Lightnews — Scholar-powered news

Reposted by @vdangioE3lab

EMBL-EBI @ebi.embl.org · Jul 22

How can we find out what’s really going on inside cells when we’re generating so much complex data?

CORNETO is an open-source tool that uses machine learning to turn tangled omics datasets into clear maps of how genes, proteins, and signalling pathways interact.

www.ebi.ac.uk/about/news/r... 🧪

CORNETO: machine learning to decode complex omics data

New tool combines biological knowledge with machine learning to help researchers extract meaningful insights from complex omics data.

www.ebi.ac.uk

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Denis Wirtz @deniswirtz.bsky.social · Jun 2

Research Saves Lives

At Hopkins, we just went live with an expansive website showing the extraordinary value of research, the impact of cuts to research, what's at stake, resources for our research community, etc.

Check it out: researchsaveslives.jhu.edu

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Samuel Maiwald @samuelmaiwald.bsky.social · May 26

Excited to share our latest study on how K29/K48-branched #ubiquitin chains are forged by the #E3 ligase TRIP12, and how this suggests a consensus mechanism for chain formation by HECT E3s!

@natsmb.nature.com

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

TRIP12 structures reveal HECT E3 formation of K29 linkages and branched ubiquitin chains - Nature Structural & Molecular Biology

Using biochemistry, chemical biology, and cryo-EM, Maiwald et al. elucidate how TRIP12 forms K29 linkages and K29/K48-linked branched ubiquitin chains, revealing a mechanism for polyubiquitylation sha...

www.nature.com

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Institute of Genetics and Cancer @uoe-igc.bsky.social · May 9

On #InternationalOvarianCancerDay, we held a Shining a Light on Ovarian Cancer event where Professor Charlie Gourley, Dr Rob Hollis and Dr Sarah Taylor talked about how their research is driving personalised patient care & BBC journalist Christine Macleod shared her story of going through treatment.

Christine Macleod, Dr Sarah Taylor, Dr Robb Hollis and Professor Charlie Gourley

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@vdangioE3lab @vdangioe3lab.bsky.social · May 7

🧬 New Research Alert! 🧬

"Pervasive phenotypic effects of FBXO42 controlled by regulation of PP4 phosphatase"
www.biorxiv.org/content/10.1...
Our findings reveal that Fbxo42 main function is to control PP4 phosphatase.
Discussions are highly welcome!
#bioRxiv #Research #Science #ubiquitin

Pervasive phenotypic effects of FBXO42 controlled by regulation of PP4 phosphatase

F-box proteins are the substrate recognition modules of the SCF (SKP1–Cullin– F-box) E3 ubiquitin ligase complex. FBXO42, an understudied member of this family, has recently emerged as a modulator of ...

www.biorxiv.org

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@vdangioE3lab @vdangioe3lab.bsky.social · May 7

nice parallel observations from David Toczyski lab :
www.biorxiv.org/content/10.1...

The regulation of Protein Phosphatase 4 by FBXO42 is required for cancer cell survival

FBXO42 is a poorly characterized F-box protein that is essential in 15% of cancer cell lines from diverse tissue types. FBXO42 has been implicated in the regulation of mitosis and p53 signaling. High-...

www.biorxiv.org

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@vdangioE3lab @vdangioe3lab.bsky.social · May 7

🧬 New Research Alert! 🧬

"Pervasive phenotypic effects of FBXO42 controlled by regulation of PP4 phosphatase"
www.biorxiv.org/content/10.1...
Our findings reveal that Fbxo42 main function is to control PP4 phosphatase.
Discussions are highly welcome!
#bioRxiv #Research #Science #ubiquitin

Pervasive phenotypic effects of FBXO42 controlled by regulation of PP4 phosphatase

F-box proteins are the substrate recognition modules of the SCF (SKP1–Cullin– F-box) E3 ubiquitin ligase complex. FBXO42, an understudied member of this family, has recently emerged as a modulator of ...

www.biorxiv.org

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Reposted by @vdangioE3lab

Serena Nik-Zainal @serenanikzainal.bsky.social · Apr 10

PAPER OUT!! 🥳🎉💃🏻🕺🏻💃🏻🕺🏻

A redefined InDel taxonomy provides insights into mutational signatures @NatureGenet

Brainchild of the amazing #GeneKoh
(Sir Jeffrey Cheah ECR)

Tweetorial below!! 👇

1/n

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

A redefined InDel taxonomy provides insights into mutational signatures - Nature Genetics

This paper describes a framework for classifying small insertions and deletions from genomic data and applies it to a large dataset comprising seven tumor types. The analysis highlights new insertion ...

www.nature.com

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Oxford Cancer @oxfordcancer.bsky.social · Mar 20

Stunning images from Francis Barr’s lab have won CRUK’s Research is Beautiful competition for February! 🌟 They capture microtubules connecting to chromosomes via kinetochores to create mitotic spindles. 🔬✨

news.cancerresearchuk.org/2025/03/13/l...

@oxfordbiochemistry.bsky.social

Latest winner in our Research is Beautiful campaign - Cancer Research UK - Cancer News

Our Research is Beautiful campaign continues to inspire with some fantastic images, but there has to be a winner, and here’s February’s…

news.cancerresearchuk.org

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Elton Zeqiraj @zeqiraj.bsky.social · Mar 17

Huge thanks to our funders @wellcometrust.bsky.social who generously funded the project. Their long-term support for our lab has made this possible especially because the project started over a decade ago, throwing many surprises along the way!

Elton Zeqiraj @zeqiraj.bsky.social · Mar 17

Excited to report our latest research on new “molecular glues” that specifically lock the BRCC36 isopeptidase complex (BRISC) in an autoinhibited state and reduce interferon signalling. This first-of-its-kind approach could reshape how we target large deubiquitylase (DUB) complexes.

rdcu.be/edRwF

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Brian Elliott @brianelliottmd.bsky.social · Mar 18

The irony of an article discussing the unpaid labor of scientists, published by a $4bn corporation reliant on the unpaid labor of scientists.

Meanwhile RJmedicine.org, a journal in which we offer $ honoraria to authors and reviewers, opened for submissions today

#academicSky #medSky #research

I spent two years organizing an international conference. How do I get compensated for my work?

It can be hard to say no to service requests in academia. Nature’s Careers team sought advice on how to ensure researchers don’t get stuck doing unpaid labour.

www.nature.com

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Elton Zeqiraj @zeqiraj.bsky.social · Mar 17

Excited to report our latest research on new “molecular glues” that specifically lock the BRCC36 isopeptidase complex (BRISC) in an autoinhibited state and reduce interferon signalling. This first-of-its-kind approach could reshape how we target large deubiquitylase (DUB) complexes.

rdcu.be/edRwF

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marcelvanvugt.bsky.social @marcelvanvugt.bsky.social · Mar 18

Happy to post a new study on BioRxiv, where we show Integrated Stress Response activation as an off-target effect of multiple clinically evaluated WEE1 inhibitors. Team effort with the lab of Dan Durocher @durocher1.bsky.social and many others. www.biorxiv.org/content/10.1...

WEE1 inhibitors trigger GCN2-mediated activation of the integrated stress response

The WEE1 kinase negatively regulates CDK1/2 to control DNA replication and mitotic entry. Genetic factors that determine sensitivity to WEE1 inhibitors (WEE1i) are largely unknown. A genome-wide inser...

www.biorxiv.org

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marcelvanvugt.bsky.social @marcelvanvugt.bsky.social · Mar 18

Thanks to the many collaborators; the labs of Thijn Brummelkamp, Alexander van Oudenaarden, Steven de Jong, Frank Sicheri, Marvin Tanenbaum @marvintanenbaum.bsky.social @jervdberg.bsky.social @rinskjetjeerdsma.bsky.social @mauritsroorda.bsky.social @daaninthelab.bsky.social

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Duncan Sproul @sproullab.bsky.social · Mar 11

Help 🚨 science Bluesky. We'd like an #GFP/#FluorescentProtein construct with an intron in the middle of the coding sequence for an experiment (not before the coding sequence). Does anyone know of anything that fits? We haven't turned up anything suitable from a quick search so far. Please repost 🙏

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James Briscoe @jamesbriscoe.bsky.social · Mar 11

Interesting idea: get the sick super-rich to pay for clinical trials

Alternative idea: get the super-rich to pay tax that allows democratically accountable governments to support clinical trials (and research and healthcare and....)

www.theguardian.com/news/2025/ma...

Many life-saving drugs fail for lack of funding. But there’s a solution: desperate rich people

Each year, hundreds of potentially world-changing treatments are discarded because scientists run out of cash. But where big pharma or altruists fear to tread, my friend and I have a solution. It’s re...

www.theguardian.com

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@vdangioE3lab @vdangioe3lab.bsky.social · Mar 7

I fully agree cutting fund and top down guidance is not the solution. It will make things a lot worse.

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@vdangioE3lab @vdangioe3lab.bsky.social · Mar 7

Probably you are right, the system is not perfect but what system is?
I overall have a positive view of the system. We are still making incredible progress at a rate that was unimaginable 10 years ago !

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@vdangioE3lab @vdangioe3lab.bsky.social · Mar 7

Probably we are much more efficient than other sectors (paradoxically this is research it just can't be efficient) but we are still striving to find ways to improve ! Only scientists can think like that !

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James Briscoe @jamesbriscoe.bsky.social · Mar 6

This is why UK gov needs to invest in PhD training & cut visa costs for scientists

Long term economic growth depends on skilled people

The UK should make the most of life sciences

Research Professional News @resprofnews.bsky.social · Mar 6

UK life sciences ‘will need 145,000 new people within 10 years’.

Report warns of skills shortage in sector at heart of government plans to boost growth.

www.researchprofessionalnews.com/rr-news-uk-i...

UK life sciences ‘will need 145,000 new people within 10 years’ - Research Professional News

Report warns of skills shortage in sector at heart of government plans to boost growth

www.researchprofessionalnews.com

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@vdangioE3lab @vdangioe3lab.bsky.social · Mar 6

It is a very well thought and meaningful piece

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Barak Rotblat @barakrotblat.bsky.social · Mar 6

I know there is not a lot of love for X on this platform but please think about Ivano's @ivanoamelio.bsky.social words

www.nature.com/articles/d41...

Should scientists ditch the social-media platform X?

Letter to the Editor

www.nature.com

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Institute of Genetics and Cancer @uoe-igc.bsky.social · Mar 5

March is #OvarianCancerAwarenessMonth. IGC researchers are leading significant advancements in our understanding of the disease. Dr Robb Hollis has written about work being undertaken at the Nicola Murray Centre for Ovarian Cancer Research into uncommon types of ovarian cancer: edin.ac/4jBEcId

Head shots of Professor Charlie Gourley (left), Professor Simon Herrington (centre) and Dr Robb Hollis (right)

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Tony Cesare @thecesarelab.bsky.social · Mar 4

Review from our lab out today: "Roles for the 3D Genome In the cell cycle, DNA replication, and double strand break repair." Written by @scientistkate.bsky.social, with her co-supervisor @piptaberlay.bsky.social and collaborator Mat Jones. www.frontiersin.org/journals/cel...

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Hartmut Vodermaier @hvodermaier.bsky.social · Feb 26

Happy that I got to handle and help publish this cool new work for @embojournal.org
And after many years of PARPi/(poly-ADP)ribose craze, exciting to see mono-ADP-ribosylation starting to reveal its secrets in so many ways now!

Mike Cohen @michaelnadbio.bsky.social · Feb 25

I'm super excited to share our study in collaboration with @jnpruneda.bsky.social, published today in @embojournal.org! We show that PARPs are modified with a non-canonical ester-linked mono-ADP-ribosylated ubiquitin species for the first time in cells: www.embopress.org/doi/full/10....

Ubiquitin is directly linked via an ester to protein-conjugated mono-ADP-ribose | The EMBO Journal

imageimageCertain E3 ligases have been found to ubiquitylate hydroxyl groups on free NAD+ and ADP-ribose in vitro, but the in vivo occurrence of this dual post-translational modification has remained ...

www.embopress.org

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