Alper Akay

We are seeing a large number of papers being published on new AI models in biology, disease, genomics. What should we look for in these papers before committing our time to test their use? I really wonder how they are reviewed as well.

Four-week timeframe for £40m AI research lab divides opinion - Research Professional News Tech advocates celebrate prospect of new UK lab, but “extremely tight” application window sparks concern

This is ridiculous but not surprising! Obviously, EPSRC must have people/organisations in mind and I wouldn’t be surprised if they have been in contact with some groups in advance. Some hard questions about why £40m is spent as such www.researchprofessionalnews.com/rr-news-uk-r...

⭐ #NARBreakthrough! ⭐
🧬 New study uncovers how #RNAstructures control stochastic exon selection in Dscam1 genes. #Balancer RNA structures and a #multi-subunit RNA architecture coordinate spatial and temporal splicing 🔬✨
Read the full article here: doi.org/10.1093/nar/...
#AlternativeSplicing

The Most Chilling Detail in the U.S. Attack on an Iranian Naval Ship The Iranian warship was taking part in an international exercise with many other countries—including the United States.

This is a chilling crime. A shame on our country. The Iranian ship was unarmed. The US knew this. The sailors were murdered by our navy, and the survivors were left to die at sea.
newrepublic.com/post/207429/...

How do RNA molecules shape genome regulation in the nervous system? (AKAY_U26CASE) | Doctoral Training Partnership This is open to Home Fee Status candidates only. This PhD project will investigate how RNA modifications influence the activity of topoisomerase I (TOP1), a crucial enzyme that regulates DNA…

PhD position in our lab - 4-year funded by BBSRC and @nrpdtp.bsky.social in collaboration with @earlhaminst.bsky.social and Inspiralis Ltd. Open to UK fee qualifying students - UK citizens and citizens of Ireland (residency requirement), etc biodtp.norwichresearchpark.ac.uk/projects/how...

🎉Proud to present our latest paper, out now in Nature Communications: www.nature.com/articles/s41...

RNA Binding Proteins (RBPs) are often full of intrinsically disordered regions (IDRs), but what these regions do during RNA recognition is often unclear. 1/10
#RNA #IDR #RBP

In Gorton & Denton, voters all feel they have been left behind — The Times and The Sunday Times There is a forgotten generation of white British voters. They feel sidelined. Confused. Swamped by mass immigration they didn’t vote for; bewildered at being told they enjoy “white privilege” while li...

I hope people of Gorton & Denton vote for a party that stands up for humanity and against genocide. Don’t believe in the lies of many politicians claiming they care about you while turning a blind eye to worst crimes of humanity of our times. apple.news/ATgPSimpARKC...

No reckoning over ethnic cleansing of Bulgaria's Turks Bulgaria's Turkish community, descendants of Ottoman settlers, suffered severe persecution under the communist regime. Yet little has been done to address the injustice.

www.dw.com/en/no-reckon...

‘Don’t go to the US – not with Trump in charge’: the UK tourist with a valid visa detained by ICE for six weeks — The Guardian Karen Newton was in America on the trip of a lifetime when she was shackled, transported and held for weeks on end. With tourism to the US under increasing strain, she says, ‘If it can happen to me, i...

I suppose if you are still organising an “international” conference in the US, you are effectively helping ICE. apple.news/AgpcB41ERTmu...

Sarajevo sniper tourists ‘killed children by day, then partied at night’ — The Times and The Sunday Times At the end of a day spent killing women and children with their expensive sniper rifles, the visitors to Sarajevo liked to celebrate until the small hours, devouring roast pork and knocking back brand...

Sarajevo sniper tourists ‘killed children by day, then partied at night’ - The Times and The Sunday Times apple.news/AP_CGjIiiS26...

Photo of UKRI CEO Professor Sir Ian Chapman.

Following an open letter on 1 February, our Chief Executive Professor Sir Ian Chapman has responded to feedback and provides an update on the changes to UKRI investment approach.

Read his letter here: www.ukri.org/news/ukri-ce...

There are a lot of similarities between how UK universities and UKRI are run. In both cases, big decisions are taken and changes made without consultation and often with dire consequences for the academic community and with little to no transparency around decisions, their impact or alternatives.

Ian Chapman makes the case that he would not be doing his job properly if he didn't deal with the cost overruns at STFC, which are causing so much grief to physicists

Physics groups are calling on ministers to intervene (presumably with more cash)

And there is now a response from a minister

...

“The goal is to break the Palestinian resistance by affecting the social base that embraces it” (...) Israel aimed to “re-engineer the Palestinian human” into a being whose sole cognitive focus is basic survival, rendering them incapable of political thought."

The way UK govt funds science is in the midst of a major transition, with creation of a much more direct link between government priorities & UKRI research funding.

My attempt to set in context the biggest upheaval in UK science funding policy since the 1980s:
softmachines.org?p=3252

The last EU Horizon programme lost £330m from UK science funding

Last week, RPN broke a string of stories on significant changes to funding across a number of research councils (see thread below)

This morning, UKRI chief executive is appearing at the Commons science committee, where he is being asked about them by MPs

Here are some key moments so far 🧵

Did a Celebrated Researcher Obscure a Baby’s Poisoning? — The New Yorker After a newborn died of opioid poisoning, a new branch of pediatrics came into being. But the evidence doesn’t add up.

We cannot rely on “science corrects itself”. We need national independent research integrity offices with powers everywhere. Here is another story about research misconduct——Did a Celebrated Researcher Obscure a Baby’s Poisoning? - The New Yorker apple.news/AO91lC8YBT-K...

The Holocaust survivor judge who issued Netanyahu’s arrest warrant — The Times and The Sunday Times At this time of year, Theodor Meron often finds himself thinking about his brother. Mietek was five years ahead of Theodor, and their early childhood was an idyllic one: summers on the Vistula, Chopin...

The Holocaust survivor judge who issued Netanyahu’s arrest warrant - The Times and The Sunday Times apple.news/AIrDM9zZ1RCK...

What's larger, a protein or its templating mRNA ?

> The mRNA is much larger.

⬛ 𝐀 𝐬𝐞𝐧𝐬𝐞 𝐨𝐟 𝐬𝐜𝐚𝐥𝐞 -- 𝐪𝐮𝐚𝐧𝐭𝐢𝐭𝐚𝐭𝐢𝐯𝐞 𝐢𝐧𝐭𝐮𝐢𝐭𝐢𝐨𝐧 & 𝐜𝐨𝐧𝐬𝐭𝐫𝐚𝐢𝐧𝐭𝐬 -- 𝐢𝐬 𝐚 𝐩𝐨𝐰𝐞𝐫𝐟𝐮𝐥 𝐞𝐧𝐚𝐛𝐥𝐞𝐫 𝐨𝐟 𝐫𝐞𝐬𝐞𝐚𝐫𝐜𝐡.

The figure shows myoglobin protein drawn to scale next to its mRNA template. The coding sequence of an mRNA ...

Why this could be final nail in coffin for an industry that was once pride of UK's economy Much has come and gone in Britain's industrial history.

news.sky.com/story/why-en...

Neat RNA papers

www.nature.com/articles/s41...
(polyamine regulation of splicing by direct binding to U2 snRNP proteins)
and
www.nature.com/articles/s41...
(impact of N1-methyl pseudo U on translation)

Just read an email about a 3 day conference organised by scientists well-known in their field with a capacity of 100 attendees, 33 invited speakers and only 10 slots for selected talks. Conferences are increasingly becoming closed circle meetings.

We've got ISSUES. Literally.

We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do?

arxiv.org/abs/2601.07563

A 🧵 1/n

Optimized murine sample sizes for RNA sequencing studies revealed from large scale comparative analysis - Nature Communications Determining the appropriate sample size (N) for bulk RNA sequencing experiments is critical to ensure reliable results. Here the authors perform an unusually large N experiment (N = 30 per group), ana...

"Results from experiments with N = 4 or less are shown to be highly misleading (...). For a cut-off of 2-fold expression differences, we find an N of 6-7 mice is required to consistently decrease the false positive rate to below 50%, and the detection sensitivity to above 50%"

FEBS Press Bacterial metabolism of tryptophan causes toxicity in C. elegans. E. coli takes up tryptophan and catabolizes it to indole via tryptophanase (TnaA). Indole can freely diffuse through lipid membranes ...

Happy to share our latest work by Shivani Gahlot and Subodh,
published in @febsj.bsky.social. We show that the amino acid Trp is highly toxic to C. elegans, and that this toxicity is driven by bacterial metabolism of Trp into indole.
febs.onlinelibrary.wiley.com/doi/10.1111/...

Don’t we, as scientists, have any responsibility in society to defend human life and humanity? Or will we continue to focus solely on research funding and impact factors in 2026? 2/2

2025 has been terrible with atrocities and indifference. I'm particularly disappointed in my scientific community. How can we claim to care about human life and health in papers and grants but stay silent when children are being killed daily? 1/2

@biouea.bsky.social @norwichrnaclub.bsky.social #UKRIFLF

Widespread intron retention and exon skipping characterise alternative splicing changes in a C. elegans model of spinal muscular atrophy Abstract. Spinal muscular atrophy (SMA) is a neurodegenerative disease caused by reduced levels of the survival motor neuron (SMN) protein, an essential co

Finally, our collaborative work with Maria Dimitriadi’s group on the spinal muscular atrophy gene SMN-1 and how it affects RNA splicing academic.oup.com/hmg/advance-...