Pedro Beltrao
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pedrobeltrao.bsky.social
Pedro Beltrao
@pedrobeltrao.bsky.social
2.6K followers 600 following 190 posts
Associate professor at ETH Zurich, studying the cellular consequences of genetic variation. Affiliated with the Swiss Institute of Bioinformatics and a part of the LOOP Zurich.
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pedrobeltrao.bsky.social
Pedro Beltrao @pedrobeltrao.bsky.social · Oct 9
new preprint: Ubiquitin is a protein modification linked with degradation but known to regulate other functions. Over 100k ubiquitination sites have been discovered and here we (@julianvangerwen.bsky.social + others) try to prioritize those most critical to the cell www.biorxiv.org/content/10.1...
The functional landscape of the human ubiquitinome
Protein ubiquitination regulates cell biology through diverse avenues, from quality control-linked protein degradation to signaling functions such as modulating protein-protein interactions and enzyme...
www.biorxiv.org
Reposted by Pedro Beltrao
zaminiqbal.bsky.social
Honoured and quite blown-over to receive this award. I have been, and continue to be, very lucky - first with great mentors, and then really prodigious students, postdocs and collaborators. Working with them has been a joy.
gensocuk.bsky.social Genetics Society UK @gensocuk.bsky.social · 21h
Congratulations to @zaminiqbal.bsky.social from @milnerevolution.bsky.social on being awarded the 2026 Mary Lyon Medal!
November 14, 2025 at 12:55 PM
Reposted by Pedro Beltrao
pmc-modularity.bsky.social
Catch our last seminar for the year on Dec 8 at 3pm CET! With Dr. Martin Rennie (@martinrennie.bsky.social), Jamal Fahoum (@hebrewuniversity.bsky.social), and Dr. Boglárka Zámbó (@zbobo2.bsky.social)

Register to attend: tinyurl.com/PMCseminar2

Previous seminars: www.youtube.com/@PMCModularity
November 14, 2025 at 8:31 AM
Reposted by Pedro Beltrao
biorxiv-biophys.bsky.social
Global Analysis of Aggregation Determinants in Small Protein Domains https://www.biorxiv.org/content/10.1101/2025.11.11.687847v1
November 13, 2025 at 1:47 AM
Reposted by Pedro Beltrao
ernstschmid.bsky.social
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Proteome-wide in silico screening for human protein-protein interactions
Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational...
biorxiv.org
November 12, 2025 at 9:26 PM
Reposted by Pedro Beltrao
hansonmark.bsky.social
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision. A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
November 11, 2025 at 11:52 AM
Reposted by Pedro Beltrao
edhuttlin.bsky.social
If you’re at #HUPO2025, be sure to stop by my poster and learn about the latest developments in the BioPlex project!
November 12, 2025 at 3:27 PM
Reposted by Pedro Beltrao
aylwyn-scally.bsky.social
Come and join us here in Cambridge! Applications open for a new faculty position, for a researcher in computational and/or theoretical biology, based jointly in Genetics and Mathematics. Happy to answer questions about research, teaching and working here.

www.cam.ac.uk/jobs/faculty...
Faculty Position in Computational Biology
Applications are invited for an Assistant/ Associate Professorship in Computational Biology to commence on 1 April 2026 or shortly thereafter. This is a joint post between the Department of Applied
www.cam.ac.uk
November 11, 2025 at 9:05 PM
pedrobeltrao.bsky.social
957 proposals were submitted in the latest round of ERC Synergy applications. They expect to fund 50 which means around 5% success rate. This is really not sustainable and a lot of people are likely avoiding doing this knowing how poor the chances are.
erc.europa.eu/news-events/...
Applications for ERC Synergy Grants 2026: Facts and figures
The ERC Synergy Grants 2026 call closed for applications on 5 November 2025. These are the preliminary data on the submitted proposals:
erc.europa.eu
November 11, 2025 at 1:22 PM
Reposted by Pedro Beltrao
bocklab.bsky.social
🗨️ Just published in Nature Biotechnology: Our CellWhisperer AI enables chat-based analysis of single-cell sequencing data. You can talk to your cells & figure out the biology without writing any computer code. Paper here: www.nature.com/articles/s41.... Annotated walkthrough in a thread below (1/11)
November 11, 2025 at 12:52 PM
pedrobeltrao.bsky.social
It has been disappointing to see the general lack of interest and investment into population genetics and genomic medicine in Switzerland. While we can resort to other national cohorts for research the country can only benefit if the know-how can be applied locally
www.sfa-phrt.ch/success-stor...
Didier Trono Interview “Switzerlands Genetic Diversity is Unique” - PHRT – Personalized Health & Related Technologies
Success Story Didier Trono While other countries are pressing ahead with the Genome of Europe, Switzerland is still hesitating. A huge mistake, says Didier Trono from the Genome Center in Geneva “I do...
www.sfa-phrt.ch
November 11, 2025 at 8:42 AM
Reposted by Pedro Beltrao
mucosalimmunology.bsky.social
1 week left to apply for a postdoc position in beautiful Switzerland doing awesome mucosal immunology. See below for details! Please re-post to spread the word!
mucosalimmunology.bsky.social Emma Slack @mucosalimmunology.bsky.social · 15d
We have an opening for a postdoctoral researcher in my group at the Botnar Institute for Immune Engineering in Basel, Switzerland. The project is aimed at developing novel mucosal adjuvants for application in oral vaccines. Deadline to apply 16.11.25! Please re-post 🔬🧬

join.com/companies/im...
Botnar Institute of Immune Engineering - BIIE (Zürich): Postdoctoral Researcher (100%): Mechanisms of action of mucosal adjuvants
Botnar Institute of Immune Engineering - BIIE has a job opening for Postdoctoral Researcher (100%): Mechanisms of action of mucosal adjuvants in Zürich (published: 30.10.2025). Apply now or check the ...
join.com
November 9, 2025 at 10:41 PM
Reposted by Pedro Beltrao
tanjastadler.bsky.social
Open position at the Swiss Institute of Bioinformatics:
We are looking for a Director of the Center of Pathogen Bioinformatics
apply.refline.ch/499599/0346/...
I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and
Director, Center for Pathogen Bioinformatics
The Centre for Pathogen Bioinformatics (CPB) is a unit of SIB which offers expertise and services in pathogen bioinformatics, computational molecular epidemiology and related multi-site project manage...
apply.refline.ch
October 25, 2025 at 1:03 PM
Reposted by Pedro Beltrao
levayerr.bsky.social
I am honnestly a bit worried by the latest fuss about qed (the IA driven review). While the results are indeed quite impressive (it is very good at listing the claim and finding potential improvement), I don't quite see how this will eventually reduce the reviewing burden or help us
November 7, 2025 at 8:33 AM
Reposted by Pedro Beltrao
jkpritch.bsky.social
Excited to share our latest work on the factors that determine what genes we find (and don't find!) in GWAS and burden tests.

We describe a critical concept that we call *specificity*.

Led by Jeff Spence and Hakhamanesh Mostafavi:
jeffspence.github.io Jeff Spence @jeffspence.github.io · 8d
How do GWAS and rare variant burden tests rank gene signals?

In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!

🧬🧪🧵

www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 4:08 AM
Reposted by Pedro Beltrao
tlemberger.bsky.social
Very cool! I agree AI scientific review can be useful if it is transparent. It is all progressing very fast and will change everything. @qedScience @bioRxiv is a great first step. We are doing some human-based eval, so more soon from @EMBOPress @ReviewCommons with @qedScience. Watch this space ;-)
November 6, 2025 at 3:21 PM
Reposted by Pedro Beltrao
odedrechavi.bsky.social
IT'S HAPPENING! 💥 I'm psyched to launch the collaboration between @qedscience.bsky.social & @openrxiv.bsky.social @biorxivpreprint.bsky.social! Preprint + q.e.d = your science is out there, and anyone can appreciate it. Let's care about making discoveries, and not on “getting published” (1/3) 👇
November 6, 2025 at 2:49 PM
Reposted by Pedro Beltrao
saezlab.bsky.social
Our revised consensus transcriptional patient map of human heart failure across patient cohorts and single-cell and bulk technologies is now published @natcomms.nature.com www.nature.com/articles/s41...
saezlab.bsky.social Saez-Rodriguez Group @saezlab.bsky.social · Nov 11
What are the key disrupted multicellular processes in heart failure? In our new work we combine 23 years of molecular data with recent single-cell atlases to draw a cross-study patient map
doi.org/10.1101/2024...
November 6, 2025 at 12:10 PM
Reposted by Pedro Beltrao
jeremy37.bsky.social
Let’s talk about rare variant association tests - we have a new method that helps you discover more with the same data! It’s called *FlexRV* to signal our approach: “flexibly modeling rare variant pathogenicity improves gene discovery for complex traits”. www.biorxiv.org/content/10.1...
Flexibly Modeling Rare Variant Pathogenicity Improves Gene Discovery for Complex Traits
Rare variant burden tests can directly identify genes that influence complex traits, but their power is limited by our ability to separate functional from benign alleles. We introduce FlexRV, an appro...
www.biorxiv.org
November 5, 2025 at 10:29 PM
Reposted by Pedro Beltrao
ostermanilya.bsky.social
Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides.
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:00 AM
Reposted by Pedro Beltrao
savitski-lab.bsky.social
Happy to see our HT-PELSA paper now published in @natsmb.nature.com 🎊 Big thanks for the constructive review process! 📖Read the manuscript here (www.nature.com/articles/s41...) & check the thread for additional information ⬇️
November 5, 2025 at 10:15 AM
Reposted by Pedro Beltrao
biorxivpreprint.bsky.social
A functional map of CDK-drug interactions at single amino acid resolution https://www.biorxiv.org/content/10.1101/2025.11.02.685764v1
November 4, 2025 at 2:49 AM
Reposted by Pedro Beltrao
hansonmark.bsky.social
Just tried q.e.d. by @odedrechavi.bsky.social et al. with a few papers including by myself & others where I knew a claim within was flawed based on a misunderstanding of the signal.

1) it was impressive. I see what the hype is about.
2) it hallucinated.

www.qedscience.com

Overly long #SciPub🧵 1/n
q.e.d Science
Critical Thinking AI for constructive criticism and science evaluation
www.qedscience.com
November 1, 2025 at 12:15 PM
Reposted by Pedro Beltrao
dudinlab.bsky.social
🚨Our collaboration with @centriolelab.bsky.social & @gautamdey.bsky.social is out today in @cp-cell.bsky.social
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky

www.cell.com/cell/fulltex...
October 31, 2025 at 2:42 PM
Reposted by Pedro Beltrao
ludwigcancer.bsky.social
Our congratulations to @skinnider.bsky.social!
October 30, 2025 at 1:59 PM