Jakub Zeman
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jakub-zeman.bsky.social
Jakub Zeman
@jakub-zeman.bsky.social
120 followers 140 following 53 posts
Postdoc with interest in ribosomes, proteins, cardiomyocytes, human embryonic cell fate... ...cats, investing, and sarcasm.
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Reposted by Jakub Zeman
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
jakub-zeman.bsky.social
A small book, big truths.
October 23, 2025 at 4:44 PM
jakub-zeman.bsky.social
@svobodalab.bsky.social This one is for you!
September 30, 2025 at 9:50 PM
jakub-zeman.bsky.social
“Just because you are offended doesn’t mean you are right.”
Ricky Gervais
September 15, 2025 at 1:19 PM
jakub-zeman.bsky.social
Our new preprint, full of exciting data, is now available. Have a look!

QKI ensures splicing fidelity during cardiogenesis by engaging the U6 tri-snRNP to activate splicing at weak 5ʹ splice sites
www.biorxiv.org/content/10.1...
www.biorxiv.org
September 8, 2025 at 6:32 AM
Reposted by Jakub Zeman
kurianlab.bsky.social
www.cell.com/cell/fulltex...

Tour de force spearheaded by brilliant Marko Jovanovic and colleagues!
SPIDR enables multiplexed mapping of RNA-protein interactions and uncovers a mechanism for selective translational suppression upon cell stress
SPIDR, a massively multiplexed method that simultaneously maps dozens of RNA-binding proteins to their RNA targets at single-nucleotide resolution, uncovers new RNA-protein interactions and provides c...
www.cell.com
July 23, 2025 at 4:47 AM
Reposted by Jakub Zeman
pastelbio.bsky.social
An Optimized SP3 Sample Processing Workflow for In-Depth and Reproducible Phosphoproteomics pubs.acs.org/doi/10....

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#proteomics #prot-paper
July 18, 2025 at 7:20 PM
Reposted by Jakub Zeman
nature.com
Researchers are making ever more sophisticated mini organs in the lab — and now they can grow their own blood vessels

go.nature.com/4nNF3ri
Mini hearts, lungs and livers made in lab now grow their own blood vessels
These sophisticated models will be used for human-development studies and drug testing.
go.nature.com
July 11, 2025 at 11:12 AM
jakub-zeman.bsky.social
One day, scientists will discover Adobe InDesign/Affinity Publisher/… for figure assembly and our lives will be much easier…
July 9, 2025 at 11:01 AM
jakub-zeman.bsky.social
A review of the history of protein-RNA friendship.
mhko.bsky.social Michal Kolář @mhko.bsky.social · Jul 9
New publication out on the evolution of protein-RNA interactions. Put together with Klára Hlouchová (@sciencecharles.bsky.social) during a lovely Czech spring.

www.sciencedirect.com/science/arti...
A scheme of chemico-biological evolution of protein-RNA interactions. It started about 4.5 billion years ago with prebiotic monomers, went through peptides, oligonucleotides, and simple complexes, reaching proteins and RNA at about 4-3.7 billion years ago.
July 9, 2025 at 10:54 AM
jakub-zeman.bsky.social
Germany of the 21st century: A place where there is a massive problem for all major personal parcel delivery companies to deliver an order.
#OrdnungMussSein
July 4, 2025 at 1:29 PM
jakub-zeman.bsky.social
Feedback without specifics is not feedback. It’s frustration.
July 3, 2025 at 9:49 AM
Reposted by Jakub Zeman
itaiyanai.bsky.social
'Night science' is what you do when you're not sure what's the question.
July 3, 2025 at 8:17 AM
Reposted by Jakub Zeman
effinbirds.com
A painting of a bird next to the words "I'm gonna need a moment to process this bullshit"
June 15, 2025 at 2:08 PM
jakub-zeman.bsky.social
Dream big. Dare to fail. Fuck dull, incremental science.
July 2, 2025 at 2:49 PM
Reposted by Jakub Zeman
apoetsch.bsky.social
We have several open postdoc positions! We do computational biology 🧬🖥️ and deep learning to understand the genomics of genome instability and (somatic) genome evolution in ageing and cancer. Interested? 👉🏻 more details: tu-dresden.de/cmcb/biotec/...
Open positions
We are looking for Postdocs! If you are interested in the lab in general as a postdoc, please feel free to apply with an open application, including a letter of motivation and a CV …
tu-dresden.de
June 26, 2025 at 9:46 AM
jakub-zeman.bsky.social
Ribosomes on an mRNA molecule are like:

youtu.be/7wm-pZp_mi0?...
Traffic Jam without bottleneck - experimental evidence
YouTube video by Francis Villatoro
youtu.be
June 26, 2025 at 5:52 AM
jakub-zeman.bsky.social
I visited the lab where I did my PhD today. They moved two floors upstairs since I left in 2020, they have got new stuff, many new students and postdocs. Yet, there are still boxes with my name around, and they are about to finish the 3C protease I purified back then. 🧡 #ProteinPutification #eIF3
June 19, 2025 at 3:05 PM
jakub-zeman.bsky.social
June 19, 2025 at 10:15 AM
jakub-zeman.bsky.social
Every. Time.
June 17, 2025 at 4:09 PM
jakub-zeman.bsky.social
- Return to work after attending #TCTeAC
- Make yourself a cappuccino
- Reflect on all the wonderful things in life
- Clear out those emails and embrace happiness
June 16, 2025 at 10:29 AM
jakub-zeman.bsky.social
The following day after coming back from #TCTeAC
June 15, 2025 at 8:55 AM
jakub-zeman.bsky.social
If any #TCTeAC survivors are staying in Prague tonight or longer, feel free to DM me for recommendations, tricks, and survival tips. Or we can have a last beer together this evening.
#AllRoadsLeadToPub
June 13, 2025 at 12:51 PM
Reposted by Jakub Zeman
svobodalab.bsky.social
#TCTeAC ... and that was all, folks! Thank you, it was fantastic.
June 13, 2025 at 8:33 AM