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Joram Mooiweer

@jorammooiweer.bsky.social
2.5K followers 998 following 220 posts

Celiac disease mucosal immunity | Engineering intestine models | iPSCs, Organoids, T cells & organ-chips🔬| PhD candidate | Dept. of Genetics 🧬 | University Medical Center Groningen | University of Groningen (@rug.nl) | 📍Groningen, the Netherlands

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Joram Mooiweer @jorammooiweer.bsky.social · 08/09/2026
Is it weird that I want to attend lectures for a master’s course that I’m helping organize?
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Vincent van Unen @vincentvanunen.bsky.social · 12/08/2026
Glad to see it out in print!! like T cell receptors and IBD? Check it out!
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Joram Mooiweer @jorammooiweer.bsky.social · 10/08/2026
We’ve been cooking something for a while, but we’re very happy to share the preprint now in its current form: "An autologous human duodenal IEL–organoid co-culture platform for studying immune–epithelial interactions" Link and threat below www.biorxiv.org/content/10.6... 🧵👇
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Vincent van Unen @vincentvanunen.bsky.social · 18/06/2026
Excited to share our new paper in @insight.jci.org How does genetic risk shape CD4 T cell recognition in inflammatory bowel disease? #IBD We linked HLA-DRB1 genotype to >3.1 million memory CD4+ TCRβ sequences in Crohn’s disease, ulcerative colitis and controls.
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bioRxivpreprint @biorxivpreprint.bsky.social · 08/08/2026
Autologous biopsy-derived co-culture platform for interrogation of intestinal epithelial-T cell crosstalk www.biorxiv.org/content/10.64898/20…
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Joram Mooiweer @jorammooiweer.bsky.social · 07/08/2026
This UMAP of mouse small intestine looks like a mouse! Right? Anyone? No?
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Karuna Ganesh @karunamdphd.bsky.social · 05/08/2026
1/ Delighted to share our paper out today in Nature: ZFP36L2 orchestrates stress-adaptive plasticity in regeneration and cancer. We found the switch that lets differentiated cells rewind into stem cells — in gut repair, and in metastasis. 🧵 doi.org/10.1038/s415...
doi.org
ZFP36L2 orchestrates stress-adaptive plasticity in regeneration and cancer - Nature
The RNA-binding protein ZFP36L2 mediates stress-adaptive plasticity in intestinal regeneration and colorectal cancer metastasis.
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Cornelia Schwayer @cschwayer.bsky.social · 01/07/2026
Excited to share that our work on ‘How the gut gets patterned during regeneration’ is out now cell.com/cell/fulltext/S0092-8674(26)00696-3 Thanks a lot to @priscaliberali.bsky.social @silviabarbiero.bsky.social @davidbrueckner.bsky.social @ehannezo.bsky.social and all co-authors! 🧵
cell.com
Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning
During regeneration, tissues must translate transient cellular variability into stable spatial organization. Tissue architecture generates a density-dependent window of heterogeneity in the mechanosen...
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Jonny Coates @jacoates.bsky.social · 14/06/2026
📢 New: State of Preprints 2026 (Version 2.0) I've added a major new section exploring what researchers actually think about preprints, drawing together evidence from 12 studies on researcher perceptions. #OpenScience #Preprints #ScholComm #AcademicPublishing #ResearchCulture
zenodo.org
State of Preprints in the Life Sciences
This is the report for the State of Preprints in the Life Sciences, investigating preprinting from 2013-2025 and the likely trends in 2026. The underlying code and figures are available from GitHub. T...
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Joram Mooiweer @jorammooiweer.bsky.social · 13/06/2026
This is seriously quite a paper!! Linking Genetic (HLA) risk with neutralizing IL10 auto-antibodies to disease mechanics
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Dr Natasha Fisher-Pearson @natashafp.bsky.social · 05/05/2026
Hello Bluesky! I'm a #microbiome researcher at the University of Oxford. I recently finished my PhD on the gut microbiome and mucosal-associated invariant T cells. Looking forward to sharing my research and connecting with other scientists interested in #immunology, #bioinformatics and microbes!
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Joram Mooiweer @jorammooiweer.bsky.social · 04/05/2026
What happened to #FluorescenceFriday?
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Xavier Trepat @xaviertrepat.bsky.social · 17/04/2026
Our latest work on shape-programmable tissues is out in @science.org. By positioning topological defects in cellular nematics, we encode frustrated 2D force fields that relax into predictable 3D shapes. Collaboration with Marino Arroyo’s lab, led by @pauguillamat.bsky.social at @ibecbarcelona.eu.
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Joram Mooiweer @jorammooiweer.bsky.social · 18/04/2026
My God… Just make it a lottery already! Basic screen on scientific strength and feasibility and then… Lottery Fair as can be, no bullshit, biased decisions or weird rejection argument. Just plain (bad)luck
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Joram Mooiweer @jorammooiweer.bsky.social · 07/04/2026
I want to win the lottery to finance my research for a few years Said no non-scientist ever
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Joram Mooiweer @jorammooiweer.bsky.social · 19/03/2026
Idk about you, but these days a “preprinted” manuscript excites me more than a “published” one 🧐 Preprints still feel alive, fresh, maybe imperfect or unfinished. Rather than published ones that have come to see the daylight after author/editorial/referee limbos for months or years
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Joram Mooiweer @jorammooiweer.bsky.social · 19/03/2026
So just when we’re building factories to produce #CAR T cells en-masse, it turns out we ourselves can be that factory!? www.nature.com/articles/s41...
nature.com
In vivo site-specific engineering to reprogram T cells - Nature
Stable and cell-specific transgene expression can be achieved through in vivo site-specific integration of large DNA payloads using a two-vector system of enveloped delivery vehicles and adeno-as...
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Stella Hurtley @smhsci.bsky.social · 13/03/2026
Just published in @science.org Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis | Science www.science.org/doi/10.1126/...
science.org
Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis
Gene expression patterns underlie development, but their systematic detection in whole embryos has remained elusive. We introduce a whole-embryo imaging platform using multiplexed error-robust fluores...
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Chris Simms @chrisnsimms.bsky.social · 12/03/2026
I'm a big fan of bioRxiv, so it was fascinating to dig into the stats behind the rise of this preprint server from its first 13 or so years for Nature News @nature.com 🧪 @biorxivpreprint.bsky.social #preprints www.nature.com/articles/d41...
nature.com
How bioRxiv changed the way biologists share ideas – in numbers
Four million articles are now downloaded from bioRxiv every month, according to an analysis of the life-science preprint server’s first 13 years of existence.
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Johannah Ruddy @johannahruddy.bsky.social · 10/03/2026
The HUNT-GWAS study shows how genetics, including HLA-DQB1, can shape gut microbes like Agathobacter, potentially influencing celiac disease risk. It highlights the promise of integrating genomics and microbiome science to better understand disease and guide future precision medicine.
medcentral.com
New Study Links Gut Makeup to Celiac Disease Pathogenesis
A genome-wide association study provided the first evidence to link genetic variation in humans to functional features of the gut microbiota.
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Joram Mooiweer @jorammooiweer.bsky.social · 10/03/2026
AI peer-review 🤝 Human peer-review 👉🏻 fair, less-biased peer-review #peerreview
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Asier Fernández Pato @asierfdezpato.bsky.social · 09/03/2026
🚨 𝗡𝗲𝘄 𝗽𝗿𝗲𝗽𝗿𝗶𝗻𝘁! After years of work, I'm excited share our manuscript "𝗣𝗿𝗲𝗴𝗻𝗮𝗻𝗰𝘆 𝗮𝗻𝗱 𝗘𝗮𝗿𝗹𝘆-𝗟𝗶𝗳𝗲 𝗚𝘂𝘁 𝗩𝗶𝗿𝗼𝗺𝗲 𝗶𝗻 𝘁𝗵𝗲 𝗟𝗶𝗳𝗲𝗹𝗶𝗻𝗲𝘀 𝗡𝗘𝗫𝗧 𝗰𝗼𝗵𝗼𝗿𝘁: 𝗢𝗿𝗶𝗴𝗶𝗻, 𝗣𝗲𝗿𝘀𝗶𝘀𝘁𝗲𝗻𝗰𝗲, 𝗜𝗻𝗳𝗹𝘂𝗲𝗻𝗰𝗶𝗻𝗴 𝗙𝗮𝗰𝘁𝗼𝗿𝘀 𝗮𝗻𝗱 𝗛𝗲𝗮𝗹𝘁𝗵 𝗜𝗺𝗽𝗹𝗶𝗰𝗮𝘁𝗶𝗼𝗻𝘀". doi.org/10.64898/202... A thread🧵👇 (1/11)
doi.org
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Joram Mooiweer @jorammooiweer.bsky.social · 08/03/2026
Capturing the microbiome in-situ It’s possible now! Can’t even begin to imagine how many new avenues this is going to open! 👇🏽
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thexavierlab.bsky.social @thexavierlab.bsky.social · 04/03/2026
New study, in collaboration with Kenya Honda, out now in @nature.com. We show how a low protein diet drives a microbiota-dependent induction of thermogenic brown adipocytes via FXR & FGF21 pathways. www.nature.com/articles/s41...
nature.com
Microbiota-mediated induction of beige adipocytes in response to dietary cues - Nature
In mice, a low-protein diet leads to a gut-microbiota-driven remodelling of adipose tissue towards brown fat, showing that gut microorganisms have a role in detecting and responding to a lack of prote...
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Nature Reviews Immunology @natrevimmunol.nature.com · 06/02/2026
In this World View article, Ruslan Medzhitov discusses the perils of too much data and not enough theory in modern immunology rdcu.be/e2DCZ
rdcu.be
On the balance of knowledge
Nature Reviews Immunology - Ruslan Medzhitov shares his thoughts on the balance between generating data and developing theories in immunology, with a focus on exploring the rules that govern...
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Joram Mooiweer @jorammooiweer.bsky.social · 22/12/2025
STOP WITH WHATEVER IT IS YOURE DOING AND READ THIS NOW!
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Mark A. Hanson @hansonmark.bsky.social · 11/11/2025
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.
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PLOS Biology @plosbiology.org · 18/12/2025
Are authors fairly judged by assessing the #journals in which their work is published? @bihutchins.bsky.social &co reveal that most influential papers are published in lower tier journals, and more authors would be better recognized with #ArticleLevelMetrics #ALMs @plosbiology.org 🧪 plos.io/4oV58Ed
Standing on the shoulders of giants. Researchers (nodes) at early (red), mid (blue) and late (grey) career stage who have built on one another's work (edges). Large nodes are researchers whose work would not be recognized with journal level metrics but would be recognized with article level metrics. Credit: B. Ian Hutchins
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Fabian Theis @fabiantheis.bsky.social · 15/12/2025
🚀 New preprint! The Human Cytokine Dictionary - 9.7M cells, 12 donors, 90 cytokines - our largest human single-cell perturbation atlas yet. Users can map cytokine activity in their own data. Huge thanks to Lukas, Sören, Larsen, Parse Bio & Seelig lab! 🔗 www.biorxiv.org/content/10.6...
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epithelial mechanics fan club @epimechfc.bsky.social · 14/12/2025
Cells can sense the geometry of their environment, from tiny subcellular features to whole-tissue patterns. How can we engineer environments to systematically probe these responses? 🧵 I'm @lhinderling.bsky.social from @olivierpertz.bsky.social lab, let’s do a short tour on microfabrication!
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Stem Cell Reports @stemcellreports.bsky.social · 11/12/2025
Do not miss the latest episode of The Stem Cell Report Podcast - Guests discuss their research on cultural conditions effects on PSC-derived intestinal epithelial cells. Listen to the episode: tinyurl.com/3s4pkj34 @jorammooiweer.bsky.social @isscr.org
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Joram Mooiweer @jorammooiweer.bsky.social · 06/12/2025
How to deal with an error in science? — This is how. Great example of clearly owning, investigating, and communicating an error - with high integrity and respect. The error analysis immediately available as a preprint👏 Kudos to the authors for this courageous move. Excited to see the new data!
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Joram Mooiweer @jorammooiweer.bsky.social · 19/11/2025
Totally psyched that our paper is out in @stemcellreports.bsky.social! For human iPSC–based gut #NAMs, which platform would you trust to behave most like real intestinal tissue? We put #organoids, Transwells and @emulatebio.bsky.social intestine-chip head to head. Spoiler: the chip wins. 🧵&🔗👇
https://www.cell.com/stem-cell-reports/fulltext/S2213-6711(25)00319-4
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Joram Mooiweer @jorammooiweer.bsky.social · 19/11/2025
THANK YOU!!! #ImmunoSky www.nature.com/articles/s41...
nature.com
Guidelines for T cell nomenclature - Nature Reviews Immunology
This Consensus Statement clarifies the existing subset-based nomenclature for T cells. Furthermore, it proposes an alternative modular nomenclature that is designed to be brief and flexible and to avo...
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Jen Gommerman @jengommerman.bsky.social · 17/11/2025
Proud to share our work now out in Cell. We hope what we learned about IgA immune responses to rotavirus can be translated into better vaccines. Congratulations Dr. Kei Haniuda, an amazing PDF. TY @uoftmedicine.bsky.social for covering. temertymedicine.utoronto.ca/news
temertymedicine.utoronto.ca
Recent News
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Joram Mooiweer @jorammooiweer.bsky.social · 08/11/2025
Yes!!! This is the way forward for fairer science evaluation: (“high-impact”) journals give stamps of interest/impact on peer-reviewed preprints (i.e. still add value). In parallel, societies can use a similar ‘approval stamp’ especially to highlight excellent work in less “sexy” fields.
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The Batlle Lab @batllelab.bsky.social · 07/11/2025
1/17 🧵 🙌Thrilled to share our first hard-core immunology paper out today in Nature Genetics! 👇 ➡️We unravel how TGFβ suppresses the innate and adaptive immune system in microsatellite stable colorectal cancer (MSS CRC). Very proud of the team and efforts behind it. www.nature.com/articles/s41...
nature.com
TGF-β builds a dual immune barrier in colorectal cancer by impairing T cell recruitment and instructing immunosuppressive SPP1+ macrophages - Nature Genetics
Targeting TGFBR1 in transplantable mouse colorectal tumor organoids improves response to anti-PD-L1 therapy. Mechanistically, TGF-β abrogates clonal expansion of T effector and memory phenotypes and i...
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Joram Mooiweer @jorammooiweer.bsky.social · 06/11/2025
🚨‼️
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Review Commons @reviewcommons.org · 03/11/2025
Big New! @elife.bsky.social @genetics-gsa.bsky.social #G3journal are joining editorial forces with @reviewcommons.org - bringing not just field-specific expertise to the process but also making #PreprintPeerReview a truly collaborative effort!🎉👏 Read more to find out👇 www.embo.org/features/pub...
embo.org
Publishers join the Review Commons peer review process  – Features – EMBO
Editors from eLife, Genetics, G3 and Journal of Cell Biology will contribute to the EMBO preprint peer review platform
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Joram Mooiweer @jorammooiweer.bsky.social · 02/11/2025
Genetically editing iPSCs is challenging. But here’s thoroughly expedited how to do it anyway 👇
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Immunity @cp-immunity.bsky.social · 31/10/2025
Online now: TCR signaling via NFATc1 constrains IL-15-induced bystander activation of human memory CD8+ T cells
dlvr.it
TCR signaling via NFATc1 constrains IL-15-induced bystander activation of human memory CD8+ T cells
Memory CD8+ T cells can undergo TCR-dependent or -independent activation. Here, Lee et al. show that IL-15-induced bystander activation of human memory CD8+ T cells is suppressed by concurrent TCR signaling through NFATc1-AP-1 interactions. Furthermore, they validate a bystander activation gene set induced by IL-15 and decreased upon TCR stimulation.
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Slater Clay @slaterc.bsky.social · 02/11/2025
Excited to share a preprint from my postdoc @theGarrettLab- now on bioRxiv! Oral acetoacetate (AcAc) suppresses tumor growth by expanding and activating MAIT cells… and the mechanism was a surprise 🧵👇 (1/10) www.biorxiv.org/content/10.1...
biorxiv.org
Acetoacetate suppresses colon cancer via an MR1-MAIT axis
Colorectal cancer (CRC) is a leading cause of cancer mortality and additional preventative, and therapeutic strategies are urgently needed. Ketogenic diets have mixed effects on tumorigenesis and comp...
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Joram Mooiweer @jorammooiweer.bsky.social · 26/10/2025
Stop 👏 judging 👏 science 👏 with 👏 bad 👏 metrics 👏!!!!!
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Joram Mooiweer @jorammooiweer.bsky.social · 23/10/2025
It’s unbelievable how side quests somehow take over your whole week. But hey; every day eventually becomes 6 PM, and you can finally start the thing you were actually supposed to do!
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Xavier Trepat @xaviertrepat.bsky.social · 22/10/2025
📣Announcing the 4th edition of the EMBL‑IBEC Conference on “Engineering Multicellular Systems”, taking place 11–13 March 2026 in Barcelona. Exploring organoids, mechanobiology, embryo models, organ-on-chip systems, multiomics and more. Abstracts open now! events.ibecbarcelona.eu/embl-ibec-co...
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Joram Mooiweer @jorammooiweer.bsky.social · 21/10/2025
Restoring Oral tolerance in 🐭 Continuous oral antigen exposure + CD28 blockade (CTLA4-Ig) = generation of CD101⁺ Tregs that enforce antigen-specific tolerance. Even in primed hosts. So pTregs can be reprogrammed into durable peacekeepers! #immunology #Tregs #immunosky
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Joram Mooiweer @jorammooiweer.bsky.social · 20/10/2025
Back to back commentaries in @natureportfolio.nature.com today. Clearly NAMs are causing a stir!
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Joram Mooiweer @jorammooiweer.bsky.social · 20/10/2025
As a researcher at the start of its career, I find this very frightening… www.nature.com/articles/d41...
nature.com
Is academic research becoming too competitive? Nature examines the data
Applications for European research grants increased in 2025. Scientists say they’re feeling the competition.
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Jeremy Barr @jeremyjbarr.bsky.social · 15/10/2025
Very excited to share the latest work from our lab, which was published today in Nature! nature.com/articles/s41... PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
nature.com
Isolation, engineering and ecology of temperate phages from the human gut - Nature
Human host-associated cellular products may act as induction agents for bacteriophages.
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Joram Mooiweer @jorammooiweer.bsky.social · 08/10/2025
In the light of “#mTOR regulates everything,” HDAC5 just gave it access to your mucus factory. Microbes → HDAC5 → 14-3-3 → mTOR → translation → mucus. Neat way to link energy status to an energy-costly process — only making #mucus when it’s worth it 🦠🧫 www.biorxiv.org/content/10.1...
biorxiv.org
Translational control of innate barrier defense by the gut microbiota
The intestinal epithelium is protected by a mucus barrier, infused with antimicrobial proteins, that restricts microbial access to host tissue. Because assembling this barrier is energetically costly,...
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