - and the British grid is heading that way. There’s a strong argument to not tackling the big economic cost to get that last 10% this decade

1